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3,174 results on '"Rafael, B"'

1. Parametric Symplectic Jet Interpolation

Author

Andrist, Rafael B., Huang, Gaofeng, Kutzschebauch, Frank, and Schott, Josua

Subjects
Mathematics - Complex Variables, 14J42, 32E30, 32M17, 32Q56
Abstract

We prove a parametric jet interpolation theorem for symplectic holomorphic automorphisms of $\mathbb{C}^{2n}$ with parameters in a Stein space. Moreover, we provide an example of an unavoidable set for symplectic holomorphic maps.

Published
2024

2. On the connectedness of the boundary of $q$-complete domains

Author

Andrist, Rafael B.

Subjects
Mathematics - Complex Variables, 32F27, 32F10, 32Q60
Abstract

The boundary of every relatively compact Stein domain in a complex manifold of dimension at least two is connected. No assumptions on the boundary regularity are necessary. The same proofs hold also for $q$-complete domains, and in the context of almost complex manifolds as well.

Published
2024

3. Nonparametric FBST for Validating Linear Models

Author

Lassance, Rodrigo F. L., Stern, Julio M., and Stern, Rafael B.

Subjects
Statistics - Methodology
Abstract

The Full Bayesian Significance Test (FBST) possesses many desirable aspects, such as not requiring a non-zero prior probability for hypotheses while also producing a measure of evidence for $H_0$. Still, few attempts have been made to bring the FBST to nonparametric settings, with the main drawback being the need to obtain the highest posterior density (HPD) in a function space. In this work, we use Gaussian processes to provide an analytically tractable FBST for hypotheses of the type $$ H_0: g(\boldsymbol{x}) = \boldsymbol{b}(\boldsymbol{x})\boldsymbol{\beta}, \quad \forall \boldsymbol{x} \in \mathcal{X}, \quad \boldsymbol{\beta} \in \mathbb{R}^k, $$ where $g(\cdot)$ is the regression function, $\boldsymbol{b}(\cdot)$ is a vector of linearly independent linear functions -- such as $\boldsymbol{b}(\boldsymbol{x}) = \boldsymbol{x}'$ -- and $\mathcal{X}$ is the covariates' domain. We also make use of pragmatic hypotheses to verify if the adherence of linear models may be approximately instead of exactly true, allowing for the inclusion of valuable information such as measurement errors and utility judgments. This contribution extends the theory of the FBST, allowing its application in nonparametric settings and providing a procedure that easily tests if linear models are adequate for the data and that can automatically perform variable selection., Comment: All code available in https://github.com/rflassance/lmFBST

Published
2024

4. On complete generators of certain Lie algebras on Danielewski surfaces

Author

Andrist, Rafael B.

Subjects
Mathematics - Complex Variables, Mathematics - Algebraic Geometry, 32M17, 32E30, 32Q56, 14R10, 14R20
Abstract

We study the Lie algebra of polynomial vector fields on a smooth Danielewski surface of the form $x y = p(z)$ with $x,y,z \in \mathbb{C}$. We provide explicitly given generators to show that: 1. The Lie algebra of polynomial vector fields is generated by $6$ complete vector fields. 2. The Lie algebra of volume-preserving polynomial vector fields is generated by finitely many vector fields, whose number depends on the degree of the defining polynomial. 3. There exists a Lie sub-algebra generated by $4$ LNDs whose flows generate a group that acts infinitely transitively on the Danielewski surface. The latter result is also generalized to higher dimensions where $z \in \mathbb{C}^N$., Comment: Sections 6 and 7 added, covering direct products and the higher-dimensional case

Published
2024

7. PROTEST: Nonparametric Testing of Hypotheses Enhanced by Experts' Utility Judgements

Author

Lassance, Rodrigo F. L., Izbicki, Rafael, and Stern, Rafael B.

