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7. 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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8. Building a Portuguese coalition for biodiversity genomics

Author

Marques, João P., Alves, Paulo C., Amorim, Isabel R., Lopes, Ricardo J., Moura, Monica, Myers, Eugene, Sim-sim, Manuela, Sousa-Santos, Carla, Alves, M. Judite, Borges, Paulo A. V., Brown, Thomas, Carneiro, Miguel, Carrapato, Carlos, Ceríaco, Luís M. P., Ciofi, Claúdio, da Silva, Luís P., Diedericks, Genevieve, Diroma, Maria Angela, Farelo, Liliana, Formenti, Giulio, Gil, Fátima, Grilo, Miguel, Iannucci, Alessio, Leitão, Henrique G., Máguas, Cristina, Mc Cartney, Ann M., Mendes, Sofia L., Moreno, João M., Morselli, Marco, Mouton, Alice, Natali, Chiara, Pereira, Fernando, Rego, Rúben M. C., Resendes, Roberto, Roxo, Guilherme, Svardal, Hannes, Trindade, Helena, Vicente, Sara, Winkler, Sylke, Alvarenga, Marcela, Amaral, Andreia J., Antunes, Agostinho, Campos, Paula F., Canário, Adelino V. M., Castilho, Rita, Castro, L. Filipe C., Crottini, Angelica, Cunha, Mónica V., Espregueira Themudo, Gonçalo, Esteves, Pedro J., Faria, Rui, Rodríguez Fernandes, Carlos, Ledoux, Jean-Baptiste, Louro, Bruno, Magalhaes, Sara, Paulo, Octávio S., Pearson, Gareth, Pimenta, João, Pina-Martins, Francisco, Santos, Teresa L., Serrão, Ester, Melo-Ferreira, José, and Sousa, Vítor C.

Published
2024
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9. 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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10. Unaccounted for nonforest vegetation loss in the Brazilian Amazon

Author

Messias, Cassiano Gustavo, de Almeida, Cláudio A., Silva, Daniel E., Soler, Luciana S., Maurano, Luis E., Camilotti, Vagner L., Alves, Fábio C., da Silva, Libério J., Reis, Mariane S., de Lima, Thiago C., Renó, Vivian, Lima, Deborah L. C., Belluzzo, Amanda P., Quadros, Camila B., Barradas, Delmina C. M., Moraes, Douglas R. V. de, Bastos, Eduardo F. M., Cunha, Igor P., Souza, Jefferson J. de, Barros, Lucélia S. de, Gusmão, Luiz Henrique A., Almeida, Rodrigo de, de Moraes, Dayane R. V., Silva, Diego M., Chrispim, Eduardo H. S., Pinto, João Felipe S. K. C., Ribeiro Neto, Manoel R., Matos, Marlon Henrique H., Moreira, Noeli Aline P., dos S. Teixeira, Raíssa C., Alves, Gabriel M. R., Andrade, Ana Carolina S. de, Perez, Letícia P., Bento, Bruna Maria P., Castro Filho, Hugo C. de, Santos, Igor S. dos, Araújo, Liliane Cristina L. de, Matias, Maira, da Silva, Murilo B., Pinheiro, Fábio da C., Carvalho, André, Xaud, Haron, Xaud, Maristela, Matos, Ana Paula, Baumann, Luis, Silva, Elaine B. da, Ferreira, Laerte Guimarães, and Adami, Marcos

Published
2024
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12. Factors associated to mortality in children with critical COVID-19 and multisystem inflammatory syndrome in a resource-poor setting

Author

de Farias, Emmerson C. F., Pavão Junior, Manoel J. C., de Sales, Susan C. D., do Nascimento, Luciana M. P. P., Pavão, Dalila C. A., Pinheiro, Anna P. S., Pinheiro, Andreza H. O., Alves, Marília C. B., Ferraro, Kíssila M. M. M., Aires, Larisse F. Q., Dias, Luana G., Machado, Mayara M. M., Serrão, Michaelle J. D., Gomes, Raphaella R., de Moraes, Sara M. P., Moura, Gabriella M. G., de Sousa, Adriana M. B., Pontes, Gabriela C. L., Carvalho, Railana D. F. P., Silva, Cristiane T. C., Lemes, Guilherme, da C. G. Diniz, Bruna, Chermont, Aurimery G., de Almeida, Kellen F. S., Saraty, Salma B., Maia, Mary L. F., Lima, Miriam R. C., Carvalho, Patricia B., de B. Braga, Renata, de O. Harada, Kathia, Justino, Maria C. A., Clemente, Gleice, Terreri, Maria Teresa, and Monteiro, Marta C.

