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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Literature update on effective environmental enrichment and light provision in broiler chickens
Souza da Silva, C. ; Jong, I.C. de - \ 2019
Wageningen : Wageningen Livestock Research (Report / Wageningen Livestock Research 1204) - 46
The results of a literature study to the effect of different types of environmental enrichment and light conditions on broiler chickens welfare are described, in order to attempt to provide an environment to slow-growing broiler chickens that better meets their behavioural requirements. With respect to environmental enrichment, a review paper has been used as a starting point and more recent information has been collected and summarised. With respect to lighting, in consultation with stakeholders we chose to limit the literature study to a fewpotential interesting areas of research (e.g. natural light provisionand its variation across the broiler house). There are several research questions in relation to enrichment provision, e.g., optimal perch design, multiple use of enrichments and the actual number of enrichments that should be provided. Currently, little is known about the need for light in slow-growing broiler chickens and how this interacts with the environmental enrichment offered. Future research priorities include theoptimization of methods of natural light provision (which is often applied in higher welfare indoor systems with slow-growing breeds), testing effects of ultraviolet wavelengths on chicken behaviour,and light colour preferences in slow-growing breeds.
Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Can timber provision from Amazonian production forests be sustainable?
Piponiot, Camille ; Rödig, Edna ; Putz, Francis E. ; Rutishauser, Ervan ; Sist, Plinio ; Ascarrunz, Nataly ; Blanc, Lilian ; Derroire, Géraldine ; Descroix, Laurent ; Guedes, Marcelino Carneiro ; Coronado, Euridice Honorio ; Huth, Andreas ; Kanashiro, Milton ; Licona, Juan Carlos ; Mazzei, Lucas ; Oliveira, Marcus Vinicio Neves D'; Peña-Claros, Marielos ; Rodney, Ken ; Shenkin, Alexander ; Souza, Cintia Rodrigues De; Vidal, Edson ; West, Thales A.P. ; Wortel, Verginia ; Hérault, Bruno - \ 2019
Environmental Research Letters 14 (2019)6. - ISSN 1748-9318
Amazonia - disturbance - ecosystem recovery - macroecology - Selective logging - tropical forestry

Around 30 Mm3 of sawlogs are extracted annually by selective logging of natural production forests in Amazonia, Earth's most extensive tropical forest. Decisions concerning the management of these production forests will be of major importance for Amazonian forests' fate. To date, no regional assessment of selective logging sustainability supports decision-making. Based on data from 3500 ha of forest inventory plots, our modelling results show that the average periodic harvests of 20 m3 ha-1 will not recover by the end of a standard 30 year cutting cycle. Timber recovery within a cutting cycle is enhanced by commercial acceptance of more species and with the adoption of longer cutting cycles and lower logging intensities. Recovery rates are faster in Western Amazonia than on the Guiana Shield. Our simulations suggest that regardless of cutting cycle duration and logging intensities, selectively logged forests are unlikely to meet timber demands over the long term as timber stocks are predicted to steadily decline. There is thus an urgent need to develop an integrated forest resource management policy that combines active management of production forests with the restoration of degraded and secondary forests for timber production. Without better management, reduced timber harvests and continued timber production declines are unavoidable.

Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

Degradation of fibres from fruit by-products allows selective modulation of the gut bacteria in an in vitro model of the proximal colon
Bussolo de Souza, Carlota ; Jonathan, Melliana ; Isay Saad, Susana Marta ; Schols, Henk A. ; Venema, Koen - \ 2019
Journal of Functional Foods 57 (2019). - ISSN 1756-4646 - p. 275 - 285.
Degradation - Fermentation - Fibre - Fruit by-products - Gut microbiota - SCFA

The potential prebiotic effect of fibres (alcohol insoluble solids fractions) from fruit by-products – orange bagasses and passion fruit peels – and their degradation by human gut microbiota was tested in an in vitro colon system. Standard medium and inulin were used as controls. Orange bagasses (A-OB1 and A-OB2) had similar chemical composition but differed regarding fermentation profile. A-OB2 resulted in a more diverse bacterial community than A-OB1 and produced more SCFA, with increased Ruminococcus and Lachnospira. Carbohydrate utilization was higher on A-OB2 probably due to higher ratio soluble to insoluble fibres. Isolated fibres from passion fruit peels presented similar chemical composition and fermentation profiling. Bacteroides and Ruminococcus were the main genera stimulated. Negligible lactate and succinate production represent slow fermentation, a protective feature against colon cancer. This study provided evidence that the tested fruit by-products have the potential to be used for selective modulation of the gut microbiota.