Subjects
Statistics - Methodology
Abstract

Instead of testing solely a precise hypothesis, it is often useful to enlarge it with alternatives that are deemed to differ from it negligibly. For instance, in a bioequivalence study one might consider the hypothesis that the concentration of an ingredient is exactly the same in two drugs. In such a context, it might be more relevant to test the enlarged hypothesis that the difference in concentration between the drugs is of no practical significance. While this concept is not alien to Bayesian statistics, applications remain confined to parametric settings and strategies on how to effectively harness experts' intuitions are often scarce or nonexistent. To resolve both issues, we introduce PROTEST, an accessible nonparametric testing framework that seamlessly integrates with Markov Chain Monte Carlo (MCMC) methods. We develop expanded versions of the model adherence, goodness-of-fit, quantile and two-sample tests. To demonstrate how PROTEST operates, we make use of examples, simulated studies - such as testing link functions in a binary regression setting, as well as a comparison between the performance of PROTEST and the PTtest (Holmes et al., 2015) - and an application with data on neuron spikes. Furthermore, we address the crucial issue of selecting the threshold - which controls how much a hypothesis is to be expanded - even when intuitions are limited or challenging to quantify., Comment: R package found in https://github.com/rflassance/protest

Published
2024

8. Regression Trees for Fast and Adaptive Prediction Intervals

Author

Cabezas, Luben M. C., Otto, Mateus P., Izbicki, Rafael, and Stern, Rafael B.

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

Predictive models make mistakes. Hence, there is a need to quantify the uncertainty associated with their predictions. Conformal inference has emerged as a powerful tool to create statistically valid prediction regions around point predictions, but its naive application to regression problems yields non-adaptive regions. New conformal scores, often relying upon quantile regressors or conditional density estimators, aim to address this limitation. Although they are useful for creating prediction bands, these scores are detached from the original goal of quantifying the uncertainty around an arbitrary predictive model. This paper presents a new, model-agnostic family of methods to calibrate prediction intervals for regression problems with local coverage guarantees. Our approach is based on pursuing the coarsest partition of the feature space that approximates conditional coverage. We create this partition by training regression trees and Random Forests on conformity scores. Our proposal is versatile, as it applies to various conformity scores and prediction settings and demonstrates superior scalability and performance compared to established baselines in simulated and real-world datasets. We provide a Python package clover that implements our methods using the standard scikit-learn interface.

Published
2024

9. Invasive non-native species in Brazil: an updated overview

Author

Zenni, Rafael D., Ziller, Sílvia R., da Rosa, Clarissa A., Sühs, Rafael B., Puechagut, Patricia B., Marterer, Beloni T. P., Heringer, Gustavo, de Matos, Ana Carolina L., Bueno, Marina L., Almeida, Jonathan W., Silva, Carlos H. T., Legracie-Júnior, José Renato, and Chapla, Tatiani E.

Published
2024
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11. The Density Property for Generalized Calogero--Moser Spaces with Inner Degrees of Freedom

Author

Andrist, Rafael B. and Huang, Gaofeng

Subjects
Mathematics - Complex Variables, Mathematical Physics, Mathematics - Algebraic Geometry, 32M17, 32Q56, 14J42, 14D21
Abstract

We prove the density property for generalized Calogero--Moser spaces with inner degrees of freedom. This allows us to describe the holomorphic automorphism group of these complex affine manifolds. These generalized Calogero--Moser spaces can also be understood as quiver varieties corresponding to moduli spaces of $\mathrm{SU}(2)$ instantons on a non-commutative $\mathbb{R}^4$.

Published
2023

12. Existence and regularity of ultradifferentiable periodic solutions to certain vector fields

Author

Gonzalez, Rafael B.

Subjects
Mathematics - Analysis of PDEs, 35A01, 35B10, 35H10
Abstract

We consider a class of first-order partial differential operators, acting on the space of ultradifferentiable periodic functions, and we describe their range by using the following conditions on the coefficients of the operators: the connectedness of certain sublevel sets, the dimension of the subspace generated by the imaginary part of the coefficients, and Diophantine conditions. In addition, we show that these properties are also linked to the regularity of the solutions. The results extend previous ones in Gevrey classes.

Published
2023

13. New Weighting Strategies for WENO Schemes

Author

Barreto, Daniel, Borges, Rafael B. de R., Costa, Bruno, and Santos, Silvaneo dos

Subjects
Mathematics - Numerical Analysis
Abstract

In this article, we propose a modified convex combination of the polynomial reconstructions of odd-order WENO schemes to maintain the central substencil prevalence over the lateral ones in all parts of the solution. New "centered" versions of the classical WENO-Z and its less dissipative counterpart, WENO-Z+, are defined through very simple modifications of the classical nonlinear weights and show significantly superior numerical properties; for instance, a well-known dispersion error for long-term runs is fixed, along with decreased dissipation and better shock-capturing abilities. Moreover, the proposed centered version of WENO-Z+ has no ad-hoc parameters and no dependence on the powers of the grid size. All the new schemes are thoroughly analyzed concerning convergence at critical points, adding to the discussion on the relevance of such convergence to the numerical simulation of typical hyperbolic conservation laws problems. Nonlinear spectral analysis confirms the enhancement achieved by the new schemes over the standard ones.