Published
2024
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14. Benchmarking the Security Protocol and Data Model (SPDM) for component authentication

Author

Alves, Renan C. A., Albertini, Bruno C., and Simplicio Jr, Marcos A.

Subjects
Computer Science - Cryptography and Security
Abstract

Efforts to secure computing systems via software traditionally focus on the operating system and application levels. In contrast, the Security Protocol and Data Model (SPDM) tackles firmware level security challenges, which are much harder (if at all possible) to detect with regular protection software. SPDM includes key features like enabling peripheral authentication, authenticated hardware measurements retrieval, and secure session establishment. Since SPDM is a relatively recent proposal, there is a lack of studies evaluating its performance impact on real-world applications. In this article, we address this gap by: (1) implementing the protocol on a simple virtual device, and then investigating the overhead introduced by each SDPM message; and (2) creating an SPDM-capable virtual hard drive based on VirtIO, and comparing the resulting read/write performance with a regular, unsecured implementation. Our results suggest that SPDM bootstrap time takes the order of tens of milliseconds, while the toll of introducing SPDM on hard drive communication highly depends on specific workload patterns. For example, for mixed random read/write operations, the slowdown is negligible in comparison to the baseline unsecured setup. Conversely, for sequential read or write operations, the data encryption process becomes the bottleneck, reducing the performance indicators by several orders of magnitude., Comment: 10 pages, 8 figures

Published
2023

16. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Author

Pearman, Peter B., Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo C., Aravanopoulos, F. A., Bertola, Laura D., Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela P., Fussi, Barbara, Godoy, José A., Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig R., Raeymaekers, Joost A. M., Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo N., Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank E., Guisan, Antoine, and Bruford, Michael

Published
2024
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17. Explanation-by-Example Based on Item Response Theory

Author

Cardoso, Lucas F. F., Ribeiro, José de S., Santos, Vitor C. A., Silva, Raíssa L., Mota, Marcelle P., Prudêncio, Ricardo B. C., and Alves, Ronnie C. O.

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, I.2.6
Abstract

Intelligent systems that use Machine Learning classification algorithms are increasingly common in everyday society. However, many systems use black-box models that do not have characteristics that allow for self-explanation of their predictions. This situation leads researchers in the field and society to the following question: How can I trust the prediction of a model I cannot understand? In this sense, XAI emerges as a field of AI that aims to create techniques capable of explaining the decisions of the classifier to the end-user. As a result, several techniques have emerged, such as Explanation-by-Example, which has a few initiatives consolidated by the community currently working with XAI. This research explores the Item Response Theory (IRT) as a tool to explaining the models and measuring the level of reliability of the Explanation-by-Example approach. To this end, four datasets with different levels of complexity were used, and the Random Forest model was used as a hypothesis test. From the test set, 83.8% of the errors are from instances in which the IRT points out the model as unreliable., Comment: 15 pages, 5 figures, 3 tables, submitted for the BRACIS'22 conference

Published
2022

18. Deriving dynamical systems for language based on the Tolerance Principle

Author

Alves, Fernando C.

Subjects
Computer Science - Computation and Language
Abstract

In this research note, I derive explicit dynamical systems for language within an acquisition-driven framework (Niyogi \& Berwick, 1997; Niyogi, 2006) assuming that children/learners follow the Tolerance Principle (Yang, 2016) to determine whether a rule is productive during the process of language acquisition. I consider different theoretical parameters such as population size (finite vs. infinite) and the number of previous generations that provide learners with data. Multiple simulations of the dynamics obtained here and applications to diacrhonic language data are in preparation, so they are not included in this first note., Comment: Fixed the year of a reference and a short comment on S-shaped curves

