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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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.

‘Opening up’ science policy: engaging with RRI in Brazil
Reyes-Galindo, Luis ; Monteiro, Marko ; Macnaghten, Phil - \ 2019
Journal of Responsible Innovation 6 (2019)3. - ISSN 2329-9460 - p. 353 - 360.
Brazil - governance of science and technology - RRI - science and technology policy

This article presents initial results from the Brazilian team in the Responsible Research and Innovation in Practice (RRI-Practice) collaboration, concurrently running in 22 countries. The project invites reflection from institutional actors through a variety of participatory exercises that focus on RRI’s potential for ‘opening up’ and impacting national science and innovation policy. After summarising the operational challenges faced during the research process, we focus on the main empirical findings. We conclude that despite its potential for opening up policy deliberation, RRI faces the inherent hurdles of surpassing longstanding Brazilian institutional traditions of hierarchical governance, autonomy and the dominance of linear models of innovation.

A comparative analysis on how different governance contexts may influence Strategic Environmental Assessment
Monteiro, Margarida B. ; Rosário Partidário, Maria do; Meuleman, Louis - \ 2018
Environmental Impact Assessment Review 72 (2018)September. - ISSN 0195-9255 - p. 79 - 87.
This paper explores the relationship between governance contexts and the development and outcomes of Strategic Environmental Assessment (SEA). The main objective of this paper is to understand if, and how, the governance context may influence the system and institutionalisation of SEA, and the capacity of SEA to reach its objectives. The research methodology is based on the comparison of six country-cases that have an established SEA system, including three European countries, two Asian countries and one in Latin American, with distinct national culture and political-administrative setting. Results show that cultural and institutional values impact how SEA is interpreted and carried out, and that SEA systems are facing constraints of a more normative and cognitive nature. Connecting governance contexts and patterns in the SEA systems confirm that SEA is not ‘context free’, but instead ‘context-influenced’, while its capacity is dependent on its level of adaptation to the governance environment.
Comparison between proton transfer reaction mass spectrometry and near infrared spectroscopy for the authentication of Brazilian coffee : A preliminary chemometric study
Monteiro, Pablo Inocêncio ; Santos, Jânio Sousa ; Alvarenga Brizola, Vitor Rafael ; Pasini Deolindo, Carolina Turnes ; Koot, Alex ; Boerrigter-Eenling, Rita ; Ruth, Saskia van; Georgouli, Konstantia ; Koidis, Anastasios ; Granato, Daniel - \ 2018
Food Control 91 (2018). - ISSN 0956-7135 - p. 276 - 283.
Authenticity - Chemometrics - Organic farming - PTR-MS - Specialty coffee - Spectroscopic methods - Volatile organic compounds

In this study, proton-transfer reaction mass spectrometry (PTR-MS) and near-infrared spectroscopy (NIRS) were compared for the authentication of geographical and farming system origins of Brazilian coffees. For this purpose, n = 19 organic (ORG) and n = 26 conventional (CONV) coffees from distinct producing regions were analyzed. Overall, differences (p ≤ 0.05) in 44 and 71 ion intensities were observed between the main producing regions and farming systems, respectively. Principal component analysis was not effective in illustrating differences between the coffees according to the farming system or geographical origin using neither PTR-MS nor NIRS data. However, when the PLS-DA was applied, which produced the best performing models compared to several other chemometric techniques, the farming system was adroitly differentiated. The fact that the classification performance (>80%) was independent of the data acquisition method used gives NIRS an edge over PTR-MS in the differentiation of the farming system because of its rapid analysis and cost. Differentiating geographic location of coffee was rather complex. The PTR-MS calibration models showed slightly better PLS-DA classification rates compared to the NIRS models (69% vs. 61%, respectively), which is even more evident when the alternative classifier is used (LDA-kNN, 69% vs. 39%, respectively). Coffee samples from either Minas Gerais (MG) or Sao Paulo (SP) were differentiated from the other regions. In conclusion, our study provides information on alternative rapid analysis coupled with chemometric techniques to differentiate the farming system and trace the geographical provenance of Brazilian specialty coffee.

