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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    ENIGMA and global neuroscience : A decade of large-scale studies of the brain in health and disease across more than 40 countries
    Thompson, Paul M. ; Jahanshad, Neda ; Ching, Christopher R.K. ; Salminen, Lauren E. ; Thomopoulos, Sophia I. ; Bright, Joanna ; Baune, Bernhard T. ; Bertolín, Sara ; Bralten, Janita ; Bruin, Willem B. ; Bülow, Robin ; Chen, Jian ; Chye, Yann ; Dannlowski, Udo ; Kovel, Carolien G.F. de; Donohoe, Gary ; Eyler, Lisa T. ; Faraone, Stephen V. ; Favre, Pauline ; Filippi, Courtney A. ; Frodl, Thomas ; Garijo, Daniel ; Gil, Yolanda ; Grabe, Hans J. ; Grasby, Katrina L. ; Hajek, Tomas ; Han, Laura K.M. ; Hatton, Sean N. ; Hilbert, Kevin ; Ho, Tiffany C. ; Holleran, Laurena ; Homuth, Georg ; Hosten, Norbert ; Houenou, Josselin ; Ivanov, Iliyan ; Jia, Tianye ; Kelly, Sinead ; Klein, Marieke ; Kwon, Jun Soo ; Laansma, Max A. ; Leerssen, Jeanne ; Lueken, Ulrike ; Nunes, Abraham ; Neill, Joseph O. ; Opel, Nils ; Piras, Fabrizio ; Piras, Federica ; Postema, Merel C. ; Pozzi, Elena ; Wang, Lei - \ 2020
    Translational Psychiatry 10 (2020)1. - ISSN 2158-3188 - 1 p.

    This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.

    Assessing the sensitivity and repeatability of permanganate oxidizable carbon as a soil health metric: An interlab comparison across soils
    Wade, Jordon ; Maltais-Landry, Gabriel ; Lucas, Dawn E. ; Bongiorno, Giulia ; Bowles, Timothy M. ; Calderón, Francisco J. ; Culman, Steve W. ; Daughtridge, Rachel ; Ernakovich, Jessica G. ; Fonte, Steven J. ; Giang, Dinh ; Herman, Bethany L. ; Guan, Lindsey ; Jastrow, Julie D. ; Loh, Bryan H.H. ; Kelly, Courtland ; Mann, Meredith E. ; Matamala, Roser ; Miernicki, Elizabeth A. ; Peterson, Brandon ; Pulleman, Mirjam M. ; Scow, Kate M. ; Snapp, Sieglinde S. ; Thomas, Vanessa ; Tu, Xinyi ; Wang, Daoyuan ; Jelinski, Nicolas A. ; Liles, Garrett C. ; Barrios-Masias, Felipe H. ; Rippner, Devin A. ; Silveira, Maria L. ; Margenot, Andrew J. - \ 2020
    Geoderma 366 (2020). - ISSN 0016-7061

    Soil organic matter is central to the soil health framework. Therefore, reliable indicators of changes in soil organic matter are essential to inform land management decisions. Permanganate oxidizable carbon (POXC), an emerging soil health indicator, has shown promise for being sensitive to soil management. However, strict standardization is required for widespread implementation in research and commercial contexts. Here, we used 36 soils—three from each of the 12 USDA soil orders—to determine the effects of sieve size and soil mass of analysis on POXC results. Using replicated measurements across 12 labs in the US and the EU (n = 7951 samples), we quantified the relative importance of 1) variation between labs, 2) variation within labs, 3) effect soil mass, and 4) effect of soil sieve size on the repeatability of POXC. We found a wide range of overall variability in POXC values across labs (0.03 to 171.8%; mean = 13.4%), and much of this variability was attributable to within-lab variation (median = 6.5%) independently of soil mass or sieve size. Greater soil mass (2.5 g) decreased absolute POXC values by a mean of 177 mg kg−1 soil and decreased analytical variability by 6.5%. For soils with organic carbon (SOC) >10%, greater soil mass (2.5 g) resulted in more frequent POXC values above the limit of detection whereas the lower soil mass (0.75 g) resulted in POXC values below the limit of detection for SOC contents <5%. A finer sieve size increased absolute values of POXC by 124 mg kg−1 while decreasing the analytical variability by 1.8%. In general, soils with greater SOC contents had lower analytical variability. These results point to potential standardizations of the POXC protocol that can decrease the variability of the metric. We recommend that the POXC protocol be standardized to use 2.5 g for soils <10% SOC. Sieve size was a relatively small contributor to analytical variability and therefore we recommend that this decision be tailored to the study purpose. Tradeoffs associated with these standardizations can be mitigated, ultimately providing guidance on how to standardize POXC for routine analysis.

