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27 results on '"Bragança, H."'

1. Spinon and bound state excitation 'light cones' in Heisenberg XXZ Chains

Author

Paula Jr, A. L. de, Bragança, H., Pereira, R. G., Drumond, R. C., and Aguiar, M. C. O.

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

We investigate the out-of-equilibrium dynamics after a local quench that connects two spin-1/2 XXZ chains prepared in the ground state of the Hamiltonian in different phases, one in the ferromagnetic phase and the other in the critical phase. We analyze the time evolution of the on-site magnetization and bipartite entanglement entropy via adaptive time-dependent density matrix renormalization group. In systems with short-range inter- actions, such as the one we consider, the velocity of information transfer is expected to be bounded, giving rise to a light-cone effect. Interestingly, our results show that, when the anisotropy parameter of the critical chain is sufficiently close to that of the isotropic ferromagnet, the light cone is determined by the velocity of spin-wave bound states that propagate faster than single-particle ("spinon") excitations. Furthermore, we investigate how the system approaches equilibrium in the inhomogeneous ground state of the connected system, in which the ferromagnetic chain induces a nonzero magnetization in the critical chain in the vicinity of the interface.

Published
2016
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2. The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola

Author

Estonian Science Foundation, Russian Academy of Sciences, Swedish Research Council, Ministry of Regional Affairs and Agriculture (Estonia), Ministry of Education and Science (Bulgaria), Università degli Studi di Firenze, European Commission, Slovenian Research Agency, Federal Office for the Environment (Switzerland), Tubby, K. [0000-0001-6864-4185], Adamčikova, K. [0000-0001-5407-5233], Adamson, K. [0000-0002-8810-8838], Akiba, M. [0000-0003-1412-9596], Barnes, Irene [0000-0002-4349-3402], Boroń, P. [0000-0002-8581-6759], Bragança, H. [0000-0002-7957-5493], Bulgakov, T. [0000-0002-4874-6851], Capretti, P. [0000-0002-1893-9871], Cech, T. [0000-0001-6681-5040], Cleary, M. [0000-0002-0318-5974], Davydenko, K. [0000-0001-6077-8533], Elvira Recuenco, Margarita [0000-0001-6749-3346], Enderle, R. [0000-0002-3436-9581], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Husson, C. [0000-0002-9148-9926], Iturritxa, Eugenia [0000-0002-6390-5873], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Piškur, B. [0000-0002-9914-4930], Queloz, V. [0000-0002-1888-4882], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Soukainen, M. [0000-0001-6686-0191], Vahalík, P. [0000-0003-3404-3095], Vester, M. [0000-0003-3596-4873], Mullett, M. [0000-0002-6013-0347], Tubby, K., Adamčikova, K., Adamson, K., Akiba, M., Barnes, Irene, Boroń, P., Bragança, H., Bulgakov, T., Burgdorf, N., Capretti, P., Cech, T., Cleary, M., Davydenko, K., Drenkhan, R., Elvira Recuenco, Margarita, Enderle, R., Gardner, J., Georgieva, M., Ghelardini, L., Husson, C., Iturritxa, Eugenia, Markovskaja, S., Mesanza, Nebai, Ogris, N., Oskay, F., Piškur, B., Queloz, V., Raitelaitytė, K., Raposo Llobet, María Rosa, Soukainen, M., Strasser, Ludwig, Vahalík, P., Vester, M., Mullett, M., Estonian Science Foundation, Russian Academy of Sciences, Swedish Research Council, Ministry of Regional Affairs and Agriculture (Estonia), Ministry of Education and Science (Bulgaria), Università degli Studi di Firenze, European Commission, Slovenian Research Agency, Federal Office for the Environment (Switzerland), Tubby, K. [0000-0001-6864-4185], Adamčikova, K. [0000-0001-5407-5233], Adamson, K. [0000-0002-8810-8838], Akiba, M. [0000-0003-1412-9596], Barnes, Irene [0000-0002-4349-3402], Boroń, P. [0000-0002-8581-6759], Bragança, H. [0000-0002-7957-5493], Bulgakov, T. [0000-0002-4874-6851], Capretti, P. [0000-0002-1893-9871], Cech, T. [0000-0001-6681-5040], Cleary, M. [0000-0002-0318-5974], Davydenko, K. [0000-0001-6077-8533], Elvira Recuenco, Margarita [0000-0001-6749-3346], Enderle, R. [0000-0002-3436-9581], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Husson, C. [0000-0002-9148-9926], Iturritxa, Eugenia [0000-0002-6390-5873], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Piškur, B. [0000-0002-9914-4930], Queloz, V. [0000-0002-1888-4882], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Soukainen, M. [0000-0001-6686-0191], Vahalík, P. [0000-0003-3404-3095], Vester, M. [0000-0003-3596-4873], Mullett, M. [0000-0002-6013-0347], Tubby, K., Adamčikova, K., Adamson, K., Akiba, M., Barnes, Irene, Boroń, P., Bragança, H., Bulgakov, T., Burgdorf, N., Capretti, P., Cech, T., Cleary, M., Davydenko, K., Drenkhan, R., Elvira Recuenco, Margarita, Enderle, R., Gardner, J., Georgieva, M., Ghelardini, L., Husson, C., Iturritxa, Eugenia, Markovskaja, S., Mesanza, Nebai, Ogris, N., Oskay, F., Piškur, B., Queloz, V., Raitelaitytė, K., Raposo Llobet, María Rosa, Soukainen, M., Strasser, Ludwig, Vahalík, P., Vester, M., and Mullett, M.

Abstract

European forests are threatened by increasing numbers of invasive pests and pathogens. Over the past century, Lecanosticta acicola, a foliar pathogen predominantly of Pinus spp., has expanded its range globally, and is increasing in impact. Lecanosticta acicola causes brown spot needle blight, resulting in premature defoliation, reduced growth, and mortality in some hosts. Originating from southern regions of North American, it devastated forests in the USA's southern states in the early twentieth century, and in 1942 was discovered in Spain. Derived from Euphresco project 'Brownspotrisk,' this study aimed to establish the current distribution of Lecanosticta species, and assess the risks of L. acicola to European forests. Pathogen reports from the literature, and new/ unpublished survey data were combined into an open-access geo-database (http://www.portalofforestpathology.com), and used to visualise the pathogen's range, infer its climatic tolerance, and update its host range. Lecanosticta species have now been recorded in 44 countries, mostly in the northern hemisphere. The type species, L. acicola, has increased its range in recent years, and is present in 24 out of the 26 European countries where data were available. Other species of Lecanosticta are largely restricted to Mexico and Central America, and recently Colombia. The geo-database records demonstrate that L. acicola tolerates a wide range of climates across the northern hemisphere, and indicate its potential to colonise Pinus spp. forests across large swathes of the Europe. Preliminary analyses suggest L. acicola could affect 62% of global Pinus species area by the end of this century, under climate change predictions. Although its host range appears slightly narrower than the similar Dothistroma species, Lecanosticta species were recorded on 70 host taxa, mostly Pinus spp., but including, Cedrus and Picea spp. Twenty-three, including species of critical ecological, environmental and economic significan

