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1. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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2. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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3. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Published
2024
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5. Decoherence of V$_{\rm B}^{-}$ spin defects in monoisotopic hexagonal boron nitride

Author

Haykal, A., Tanos, R., Minotto, N., Durand, A., Fabre, F., Li, J., Edgar, J. H., Ivady, V., Gali, A., Michel, T., Dréau, A., Gil, B., Cassabois, G., and Jacques, V.

Subjects
Condensed Matter - Materials Science, Quantum Physics
Abstract

Spin defects in hexagonal boron nitride (hBN) are promising quantum systems for the design of flexible two-dimensional quantum sensing platforms. Here we rely on hBN crystals isotopically enriched with either $^{10}$B or $^{11}$B to investigate the isotope-dependent properties of a spin defect featuring a broadband photoluminescence signal in the near infrared. By analyzing the hyperfine structure of the spin defect while changing the boron isotope, we first unambiguously confirm that it corresponds to the negatively-charged boron-vacancy center (${\rm V}_{\rm B}^-$). We then show that its spin coherence properties are slightly improved in $^{10}$B-enriched samples. This is supported by numerical simulations employing cluster correlation expansion methods, which reveal the importance of the hyperfine Fermi contact term for calculating the coherence time of point defects in hBN. Using cross-relaxation spectroscopy, we finally identify dark electron spin impurities as an additional source of decoherence. This work provides new insights into the properties of ${\rm V}_{\rm B}^-$ spin defects, which are valuable for the future development of hBN-based quantum sensing foils., Comment: 8 pages, 5 figures

Published
2021
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6. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Published
2024
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7. COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project [version 3; peer review: 2 approved, 1 approved with reservations]

Author

Guy Cochrane, Estelle Kilias, Felix Shaw, Josephine Burgin, Mara K.N. Lawniczak, Seanna McTaggart, Alice Minotto, Aaliyah Providence, Joana Paupério, Peter Harrison, Robert Davey, and Jeena Rajan

Subjects
biodiversity, standards, sharing, metadata, samples, Darwin Tree of Life, eng, Medicine, Science
Abstract

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Published
2024
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8. A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project [version 1; peer review: 2 approved]

Author

Silvia Salatino, Rebekka Uhl, Peter O. Mulhair, Freja Azzopardi, Jordan Beasley, Alex D. Twyford, Lucia Campos-Dominguez, Michelle L. Hart, Olga Sivell, David Bell, Gavin Broad, Felix Shaw, Piotr Cuber, Darren Choonea, Peter M. Hollingsworth, Laura L. Forrest, Sahr Mian, Alexandra Dombrowski, Mara K.N. Lawniczak, Claire Griffin, Clementine Greeves, Peter W.H. Holland, Joanna Harley, Owen T. Lewis, Amanda Jones, Ben W. Price, Raju Misra, Estelle Kilias, Ian Barnes, Laura Sivess, Heather Allen, Alice Minotto, Inez Januszczak, Michael Cunliffe, Mark L. Blaxter, Liam Crowley, Lyndall Pereira da Conceicoa, Brian Douglas, Kieran Woof, Ester Gaya, and Paul Kersey

Subjects
DNA barcoding, species identification, taxonomy, Britain and Ireland, biodiversity, eng, Medicine, Science
Abstract

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

Published
2024
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9. Crosstalk between MicroRNAs and Oxidative Stress in Coeliac Disease

Author

Filippo Pelizzaro, Romilda Cardin, Giulia Sarasini, Milena Minotto, Chiara Carlotto, Matteo Fassan, Michela Palo, Fabio Farinati, and Fabiana Zingone

Subjects
coeliac disease, micrornas, oxidative stress, inflammation, diagnosis, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

MicroRNAs (miRNAs) are small, non-coding RNA molecules involved in regulating gene expression. Many studies, mostly conducted on pediatric patients, suggested that oxidative stress and several miRNAs may play an important role in coeliac disease (CeD) pathogenesis. However, the interplay between oxidative stress and miRNA regulatory functions in CeD remains to be clarified. In this review, we aimed to perform a literature review on the role of miRNAs and oxidative stress in adult CeD patients and to analyze their potential interactions. In this direction, we also reported the preliminary results of a pilot study we recently performed.