Published
2023

15. REACT to NHST: Sensible conclusions to meaningful hypotheses

Author

Izbicki, Rafael, Cabezas, Luben M. C., Colugnatti, Fernando A. B., Lassance, Rodrigo F. L., de Souza, Altay A. L., and Stern, Rafael B.

Subjects
Statistics - Methodology
Abstract

While Null Hypothesis Significance Testing (NHST) remains a widely used statistical tool, it suffers from several shortcomings, such as conflating statistical and practical significance, sensitivity to sample size, and the inability to distinguish between accepting the null hypothesis and failing to reject it. Recent efforts have focused on developing alternatives to NHST to address these issues. Despite these efforts, conventional NHST remains dominant in scientific research due to its simplicity and perceived ease of interpretation. Our work presents a novel alternative to NHST that is just as accessible and intuitive: REACT. It not only tackles the shortcomings of NHST but also offers additional advantages over existing alternatives. For instance, REACT is easily applicable to multiparametric hypotheses and does not require stringent significance-level corrections when conducting multiple tests. We illustrate the practical utility of REACT through real-world data examples, using criteria aligned with common research practices to distinguish between the absence of evidence and evidence of absence.

Published
2023

16. A Criterion for the Density Property of Stein Manifolds

Author

Andrist, Rafael B., Freudenburg, Gene, Huang, Gaofeng, Kutzschebauch, Frank, and Schott, Josua

Subjects
Mathematics - Complex Variables, 32M25 (Primary), 14R20, 20G35, 32M05, 32M17, 32Q56 (Secondary)
Abstract

We generalize a criterion for the density property of Stein manifolds. As an application, we give a new, simple proof of the fact that the Danielewski surfaces have the algebraic density property. Furthermore, we have found new examples of Stein manifolds with the density property.

Published
2023

17. Flexible conditional density estimation for time series

Author

Grivol, Gustavo, Izbicki, Rafael, Okuno, Alex A., and Stern, Rafael B.

Subjects
Statistics - Methodology, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

This paper introduces FlexCodeTS, a new conditional density estimator for time series. FlexCodeTS is a flexible nonparametric conditional density estimator, which can be based on an arbitrary regression method. It is shown that FlexCodeTS inherits the rate of convergence of the chosen regression method. Hence, FlexCodeTS can adapt its convergence by employing the regression method that best fits the structure of data. From an empirical perspective, FlexCodeTS is compared to NNKCDE and GARCH in both simulated and real data. FlexCodeTS is shown to generally obtain the best performance among the selected methods according to either the CDE loss or the pinball loss., Comment: 19 pages, 7 figures

Published
2023

18. The symplectic holomorphic density property for Calogero-Moser spaces

Author

Andrist, Rafael B. and Huang, Gaofeng

Subjects
Mathematics - Complex Variables, Mathematics - Algebraic Geometry, Mathematics - Symplectic Geometry, 32M17, 32Q56, 14J42, 14L24
Abstract

We introduce the symplectic holomorphic density property and the Hamiltonian holomorphic density property together with the corresponding version of Anders\'en-Lempert theory. We establish these properties for the Calogero-Moser space $\mathcal{C}_n$ of $n$ particles and describe its group of holomorphic symplectic automorphisms., Comment: 29 pages, email addresses added

Published
2023

19. Molecular genetics in adult-onset Still’s disease: next-generation sequencing in 24 patients and literature review

Author

Diana Prieto-Peña, Eztizen Labrador-Sánchez, Rafael B. Melero-González, Fred Antón-Pagés, Natalia Palmou-Fontana, Carmen Alvarez-Reguera, Nerea Paz-Gandiaga, and Ricardo Blanco

Subjects
genetics, adult-onset Still’s disease, NGS, molecular genetic techniques, autoinflammatory diseases, Immunologic diseases. Allergy, RC581-607
Abstract