Published
2022

19. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Author

Nilson, Sara M, Gandolfi, Barbara, Grahn, Robert A, Kurushima, Jennifer D, Lipinski, Monika J, Randi, Ettore, Waly, Nashwa E, Driscoll, Carlos, Murua Escobar, Hugo, Schuster, Rolf K, Maruyama, Soichi, Labarthe, Norma, Chomel, Bruno B, Ghosh, Sankar Kumar, Ozpinar, Haydar, Rah, Hyung-Chul, Millán, Javier, Mendes-de-Almeida, Flavya, Levy, Julie K, Heitz, Elke, Scherk, Margie A, Alves, Paulo C, Decker, Jared E, and Lyons, Leslie A

Subjects
Biological Sciences, Genetics, Animals, Cats, Domestication, Genotype, Microsatellite Repeats, Middle East, Evolutionary Biology, Evolutionary biology
Abstract

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

Published
2022

22. Data vs classifiers, who wins?

Author

Cardoso, Lucas F. F., Santos, Vitor C. A., Francês, Regiane S. Kawasaki, Prudêncio, Ricardo B. C., and Alves, Ronnie C. O.

Subjects
Computer Science - Machine Learning, I.2.6
Abstract

The experiments covered by Machine Learning (ML) must consider two important aspects to assess the performance of a model: datasets and algorithms. Robust benchmarks are needed to evaluate the best classifiers. For this, one can adopt gold standard benchmarks available in public repositories. However, it is common not to consider the complexity of the dataset when evaluating. This work proposes a new assessment methodology based on the combination of Item Response Theory (IRT) and Glicko-2, a rating system mechanism generally adopted to assess the strength of players (e.g., chess). For each dataset in a benchmark, the IRT is used to estimate the ability of classifiers, where good classifiers have good predictions for the most difficult test instances. Tournaments are then run for each pair of classifiers so that Glicko-2 updates performance information such as rating value, rating deviation and volatility for each classifier. A case study was conducted hereby which adopted the OpenML-CC18 benchmark as the collection of datasets and pool of various classification algorithms for evaluation. Not all datasets were observed to be really useful for evaluating algorithms, where only 10% were considered really difficult. Furthermore, the existence of a subset containing only 50% of the original amount of OpenML-CC18 was verified, which is equally useful for algorithm evaluation. Regarding the algorithms, the methodology proposed herein identified the Random Forest as the algorithm with the best innate ability., Comment: 34 pages, 7 figures and 9 tables

Published
2021

23. Ultrabroadband nanocavity of hyperbolic phonon polaritons in 1D-like {\alpha}-MoO3

Author

Barcelos, Ingrid D., Canassa, Thalita A., Mayer, Rafael A., Feres, Flavio H., de Oliveira, Eynara G., Goncalves, Alem-Mar B., Bechtel, Hans A., Freitas, Raul O., Maia, Francisco C. B., and Alves, Diego C. B.

Subjects
Condensed Matter - Materials Science, Physics - Optics
Abstract

The exploitation of phonon-polaritons in nanostructured materials offers a pathway to manipulate infrared (IR) light for nanophotonic applications. Notably, hyperbolic phonons polaritons (HP2) in polar bidimensional crystals have been used to demonstrate strong electromagnetic field confinement, ultraslow group velocities, and long lifetimes (~ up to 8 ps). Here we present nanobelts of {\alpha}-phase molybdenum trioxide ({\alpha}-MoO3) as a low-dimensional medium supporting HP2 modes in the mid- and far-IR ranges. By real-space nanoimaging, with IR illuminations provided by synchrotron and tunable lasers, we observe that such HP2 response happens via formation of Fabry-Perot resonances. We remark an anisotropic propagation which critically depends on the frequency range. Our findings are supported by the convergence of experiment, theory, and numerical simulations. Our work shows that the low dimensionality of natural nanostructured crystals, like {\alpha}-MoO3 nanobelts, provides an attractive platform to study polaritonic light-matter interactions and offer appealing cavity properties that could be harnessed in future designs of compact nanophotonic devices.

Published
2021

24. Language learnability in the limit for general metrics: a Gold-Angluin result

Author

Alves, Fernando C.