Published
2023

3. Climate, host and geography shape insect and fungal communities of trees

Author

Swiss National Science Foundation, Federal Office for the Environment (Switzerland), European Commission, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Australian Centre for International Agricultural Research, Agriculture and Agri-Food Canada, Swiss Agency for Development and Cooperation, Slovak Research and Development Agency, National Research, Development and Innovation Office (Hungary), Estonian Research Council, Ministry of Science and Higher Education (Poland), Ministry of Education, Science and Technological Development (Serbia), Franić, Iva [0000-0002-3352-0956], Allan, Eric [0000-0001-9641-9436], Prospero, Simone [0000-0002-9129-8556], Adamson, K. [0000-0002-8810-8838], Attorre, Fabio [0000-0002-7744-2195], Auger-Rozenberg, Marie-Anne [0000-0002-2455-2438], Avtzis, Dimitrios [0000-0002-7772-6892], Baert, Wim [0009-0003-2767-3053], Barta, Marek [0000-0003-2450-1769], Bauters, Kenneth [0000-0003-3356-0306], Bellahirech, Amani [0000-0002-5801-6051], Boroń, P. [0000-0002-8581-6759], Bragança, H. [0000-0002-7957-5493], Brestovanská, Tereza [0000-0003-4907-2542], Brurberg, May Bente [0000-0002-1293-1916], Burgess, Treena [0000-0002-7962-219X], Burokienė, Daiva [0000-0001-5965-5210], Cleary, M. [0000-0002-0318-5974], Corley, Juan [0000-0002-8032-2223], Coyle, David [0000-0003-3074-0440], Csóka, György [0000-0001-9132-4825], Černý, Karel [0000-0003-3492-0940], Davydenko, Kateryna [0000-0001-6077-8533], de Groot, Maarten [0000-0002-5721-6676], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Edwards, Jacqueline [0000-0003-0310-7236], Elsafy, Mohammed [0000-0002-2008-5182], Eötvös, Csaba Béla [0000-0001-5534-4597], Falko, Roman [0000-0003-2270-9216], Fan, G. [0000-0003-4154-3143], Feddern, Nina [0000-0002-5104-1473], Fürjes-Mikó, Ágnes [0009-0007-5250-7574], Gossner, Martin M. [0000-0003-1516-6364], Grad, Bartłomiej [0000-0001-6600-9348], Hartmann, Martin [0000-0001-8069-5284], Havrdova, Ludmila [0000-0003-3330-1857], Kádasi Horáková, Miriam [0000-0003-1310-8451], Hrabětová, Markéta [0000-0003-1866-2785], Justesen, Mathias Just [0000-0002-5252-7045], Kacprzyk, Magdalena [0000-0001-9679-5423], Kenis, Marc [0000-0002-3179-0872], Kirichenko, Natalia [0000-0002-7362-6464], Kovač, Marta [0000-0002-0116-7545], Kramarets, Volodymyr [0000-0002-5978-3711], Lacković, Nikola [0000-0003-3739-1220], Lantschner, Maria Victoria [0000-0002-2012-1366], Lazarević, Jelena [0000-0002-9460-7342], Li, Hongmei [0000-0001-6509-400X], Madsen, Corrie Lynne [0000-0002-3796-399X], Matošević, Dinka [0000-0001-7380-688X], Matsiakh, Iryna [0000-0003-2249-1296], May, Tom W. [0000-0003-2214-4972], Nikolov, Christo [0000-0003-1126-459X], O'Hanlon, Richard [0000-0002-0595-0246], Oskay, F. [0000-0002-8918-5595], Paap, Trudy [0000-0003-1364-4350], Parpan, Taras [0000-0002-8459-0479], Piškur, B. [0000-0002-9914-4930], Ravn, Hans Peter [0000-0001-5090-3273], Richard, John [0000-0002-9146-530X], Ronse, Anne [0000-0001-7446-9205], Roques, Alain [0000-0002-3734-3918], Ruffner, Beat [0000-0001-9848-2500], Santini, Alberto [0000-0002-7955-9207], Sivickis, Karolis [0000-0003-2304-130X], Soliani, Carolina [0000-0003-0388-2291], Talgø, Venche [0000-0002-2146-9938], Tomoshevich, Maria [0000-0002-0307-5919], Uimari, Anne [0000-0001-7136-685X], Ulyshen, Michael [0000-0001-6614-1242], Vettraino, A. M. [0000-0003-0797-3297], Villari, C. [0000-0003-3259-9866], Wang, Yongjun [0000-0002-8488-3423], Witzell, Johanna [0000-0003-1741-443X], Zlatković, Milica [0000-0003-4514-3980], Eschen, René [0000-0002-0464-6680], Franić, Iva, Allan, Eric, Prospero, Simone, Adamson, K., Attorre, Fabio, Auger-Rozenberg, Marie-Anne, Augustin, Sylvie, Avtzis, Dimitrios, Baert, Wim, Barta, Marek, Bauters, Kenneth, Bellahirech, Amani, Boroń, P., Bragança, H., Brestovanská, Tereza, Brurberg, May Bente, Burgess, Treena, Burokienė, Daiva, Cleary, M., Corley, Juan, Coyle, David, Csóka, György, Černý, Karel, Davydenko, Kateryna, de Groot, Maarten, Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Drenkhan, R., Edwards, Jacqueline, Elsafy, Mohammed, Eötvös, Csaba Béla, Falko, Roman, Fan, G., Feddern, Nina, Fürjes-Mikó, Ágnes, Gossner, Martin M., Grad, Bartłomiej, Hartmann, Martin, Havrdova, Ludmila, Kádasi Horáková, Miriam, Hrabětová, Markéta, Justesen, Mathias Just, Kacprzyk, Magdalena, Kenis, Marc, Kirichenko, Natalia, Kovač, Marta, Kramarets, Volodymyr, Lacković, Nikola, Lantschner, Maria Victoria, Lazarević, Jelena, Leskiv, Marianna, Li, Hongmei, Madsen, Corrie Lynne, Malumphy, Chris, Matošević, Dinka, Matsiakh, Iryna, May, Tom W., Meffert, Johan, Migliorini, Duccio, Nikolov, Christo, O'Hanlon, Richard, Oskay, F., Paap, Trudy, Parpan, Taras, Piškur, B., Ravn, Hans Peter, Richard, John, Ronse, Anne, Roques, Alain, Ruffner, Beat, Santini, Alberto, Sivickis, Karolis, Soliani, Carolina, Talgø, Venche, Tomoshevich, Maria, Uimari, Anne, Ulyshen, Michael, Vettraino, A. M., Villari, C., Wang, Yongjun, Witzell, Johanna, Zlatković, Milica, Eschen, René, Swiss National Science Foundation, Federal Office for the Environment (Switzerland), European Commission, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Australian Centre for International Agricultural Research, Agriculture and Agri-Food Canada, Swiss Agency for Development and Cooperation, Slovak Research and Development Agency, National Research, Development and Innovation Office (Hungary), Estonian Research Council, Ministry of Science and Higher Education (Poland), Ministry of Education, Science and Technological Development (Serbia), Franić, Iva [0000-0002-3352-0956], Allan, Eric [0000-0001-9641-9436], Prospero, Simone [0000-0002-9129-8556], Adamson, K. [0000-0002-8810-8838], Attorre, Fabio [0000-0002-7744-2195], Auger-Rozenberg, Marie-Anne [0000-0002-2455-2438], Avtzis, Dimitrios [0000-0002-7772-6892], Baert, Wim [0009-0003-2767-3053], Barta, Marek [0000-0003-2450-1769], Bauters, Kenneth [0000-0003-3356-0306], Bellahirech, Amani [0000-0002-5801-6051], Boroń, P. [0000-0002-8581-6759], Bragança, H. [0000-0002-7957-5493], Brestovanská, Tereza [0000-0003-4907-2542], Brurberg, May Bente [0000-0002-1293-1916], Burgess, Treena [0000-0002-7962-219X], Burokienė, Daiva [0000-0001-5965-5210], Cleary, M. [0000-0002-0318-5974], Corley, Juan [0000-0002-8032-2223], Coyle, David [0000-0003-3074-0440], Csóka, György [0000-0001-9132-4825], Černý, Karel [0000-0003-3492-0940], Davydenko, Kateryna [0000-0001-6077-8533], de Groot, Maarten [0000-0002-5721-6676], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Edwards, Jacqueline [0000-0003-0310-7236], Elsafy, Mohammed [0000-0002-2008-5182], Eötvös, Csaba Béla [0000-0001-5534-4597], Falko, Roman [0000-0003-2270-9216], Fan, G. [0000-0003-4154-3143], Feddern, Nina [0000-0002-5104-1473], Fürjes-Mikó, Ágnes [0009-0007-5250-7574], Gossner, Martin M. [0000-0003-1516-6364], Grad, Bartłomiej [0000-0001-6600-9348], Hartmann, Martin [0000-0001-8069-5284], Havrdova, Ludmila [0000-0003-3330-1857], Kádasi Horáková, Miriam [0000-0003-1310-8451], Hrabětová, Markéta [0000-0003-1866-2785], Justesen, Mathias Just [0000-0002-5252-7045], Kacprzyk, Magdalena [0000-0001-9679-5423], Kenis, Marc [0000-0002-3179-0872], Kirichenko, Natalia [0000-0002-7362-6464], Kovač, Marta [0000-0002-0116-7545], Kramarets, Volodymyr [0000-0002-5978-3711], Lacković, Nikola [0000-0003-3739-1220], Lantschner, Maria Victoria [0000-0002-2012-1366], Lazarević, Jelena [0000-0002-9460-7342], Li, Hongmei [0000-0001-6509-400X], Madsen, Corrie Lynne [0000-0002-3796-399X], Matošević, Dinka [0000-0001-7380-688X], Matsiakh, Iryna [0000-0003-2249-1296], May, Tom W. [0000-0003-2214-4972], Nikolov, Christo [0000-0003-1126-459X], O'Hanlon, Richard [0000-0002-0595-0246], Oskay, F. [0000-0002-8918-5595], Paap, Trudy [0000-0003-1364-4350], Parpan, Taras [0000-0002-8459-0479], Piškur, B. [0000-0002-9914-4930], Ravn, Hans Peter [0000-0001-5090-3273], Richard, John [0000-0002-9146-530X], Ronse, Anne [0000-0001-7446-9205], Roques, Alain [0000-0002-3734-3918], Ruffner, Beat [0000-0001-9848-2500], Santini, Alberto [0000-0002-7955-9207], Sivickis, Karolis [0000-0003-2304-130X], Soliani, Carolina [0000-0003-0388-2291], Talgø, Venche [0000-0002-2146-9938], Tomoshevich, Maria [0000-0002-0307-5919], Uimari, Anne [0000-0001-7136-685X], Ulyshen, Michael [0000-0001-6614-1242], Vettraino, A. M. [0000-0003-0797-3297], Villari, C. [0000-0003-3259-9866], Wang, Yongjun [0000-0002-8488-3423], Witzell, Johanna [0000-0003-1741-443X], Zlatković, Milica [0000-0003-4514-3980], Eschen, René [0000-0002-0464-6680], Franić, Iva, Allan, Eric, Prospero, Simone, Adamson, K., Attorre, Fabio, Auger-Rozenberg, Marie-Anne, Augustin, Sylvie, Avtzis, Dimitrios, Baert, Wim, Barta, Marek, Bauters, Kenneth, Bellahirech, Amani, Boroń, P., Bragança, H., Brestovanská, Tereza, Brurberg, May Bente, Burgess, Treena, Burokienė, Daiva, Cleary, M., Corley, Juan, Coyle, David, Csóka, György, Černý, Karel, Davydenko, Kateryna, de Groot, Maarten, Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Drenkhan, R., Edwards, Jacqueline, Elsafy, Mohammed, Eötvös, Csaba Béla, Falko, Roman, Fan, G., Feddern, Nina, Fürjes-Mikó, Ágnes, Gossner, Martin M., Grad, Bartłomiej, Hartmann, Martin, Havrdova, Ludmila, Kádasi Horáková, Miriam, Hrabětová, Markéta, Justesen, Mathias Just, Kacprzyk, Magdalena, Kenis, Marc, Kirichenko, Natalia, Kovač, Marta, Kramarets, Volodymyr, Lacković, Nikola, Lantschner, Maria Victoria, Lazarević, Jelena, Leskiv, Marianna, Li, Hongmei, Madsen, Corrie Lynne, Malumphy, Chris, Matošević, Dinka, Matsiakh, Iryna, May, Tom W., Meffert, Johan, Migliorini, Duccio, Nikolov, Christo, O'Hanlon, Richard, Oskay, F., Paap, Trudy, Parpan, Taras, Piškur, B., Ravn, Hans Peter, Richard, John, Ronse, Anne, Roques, Alain, Ruffner, Beat, Santini, Alberto, Sivickis, Karolis, Soliani, Carolina, Talgø, Venche, Tomoshevich, Maria, Uimari, Anne, Ulyshen, Michael, Vettraino, A. M., Villari, C., Wang, Yongjun, Witzell, Johanna, Zlatković, Milica, and Eschen, René

