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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    Effects and moderators of coping skills training on symptoms of depression and anxiety in patients with cancer : Aggregate data and individual patient data meta-analyses
    Buffart, L.M. ; Schreurs, M.A.C. ; Abrahams, H.J.G. ; Kalter, J. ; Aaronson, N.K. ; Jacobsen, P.B. ; Newton, R.U. ; Courneya, K.S. ; Armes, J. ; Arving, C. ; Braamse, A.M. ; Brandberg, Y. ; Dekker, J. ; Ferguson, R.J. ; Gielissen, M.F. ; Glimelius, B. ; Goedendorp, M.M. ; Graves, K.D. ; Heiney, S.P. ; Horne, R. ; Hunter, M.S. ; Johansson, B. ; Northouse, L.L. ; Oldenburg, H.S. ; Prins, J.B. ; Savard, J. ; Beurden, M. van; Berg, S.W. van den; Brug, J. ; Knoop, H. ; Verdonck-de Leeuw, I.M. - \ 2020
    Clinical Psychology Review 80 (2020). - ISSN 0272-7358
    (individual patient data) meta-analysis - Anxiety - Coping skills training - Depression - Neoplasm - Psychosocial care

    Purpose: This study evaluated the effects of coping skills training (CST) on symptoms of depression and anxiety in cancer patients, and investigated moderators of the effects. Methods: Overall effects and intervention-related moderators were studied in meta-analyses of pooled aggregate data from 38 randomized controlled trials (RCTs). Patient-related moderators were examined using linear mixed-effect models with interaction tests on pooled individual patient data (n = 1953) from 15 of the RCTs. Results: CST had a statistically significant but small effect on depression (g = −0.31,95% confidence interval (CI) = −0.40;-0.22) and anxiety (g = −0.32,95%CI = -0.41;-0.24) symptoms. Effects on depression symptoms were significantly larger for interventions delivered face-to-face (p =.003), led by a psychologist (p =.02) and targeted to patients with psychological distress (p =.002). Significantly larger reductions in anxiety symptoms were found in younger patients (pinteraction < 0.025), with the largest reductions in patients <50 years (β = −0.31,95%CI = -0.44;-0.18) and no significant effects in patients ≥70 years. Effects of CST on depression (β = −0.16,95%CI = -0.25;-0.07) and anxiety (β = −0.24,95%CI = -0.33;-0.14) symptoms were significant in patients who received chemotherapy but not in patients who did not (pinteraction < 0.05). Conclusions: CST significantly reduced symptoms of depression and anxiety in cancer patients, and particularly when delivered face-to-face, provided by a psychologist, targeted to patients with psychological distress, and given to patients who were younger and received chemotherapy.

    Zooming in on mechanistic predator–prey ecology : Integrating camera traps with experimental methods to reveal the drivers of ecological interactions
    Smith, Justine A. ; Suraci, Justin P. ; Hunter, Jennifer S. ; Gaynor, Kaitlyn M. ; Keller, Carson B. ; Palmer, Meredith S. ; Atkins, Justine L. ; Castañeda, Irene ; Cherry, Michael J. ; Garvey, Patrick M. ; Huebner, Sarah E. ; Morin, Dana J. ; Teckentrup, Lisa ; Weterings, Martijn J.A. ; Beaudrot, Lydia - \ 2020
    Journal of Animal Ecology 89 (2020)9. - ISSN 0021-8790 - p. 1997 - 2012.
    antipredator behaviour - camera trap - detection - experiments - landscape of fear - predator recognition - prey selection

    Camera trap technology has galvanized the study of predator–prey ecology in wild animal communities by expanding the scale and diversity of predator–prey interactions that can be analysed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator–prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive predator and prey behaviour, incorporating environmental realism not possible in the laboratory while benefiting from the distinct capacity of camera traps to generate large datasets from multiple species with minimal observer interference. However, such pairings of camera traps with experimental methods remain underutilized. We review recent advances in the experimental application of camera traps to investigate fundamental mechanisms underlying predator–prey ecology and present a conceptual guide for designing experimental camera trap studies. Only 9% of camera trap studies on predator–prey ecology in our review use experimental methods, but the application of experimental approaches is increasing. To illustrate the utility of camera trap-based experiments using a case study, we propose a study design that integrates observational and experimental techniques to test a perennial question in predator–prey ecology: how prey balance foraging and safety, as formalized by the risk allocation hypothesis. We discuss applications of camera trap-based experiments to evaluate the diversity of anthropogenic influences on wildlife communities globally. Finally, we review challenges to conducting experimental camera trap studies. Experimental camera trap studies have already begun to play an important role in understanding the predator–prey ecology of free-living animals, and such methods will become increasingly critical to quantifying drivers of community interactions in a rapidly changing world. We recommend increased application of experimental methods in the study of predator and prey responses to humans, synanthropic and invasive species, and other anthropogenic disturbances.