Subjects
Computer Science - Computation and Language, Computer Science - Formal Languages and Automata Theory
Abstract

In his pioneering work in the field of Inductive Inference, Gold (1967) proved that a set containing all finite languages and at least one infinite language over the same fixed alphabet is not learnable in the exact sense. Within the same framework, Angluin (1980) provided a complete characterization for the learnability of language families. Mathematically, the concept of exact learning in that classical setting can be seen as the use of a particular type of metric for learning in the limit. In this short research note we use Niyogi's extended version of a theorem by Blum and Blum (1975) on the existence of locking data sets to prove a necessary condition for learnability in the limit of any family of languages in any given metric. This recovers Gold's theorem as a special case. Moreover, when the language family is further assumed to contain all finite languages, the same condition also becomes sufficient for learnability in the limit.

Published
2021

25. New Coalescences for the Painlev\'e Equations

Author

Alves, V. C. C.

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems, Mathematics - Classical Analysis and ODEs, 33E17, 33E05, 34A34
Abstract

The Painlev\'e equations are here connected to other classes of equations with the Painlev\'e Property (Ince's equations) by the same degeneracy procedure that connects the Painlev\'e equations (coalescence). These Ince's equations here are also connected among themselves like in the traditional Painlev\'e's coalescence cascade. Such degeneracy is considered also for the special equations, symmetric equations and B\"acklund transformations.

Published
2021

26. Gauge Symmetry Origin of B\'acklund Transformations for Painlev\'e Equations

Author

Alves, V. C. C., Aratyn, H., Gomes, J. F., and Zimerman, A. H.

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

We identify the self-similarity limit of the second flow of $sl(N)$ mKdV hierarchy with the periodic dressing chain thus establishing % a connection to $A^{(1)}_{N-1}$ invariant Painlev\'e equations. The $A^{(1)}_{N-1}$ B\"acklund symmetries of dressing equations and Painlev\'e equations are obtained in the self-similarity limit of gauge transformations of the mKdV hierarchy realized as zero-curvature equations on the loop algebra $\widehat{sl}(N)$ endowed with a principal gradation.

Published
2021
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27. Coalescence, Deformation and B\'acklund Symmetries of Painlev\'e IV and II Equations

Author

Alves, V. C. C., Aratyn, H., Gomes, J. F., and Zimerman, A. H.

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

We extend Painlev\'e IV model by adding quadratic terms to its Hamiltonian obtaining two classes of models (coalescence and deformation) that interpolate between Painlev\'e IV and II equations for special limits of the underlying parameters. We derive the underlying B\"acklund transformations, symmetry structure and requirements to satisfy Painlev\'e property., Comment: 21 pages, to appear in J. Phys. A: Math. Theor. (2020)

Published
2020
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28. NASirt: AutoML based learning with instance-level complexity information

Author

Neto, Habib Asseiss, Alves, Ronnie C. O., and Campos, Sergio V. A.

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning, I.2.6
Abstract

Designing adequate and precise neural architectures is a challenging task, often done by highly specialized personnel. AutoML is a machine learning field that aims to generate good performing models in an automated way. Spectral data such as those obtained from biological analysis have generally a lot of important information, and these data are specifically well suited to Convolutional Neural Networks (CNN) due to their image-like shape. In this work we present NASirt, an AutoML methodology based on Neural Architecture Search (NAS) that finds high accuracy CNN architectures for spectral datasets. The proposed methodology relies on the Item Response Theory (IRT) for obtaining characteristics from an instance level, such as discrimination and difficulty, and it is able to define a rank of top performing submodels. Several experiments are performed in order to demonstrate the methodology's performance with different spectral datasets. Accuracy results are compared to other benchmarks methods, such as a high performing, manually crafted CNN and the Auto-Keras AutoML tool. The results show that our method performs, in most cases, better than the benchmarks, achieving average accuracy as high as 97.40%., Comment: to be published

Published
2020

29. Decoding machine learning benchmarks

Author

Cardoso, Lucas F. F., Santos, Vitor C. A., Francês, Regiane S. K., Prudêncio, Ricardo B. C., and Alves, Ronnie C. O.

