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5. The GenTree Platform:growth traits and tree-level environmental data in 12 European forest tree species

Author

Opgenoorth, L. (Lars), Benjamin, D. (Dauphin), Benavides, R. (Raquel), Heer, K. (Katrin), Alizoti, P. (Paraskevi), Martinez-Sancho, E. (Elisabet), Alia, R. (Ricardo), Ambrosio, O. (Olivier), Audrey, A. (Albet), Aunon, F. (Francisco), Avanzi, C. (Camilla), Avramidou, E. (Evangelia), Bagnoli, F. (Francesca), Barbas, E. (Evangelos), Bastias, C. C. (Cristina C.), Bastien, C. (Catherine), Ballesteros, E. (Eduardo), Beffa, G. (Giorgia), Bernier, F. (Frederic), Bignalet, H. (Henri), Bodineau, G. (Guillaume), Bouic, D. (Damien), Brodbeck, S. (Sabine), Brunetto, W. (William), Buchovska, J. (Jurata), Buy, M. (Melanie), Cabanillas-Saldana, A. M. (Ana M.), Carvalho, B. (Barbara), Cheval, N. (Nicolas), Climent, J. M. (Jose M.), Correard, M. (Marianne), Cremer, E. (Eva), Danusevicius, D. (Darius), Del Cano, F. (Fernando), Denou, J.-L. (Jean-Luc), di Gerardi, N. (Nicolas), Dokhelar, B. (Bernard), Ducousso, A. (Alexis), Nilsen, A. E. (Anne Eskild), Farsakoglou, A.-M. (Anna-Maria), Fonti, P. (Patrick), Ganopoulos, I. (Ioannis), Garcia del Barrio, J. M. (Jose M.), Gilg, O. (Olivier), Gonzalez-Martinez, S. C. (Santiago C.), Graf, R. (Rene), Gray, A. (Alan), Grivet, D. (Delphine), Gugerli, F. (Felix), Hartleitner, C. (Christoph), Hollenbach, E. (Enja), Hurel, A. (Agathe), Issehut, B. (Bernard), Jean, F. (Florence), Jorge, V. (Veronique), Jouineau, A. (Arnaud), Kappner, J.-P. (Jan-Philipp), Karkkainen, K. (Katri), Kesälahti, R. (Robert), Knutzen, F. (Florian), Kujala, S. T. (Sonja T.), Kumpula, T. A. (Timo A.), Labriola, M. (Mariaceleste), Lalanne, C. (Celine), Lambertz, J. (Johannes), Lascoux, M. (Martin), Lejeune, V. (Vincent), Le-Provost, G. (Gregoire), Levillain, J. (Joseph), Liesebach, M. (Mirko), Lopez-Quiroga, D. (David), Meier, B. (Benjamin), Malliarou, E. (Ermioni), Marchon, J. (Jeremy), Mariotte, N. (Nicolas), Mas, A. (Antonio), Matesanz, S. (Silvia), Meischner, H. (Helge), Michotey, C. (Celia), Milesi, P. (Pascal), Morganti, S. (Sandro), Nievergelt, D. (Daniel), Notivol, E. (Eduardo), Ostreng, G. (Geir), Pakull, B. (Birte), Perry, A. (Annika), Piotti, A. (Andrea), Plomion, C. (Christophe), Poinot, N. (Nicolas), Pringarbe, M. (Mehdi), Puzos, L. (Luc), Pyhajarvi, T. (Tanja), Raffin, A. (Annie), Ramirez-Valiente, J. A. (Jose A.), Rellstab, C. (Christian), Remi, D. (Dourthe), Richter, S. (Sebastian), Robledo-Arnuncio, J. J. (Juan J.), San Segundo, S. (Sergio), Savolainen, O. (Outi), Schueler, S. (Silvio), Schneck, V. (Volker), Scotti, I. (Ivan), Semerikov, V. (Vladimir), Slamova, L. (Lenka), Sonstebo, J. H. (Jorn Henrik), Spanu, I. (Ilaria), Thevenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), von Arx, G. (Georg), Westin, J. (Johan), Fady, B. (Bruno), Myking, T. (Tor), Valladares, F. (Fernando), Aravanopoulos, F. A. (Filippos