    Uncertainty in times of medical emergency: Knowledge gaps and structural ignorance during the Brazilian Zika crisis
    Kelly, Ann H. ; Lezaun, Javier ; Löwy, Ilana ; Matta, Gustavo Corrêa ; Oliveira Nogueira, Carolina de; Rabello, Elaine Teixeira - \ 2020
    Social Science and Medicine 246 (2020). - ISSN 0277-9536
    Brazil - Emergency research - Public health emergency - Uncertainty - Zika

    Uncertainty was a defining feature of the Brazilian Zika crisis of 2015–2016. The cluster of cases of neonatal microcephaly detected in the country's northeast in the second half of 2015, and the possibility that a new virus transmitted by Aedes mosquitoes was responsible for this new syndrome, created a deep sense of shock and confusion in Brazil and around the world. When in February 2016 the WHO declared a Public Health Emergency of International Concern (PHEIC), it noted that it did so on the basis of what was not known about the virus and its pathogenic potential. To better understand the role that non-knowledge played in the unfolding of the Brazilian Zika crisis we differentiate between three different kinds of uncertainty: global health uncertainty, public health uncertainty, and clinical uncertainty. While these three forms of uncertainty were difficult to disentangle in the early weeks of the crisis, very soon each one began to trace a distinct trajectory. Global health uncertainty centered on the question of the causative link between Zika virus infection and congenital malformations, and was declared resolved by the time the PHEIC was lifted in November 2016. Public health and clinical uncertainty, in contrast, persisted over a longer period of time and did, in some important ways, become entrenched. This taxonomy of uncertainties allows us to explore the systematic nonproduction of knowledge in times of medical emergency, and suggests structural limitations in the framework of “emergency research” that global health institutions have developed to deal with unexpected threats.

    The importance of vector control for the control and elimination of vector-borne diseases
    Wilson, Anne L. ; Courtenay, Orin ; Kelly-Hope, Louise A. ; Scott, Thomas W. ; Takken, Willem ; Torr, Steve J. ; Lindsay, Steve W. - \ 2020
    PLoS Neglected Tropical Diseases 14 (2020)1. - ISSN 1935-2727 - p. e0007831 - e0007831.

    Vector-borne diseases (VBDs) such as malaria, dengue, and leishmaniasis exert a huge burden of morbidity and mortality worldwide, particularly affecting the poorest of the poor. The principal method by which these diseases are controlled is through vector control, which has a long and distinguished history. Vector control, to a greater extent than drugs or vaccines, has been responsible for shrinking the map of many VBDs. Here, we describe the history of vector control programmes worldwide from the late 1800s to date. Pre 1940, vector control relied on a thorough understanding of vector ecology and epidemiology, and implementation of environmental management tailored to the ecology and behaviour of local vector species. This complex understanding was replaced by a simplified dependency on a handful of insecticide-based tools, particularly for malaria control, without an adequate understanding of entomology and epidemiology and without proper monitoring and evaluation. With the rising threat from insecticide-resistant vectors, global environmental change, and the need to incorporate more vector control interventions to eliminate these diseases, we advocate for continued investment in evidence-based vector control. There is a need to return to vector control approaches based on a thorough knowledge of the determinants of pathogen transmission, which utilise a range of insecticide and non-insecticide-based approaches in a locally tailored manner for more effective and sustainable vector control.