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning, I.2.6
Abstract

Despite the availability of benchmark machine learning (ML) repositories (e.g., UCI, OpenML), there is no standard evaluation strategy yet capable of pointing out which is the best set of datasets to serve as gold standard to test different ML algorithms. In recent studies, Item Response Theory (IRT) has emerged as a new approach to elucidate what should be a good ML benchmark. This work applied IRT to explore the well-known OpenML-CC18 benchmark to identify how suitable it is on the evaluation of classifiers. Several classifiers ranging from classical to ensembles ones were evaluated using IRT models, which could simultaneously estimate dataset difficulty and classifiers' ability. The Glicko-2 rating system was applied on the top of IRT to summarize the innate ability and aptitude of classifiers. It was observed that not all datasets from OpenML-CC18 are really useful to evaluate classifiers. Most datasets evaluated in this work (84%) contain easy instances in general (e.g., around 10% of difficult instances only). Also, 80% of the instances in half of this benchmark are very discriminating ones, which can be of great use for pairwise algorithm comparison, but not useful to push classifiers abilities. This paper presents this new evaluation methodology based on IRT as well as the tool decodIRT, developed to guide IRT estimation over ML benchmarks., Comment: Paper published at the BRACIS 2020 conference, 15 pages, 4 figures

Published
2020
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36. Mining the 99 Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus)

Author

Lyons, LA, Buckley, RM, Harvey, RJ, Abitbol, Marie, Aberdein, Danielle, Alves, Paulo C, Andersson, Asa Ohlsson, Bellone, Rebecca R, Bergström, Tomas F, Bilgen, Nuket, Boyko, Adam R, Brockman, Jeffrey A, Casal, Margret L, Castelhano, Marta G, Davis, Brian W, Davison, Lucy, Distl, Ottmar, Dodman, Nicholas H, Ellinwood, N Matthew, Fogle, Jonathan E, Forman, Oliver P, Garrick, Dorian J, Ginns, Edward I, Häggström, Jens, Hasegawa, Daisuke, Haase, Bianca, Jagannathan, Vidhya, Lait, Philippa, Hernandez, Isabel, Hytönen, Marjo K, Kaukonen, Maria, Kosho, Tomoki, Leclerc, Emilie, Lear, Teri L, Leeb, Tosso, Li, Ronald HL, Lohi, Hannes, Longeri, Maria, Magnuson, Mark A, Malik, Richard, Mane, Shrinivasrao P, Middleton, Rondo, Munday, John S, Murphy, William J, Myers, Alexandra N, Pedersen, Niels C, Peterson‐Jones, Simon M, Rothschild, Max F, Rusbridge, Clare, Schoenebeck, Jeffrey J, Shapiro, Beth, Stern, Joshua A, Swanson, William F, Terio, Karen A, Todhunter, Rory J, Warren, Wesley C, Wilcox, Elizabeth A, Wildschutte, Julia H, and Yu, Yoshihiko

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Amino Acid Sequence, Animals, Breeding, Cats, Genome, Hair Color, Intercellular Signaling Peptides and Proteins, Phenotype, Abyssinian, coat pattern, Dickkopf&#160, Wnt&#160, Signaling&#160, Pathway Inhibitor 4, DKK4, Tabby, Lives Cat Genome Consortium, DKK4, Dickkopf Wnt Signaling Pathway Inhibitor 4, Tabby, Zoology, Veterinary Sciences, Dairy & Animal Science
Abstract

Tabby patterns of fur coats are defining characteristics in wild and domestic felids. Historically, three autosomal alleles at one locus (Tabby): Abyssinian (Ta ; a.k.a. ticked), mackerel (Tm ; a.k.a. striped) and blotched (tb ; a.k.a. classic, blotched) were thought to control these patterns in domestic cats and their breeds. Currently, at least three loci influence cat tabby markings, two of which are designated Tabby and Ticked. The Tabby locus is laeverin (LVRN) and affects the mackerel and blotched patterns. The unidentified gene for the Ticked locus on cat chromosome B1 was suggested to control the presence or absence of the ticked pattern (Tabby - Abyssinian (Ta ; a.k.a. ticked). The cat reference genome (Cinnamon, the Abyssinian) has the ticked phenotype and the variant dataset and coat phenotypes from the 99 Lives Cat Genome Consortium (195 cats) were used to identify candidate genes and variants associated with the Ticked locus. Two strategies were used to find the Ticked allele(s), one considered Cinnamon with the reference allele or heterozygous (Strategy A) and the other considered Cinnamon as having the variant allele or heterozygous (Strategy B). For Strategy A, two variants in Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4), a p.Cys63Tyr (B1:41621481, c.188G>A) and a less common p.Ala18Val (B1:42620835, c.53C>T) variant are suggested as two alleles influencing the Ticked phenotype. Bioinformatic and molecular modeling analysis suggests that these changes disrupt a key disulfide bond in the Dkk4 cysteine-rich domain 1 or Dkk4 signal peptide cleavage respectively. All coding variants were excluded as Ticked alleles using Strategy B.