Exploring Ecosystem Network Analysis to Balance Resilience and Performance in Sustainable Supply Chain Design
Miranda de Souza, Vitor ; Bloemhof-Ruwaard, J.M. ; Borsato, Milton - \ 2019
International Journal of Advanced Operations Management 11 (2019)1/2. - ISSN 1758-938X - p. 26 - 45.
resilience - ecosystem network analysis - sustainable supply chain - multi-objective programming
Sustainable Supply Chain Design can be performed using optimization strategies for minimizing environmental impacts while maximizing profit. It is not clear how such strategies influence the resilience of a supply chain its ability to cope with disruptions without compromising its function. This research used the Ecosystem Network Analysis (ENA), a model from Ecological Economics, to evaluate the resilience during the design of a sugar beet supply chain. The Ɛ-constraint method was used to solve a multi-objective, mixed-integer linear programming model (MOMILP). Results showed that ENA results are compromised when the strategy of minimizing environmental impacts is used, due to the increased fragility of the configuration, compared with the configuration from the profit maximization strategy. Sensitivity analysis also revealed that, when the number of facilities is increased, ENA results improve while profit is decreased. ENA showed an interesting potential to support the pursuit of balance between resilience and performance, bringing insights during early design stages.
Towards Regenerative Supply Networks : A design framework proposal
Souza, Vitor de; Bloemhof-Ruwaard, Jacqueline ; Borsato, Milton - \ 2019
Journal of Cleaner Production 221 (2019). - ISSN 0959-6526 - p. 145 - 156.
Regenerative development - Resilience - Sustainable supply network design - Systems approach - Transdisciplinary research

Anthropocentrism and disciplinary research have not led to effective solutions to sustainability problems. A shift is required towards biocentric, transdisciplinarity-based solutions, to mitigate rebound effects and unintended, negative effects. In the field of Sustainable Supply Network Design, such shift implies on developing resilient solutions that maximize environmental benefits instead of minimizing environmental impacts. Recent researches have showed progress in this direction proposing more integrative approaches, but a framework to design supply networks with the purpose of environmental regeneration is yet to be proposed. This research aims to fill this gap, merging concepts from Regenerative Design, Transdisciplinary Research, Systems Thinking, Social Sciences and Design Sciences. Such framework is regarded as an artefact, and Design Science Research Methodology used for its development: a main problem is identified, objectives for a solution are drawn and the framework is designed. First, the Regenerative Supply Network Design is defined, to guide the elaboration of the Regenerative Supply Chain Design framework, consisting of six steps: (i) description of the network surroundings and identification of a regenerative purpose; (ii) redesign of outputs (iii) network conceptualization, (iv) optimize performance, (v) choose configuration, and (vi) implementation. Among the implications of this research are that (i) practitioners basing their design process in this framework are effectively shifting from anthropocentrism to biocentrism with a clear, defined purpose of environmental restoration and (ii), that the supply networks evolve in the integration with the environment, enhancing eco-systems resilience.

Molybdenum/tungsten-carbide and nickel-phosphide as emerging catalysts for deoxygenation reactions
Souza Macedo, Luana - \ 2019
Wageningen University. Promotor(en): J.H. Bitter; V. Teixeira da Silva. - Wageningen : Wageningen University - ISBN 9789463435475 - 195
Embolism resistance drives the distribution of Amazonian rainforest tree species along hydro-topographic gradients
Oliveira, Rafael S. ; Costa, Flavia R.C. ; Baalen, Emma van; Jonge, Arjen de; Bittencourt, Paulo R. ; Almanza, Yanina ; V. Barros, Fernanda de; Cordoba, Edher C. ; Fagundes, Marina V. ; Garcia, Sabrina ; Guimaraes, Zilza T.T.M. ; Hertel, Mariana ; Schietti, Juliana ; Rodrigues-Souza, Jefferson ; Poorter, Lourens - \ 2019
New Phytologist 221 (2019)3. - ISSN 0028-646X - p. 1457 - 1465.
drought vulnerability - forest resilience - functional ecology - hydrological niches - P - phosphorus - tropical forests - water table

Species distribution is strongly driven by local and global gradients in water availability but the underlying mechanisms are not clear. Vulnerability to xylem embolism (P50) is a key trait that indicates how species cope with drought and might explain plant distribution patterns across environmental gradients. Here we address its role on species sorting along a hydro-topographical gradient in a central Amazonian rainforest and examine its variance at the community scale. We measured P50 for 28 tree species, soil properties and estimated the hydrological niche of each species using an indicator of distance to the water table (HAND). We found a large hydraulic diversity, covering as much as 44% of the global angiosperm variation in P50. We show that P50: contributes to species segregation across a hydro-topographic gradient in the Amazon, and thus to species coexistence; is the result of repeated evolutionary adaptation within closely related taxa; is associated with species tolerance to P-poor soils, suggesting the evolution of a stress-tolerance syndrome to nutrients and drought; and is higher for trees in the valleys than uplands. The large observed hydraulic diversity and its association with topography has important implications for modelling and predicting forest and species resilience to climate change.

