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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    A Combined Nutrition and Exercise Intervention Influences Serum Vitamin B-12 and 25-Hydroxyvitamin D and Bone Turnover of Healthy Chinese Middle-Aged and Older Adults
    Groenendijk, Inge ; Chan, Ruth ; Woo, Jean ; Ong, Sherlin ; Parikh, Panam ; Bragt, Marjolijn C.E. ; Groot, Lisette C.P.G.M. de - \ 2020
    The Journal of Nutrition 150 (2020)8. - ISSN 0022-3166 - p. 2112 - 2119.
    25(OH)D - 25-hydroxyvitamin D - bone turnover - exercise - middle-aged adults - nutrition - older adults - vitamin B-12

    BACKGROUND: Hong Kong faces several public health problems including malnutrition and osteoporosis. Considering the typical Chinese diet and overall low physical activity levels of Chinese adults, timely interventions to improve nutritional status and bone health are needed. OBJECTIVES: We examined the effects of a nutrition plus exercise intervention on serum vitamin B-12 and 25-hydroxyvitamin D [25(OH)D], bone turnover markers, and parathyroid hormone (PTH) concentrations in apparently healthy Chinese middle-aged and older adults. METHODS: In this 24-wk randomized controlled trial, 180 Chinese adults (85 women, mean ± SD age: 61 ± 6 y) were randomly assigned to receive a fortified milk supplement (2 × 30 g/d) and an exercise program (2 × 1 h/wk including resistance, balance, and aerobic training) or no intervention. The primary outcome was physical performance. In this article we analyzed the secondary outcomes serum vitamin B-12 and 25(OH)D concentrations, assessed at baseline, 12 wk, and 24 wk. Also, bone turnover markers and PTH concentrations were studied. Linear mixed models evaluated group differences over time. RESULTS: A significant time × group interaction (P < 0.001) was found for serum vitamin B-12 and 25(OH)D concentrations and the bone turnover markers, but not for serum PTH concentrations (P = 0.09). The intervention increased mean ± SD vitamin B-12 concentrations from baseline (345 ± 119 pmol/L) to 24 wk (484 ± 136 pmol/L), whereas concentrations remained stable within the control. For 25(OH)D concentrations, the intervention group had a greater increase from baseline (54.7 ± 14.2 nmol/L) to 24 wk (80.1 ± 19.2 nmol/L) than the control (60.6 ± 15.2 compared with 65.6 ± 14.6 nmol/L). The ratio of the net effect of bone formation and resorption was greater in the intervention group, suggesting less bone remodeling, irrespective of sex. CONCLUSIONS: A fortified milk supplement and exercise intervention successfully improved vitamin B-12 and 25(OH)D concentrations as well as the balance of bone turnover markers of Chinese middle-aged and older adults.This trial was registered at trialregister.nl as NTR6214.