Published
2021

41. Learning Calculus through PBL in an Industrial Engineering and Management Program - A Seven-Year Study

Author

Cargnin-Stieler, Marinez, Malheiro, M. Teresa, Alves, Anabela C., Lima, Rui M., and Teixeira, Marcelo C. M.

Abstract

This paper aims to study ways of contributing to the development of Calculus through a Project-Based Learning (PBL) approach, which involves students in their first semester of the Integrated Master's program in Industrial Engineering and Management (IEM) at the University of Minho. The study presents the analysis of forty-two interdisciplinary project reports developed by students over a seven-year period. The reports offer good evidence for the application of the requested Calculus learning outcomes, demonstrating that the application of Calculus content occurred during the development of the project. This finding means that PBL was successful as a truly active learning process for Calculus that involves students learning independently through the interdisciplinary resolution of problems related to their engineering professional profiles.

Published
2019

42. Symmetries and hamiltonians of Ince's XXXVIII and XLIX equations

Author

Alves, V. C. C., Aratyn, H., Gomes, J. F., and Zimerman, A. H.

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

We discuss symmetries of Hamiltonians of I$_{38}$ and I$_{49}$ equations that appear on Ince's list of fifty second-order differential equations with Painlev\'e property. This study is informed by structure of Weyl symmetries of Painlev\'e P$_{III}$ and mixed Painlev\'e P$_{III-V}$ equations and provides insights into differences between the symmetries of Painlev\'e equations and symmetries of solvable equations on Ince's list., Comment: 9 pages, Proc. of the 32nd International Colloquium on Group Theoretical Methods in Physics (Group32), 2018, Prague, Czech Republic

Published
2019
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43. On special limits of the Mixed Painlev\'e P$_{\mathbf{III-V}}$ Model

Author

Alves, V C C, Aratyn, H, Gomes, J F, and Zimerman, A H

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

The paper discusses P$_{III-V}$ equation for special values of its parameters for which this equation reduces to P$_{III}$, I$_{12}$, as well as, to some special cases of I$_{38}$ and I$_{49}$ equations from the Ince's list of $50$ second order differential equations possessing Painlev\'e property. These reductions also yield symmetries governing the reduced models obtained from the P$_{III-V}$ equation. We point out that the solvable equations on Ince's list emerge in this reduction scheme when the underlying reflections of the Weyl symmetry group no longer include an affine reflection through the hyperplane orthogonal to the highest root and therefore do not give rise to an affine Weyl group. We hypothesize that on the level of the underlying algebra and geometry this might be a fundamental feature that distinguishes the six Painlev\'e equations from the remaining $44$ solvable equations on the Ince's list., Comment: 10 pages, Proc. of the 32nd International Colloquium on Group Theoretical Methods in Physics (Group32), 2018, Prague, Czech Republic

Published
2019
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45. Solutions of Mixed Painlev\'e P$_{\mathbf{III-V}}$ Model

Author

Alves, V. C. C., Aratyn, H., Gomes, J. F., and Zimerman, A. H.

Subjects
Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

We review the construction of the mixed Painlev\'e P$_{III-V}$ system in terms of a 4-boson integrable model and discuss its symmetries. Such a mixed system consist of an hybrid differential equation that for special limits of its parameters reduces to either Painlev\'e P$_{III}$ or P$_{V}$. The aim of this paper is to describe solutions of P$_{III-V}$ model. In particular, we determine and classify rational, power series and transcendental solutions of P$_{III-V}$. A class of power series solutions is shown to be convergent in accordance with the Briot-Bouquet theorem. Moreover, the P$_{III-V}$ equations are reduced to Riccati equations and solved for special values of parameters. The corresponding Riccati solutions can be expressed as Whittaker functions or alternatively confluent hypergeometric and Laguerre functions and are given by ratios of polynomials of order $n$ when the parameter of P$_{III-V}$ equation is quantized by integer $n \in \mathbb{Z}$., Comment: 27 pages , to appear in J. Phys. A, (2018)

Published
2018
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46. Electrical and Optical Properties of Heavily Ge-Doped AlGaN

Author

Blasco, R., Ajay, A., Robin, E., Bougerol, C., Lorentz, K., Alves, L. C., Mouton, I., Amichi, L., Grenier, A., and Monroy, E.