ObjectiveNext-generation sequencing (NGS) panels are increasingly used for the diagnosis of monogenic systemic autoinflammatory diseases (SAIDs). However, their role in patients with adult-onset Still’s disease (AOSD) remains unknown. This study aims to assess the usefulness of NGS panels in AOSD patients to improve diagnosis and management of the disease.MethodsThis observational, multicenter study included all patients with AOSD diagnosis who underwent NGS panel testing in northern Spain. Clinical manifestations, laboratory parameters, complications, and therapeutic responses were recorded.ResultsA total of 24 patients (16 men, 8 women) with an average age of 42.2 ± 17.9 (mean ± SD) years, in whom NGS was performed, fulfilled the Yamaguchi and/or Fautrel criteria for AOSD. The most common symptoms, apart from fever, were skin rash (75%), asthenia (91.7%), and articular manifestations (91.7%). All patients had elevated acute-phase reactant levels and hyperferritinemia. Almost all patients received oral glucocorticoids as initial therapy. Conventional disease-modifying antirheumatic drugs (cDMARDs) were used in 17 (70.8%) patients and biologic therapy in 13 (54.1%) patients. Genetic variants were observed in 5 (20.8%) patients. None of them were classified as pathogenic. Variants of uncertain significance (VUS) were identified in NOD2 (c.2104C>T and c.2251G>A), TNFRSF1A (c.224C>T), TNFAIP3 (c.1939A>C), and SCN9A (c.2617G>A). Atypical manifestations and/or therapeutic refractoriness were observed in patients carrying genetic variants, except for one patient with the TNFAIP3 VUS. Four out of five patients with VUS had a severe and refractory course of the disease and required biologic therapy.ConclusionNGS was useful to rule out the presence of pathogenic genetic variants related to other SAIDs and to detect VUS that may help identify patients at risk for atypical and severe manifestations and poor response to conventional therapy.

Published
2024
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20. DNA barcode shows discordant cases among morphological and molecular species identification in Isbrueckerichthys (Siluriformes: Loricariidae)

Author

Rafael B. de Almeida, Matheus Azambuja, Viviane Nogaroto, Claudio Oliveira, Fábio F. Roxo, Cláudio H. Zawadzki, and Marcelo R. Vicari

Subjects
Incipient speciation, Integrative taxonomy, Molecular operational taxonomic units, Molecular species delimitation, Systematics, Zoology, QL1-991
Abstract

Abstract Isbrueckerichthys is a genus of armored catfish (Siluriformes: Loricariidae) with five species in the lowlands from the Ribeira de Iguape basin and in the uplands of the Tibagi River basin. Despite the validation of the morphological species, molecular data to investigate gene flow and species delimitation have not been completed for all species. For this purpose, we compared sequences of COI region associated with barcoding molecular identification, aiming for a species delimitation analysis and generating population data of I. alipionis, I. epakmos, I. duseni, I. cf. duseni, I. saxicola, and I. calvus. The K2P genetic distance, molecular species delimitation analysis, and well-sustained branches in the phylogenetic tree validate I. alipionis, I. epakmos, and I. duseni, and suggest I. cf. duseni as a valid molecular operational taxonomic unit. However, no differences were detected between I. saxicola and I. calvus. The discordance between molecular and morphological species may be due to the recent dispersal of some Isbrueckerichthys representatives at the border between the Ribeira de Iguape and Tibagi basins. The isolation features of the mountainous region of Ribeira de Iguape basin and headwaters captures to uplands are presented to explain the dispersion and the cases of incipient speciation in Isbrueckerichthys lineages.

Published
2024
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26. How to enhance Atlantic Forest protection? Dealing with the shortcomings of successional stages classification

Author

Angélica F. Resende, Felipe Rosafa Gavioli, Rafael B. Chaves, Jean Paul Metzger, Luís Fernando Guedes Pinto, Pedro R. Piffer, Pedro M. Krainovic, Matheus S. Fuza, Ricardo R. Rodrigues, Marcelo Pinho, Catherine T. Almeida, Danilo R.A. Almeida, Paulo G. Molin, Thiago S.F. Silva, and Pedro H.S. Brancalion

Subjects
Tropical forest, Law enforcement, Environmental legislation, Environmental permitting, Offset policies, Ecological succession, Ecology, QH540-549.5, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