Mutation of adjacent cysteine residues in the NSs protein of Rift Valley fever virus results in loss of virulence in mice
Monteiro, Gaby E.R. ; Jansen van Vuren, Petrus ; Wichgers Schreur, Paul J. ; Odendaal, Lieza ; Clift, Sarah J. ; Kortekaas, Jeroen ; Paweska, Janusz T. - \ 2018
Virus Research 249 (2018). - ISSN 0168-1702 - p. 31 - 44.
Attenuation - Cysteine - Mutations - NSs protein - Rift Valley fever virus - Virulence
The NSs protein encoded by the S segment of Rift Valley fever virus (RVFV) is the major virulence factor, counteracting the host innate antiviral defence. It contains five highly conserved cysteine residues at positions 39, 40, 149, 178 and 194, which are thought to stabilize the tertiary and quaternary structure of the protein. Here, we report significant differences between clinical, virological, histopathological and host gene responses in BALB/c mice infected with wild-type RVFV (wtRVFV) or a genetic mutant having a double cysteine-to-serine substitution at residues 39 and 40 of the NSs protein (RVFV-C39S/C40S). Mice infected with the wtRVFV developed a fatal acute disease; characterized by high levels of viral replication, severe hepatocellular necrosis, and massive up-regulation of transcription of genes encoding type I and −II interferons (IFN) as well as pro-apoptotic and pro-inflammatory cytokines. The RVFV-C39S/C40S mutant did not cause clinical disease and its attenuated virulence was consistent with virological, histopathological and host gene expression findings in BALB/c mice. Clinical signs in mice infected with viruses containing cysteine-to-serine substitutions at positions 178 or 194 were similar to those occurring in mice infected with the wtRVFV, while a mutant containing a substitution at position 149 caused mild, non-fatal disease in mice. As mutant RVFV-C39S/C40S showed an attenuated phenotype in mice, the molecular mechanisms behind this attenuation were further investigated. The results show that two mechanisms are responsible for the attenuation; (1) loss of the IFN antagonistic propriety characteristic of the wtRVFV NSs and (2) the inability of the attenuated mutant to degrade Proteine Kinase R (PKR).
Global Carbon Budget 2017
Quéré, Corinne Le; Andrew, Robbie M. ; Friedlingstein, Pierre ; Sitch, Stephen ; Pongratz, Julia ; Manning, Andrew C. ; Ivar Korsbakken, Jan ; Peters, Glen P. ; Canadell, Josep G. ; Jackson, Robert B. ; Boden, Thomas A. ; Tans, Pieter P. ; Andrews, Oliver D. ; Arora, Vivek K. ; Bakker, Dorothee C.E. ; Barbero, Leticia ; Becker, Meike ; Betts, Richard A. ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Cosca, Catherine E. ; Cross, Jessica ; Currie, Kim ; Gasser, Thomas ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Houghton, Richard A. ; Hunt, Christopher W. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Kato, Etsushi ; Kautz, Markus ; Keeling, Ralph F. ; Klein Goldewijk, Kees ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lima, Ivan ; Lombardozzi, Danica ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Nojiri, Yukihiro ; Padin, X.A. ; Peregon, Anna ; Pfeil, Benjamin ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Reimer, Janet ; Rödenbeck, Christian ; Schwinger, Jörg ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Laan-Luijkx, Ingrid T. van der; Werf, Guido R. van der; Heuven, Steven Van; Viovy, Nicolas ; Vuichard, Nicolas ; Walker, Anthony P. ; Watson, Andrew J. ; Wiltshire, Andrew J. ; Zaehle, Sönke ; Zhu, Dan - \ 2018
Earth System Science Data 10 (2018)1. - ISSN 1866-3508 - p. 405 - 448.
Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on land-cover change data and bookkeeping models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1δ. For the last decade available (2007-2016), EFF was 9.4±0.5 GtC yr-1, ELUC 1.3±0.7 GtC yr-1, GATM 4.7±0.1 GtC yr-1, SOCEAN 2.4±0.5 GtC yr-1, and SLAND 3.0±0.8 GtC yr-1, with a budget imbalance BIM of 0.6 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For year 2016 alone, the growth in EFF was approximately zero and emissions remained at 9.9±0.5 GtC yr-1. Also for 2016, ELUC was 1.3±0.7 GtC yr-1, GATM was 6.1±0.2 GtC yr-1, SOCEAN was 2.6±0.5 GtC yr-1, and SLAND was 2.7±1.0 GtC yr-1, with a small BIM of-0.3 GtC. GATM continued to be higher in 2016 compared to the past decade (2007-2016), reflecting in part the high fossil emissions and the small SLAND consistent with El Ninõ conditions. The global atmospheric CO2 concentration reached 402.8±0.1 ppm averaged over 2016. For 2017, preliminary data for the first 6-9 months indicate a renewed growth in EFF of C2.0% (range of 0.8 to 3.0 %) based on national emissions projections for China, USA, and India, and projections of gross domestic product (GDP) corrected for recent changes in the carbon intensity of the economy for the rest of the world. This living data update documents changes in the methods and data sets used in this new global carbon budget compared with previous publications of this data set (Le Quéré et al., 2016, 2015b, a, 2014, 2013). All results presented here can be downloaded from https://doi.org/10.18160/GCP-2017 (GCP, 2017).
Effects of animal type (wild vs. domestic) and diet alfalfa level on intake and digestibility of European adult rabbits (Oryctolagus cuniculus)
Pinheiro, Victor ; Outor-Monteiro, D. ; Mourão, J.L. ; Cone, J.W. ; Guimaraes Dias Lourenco, Ana - \ 2018
Journal of Animal Physiology and Animal Nutrition 102 (2018)1. - ISSN 0931-2439 - p. e460 - e467.
alfalfa level - digestibility - domestic - intake - rabbit - wild
The aim of this study was to evaluate the effect of the level of alfalfa in the diet on feed intake and digestibility of two types of rabbits, wild (Oryctolagus cuniculus algirus) vs. domestic (O. cuniculus cuniculus). Ten wild (W; mean LW = 927 g) and 10 domestic (D; mean LW = 4,645 g) adult rabbit does were fed ad libitum two pelleted diets: a control diet (C) with 15% of dehydrated alfalfa hay (as feed basis) and a test diet (A) with 36% of dehydrated alfalfa hay (as feed basis), according to a change-over design. Wild does dry matter (DM) intake per kg live weight (BW) was 55% higher (p < .001) than the intake of the D ones (58 g vs. 37 g DM per kg BW respectively). However, no difference (p > .05) was found when intake was expressed per kg0.75 BW (ca. 56 g DM) and tended to be higher (p = .07) in D does when expressed per kg0.67 BW (62 g vs. 55 g DM). Domestic does showed a higher (p < .05) DM, organic matter, crude energy and neutral detergent fibre digestibility (3; 2; 3; 3 percentage points respectively) than W does. The amount of nutrients and energy digested by D does was lower per kg BW (p < .001), similar per kg0.75 BW (p > .05) and tended to be higher per kg0.67 BW (p < .1) than in W does. The diet content of alfalfa did not affect (p > .05) the feed intake nor the diet digestibility. This study suggests that W rabbits exhibit a higher intake per kg BW and a lower digestibility than their D counterparts, which results in similar digestible nutrient and energy intake per kg BW powered to 0.75. The nutritive value of dehydrated alfalfa for rabbits, evaluated through intake and digestibility, seems to be equivalent to their base diets (forage plus concentrate).
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
Nowell, Reuben W. ; Elsworth, Ben ; Oostra, Vicencio ; Zwaan, Bas J. ; Wheat, Christopher W. ; Saastamoinen, Marjo ; Saccheri, Ilik J. ; Hof, Arjen E. van 't; Wasik, Bethany R. ; Connahs, Heidi ; Aslam, Muhammad L. ; Kumar, Sujai ; Challis, Richard J. ; Monteiro, Antónia ; Brakefield, Paul M. ; Blaxter, Mark - \ 2017
GigaScience 6 (2017)7. - ISSN 2047-217X
Bicyclus anynana - Lepidopteran genome - Nymphalid - Nymphalidae - Satyrid - Squinting bush brown