    Data underlying the publication: Mitigating ecosystem impacts of bottom trawl fisheries for North Sea sole Solea solea by replacing mechanical with electrical stimulation
    Rijnsdorp, Adriaan ; Depestele, J. ; Eigaard, O.R. ; Hintzen, Niels ; Ivanovic, A. ; Molenaar, Pieke ; O'Neill, F. ; Polet, H. ; Poos, Jan Jaap ; Kooten, Tobias van - \ 2020
    Wageningen University & Research
    beam trawl - Dutch fleet - habitat - North Sea - pulse trawl
    The csv data file “SAR_TBB.csv” contains data on habitat characteristics and fishing effort of the Dutch beam trawl fleet by grid cells of 1 minute longitude * 1 minute latitude in the North Sea used to study the changes in trawling impact on the benthic ecosystem due to the transition from conventional beam trawling to pulse trawling. Habitat variables include %sand, %gravel, %mud, bed shear stress (N.m-2) and level 3 EUNIS habitat type. Fishing effort, expressed as the annual swept area ratio (area swept by the gear in km2 / surface area of the grid cell (km2)), is given for the total Dutch beam trawl fleet and for a subset of vessels holding a pulse license (PLH) when fishing with the conventional beam trawl gear (PLH.T.year) or with the innovative pulse trawl (PLH.P.year).
    Fysisch-chemische inductie van plantweerbaarheid
    Stevens, L.H. ; Breeuwsma, S.J. ; Griekspoor, Y. ; Rutgers, B. - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research Biointeracties en Plantgezondheid - 67
    In dit rapport wordt verslag gedaan van onderzoek naar de interactie tussen rood/verrood-LED-stuurlicht en inductie van plantweerbaarheid middels elicitors. Het onderzoek bestond uit een reeks min of meer uniforme kasexperimenten uitgevoerd met groepen van jonge tomatenplanten als modelgewas, aangevuld met gerbera en enkele perkplanten als sierteeltgewassen. Het beoogde weerbaarheidseffect betrof het zogenoemde systemic acquired resistance (SAR). De effecten van de behandelingen werden vastgesteld door bepaling van salicylzuur, van expressie van pathogenesis related (PR) proteins, en van de meeldauwontwikkeling.
    Angular-Based Radiometric Slope Correction for Sentinel-1 on Google Earth Engine
    Vollrath, Andreas ; Mullissa, Adugna ; Reiche, Johannes - \ 2020
    Remote Sensing 12 (2020)11. - ISSN 2072-4292 - 14 p.
    This article provides an angular-based radiometric slope correction routine for Sentinel-1 SAR imagery on the Google Earth Engine platform. Two established physical reference models are implemented. The first model is optimised for vegetation applications by assuming volume scattering on the ground. The second model is optimised for surface scattering, and therefore targeted at urban environments or analysis of soil characteristics. The framework of both models is extended to simultaneously generate masks of invalid data in active layover and shadow affected areas. A case study, using openly available and reproducible code, exemplarily demonstrates the improvement of the backscatter signal in a mountainous area of the Austrian Alps. Furthermore, suggestions for specific use cases are discussed and drawbacks of the method with respect to pixel-area based methods are highlighted. The radiometrically corrected radar backscatter products are overcoming current limitations and are compliant with recent CEOS specifications for SAR backscatter over land. This improves a wide range of potential usage scenarios of the Google Earth Engine platform in mapping various land surface parameters with Sentinel-1 on a large scale and in a rapid manner. The provision of an openly accessible Earth Engine module allows users a smooth integration of the routine into their own workflows.
    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    Polsarnet: A deep fully convolutional network for polarimetric sar image classification
    Mullissa, Adugna G. ; Persello, Claudio ; Stein, Alfred - \ 2019
    IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 12 (2019)12. - ISSN 1939-1404 - p. 5300 - 5309.
    Convolutional neural network (CNN) - deep learning - image classification - machine learning - polarimetric SAR (PolSAR)

    Deep learning has successfully improved the classification accuracy of optical remote sensing images. Recent works attempted to transfer the success of these techniques to the microwave domain to classify Polarimetric SAR data. So far, most deep learning networks separate amplitude and phase as separate input images. In this article, we present a deep fully convolutional network that uses real-valued weight kernels to perform pixel-wise classification of complex-valued images. We evaluated the performance of this network by comparing it with support vector machine, Random Forest, complex-valued convolutional neural network (CV-CNN), and a network that uses amplitude and phase information separately as real channels. The evaluation was done on a quad-polarized AIRSAR image and a dual-polarimetric multitemporal Sentinel-1 data acquired over Flevoland, the Netherlands. The proposed method achieved higher accuracy compared to all other networks with the same architecture.

