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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    2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
    Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
    Archives of Virology (2020). - ISSN 0304-8608

    In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

    Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene
    Dhillon, Braham ; Kema, Gert H.J. ; Hamelin, Richard C. ; Bluhm, Burt H. ; Goodwin, Stephen B. - \ 2019
    Mobile DNA 10 (2019)1. - ISSN 1759-8753
    Fungal evolution - Genome evolution - Purifying selection - Transduplication

    Background: Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-Aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis, was analyzed in greater detail. Results: These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina. Conclusions: These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.

    Comparison of the Health Benefits of Different Types of Nature
    Vries, Sjerp De - \ 2019
    JAMA Network Open 2 (2019)7. - ISSN 2574-3805 - 2 p.
    In their study, Astell-Burt and Feng1 address 2 important limitations of much of the research on contact with nearby nature and human health and well-being.2 The first one is its cross-sectional design, preventing the ability to draw firm conclusions regarding the causality of observed associations. The second one is that most studies do not distinguish between different types of green and/or blue space and consequently tell us little about which type of nature is most beneficial. In their study, they begin to address this gap by making efficient use of longitudinal health data already collected for other purposes and enriching these data with land-use data on the availability of green and blue space in the residential environment. Consequently, in addition to prevalence data, incidence data were available on high risk of psychological distress, physician-diagnosed anxiety and/or depression, and less than good self-rated health. Furthermore, they distinguished 3 types of vegetation: tree canopy, grass, and low-lying vegetation. They concluded that tree canopy may be more beneficial than the other 2 types.
    An architectural understanding of natural sway frequencies in trees
    Jackson, T. ; Shenkin, A. ; Moore, J. ; Bunce, A. ; Emmerik, T. Van; Kane, B. ; Burcham, D. ; James, K. ; Selker, J. ; Calders, K. ; Origo, N. ; Disney, M. ; Burt, A. ; Wilkes, P. ; Raumonen, P. ; Gonzalez De Tanago Menaca, J. ; Lau, A. ; Herold, M. ; Goodman, R.C. ; Fourcaud, T. ; Malhi, Y. - \ 2019
    Journal of the Royal Society, Interface 16 (2019)155. - ISSN 1742-5689 - 9 p.
    The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.
    Clostridium difficile in wild rodents and insectivores in the Netherlands
    Krijger, I.M. ; Meerburg, B.G. ; Harmanus, C. ; Burt, S.A. - \ 2019
    Letters in Applied Microbiology (2019). - ISSN 0266-8254
    animal to human - Clostridioides difficile - farms - house mouse - Mus musculus - Rattus rattus - transmission - zoonotic pathogen

    With wild rodents and insectivores being present around humans and their living, working and food production environments, it is important to gain knowledge of the zoonotic pathogens present in these animals. The enteropathogen Clostridium difficile, an opportunistic anaerobic bacteria, can be carried by both animals and humans, and is distributed globally. It is known that there is genetic overlap between human and animal sources of C. difficile. In this study, the aim was to assess the presence of C. difficile in rodents and insectivores trapped on and around pig and cattle farms in the Netherlands. In total 347 rodents and insectivores (10 different species) were trapped and 39·2% tested positive for presence of C. difficile. For all positive samples the ribotype (RT) was determined, and in total there were 13 different RTs found (in descending order of frequency: 057, 010, 029, 005, 073, 078, 015, 035, 454, 014, 058, 062, 087). Six of the RTs isolated from rodents and insectivores are known to be associated with human C. difficile infection; RT005, RT010, RT014, RT015, RT078 and RT087. The presence of rodents and insectivores in and around food production buildings (e.g. farms) could contribute to the spread of C. difficile in the human environment. In order to enable on-farm management for pathogen control, it is essential to comprehend the role of wild rodents and insectivores that could potentially affect the ecology of disease agents on farms. Significance and Impact of the Study: This study shows that rodents and insectivores in and around food production buildings (e.g. farms) can carry Clostridium difficile ribotypes associated with human C. difficile infection (CDI). C. difficile spores in rodent and insectivore droppings are able to survive in the environment for prolonged periods, leading to host-to-host exposure and transmission. Therefore we can state that rodent and insectivore presence on farms is a risk for zoonotic pathogen transmission of C. difficile.