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (~×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).

It takes three to tango : biobased innovaties: een samenwerking tussen overheid, onderwijs en ondernemers
Monteiro da Fonseca, Wendy ; Otterloo, Laura van; Simons, Ralph ; Ankersmit, Elis ; Vilsteren, Gerlinde van - \ 2017
Netherlands : CoE BBE - 47
samenwerking - publiek-private samenwerking - innovaties - biobased economy - kennisoverdracht - colleges - onderzoek - nederland - beroepsopleiding (hoger) - cooperation - public-private cooperation - innovations - knowledge transfer - research - netherlands - professional education
De transitie naar een Biobased Economy (BBE) is al jaren een 'hot item' in Nederland, zowel binnen de Nationaal Wetenschapsagenda als binnen de topsectoren. De MKB-erst, elk in eigen niches, spelen hierbij een bepalende rol. Hiernaast hebben de hogescholen op dit domein de ambitie om een belangrijke rol voor het MKB als kennisleverancier te spelen (onderwijs en onderzoek). In dit rapport probeert helderheid te creëren over hoe dit proces verloopt.
Os desafios de transferência de tecnologia no setor produtivo do leite : O estudo de caso do Projeto Balde Cheio
Monteiro Novo, A.L. ; Jansen, C.E.P. ; Slingerland, M.A. ; Ismail, Ramalho Haddade ; Chinelato de Camargo, Artur - \ 2016
In: Pecuária de leite no Brasil / Vilela, Duarte, de Paula Ferreira, Reinaldo, Nogueira Fernandes, Ellizabeth, Vieiera Juntolli, Fabrício, Embrapa - ISBN 9788570356444 - p. 285 - 304.
Global Carbon Budget 2016
Quéré, C. Le; Andrew, R.M. ; Canadell, J.G. ; Sitch, Stephen ; Korsbakken, Jan Ivar ; Peters, Glen P. ; Manning, Andrew C. ; Boden, Thomas A. ; Tans, Pieter P. ; Houghton, Richard A. ; Keeling, Ralph F. ; Alin, Simone ; Andrews, Oliver D. ; Anthoni, Peter ; Barbero, Leticia ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Currie, Kim ; Delire, Christine ; Doney, Scott C. ; Friedlingstein, Pierre ; Gkritzalis, Thanos ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Hoppema, Mario ; Klein Goldewijk, Kees ; Jain, Atul K. ; Kato, Etsushi ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lombardozzi, Danica ; Melton, Joe R. ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin-Ichiro ; O'Brien, Kevin ; Olsen, Are ; Omar, Abdirahman M. ; Ono, Tsuneo ; Pierrot, Denis ; Poulter, Benjamin ; Rödenbeck, Christian ; Salisbury, Joe ; Schuster, Ute ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Sutton, Adrienne J. ; Takahashi, Taro ; Tian, Hanqin ; Tilbrook, Bronte ; Laan-Luijkx, I.T. van der; Werf, Guido R. Van Der; Viovy, Nicolas ; Walker, Anthony P. ; Wiltshire, Andrew J. ; Zaehle, Sönke - \ 2016
Global Carbon Budget 2016
Quéré, Corinne Le; Andrew, Robbie M. ; Canadell, Josep G. ; Sitch, Stephen ; Korsbakken, Jan Ivar ; Peters, Glen P. ; Manning, Andrew C. ; Boden, Thomas A. ; Tans, Pieter P. ; Houghton, Richard A. ; Keeling, Ralph F. ; Alin, Simone ; Andrews, Oliver D. ; Anthoni, Peter ; Barbero, Leticia ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Currie, Kim ; Delire, Christine ; Doney, Scott C. ; Friedlingstein, Pierre ; Gkritzalis, Thanos ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Hoppema, Mario ; Klein Goldewijk, Kees ; Jain, Atul K. ; Kato, Etsushi ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lombardozzi, Danica ; Melton, Joe R. ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, S. ; O'Brien, Kevin ; Olsen, Are ; Omar, Abdirahman M. ; Ono, Tsuneo ; Pierrot, Denis ; Poulter, Benjamin ; Rödenbeck, Christian ; Salisbury, Joe ; Schuster, Ute ; Schwinger, Jörg ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Sutton, Adrienne J. ; Takahashi, Taro ; Tian, Hanqin ; Tilbrook, Bronte ; Laan-Luijkx, Ingrid T. van der; Werf, Guido R. van der; Viovy, Nicolas ; Walker, Anthony P. ; Wiltshire, Andrew J. ; Zaehle, Sönke - \ 2016
Earth System Science Data 8 (2016)2. - ISSN 1866-3508 - p. 605 - 649.
Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere – the “global carbon budget” – is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates and consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models. We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2006–2015), EFF was 9.3 ± 0.5 GtC yr−1, ELUC 1.0 ± 0.5 GtC yr−1, GATM 4.5 ± 0.1 GtC yr−1, SOCEAN 2.6 ± 0.5 GtC yr−1, and SLAND 3.1 ± 0.9 GtC yr−1. For year 2015 alone, the growth in EFF was approximately zero and emissions remained at 9.9 ± 0.5 GtC yr−1, showing a slowdown in growth of these emissions compared to the average growth of 1.8 % yr−1 that took place during 2006–2015. Also, for 2015, ELUC was 1.3 ± 0.5 GtC yr−1, GATM was 6.3 ± 0.2 GtC yr−1, SOCEAN was 3.0 ± 0.5 GtC yr−1, and SLAND was 1.9 ± 0.9 GtC yr−1. GATM was higher in 2015 compared to the past decade (2006–2015), reflecting a smaller SLAND for that year. The global atmospheric CO2 concentration reached 399.4 ± 0.1 ppm averaged over 2015. For 2016, preliminary data indicate the continuation of low growth in EFF with +0.2 % (range of −1.0 to +1.8 %) based on national emissions projections for China and USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. In spite of the low growth of EFF in 2016, the growth rate in atmospheric CO2 concentration is expected to be relatively high because of the persistence of the smaller residual terrestrial sink (SLAND) in response to El Niño conditions of 2015–2016. From this projection of EFF and assumed constant ELUC for 2016, cumulative emissions of CO2 will reach 565 ± 55 GtC (2075 ± 205 GtCO2) for 1870–2016, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quéré et al., 2015b, a, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center.
Resilience of Amazonian forests : the roles of fire, flooding and climate
Monteiro Flores, B. - \ 2016
Wageningen University. Promotor(en): Marten Scheffer, co-promotor(en): Milena Holmgren Urba; Jose de Attayde. - Wageningen : Wageningen University - ISBN 9789462578876 - 128
forests - resilience of nature - fire - flooding - floods - climate - floodplains - vegetation - amazonia - bossen - veerkracht van de natuur - brand - inundatie - overstromingen - klimaat - stroomvlakten - vegetatie - amazonia