A.), Cavers, S. (Stephen), Opgenoorth, L. (Lars), Benjamin, D. (Dauphin), Benavides, R. (Raquel), Heer, K. (Katrin), Alizoti, P. (Paraskevi), Martinez-Sancho, E. (Elisabet), Alia, R. (Ricardo), Ambrosio, O. (Olivier), Audrey, A. (Albet), Aunon, F. (Francisco), Avanzi, C. (Camilla), Avramidou, E. (Evangelia), Bagnoli, F. (Francesca), Barbas, E. (Evangelos), Bastias, C. C. (Cristina C.), Bastien, C. (Catherine), Ballesteros, E. (Eduardo), Beffa, G. (Giorgia), Bernier, F. (Frederic), Bignalet, H. (Henri), Bodineau, G. (Guillaume), Bouic, D. (Damien), Brodbeck, S. (Sabine), Brunetto, W. (William), Buchovska, J. (Jurata), Buy, M. (Melanie), Cabanillas-Saldana, A. M. (Ana M.), Carvalho, B. (Barbara), Cheval, N. (Nicolas), Climent, J. M. (Jose M.), Correard, M. (Marianne), Cremer, E. (Eva), Danusevicius, D. (Darius), Del Cano, F. (Fernando), Denou, J.-L. (Jean-Luc), di Gerardi, N. (Nicolas), Dokhelar, B. (Bernard), Ducousso, A. (Alexis), Nilsen, A. E. (Anne Eskild), Farsakoglou, A.-M. (Anna-Maria), Fonti, P. (Patrick), Ganopoulos, I. (Ioannis), Garcia del Barrio, J. M. (Jose M.), Gilg, O. (Olivier), Gonzalez-Martinez, S. C. (Santiago C.), Graf, R. (Rene), Gray, A. (Alan), Grivet, D. (Delphine), Gugerli, F. (Felix), Hartleitner, C. (Christoph), Hollenbach, E. (Enja), Hurel, A. (Agathe), Issehut, B. (Bernard), Jean, F. (Florence), Jorge, V. (Veronique), Jouineau, A. (Arnaud), Kappner, J.-P. (Jan-Philipp), Karkkainen, K. (Katri), Kesälahti, R. (Robert), Knutzen, F. (Florian), Kujala, S. T. (Sonja T.), Kumpula, T. A. (Timo A.), Labriola, M. (Mariaceleste), Lalanne, C. (Celine), Lambertz, J. (Johannes), Lascoux, M. (Martin), Lejeune, V. (Vincent), Le-Provost, G. (Gregoire), Levillain, J. (Joseph), Liesebach, M. (Mirko), Lopez-Quiroga, D. (David), Meier, B. (Benjamin), Malliarou, E. (Ermioni), Marchon, J. (Jeremy), Mariotte, N. (Nicolas), Mas, A. (Antonio), Matesanz, S. (Silvia), Meischner, H. (Helge), Michotey, C. (Celia), Milesi, P. (Pascal), Morganti, S. (Sandro), Nievergelt, D. (Daniel), Notivol, E. (Eduardo), Ostreng, G. (Geir), Pakull, B. (Birte), Perry, A. (Annika), Piotti, A. (Andrea), Plomion, C. (Christophe), Poinot, N. (Nicolas), Pringarbe, M. (Mehdi), Puzos, L. (Luc), Pyhajarvi, T. (Tanja), Raffin, A. (Annie), Ramirez-Valiente, J. A. (Jose A.), Rellstab, C. (Christian), Remi, D. (Dourthe), Richter, S. (Sebastian), Robledo-Arnuncio, J. J. (Juan J.), San Segundo, S. (Sergio), Savolainen, O. (Outi), Schueler, S. (Silvio), Schneck, V. (Volker), Scotti, I. (Ivan), Semerikov, V. (Vladimir), Slamova, L. (Lenka), Sonstebo, J. H. (Jorn Henrik), Spanu, I. (Ilaria), Thevenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), von Arx, G. (Georg), Westin, J. (Johan), Fady, B. (Bruno), Myking, T. (Tor), Valladares, F. (Fernando), Aravanopoulos, F. A. (Filippos A.), and Cavers, S. (Stephen)