Abstract

Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance indicating that human-mediated transport may serve as a pathway of the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.

Published
2023

4. Work and Quantum Phase Transitions: Is there Quantum Latency?

Author

Mascarenhas, E., Braganca, H., Dorner, R., Santos, M. Franca, Vedral, V., Modi, K., and Goold, J.

Subjects
Quantum Physics, Condensed Matter - Statistical Mechanics
Abstract

We study the physics of quantum phase transitions from the perspective of non-equilibrium thermodynamics. For first order quantum phase transitions, we find that the average work done per quench in crossing the critical point is discontinuous. This leads us to introduce the quantum latent work in analogy with the classical latent heat of first order classical phase transitions. For second order quantum phase transitions the irreversible work is closely related to the fidelity susceptibility for weak sudden quenches of the system Hamiltonian. We demonstrate our ideas with numerical simulations of first, second, and infinite order phase transitions in various spin chain models., Comment: accepted in PRE

Published
2013
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5. The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola

Author

Tubby K., Adamčikova K., Adamson K., Akiba M., Barnes I., Boroń P., Bragança H., Bulgakov T., Burgdorf N., Capretti P., Cech T., Cleary M., Davydenko K., Drenkhan R., Elvira-Recuenco M., Enderle R., Gardner J., Georgieva M., Ghelardini L., Husson C., Iturritxa E., Markovskaja S., Mesanza N., Ogris N., Oskay F., Piškur B., Queloz V., Raitelaitytė K., Raposo R., Soukainen M., Strasser L., Vahalík P., Vester M., Mullett M., Tubby K., Adamčikova K., Adamson K., Akiba M., Barnes I., Boroń P., Bragança H., Bulgakov T., Burgdorf N., Capretti P., Cech T., Cleary M., Davydenko K., Drenkhan R., Elvira-Recuenco M., Enderle R., Gardner J., Georgieva M., Ghelardini L., Husson C., Iturritxa E., Markovskaja S., Mesanza N., Ogris N., Oskay F., Piškur B., Queloz V., Raitelaitytė K., Raposo R., Soukainen M., Strasser L., Vahalík P., Vester M., and Mullett M.