Published
2024
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11. A real‐world retrospective–prospective analysis of efficacy and safety of combined ixazomib, lenalidomide, and dexamethasone in relapsed/refractory multiple myeloma: The northern Italy experience

Author

Anna Furlan, Michele Cea, Laura Pavan, Monica Galli, Cristina Clissa, Silvia Mangiacavalli, Anna Maria Cafro, Stefania Girlanda, Francesca Patriarca, Claudia Minotto, Giovanni Bertoldero, Gregorio Barilà, Anna Pascarella, Albana Lico, Rossella Paolini, Nicholas Rabassi, Norbert Pescosta, Marika Porrazzo, Giovanni De Sabbata, Alessandra Pompa, Giulia Bega, Stefania Cavallin, Francesca Guidotti, Magda Marcatti, Maurizio Rupolo, Angelo Belotti, Filippo Gherlinzoni, and Renato Zambello

Subjects
efficacy, ixazomib–lenalidomide–dexamethasone, lenalidomide‐exposed, lenalidomide‐refractory, real‐life, relapsed/refractory multiple myeloma, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Introduction Ixazomib, lenalidomide, and dexamethasone (IRd) have been approved for the treatment of relapsed/refractory multiple myeloma (RRMM) based on the results of the TOURMALINE‐MM1. Objectives and Methods We conducted a retrospective–prospective analysis of 106 RRMM patients (pts) treated with IRd in 21 centers in Northern Italy, with the aim to evaluate the efficacy and safety of IRd in real life. Results At IRd initiation, 34% of pts were aged ≥75 (median 72.5), 8.5% had an ECOG performance status ≥2, 54.7% of evaluable pts carried high‐risk cytogenetic abnormalities [del17p and/or t(4;14) and/or t(14;16) and/or 1 g gain/amp], 60.2% had received ≥2 prior lines of therapy (pLoT), 57.5% were lenalidomide (Len)‐exposed (including both Len‐sensitive and Len‐refractory pts), and 22% were Len‐refractory. Main G ≥3 adverse events (AEs) were thrombocytopenia (16%) and neutropenia (12.3%). G ≥3 non‐hematologic AEs included infections (9.4%) and GI toxicity (diarrhea 5.7%, hepatotoxicity 2.8%), VTE, skin rash, and peripheral neuropathy were mainly G1‐2. The overall response rate was 56.4% (≥VGPR 30%). With a median follow‐up of 38 m, median PFS (mPFS) was 16 m and the 1‐year OS rate was 73%. By subgroup analysis, an extended PFS was observed for pts achieving ≥VGPR (mPFS 21.2 m), time from diagnosis to IRd ≥5 years (26.2 m), 1 pLoT (34.4 m), Len‐naïve (NR), age ≥70 (20 m). In pts exposed to Len, non‐refractory in any prior line and immediately prior to IRd, mPFS was 16 and 18 m, respectively. An inferior PFS was seen in Len‐refractory pts (4.6 m). By multivariate analysis, independent predictors of PFS were age ≥70 (HR 0.6), time from diagnosis ≥5 years (HR 0.32), refractoriness to Len in any prior line (HR 3.33), and immediately prior (HR 4.31). Conclusion IRd might be effective and safe in RRMM pts with an indolent disease, in early lines of treatment, and who proved Len‐sensitive, independent of age, and cytogenetic risk.

Published
2024
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12. Nail Diseases

Author

Minotto, Renan, Corte, Liliam Dalla, Millán, Thaís, Furtado, Bianca Coelho, and Rangel Bonamigo, Renan, editor

Published
2023
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13. Uma Revisão sobre Instrumentos de Avaliação do Burnout na Segurança Pública

Author

Germano Gabriel Lima Esteves, Daniela Sacramento Zanini, Giulia Veiga de Leite Ribeiro Melo, Sebastião Venâncio Pereira Júnior, Sérgio Eduardo Silva de Oliveira, Felipe Minotto Corrêa, Wladimir Rodrigues da Fonseca, Thiago Gomes Nascimento, Lara Letícia Pinto Barbosa, Francisco Guilherme Lima Macedo, and Cristiane Faiad