    Ecomorphology of largemouth bass relative to a native trophic analogue explains its high invasive impact
    Luger, A.M. ; South, J. ; Alexander, M.E. ; Ellender, B.R. ; Weyl, O.L.F. ; Nagelkerke, L.A.J. - \ 2020
    Biological Invasions 22 (2020). - ISSN 1387-3547 - p. 2223 - 2233.
    Competition - Conservation - Freshwater - Functional traits - Handling time

    Predicting and understanding the impact of biological invaders is a global ecological imperative. Progress has been made through the application of phenomenological analysis via comparative functional response analysis. However, little is known about the mechanisms which drive high-magnitude functional responses of invasive species, especially when compared to trophically analogous natives. Largemouth bass Micropterus salmoides is a freshwater invasive species evaluated as a more efficient predator, with a higher-magnitude functional response, compared to a native analogue, the Cape kurper Sandelia capensis. In order to determine what traits drive this difference we quantified handling time behaviours (detection time, catch time, processing time) of both predator species and prey/predator size ratio, and employ an ecomorphological approach to determine whether largemouth bass is a more specialised predator than Cape kurper. There was no difference in detection time between the species, but largemouth bass were significantly and on average five times faster at catching prey than Cape kurper. Both species’ processing time was positively related to prey size, but Cape kurper was on average 4.5 times faster than largemouth bass. Ecomorphological data indicate that largemouth bass was the more specialised pursuit hunter for fish, whereas Cape kurper was better at ambush hunting. This suggests that the ecological impact of largemouth bass may be exacerbated in areas where there is habitat simplification which can lead to the extirpation of local small-bodied fish. In addition, there may be non-consumptive detrimental effects on trophically analogous natives through competitive exclusion.

    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    From Bush Mangoes to Bouillon Cubes : Wild Plants and Diet among the Baka, Forager-Horticulturalists from Southeast Cameroon
    Gallois, Sandrine ; Heger, Thomas ; Andel, Tinde van; Sonké, Bonaventure ; Henry, Amanda G. - \ 2020
    Economic Botany 74 (2020). - ISSN 0013-0001 - p. 46 - 58.
    Edibles - Ethnobotany - Food behavior - Food preferences - Hunter-gatherers - Nutritional transition

    Increasing deforestation affects tropical forests, threatening the livelihoods of local populations who subsist on forest resources. The disappearance of wild plants and animals and the increasing influence of market economies affect local health, well-being, and diet. The impact of these changes on wild meat consumption has been well documented, but little attention has been given to wild edible plants, despite their importance as sources of calories and micronutrients. Furthermore, the relationships among food behavior strategies adopted by local populations, their psycho-cultural representations of food, and their food preferences have been poorly explored. In this study, we investigate food behaviors with an emphasis on the role of wild edible plants among a forager-horticulturalist society from the Congo Basin: the Baka. By combining an ethnobotanical survey with data from interviews (n = 536) related to food behaviors and representations of food, our data show that the Baka valorize both agricultural and marketable foods, and that wild plants represent a minor part of their diet, both in frequency and diversity. Finally, by examining how some wild edible plants have shifted from being eaten to being sold, we explore how market-oriented uses of wild edible plants may affect dietary behaviors and biocultural resilience.

    Forensic microbiology reveals that Neisseria animaloris infections in harbour porpoises follow traumatic injuries by grey seals
    Foster, Geoffrey ; Whatmore, Adrian M. ; Dagleish, Mark P. ; Malnick, Henry ; Gilbert, Maarten J. ; Begeman, Lineke ; Macgregor, Shaheed K. ; Davison, Nicholas J. ; Roest, Hendrik Jan ; Jepson, Paul ; Howie, Fiona ; Muchowski, Jakub ; Brownlow, Andrew C. ; Wagenaar, Jaap A. ; Kik, Marja J.L. ; Deaville, Rob ; Doeschate, Mariel T.I. ten; Barley, Jason ; Hunter, Laura ; IJsseldijk, Lonneke L. - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    Neisseria animaloris is considered to be a commensal of the canine and feline oral cavities. It is able to cause systemic infections in animals as well as humans, usually after a biting trauma has occurred. We recovered N. animaloris from chronically inflamed bite wounds on pectoral fins and tailstocks, from lungs and other internal organs of eight harbour porpoises. Gross and histopathological evidence suggest that fatal disseminated N. animaloris infections had occurred due to traumatic injury from grey seals. We therefore conclude that these porpoises survived a grey seal predatory attack, with the bite lesions representing the subsequent portal of entry for bacteria to infect the animals causing abscesses in multiple tissues, and eventually death. We demonstrate that forensic microbiology provides a useful tool for linking a perpetrator to its victim. Moreover, N. animaloris should be added to the list of potential zoonotic bacteria following interactions with seals, as the finding of systemic transfer to the lungs and other tissues of the harbour porpoises may suggest a potential to do likewise in humans.

    Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
    Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
    Nature 571 (2019)7765. - ISSN 0028-0836

    In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following, https://inventaire-forestier.ign.fr/spip.php?rubrique159, site accessed on 01 January 2015)’. All of these errors have been corrected online.

    Hunting communities of practice : Factors behind the social differentiation of hunters in modernity
    Essen, Erica von; Heijgen, Eugenie van; Gieser, Thorsten - \ 2019
    Journal of Rural Studies 68 (2019). - ISSN 0743-0167 - p. 13 - 21.
    Defensive localism - Hunting - Landscapes - Urban outsiders - Wildlife management

    Hunting is a social world in which members socially differentiate themselves into smaller social worlds on the basis of adhering to a particular method, aesthetic, or game. Such identity constitution has been understood as forming communities of practice of hunters. Importantly, these communities frequently take pride in their distinct identities and assert theirs is the ‘real’ way of hunting. In this paper, we canvass the diverse factors that make up hunter identities and examine them for patterns and meaning. Our analysis places the phenomenon of social differentiation as it currently takes place in hunting in the context of responses to modernization. On this analysis, hunter identities are found to be rooted in defensive localism, class competition over resources, gender and moral affiliation, and the protection of the social legitimacy of hunting before an increasingly critical society. Our work is at once a synthesis of recurring hunting profiles across literature and field sites in Europe and a critical analysis of the significance of hunting communities of practice in future research, including serious leisure studies, nature-based recreation, criminology and rural sociology.

    Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records
    Hines, Hunter N. ; Onsbring, Henning ; Ettema, Thijs J.G. ; Esteban, Genoveva F. - \ 2018
    Protist 169 (2018)6. - ISSN 1434-4610 - p. 875 - 886.
    anaerobic respiration - Heterotrich. - Protist - RNA-seq - stop codon - symbiotic algae

    The ciliate Spirostomum semivirescens is a large freshwater protist densely packed with endosymbiotic algae and capable of building a protective coating from surrounding particles. The species has been rarely recorded and it lacks any molecular investigations. We obtained such data from S. semivirescens isolated in the UK and Sweden. Using single-cell RNA sequencing of isolates from both countries, the transcriptome of S. semivirescens was generated. A phylogenetic analysis identified S. semivirescens as a close relative to S. minus. Additionally, rRNA sequence analysis of the green algal endosymbiont revealed that it is closely related to Chlorella vulgaris. Along with the molecular species identification, an analysis of the ciliates’ stop codons was carried out, which revealed a relationship where TGA stop codon frequency decreased with increasing gene expression levels. The observed codon bias suggests that S. semivirescens could be in an early stage of reassigning the TGA stop codon. Analysis of the transcriptome indicates that S. semivirescens potentially uses rhodoquinol-dependent fumarate reduction to respire in the oxygen-depleted habitats where it lives. The data also shows that despite large geographical distances (over 1,600 km) between the sampling sites investigated, a morphologically-identical species can share an exact molecular signature, suggesting that some ciliate species, even those over 1 mm in size, could have a global biogeographical distribution.

    A review of system dynamics models applied in social and humanitarian researches
    Allahi, Fahimeh ; Leeuw, Sander De; Sabet, Ehsan ; Kian, Ramez ; Damiani, Lorenzo ; Giribone, Pietro ; Revetria, Roberto ; Cianci, Roberto - \ 2018
    In: Proceedings of the World Congress on Engineering 2018, WCE 2018. - Newswood Limited (Lecture Notes in Engineering and Computer Science ) - ISBN 9789881404794 - p. 789 - 794.
    Complex systems - Decision-making - Humanitarian - Literature review - System dynamic