Abstract

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusions: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data c

Published
2021

6. The GenTree Leaf Collection:inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, R. (Raquel), Carvalho, B. (Barbara), Bastias, C. C. (Cristina C.), Lopez-Quiroga, D. (David), Mas, A. (Antonio), Cavers, S. (Stephen), Gray, A. (Alan), Albet, A. (Audrey), Alia, R. (Ricardo), Ambrosio, O. (Olivier), Aravanopoulos, F. (Filippos), Aunon, F. (Francisco), Avanzi, C. (Camilla), Avramidou, E. V. (Evangelia V.), Bagnoli, F. (Francesca), Ballesteros, E. (Eduardo), Barbas, E. (Evangelos), Bastien, C. (Catherine), Bernier, F. (Frederic), Bignalet, H. (Henry), Bouic, D. (Damien), Brunetto, W. (William), Buchovska, J. (Jurata), Cabanillas-Saldana, A. M. (Ana M.), Cheval, N. (Nicolas), Climent, J. M. (Jose M.), Correard, M. (Marianne), Cremer, E. (Eva), Danusevicius, D. (Darius), Dauphin, B. (Benjamin), Del Cano, F. (Fernando), Denou, J.-L. (Jean-Luc), Dokhelar, B. (Bernard), Dourthe, R. (Remi), Farsakoglou, A.-M. (Anna-Maria), Fera, A. (Andreas), Fonti, P. (Patrick), Ganopoulos, I. (Ioannis), Garcia del Barrio, J. M. (Jose M.), Gilg, O. (Olivier), Gonzalez-Martinez, S. C. (Santiago C.), Graf, R. (Rene), Grivet, D. (Delphine), Gugerli, F. (Felix), Hartleitner, C. (Christoph), Heer, K. (Katrin), Hollenbach, E. (Enja), Hurel, A. (Agathe), Issehuth, B. (Bernard), Jean, F. (Florence), Jorge, V. (Veronique), Jouineau, A. (Arnaud), Kappner, J.-P. (Jan-Philipp), Kärkkainen, K. (Katri), Kesälahti, R. (Robert), Knutzen, F. (Florian), Kujala, S. T. (Sonja T.), Kumpula, T. (Timo), Labriola, M. (Mariaceleste), Lalanne, C. (Celine), Lambertz, J. (Johannes), Lascoux, M. (Martin), Le Provost, G. (Gregoire), Liesebach, M. (Mirko), Malliarou, E. (Ermioni), Marchon, J. (Jeremy), Mariotte, N. (Nicolas), Martinez-Sancho, E. (Elisabet), Matesanz, S. (Silvia), Meischner, H. (Helge), Michotey, C. (Celia), Milesi, P. (Pascal), Morganti, S. (Sandro), Myking, T. (Tor), Nilsen, A. E. (Anne E.), Notivol, E. (Eduardo), Opgenoorth, L. (Lars), ostreng, G. (Geir), Pakull, B. (Birte), Piotti, A. (Andrea), Plomion, C. (Christophe), Poinot, N. (Nicolas), Pringarbe, M. (Mehdi), Puzos, L. (Luc), Pyhajarvi, T. (Tanja), Raffin, A. (Annie), Ramirez-Valiente, J. A. (Jose A.), Rellstab, C. (Christian), Richter, S. (Sebastian), Robledo-Arnuncio, J. J. (Juan J.), San Segundo, S. (Sergio), Savolainen, O. (Outi), Schneck, V. (Volker), Schueler, S. (Silvio), Scotti, I. (Ivan), Semerikov, V. (Vladimir), Henrik Sonstebo, J. (Jorn), Spanu, I. (Ilaria), Thevenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), Westin, J. (Johan), Fady, B. (Bruno), Valladares, F. (Fernando), Benavides, R. (Raquel), Carvalho, B. (Barbara), Bastias, C. C. (Cristina