    Taxonomy of the order Bunyavirales : second update 2018
    Maes, Piet ; Adkins, Scott ; Alkhovsky, Sergey V. ; Avšič-Županc, Tatjana ; Ballinger, Matthew J. ; Bente, Dennis A. ; Beer, Martin ; Bergeron, Éric ; Blair, Carol D. ; Briese, Thomas ; Buchmeier, Michael J. ; Burt, Felicity J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, J.C.S. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; DeRisi, Joseph L. ; Digiaro, Michele ; Drebot, Mike ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fulhorst, Charles F. ; Garrison, Aura R. ; Gāo, George Fú ; Gonzalez, Jean Paul J. ; Groschup, Martin H. ; Günther, Stephan ; Haenni, Anne Lise ; Hall, Roy A. ; Hewson, Roger ; Hughes, Holly R. ; Jain, Rakesh K. ; Jonson, Miranda Gilda ; Junglen, Sandra ; Klempa, Boris ; Klingström, Jonas ; Kormelink, Richard ; Lambert, Amy J. ; Langevin, Stanley A. ; Lukashevich, Igor S. ; Marklewitz, Marco ; Martelli, Giovanni P. ; Mielke-Ehret, Nicole ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Naidu, Rayapati ; Zhang, Yong Zhen - \ 2019
    Archives of Virology 164 (2019)3. - ISSN 0304-8608 - p. 927 - 941.

    In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

    Finite element analysis of trees in the wind based on terrestrial laser scanning data
    Jackson, T. ; Shenkin, A. ; Wellpott, A. ; Calders, K. ; Origo, N. ; Disney, M. ; Burt, A. ; Raumonen, P. ; Gardiner, B. ; Herold, M. ; Fourcaud, T. ; Malhi, Y. - \ 2019
    Agricultural and Forest Meteorology 265 (2019). - ISSN 0168-1923 - p. 137 - 144.
    Critical wind speed - Finite element analysis - Resonant frequency - Terrestrial laser scanning - TLS - Wind damage

    Wind damage is an important driver of forest structure and dynamics, but it is poorly understood in natural broadleaf forests. This paper presents a new approach in the study of wind damage: combining terrestrial laser scanning (TLS) data and finite element analysis. Recent advances in tree reconstruction from TLS data allowed us to accurately represent the 3D geometry of a tree in a mechanical simulation, without the need for arduous manual mapping or simplifying assumptions about tree shape. We used this simulation to predict the mechanical strains produced on the trunks of 21 trees in Wytham Woods, UK, and validated it using strain data measured on these same trees. For a subset of five trees near the anemometer, the model predicted a five-minute time-series of strain with a mean cross-correlation coefficient of 0.71, when forced by the locally measured wind speed data. Additionally, the maximum strain associated with a 5 ms−1 or 15 ms-1 wind speed was well predicted by the model (N = 17, R2 = 0.81 and R2 = 0.79, respectively). We also predicted the critical wind speed at which the trees will break from both the field data and models and find a good overall agreement (N = 17, R2 = 0.40). Finally, the model predicted the correct trend in the fundamental frequencies of the trees (N = 20, R2 = 0.38) although there was a systematic underprediction, possibly due to the simplified treatment of material properties in the model. The current approach relies on local wind data, so must be combined with wind flow modelling to be applicable at the landscape-scale or over complex terrain. This approach is applicable at the plot level and could also be applied to open-grown trees, such as in cities or parks.