The Atlantic Forest is a global biodiversity hotspot and a significant provider of ecosystem services to 65% of the Brazilian population. Due to being highly threatened, it is protected by federal law 11,428/2006, which establishes forest use restrictions based on native vegetation successional stages in the Atlantic Forest, with more advanced stages receiving more protection. The classification parameters are established at the state level. However, the parameters employed to classify forest fragments in different successional stages are subjective and imprecise, negatively impacting environmental permitting and related offset policies. Here, we critically assessed the major limitations in applying the 11,428/2006 law and presented alternatives for establishing a more transparent, applicable, legally safe, and effective protocol for identifying the conservation value of forest fragments. We also highlight problems related to sampling, indicators, and methodologies and present guidelines for revising the parameters for applying the Atlantic Forest law and associated state-level resolutions. We suggest an inclusive two-step analysis based on vegetation structure, forest cover history, biodiversity, ecosystem services (social), and landscape indicators. By employing a more technological approach and transferring part of the assessment responsibility to the state-level environmental agencies instead of allowing self-declared reports by landowners, our proposal focuses on the potential for evaluating ecological integrity among different successional classes by forest types. As nearly 90% of the remaining Brazilian Atlantic Forest is located within private lands, improving this legal instrument is essential for protecting the vulnerable biodiversity of this unique and threatened biome.

Published
2024
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27. Integrable generators of Lie algebras of vector fields on $\mathrm{SL}_2(\mathbb{C})$ and on $xy = z^2$

Author

Andrist, Rafael B.

Subjects
Mathematics - Complex Variables, Mathematics - Algebraic Geometry, 32M17, 32E30, 32M25, 32Q56, 14R10
Abstract

For the special linear group $\mathrm{SL}_2(\mathbb{C})$ and for the singular quadratic Danielewski surface $x y = z^2$ we give explicitly a finite number of complete polynomial vector fields that generate the Lie algebra of all polynomial vector fields on them. Moreover, we give three unipotent one-parameter subgroups that generate a subgroup of algebraic automorphisms acting infinitely transitively on $x y = z^2$.

Published
2022

28. Macroecological links between the Linnean, Wallacean, and Darwinian shortfalls

Author

Diniz Filho, Jose Alexandre F., Jardim, Lucas, Guedes, Jhonny J.M., Meyer, Leila, Stropp, Juliana, Frateles, Livia Estéfane Fernandes, Pinto, Rafael B., Lohmann, Lucía G., Tessarolo, Geiziane, de Carvalho, Claudio J.B., Ladle, Richard J., and Hortal, Joaquin

Subjects
biodiversity bias, Darwinian shortfall, diversity gradients, knowledge shortfalls, latitudinal taxonomy gradient, Linnean shortfall, macroecology, uncertainty, species diversity, Wallacean shortfall
Abstract

Species are the currency of most biodiversity studies. However, many shortfalls and biases remain in our biodiversity estimates, preventing a comprehensive understanding of the eco-evolutionary processes that have shaped the biodiversity currently available on Earth. Biased biodiversity estimates also jeopardize the effective implementation of data-driven conservation strategies, ultimately leading to biodiversity loss. Here, we delve into the concept of the Latitudinal Taxonomy Gradient (LTG) and show how this new idea provides an interesting conceptual link between the Linnean (i.e., our ignorance of how many species there are on Earth), Darwinian (i.e., our ignorance of species evolutionary relationships), and Wallacean (i.e., our ignorance on species distribution) shortfalls. More specifically, we contribute to an improved understanding of LTGs and establish the basis for the development of new methods that allow us to: (i) better account for the integration between different shortfalls and, (ii) estimate how these interactions may affect our understanding about the evolutionary components of richness gradients at macroecological scales.

Published
2023

29. Complexity and phase transitions in citation networks: insights from artificial intelligence research

Author

Ariadne A. Costa and Rafael B. Frigori

Subjects
citation network, artificial intelligence, Shannon entropy, fractal dimension, complex networks, Bibliography. Library science. Information resources
Abstract

In this study, we analyze the changes over time in the complexity and structure of words used in article titles and the connections between articles in citation networks, focusing on the topic of artificial intelligence (AI) up to 2020. By measuring unpredictability in word usage and changes in the connections between articles, we gain insights into shifts in research focus and diversity of themes. Our investigation reveals correspondence between fluctuations in word complexity and changes in the structure of citation networks, highlighting links between thematic evolution and network dynamics. This approach not only enhances our understanding of scientific progress but also may help in anticipating emerging fields and fostering innovation, providing a quantitative lens for studying scientific domains beyond AI.