Influence of synthesis method on molybdenum carbide crystal structure and catalytic performance in stearic acid hydrodeoxygenation
Souza Macedo, Luana ; Oliveira, Ricardo R. ; Haasterecht, Tomas van; Teixeira da Silva, Victor ; Bitter, Harry - \ 2019
Applied Catalysis B-Environmental 241 (2019). - ISSN 0926-3373 - p. 81 - 88.
Crystal structure - Hydrodeoxygenation - Molybdenum carbide - Site density - Synthesis method

The role of the synthesis method of molybdenum carbide nanoparticle catalysts supported on carbon nanofibers on crystal structure and on catalytic performance in hydrodeoxygenation of stearic acid was investigated. We obtained the cubic phase of molybdenum carbide (α-MoC1-x) by impregnating carbon nanofibers with a solution of (NH4)2MoO4, then exposing them to 20% CH4/H2 at 650 °C for 2 h. When increasing the Mo loading from 7.5 wt% to 20 wt% or using the carbothermal reduction method, i.e. using carbon from the support to reduce the (NH4)2MoO4 precursor at 800 °C for 6 h, the hexagonal phase (β-Mo2C) resulted. Experiments with stearic acid hydrodeoxygenation showed that both phases (7.5 wt% Mo) displayed similar intrinsic activities. However, α-MoC1-x/CNF reached 80% stearic acid conversion after 240 min while the β-Mo2C/CNF catalyst attained the same conversion after 360 min. CO chemisorption results showed that α-MoC1-x/CNF and β-Mo2C/CNF have a similar number of potential active sites (66 and 56 μmol g−1, respectively). We attribute the difference in catalytic performance between α-MoC1-x/CNF and β-Mo2C/CNF to differences in the catalyst's crystal structure, more specifically, the associated site density. The face-centered cubic α-MoC1-x/CNF has a lower site density (0.1096 Mo atoms Ų) than the hexagonal close-packed β-Mo2C/CNF (0.1402 Mo atoms Ų), making the Mo atoms at the surface of the α-MoC1-x phase more accessible for large reactant molecules such as stearic acid thus allowing its convertion in shorter times.

The role of fertile anthropogenic soils in the conservation of native and exotic agrobiodiversity in Amazonian homegardens
Souza, Nathalia B. de; Junqueira, André Braga ; Struik, Paul C. ; Stomph, Tjeerdjan ; Clement, Charles R. - \ 2019
Agroforestry Systems 93 (2019)2. - ISSN 0167-4366 - p. 471 - 482.
Agroecosystems - Amazonian dark earths - Geographical origin of species - Soil fertility - Spontaneous plants

Amazonian dark earths (ADE) are anthropogenic soils mostly created between 500 and 2500 years ago by pre-Columbian populations. ADE are currently used by local people for different agricultural and agroforestry systems. Because of their high fertility they may play an important role in the conservation of non-native agrobiodiversity. This study aimed to investigate the variation in richness and abundance of exotic and native species in homegardens along the ADE-background soil continuum. We conducted floristic inventories in 70 homegardens located in 7 riverside communities along the lower and middle Madeira River, Central Amazonia. Each species sampled was classified according to its origin: native Amazonian, American (from outside Amazonia) and non-American, and each individual was classified according to its form of establishment: cultivated or spontaneous. The floristic diversity was significantly related to soil fertility, texture and homegarden size. We found a positive relationship between soil fertility and richness of species and landraces. Homegardens on more fertile soils tended to have a higher richness and abundance of cultivated non-American species, as well as a higher richness and abundance of spontaneously established American species. Homegardens at the fertile end of the fertility gradient provided conditions for the establishment and growth of many species, especially exotic species, that are generally more nutrient-demanding than Amazonian species. Our results show that homegarden agroecosystems on ADE favour experimentation with the introduction of a wide range of species from various regions of the globe.