Subjects
estresse ocupacional, avaliação psicológica, saúde ocupacional, psicometria, Psychology, BF1-990
Abstract

Resumo Objetivou-se mapear os instrumentos utilizados na avaliação da síndrome de Burnout em profissionais da segurança pública, indicando os aspectos psicométricos, amostras e variáveis associadas. Foram selecionados 19 estudos nas bases de dados pesquisadas (PsycINFO, PubMED e Google Scholar). Os resultados indicaram a utilização dos instrumentos MBI-GS, MBI-HSS, BM-S, CBI e CESQT, mas apenas um dos instrumentos apresentou evidência de validade nesse contexto. Constatou-se a associação do Burnout com variáveis pessoais, organizacionais e específicas. A comparação dos estudos e dos índices de Burnout foi limitada devido à falta de padronização. A ausência de evidências de validade e de padronização dos resultados acarreta problemas como a falta de suporte empírico das pontuações e dificuldade na comparação dos estudos. Os dados revelam limitações na avaliação dos níveis de Burnout utilizadas no contexto de segurança pública, uma vez que as medidas não apresentam evidências de validade para esse contexto, indicando a necessidade de pesquisas na área.

Published
2023
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14. Experimental Demonstration of Staggered CAP Modulation for Low Bandwidth Red-Emitting Polymer-LED based Visible Light Communications

Author

Haigh, Paul Anthony, Minotto, Alessandro, Burton, Andrew, Ghassemlooy, Zabih, Murto, Petri, Genene, Zewdneh, Mammo, Wendimagegn, Andersson, Mats R., Wang, Ergang, Cacialli, Franco, and Darwazeh, Izzat

Subjects
Computer Science - Networking and Internet Architecture, Electrical Engineering and Systems Science - Signal Processing, Physics - Applied Physics
Abstract

In this paper we experimentally demonstrate, for the first time, staggered carrier-less amplitude and phase (sCAP) modulation for visible light communication systems based on polymer light-emitting diodes emitting at ~639 nm. The key advantage offered by sCAP in comparison to conventional multiband CAP is its full use of the available spectrum. In this work, we compare sCAP, which utilises four orthogonal filters to generate the signal, with a conventional 4-band multi-CAP system and on-off keying (OOK). We transmit each modulation format with equal energy and present a record un-coded transmission speed of ~6 Mb/s. This represents gains of 25% and 65% over the achievable rate using 4-CAP and OOK, respectively., Comment: 6 pages, 9 figures, IEEE ICC 2019 conference

Published
2019

15. P970: A REAL-WORLD RETROSPECTIVE-PROSPECTIVE ANALYSIS OF EFFICACY AND SAFETY OF COMBINED IXAZOMIB, LENALIDOMIDE AND DEXAMETHASONE IN RELAPSED/REFRACTORY MULTIPLE MYELOMA: THE NORTHERN ITALY EXPERIENCE

Author

Anna Furlan, Michele Cea, Renato Zambello, Laura Pavan, Monica Galli, Cristina Clissa, Silvia Mangiacavalli, Anna Maria Cafro, Stefania Girlanda, Francesca Patriarca, Claudia Minotto, Giovanni Bertoldero, Gregorio Barilà, Anna Pascarella, Albana Lico, Rossella Paolini, Nicholas Rabassi, Norbert Pescosta, Marika Porrazzo, and Filippo Gherlinzoni

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Published
2023
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16. Novel 4-aminoquinolines: Synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase, antitubercular activity, SAR, and preclinical evaluation

Author

Paz, Josiane Delgado, Denise de Moura Sperotto, Nathalia, Ramos, Alessandro Silva, Pissinate, Kenia, da Silva Rodrigues Junior, Valnês, Abbadi, Bruno Lopes, Borsoi, Ana Flávia, Rambo, Raoní Scheibler, Corso Minotto, Ana Carolina, da Silva Dadda, Adilio, Galina, Luiza, Macchi Hopf, Fernanda Souza, Muniz, Mauro Neves, Borges Martinelli, Leonardo Kras, Roth, Candida Deves, Madeira Silva, Rodrigo Braccini, Perelló, Marcia Alberton, de Matos Czeczot, Alexia, Neves, Christiano Ev, Duarte, Lovaine Silva, Leyser, Mariana, Dias de Oliveira, Sílvia, Bizarro, Cristiano Valim, Machado, Pablo, and Basso, Luiz Augusto