C.), Lopez-Quiroga, D. (David), Mas, A. (Antonio), Cavers, S. (Stephen), Gray, A. (Alan), Albet, A. (Audrey), Alia, R. (Ricardo), Ambrosio, O. (Olivier), Aravanopoulos, F. (Filippos), Aunon, F. (Francisco), Avanzi, C. (Camilla), Avramidou, E. V. (Evangelia V.), Bagnoli, F. (Francesca), Ballesteros, E. (Eduardo), Barbas, E. (Evangelos), Bastien, C. (Catherine), Bernier, F. (Frederic), Bignalet, H. (Henry), Bouic, D. (Damien), Brunetto, W. (William), Buchovska, J. (Jurata), Cabanillas-Saldana, A. M. (Ana M.), Cheval, N. (Nicolas), Climent, J. M. (Jose M.), Correard, M. (Marianne), Cremer, E. (Eva), Danusevicius, D. (Darius), Dauphin, B. (Benjamin), Del Cano, F. (Fernando), Denou, J.-L. (Jean-Luc), Dokhelar, B. (Bernard), Dourthe, R. (Remi), Farsakoglou, A.-M. (Anna-Maria), Fera, A. (Andreas), Fonti, P. (Patrick), Ganopoulos, I. (Ioannis), Garcia del Barrio, J. M. (Jose M.), Gilg, O. (Olivier), Gonzalez-Martinez, S. C. (Santiago C.), Graf, R. (Rene), Grivet, D. (Delphine), Gugerli, F. (Felix), Hartleitner, C. (Christoph), Heer, K. (Katrin), Hollenbach, E. (Enja), Hurel, A. (Agathe), Issehuth, B. (Bernard), Jean, F. (Florence), Jorge, V. (Veronique), Jouineau, A. (Arnaud), Kappner, J.-P. (Jan-Philipp), Kärkkainen, K. (Katri), Kesälahti, R. (Robert), Knutzen, F. (Florian), Kujala, S. T. (Sonja T.), Kumpula, T. (Timo), Labriola, M. (Mariaceleste), Lalanne, C. (Celine), Lambertz, J. (Johannes), Lascoux, M. (Martin), Le Provost, G. (Gregoire), Liesebach, M. (Mirko), Malliarou, E. (Ermioni), Marchon, J. (Jeremy), Mariotte, N. (Nicolas), Martinez-Sancho, E. (Elisabet), Matesanz, S. (Silvia), Meischner, H. (Helge), Michotey, C. (Celia), Milesi, P. (Pascal), Morganti, S. (Sandro), Myking, T. (Tor), Nilsen, A. E. (Anne E.), Notivol, E. (Eduardo), Opgenoorth, L. (Lars), ostreng, G. (Geir), Pakull, B. (Birte), Piotti, A. (Andrea), Plomion, C. (Christophe), Poinot, N. (Nicolas), Pringarbe, M. (Mehdi), Puzos, L. (Luc), Pyhajarvi, T. (Tanja), Raffin, A. (Annie), Ramirez-Valiente, J. A. (Jose A.), Rellstab, C. (Christian), Richter, S. (Sebastian), Robledo-Arnuncio, J. J. (Juan J.), San Segundo, S. (Sergio), Savolainen, O. (Outi), Schneck, V. (Volker), Schueler, S. (Silvio), Scotti, I. (Ivan), Semerikov, V. (Vladimir), Henrik Sonstebo, J. (Jorn), Spanu, I. (Ilaria), Thevenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), Westin, J. (Johan), Fady, B. (Bruno), and Valladares, F. (Fernando)

Abstract

Motivation: Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU‐Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra‐ and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained: We chose morphological and chemical characters linked to trade‐offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope ¹³C and ¹⁵N in leaves. Spatial location and grain: We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period: Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement: We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format: The data files are in ASCII text, tab delimited, not compressed.