    Chlamydia psittaci and C. avium in feral pigeon (Columba livia domestica) droppings in two cities in the Netherlands
    Burt, Sara A. ; Röring, Romy E. ; Heijne, Marloes - \ 2018
    Veterinary Quarterly 38 (2018)1. - ISSN 0165-2176 - p. 63 - 66.
    Chlamydia avium - Chlamydia psittaci - feral - Pigeon - psittacosis
    Background: Feral pigeons (Columba livia domestica) live and breed in many city centres and contact with their droppings can be a hazard for human health if the birds carry Chlamydia psittaci. Objective: The aim of this study was to establish whether pigeon droppings in two Dutch cities (Utrecht and Haarlem) contain C. psittaci and/or C. avium, which could be a potential hazard for transmission to humans. Methods: In May 2017 seven feral pigeon ‘hot spots’ with between 5 and 40+ pigeons present were identified in two cities by visual observations over two days. During the following ten days fresh droppings were collected at these hot spots and the samples were pooled per three droppings to achieve 40–41 samples per city. Samples were analysed for Chlamydia DNA with a broad range 23S Chlamydiaceae Real-Time PCR and positive samples were tested with a specific C. psittaci and C. avium Real-Time PCR. Positive C. psittaci samples were genotyped. Results: C. psittaci and C. avium were detected in both cities. For C. psittaci the prevalences in Utrecht and Haarlem were 2.4% and 7.5%, respectively; for C. avium 36.6% and 20.0%, respectively. One sample contained both species. All C. psittaci samples belonged to genotype B. Conclusion: C. psittaci and C. avium are present in feral pigeon droppings in Utrecht and Haarlem. Human contact with droppings from infected pigeons or inhalation of dust from dried droppings represent a potential hazard to public health.
    Estimation of above-ground biomass of large tropical trees with terrestrial LiDAR
    Gonzalez De Tanago, Jose ; Lau, Alvaro ; Bartholomeus, Harm ; Herold, Martin ; Avitabile, Valerio ; Raumonen, Pasi ; Martius, Christopher ; Goodman, Rosa C. ; Disney, Mathias ; Manuri, Solichin ; Burt, Andrew ; Calders, Kim - \ 2018
    Methods in Ecology and Evolution 9 (2018)2. - ISSN 2041-210X - p. 223 - 234.
    1. Tropical forest biomass is a crucial component of global carbon emission estimations. However, calibration and validation of such estimates require accurate and effective methods to estimate in situ above-ground biomass (AGB). Present methods rely on allometric models that are highly uncertain for large tropical trees. Terrestrial laser scanning (TLS) tree modelling has demonstrated to be more accurate than these models to infer forest AGB. Nevertheless, applying TLS methods on tropical large trees is still challenging. We propose a method to estimate AGB of large tropical trees by three-dimensional (3D) tree modelling of TLS point clouds. 2. Twenty-nine plots were scanned with a TLS in three study sites (Peru, Indonesia and Guyana). We identified the largest tree per plot (mean diameter at breast height of 73.5 cm), extracted its point cloud and calculated its volume by 3D modelling its structure using quantitative structure models (QSM) and converted to AGB using species-specific wood density. We also estimated AGB using pantropical and local allometric models. To assess the accuracy of our and allometric methods, we harvest the trees and took destructive measurements. 3. AGB estimates by the TLS–QSM method showed the best agreement in comparison to destructive harvest measurements (28.37% coefficient of variation of root mean square error [CV-RMSE] and concordance correlation coefficient [CCC] of 0.95), outperforming the pantropical allometric models tested (35.6%–54.95% CV-RMSE and CCC of 0.89–0.73). TLS–QSM showed also the lowest bias (overall underestimation of 3.7%) and stability across tree size range, contrasting with the allometric models that showed a systematic bias (overall underestimation ranging 15.2%–35.7%) increasing linearly with tree size. The TLS–QSM method also provided accurate tree wood volume estimates (CV RMSE of 23.7%) with no systematic bias regardless the tree structural characteristics. 4. Our TLS–QSM method accounts for individual tree biophysical structure more effectively than allometric models, providing more accurate and less biased AGB estimates for large tropical trees, independently of their morphology. This non-destructive method can be further used for testing and calibrating new allometric models, reducing the current under-representation of large trees in and enhancing present and past estimates of forest biomass and carbon emissions from tropical forests.
    Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements
    Pfeifer, Marion ; Gonsamo, Alemu ; Woodgate, William ; Cayuela, Luis ; Marshall, Andrew R. ; Ledo, Alicia ; Paine, Timothy C.E. ; Marchant, Rob ; Burt, Andrew ; Calders, Kim ; Courtney-mustaphi, Colin ; Cuni-sanchez, Aida ; Deere, Nicolas J. ; Denu, Dereje ; Gonzalez De Tanago Meñaca, J. ; Hayward, Robin ; Lau Sarmiento, A.I. ; Macía, Manuel J. ; Olivier, Pieter I. ; Pellikka, Petri ; Seki, Hamidu ; Shirima, Deo ; Trevithick, Rebecca ; Wedeux, Beatrice ; Wheeler, Charlotte ; Munishi, Pantaleo K.T. ; Martin, Thomas ; Mustari, Abdul ; Platts, Philip J. - \ 2018
    Forest Ecosystems 5 (2018). - ISSN 2095-6355 - 14 p.
    Background: Canopy structure, defined by leaf area index (LAI), fractional vegetation cover (FCover) and fraction of absorbed photosynthetically active radiation (fAPAR), regulates a wide range of forest functions and ecosystem services. Spatially consistent field-measurements of canopy structure are however lacking, particularly for the tropics. Methods: Here, we introduce the Global LAI database: a global dataset of field-based canopy structure measurements spanning tropical forests in four continents (Africa, Asia, Australia and the Americas). We use these measurements to test for climate dependencies within and across continents, and to test for the potential of anthropogenic disturbance and forest protection to modulate those dependences. Results: Using data collected from 887 tropical forest plots, we show that maximum water deficit, defined across the most arid months of the year, is an important predictor of canopy structure, with all three canopy attributes declining significantly with increasing water deficit. Canopy attributes also increase with minimum temperature, and with the protection of forests according to both active (within protected areas) and passive measures (through topography). Once protection and continent effects are accounted for, other anthropogenic measures (e.g. human population) do not improve the model. Conclusions: We conclude that canopy structure in the tropics is primarily a consequence of forest adaptation to the maximum water deficits historically experienced within a given region. Climate change, and in particular changes in drought regimes may thus affect forest structure and function, but forest protection may offer some resilience against this effect.
    Above-ground biomass assessment of tropical trees with Terrestrial LiDAR and 3D architecture models
    Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Bartholomeus, H.M. ; Herold, M. ; Avitabile, V. ; Raumonen, Pasi ; Martius, Christopher ; Goodman, R.C. ; Disney, Mathias ; Manuri, Solichin ; Burt, Andrew ; Calders, Kim - \ 2017
    In: SilviLaser 2017 Program. - Blacksburg : Virginia Tech - p. 123 - 124.
    Exploring pathways linking greenspace to health : Theoretical and methodological guidance
    Markevych, Iana ; Schoierer, Julia ; Hartig, Terry ; Chudnovsky, Alexandra ; Hystad, Perry ; Dzhambov, Angel M. ; Vries, Sjerp de; Triguero-Mas, Margarita ; Brauer, Michael ; Nieuwenhuijsen, Mark J. ; Lupp, Gerd ; Richardson, Elizabeth A. ; Astell-Burt, Thomas ; Dimitrova, Donka ; Feng, Xiaoqi ; Sadeh, Maya ; Standl, Marie ; Heinrich, Joachim ; Fuertes, Elaine - \ 2017
    Environmental Research 158 (2017). - ISSN 0013-9351 - p. 301 - 317.
    Green spaces - Greenness - Greenspace - Mediation analysis - Pathways