Published
2023
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18. Decoherence of V $${}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$ B − spin defects in monoisotopic hexagonal boron nitride

Author

A. Haykal, R. Tanos, N. Minotto, A. Durand, F. Fabre, J. Li, J. H. Edgar, V. Ivády, A. Gali, T. Michel, A. Dréau, B. Gil, G. Cassabois, and V. Jacques

Subjects
Science
Abstract

Recently, coherent control of spin defects in hBN has been realized, enabling future applications in quantum sensing technologies. Here the authors perform a systematic study of isotope-dependent spin coherence properties of the negatively-charged boron-vacancy defect in monoisotopic hBN crystals.

Published
2022
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19. Drug-Induced Liver Injury: Role of Circulating Liver-Specific microRNAs and Keratin-18.

Author

Cardin, Romilda, Bizzaro, Debora, Russo, Francesco Paolo, D'Arcangelo, Francesca, Ideo, Francesco, Pelizzaro, Filippo, Carlotto, Chiara, Minotto, Milena, Farinati, Fabio, Burra, Patrizia, and Germani, Giacomo

Subjects
LIVER injuries, LIVER diseases, ACUTE diseases, SENSITIVITY & specificity (Statistics), HEPATITIS
Abstract

Background and Objective: Drug-induced liver injury (DILI) is increasingly becoming a cause of acute hepatitis. The study evaluated the role of liver-specific microRNAs (miRNAs) and keratin-18 (K-18) markers M30 (apoptosis) and M65 (necrosis) as biomarkers of acute hepatitis. Methods: Sixty-eight patients were sub-grouped as DILI, HBV- and alcohol-related acute hepatitis. Five healthy controls were included. The expression of plasma miR-21-5p, miR-34a-5p and miR-122-5p was evaluated by RT-qPCR analysis using healthy volunteers as reference. M30 and M65 were determined with ELISA kits. Results: All markers were significantly higher in the acute liver disease patients compared to controls. In DILI, miRNA levels positively correlated with M30, M65 and ALT. miR-122-5p had the highest AUC of 0.73, sensitivity of 76.2 and specificity of 72.2 in identifying DILI from other groups. Patients with hepatocellular-pattern DILI showed higher miR-122-5p and miR-21-5p compared to patients with cholestatic or mixed pattern. A new score to discriminate DILI versus other causes of acute hepatitis was developed using the identified risk factors as follows: 0.012 × miR-34a-5p + 0.012 × miR-122-5p − 0.001 × M30 + 2.642 × 1 (if mixed pattern) + 0.014 × 1 (if hepatocellular pattern) + 1.887. The AUC of the score was 0.86, with a sensitivity and specificity of 81%, better than the values of the single markers. Conclusions: Liver-specific miRNAs and K-18 could be promising serum biomarkers of DILI, especially when used in combination. [ABSTRACT FROM AUTHOR]

Published
2024
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22. COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project

Author

Shaw, Felix, primary, Minotto, Alice, additional, McTaggart, Seanna, additional, Providence, Aaliyah, additional, Harrison, Peter, additional, Paupério, Joana, additional, Rajan, Jeena, additional, Burgin, Josephine, additional, Cochrane, Guy, additional, Kilias, Estelle, additional, Lawniczak, Mara K.N., additional, and Davey, Robert, additional

Published
2024
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23. P49 A REAL-WORLD RETROSPECTIVE-PROSPECTIVE ANALYSIS OF EFFICACY AND SAFETY OF COMBINED IXAZOMIB, LENALIDOMIDE AND DEXAMETHASONE IN RELAPSED/REFRACTORY MULTIPLE MYELOMA: THE NORTHERN ITALY EXPERIENCE

Author

A. Furlan, M. Cea, R. Zambello, L. Pavan, M Galli, C. Clissa, S. Mangiacavalli, A. Cafro, S. Girlanda, F. Patriarca, C. Minotto, G. Bertoldero, G. Barilà, A. Pascarella, A. Lico, R. Paolini, N. Rabassi, N. Pescosta, M. Porrazzo, G. De Sabbata, A. Pompa, G. Bega, S. Cavallin, F. Guidotti, G. Semenzato, C. Zaina, and F. Gherlinzoni