Published
2023

6. Global geographic distribution and host range of fusarium circinatum, the causal agent of pine pitch canker

Author

European Commission, Estonian Science Foundation, Agence Nationale de la Recherche (France), Scottish Government, Office fédéral de l'environnement (Suisse), Martín-García, Jorge [0000-0002-3057-3710], Vahalík, P. [0000-0003-3404-3095], Adamson, K. [0000-0002-8810-8838], Adamčikova, K. [0000-0001-5407-5233], Ahumada, Rodrigo [0000-0002-2397-2721], Blank, Lior [0000-0002-8753-0113], Bragança, H. [0000-0002-7957-5493], Capretti, P. [0000-0002-1893-9871], Cleary, M. [0000-0002-0318-5974], Cornejo, Carolina [0000-0003-3259-6198], Davydenko, K. [0000-0001-6077-8533], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Dvorák, Milon [0000-0002-4390-4718], Enderle, R. [0000-0002-3436-9581], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Hantula, Jarkko [0000-0002-1016-0636], Ioos, Renaud [0000-0001-9359-5098], Iturritxa, Eugenia [0000-0002-6390-5873], Kanetis, Loukas [0000-0002-1869-558X], Karpun, Natalia N. [0000-0002-7696-3618], Koltay, András [0000-0001-6865-2601], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Milenkovic, Ivan [0000-0003-2792-0221], Musolin, Dmitry L. [0000-0002-3913-3674], Nowakowska, Justyna A. [0000-0001-5863-053X], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Paraschiv, Marius [0000-0001-6916-8600], Pasquali, Matias [0000-0002-9102-2066], Pecori, Francesco [0000-0002-6577-7190], Rafoss, Trond [0000-0002-8489-4771], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Robin, Cecile [0000-0002-8145-245X], Rodas, Carlos A. [0000-0002-8895-8883], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Selikhovkin, Andrey V. [0000-0003-4227-9647], Solla, A. [0000-0002-2596-1612], Soukainen, M. [0000-0001-6686-0191], Soulioti, Nikoleta [0000-0001-5011-0863], Steenkamp, Emma T. [0000-0003-0217-8219], Tsopelas, Panaghiotis [0000-0002-7853-4534], Vemic, Aleksandar [0000-0001-9195-8967], Vettraino, A. M. [0000-0003-0797-3297], Wingfield, Michael J. [0000-0001-9346-2009], Woodward, Stephen [0000-0002-6627-7702], Zamora-Ballesteros, Cristina [0000-0002-9728-5553], Mullett, M. [0000-0002-6013-0347], Drenkhan, R., Ganley, Beccy, Martín-García, Jorge, Vahalík, P., Adamson, K., Adamčikova, K., Ahumada, Rodrigo, Blank, Lior, Bragança, H., Capretti, P., Cleary, M., Cornejo, Carolina, Davydenko, K., Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Dvorák, Milon, Enderle, R., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hantula, Jarkko, Ioos, Renaud, Iturritxa, Eugenia, Kanetis, Loukas, Karpun, Natalia N., Koltay, András, Landeras, Elena, Markovskaja, S., Mesanza, Nebai, Milenkovic, Ivan, Musolin, Dmitry L., Nikolaou, Konstantinos, Nowakowska, Justyna A., Ogris, N., Oskay, F., Oszako, Tomasz, Papazova-Anakieva, Irena, Paraschiv, Marius, Pasquali, Matias, Pecori, Francesco, Rafoss, Trond, Raitelaitytė, K., Raposo Llobet, María Rosa, Robin, Cecile, Rodas, Carlos A., Santini, Alberto, Sanz-Ros, Antonio V., Selikhovkin, Andrey V., Solla, A., Soukainen, M., Soulioti, Nikoleta, Steenkamp, Emma T., Tsopelas, Panaghiotis, Vemic, Aleksandar, Vettraino, A. M., Wingfield, Michael J., Woodward, Stephen, Zamora-Ballesteros, Cristina, Mullett, M., European Commission, Estonian Science Foundation, Agence Nationale de la Recherche (France), Scottish Government, Office fédéral de l'environnement (Suisse), Martín-García, Jorge [0000-0002-3057-3710], Vahalík, P. [0000-0003-3404-3095], Adamson, K. [0000-0002-8810-8838], Adamčikova, K. [0000-0001-5407-5233], Ahumada, Rodrigo [0000-0002-2397-2721], Blank, Lior [0000-0002-8753-0113], Bragança, H. [0000-0002-7957-5493], Capretti, P. [0000-0002-1893-9871], Cleary, M. [0000-0002-0318-5974], Cornejo, Carolina [0000-0003-3259-6198], Davydenko, K. [0000-0001-6077-8533], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Dvorák, Milon [0000-0002-4390-4718], Enderle, R. [0000-0002-3436-9581], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Hantula, Jarkko [0000-0002-1016-0636], Ioos, Renaud [0000-0001-9359-5098], Iturritxa, Eugenia [0000-0002-6390-5873], Kanetis, Loukas [0000-0002-1869-558X], Karpun, Natalia N. [0000-0002-7696-3618], Koltay, András [0000-0001-6865-2601], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Milenkovic, Ivan [0000-0003-2792-0221], Musolin, Dmitry L. [0000-0002-3913-3674], Nowakowska, Justyna A. [0000-0001-5863-053X], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Paraschiv, Marius [0000-0001-6916-8600], Pasquali, Matias [0000-0002-9102-2066], Pecori, Francesco [0000-0002-6577-7190], Rafoss, Trond [0000-0002-8489-4771], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Robin, Cecile [0000-0002-8145-245X], Rodas, Carlos A. [0000-0002-8895-8883], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Selikhovkin, Andrey V. [0000-0003-4227-9647], Solla, A. [0000-0002-2596-1612], Soukainen, M. [0000-0001-6686-0191], Soulioti, Nikoleta [0000-0001-5011-0863], Steenkamp, Emma T. [0000-0003-0217-8219], Tsopelas, Panaghiotis [0000-0002-7853-4534], Vemic, Aleksandar [0000-0001-9195-8967], Vettraino, A. M. [0000-0003-0797-3297], Wingfield, Michael J. [0000-0001-9346-2009], Woodward, Stephen [0000-0002-6627-7702], Zamora-Ballesteros, Cristina [0000-0002-9728-5553], Mullett, M. [0000-0002-6013-0347], Drenkhan, R., Ganley, Beccy, Martín-García, Jorge, Vahalík, P., Adamson, K., Adamčikova, K., Ahumada, Rodrigo, Blank, Lior, Bragança, H., Capretti, P., Cleary, M., Cornejo, Carolina, Davydenko, K., Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Dvorák, Milon, Enderle, R., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hantula, Jarkko, Ioos, Renaud, Iturritxa, Eugenia, Kanetis, Loukas, Karpun, Natalia N., Koltay, András, Landeras, Elena, Markovskaja, S., Mesanza, Nebai, Milenkovic, Ivan, Musolin, Dmitry L., Nikolaou, Konstantinos, Nowakowska, Justyna A., Ogris, N., Oskay, F., Oszako, Tomasz, Papazova-Anakieva, Irena, Paraschiv, Marius, Pasquali, Matias, Pecori, Francesco, Rafoss, Trond, Raitelaitytė, K., Raposo Llobet, María Rosa, Robin, Cecile, Rodas, Carlos A., Santini, Alberto, Sanz-Ros, Antonio V., Selikhovkin, Andrey V., Solla, A., Soukainen, M., Soulioti, Nikoleta, Steenkamp, Emma T., Tsopelas, Panaghiotis, Vemic, Aleksandar, Vettraino, A. M., Wingfield, Michael J., Woodward, Stephen, Zamora-Ballesteros, Cristina, and Mullett, M.

Abstract

Fusarium circinatum, the causal agent of pine pitch canker (PPC), is currently one of the most important threats of Pinus spp. globally. This pathogen is known in many pine-growing regions, including natural and planted forests, and can affect all life stages of trees, from emerging seedlings to mature trees. Despite the importance of PPC, the global distribution of F. circinatum is poorly documented, and this problem is also true of the hosts within countries that are affected. The aim of this study was to review the global distribution of F. circinatum, with a particular focus on Europe. We considered (1) the current and historical pathogen records, both positive and negative, based on confirmed reports from Europe and globally; (2) the genetic diversity and population structure of the pathogen; (3) the current distribution of PPC in Europe, comparing published models of predicted disease distribution; and (4) host susceptibility by reviewing literature and generating a comprehensive list of known hosts for the fungus. These data were collated from 41 countries and used to compile a specially constructed geo-database. A review of 6297 observation records showed that F. circinatum and the symptoms it causes on conifers occurred in 14 countries, including four in Europe, and is absent in 28 countries. Field observations and experimental data from 138 host species revealed 106 susceptible host species including 85 Pinus species, 6 non-pine tree species and 15 grass and herb species. Our data confirm that susceptibility to F. circinatum varies between different host species, tree ages and environmental characteristics. Knowledge on the geographic distribution, host range and the relative susceptibility of different hosts is essential for disease management, mitigation and containment strategies. The findings reported in this review will support countries that are currently free of F. circinatum in implementing effective procedures and restrictions and prevent further