Published
2021

7. Resilience learning through self adaptation in digital twins of human-cyber-physical systems

Author

Bellini, E., Bagnoli, F., Caporuscio, M., Damiani, E, Flammini, Francesco, Linkov, I., Liò, P., Marrone, S., Bellini, E., Bagnoli, F., Caporuscio, M., Damiani, E, Flammini, Francesco, Linkov, I., Liò, P., and Marrone, S.

Abstract

Human-Cyber-Physical-Systems (HPCS), such as critical infrastructures in modern society, are subject to several systemic threats due to their complex interconnections and interdependencies. Management of systemic threats requires a paradigm shift from static risk assessment to holistic resilience modeling and evaluation using intelligent, data-driven and run-time approaches. In fact, the complexity and criticality of HCPS requires timely decisions considering many parameters and implications, which in turn require the adoption of advanced monitoring frameworks and evaluation tools. In order to tackle such challenge, we introduce those new paradigms in a framework named RESILTRON, envisioning Digital Twins (DT) to support decision making and improve resilience in HCPS under systemic stress. In order to represent possibly complex and heterogeneous HCPS, together with their environment and stressors, we leverage on multi-simulation approaches, combining multiple formalisms, data-driven approaches and Artificial Intelligence (AI) modelling paradigms, through a structured, modular and compositional framework. DT are used to provide an adaptive abstract representation of the system in terms of multi-layered spatially-embedded dynamic networks, and to apply self-adaptation to time-warped What-If analyses, in order to find the best sequence of decisions to ensure resilience under uncertainty and continuous HPCS evolution.

Published
2021
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8. JAK2-mutated Langerhans cell histiocytosis associated with primary myelofibrosis treated with ruxolitinib

Author

Bonometti, A, Bagnoli, F, Fanoni, D, Venegoni, L, Corti, L, Bianchi, P, Elli, E, Isimbaldi, G, L'Imperio, V, Nazzaro, G, Passoni, E, Berti, E, Bonometti A., Bagnoli F., Fanoni D., Venegoni L., Corti L., Bianchi P., Elli E. M., Isimbaldi G., L'Imperio V., Nazzaro G., Passoni E., Berti E., Bonometti, A, Bagnoli, F, Fanoni, D, Venegoni, L, Corti, L, Bianchi, P, Elli, E, Isimbaldi, G, L'Imperio, V, Nazzaro, G, Passoni, E, Berti, E, Bonometti A., Bagnoli F., Fanoni D., Venegoni L., Corti L., Bianchi P., Elli E. M., Isimbaldi G., L'Imperio V., Nazzaro G., Passoni E., and Berti E.

Abstract

The pathogenesis and cellular origin of Langerhans cell histiocytosis (LCH) are debated. Recently, mutations on MAPK and PI3K pathways have been linked to disrupted cell proliferation in LCH. Janus Kinase 2 (JAK2) mutations play the same role in Philadelphia-negative chronic myeloproliferative neoplasms. We describe the case of a patient affected by JAK2-positive primary myelofibrosis (PMF) who developed a clonally related LCH while in treatment with ruxolitinib. JAK inhibitors are well known to affect function and differentiation of different hematological lineages, including mononuclear phagocytes precursors. Nevertheless, the literature describes cases of LCH clonally associated with non-LCH hematological neoplasm, suggesting how multilinear myeloid neoplasms may arise from bone marrow. Hence, we briefly discuss the possible pathogenic roles of genetic mutations and JAK inhibition therapy in the pathogenesis of LCH and associated neoplasms.