    Background In a rapidly urbanizing world, many people have little contact with natural environments, which may affect health and well-being. Existing reviews generally conclude that residential greenspace is beneficial to health. However, the processes generating these benefits and how they can be best promoted remain unclear. Objectives During an Expert Workshop held in September 2016, the evidence linking greenspace and health was reviewed from a transdisciplinary standpoint, with a particular focus on potential underlying biopsychosocial pathways and how these can be explored and organized to support policy-relevant population health research. Discussions Potential pathways linking greenspace to health are here presented in three domains, which emphasize three general functions of greenspace: reducing harm (e.g. reducing exposure to air pollution, noise and heat), restoring capacities (e.g. attention restoration and physiological stress recovery) and building capacities (e.g. encouraging physical activity and facilitating social cohesion). Interrelations between among the three domains are also noted. Among several recommendations, future studies should: use greenspace and behavioural measures that are relevant to hypothesized pathways; include assessment of presence, access and use of greenspace; use longitudinal, interventional and (quasi)experimental study designs to assess causation; and include low and middle income countries given their absence in the existing literature. Cultural, climatic, geographic and other contextual factors also need further consideration. Conclusions While the existing evidence affirms beneficial impacts of greenspace on health, much remains to be learned about the specific pathways and functional form of such relationships, and how these may vary by context, population groups and health outcomes. This Report provides guidance for further epidemiological research with the goal of creating new evidence upon which to develop policy recommendations.