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Published
2023
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24. The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

Author

Pavlović, Milena, Scheffer, Lonneke, Motwani, Keshav, Kanduri, Chakravarthi, Kompova, Radmila, Vazov, Nikolay, Waagan, Knut, Bernal, Fabian L. M., Costa, Alexandre Almeida, Corrie, Brian, Akbar, Rahmad, Al Hajj, Ghadi S., Balaban, Gabriel, Brusko, Todd M., Chernigovskaya, Maria, Christley, Scott, Cowell, Lindsay G., Frank, Robert, Grytten, Ivar, Gundersen, Sveinung, Haff, Ingrid Hobæk, Hovig, Eivind, Hsieh, Ping-Han, Klambauer, Günter, Kuijjer, Marieke L., Lund-Andersen, Christin, Martini, Antonio, Minotto, Thomas, Pensar, Johan, Rand, Knut, Riccardi, Enrico, Robert, Philippe A., Rocha, Artur, Slabodkin, Andrei, Snapkov, Igor, Sollid, Ludvig M., Titov, Dmytro, Weber, Cédric R., Widrich, Michael, Yaari, Gur, Greiff, Victor, and Sandve, Geir Kjetil

Published
2021
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25. Making Treatment-Free Remission (TFR) Easier in Chronic Myeloid Leukemia: Fact-Checking and Practical Management Tools

Author

Castagnetti, Fausto, Binotto, Gianni, Capodanno, Isabella, Billio, Atto, Calistri, Elisabetta, Cavazzini, Francesco, Crugnola, Monica, Gozzini, Antonella, Gugliotta, Gabriele, Krampera, Mauro, Lucchesi, Alessandro, Merli, Anna, Miggiano, Maria Cristina, Minotto, Claudia, Poggiaspalla, Monica, Salvucci, Marzia, Scappini, Barbara, Tiribelli, Mario, Trabacchi, Elena, Rosti, Gianantonio, Galimberti, Sara, and Bonifacio, Massimiliano

Published
2021
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26. Harpoon nail: an unusual form of onychocryptosis

Author

Andréa Abê Pereira, Jéssica Lüders Bueno, Raquel Kupske, Leonardo Albarello, and Renan Minotto

Subjects
nail diseases, nails ingrown, hallux, Dermatology, RL1-803
Abstract

Onychocryptosis is a frequent nail disease, which most commonly affects the toes. It has some variants, including the little known "Harpoon Nail". The diagnosis is usually clinical, and the treatment is surgical, with different techniques described in the literature. We report the case of a 25-year-old man with a harpoon nail on the left hallux and the surgical method used for treatment with excellent results

Published
2022
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27. Surgical approach to retronychia refractory to clinical treatments

Author

Iago Gonçalves Ferreira, Livia Giacomet, Ana Cristina Dornelles, and Renan Minotto

Subjects
nail diseases, nails, nails ingrown, Dermatology, RL1-803
Abstract

Retronychia is an inflammatory onychopathy characterized by the disordered growth and stacking of nail plates, associated with an imbalance in the matrix production of plaques, which tend to overlap. This condition may be associated with trauma, evolving with an inflammatory reaction along the proximal nail fold and granulation tissue formation. We report the case of a patient with retronychia in the left hallux, submitted to surgical treatment after failure of therapeutic responses with previous clinical treatments. The surgical approach led to the avulsion of the overlapping nail plates and the excision of voluminous granulation tissues, achieving adequate postoperative evolution.

Published
2022
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30. Uma métrica para avaliação da ocupação docente em instituições de ensino superior

Author

Atilio Minotto Neto, Leandro Luis Corso, and Guilherme Holsbach Costa

Subjects
Carga de trabalho, Ocupação docente, Processo analítico hierárquico, Education (General), L7-991
Abstract

A gestão da ocupação docente em instituições de ensino superior é um problema que afeta universidades públicas e, principalmente, as privadas. Uma distribuição justa de tarefas aos docentes repercute diretamente na qualidade do ensino, na produção de conhecimento, na sustentabilidade institucional e, principalmente, na saúde dos docentes. Neste trabalho é proposto um método para avaliação da composição da carga de trabalho com base em uma ferramenta chamada Processo Analítico Hierárquico, visando a equidade em termos de carga de trabalho (o que não significa o mesmo que equidade das cargas-horárias nas diferentes atividades docentes). Como principal contribuição, é proposta uma métrica, chamada Coeficiente de Carga de Trabalho, que pode ser facilmente adaptada a realidade de cada instituição. Apesar das bases matemáticas, quando implementada computacionalmente, a utilização dessa métrica passa a ser simples e acessível a gestores de qualquer formação.