    Climate Change and Cereal Production Evolution Trend in the Sahel: Case Study in Mali from 1951 to 2010
    Claessens, L.F.G. - \ 2019
    Sustainable Agriculture Research 8 (2019)2. - ISSN 1927-050X - p. 68 - 89.
    Mali is a Sahelian country with a large climatic contrast from North to South. The current climatic and production evolutionary study is focused on the six major agro-climatic cereal production zones ranging from Kayes (400 mm) to Sikasso (>1000 mm) of rainfalls. Climatic data are rainfall records, daily maximum and minimum temperatures from 60 years of the six major synoptic weather observation stations. Data were analyzed on comparing average decades of the two normal periods of 30 years (1951-1980) and (1981-2010). Annual agronomic production data for millet, sorghum, maize and rice are derived from Mali's agricultural statistics base from 1984 to 2013. Main climatic results analyses indicate that climate change resulted in a decrease of 100 mm isohyets between the 2 periods of 30 years. The structure of the rainy season was little changed between these two periods since the average start of the season was delayed by 6 days and the average end date of the season became earlier by 4 days. Maximum temperatures increased significantly from + 0.44°C to + 1.53°C and minimum temperatures significantly increased from + 1.05°C to + 1.93°C in varying way depending on the sites. Statistics of major agronomic food crop production in Mali from 1984 to 2013 indicate an average increase of 985 to 4492 thousand tones, or 22% increase per year. There is a positive upward in saw tooth trend in Malian production from 1984 to 2013. This positive trend is the result of a combination of agricultural extension, agronomic research application and the management of small farmer holder in the Sahel. This evolution needs better study for drawing necessary right conclusions.
    Robust Visual-Aided Autonomous Takeoff, Tracking, and Landing of a Small UAV on a Moving Landing Platform for Life-Long Operation
    Palafox, Pablo R. ; Garzón, Mario ; Pereira Valente, J.R. ; Roldán, Juan Jesús ; Barrientos, Antonio - \ 2019
    Applied Sciences 9 (2019)13. - ISSN 2076-3417
    Robot cooperation is key in Search and Rescue (SaR) tasks. Frequently, these tasks take place in complex scenarios affected by different types of disasters, so an aerial viewpoint is useful for autonomous navigation or human tele-operation. In such cases, an Unmanned Aerial Vehicle (UAV) in cooperation with an unmanned Ground Vehicle (UGV) can provide valuable insight into the
    area. To carry out its work successfully, such as multi-robot system requires the autonomous takeoff, tracking, and landing of the UAV on the moving UGV. Furthermore, it needs to be robust and capable of life-long operation. In this paper, we present an autonomous system that enables a UAV to take off
    autonomously from a moving landing platform, locate it using visual cues, follow it, and robustly land on it. The system relies on a finite state machine, which together with a novel re-localization module allows the system to operate robustly for extended periods of time and to recover from potential failed landing maneuvers. Two approaches for tracking and landing are developed, implemented, and tested. The first variant is based on a novel height-adaptive PID controller that uses the current position of the landing platform as the target. The second one combines this height-adaptive PID controller with a Kalman filter in order to predict the future positions of the platform and provide them as input to the PID controller. This facilitates tracking and, mainly, landing. Both the system as a whole and the re-localization module in particular have been tested extensively in a simulated environment (Gazebo). We also present a qualitative evaluation of the system on the real robotic platforms, demonstrating that our system can also be deployed on real robotic platforms. For the benefit of the community, we make our software open source.
    Domain-Driven Analysis of Architecture Reconstruction Methods
    Tekinerdogan, B. ; Uzun, Burak - \ 2019
    In: Model Management and Analytics for Large Scale Systems / Tekinerdogan, B., Babur, Ö, Cleophas, L., van den Brand, M., Aksit, M., Elsevier Academic Press - ISBN 9780128166499 - p. 67 - 84.
    Software architecture reconstruction (SAR) is a process which aims to obtain the architecture information of any system using various sources. These sources contain documentations, logs, codes, and stakeholder concerns. Various automated and manual approaches have been proposed in the literature for SAR. Manual architecture reconstruction is usually time consuming, costly, error-prone, and complex. Hence different studies have addressed these problems by proposing automatized methods and tools for SAR. In this chapter we present a systematic characterization of the published architecture reconstruction methods. We apply a domain analysis process in which we first define the generic domain model of architecture reconstruction. The model is represented as a set of key terms, a generic business process model, and a feature diagram that represents the common and variant features of architecture reconstruction. We also present the method for deriving concrete architecture reconstruction methods from the generic domain model. We illustrate our approach for deriving two different concrete architecture reconstruction methods.
    Predicting estrogen receptor binding of chemicals using a suite of in silico methods – Complementary approaches of (Q)SAR, molecular docking and molecular dynamics
    Cotterill, J.V. ; Palazzolo, L. ; Ridgway, C. ; Price, N. ; Rorije, E. ; Moretto, A. ; Peijnenburg, A. ; Eberini, I. - \ 2019
    Toxicology and Applied Pharmacology 378 (2019). - ISSN 0041-008X
    Estrogen receptor - In Silico - Low-mode molecular dynamics simulation - Molecular docking - QSAR