On the Stability of Supported Carbides for Deoxygenation Reactions
Bitter, J.H. ; Gosselink, R.W. ; Stellwagen, Daniel ; Souza Macêdo, L. ; Wiegersma, Tijmen ; Haasterecht, T. van; Teixeira da Silva, V. - \ 2018
Carbon supported metal-carbides and metal phosphide for biomass-based conversions
Bitter, J.H. ; Souza Macêdo, L. ; Oliveira Jr, R.R. ; Haasterecht, T. van; Auxiliadora, M. ; Baldanza, S. ; Teixeira da Silva, V. - \ 2018
Eighty Years of Mycopathologia: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens
Chaturvedi, Vishnu ; Bouchara, Jean Philippe ; Hagen, Ferry ; Alastruey-Izquierdo, Ana ; Badali, Hamid ; Bocca, Anamelia Lorenzetti ; Cano-Lira, Jose F. ; Cao, Cunwei ; Chaturvedi, Sudha ; Chotirmall, Sanjay H. ; Diepeningen, Anne D. Van; Gangneux, Jean Pierre ; Guinea, Jesus ; Hoog, Sybren De; Ilkit, Macit ; Kano, Rui ; Liu, Weida ; Martinez-Rossi, Nilce M. ; Souza Carvalho Melhem, Marcia De; Ono, Mario Augusto ; Ran, Yuping ; Ranque, Stephane ; Almeida Soares, Celia Maria De; Sugita, Takashi ; Thomas, Philip A. ; Vecchiarelli, Anna ; Wengenack, Nancy L. ; Woo, Patrick C.Y. ; Xu, Jianping ; Zancope-Oliveira, Rosely M. - \ 2018
Mycopathologia 183 (2018)6. - ISSN 0301-486X - p. 859 - 877.
Mycopathologia was founded in 1938 to ‘diffuse the understanding of fungal diseases in man and animals among mycologists.’ This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5–5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of ‘classic papers’ since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host–pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other’s language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.
Identification of the Bisabolol Synthase in the Endangered Candeia Tree (Eremanthus erythropappus (DC) McLeisch)
Alves Gomes Albertti, Leticia ; Delatte, T.L. ; Souza Farias, Katyuce de; Boaretto, A.G. ; Verstappen, F.W.A. ; Houwelingen, A.M.M.L. van; Cankar, K. ; Bouwmeester, H.J. ; Beekwilder, M.J. - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Candeia (Eremanthus erythropappus (DC) McLeisch, Asteraceae) is a Brazilian tree, mainly occurring in the cerrado areas. From ethnobotanical information its essential oil is known to have wound healing and nociceptive properties. These properties are ascribed to result from a sesquiterpene alcohol, (–)-α-bisabolol, which is present at high concentrations in this oil. Bisabolol is highly valued by the cosmetic industry because of its antibacterial, anti-inflammatory, skin-smoothing and wound healing properties. Over the past decades, Candeia timber has been collected at large scale for bisabolol extraction from wild reserves and the species is thereby at risk of extinction. To support the development of breeding and nursing practices that would facilitate sustainable cultivation of Candeia, we identified a terpene synthase gene, EeBOS1, that appears to control biosynthesis (–)-α-bisabolol in the plant. Expression of this gene in E. coli showed that EeBOS1 protein is capable of producing (–)-α-bisabolol from farnesyl pyrophosphate in vitro. Analysis of gene expression in different tissues from Candeia plants in different life stages showed a high correlation of EeBOS1 expression and accumulation of (–)-α-bisabolol. This work is the first step to unravel the pathway toward (–)-α-bisabolol in Candeia, and in the further study of the control of (–)-α-bisabolol production
Characterization and in vitro digestibility of by-products from Brazilian food industry : Cassava bagasse, orange bagasse and passion fruit peel
Bussolo de Souza, Carlota ; Jonathan, Melliana ; Isay Saad, Susana Marta ; Schols, Henk A. ; Venema, Koen - \ 2018
Bioactive Carbohydrates and Dietary Fibre 16 (2018). - ISSN 2212-6198 - p. 90 - 99.
Bagasse - By-product - Digestibility - Fibre - Peel - Sustainability