Published
2024
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30. Catálogo Taxonômico da Fauna do Brasil: Setting the baseline knowledge on the animal diversity in Brazil

Author

Walter A. Boeger, Michel P. Valim, Hussam Zaher, José A. Rafael, Rafaela C. Forzza, Alexandre R. Percequillo, Cristiana S. Serejo, André R.S. Garraffoni, Adalberto J. Santos, Adam Slipinski, Adelita M. Linzmeier, Adolfo R. Calor, Adrian A. Garda, Adriano B. Kury, Agatha C.S. Fernandes, Aisur I. Agudo-Padrón, Alberto Akama, Alberto M. da Silva Neto, Alejandro L. Burbano, Aleksandra Menezes, Alessandre Pereira-Colavite, Alexander Anichtchenko, Alexander C. Lees, Alexandra M.R. Bezerra, Alexandre C. Domahovski, Alexandre D. Pimenta, Alexandre L.P. Aleixo, Alexandre P. Marceniuk, Alexandre S. de Paula, Alexandre Somavilla, Alexandre Specht, Alexssandro Camargo, Alfred F. Newton, Aline A.S. da Silva, Aline B. dos Santos, Aline D. Tassi, Allan C. Aragão, Allan P.M. Santos, Alvaro E. Migotto, Amanda C. Mendes, Amanda Cunha, Amazonas Chagas Júnior, Ana A.T. de Sousa, Ana C. Pavan, Ana C.S. Almeida, Ana L.B.G. Peronti, Ana L. Henriques-Oliveira, Ana L. Prudente, Ana L. Tourinho, Ana M.O. Pes, Ana P. Carmignotto, Ana P.G. da Silva Wengrat, Ana P.S. Dornellas, Anamaria Dal Molin, Anderson Puker, André C. Morandini, André da S. Ferreira, André L. Martins, André M. Esteves, André S. Fernandes, André S. Roza, Andreas Köhler, Andressa Paladini, Andrey J. de Andrade, Ângelo P. Pinto, Anna C. de A. Salles, Anne I. Gondim, Antonia C.Z. Amaral, Antonio A.A. Rondón, Antonio Brescovit, Antônio C. Lofego, Antonio C. Marques, Antonio Macedo, Artur Andriolo, Augusto L. Henriques, Augusto L. Ferreira Júnior, Aurino F. de Lima, Ávyla R. de A. Barros, Ayrton do R. Brito, Bárbara L.V. Romera, Beatriz M.C. de Vasconcelos, Benjamin W. Frable, Bernardo F. Santos, Bernardo R. Ferraz, Brunno B. Rosa, Brunno H.L. Sampaio, Bruno C. Bellini, Bruno Clarkson, Bruno G. de Oliveira, Caio C.D. Corrêa, Caleb C. Martins, Camila F. de Castro-Guedes, Camilla Souto, Carla de L. Bicho, Carlo M. Cunha, Carlos A. de M. Barboza, Carlos A.S. de Lucena, Carlos Barreto, Carlos D.C.M. de Santana, Carlos E.Q. Agne, Carlos G.C. Mielke, Carlos H.S. Caetano, Carlos H.W. Flechtmann, Carlos J.E. Lamas, Carlos Rocha, Carolina S. Mascarenhas, Cecilia B. Margaría, Cecilia Waichert, Celina Digiani, Célio F.B. Haddad, Celso O. Azevedo, Cesar J. Benetti, Charles M.D. dos Santos, Charles R. Bartlett, Cibele Bonvicino, Cibele S. Ribeiro-Costa, Cinthya S.G. Santos, Cíntia E.L. Justino, Clarissa Canedo, Claudia C. Bonecker, Cláudia P. Santos, Claudio J.B. de Carvalho, Clayton C. Gonçalves, Cleber Galvão, Cleide Costa, Cléo D.C. de Oliveira, Cristiano F. Schwertner, Cristiano L. Andrade, Cristiano M. Pereira, Cristiano Sampaio, Cristina de O. Dias, Daercio A. de A. Lucena, Daiara Manfio, Dalton de S. Amorim, Dalva L. de Queiroz, Daniara Colpani, Daniel Abbate, Daniel A. Aquino, Daniel Burckhardt, Daniel C. Cavallari, Daniel de C. Schelesky Prado, Daniel