Subjects
Condensed Matter - Materials Science
Abstract

We report the effect of germanium as n-type dopant on the electrical and optical properties of AlxGa1-xN layers grown by plasma assisted molecular-beam epitaxy. The Al content has been varied from x = 0 to 0.66, confirmed by Rutherford backscattering spectrometry, and the Ge concentration was increased up to [Ge] = 1E21 cm-3. Even at these high doping levels Ge does not induce any structural degradation in AlxGa1-xN layers with x below 0.15. However, for higher Al compositions, clustering of Ge forming crystallites were observed. Hall effect measurements show a gradual decrease of the carrier concentration when increasing the Al mole fraction, which is already noticeable in samples with x = 0.24. Samples with x = 0.64-0.66 remain conductive, but the donor activation rate drops to around 0.1% (carrier concentration around 1E18 cm-3 for [Ge] = 1E21 cm-3). From the optical point of view, the low temperature photoluminescence is dominated by the band-to-band emission, which show only spectral shift and broadening associated to the Burstein-Moss effect. The evolution of the photoluminescence peak position with temperature shows that the free carriers due to Ge doping can efficiently screen the potential fluctuations induced by alloy disorder.

Published
2018
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47. Mitochondrial GTP Links Nutrient Sensing to β Cell Health, Mitochondrial Morphology, and Insulin Secretion Independent of OxPhos

Author

Jesinkey, Sean R, Madiraju, Anila K, Alves, Tiago C, Yarborough, OrLando H, Cardone, Rebecca L, Zhao, Xiaojian, Parsaei, Yassmin, Nasiri, Ali R, Butrico, Gina, Liu, Xinran, Molina, Anthony J, Rountree, Austin M, Neal, Adam S, Wolf, Dane M, Sterpka, John, Philbrick, William M, Sweet, Ian R, Shirihai, Orian H, and Kibbey, Richard G

Subjects
Biochemistry and Cell Biology, Biological Sciences, Diabetes, Nutrition, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Metabolic and endocrine, Adenosine Triphosphate, Animals, Cell Differentiation, Cell Line, Cell Proliferation, Citric Acid Cycle, Glucose, Guanosine Triphosphate, Homeostasis, Humans, Insulin, Insulin Secretion, Insulin-Secreting Cells, Mice, Mice, Inbred C57BL, Mice, Transgenic, Microscopy, Electron, Transmission, Mitochondria, Mitochondrial Membranes, Oxidative Phosphorylation, Phosphoenolpyruvate Carboxykinase (ATP), Succinate-CoA Ligases, Up-Regulation, MIMOSA, PEPCK-M, anaplerosis, insulin secretion, metabolic flux, mitochondrial GTP, oxidative phosphorylation, phosphoenolpyruvate, stable isotope, succinyl-CoA synthetase, Medical Physiology, Biological sciences
Abstract

Mechanisms coordinating pancreatic β cell metabolism with insulin secretion are essential for glucose homeostasis. One key mechanism of β cell nutrient sensing uses the mitochondrial GTP (mtGTP) cycle. In this cycle, mtGTP synthesized by succinyl-CoA synthetase (SCS) is hydrolyzed via mitochondrial PEPCK (PEPCK-M) to make phosphoenolpyruvate, a high-energy metabolite that integrates TCA cycling and anaplerosis with glucose-stimulated insulin secretion (GSIS). Several strategies, including xenotopic overexpression of yeast mitochondrial GTP/GDP exchanger (GGC1) and human ATP and GTP-specific SCS isoforms, demonstrated the importance of the mtGTP cycle. These studies confirmed that mtGTP triggers and amplifies normal GSIS and rescues defects in GSIS both in vitro and in vivo. Increased mtGTP synthesis enhanced calcium oscillations during GSIS. mtGTP also augmented mitochondrial mass, increased insulin granule number, and membrane proximity without triggering de-differentiation or metabolic fragility. These data highlight the importance of the mtGTP signal in nutrient sensing, insulin secretion, mitochondrial maintenance, and β cell health.

Published
2019

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