The aim of the present study was to characterize selected by-products from Brazilian food industry and their in vitro digestibility. These by-products (cassava and orange bagasses and passion fruit peels) are potentially rich sources of dietary fibres, but currently they are mostly disposed. Their analysis revealed differences in composition for the same by-product type from different suppliers. Cassava bagasses were mainly composed of starch, with high variability among tested by-products (45–77.5% starch). In vitro experiments indicated that cassava bagasses had ~ 12% of resistant starch. The orange bagasses had free glucose and highly methyl esterified pectin as the main constituents (~23.5% of total pectin). Seventy-seven % of digestible glucose present in the orange bagasse were absorbed within 3 h experimental run. Passion fruit peels were a good source of fibres, especially pectin (~19%) and (hemi)cellulose (~16%). These in vitro experiments indicated that passion fruit peel had slower absorption of glucose than the other by-products, with 80% of digestible glucose absorbed within 5 h. In conclusion, the tested by-products are good sources of diverse types of fibres and have a great potential to be incorporated into different food products, decreasing food waste and contributing to a sustainable food system.

Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables
Souza Iung, Laiza Helena de; Mulder, Herman Arend ; Rezende Neves, Haroldo Henrique de; Carvalheiro, Roberto - \ 2018
BMC Genomics 19 (2018). - ISSN 1471-2164
Beef cattle - DHGLM - Genetic heterogeneity of residual variance - Growth traits - GWAS - Micro-environmental sensitivity

Background: In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N=423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv=0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_ σ ě 2 $$ (\upsigma)_(\widehat(\mathrm(e)))^2 $$ ). Results: The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor>20) with dEBVv and ln_ σ ě 2 $$ (\upsigma)_(\widehat(\mathrm(e)))^2 $$ , respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. Conclusions: It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.

The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon
Maezumi, S.Y. ; Alves, Daiana ; Robinson, Mark ; Souza, Jonas Gregorio de; Levis, Carolina ; Barnett, Robert L. ; Almeida de Oliveira, Edemar ; Urrego, Dunia ; Schaan, Denise ; Iriarte, José - \ 2018
Nature Plants 4 (2018)8. - ISSN 2055-026X - p. 540 - 547.

The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1–10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

Ten essentials for action-oriented and second order energy transitions, transformations and climate change research
Fazey, Ioan ; Schäpke, Niko ; Caniglia, Guido ; Patterson, James ; Hultman, Johan ; Mierlo, Barbara Van; Säwe, Filippa ; Wiek, Arnim ; Wittmayer, Julia ; Aldunce, Paulina ; Waer, Husam Al; Battacharya, Nandini ; Bradbury, Hilary ; Carmen, Esther ; Colvin, John ; Cvitanovic, Christopher ; D’Souza, Marcella ; Gopel, Maja ; Goldstein, Bruce ; Hämäläinen, Timo ; Harper, Gavin ; Henfry, Tom ; Hodgson, Anthony ; Howden, Mark S. ; Kerr, Andy ; Klaes, Matthias ; Lyon, Christopher ; Midgley, Gerald ; Moser, Susanne ; Mukherjee, Nandan ; Müller, Karl ; O’brien, Karen ; O’Connell, Deborah A. ; Olsson, Per ; Page, Glenn ; Reed, Mark S. ; Searle, Beverley ; Silvestri, Giorgia ; Spaiser, Viktoria ; Strasser, Tim ; Tschakert, Petra ; Uribe-Calvo, Natalia ; Waddell, Steve ; Rao-Williams, Jennifer ; Wise, Russel ; Wolstenholme, Ruth ; Woods, Mel ; Wyborn, Carina - \ 2018
Energy Research & Social Science 40 (2018). - ISSN 2214-6296 - p. 54 - 70.
The most critical question for climate research is no longer about the problem, but about how to facilitate the transformative changes necessary to avoid catastrophic climate-induced change. Addressing this question, however, will require massive upscaling of research that can rapidly enhance learning about transformations. Ten essentials for guiding action-oriented transformation and energy research are therefore presented, framed in relation to second-order science. They include: (1) Focus on transformations to low-carbon, resilient living; (2) Focus on solution processes; (3) Focus on ‘how to’ practical knowledge; (4) Approach research as occurring from within the system being intervened; (5) Work with normative aspects; (6) Seek to transcend current thinking; (7) Take a multi-faceted approach to understand and shape change; (8) Acknowledge the value of alternative roles of researchers; (9) Encourage second-order experimentation; and (10) Be reflexive. Joint application of the essentials would create highly adaptive, reflexive, collaborative and impact-oriented research able to enhance capacity to respond to the climate challenge. At present, however, the practice of such approaches is limited and constrained by dominance of other approaches. For wider transformations to low carbon living and energy systems to occur, transformations will therefore also be needed in the way in which knowledge is produced and used.
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