Published
2021
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33. The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.

Author

Milena Pavlovic, Lonneke Scheffer, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, Fabian L. M. Bernal, Alexandre Almeida Costa, Brian Corrie, Rahmad Akbar, Ghadi S. Al Hajj, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank 0006, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini 0001, Thomas Minotto, Johan Pensar, Knut D. Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig Magne Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, and Geir Kjetil Sandve

Published
2021
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34. Tailoring the optical properties of rubrene films through epitaxy-induced amorphous-to-crystal transition.

Author

Trabattoni, Silvia, Raimondo, Luisa, Minotto, Alessandro, Monguzzi, Angelo, Meinardi, Francesco, and Sassella, Adele

Abstract

Crystalline rubrene (RUB) with the orthorhombic structure can be regarded as a workhorse in organic optoelectronics. So far, however, its great potential for device integration has been held back by the struggle to obtain high-quality and photo-oxidation-resistant RUB thin films. Here, we propose an effective strategy to obtain homogeneous, highly crystalline, and oriented RUB thin films, which relies on the spontaneous amorphous-to-crystal transition driven by organic epitaxy occurring at room temperature in vacuum; this crucial process dictates the final morphological, structural, and optoelectronic properties of the film. To probe the kinetics of the transition, we combine ex situ analysis via polarized optical spectroscopy and atomic force microscopy with a photoluminescence investigation carried out in situ, based on monitoring the efficiency of the singlet fission process typical of crystalline RUB. Building on the insights gained, we tune the thin film growth and post-growth parameters to obtain centimeter-scale, highly homogeneous and crystalline RUB thin films, consisting of several μm-sized and coherently oriented domains, featuring oxidation resistance. [ABSTRACT FROM AUTHOR]

Published
2024
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36. A real‐world retrospective–prospective analysis of efficacy and safety of combined ixazomib, lenalidomide, and dexamethasone in relapsed/refractory multiple myeloma: The northern Italy experience

Author

Furlan, Anna, primary, Cea, Michele, additional, Pavan, Laura, additional, Galli, Monica, additional, Clissa, Cristina, additional, Mangiacavalli, Silvia, additional, Cafro, Anna Maria, additional, Girlanda, Stefania, additional, Patriarca, Francesca, additional, Minotto, Claudia, additional, Bertoldero, Giovanni, additional, Barilà, Gregorio, additional, Pascarella, Anna, additional, Lico, Albana, additional, Paolini, Rossella, additional, Rabassi, Nicholas, additional, Pescosta, Norbert, additional, Porrazzo, Marika, additional, De Sabbata, Giovanni, additional, Pompa, Alessandra, additional, Bega, Giulia, additional, Cavallin, Stefania, additional, Guidotti, Francesca, additional, Marcatti, Magda, additional, Rupolo, Maurizio, additional, Belotti, Angelo, additional, Gherlinzoni, Filippo, additional, and Zambello, Renato, additional

Published
2024
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37. Towards efficient near-infrared fluorescent organic light-emitting diodes

Author

Alessandro Minotto, Ibrahim Bulut, Alexandros G. Rapidis, Giuseppe Carnicella, Maddalena Patrini, Eugenio Lunedei, Harry L. Anderson, and Franco Cacialli

Subjects
Applied optics. Photonics, TA1501-1820, Optics. Light, QC350-467
Abstract

Light-emitting diodes: Near-infrared fluorescence from organic molecules Organic (carbon-based) light-emitting diodes (LEDs) that emit near-infrared light can be built by linking together large organic molecules called porphyrins, offering many potential industrial and medical applications. Organic near-infrared LEDs have several advantages over conventional LEDs based on inorganic semiconductors, including mechanical flexibility, biocompatibility and the absence of polluting heavy metals. Researchers in the UK and Italy led by Harry Anderson at the University of Oxford and Franco Cacialli at University College London explored the potential of linked porphyrin structures that fluoresce at near-infrared wavelengths. The optical properties of the materials are improved by engineering the molecular structure and a quantitative model is presented to explain the efficient emission. This research provides understanding of exciton dynamics and points towards innovative uses of near-infrared light in applications including light therapy, optical communications, biosensors and biometric systems.