Published
2020

7. Potential interactions between invasive Fusarium circinatum and other pine pathogens in Europe

Author

European Commission, Russian Foundation for Basic Research, Ministerio de Economía y Competitividad (España), Ministry of Education, Youth and Sports (Czech Republic), Fundação para a Ciência e a Tecnologia (Portugal), Elvira Recuenco, Margarita [0000-0001-6749-3346], Cacciola, Santa Olga [0000-0001-7926-3601], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Garbelotto, Matteo [0000-0001-9737-0128], Aguayo, Jaime [0000-0002-7552-0655], Solla, A. [0000-0002-2596-1612], Mullett, M. [0000-0002-6013-0347], Drenkhan, Tiia [0000-0001-9865-2549], Oskay, F. [0000-0002-8918-5595], Kaya, Ayse Gülden Aday [0000-0002-5631-6026], Iturritxa, Eugenia [0000-0002-6390-5873], Cleary, M. [0000-0002-0318-5974], Witzell, Johanna [0000-0003-1741-443X], Georgieva, M. [0000-0003-3165-1992], Papazova-Anakieva, Irena [0000-0002-7260-4685], Chira, Danut [0000-0002-7402-4975], Paraschiv, Marius [0000-0001-6916-8600], Musolin, Dmitry L. [0000-0002-3913-3674], Selikhovkin, Andrey V. [0000-0003-4227-9647], Varentsova, Elena Yu [0000-0002-4616-2289], Adamčikova, K. [0000-0001-5407-5233], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Davydenko, K. [0000-0001-6077-8533], Capretti, P. [0000-0002-1893-9871], Scanu, Bruno [0000-0002-0690-580X], Gonthier, Paolo [0000-0002-7242-8239], Tsopelas, Panaghiotis [0000-0002-7853-4534], Martín-García, Jorge [0000-0002-3057-3710], Morales-Rodríguez, Carmen [0000-0002-2971-2840], Lehtijärvi, Asko [0000-0002-0367-0849], Lehtijärvi, H. Tugba Dogmus [0000-0002-1050-8823], Oszako, Tomasz [0000-0003-4688-2582], Nowakowska, Justyna A. [0000-0001-5863-053X], Bragança, H. [0000-0002-7957-5493], Fernández-Fernández, Mercedes M. [0000-0002-1646-5027], Hantula, Jarkko [0000-0002-1016-0636], Díez, Julio Javier [0000-0003-0558-8141], Elvira Recuenco, Margarita, Cacciola, Santa Olga, Sanz-Ros, Antonio V., Garbelotto, Matteo, Aguayo, Jaime, Solla, A., Mullett, M., Drenkhan, Tiia, Oskay, F., Kaya, Ayse Gülden Aday, Iturritxa, Eugenia, Cleary, M., Witzell, Johanna, Georgieva, M., Papazova-Anakieva, Irena, Chira, Danut, Paraschiv, Marius, Musolin, Dmitry L., Selikhovkin, Andrey V., Varentsova, Elena Yu, Adamčikova, K., Markovskaja, S., Mesanza, Nebai, Davydenko, K., Capretti, P., Scanu, Bruno, Gonthier, Paolo, Tsopelas, Panaghiotis, Martín-García, Jorge, Morales-Rodríguez, Carmen, Lehtijärvi, Asko, Lehtijärvi, H. Tugba Dogmus, Oszako, Tomasz, Nowakowska, Justyna A., Bragança, H., Fernández-Fernández, Mercedes M., Hantula, Jarkko, Díez, Julio Javier, European Commission, Russian Foundation for Basic Research, Ministerio de Economía y Competitividad (España), Ministry of Education, Youth and Sports (Czech Republic), Fundação para a Ciência e a Tecnologia (Portugal), Elvira Recuenco, Margarita [0000-0001-6749-3346], Cacciola, Santa Olga [0000-0001-7926-3601], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Garbelotto, Matteo [0000-0001-9737-0128], Aguayo, Jaime [0000-0002-7552-0655], Solla, A. [0000-0002-2596-1612], Mullett, M. [0000-0002-6013-0347], Drenkhan, Tiia [0000-0001-9865-2549], Oskay, F. [0000-0002-8918-5595], Kaya, Ayse Gülden Aday [0000-0002-5631-6026], Iturritxa, Eugenia [0000-0002-6390-5873], Cleary, M. [0000-0002-0318-5974], Witzell, Johanna [0000-0003-1741-443X], Georgieva, M. [0000-0003-3165-1992], Papazova-Anakieva, Irena [0000-0002-7260-4685], Chira, Danut [0000-0002-7402-4975], Paraschiv, Marius [0000-0001-6916-8600], Musolin, Dmitry L. [0000-0002-3913-3674], Selikhovkin, Andrey V. [0000-0003-4227-9647], Varentsova, Elena Yu [0000-0002-4616-2289], Adamčikova, K. [0000-0001-5407-5233], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Davydenko, K. [0000-0001-6077-8533], Capretti, P. [0000-0002-1893-9871], Scanu, Bruno [0000-0002-0690-580X], Gonthier, Paolo [0000-0002-7242-8239], Tsopelas, Panaghiotis [0000-0002-7853-4534], Martín-García, Jorge [0000-0002-3057-3710], Morales-Rodríguez, Carmen [0000-0002-2971-2840], Lehtijärvi, Asko [0000-0002-0367-0849], Lehtijärvi, H. Tugba Dogmus [0000-0002-1050-8823], Oszako, Tomasz [0000-0003-4688-2582], Nowakowska, Justyna A. [0000-0001-5863-053X], Bragança, H. [0000-0002-7957-5493], Fernández-Fernández, Mercedes M. [0000-0002-1646-5027], Hantula, Jarkko [0000-0002-1016-0636], Díez, Julio Javier [0000-0003-0558-8141], Elvira Recuenco, Margarita, Cacciola, Santa Olga, Sanz-Ros, Antonio V., Garbelotto, Matteo, Aguayo, Jaime, Solla, A., Mullett, M., Drenkhan, Tiia, Oskay, F., Kaya, Ayse Gülden Aday, Iturritxa, Eugenia, Cleary, M., Witzell, Johanna, Georgieva, M., Papazova-Anakieva, Irena, Chira, Danut, Paraschiv, Marius, Musolin, Dmitry L., Selikhovkin, Andrey V., Varentsova, Elena Yu, Adamčikova, K., Markovskaja, S., Mesanza, Nebai, Davydenko, K., Capretti, P., Scanu, Bruno, Gonthier, Paolo, Tsopelas, Panaghiotis, Martín-García, Jorge, Morales-Rodríguez, Carmen, Lehtijärvi, Asko, Lehtijärvi, H. Tugba Dogmus, Oszako, Tomasz, Nowakowska, Justyna A., Bragança, H., Fernández-Fernández, Mercedes M., Hantula, Jarkko, and Díez, Julio Javier

Abstract

Pines are major components of native forests and plantations in Europe, where they have both economic significance and an important ecological role. Diseases of pines are mainly caused by fungal and oomycete pathogens, and can significantly reduce the survival, vigor, and yield of both individual trees and entire stands or plantations. Pine pitch canker (PPC), caused by Fusarium circinatum (Nirenberg and O'Donnell), is among the most devastating pine diseases in the world, and is an example of an emergent invasive disease in Europe. The effects of microbial interactions on plant health, as well as the possible roles plant microbiomes may have in disease expression, have been the focus of several recent studies. Here, we describe the possible effects of co-infection with pathogenic fungi and oomycetes with F. circinatum on the health of pine seedlings and mature plants, in an attempt to expand our understanding of the role that biotic interactions may play in the future of PPC disease in European nurseries and forests. The available information on pine pathogens that are able to co-occur with F. circinatum in Europe is here reviewed and interpreted to theoretically predict the effects of such co-occurrences on pine survival, growth, and yield. Beside the awareness that F. circinatum may co-occurr on pines with other pathogens, an additional outcome from this review is an updating of the literature, including the so-called grey literature, to document the geographical distribution of the relevant pathogens and to facilitate differential diagnoses, particularly in nurseries, where some of them may cause symptoms similar to those induced by F. circinatum. An early and accurate diagnosis of F. circinatum, a pathogen that has been recently introduced and that is currently regulated in Europe, is essential to prevent its introduction and spread in plantings and forests.

Published
2020

8. Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs

Author

Franić, I., Prospero, S., Adamson, K., Allan, E., Attorre, F., Auger-Rozenberg, M.A., Augustin, S., Avtzis, D., Baert, W., Barta, M., Bauters, K., Bellahirech, A., Boroń, P., Bragança, H., Brestovanská, T., Brurberg, M.B., Burgess, T., Burokienė, D., Cleary, M., Corley, J., Coyle, D.R., Csóka, G., Černý, K., Davydenko, K., de Groot, M., Diez, J.J., Doğmuş Lehtijärvi, H.T., Drenkhan, R., Edwards, J., Elsafy, M., Eötvös, C.B., Falko, R., Fan, J., Feddern, N., Fürjes-Mikó, Á., Gossner, M.M., Grad, B., Hartmann, M., Havrdova, L., Horáková, M.K., Hrabětová, M., Justesen, M.J., Kacprzyk, M., Kenis, M., Kirichenko, N., Kovač, M., Kramarets, V., Lacković, N., Lantschner, M.V., Lazarević, J., Leskiv, M., Li, H., Madsen, C.L., Malumphy, C., Matošević, D., Matsiakh, I., May, T.W., Meffert, J., Migliorini, D., Nikolov, C., O’Hanlon, R., Oskay, F., Paap, T., Parpan, T., Piškur, B., Ravn, H.P., Richard, J., Ronse, A., Roques, A., Ruffner, B., Sivickis, K., Soliani, C., Talgø, V., Tomoshevich, M., Uimari, A., Ulyshen, M., Vettraino, A.M., Villari, C., Wang, Y., Witzell, J., Zlatković, M., Eschen, R., Franić, I., Prospero, S., Adamson, K., Allan, E., Attorre, F., Auger-Rozenberg, M.A., Augustin, S., Avtzis, D., Baert, W., Barta, M., Bauters, K., Bellahirech, A., Boroń, P., Bragança, H., Brestovanská, T., Brurberg, M.B., Burgess, T., Burokienė, D., Cleary, M., Corley, J., Coyle, D.R., Csóka, G., Černý, K., Davydenko, K., de Groot, M., Diez, J.J., Doğmuş Lehtijärvi, H.T., Drenkhan, R., Edwards, J., Elsafy, M., Eötvös, C.B., Falko, R., Fan, J., Feddern, N., Fürjes-Mikó, Á., Gossner, M.M., Grad, B., Hartmann, M., Havrdova, L., Horáková, M.K., Hrabětová, M., Justesen, M.J., Kacprzyk, M., Kenis, M., Kirichenko, N., Kovač, M., Kramarets, V., Lacković, N., Lantschner, M.V., Lazarević, J., Leskiv, M., Li, H., Madsen, C.L., Malumphy, C., Matošević, D., Matsiakh, I., May, T.W., Meffert, J., Migliorini, D., Nikolov, C., O’Hanlon, R., Oskay, F., Paap, T., Parpan, T., Piškur, B., Ravn, H.P., Richard, J., Ronse, A., Roques, A., Ruffner, B., Sivickis, K., Soliani, C., Talgø, V., Tomoshevich, M., Uimari, A., Ulyshen, M., Vettraino, A.M., Villari, C., Wang, Y., Witzell, J., Zlatković, M., and Eschen, R.