The Amazon has recently been portrayed as a resilient forest system based on quick recovery of biomass after human disturbance. Yet with climate change, the frequency of droughts and wildfires may increase, implying that parts of this massive forest may shift into a savanna state. Although the Amazon basin seems quite homogeneous, 14% is seasonally inundated. In my thesis I combine analyses of satellite data with field measurements and experiments to assess the role of floodplain ecosystems in shaping the resilience of Amazonian forests.

First, I analyse tree cover distribution for the whole Amazon to reveal that savannas are relatively more common on floodplains. This suggests that compared to uplands, floodplains spend more time in the savanna state. Also, floodplain forests seem to have a tipping point at 1500 mm of annual rainfall in which forests may shift to savanna, whereas the tipping point for upland forests seems to be at 1000 mm of rainfall. Combining satellite and field measurements, I show that the higher frequency of savannas on floodplain ecosystems may be due to a higher sensitivity to fire. After a forest fire, floodplains lose more tree cover and soil fertility, and recover more slowly than uplands (chapter 2).

In floodplains of the Negro river, I studied the recovery of blackwater forests after repeated fires, using field data on tree basal area, species richness, seed availability, and herbaceous cover. Results indicate that repeated fires may easily trap blackwater floodplains in an open-vegetation state, due the sudden loss of forest resilience after a second fire event (chapter 3).

Analyses of the soil and tree composition of burnt floodplain forests, reveal that a first fire is the onset of the loss of soil fertility that intensifies while savanna trees dominate the tree community. A tree compositional shift happens within four decades, possibly accelerated by fast nutrient leaching. The rapid savannization of floodplain forests after fire implies that certain mechanisms such as environmental filtering may favor the recruitment of savanna trees over forest trees (chapter 4).

In chapter 5, I experimentally tested in the field the roles of dispersal limitation, and environmental filtering for tree recruitment in burnt floodplain forests. I combine inventories of seed availability in burnt sites with experiments using planted seeds and seedlings of six floodplain tree species. Repeated fires strongly reduce the availability of tree seeds, yet planted trees thrive despite degraded soils and high herbaceous cover. Moreover, degraded soils on twice burnt sites seem to limit the growth of most pioneer trees, but not of savanna trees with deeper roots. Our results suggest a limitation of forest trees to disperse into open burnt sites.