    Mass spectrometry searches using MASST
    Wang, Mingxun ; Jarmusch, Alan K. ; Vargas, Fernando ; Aksenov, Alexander A. ; Gauglitz, Julia M. ; Weldon, Kelly ; Petras, Daniel ; Silva, Ricardo da; Quinn, Robert ; Melnik, Alexey V. ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Aceves, Christine M. ; Panitchpakdi, Morgan ; Brown, Elizabeth ; Ottavio, Francesca Di; Sikora, Nicole ; Elijah, Emmanuel O. ; Labarta-Bajo, Lara ; Gentry, Emily C. ; Shalapour, Shabnam ; Kyle, Kathleen E. ; Puckett, Sara P. ; Watrous, Jeramie D. ; Carpenter, Carolina S. ; Bouslimani, Amina ; Ernst, Madeleine ; Swafford, Austin D. ; Zúñiga, Elina I. ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Loomba, Rohit ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Biotechnology 38 (2020). - ISSN 1087-0156 - p. 23 - 26.
    Mud Motor Sedimentation Erosion bars dataset
    Puijenbroek, Marinka van; Baptist, Martin ; Elschot, Kelly ; Regteren, Marin van; Groot, Alma de - \ 2020
    Wageningen University & Research
    Salt marsh - Sediment dynamics - Vegetation
    Data of the sedimentation and vegetation at the Mud Motor salt marsh and a control site. The data is collected from 2015 - 2019. The sedimentation is collected with a Sedimentation Erosion Bar every two months, the presence and cover of plants species is recorded every year in August/September.
    Towards an integrative understanding of soil biodiversity
    Thakur, Madhav P. ; Phillips, Helen R.P. ; Brose, Ulrich ; Vries, Franciska T. De; Lavelle, Patrick ; Loreau, Michel ; Mathieu, Jerome ; Mulder, Christian ; Putten, Wim H. Van der; Rillig, Matthias C. ; Wardle, David A. ; Bach, Elizabeth M. ; Bartz, Marie L.C. ; Bennett, Joanne M. ; Briones, Maria J.I. ; Brown, George ; Decaëns, Thibaud ; Eisenhauer, Nico ; Ferlian, Olga ; Guerra, Carlos António ; König-Ries, Birgitta ; Orgiazzi, Alberto ; Ramirez, Kelly S. ; Russell, David J. ; Rutgers, Michiel ; Wall, Diana H. ; Cameron, Erin K. - \ 2020
    Biological Reviews 95 (2020)2. - ISSN 1464-7931 - p. 350 - 364.
    alpha diversity - beta diversity - biodiversity theory - metacommunity theory - neutral theory - niche theory - spatial scale - species–energy relationship - theory of island biogeography

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

    A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
    Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick A. ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Zvoleff, Alexander ; Sutherland, Chris ; Tenan, Simone - \ 2020
    Ecography 43 (2020)1. - ISSN 0906-7590 - p. 75 - 84.
    The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
    Environmental impact assessment of water-saving irrigation systems across 60 irrigation construction projects in northern China
    Chen, Xiuzhi ; Thorp, Kelly R. ; Oel, Pieter R. van; Xu, Zhenci ; Zhou, Bo ; Li, Yunkai - \ 2020
    Journal of Cleaner Production 245 (2020). - ISSN 0959-6526
    Carbon footprint - Environmental impact - Irrigation project - Life cycle assessment - Scenario - Water footprint

    With increasing water shortages partly due to increasing demands, water has become a globally relevant issue especially in arid and semi-arid regions. Water-saving irrigation technologies provide new ways for improving the efficiency of water use for agricultural production. Although efficient irrigation management could lead to water savings and increased yields, the water consumption and greenhouse gas emissions during the construction of irrigation projects also puts pressure on environmental health. However, little research has considered the environmental impact of the construction process and materials. To fill this gap, the water footprint (WF) and carbon footprint (CF) of irrigation projects were calculated using life cycle assessment (LCA) methods. The results for sixty typical irrigation projects in northern China showed that the WF accounted for only 0.2–1.5% of the total agricultural WF and 2.3–8.8% of the water saved. When the WF to construct modern irrigation systems is not considered, the water-saving effects of these systems are generally overestimated by 13%. The CF for irrigation projects was 42.0% of all agricultural activities. Due to the difficulty to obtain detailed information for irrigation projects, this paper established the relationship between financial investment or area and CF for three kinds of irrigation projects. It provided a simple quantitative method for assessing its environmental impacts. By comparing environmental impacts and production benefits under different scenarios, using drip irrigation over the long-term could increase crop yield and reduce water footprint, but carbon footprint was increased at the same time. This study suggests that it is necessary to assess the environmental impacts of irrigation construction projects from a life cycle perspective rather focusing only on yield increases and reductions in irrigation amounts.