Abstract

International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees.

Published
2022

10. Sampling and detection strategies for the pine pitch canker (PPC) disease pathogen Fusarium Circinatum in Europe

Author

European Commission, Ministerio de Economía y Competitividad (España), Fundação para a Ciência e a Tecnologia (Portugal), Vainio, Eeva [0000-0002-6739-7968], Bezos, Diana [0000-0002-0423-4627], Bragança, H. [0000-0002-4554-2722], Cleary, M. [0000-0002-0318-5974], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0001-6580-4147], Ghelardini, L. [0000-0002-3180-4226], Hannunen, Salla [0000-0002-0998-4240], Ioos, Renaud [0000-0001-9359-5098], Martín-García, Jorge [0000-0002-3057-3710], Martínez-Álvarez, Pablo [0000-0002-4605-7702], Mullett, M. [0000-0002-6013-0347], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Piškur, B. [0000-0002-9914-4930], Romeralo, Carmen [0000-0002-8510-9915], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Steenkamp, Emma T. [0000-0003-0217-8219], Tubby, K. [0000-0001-6864-4185], Wingfield, Michael J. [0000-0001-9346-2009], Díez, Julio Javier [0000-0003-0558-8141], Vainio, Eeva, Bezos, Diana, Bragança, H., Cleary, M., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hannunen, Salla, Ioos, Renaud, Martín-García, Jorge, Martínez-Álvarez, Pablo, Mullett, M., Oszako, Tomasz, Papazova-Anakieva, Irena, Piškur, B., Romeralo, Carmen, Sanz-Ros, Antonio V., Steenkamp, Emma T., Tubby, K., Wingfield, Michael J., Díez, Julio Javier, European Commission, Ministerio de Economía y Competitividad (España), Fundação para a Ciência e a Tecnologia (Portugal), Vainio, Eeva [0000-0002-6739-7968], Bezos, Diana [0000-0002-0423-4627], Bragança, H. [0000-0002-4554-2722], Cleary, M. [0000-0002-0318-5974], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0001-6580-4147], Ghelardini, L. [0000-0002-3180-4226], Hannunen, Salla [0000-0002-0998-4240], Ioos, Renaud [0000-0001-9359-5098], Martín-García, Jorge [0000-0002-3057-3710], Martínez-Álvarez, Pablo [0000-0002-4605-7702], Mullett, M. [0000-0002-6013-0347], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Piškur, B. [0000-0002-9914-4930], Romeralo, Carmen [0000-0002-8510-9915], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Steenkamp, Emma T. [0000-0003-0217-8219], Tubby, K. [0000-0001-6864-4185], Wingfield, Michael J. [0000-0001-9346-2009], Díez, Julio Javier [0000-0003-0558-8141], Vainio, Eeva, Bezos, Diana, Bragança, H., Cleary, M., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hannunen, Salla, Ioos, Renaud, Martín-García, Jorge, Martínez-Álvarez, Pablo, Mullett, M., Oszako, Tomasz, Papazova-Anakieva, Irena, Piškur, B., Romeralo, Carmen, Sanz-Ros, Antonio V., Steenkamp, Emma T., Tubby, K., Wingfield, Michael J., and Díez, Julio Javier

Abstract

Fusarium circinatum Nirenberg & O'Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions-via contaminated seeds, wood material, soil and growing substrates, natural means and human activities-into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the "bridgehead effect", where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspec

Published
2019

11. Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum

Author

Universitat Politècnica de València. Instituto Agroforestal Mediterráneo - Institut Agroforestal Mediterrani, Estonian Science Foundation, Forestry Commission, Reino Unido, Slovenian Research Agency, European Cooperation in Science and Technology, Ministry for Primary Industries, Nueva Zelanda, Fundação para a Ciência e a Tecnologia, Portugal, Ministry of Agriculture, Forestry and Food, Eslovenia, Instituto Nacional de Investigação Agrária e Veterinária, Portugal, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Francia, Ioos, R., Aloi, F., Piskur, B., Guinet, C., Mullett, M., Berbegal Martinez, Monica, Bragança, H., Cacciola, S.O., Oskay, F., Cornejo, C., Adamson, K., Kacergius, A., Martínez-Álvarez, P., Nowakowska, J.A., Luchi, N., Universitat Politècnica de València. Instituto Agroforestal Mediterráneo - Institut Agroforestal Mediterrani, Estonian Science Foundation, Forestry Commission, Reino Unido, Slovenian Research Agency, European Cooperation in Science and Technology, Ministry for Primary Industries, Nueva Zelanda, Fundação para a Ciência e a Tecnologia, Portugal, Ministry of Agriculture, Forestry and Food, Eslovenia, Instituto Nacional de Investigação Agrária e Veterinária, Portugal, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Francia, Ioos, R., Aloi, F., Piskur, B., Guinet, C., Mullett, M., Berbegal Martinez, Monica, Bragança, H., Cacciola, S.O., Oskay, F., Cornejo, C., Adamson, K., Kacergius, A., Martínez-Álvarez, P., Nowakowska, J.A., and Luchi, N.

Abstract

[EN] Fusarium circinatum is a harmful pathogenic fungus mostly attacking Pinus species and also Pseudotsuga menziesii, causing cankers in trees of all ages, damping-off in seedlings, and mortality in cuttings and mother plants for clonal production. This fungus is listed as a quarantine pest in several parts of the world and the trade of potentially contaminated pine material such as cuttings, seedlings or seeds is restricted in order to prevent its spread to disease-free areas. Inspection of plant material often relies on DNA testing and several conventional or real-time PCR based tests targeting F. circinatum are available in the literature. In this work, an international collaborative study joined 23 partners to assess the transferability and the performance of nine molecular protocols, using a wide panel of DNA from 71 representative strains of F. circinatum and related Fusarium species. Diagnostic sensitivity, specificity and accuracy of the nine protocols all reached values >80%, and the diagnostic specificity was the only parameter differing significantly between protocols. The rates of false positives and of false negatives were computed and only the false positive rates differed significantly, ranging from 3.0% to 17.3%. The difference between protocols for some of the performance values were mainly due to cross-reactions with DNA from non-target species, which were either not tested or documented in the original articles. Considering that participating laboratories were free to use their own reagents and equipment, this study demonstrated that the diagnostic protocols for F. circinatum were not easily transferable to end-users. More generally, our results suggest that the use of protocols using conventional or real-time PCR outside their initial development and validation conditions should require careful characterization of the performance data prior to use under modified conditions (i.e. reagents and equipment). Suggestions to improve the transfer are pr

Published
2019

12. Global geographic distribution and host range of Dothistroma species:a comprehensive review

Author

Drenkhan, R., Tomešová-haataja, V., Fraser, S., Bradshaw, R. E., Vahalík, P., Mullett, M. S., Martín-García, J., Bulman, L. S., Wingfield, M. J., Kirisits, T., Cech, T. L., Schmitz, S., Baden, R., Tubby, K., Brown, A., Georgieva, M., Woods, A., Ahumada, R., Jankovský, L., Thomsen, Iben Margrete, Adamson, K., Marçais, B., Vuorinen, M., Tsopelas, P., Koltay, A., Halasz, A., La Porta, N., Anselmi, N., Kiesnere, R., Markovskaja, S., Kačergius, A., Papazova-anakieva, I., Risteski, M., Sotirovski, K., Lazarević, J., Solheim, H., Boroń, P., Bragança, H., Chira, D., Musolin, D. L., Selikhovkin, A. V., Bulgakov, T. S., Keča, N., Karadžić, D., Galovic, V., Pap, P., Markovic, M., Poljakovic Pajnik, L., Vasic, V., Ondrušková, E., Piškur, B., Sadiković, D., Diez, J. J., Solla, A., Millberg, H., Stenlid, J., Angst, A., Queloz, V., Lehtijärvi, A., Doğmuş-lehtijärvi, H. T., Oskay, F., Davydenko, K., Meshkova, V., Craig, D., Woodward, S., Barnes, I., Drenkhan, R., Tomešová-haataja, V., Fraser, S., Bradshaw, R. E., Vahalík, P., Mullett, M. S., Martín-García, J., Bulman, L. S., Wingfield, M. J., Kirisits, T., Cech, T. L., Schmitz, S., Baden, R., Tubby, K., Brown, A., Georgieva, M., Woods, A., Ahumada, R., Jankovský, L., Thomsen, Iben Margrete, Adamson, K., Marçais, B., Vuorinen, M., Tsopelas, P., Koltay, A., Halasz, A., La Porta, N., Anselmi, N., Kiesnere, R., Markovskaja, S., Kačergius, A., Papazova-anakieva, I., Risteski, M., Sotirovski, K., Lazarević, J., Solheim, H., Boroń, P., Bragança, H., Chira, D., Musolin, D. L., Selikhovkin, A. V., Bulgakov, T. S., Keča, N., Karadžić, D., Galovic, V., Pap, P., Markovic, M., Poljakovic Pajnik, L., Vasic, V., Ondrušková, E., Piškur, B., Sadiković, D., Diez, J. J., Solla, A., Millberg, H., Stenlid, J., Angst, A., Queloz, V., Lehtijärvi, A., Doğmuş-lehtijärvi, H. T., Oskay, F., Davydenko, K., Meshkova, V., Craig, D., Woodward, S., and Barnes, I.