The combined evidence presented in this thesis support the hypothesis that Amazonian forests on floodplains are less resilient than forests on uplands, and more likely to shift into a savanna state. The lower ability of floodplains to retain soil fertility and recover forest structure after fire, may accelerate the transition to savanna. I also present some evidence of dispersal limitation of floodplain forest trees. Broad-scale analyses of tree cover as a function of rainfall suggest that savannas are likely to expand first in floodplains if Amazonian climate becomes drier. Savanna expansion through floodplain ecosystems to the core of the Amazon may spread fragility from an unsuspected place.

Advantages and limitations of chemical extraction tests to predict mercury soil-plant transfer in soil risk evaluations
Monteiro, R.J.R. ; Rodrigues, S.M. ; Cruz, N. ; Henriques, B. ; Duarte, A.C. ; Römkens, P.F.A.M. ; Pereira, E. - \ 2016
Environmental Science and Pollution Research 23 (2016)14. - ISSN 0944-1344 - p. 14327 - 14337.
Agricultural soils - Chemical availability - Mercury - Plant uptake - Risk assessment - Soil tests

In this study, we compared the size of the mobile Hg pool in soil to those obtained by extractions using 2 M HNO3, 5 M HNO3, and 2 M HCl. This was done to evaluate their suitability to be used as proxies in view of Hg uptake by ryegrass. Total levels of Hg in soil ranged from 0.66 to 70 mg kg−1 (median 17 mg kg−1), and concentrations of Hg extracted increased in the order: mobile Hg <2 M HNO3 <5 M HNO3 <2 M HCl. The percentage of Hg extracted relative to total Hg in soil varied from 0.13 to 0.79 % (for the mobile pool) to 4.8–82 % (for 2 M HCl). Levels of Hg in ryegrass ranged from 0.060 to 36 mg kg−1 (median 0.65 mg kg−1, in roots) and from 0.040 to 5.4 mg kg−1 (median 0.34 mg kg−1, in shoots). Although results from the 2 M HNO3 extraction appeared to the most comparable to the actual total Hg levels measured in plants, the 2 M HCl extraction better expressed the variation in plant pools. In general, soil tests explained between 66 and 86 % of the variability of Hg contents in ryegrass shoots. Results indicated that all methods tested here can be used to estimate the plant total Hg pool at contaminated areas and can be used in first tier soil risk evaluations. This study also indicates that a relevant part of Hg in plants is from deposition of soil particles and that splashing of soil can be more significant for plant contamination than actual uptake processes. [Figure not available: see fulltext.]

Root-to-shoot ABA signaling does not contribute to genotypic variation in stomatal functioning induced by high relative air humidity
Carvalho, Dália R.A. ; Fanourakis, D. ; Correia, M.J. ; Monteiro, J.A. ; Araújo-Alves, J.P.L. ; Vasconcelos, M.W. ; Almeida, D.P.F. ; Heuvelink, E. ; Pinto de Carvalho, S. - \ 2016
Environmental and Experimental Botany 123 (2016). - ISSN 0098-8472 - p. 13 - 21.
Abscisic acid - Relative water content - Rosa×hybrida - Stomatal anatomy - Vapor pressure deficit - Water loss

High relative air humidity (RH ≥85%) during leaf expansion hampers stomatal responsiveness to closing stimuli, a genotype-dependent effect. Genotypes with reduced stomatal closure in response to closing stimuli (i.e., sensitive genotypes) show low bulk leaf abscisic acid concentration ([ABA]). We hypothesized that the amount of ABA produced in the roots and delivered with the transpiration stream to the leaves is a critical step for a proper stomatal functioning in high RH-grown plants. Ten genotypes from a cut rose tetraploid population were grown at moderate (62%) or high (89%) RH. Stomatal anatomy and responsiveness to desiccation or ABA feeding were evaluated. Root and leaf petiole xylem sap [ABA] were quantified, and ABA delivery rate from root-to-shoot was estimated. High RH reduced stomatal responsiveness to both closing stimuli in the sensitive genotypes, whereas it had a non-significant effect in the tolerant ones. Estimates of [ABA] in root xylem sap at transpirational flow rate were not related to the genotypic differences in the sensitivity to high RH. However, high RH increased this concentration irrespective of the genotype, probably due to a reduced dilution of the [ABA] in the xylem sap as a result of a lower transpiration rate compared to moderate RH-grown plants. Leaf petiole xylem sap [ABA] was neither related to the genotypic differences in the sensitivity to high RH nor it was affected by RH. We concluded that genotypic differences in the stomatal sensitivity to high RH cannot be explained by changes in the [ABA] delivered with the transpiration stream from the roots to the leaves.