    Over the past decades, the number of disasters has been on the rise, including earthquakes, war, flood and other incidents that cause destruction of society, such as education and health services. Forecasts show that over the next 50 years, natural and manmade disasters are expected to increase five-folds both in the number and impact. Therefore, there is a need for effective and efficient disaster support actions during emergencies. This compels humanitarian organizations to improve the effectiveness and efficiency of their approaches and facilitate decision making in resolving such complicated problems characterized by numerous parameters. Besides, humanitarian organizations face situations with multiple critical events, inadequate funding, limited time to plan and react, and operating in increasingly challenging circumstances. Useful approaches for tackling problems in such dynamic conditions require methods and tools that take into account uncertainty and enable managers to evaluate the dynamic complexity of such systems, to facilitate decision making. Among the large amount of decision-aid tools for humanitarian organizations, System Dynamic (SD) is a method used for the evaluation of complex system behavior and for presenting the effect of decisions over time in an easy-to-use model. This method has been applied in humanitarian problems, and this paper aims to present a review of the most relevant humanitarian publications associated with system dynamics. This literature review is a structured review of the papers published since 2003 onwards. The finding of this research can be used to facilitate further research in developing the system dynamic methodology for humanitarian organizations and to present the essential requirement of SD tools for modeling complex environments.

    Hunting for strong seeds
    Kik, C. - \ 2018

    Onderzoeker en "seed hunter" Chris Kik reist de hele wereld over om wilde groente zaden te zoeken. Dankzij die zaden kunnen we sterke groenten kweken. Hoe zit dat precies?

    The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera
    Linard, Benjamin ; Crampton-Platt, Alex ; Moriniere, Jerome ; Timmermans, Martijn J.T.N. ; Andújar, Carmelo ; Arribas, Paula ; Miller, Kirsten E. ; Lipecki, Julia ; Favreau, Emeline ; Hunter, Amie ; Gómez-Rodríguez, Carola ; Barton, Christopher ; Nie, Ruie ; Gillett, Conrad P.D.T. ; Breeschoten, Thijmen ; Bocak, Ladislav ; Vogler, Alfried P. - \ 2018
    Molecular Phylogenetics and Evolution 128 (2018). - ISSN 1055-7903 - p. 1 - 11.
    Biodiversity discovery - Coleoptera - Mass-trapped samples - Metagenome skimming - Mitochondrial metagenomics

    A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

    Accounting for non-stationary variance in geostatistical mapping of soil properties
    Wadoux, Alexandre M.J.C. ; Brus, Dick J. ; Heuvelink, Gerard B.M. - \ 2018
    Geoderma 324 (2018). - ISSN 0016-7061 - p. 138 - 147.
    Geostatistics - Kriging - Non-stationarity - Pedometrics - REML - Uncertainty assessment

    Simple and ordinary kriging assume a constant mean and variance of the soil variable of interest. This assumption is often implausible because the mean and/or variance are linked to terrain attributes, parent material or other soil forming factors. In kriging with external drift (KED) non-stationarity in the mean is accounted for by modelling it as a linear combination of covariates. In this study, we applied an extension of KED that also accounts for non-stationary variance. Similar to the mean, the variance is modelled as a linear combination of covariates. The set of covariates for the mean may differ from the set for the variance. The best combinations of covariates for the mean and variance are selected using Akaike's information criterion. Model parameters of the selected model are then estimated by differential evolution using the Restricted Maximum Likelihood (REML) in the objective function. The methodology was tested in a small area of the Hunter Valley, NSW Australia, where samples from a fine grid with gamma K measurements were treated as measurements of the variable of interest. Terrain attributes were used as covariates. Both a non-stationary variance and a stationary variance model were calibrated. The mean squared prediction errors of the two models were somewhat comparable. However, the uncertainty about the predictions was much better quantified by the non-stationary variance model, as indicated by the mean and median of the standardized squared prediction error and by accuracy plots. We conclude that the non-stationary variance model is more flexible and better suited for uncertainty quantification of a mapped soil property. However, parameter estimation of the non-stationary variance model requires more attention due to possible singularity of the covariance matrix.