    With the aim of obtaining reliable estimates of Estrogen Receptor (ER) binding for diverse classes of compounds, a weight of evidence approach using estimates from a suite of in silico models was assessed. The predictivity of a simple Majority Consensus of (Q)SAR models was assessed using a test set of compounds with experimental Relative Binding Affinity (RBA) data. Molecular docking was also carried out and the binding energies of these compounds to the ERα receptor were determined. For a few selected compounds, including a known full agonist and antagonist, the intrinsic activity was determined using low-mode molecular dynamics methods. Individual (Q)SAR model predictivity varied, as expected, with some models showing high sensitivity, others higher specificity. However, the Majority Consensus (Q)SAR prediction showed a high accuracy and reasonably balanced sensitivity and specificity. Molecular docking provided quantitative information on strength of binding to the ERα receptor. For the 50 highest binding affinity compounds with positive RBA experimental values, just 5 of them were predicted to be non-binders by the Majority QSAR Consensus. Furthermore, agonist-specific assay experimental values for these 5 compounds were negative, which indicates that they may be ER antagonists. We also showed different scenarios of combining (Q)SAR results with Molecular docking classification of ER binding based on cut-off values of binding energies, providing a rational combined strategy to maximize terms of toxicological interest.

    Digital mapping of peatlands – A critical review
    Minasny, Budiman ; Berglund, Örjan ; Connolly, John ; Hedley, Carolyn ; Vries, Folkert de; Gimona, Alessandro ; Kempen, Bas ; Kidd, Darren ; Lilja, Harry ; Malone, Brendan ; McBratney, Alex ; Roudier, Pierre ; O'Rourke, Sharon ; Rudiyanto, ; Padarian, José ; Poggio, Laura ; Caten, Alexandre ten; Thompson, Daniel ; Tuve, Clint ; Widyatmanti, Wirastuti - \ 2019
    Earth-Science Reviews 196 (2019). - ISSN 0012-8252

    Peatlands offer a series of ecosystem services including carbon storage, biomass production, and climate regulation. Climate change and rapid land use change are degrading peatlands, liberating their stored carbon (C) into the atmosphere. To conserve peatlands and help in realising the Paris Agreement, we need to understand their extent, status, and C stocks. However, current peatland knowledge is vague—estimates of global peatland extent ranges from 1 to 4.6 million km2, and C stock estimates vary between 113 and 612 Pg (or billion tonne C). This uncertainty mostly stems from the coarse spatial scale of global soil maps. In addition, most global peatland estimates are based on rough country inventories and reports that use outdated data. This review shows that digital mapping using field observations combined with remotely-sensed images and statistical models is an avenue to more accurately map peatlands and decrease this knowledge gap. We describe peat mapping experiences from 12 countries or regions and review 90 recent studies on peatland mapping. We found that interest in mapping peat information derived from satellite imageries and other digital mapping technologies is growing. Many studies have delineated peat extent using land cover from remote sensing, ecology, and environmental field studies, but rarely perform validation, and calculating the uncertainty of prediction is rare. This paper then reviews various proximal and remote sensing techniques that can be used to map peatlands. These include geophysical measurements (electromagnetic induction, resistivity measurement, and gamma radiometrics), radar sensing (SRTM, SAR), and optical images (Visible and Infrared). Peatland is better mapped when using more than one covariate, such as optical and radar products using nonlinear machine learning algorithms. The proliferation of satellite data available in an open-access format, availability of machine learning algorithms in an open-source computing environment, and high-performance computing facilities could enhance the way peatlands are mapped. Digital soil mapping allows us to map peat in a cost-effective, objective, and accurate manner. Securing peatlands for the future, and abating their contribution to atmospheric C levels, means digitally mapping them now.