L. Praciano, Daniel S. Basílio, Daniela de C. Bená, Daniela G.P. de Toledo, Daniela M. Takiya, Daniell R.R. Fernandes, Danilo C. Ament, Danilo P. Cordeiro, Darliane E. Silva, Darren A. Pollock, David B. Muniz, David I. Gibson, David S. Nogueira, Dayse W.A. Marques, Débora Lucatelli, Deivys M.A. Garcia, Délio Baêta, Denise N.M. Ferreira, Diana Rueda-Ramírez, Diego A. Fachin, Diego de S. Souza, Diego F. Rodrigues, Diego G. de Pádua, Diego N. Barbosa, Diego R. Dolibaina, Diogo C. Amaral, Donald S. Chandler, Douglas H.B. Maccagnan, Edilson Caron, Edrielly Carvalho, Edson A. Adriano, Edson F. de Abreu Júnior, Edson H.L. Pereira, Eduarda F.G. Viegas, Eduardo Carneiro, Eduardo Colley, Eduardo Eizirik, Eduardo F. dos Santos, Eduardo M. Shimbori, Eduardo Suárez-Morales, Eliane P. de Arruda, Elisandra A. Chiquito, Élison F.B. Lima, Elizeu B. de Castro, Elton Orlandin, Elynton A. do Nascimento, Emanuel Razzolini, Emanuel R.R. Gama, Enilma M. de Araujo, Eric Y. Nishiyama, Erich L. Spiessberger, Érika C.L. dos Santos, Eugenia F. Contreras, Eunice A.B. Galati, Evaldo C. de Oliveira Junior, Fabiana Gallardo, Fabio A. Hernandes, Fábio A. Lansac-Tôha, Fabio B. Pitombo, Fabio Di Dario, Fábio L. dos Santos, Fabio Mauro, Fabio O. do Nascimento, Fabio Olmos, Fabio R. Amaral, Fabio Schunck, Fábio S. P. de Godoi, Fabrizio M. Machado, Fausto E. Barbo, Federico A. Agrain, Felipe B. Ribeiro, Felipe F.F. Moreira, Felipe F. Barbosa, Fenanda S. Silva, Fernanda F. Cavalcanti, Fernando C. Straube, Fernando Carbayo, Fernando Carvalho Filho, Fernando C.V. Zanella, Fernando de C. Jacinavicius, Fernando H.A. Farache, Fernando Leivas, Fernando M.S. Dias, Fernando Mantellato, Fernando Z. Vaz-de-Mello, Filipe M. Gudin, Flávio Albuquerque, Flavio B. Molina, Flávio D. Passos, Floyd W. Shockley, Francielly F. Pinheiro, Francisco de A.G. de Mello, Francisco E. de L. Nascimento, Francisco L. Franco, Francisco L. de Oliveira, Francisco T. de V. Melo, Freddy R.B. Quijano, Frederico F. Salles, Gabriel Biffi, Gabriel C. Queiroz, Gabriel L. Bizarro, Gabriela Hrycyna, Gabriela Leviski, Gareth S. Powell, Geane B. dos Santos, Geoffrey E. Morse, George Brown, George M.T. Mattox, Geraldo Zimbrão, Gervásio S. Carvalho, Gil F.G. Miranda, Gilberto J. de Moraes, Gilcélia M. Lourido, Gilmar P. Neves, Gilson R.P. Moreira, Giovanna G. Montingelli, Giovanni N. Maurício, Gláucia Marconato, Guilherme E.L. Lopez, Guilherme L. da Silva, Guilherme Muricy, Guilherme R.R. Brito, Guilherme S.T. Garbino, Gustavo E. Flores, Gustavo Graciolli, Gustavo S. Libardi, Heather C. Proctor, Helcio R. Gil-Santana, Henrique R. Varella, Hermes E. Escalona, Hermes J. Schmitz, Higor D.D. Rodrigues, Hilton de C. Galvão Filho, Hingrid Y.S. Quintino, Hudson A. Pinto, Hugo L. Rainho, Igor C. Miyahira, Igor de S. Gonçalves, Inês X. Martins, Irene A. Cardoso, Ismael B. de Oliveira, Ismael Franz, Itanna O. Fernandes, Ivan F. Golfetti, Ivanklin S. Campos-Filho, Ivo de S. Oliveira, Jacques H.C. Delabie, Jader de Oliveira, Jadila S. Prando, James L. Patton, Jamille