    Aquaculture
    Bardocz, Tamas ; Jansen, H.M. ; Cai, Junning ; Aguilar-Manjarrez, Jose ; Barrento, Sara ; Hunter, Shane A. ; Poelman, M. - \ 2018
    In: Building Industries at Sea: 'Blue Growth' and the New Maritime Economy / Johnson, Kate, Dalton, Gordon, Masters, Ian, River Publishers (River Publishers Series in Renewable Energy ) - ISBN 9788793609266 - p. 11 - 38.
    Quantifying the scale and socioeconomic drivers of bird hunting in Central African forest communities
    Whytock, Robin C. ; Morgan, Bethan J. ; Awa, Taku ; Bekokon, Zacharie ; Abwe, Ekwoge A. ; Buij, Ralph ; Virani, Munir ; Vickery, Juliet A. ; Bunnefeld, Nils - \ 2018
    Biological Conservation 218 (2018). - ISSN 0006-3207 - p. 18 - 25.
    Cameroon - Hornbills - Illegal hunting - Raptors - Wild meat
    Global biodiversity is threatened by unsustainable exploitation for subsistence and commerce, and tropical forests are facing a hunting crisis. In Central African forests, hunting pressure has been quantified by monitoring changes in the abundance of affected species and by studying wild meat consumption, trade and hunter behaviour. However, a proportion of offtake is also discarded as bycatch or consumed by hunters when working, which can be overlooked by these methods. For example, remains of hornbills and raptors are found regularly in hunting camps but relatively few birds are consumed in households or traded in markets. Hornbill and raptor populations are sensitive to small increases in mortality because of their low intrinsic population growth rates, however, the scale and socioeconomic drivers of the cryptic hunting pressure affecting these species have not been quantified. We used direct and indirect questioning and mixed-effects models to quantify the socioeconomic predictors, scale and seasonality of illegal bird hunting and consumption in Littoral Region, Cameroon. We predicted that younger, unemployed men with low educational attainment (i.e. hunters) would consume birds more often than other demographics, and that relative offtake would be higher than expected based on results from village and market-based studies. We found that birds were primarily hunted and consumed by unemployed men during the dry season but, in contrast to expectations, we found that hunting prevalence increased with educational attainment. Within unemployed men educated to primary level (240 of 675 respondents in 19 villages), we estimated an average of 29 hornbills and eight raptors (compared with 19 pangolins) were consumed per month during the study period (Feb–Jun 2015) in a catchment of c.1135 km2. We conclude that large forest birds face greater hunting pressure than previously recognised, and birds are a regular source of protein for men during unemployment. Offtake levels may be unsustainable for some raptors and hornbills based on life history traits but in the absence of sufficient baseline ecological and population data we recommend that a social-ecological modeling approach is used in future to quantify hunting sustainability.
    Climate change effects on wildland fire risk in the Northeastern and Great Lakes states predicted by a downscaled multi-model ensemble
    Kerr, Gaige Hunter ; DeGaetano, Arthur T. ; Stoof, Cathelijne R. ; Ward, Daniel - \ 2018
    Theoretical and Applied Climatology 131 (2018)1-2. - ISSN 0177-798X - p. 625 - 639.

    This study is among the first to investigate wildland fire risk in the Northeastern and the Great Lakes states under a changing climate. We use a multi-model ensemble (MME) of regional climate models from the Coordinated Regional Downscaling Experiment (CORDEX) together with the Canadian Forest Fire Weather Index System (CFFWIS) to understand changes in wildland fire risk through differences between historical simulations and future projections. Our results are relatively homogeneous across the focus region and indicate modest increases in the magnitude of fire weather indices (FWIs) during northern hemisphere summer. The most pronounced changes occur in the date of the initialization of CFFWIS and peak of the wildland fire season, which in the future are trending earlier in the year, and in the significant increases in the length of high-risk episodes, defined by the number of consecutive days with FWIs above the current 95th percentile. Further analyses show that these changes are most closely linked to expected changes in the focus region’s temperature and precipitation. These findings relate to the current understanding of particulate matter vis-à-vis wildfires and have implications for human health and local and regional changes in radiative forcings. When considering current fire management strategies which could be challenged by increasing wildland fire risk, fire management agencies could adapt new strategies to improve awareness, prevention, and resilience to mitigate potential impacts to critical infrastructure and population.

    People's Involvement in Residential PV and their Experiences
    Mierlo, Barbara Van - \ 2017
    In: Photovoltaic Solar Energy / Reinders, A., Verlinden, P., van Stark, W., Freundlich, A., Wiley - ISBN 9781118927465 - p. 634 - 645.
    This chapter takes stock of the current knowledge and understanding of people's involvement in and experiences of photovoltaics (PVs), which is important for the design of PV systems as well as wise market introduction and support. It also takes an interest in everybody who is not professionally involved, as a 'prosumer', an active citizen or a gadget hunter, and more. Suggestions are provided on how to engage in a more effective learning process to improve further socio‐technological development. People who own a single house can individually purchase a PV system to be mounted on or integrated into their rooftops or facades if the physical conditions and their financial resources allow it. In this role they are most frequently addressed in PV campaigns and policy. People living in an apartment or rental house are confined to becoming involved in collective initiatives or buying a small add‐on system.
    Seed hunter explores Uzbekistan and Jordan
    Kik, C. - \ 2017
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