Assessing the effects of land cover and future climate conditions on the provision of hydrological services in a medium-sized watershed of Portugal
Carvalho-Santos, Claudia ; Nunes, João Pedro ; Monteiro, António T. ; Hein, Lars ; Honrado, João Pradinho - \ 2016
Hydrological Processes 30 (2016)5. - ISSN 0885-6087 - p. 720 - 738.
Future climate - Hydrological services - Land-cover scenarios - RCP 4.5 scenario - SWAT - Vez watershed

The separated and combined effects of land-cover scenarios and future climate on the provision of hydrological services were evaluated in Vez watershed, northern Portugal. Soil and Water Assessment Tool was calibrated against daily discharge, sediments and nitrates, with good agreements between model predictions and field observations. Four hypothetical land-cover scenarios were applied under current climate conditions (eucalyptus/pine, oak, agriculture/vine and low vegetation). A statistical downscaling of four General Circulation Models, bias-corrected with ground observations, was carried out for 2021-2040 and 2041-2060, using representative concentration pathway 4.5 scenario. Also, the combined effects of future climate conditions were evaluated under eucalyptus/pine and agriculture/vine scenario. Results for land cover revealed that eucalyptus/pine scenario reduced by 7% the annual water quantity and up to 17% in the summer period. Although climate change has only a modest effect on the reduction of the total annual discharge (-7%), the effect on the water levels during summer was more pronounced, between -15% and -38%. This study shows that climate change can affect the provision of hydrological services by reducing dry season flows and by increasing flood risks during the wet months. Regarding the combined effects, future climate may reduce the low flows, which can be aggravated with eucalyptus/pine scenario. In turn, peak flows and soil erosion can be offset. Future climate may increase soil erosion and nitrate concentration, which can be aggravated with agriculture scenario. Results moreover emphasize the need to consider both climate and land-cover impacts in adaptation and land management options at the watershed scale.

Inovação responsável através de fronteiras: tensões, paradoxos e possibilidades
Macnaghten, Phil ; Owen, Richard ; Stilgoe, Jack ; Wynne, Brian ; Azevedo, Adalberto ; Campo, André Luiz Sica De ; Chilvers, Jason ; Dagnino, Renato ; Giulio, Gabriela Di ; Frow, Emma ; Garvey, Brian ; Groves, Christopher ; Hartley, Sarah ; Knobel, Marcelo ; Kobayashi, Elizabete ; Lehtonen, Markku ; Martin, Javier Lezaun James ; Mello, Leonardo Freire De ; Monteiro, Marko ; Costa, Janaina Pamplona Da ; Rigolin, Camila ; Rondani, Bruno ; Staykova, Margarita ; Taddei, Renzo ; Till, Chris ; Tyfield, David ; Velho, Léa ; Wilford, Sara - \ 2015
Teoria e Pesquisa 24 (2015)2. - ISSN 0104-0103 - p. 18 - 24.
In March 2014 a group of early career researchers
and academics from São Paulo state and from the UK met
at the University of Campinas to participate in a workshop
on ‘ResponsibleInnovation and the Governance of Socially
Controversial Technologies’. In this Perspective we describe key
reflections and observations from the workshop discussions, paying
particular attention to the discourse of responsible innovation from
a cross-cultural perspective. We describe a number of important
tensions, paradoxes and opportunities that emerged over the
three days of the workshop.
Testing single extraction methods and in vitro tests to assess the geochemical reactivity and human bioaccessibility of silver in urban soils amended with silver nanoparticles
Cruz, N. ; Rodrigues, S.M. ; Tavares, D. ; Monteiro, R.J.R. ; Carvalho, L. ; Trindade, T. ; Duarte, A.C. ; Pereira, E. ; Romkens, Paul - \ 2015
Chemosphere 135 (2015). - ISSN 0045-6535 - p. 304 - 311.
Bioavailability - Engineered silver nanoparticles - Geochemical reactivity - In vitro bioaccessibility - Soil pollution