    Linking Terrestrial LiDAR Scanner and Conventional Forest Structure Measurements with Multi-Modal Satellite Data
    Mulatu, Kalkidan ; Decuyper, Mathieu ; Brede, Benjamin ; Kooistra, Lammert ; Reiche, Johannes ; Mora, Brice ; Herold, Martin - \ 2019
    Forests 10 (2019)3. - ISSN 1999-4907 - 19 p.
    Obtaining information on vertical forest structure requires detailed data acquisition and analysis which is often performed at a plot level. With the growing availability of multi-modal satellite remote sensing (SRS) datasets, their usability towards forest structure estimation is increasing. We assessed the relationship of PlanetScope-, Sentinel-2-, and Landsat-7-derived vegetation indices (VIs), as well as ALOS-2 PALSAR-2- and Sentinel-1-derived backscatter intensities with a terrestrial laser scanner (TLS) and conventionally measured forest structure parameters acquired from 25 field plots in a tropical montane cloud forest in Kafa, Ethiopia. Results showed that canopy gap-related forest structure parameters had their highest correlation (|r| = 0.4 − 0.48) with optical sensor-derived VIs, while vegetation volume-related parameters were mainly correlated with red-edge- and short-wave infrared band-derived VIs (i.e., inverted red-edge chlorophyll index (IRECI), normalized difference moisture index), and synthetic aperture radar (SAR) backscatters (|r| = −0.57 − 0.49). Using stepwise multi-linear regression with the Akaike information criterion as evaluation parameter, we found that the fusion of different SRS-derived variables can improve the estimation of field-measured structural parameters. The combination of Sentinel-2 VIs and SAR backscatters was dominant in most of the predictive models, while IRECI was found to be the most common predictor for field-measured variables. The statistically significant regression models were able to estimate cumulative plant area volume density with an R2 of 0.58 and with the lowest relative root mean square error (RRMSE) value (0.23). Mean gap and number of gaps were also significantly estimated, but with higher RRMSE (R2 = 0.52, RRMSE = 1.4, R2 = 0.68, and RRMSE = 0.58, respectively). The models showed poor performance in predicting tree density and number of tree species (R2 = 0.28, RRMSE = 0.41, and R2 = 0.21, RRMSE = 0.39, respectively). This exploratory study demonstrated that SRS variables are sensitive to retrieve structural differences of tropical forests and have the potential to be used to upscale biodiversity relevant field-based forest structure estimates.
    QSAR of 1,4-benzoxazin-3-one antimicrobials and their drug design perspectives
    Bruijn, Wouter J.C. de; Hageman, Jos A. ; Araya-Cloutier, Carla ; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
    Bioorganic and Medicinal Chemistry 26 (2018)23-24. - ISSN 0968-0896 - p. 6105 - 6114.
    2H-1,4-benzoxazin-3(4H)-one - Antibacterial - Antifungal - Benzoxazinoid - Benzoxazinone - Drug design - QSAR - SAR

    Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in literature were curated into an extensive dataset of 111 compounds. Descriptor selection was performed by a genetic algorithm. QSAR models revealed differences in requirements for activity against fungi, gram-positive and gram-negative bacteria. Shape, VolSurf, and H-bonding property descriptors were frequently picked in all models. The models obtained for gram-positive and gram-negative bacteria showed good predictive power (Q2 Ext 0.88 and 0.85, respectively). Based on the models generated, an additional set of 1,4-benzoxazin-3-ones, for which no antimicrobial activity had been determined in literature, were evaluated in silico. Additionally, newly designed lead compounds with a 1,4-benzoxazin-3-one scaffold were generated in silico by varying the positions and combinations of substituents. Two of these were predicted to be up to 5 times more active than any of the compounds in the current dataset. The 1,4-benzoxazin-3-one scaffold was concluded to possess potential for the design of new antimicrobial compounds with potent antibacterial activity, a multitarget mode of action, and possibly reduced susceptibility to gram negatives’ efflux pumps.