Published
2018

9. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, E. (Elisabet), Slámová, L. (Lenka), Morganti, S. (Sandro), Grefen, C. (Claudio), Carvalho, B. (Barbara), Dauphin, B. (Benjamin), Rellstab, C. (Christian), Gugerli, F. (Felix), Opgenoorth, L. (Lars), Heer, K. (Katrin), Knutzen, F. (Florian), von Arx, G. (Georg), Valladares, F. (Fernando), Cavers, S. (Stephen), Fady, B. (Bruno), Alía, R. (Ricardo), Aravanopoulos, F. (Filippos), Avanzi, C. (Camilla), Bagnoli, F. (Francesca), Barbas, E. (Evangelos), Bastien, C. (Catherine), Benavides, R. (Raquel), Bernier, F. (Frédéric), Bodineau, G. (Guillaume), Bastias, C. C. (Cristina C.), Charpentier, J.-P. (Jean-Paul), Climent, J. M. (José M.), Corréard, M. (Marianne), Courdier, F. (Florence), Danusevicius, D. (Darius), Farsakoglou, A.-M. (Anna-Maria), García del Barrio, J. M. (José M.), Gilg, O. (Olivier), González-Martínez, S. C. (Santiago C.), Gray, A. (Alan), Hartleitner, C. (Christoph), Hurel, A. (Agathe), Jouineau, A. (Arnaud), Kärkkäinen, K. (Katri), Kujala, S. T. (Sonja T.), Labriola, M. (Mariaceleste), Lascoux, M. (Martin), Lefebvre, M. (Marlène), Lejeune, V. (Vincent), Le-Provost, G. (Grégoire), Liesebach, M. (Mirko), Malliarou, E. (Ermioni), Mariotte, N. (Nicolas), Matesanz, S. (Silvia), Michotey, C. (Célia), Milesi, P. (Pascal), Myking, T. (Tor), Notivol, E. (Eduardo), Pakull, B. (Birte), Piotti, A. (Andrea), Plomion, C. (Christophe), Pringarbe, M. (Mehdi), Pyhäjärvi, T. (Tanja), Raffin, A. (Annie), Ramírez-Valiente, J. A. (José A.), Ramskogler, K. (Kurt), Robledo-Arnuncio, J. J. (Juan J.), Savolainen, O. (Outi), Schueler, S. (Silvio), Semerikov, V. (Vladimir), Spanu, I. (Ilaria), Thévenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Veisse, D. (Dominique), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), Westin, J. (Johan), Fonti, P. (Patrick), Martínez-Sancho, E. (Elisabet), Slámová, L. (Lenka), Morganti, S. (Sandro), Grefen, C. (Claudio), Carvalho, B. (Barbara), Dauphin, B. (Benjamin), Rellstab, C. (Christian), Gugerli, F. (Felix), Opgenoorth, L. (Lars), Heer, K. (Katrin), Knutzen, F. (Florian), von Arx, G. (Georg), Valladares, F. (Fernando), Cavers, S. (Stephen), Fady, B. (Bruno), Alía, R. (Ricardo), Aravanopoulos, F. (Filippos), Avanzi, C. (Camilla), Bagnoli, F. (Francesca), Barbas, E. (Evangelos), Bastien, C. (Catherine), Benavides, R. (Raquel), Bernier, F. (Frédéric), Bodineau, G. (Guillaume), Bastias, C. C. (Cristina C.), Charpentier, J.-P. (Jean-Paul), Climent, J. M. (José M.), Corréard, M. (Marianne), Courdier, F. (Florence), Danusevicius, D. (Darius), Farsakoglou, A.-M. (Anna-Maria), García del Barrio, J. M. (José M.), Gilg, O. (Olivier), González-Martínez, S. C. (Santiago C.), Gray, A. (Alan), Hartleitner, C. (Christoph), Hurel, A. (Agathe), Jouineau, A. (Arnaud), Kärkkäinen, K. (Katri), Kujala, S. T. (Sonja T.), Labriola, M. (Mariaceleste), Lascoux, M. (Martin), Lefebvre, M. (Marlène), Lejeune, V. (Vincent), Le-Provost, G. (Grégoire), Liesebach, M. (Mirko), Malliarou, E. (Ermioni), Mariotte, N. (Nicolas), Matesanz, S. (Silvia), Michotey, C. (Célia), Milesi, P. (Pascal), Myking, T. (Tor), Notivol, E. (Eduardo), Pakull, B. (Birte), Piotti, A. (Andrea), Plomion, C. (Christophe), Pringarbe, M. (Mehdi), Pyhäjärvi, T. (Tanja), Raffin, A. (Annie), Ramírez-Valiente, J. A. (José A.), Ramskogler, K. (Kurt), Robledo-Arnuncio, J. J. (Juan J.), Savolainen, O. (Outi), Schueler, S. (Silvio), Semerikov, V. (Vladimir), Spanu, I. (Ilaria), Thévenet, J. (Jean), Tollefsrud, M. M. (Mari Mette), Turion, N. (Norbert), Veisse, D. (Dominique), Vendramin, G. G. (Giovanni Giuseppe), Villar, M. (Marc), Westin, J. (Johan), and Fonti, P. (Patrick)

Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Published
2020

10. Cognitive and Physiological Response for Health Monitoring in an Ageing Population: A Multi-modal System

Author

El Yacoubi, S, Bagnoli, F, Pacini, G, Saibene, A, Gasparini, F, El Yacoubi, S, Bagnoli, F, Pacini, G, Saibene, A, and Gasparini, F

Abstract

In the last years, a rapid increase of life expectancy has been observed and thus ageing is becoming a hot topic in different research fields. Ensuring the wellbeing of elderly people has a positive impact on healthcare, economy and social equality and thus developing a system that takes into account and integrates physiological parameters, cognitive and physical training, elderly-user experience and perception of the system itself, may represent an innovative multi-modal mean through which ameliorate older people wellbeing.

Published
2019

11. Intralymphatic vaccination

Author

Rappuoli, R, Bagnoli, F, Rappuoli, R ( R ), Bagnoli, F ( F ), Kündig, T M, Johansen, P; https://orcid.org/0000-0002-5055-6299, Senti, G, Rappuoli, R, Bagnoli, F, Rappuoli, R ( R ), Bagnoli, F ( F ), Kündig, T M, Johansen, P; https://orcid.org/0000-0002-5055-6299, and Senti, G

Published
2011

12. High-density SNP assay development for genetic analysis in maritime pine (#Pinus pinaster#)

Author

Plomion, Christophe, Bartholomé, Jérôme, Lesur, Isabelle, Boury, Christophe, Rodríguez-Quilón, I., Lagraulet, Hélène, Ehrenmann, François, Bouffier, L., Gion, Jean-Marc, Grivet, D., de Miguel, Marina, de Maria, Nuria, Cervera, María-Teresa, Bagnoli, F., Isik, F., Vendramin, Giovanni G., González-Martínez, S.C., Plomion, Christophe, Bartholomé, Jérôme, Lesur, Isabelle, Boury, Christophe, Rodríguez-Quilón, I., Lagraulet, Hélène, Ehrenmann, François, Bouffier, L., Gion, Jean-Marc, Grivet, D., de Miguel, Marina, de Maria, Nuria, Cervera, María-Teresa, Bagnoli, F., Isik, F., Vendramin, Giovanni G., and González-Martínez, S.C.

Abstract

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. (Résumé d'auteur)

Published
2016

13. First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill

Author

Pinosio, S., González-Martínez, S. C., Bagnoli, F., Cattonaro, F., Grivet Delphine, Delphine, Marroni, F., Lorenzo, Z., Pausas, J. G., Verdú, M., Vendramin, G. G., Pinosio, S., González-Martínez, S. C., Bagnoli, F., Cattonaro, F., Grivet Delphine, Delphine, Marroni, F., Lorenzo, Z., Pausas, J. G., Verdú, M., and Vendramin, G. G.

Abstract

Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48 629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34 014 SNPs across species, with a Ka/Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28 236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes. © 2014 John Wiley & Sons Ltd.