    Data acquisition considerations for Terrestrial Laser Scanning of forest plots
    Wilkes, Phil ; Lau Sarmiento, Alvaro ; Disney, Mathias ; Calders, Kim ; Burt, Andrew ; Gonzalez De Tanago Meñaca, J. ; Bartholomeus, Harm ; Brede, Benjamin ; Herold, Martin - \ 2017
    Remote Sensing of Environment 196 (2017). - ISSN 0034-4257 - p. 140 - 153.
    The poor constraint of forest Above Ground Biomass (AGB) is responsible, in part, for large uncertainties in modelling future climate scenarios. Terrestrial Laser Scanning (TLS) can be used to derive unbiased and non-destructive estimates of tree structure and volume and can, therefore, be used to address key uncertainties in forest AGB estimates. Here we review our experience of TLS sampling strategies from 27 campaigns conducted over the past 5 years, across tropical and temperate forest plots, where data was captured with a RIEGL VZ-400 laser scanner. The focus is on strategies to derive Geometrical Modelling metrics (e.g. tree volume) over forest plots (≥1 ha) which require the accurate co-registration of 10s to 100s of individual point clouds. We recommend a 10 m × 10 m sampling grid as an approach to produce a point cloud with a uniform point distribution, that can resolve higher order branches (down to a few cm in diameter) towards the top of 30+ m canopies and can be captured in a timely fashion i.e. ∼3–6 days per ha. A data acquisition protocol, such as presented here, would facilitate data interoperability and inter-comparison of metrics between instruments/groups, from plot to plot and over time.
    Evaluation of the Range Accuracy and the Radiometric Calibration of Multiple Terrestrial Laser Scanning Instruments for Data Interoperability
    Calders, Kim ; Disney, Mathias I. ; Armston, John ; Burt, Andrew ; Brede, Benjamin ; Origo, Niall ; Muir, Jasmine ; Nightingale, Joanne - \ 2017
    IEEE Transactions on Geoscience and Remote Sensing 55 (2017)5. - ISSN 0196-2892 - p. 2716 - 2724.
    Terrestrial laser scanning (TLS) data provide 3-D measurements of vegetation structure and have the potential to support the calibration and validation of satellite and airborne sensors. The increasing range of different commercial and scientific TLS instruments holds challenges for data and instrument interoperability. Using data from various TLS sources will be critical to upscale study areas or compare data. In this paper, we provide a general framework to compare the interoperability of TLS instruments. We compare three TLS instruments that are the same make and model, the RIEGL VZ-400. We compare the range accuracy and evaluate the manufacturer's radiometric calibration for the uncalibrated return intensities. Our results show that the range accuracy between instruments is comparable and within the manufacturer's specifications. This means that the spatial XYZ data of different instruments can be combined into a single data set. Our findings demonstrate that radiometric calibration is instrument specific and needs to be carried out for each instrument individually before including reflectance information in TLS analysis. We show that the residuals between the calibrated reflectance panels and the apparent reflectance measured by the instrument are greatest for highest reflectance panels (residuals ranging from 0.058 to 0.312).
    Data from: "African savanna-forest boundary dynamics: a 20-year study"
    Cuni-sanchez, Aida ; White, Lee J.T. ; Calders, K. ; Jeffery, Kathryn J. ; Abernethy, Katharine ; Burt, Andrew ; Disney, Mathias ; Gilpin, Martin ; Gomez-dans, Jose L. ; Lewis, Simon L. - \ 2016
    Wageningen University & Research
    Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of forest-savanna boundary change over time. Using long-term inventory plots we quantify changes in above-ground biomass (AGB), vegetation structure and biodiversity over 20 years for five vegetation types (savanna, colonising forest or F1, successional monodominant forest or F2, Marantaceae forest or F3 and mixed forest or F4) along a savanna-forest transition of central Gabon, all occurring on similar soils. Additionally, we use novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences across the transition. Overall, F1 and F2 forests increased in AGB, mainly as a result of adding stems (recruitment in F1) or increased Basal Area (F2). Some plots of F3 and F4 increased in AGB while some decreased. Changes in biodiversity and species’ dominance were small. After 20 years no plot could be classified as having moved to the next stage in the succession. TLS vertical plant profiles showed very distinctive differences amongst the vegetation types. We highlight two relevant points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store important quantities of Carbon. Decades long-term monitoring is likely to be required to assess the speed of transition between vegetation types, ideally with TLS, as this provides more objective forest classifications than inventory monitoring.
    3D Measurements of Tropical Forest Structure for BIOMASS, Morphology and Calibration and Validation of Satellite Observations
    Disney, Mathias ; Burt, Andrew ; Calders, K. ; Raumonen, P. ; Herold, M. ; Lewis, P. ; Lewis, S. ; Boni Vicari, M. ; Rowland, L. ; Meir, P. ; Mitchard, Edward - \ 2016
    Erratum to: Hepatitis E Virus in Farmed Rabbits, Wild Rabbits and Petting Farm Rabbits in the Netherlands
    Burt, Sara A. ; Veltman, Jorg ; Honing-Hakze, Renate van der; Schmitt, Heike ; Poel, Wim H.M. van der - \ 2016
    Food and Environmental Virology 8 (2016)4. - ISSN 1867-0334 - p. 313 - 313.
    African Savanna-Forest Boundary Dynamics: A 20-Year Study
    Cuni-Sanchez, Aida ; White, Lee J.T. ; Calders, Kim ; Jeffery, Kathryn J. ; Abernethy, Katharine ; Burt, Andrew ; Disney, Mathias ; Gilpin, Martin ; Gomez-Dans, Jose L. ; Lewis, Simon L. - \ 2016
    PLoS ONE 11 (2016)6. - ISSN 1932-6203
    Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types.
    Hepatitis E Virus in Farmed Rabbits, Wild Rabbits and Petting Farm Rabbits in the Netherlands
    Burt, Sara A. ; Veltman, Jorg ; Hakze-van der Honing, Renate ; Schmitt, Heike ; Poel, Wim H.M. van der - \ 2016
    Food and Environmental Virology 8 (2016)3. - ISSN 1867-0334 - p. 227 - 229.
    Hepatitis E - HEV - Rabbits - Zoonosis

    Rabbits have been suggested as a zoonotic source of Hepatitis E virus. Phylogenetic analysis of HEV isolates from farmed, wild and pet rabbits in the Netherlands (23, 0, and 60 % respectively) showed them to be grouped amongst published rabbit HEV sequences and distinct from most human isolates. Dutch rabbits are unlikely to be a zoonotic source.

    New measurements of biomass and structure in tropical forests
    Disney, M. ; Burt, A. ; Calders, K. ; Cuni Sanchez, A. ; Avitabile, V. ; Lewis, S. ; Gonzalez de Tanago Meñaca, J. ; Herold, M. ; Raumonen, P. ; Lewis, P. - \ 2015
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