To assess if the geochemical reactivity and human bioaccessibility of silver nanoparticles (AgNPs) in soils can be determined by routine soil tests commonly applied to other metals in soil, colloidal Ag was introduced to five pots containing urban soils (equivalent to 6.8mgAgkg-1 soil). Following a 45days stabilization period, the geochemical reactivity was determined by extraction using 0.43M and 2M HNO3. The bioaccessibility of AgNPs was evaluated using the Simplified Bioaccessibility Extraction Test (SBET) the "Unified BARGE Method" (UBM), and two simulated lung fluids (modified Gamble's solution (MGS) and artificial lysosomal fluid (ALF)).The amount of Ag extracted by 0.43M and 2M HNO3 soil tests was

The ‘Ilhas’ of Porto and ‘self-improvement urbanism’: the inhabitants as engine of urban transformation
Holz Amorim de Sena, N.H. ; Doevendans, P. ; Rousseau, S. - \ 2014
In: 21st International Seminar on Urban Form "Our common future in Urban Morphology". - Porto : FEUP - ISBN 9789729910166 - p. 583 - 597.
An ‘Ilha’ in Porto is a typology of low cost housing which spread within the city in the 19th Century as a result of the industrial development. The extremely small dwellings (around 4x4m) were established within backyards of middle class houses, connected to the street through a narrow corridor. Despite all public trials of destruction, more than 1.000 ‘Ilhas’ still shelter more than 13.000 people within the city of Porto. The subject of this article is the analysis of the morphology of the ‘Ilhas’ of Porto, Portugal. The objective is to illustrate what the typology currently means for its inhabitants and for the urban space and propose methods of improving their living standards. The social and spatial dimension of the ‘Ilhas’ as an ‘assemblage’ of the city determines the research method, focusing on a) an analysis of the morphology and typology of a selected cluster of ‘Ilhas’ in different scales; b) participatory research involving the inhabitants, including interviews and observation of daily practices and community values. Despite the low quality living conditions, the inhabitants of the ‘Ilhas’ show an impressive attachment to their living space, forming a strong community. This quality is used as a foundation for the ‘selfimprovement’ urbanism, where the community operates as the main engine of the urban transformation. The main finding of the research is that the ‘Ilhas’ could be an inexpensive solution for the current housing crisis through the further development of the ‘self-improvement’ urbanism. This innovative approach includes strong public participation and an innovative position of the planner within the process.
Oral bioaccessibility and human exposure to anthropogenic and geogenic mercury in urban, industrial and mining areas
Rodrigues, S.M. ; Coelho, C. ; Cruz, N. ; Monteiro, R.J.R. ; Henriques, B. ; Duarte, A.C. ; Romkens, P.F.A.M. ; Pereira, E. - \ 2014
Science of the Total Environment 496 (2014). - ISSN 0048-9697 - p. 649 - 661.
atomic-absorption-spectrometry - potentially toxic elements - chloralkali plant - inorganic mercury - part i - contaminated soils - asturias spain - speciation - sediments - portugal
The objective of this study was to characterize the link between bioaccessibility and fractionation of mercury (Hg) in soils and to provide insight into human exposure to Hg due to inhalation of airborne soil particles and hand-to-mouth ingestion of Hg-bearing soil. Mercury in soils from mining, urban and industrial areas was fractionated in organometallic forms; mobile; semi-mobile; and non-mobile forms as well as HCl-extractable Hg. The in vitro bioaccessibility of Hg was obtained by extracting soils with (1) a simulated human gastric fluid (pH 1.5), and (2) a simulated human lung fluid (pH 7.4). Total soil Hg concentrations ranged from 0.72 to 1.8 mg kg- 1 (urban areas), 0.28 to 94 mg kg- 1 (industrial area) and 0.92 to 37 mg kg- 1 (mining areas). Both organometallic Hg as well as 0.1 M HCl extractable Hg were lower (<0.5% of total Hg) than Hg extracted by gastric fluid (up to 1.8% of total Hg) and lung fluid (up to 12% of total Hg). In addition, Hg extracted by lung fluid was significantly higher in urban and industrial soils (average 5.0–6.6% of total Hg) compared to mining soils. Such differences were related to levels of mobile Hg species in urban and industrial soils compared to mining soils. These results strengthen the need to measure site-specific Hg fractionation when determining Hg bioaccessibility. Results also show that ingestion and/or inhalation of Hg from soil particles can contribute up to 8% of adult total Hg intake when compared to total Hg intake via consumption of contaminated fish and animal products from contaminated areas.
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