Published
2014

14. Comparative mapping in the Fagaceae and beyond with EST-SSRs

Author

Bodenes, C., Chancerel, E., Gailing, O., Vendramin, G.G., Bagnoli, F., Durand, J., Goicoechea, P.G., Soliani, C., Villani, F., Mattioni, C., Koelewijn, H.P., Murat, F., Salse, J., Roussel, G., Boury, C., Alberto, F., Kremer, A., Plomion, C., Bodenes, C., Chancerel, E., Gailing, O., Vendramin, G.G., Bagnoli, F., Durand, J., Goicoechea, P.G., Soliani, C., Villani, F., Mattioni, C., Koelewijn, H.P., Murat, F., Salse, J., Roussel, G., Boury, C., Alberto, F., Kremer, A., and Plomion, C.

Abstract

Background: Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results: We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions: This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.

Published
2012

15. Information dynamics algorithm for detecting communities in networks

Author

Massaro, E., Guazzini, A., Bagnoli, F., Liò, P., Massaro, E., Guazzini, A., Bagnoli, F., and Liò, P.

Abstract

The problem of community detection is relevant in many scientific disciplines, from social science to statistical physics. Given the impact of community detection in many areas, such as psychology and social sciences, we have addressed the issue of modifying existing well performing algorithms by incorporating elements of the domain application fields, i.e. domain-inspired. We have focused on a psychology and social network - inspired approach which may be useful for further strengthening the link between social network studies and mathematics of community detection. Here we introduce a community-detection algorithm derived from the van Dongen's Markov Cluster algorithm (MCL) method by considering networks' nodes as agents capable to take decisions. In this framework we have introduced a memory factor to mimic a typical human behavior such as the oblivion effect. The method is based on information diffusion and it includes a non-linear processing phase. We test our method on two classical community benchmark and on computer generated networks with known community structure. Our approach has three important features: the capacity of detecting overlapping communities, the capability of identifying communities from an individual point of view and the fine tuning the community detectability with respect to prior knowledge of the data. Finally we discuss how to use a Shannon entropy measure for parameter estimation in complex networks., Comment: Submitted to "Communication in Nonlinear Science and Numerical Simulation"

Published
2011
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16. Application Design and Engagement Strategy of a Game with a Purpose for Climate Change Awareness

Author

Bagnoli, F, Scharl, Arno, Föls, Michael, Piccolo, Lara, Fernandez, Miriam, Alani, Harith, Bagnoli, F, Scharl, Arno, Föls, Michael, Piccolo, Lara, Fernandez, Miriam, and Alani, Harith

Abstract

The Climate Challenge is an online application in the tradition of games with a purpose that combines practical steps to reduce carbon footprint with predictive tasks to estimate future climate-related conditions. As part of the Collective Awareness Platform, the application aims to increase environmental literacy and motivate users to adopt more sustainable lifestyles. It has been deployed in conjunction with the Media Watch on Climate Change, a publicly available knowledge aggregator and visual analytics system for exploring environmental content from multiple online sources. This paper presents the motivation and goals of the Climate Challenge from an interdisciplinary perspective, outlines the application design including the types of tasks built into the application, discusses incentive mechanisms, and analyses the pursued user engagement strategies.

17. Application Design and Engagement Strategy of a Game with a Purpose for Climate Change Awareness

Author

Bagnoli, F, Scharl, Arno, Föls, Michael, Piccolo, Lara, Fernandez, Miriam, Alani, Harith, Bagnoli, F, Scharl, Arno, Föls, Michael, Piccolo, Lara, Fernandez, Miriam, and Alani, Harith

Abstract

The Climate Challenge is an online application in the tradition of games with a purpose that combines practical steps to reduce carbon footprint with predictive tasks to estimate future climate-related conditions. As part of the Collective Awareness Platform, the application aims to increase environmental literacy and motivate users to adopt more sustainable lifestyles. It has been deployed in conjunction with the Media Watch on Climate Change, a publicly available knowledge aggregator and visual analytics system for exploring environmental content from multiple online sources. This paper presents the motivation and goals of the Climate Challenge from an interdisciplinary perspective, outlines the application design including the types of tasks built into the application, discusses incentive mechanisms, and analyses the pursued user engagement strategies.

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