Published
2021
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38. Avaliação do potencial de desenvolvimento in vitro de sementes de calendula officinalis em meio de cultura MS

Author

Rafaela Ansiliero, Nathalia Turkot Candiago, Elisandra Minotto, Cristian Antunes de Almeida, and César Milton Baratto

Subjects
calêndula, micropropagação, corante alimentício, germinação, Biotechnology, TP248.13-248.65, Food processing and manufacture, TP368-456
Abstract

Callendula officinalis é uma planta herbácea pertencente à família Asteraceae, a qual é capaz de apresentar atividades antioxidante e antibacteriana contra variados microrganismos. A técnica de micropropagação in vitro da espécie é alternativa para obter-se plantas com melhor qualidade e uniformidade, com produção de plantas sadias e com crescimento rápido. Com base nisso, este estudo busca avaliar o potencial de desenvolvimento in vitro, de sementes de Calendula officinalis, avaliando fatores como germinação, estabelecimento e crescimento. As sementes utilizadas foram colhidas de plantas matrizes cultivadas em propriedade privada na cidade de Iomerê-SC/Brasil em março/2019, sendo transportadas até o laboratório da UNOESC. Após o preparo do meio de cultivo MS, as sementes foram lavadas, desinfestadas e posicionadas no meio de cultivo em tubos. Dez tubos continham corante artificial alimentício rosa e outros 10 não possuíam adição do corante, foram mantidas no escuro por 7 dias a 25ºC, decorrido tempo, transferidas para fotoperíodo de 16 horas. Após 36 dias, realizou-se a multiplicação in vitro em vidros com meio MS sem adição de corante e mantido nas mesmas condições. As sementes de calêndula apresentaram baixo desenvolvimento in vitro, sendo que as que desenvolveram são oriundas do meio de cultivo MS com adição do corante artificial alimentício rosa, atingido em 43 dias de cultivo uma média de 4 cm de comprimento. Apesar do corante artificial ter apresentado resultado positivo no desenvolvimento dos explantes, demais estudos são necessários para aprimorar técnicas mecânicas e químicas que auxiliem na germinação in vitro de sementes de calêndula.

Published
2020
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39. Onicomatricoma gigante: relato de um caso

Author

Manoella Freitas Santos, Maria Emilia Vieira de Souza, Laura Luzzatto, Leonardo Albarello, and Renan Minotto

Subjects
doenças da unha, neoplasias, unhas, Dermatology, RL1-803
Abstract

Introdução: Onicomatricoma é um tumor benigno, raro, caracterizado pela tétrade clínica de faixa longitudinal amarelada de espessura variável, hemorragias em estilhaço, hipercurvatura longitudinal e transversa da placa ungueal e projeções digitiformes que emergem da matriz ungueal, deixando cavitações na placa ungueal. Relatamos um caso de paciente feminina, 49 anos, com queixa de lesão tumoral em terceiro quirodáctilo esquerdo há cerca de quatro anos, com aumento progressivo no período. Ao exame, apresentava lesão tumoral exuberante clinicamente compatível com onicomatricoma, confirmado pelo exame anatomopatológico após exérese completa do tumor.