    The Ecological Functions and Ecosystem Services of Urban and Technogenic Soils : from Theory to Practice (A Review)
    Vasenev, V.I. ; Oudenhoven, A.P.E. van; Romzaykina, O.N. ; Hajiaghaeva, R.A. - \ 2018
    Eurasian Soil Science 51 (2018)10. - ISSN 1064-2293 - p. 1119 - 1132.
    decision-making support - ecologic and economic assessment - sustainable development of cities - urbanization

    A review of Russian and foreign approaches to analyze and assess the ecological and socioeconomic role of urban and technogenic soils is made in the context of the two popular concepts: the ecological functions of soils and ecosystem services. The modern definitions, classification, and evaluation of ecosystem services and their relationships with soil functions are considered both in general and in relation to urban and technogenic soils. Despite some methodological differences, the work shows that the concepts are closely related, and their joint use is highly promising. Three practical examples for the cities of Moscow, Hangzhou, and Hong Kong show a consistent transition from the analysis of soil properties and functions to the assessment of ecosystem services and decision making in engineering, urban improvement, and sustainable urban development.

    Bottom trawl fishing footprints on the world’s continental shelves
    Amoroso, Ricardo O. ; Pitcher, C.R. ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Parma, Ana M. ; Suuronen, Petri ; Eigaard, Ole R. ; Bastardie, Francois ; Hintzen, Niels T. ; Althaus, Franziska ; Baird, Susan Jane ; Black, Jenny ; Buhl-Mortensen, Lene ; Campbell, Alexander B. ; Catarino, Rui ; Collie, Jeremy ; Cowan, James H. ; Durholtz, Deon ; Engstrom, Nadia ; Fairweather, Tracey P. ; Fock, Heino O. ; Ford, Richard ; Gálvez, Patricio A. ; Gerritsen, Hans ; Góngora, María Eva ; González, Jessica A. ; Hiddink, Jan G. ; Hughes, Kathryn M. ; Intelmann, Steven S. ; Jenkins, Chris ; Jonsson, Patrik ; Kainge, Paulus ; Kangas, Mervi ; Kathena, Johannes N. ; Kavadas, Stefanos ; Leslie, Rob W. ; Lewis, Steve G. ; Lundy, Mathieu ; Makin, David ; Martin, Julie ; Mazor, Tessa ; Gonzalez-Mirelis, Genoveva ; Newman, Stephen J. ; Papadopoulou, Nadia ; Posen, Paulette E. ; Rochester, Wayne ; Russo, Tommaso ; Sala, Antonello ; Semmens, Jayson M. ; Silva, Cristina - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)43. - ISSN 0027-8424 - p. E10275 - E10282.
    Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when highresolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, therewas >95% probability that >90%of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
    Speckle reduction in PolSAR by multi-channel variance stabilization and Gaussian denoising: MuLoG
    Deledalle, Charles Alban ; Denis, Loïc ; Tupin, Florence ; Lobry, Sylvain - \ 2018
    In: EUSAR 2018 - 12th European Conference on Synthetic Aperture Radar, Proceedings. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9783800746361 - p. 539 - 543.

    Due to speckle phenomenon, some form of filtering must be applied to SAR data prior to performing any polarimetric analysis. Beyond the simple multilooking operation (i.e., moving average), several methods have been designed specifically for PolSAR filtering. The specifics of speckle noise and the correlations between polarimetric channels make PolSAR filtering more challenging than usual image restoration problems. Despite their striking performance, existing image denoising algorithms, mostly designed for additive white Gaussian noise, cannot be directly applied to PolSAR data. We bridge this gap with MuLoG by providing a general scheme that stabilizes the variance of the polarimetric channels and that can embed almost any Gaussian denoiser. We describe MuLoG approach and illustrate its performance on airborne PolSAR data using a very recent Gaussian denoiser based on a convolutional neural network.

    Function, localization and evolution of SOSEKI polar proteins
    Dop, Maritza van - \ 2018
    Wageningen University. Promotor(en): D. Weijers. - Wageningen : Wageningen University - ISBN 9789463434799 - 173

    The evolution of multi-cellular plants went hand in hand with the establishment of a complex polarity system to guide development and survival. Within the cell, polarity cues need to be established, read and translated into sub-cellular processes. Yet, the exact mechanisms that translate polarity into sub-cellular processes remain elusive. In Chapter 1, we discuss polarity and several proteins that use polar information to guide their localization. The Arabidopsis embryo is introduced as an excellent model for studying cell polarity.