Published
2016

15. Principal toxicant plants that cause sudden death in bovine in Espírito Santo State - Brazil

Author

Carvalho, G. D., Nunes, L. C., Bragança, H. B. N., Porfírio, L. C., Carvalho, G. D., Nunes, L. C., Bragança, H. B. N., and Porfírio, L. C.

Abstract

In Brazil is very frequent the occurrence of sudden death in bovine, caused by the ingestion of toxicant plants. Those sudden deaths in general show none previous clinical signs and absence of significant post mortem discoveries, promoting economical losses with difficulties to be considered. The ignorance of the toxicant vegetable species is pointed as the principal factor for occurrence of those accidents, in that way, the best form to prevent this is the knowledge and the popularization regarding about the subject. In that context, this work exposes the principal toxicant plants that cause sudden death in bovine in Espírito Santo State (Palicourea marcgravii, Mascagnia rigida, Tetrapterys acutifolia and Oxypetalum banksii), tends in view the great number of intoxication cases that happened in this region., No Brasil é muito freqüente a ocorrência de morte súbita em bovinos, causada por ingestão de plantas tóxicas. Estas mortes repentinas em geral se manifestam sem sinais clínicos prévios e ausência de achados necroscópicos significativos, promovendo perdas econômicas difíceis de serem estimadas. O desconhecimento das espécies vegetais tóxicas é apontado como o principal fator para ocorrência desses acidentes, desse modo, a melhor forma de prevenir é o conhecimento e a divulgação a respeito do assunto. Neste contexto, este trabalho expõe as principais plantas tóxicas relatadas, até o momento, como causadoras de morte súbita em bovinos no Estado do Espírito Santo (Palicourea marcgravii, Mascagnia rigida, Tetrapterys acutifolia e Oxypetalum banksii), tendo em vista o grande número de casos de intoxicação ocorridos nessa região.

Published
2009

18. Vibration sensor dataset for estimating fan coil motor health.

Author

Lifsitch H, Rocha G, Bragança H, Filho C, Okimoto L, Amorin A, and Cardoso F

Abstract

To enhance the field of continuous motor health monitoring, we present FAN-COIL-I, an extensive vibration sensor dataset derived from a Fan Coil motor. This dataset is uniquely positioned to facilitate the detection and prediction of motor health issues, enabling a more efficient maintenance scheduling process that can potentially obviate the need for regular checks. Unlike existing datasets, often created under controlled conditions or through simulations, FAN-COIL-I is compiled from real-world operational data, providing an invaluable resource for authentic motor diagnosis and predictive maintenance research. Gathered using a high-resolution 32 KHz sampling rate, the dataset encompasses comprehensive vibration readings from both the forward and rear sides of the Fan Coil motor over a continuous two-week period, offering a rare glimpse into the dynamic operational patterns of these systems in a corporate setting. FAN-COIL-I stands out not only for its real-world applicability but also for its potential to serve as a reliable benchmark for researchers and practitioners seeking to validate their models against genuine engine conditions., (© 2024 The Author(s).)

Published
2024
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19. Performance counter dataset for behavioural biometric purpose.

Author

Andrade C, Bragança H, Feitosa E, and Souto E

Abstract

In the pursuit of advancing research in continuous user authentication, we introduce COUNT-OS-I and COUNT-OS-II, two distinct performance counter datasets from Windows operating systems, crafted to bolster research in continuous user authentication. Encompassing data from 63 computers and users, the datasets offer rich, real-world insights for developing and evaluating authentication models. COUNT-OS-I spans 26 users in an IT department, capturing 159 attributes across diverse hardware and software environments over 26 h on average per user. COUNT-OS-II, on the other hand, encompasses 37 users with identical system configurations, recording 218 attributes per sample over a 48-hour period. Both datasets utilize pseudonymization to safeguard user identities while maintaining data integrity and statistical accuracy. The well-balanced nature of the data, confirmed by comprehensive statistical analysis, positions these datasets as reliable benchmarks for the continuous user authentication domain. Through their release, we aim to empower the development of robust, real-world applicable authentication models, contributing to enhanced system security and user trust., (© 2023 The Author(s).)

Published
2023
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20. Android malware detection with MH-100K: An innovative dataset for advanced research.

Author

Bragança H, Rocha V, Barcellos L, Souto E, Kreutz D, and Feitosa E

Abstract

High-quality datasets are crucial for building realistic and high-performance supervised malware detection models. Currently, one of the major challenges of machine learning-based solutions is the scarcity of datasets that are both representative and of high quality. To foster future research and provide updated and public data for comprehensive evaluation and comparison of existing classifiers, we introduce the MH-100K dataset [1], an extensive collection of Android malware information comprising 101,975 samples. It encompasses a main CSV file with valuable metadata, including the SHA256 hash (APK's signature), file name, package name, Android's official compilation API, 166 permissions, 24,417 API calls, and 250 intents. Moreover, the MH-100K dataset features an extensive collection of files containing useful metadata of the VirusTotal1 analysis. This repository of information can serve future research by enabling the analysis of antivirus scan result patterns to discern the prevalence and behaviour of various malware families. Such analysis can help to extend existing malware taxonomies, the identification of novel variants, and the exploration of malware evolution over time., (© 2023 The Author(s).)

Published
2023
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21. Climate, host and geography shape insect and fungal communities of trees.

Author

Franić I, Allan E, Prospero S, Adamson K, Attorre F, Auger-Rozenberg MA, Augustin S, Avtzis D, Baert W, Barta M, Bauters K, Bellahirech A, Boroń P, Bragança H, Brestovanská T, Brurberg MB, Burgess T, Burokienė D, Cleary M, Corley J, Coyle DR, Csóka G, Černý K, Davydenko K, de Groot M, Diez JJ, Doğmuş Lehtijärvi HT, Drenkhan R, Edwards J, Elsafy M, Eötvös CB, Falko R, Fan J, Feddern N, Fürjes-Mikó Á, Gossner MM, Grad B, Hartmann M, Havrdova L, Kádasi Horáková M, Hrabětová M, Justesen MJ, Kacprzyk M, Kenis M, Kirichenko N, Kovač M, Kramarets V, Lacković N, Lantschner MV, Lazarević J, Leskiv M, Li H, Madsen CL, Malumphy C, Matošević D, Matsiakh I, May TW, Meffert J, Migliorini D, Nikolov C, O'Hanlon R, Oskay F, Paap T, Parpan T, Piškur B, Ravn HP, Richard J, Ronse A, Roques A, Ruffner B, Santini A, Sivickis K, Soliani C, Talgø V, Tomoshevich M, Uimari A, Ulyshen M, Vettraino AM, Villari C, Wang Y, Witzell J, Zlatković M, and Eschen R

Subjects
Animals, Humans, Phylogeny, Forests, Geography, Climate Change, Insecta, Ecosystem, Mycobiome
Abstract

Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance indicating that human-mediated transport may serve as a pathway of the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate., (© 2023. The Author(s).)

Published
2023
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22. How Validation Methodology Influences Human Activity Recognition Mobile Systems.

Author

Bragança H, Colonna JG, Oliveira HABF, and Souto E

Subjects
Algorithms, Humans, Human Activities, Machine Learning
Abstract

In this article, we introduce explainable methods to understand how Human Activity Recognition (HAR) mobile systems perform based on the chosen validation strategies. Our results introduce a new way to discover potential bias problems that overestimate the prediction accuracy of an algorithm because of the inappropriate choice of validation methodology. We show how the SHAP (Shapley additive explanations) framework, used in literature to explain the predictions of any machine learning model, presents itself as a tool that can provide graphical insights into how human activity recognition models achieve their results. Now it is possible to analyze which features are important to a HAR system in each validation methodology in a simplified way. We not only demonstrate that the validation procedure k -folds cross-validation ( k -CV), used in most works to evaluate the expected error in a HAR system, can overestimate by about 13% the prediction accuracy in three public datasets but also choose a different feature set when compared with the universal model. Combining explainable methods with machine learning algorithms has the potential to help new researchers look inside the decisions of the machine learning algorithms, avoiding most times the overestimation of prediction accuracy, understanding relations between features, and finding bias before deploying the system in real-world scenarios.