Published
2020
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40. Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth

Author

Jose J. De Vega, Robert P. Davey, Jorge Duitama, Dairo Escobar, Marco A. Cristancho‐Ardila, Graham J. Etherington, Alice Minotto, Nelson E. Arenas‐Suarez, Juan D. Pineda‐Cardenas, Javier Correa‐Alvarez, Anyela V. Camargo Rodriguez, Wilfried Haerty, Juan P. Mallarino‐Robayo, Emiliano Barreto‐Hernandez, Monica Muñoz‐Torres, Narcis Fernandez‐Fuentes, Federica Di Palma, and the Colombian Cyberinfrastructure Consortium for Biodiversity

Subjects
biodiversity, data management, e‐infrastructure, innovation, research policy, Environmental sciences, GE1-350, Botany, QK1-989
Abstract

Societal Impact Statement Colombia is a “megadiverse” country with vast natural resources. A history of recent conflict means that information is only now being collected on the natural capital of regions that were previously unexplored. Better access to data, tools, and expertise is required for evidence‐supported decisions on the conservation of these resources. The development of a bespoke cyberinfrastructure could help fulfill this need by providing access to digital resources in a collaborative cyberenvironment. We outline key priorities and develop a reference framework for building cyberinfrastructure in Colombia. This framework could be applied to other fields and countries to promote knowledge exchange, scientific innovation, and socioeconomic growth.

Published
2020
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44. A Transparent Ultrasound Array for Real-Time Optical, Ultrasound, and Photoacoustic Imaging

Author

Haoyang Chen, Sumit Agrawal, Mohamed Osman, Josiah Minotto, Shubham Mirg, Jinyun Liu, Ajay Dangi, Quyen Tran, Thomas Jackson, and Sri-Rajasekhar Kothapalli

Subjects
Medical technology, R855-855.5, Biotechnology, TP248.13-248.65
Abstract

Objective and Impact Statement. Simultaneous imaging of ultrasound and optical contrasts can help map structural, functional, and molecular biomarkers inside living subjects with high spatial resolution. There is a need to develop a platform to facilitate this multimodal imaging capability to improve diagnostic sensitivity and specificity. Introduction. Currently, combining ultrasound, photoacoustic, and optical imaging modalities is challenging because conventional ultrasound transducer arrays are optically opaque. As a result, complex geometries are used to coalign both optical and ultrasound waves in the same field of view. Methods. One elegant solution is to make the ultrasound transducer transparent to light. Here, we demonstrate a novel transparent ultrasound transducer (TUT) linear array fabricated using a transparent lithium niobate piezoelectric material for real-time multimodal imaging. Results. The TUT-array consists of 64 elements and centered at ~6 MHz frequency. We demonstrate a quad-mode ultrasound, Doppler ultrasound, photoacoustic, and fluorescence imaging in real-time using the TUT-array directly coupled to the tissue mimicking phantoms. Conclusion. The TUT-array successfully showed a multimodal imaging capability and has potential applications in diagnosing cancer, neurological, and vascular diseases, including image-guided endoscopy and wearable imaging.

Published
2022
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48. Acute Vascular Reactive Inflammatory Acral Skin Lesions and SARS-CoV-2

Author

Renan Minotto, Joana R. Fitz, Bruna M. Bauer, and Ana Helena Choi

Subjects
COVID-19, Chilblains, Nail Diseases, Paronychia, SARS-CoV-2, Skin Diseases, Dermatology, RL1-803, Infectious and parasitic diseases, RC109-216
Abstract

Introduction: Coronavirus disease 2019 (COVID-19) predominantly affects the respiratory system, but there have been many reports of skin involvement. Several cutaneous manifestations associated with COVID-19 have been identified, including acral lesions (pernio-like), which we intend to better characterize in this study. Methods: Demographic, clinical and major histopathologic characteristics of acral skin lesions occurring during the acute infection stage of COVID-19 disease were evaluated in this survey conducted in the Dermatology Division of Santa Casa Hospital Complex, Federal University of Health Sciences, Porto Alegre, Brazil. Results: In the present study, we evaluated eight female patients with acute SARS-CoV-2 infection confirmed by PCR with acral skin lesions including pernio-like. The mean age was 43.6 and with no other acute disease, who had a good outcome with need for hospitalization only in 2 cases. Pernio-like lesions were observed under hot weather conditions in patients who denied any previous history of similar cutaneous manifestations. Some acral lesions resembled those of lupus erythematosus and of herpes simplex paronychia, but laboratory tests were negative for those conditions. Unusual nail involvement was present, characterized by half-moon shaped erythematous bands at the distal margin of the lunula. Conclusion: Recognition of these skin lesions is important in that they could be potential markers, aiding in the diagnosis and prognosis of COVID-19 disease.

Published
2021
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