    In Chapter 2, we take a closer look at development of the Arabidopsis embryo. Hereby we focus specifically on how oriented divisions are generated by developmental regulators and the division machinery. Recent advancement in 3D imaging of the embryo revealed that cell division abides to a ‘smallest plane’ rule, and that auxin can prevent adherence to this rule. Studying how auxin effectors are linked to cell division regulators and cell polarity may provide a greater understanding of oriented cell division in the embryo.

    Using the Arabidopsis embryo as model for auxin-regulated development, we identify a novel family of polarly localized proteins in Chapter 3. Unlike previously published polar proteins, this new family shows a robust localization to specific cell edges, which coined the name SOSEKI (SOK, Japanese for cornerstone). SOK localization is guided by integration of plant-wide apico-basal and radial polarity. Pharmacological inhibition of pathways commonly used by polarly localized proteins showed that SOK is localized through a novel mechanism. Mis-expression of SOK1 caused oblique cell divisions and polar localization was required for this activity. We identified a highly conserved N-terminal domain that structurally resembles the DIX domain found in Wnt polarity signalling proteins in animals (Ehebauer & Arias, 2009; Schwarz-Romond et al., 2007). In animals, this domain shows autocatalytic polymerization. SOK1 DIX-LIKE can dimerize and is required for polar edge clustering and biological activity, which shows that the fundamental function of DIX is conserved. Taken together, this chapter revealed a compass of polar axes that guides SOK polar edge localization. In addition, we showed that both plants and animals use the DIX domain in the context of polarity.

    SOK showed striking localization and behavior, but nothing was known about the function of this protein family. In Chapter 4, we studied SOK function by generating sok mutants. We found that small mutations near the N-terminal end of SOK1 sometimes caused fertility defects, but that larger deletions had no effect. The sok1 deletion mutant showed upregulation of the SOK4 gene, which suggests that there may be a compensation mechanism or feedback loop. The potential redundancy between SOK1 and SOK4 led to further investigation of SOK expression and localization throughout the plant. Based on our findings, SOK2 and 3 may be redundant in the leaf, while SOK2, 3 and 5 overlap in the gynoecium.

    As SOK was a completely novel protein family with unknown origin, we aimed to learn more about its evolutionary history. Therefore we investigated the protein sequence, properties and polar localization throughout plant evolution in Chapter 5. We showed that SOK first arose in early land plants, and that they contain several conserved domains that separate SOKs in an ancestral and a more recently evolved type. To assess the conservation of polarity, we studied four SOKs in the moss Physcomitrella patens. One of these tested PpSOKs showed polar edge accumulation in the gametophore, which suggests that edge polarity of SOK proteins is conserved throughout evolution. Next we performed phylogenetic and functional analysis on the DIX domain, which is the most highly conserved domain of SOK. Our results revealed that DIX is present in land plants, animals and the SAR group, and that it is capable of polymerization in all these clades.

    The molecular context of a protein can reveal how it functions within the cell and how it obtains its localization. To address these questions in Chapter 6, we combined biochemistry and cell biology and identified shared and unique interactors of SOK1, SOK2 and SOK3. At least one of these interactors was recruited to the polar SOK1 site in a DIX-LIKE-dependent manner. We extended the network of interaction partners and found that SOK1 interacts with a network of laterally-polar proteins. The secondary interactors revealed links with amongst others the cytoskeleton. Based on these findings, we propose that DIX-like-mediated polymerization creates a polar scaffold that recruits interactors for local tasks. Such tasks may be modification of the cytoskeleton during cell growth or mechanical stress.

    To conclude this thesis, the context and implications of our results were discussed in Chapter 7. In this discussion, we also provide an outlook for the future and suggestions for application of our results in research and biotechnology.

    Arabidopsis WRKY50 and TGA transcription factors synergistically activate expression of PR1
    Hussain, Rana M.F. ; Sheikh, Arsheed H. ; Haider, Imran ; Quareshy, Mussa ; Linthorst, Huub J.M. - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Arabidopsis - AtWRKY50 - EMSA - PR1 - SAR - TGA