Published
2022
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23. Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs.

Author

Franić I, Prospero S, Adamson K, Allan E, Attorre F, Auger-Rozenberg MA, Augustin S, Avtzis D, Baert W, Barta M, Bauters K, Bellahirech A, Boroń P, Bragança H, Brestovanská T, Brurberg MB, Burgess T, Burokienė D, Cleary M, Corley J, Coyle DR, Csóka G, Černý K, Davydenko K, de Groot M, Diez JJ, Doğmuş Lehtijärvi HT, Drenkhan R, Edwards J, Elsafy M, Eötvös CB, Falko R, Fan J, Feddern N, Fürjes-Mikó Á, Gossner MM, Grad B, Hartmann M, Havrdova L, Horáková MK, Hrabětová M, Justesen MJ, Kacprzyk M, Kenis M, Kirichenko N, Kovač M, Kramarets V, Lacković N, Lantschner MV, Lazarević J, Leskiv M, Li H, Madsen CL, Malumphy C, Matošević D, Matsiakh I, May TW, Meffert J, Migliorini D, Nikolov C, O'Hanlon R, Oskay F, Paap T, Parpan T, Piškur B, Ravn HP, Richard J, Ronse A, Roques A, Ruffner B, Sivickis K, Soliani C, Talgø V, Tomoshevich M, Uimari A, Ulyshen M, Vettraino AM, Villari C, Wang Y, Witzell J, Zlatković M, and Eschen R

Subjects
Animals, Biodiversity, Trees, Endophytes, Fungi, Insecta
Abstract

International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees., (© 2022. The Author(s).)

Published
2022
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24. A New Double-Stranded RNA Mycovirus in Cryphonectria naterciae Is Able to Cross the Species Barrier and Is Deleterious to a New Host.

Author

Cornejo C, Hisano S, Bragança H, Suzuki N, and Rigling D

Abstract

Cryphonectria is a fungal genus associated with economically significant disease of trees. Herein we characterized a novel double-stranded RNA virus from the fungal species Cryphonectria naterciae , a species unexplored as a virus host. De novo assembly of RNA-seq data and Sanger sequencing of RACE (rapid amplification of cDNA ends) clones gave the complete, non-segmented genome (10,164 bp) of the virus termed Cryphonectria naterciae fusagravirus (CnFGV1) that was phylogenetically placed within the previously proposed viral family Fusagraviridae. Of 31 field-collected strains of C. naterciae , 40% tested CnFGV1-positive. Cocultivation resulted in within-species transmission of CnFGV1 to virus-free strains of C. naterciae . Comparison of the mycelium phenotype and the growth rate of CnFGV1-infected and virus-free isogenic strains revealed frequent sectoring and growth reduction in C. naterciae upon virus infection. Co-culturing also led to cross-species transmission of CnFGV1 to Cryphonectria carpinicola and Cryphonectria radicalis , but not to Cryphonectria parasitica . The virus-infected C. naterciae and the experimentally infected Cryphonectria spp. readily transmitted CnFGV1 through asexual spores to the next generation. CnFGV1 strongly reduced conidiation and in some cases vegetative growth of C. carpinicola , which is involved in the European hornbeam disease. This study is the first report of a fusagravirus in the family Cryphonectriaceae and lays the groundwork for assessing a hypovirulence effect of CnFGV1 against the hornbeam decline in Europe.

Published
2021
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25. A Smartphone Lightweight Method for Human Activity Recognition Based on Information Theory.

Author

Bragança H, Colonna JG, Lima WS, and Souto E

Subjects
Accelerometry, Algorithms, Databases, Factual, Humans, Smartphone, Human Activities, Information Theory, Machine Learning, Monitoring, Physiologic
Abstract

Smartphones have emerged as a revolutionary technology for monitoring everyday life, and they have played an important role in Human Activity Recognition (HAR) due to its ubiquity. The sensors embedded in these devices allows recognizing human behaviors using machine learning techniques. However, not all solutions are feasible for implementation in smartphones, mainly because of its high computational cost. In this context, the proposed method, called HAR-SR, introduces information theory quantifiers as new features extracted from sensors data to create simple activity classification models, increasing in this way the efficiency in terms of computational cost. Three public databases (SHOAIB, UCI, WISDM) are used in the evaluation process. The results have shown that HAR-SR can classify activities with 93% accuracy when using a leave-one-subject-out cross-validation procedure (LOSO).

Published
2020
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26. Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum.

Author

Ioos R, Aloi F, Piškur B, Guinet C, Mullett M, Berbegal M, Bragança H, Cacciola SO, Oskay F, Cornejo C, Adamson K, Douanla-Meli C, Kačergius A, Martínez-Álvarez P, Nowakowska JA, Luchi N, Vettraino AM, Ahumada R, Pasquali M, Fourie G, Kanetis L, Alves A, Ghelardini L, Dvořák M, Sanz-Ros A, Diez JJ, Baskarathevan J, and Aguayo J

Subjects
DNA, Fungal analysis, DNA, Plant, False Positive Reactions, Fusarium genetics, International Cooperation, Real-Time Polymerase Chain Reaction, Reproducibility of Results, Sensitivity and Specificity, Fusarium isolation & purification, Molecular Biology standards, Pinus microbiology, Plant Diseases microbiology, Polymerase Chain Reaction methods
Abstract

Fusarium circinatum is a harmful pathogenic fungus mostly attacking Pinus species and also Pseudotsuga menziesii, causing cankers in trees of all ages, damping-off in seedlings, and mortality in cuttings and mother plants for clonal production. This fungus is listed as a quarantine pest in several parts of the world and the trade of potentially contaminated pine material such as cuttings, seedlings or seeds is restricted in order to prevent its spread to disease-free areas. Inspection of plant material often relies on DNA testing and several conventional or real-time PCR based tests targeting F. circinatum are available in the literature. In this work, an international collaborative study joined 23 partners to assess the transferability and the performance of nine molecular protocols, using a wide panel of DNA from 71 representative strains of F. circinatum and related Fusarium species. Diagnostic sensitivity, specificity and accuracy of the nine protocols all reached values >80%, and the diagnostic specificity was the only parameter differing significantly between protocols. The rates of false positives and of false negatives were computed and only the false positive rates differed significantly, ranging from 3.0% to 17.3%. The difference between protocols for some of the performance values were mainly due to cross-reactions with DNA from non-target species, which were either not tested or documented in the original articles. Considering that participating laboratories were free to use their own reagents and equipment, this study demonstrated that the diagnostic protocols for F. circinatum were not easily transferable to end-users. More generally, our results suggest that the use of protocols using conventional or real-time PCR outside their initial development and validation conditions should require careful characterization of the performance data prior to use under modified conditions (i.e. reagents and equipment). Suggestions to improve the transfer are proposed.

Published
2019
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27. Dark-exciton valley dynamics in transition metal dichalcogenide alloy monolayers.

Author

Bragança H, Riche F, Qu F, Lopez-Richard V, and Marques GE

Abstract

We report a comprehensive theory to describe exciton and biexciton valley dynamics in monolayer Mo 1-x W x Se 2 alloys. To probe the impact of different excitonic channels, including bright and dark excitons, intravalley biexcitons, intervalley scattering between bright excitons, as well as bright biexcitons, we have performed a systematic study from the simplest system to the most complex one. In contrast to the binary WSe 2 monolayer with weak photoluminescence (PL) and high valley polarization at low temperatures and the MoSe 2 , that presents high PL intensity, but low valley polarization, our results demonstrate that it is possible to set up a ternary alloy with intermediate W-concentration that holds simultaneously a considerably robust light emission and an efficient optical orientation of the valley pseudospin. We find the critical value of W-concentration, x c , that turns alloys from bright to darkish. The dependence of the PL intensity on temperature shows three regimes: while bright monolayer alloys display a usual temperature dependence in which the intensity decreases with rising temperature, the darkish alloys exhibit the opposite behavior, and the alloys with x around x c show a non-monotonic temperature response. Remarkably, we observe that the biexciton enhances significantly the stability of the exciton emission against fluctuations of W-concentration for bright alloys. Our findings pave the way for developing high-performance valleytronic and photo-emitting devices.

Published
2019
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