    Understanding the acceptability of wolf management actions: Roles of cognition and emotion
    Straka, Tanya M. ; Miller, Kelly ; Jacobs, M.H. - \ 2020
    Human Dimensions of Wildlife 25 (2020)1. - ISSN 1087-1209 - p. 33 - 46.
    Wolf management actions are seldom universally accepted and understanding diverse opinions is of value for conservation practitioners. Previous research has either investigated cognitions or emotions to understand public acceptability of wolf management actions. We investigated both concepts simultaneously to identify whether their predictive potentials are mutually exclusive. A survey measuring wildlife value orientations, valence (positive-negative emotions) toward wolves, and responses to wolf management actions (doing nothing, public education, lethal control) was completed by 597 Dutch and German university students. Valence predicted the acceptability of all wolf management actions. Wildlife value orientations predicted the acceptability of lethal control and partially public education but not of doing nothing. Emotions thus added predictive potential next to cognitions to understand responses to wolf management actions. For both research and practice, it is important to acknowledge that the acceptability of wolf management actions is not only guided by what people think, but also by what they feel.
    Essential amino acid profile of metabolizable protein affects mammary gland amino acid metabolism in diary cattle
    Nichols, Kelly - \ 2019
    Feeding the mammary gland: energy and amino acid partitioning in lactating dairy cattle
    Nichols, Kelly - \ 2019
    Protein efficiency in dairy cows: Feeding the mammary gland
    Nichols, Kelly - \ 2019
    FACCE ERA-GAS Overview of the ERA-NET Cofund Action, highlights of the joint transnational research calls & abstracts of the funded research projects
    Kuzniar-van der Zee, Brenda ; Zisopoulos, F.K. ; Bunthof, C.J. ; Kelly, R. - \ 2019
    FACCE ERA-GAS - 20 p.
    Protein efficiency in dairy cows: Feeding the mammary gland
    Nichols, Kelly - \ 2019
    A large-scale field experiments on salt marsh construction in the Ems estuary, the Netherlands
    Baptist, M.J. ; Dankers, P. ; Cleveringa, J. ; Sittoni, L. ; Willemsen, P. ; Elschot, Kelly ; Puijenbroek, M.E.B. van; Hendriks, M. - \ 2019
    In: RCEM 2019" the 11th symposium on river, coastal and estuarine morphodynamics: book of abstracs. - - p. 95 - 95.
    Impact of postabsorptive energy source on mammary gland amino acid metabolism in dairy cattle
    Nichols, Kelly - \ 2019
    TMAP Kwelders (2019) : Tussenrapportage WOT-04-009-035.02
    Elschot, Kelly ; Puijenbroek, M.E.B. van; Wal, J.T. van der; Sonneveld, C. ; Lagendijk, D.D.G. - \ 2019
    The Nitrogen issue: Typically Dutch?
    Giller, Ken ; Parodi, Alejandro ; Nichols, Kelly ; Schmidt, Alena - \ 2019
    Digitalisation in the New Zealand Agricultural Knowledge and Innovation System : Initial understandings and emerging organisational responses to digital agriculture
    Rijswijk, Kelly ; Klerkx, Laurens ; Turner, James A. - \ 2019
    NJAS Wageningen Journal of Life Sciences 90-91 (2019). - ISSN 1573-5214
    Advisors - AKIS - Digital agriculture - Digitalisation - Organisational change - Organisational identity - Research organisations - Smart farming

    Digital agriculture is likely to transform productive processes both on- and off- farm, as well as the broader social and institutional context using digital technologies. It is largely unknown how agricultural knowledge providing organisations, such as advisors and science organisations, understand and respond to digital agriculture. The concept of ‘organisational identity’ is used to describe both initial understandings of, and emerging responses, to digital agriculture, which together show how organisations ‘digi-grasp’, i.e. make sense of and enact digitalisation in their organisations. The understanding is described using aspects of identity change (i.e. the nature, pace, source and context of digital agriculture), while the responses are outlined through the various attributes of organisational identity (i.e. capabilities, practices, services, clients, partners, purpose and values). We explore this question in the context of New Zealand through 29 semi-structured interviews with different types of agricultural knowledge providers, including farm advisors, science organisations, as well as technology providers. The findings show that digitalisation is often understood as farm-centric, despite being considered disruptive both on- and off-farm. These understandings influence an organisation's digitalisation responses to digital agriculture. The responses were often ad-hoc, starting with adapting organisational capabilities, practices and services as their clients and partners require, rather than a strategic approach allowing for more flexibility of roles and processes and changing business models. The ad-hoc approach appears to be a response to uncertainty as digital agriculture is in early stages of development. This indicates that agricultural knowledge and innovation system should better support agricultural knowledge providers in digi-grasping and developing a digitalisation strategy, by anticipating possible futures and reflecting on the consequences of these for value propositions, business models and organisational identities of agricultural knowledge providers.

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