    Arabidopsis PR1 is a salicylic acid (SA) inducible marker gene for systemic acquired resistance (SAR). However, the regulation of PR1 in plants is poorly understood. In this study, we showed that AtWRKY50 transcription factor binds to two promoter elements of PR1 via its DNA binding domain. Interestingly, the DNA-binding sites for AtWRKY50 deviate significantly from the consensus WRKY binding W-box. The binding sites are located in close proximity to the binding sites for TGA transcription factors. Transactivation experiments in Arabidopsis protoplasts derived from wild type, npr1-1 and tga256 mutant plants indicated that AtWRKY50 alone was able to induce expression of a PR1::β-glucuronidase (GUS) reporter gene, independent of TGAs or NPR1. However, co-expression of TGA2 or TGA5 with AtWRKY50 synergistically enhanced expression to high levels. Yeast-2-hybrid assays and bimolecular fluorescence complementation (BiFC) experiments revealed that AtWRKY50 could interact with TGA2 and TGA5. Using electrophoretic mobility shift assays (EMSA) it was established that AtWRKY50 and TGA2 or TGA5 simultaneously bind to the PR1 promoter. Taken together, these results support a role of AtWRKY50 in SA-induced expression of PR1. Highlights: AtWRKY50 specifically binds to LS10 region of PR1 promoter and interacts with TGAs to synergistically activate PR1 expression.

    Experimenting with a novel technology for provision of safe drinking water in rural Bangladesh: The case of sub-surface arsenic removal (SAR)
    Kundu, D.K. ; Gupta, A. ; Mol, A.P.J. ; Rahman, M.M. ; Halem, Doris van - \ 2018
    Technology in Society 53 (2018). - ISSN 0160-791X - p. 161 - 172.
    Arsenic contamination - Safe drinking water - Socio-technical experiment - Sub-surface arsenic removal - Bangladesh
    Subsurface Arsenic Removal (SAR) is a technique used for in-situ removal of naturally occurring arsenic in groundwater. This new technology was deployed recently on an experimental basis in two sites in rural Bangladesh, to address the pressing problem of rural drinking water supplies contaminated by arsenic. This article assesses whether and to what extent these first field experiments with SAR can be conceptualized as “socio-technical experiments” designed to incubate and improve radical technological innovations by serving as ‘living lab”, “window” and/or “agent of change”. As per writings in transition theory, an experiment functions as a living lab if it permits testing, learning and improving upon a technological innovation. It functions as a window if it is able to facilitate communication and conversation by raising actors’ interest and enrolling new actors. It functions as an agent of change if it can successfully stimulate changes in potential users' practices and behaviours. Through studying two SAR experiments, this article finds that this novel technology served as a living lab and window, but not (yet) as agent of change, partly because integrating social considerations (such as community buy-in, appropriate site selection and post-installation support) into SAR prototype design during field experimentation proved very difficult. A key obstacle was that the technical efficacy of the technology remained a primary concern during experimentation, and it was unsafe to make water deriving from experimental SAR units available to users. The technology thus remained an abstract idea and provided unable to stimulate behavioural changes amongst users. We conclude that there is a need to identify conditions under which real world experiments can serve as agents of change to facilitate sustainable uptake of arsenic safe technologies in rural developing country contexts.
    The Perfect Match: Simultaneous Strawberry Pollination and Bio-Sampling of the Plant Pathogenic Bacterium Erwinia pyrifoliae by Honey Bees Apis mellifera
    Steen, Sjef van der; Bergsma-Vlami, M. ; Wenneker, M. - \ 2018
    Sustainable Agriculture Research 7 (2018)1. - ISSN 1927-050X - p. 25 - 32.
    In this study we show that honey bee colonies placed in a greenhouse for pollination of strawberry can simultaneously be used to indicate the presence of the plant pathogenic bacterium Erwinia pyrifoliae. This was demonstrated by using two methods of qualitative sacrificial and non-sacrificial bio sampling of the honey bee colony. A novel method for non-sacrificial subsampling, named the Beehold device, was applied. Applying the Beehold device did not disturb or affect negatively the honey bee colony. The study demonstrated that the integration of pollination service and bio-sampling functioned. In the sacrificially derived honey bee subsamples, E. pyrifoliae was detected prior to any visible infection in the plant; however, E. pyrifoliae was detected via non-sacrificial sampling at the same time as plant infection was first observed. The Beehold device is a practical tool for monitoring plant pathogens via forager bees during flowering until fruit onset, but is not as sensitive as directly sampling honey bees.
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