de A. Bitencourt, Janaina M. Silva, Jandir C. Santos, Janine O. Arruda, Jefferson S. Valderrama, Jeronymo Dalapicolla, Jéssica P. Oliveira, Jiri Hájek, João P. Morselli, João P. Narita, João P.I. Martin, Jocélia Grazia, Joe McHugh, Jorge J. Cherem, José A.S. Farias Júnior, Jose A.M. Fernandes, José F. Pacheco, José L.O. Birindelli, José M. Rezende, Jose M. Avendaño, José M. Barbanti Duarte, José R. Inácio Ribeiro, José R.M. Mermudes, José R. Pujol-Luz, Josenilson R. dos Santos, Josenir T. Câmara, Joyce A. Teixeira, Joyce R. do Prado, Juan P. Botero, Julia C. Almeida, Julia Kohler, Julia P. Gonçalves, Julia S. Beneti, Julian P. Donahue, Juliana Alvim, Juliana C. Almeida, Juliana L. Segadilha, Juliana M. Wingert, Julianna F. Barbosa, Juliano Ferrer, Juliano F. dos Santos, Kamila M.D. Kuabara, Karine B. Nascimento, Karine Schoeninger, Karla M. Campião, Karla Soares, Kássia Zilch, Kim R. Barão, Larissa Teixeira, Laura D. do N.M. de Sousa, Leandro L. Dumas, Leandro M. Vieira, Leonardo H.G. Azevedo, Leonardo S. Carvalho, Leonardo S. de Souza, Leonardo S.G. Rocha, Leopoldo F.O. Bernardi, Letícia M. Vieira, Liana Johann, Lidianne Salvatierra, Livia de M. Oliveira, Lourdes M.A. El-moor Loureiro, Luana B. Barreto, Luana M. Barros, Lucas Lecci, Lucas M. de Camargos, Lucas R.C. Lima, Lucia M. Almeida, Luciana R. Martins, Luciane Marinoni, Luciano de A. Moura, Luciano Lima, Luciano N. Naka, Lucília S. Miranda, Lucy M. Salik, Luis E.A. Bezerra, Luis F. Silveira, Luiz A. Campos, Luiz A.S. de Castro, Luiz C. Pinho, Luiz F.L. Silveira, Luiz F.M. Iniesta, Luiz F.C. Tencatt, Luiz R.L. Simone, Luiz R. Malabarba, Luiza S. da Cruz, Lukas Sekerka, Lurdiana D. Barros, Luziany Q. Santos, Maciej Skoracki, Maira A. Correia, Manoel A. Uchoa, Manuella F.G. Andrade, Marcel G. Hermes, Marcel S. Miranda, Marcel S. de Araújo, Marcela L. Monné, Marcelo B. Labruna, Marcelo D. de Santis, Marcelo Duarte, Marcelo Knoff, Marcelo Nogueira, Marcelo R. de Britto, Marcelo R.S. de Melo, Marcelo R. de Carvalho, Marcelo T. Tavares, Marcelo V. Kitahara, Marcia C.N. Justo, Marcia J.C. Botelho, Márcia S. Couri, Márcio Borges-Martins, Márcio Felix, Marcio L. de Oliveira, Marco A. Bologna, Marco S. Gottschalk, Marcos D.S. Tavares, Marcos G. Lhano, Marcus Bevilaqua, Marcus T.T. Santos, Marcus V. Domingues, Maria A.M. Sallum, María C. Digiani, Maria C.A. Santarém, Maria C. do Nascimento, María de los A.M. Becerril, Maria E.A. dos Santos, Maria I. da S. dos Passos, Maria L. Felippe-Bauer, Mariana A. Cherman, Mariana Terossi, Marie L.C. Bartz, Marina F. de C. Barbosa, Marina V. Loeb, Mario Cohn-Haft, Mario Cupello, Marlúcia B. Martins, Martin L. Christofersen, Matheus Bento, Matheus dos S. Rocha, Maurício L. Martins, Melissa O. Segura, Melissa Q. Cardenas, Mércia E. Duarte, Michael A. Ivie, Michael M. Mincarone, Michela Borges, Miguel A. Monné, Mirna M. Casagrande, Monica A. Fernandez, Mônica Piovesan, Naércio A. Menezes, Natalia P. Benaim, Natália S. Reategui, Natan C. Pedro, Nathalia H. Pecly, Nelson Ferreira Júnior, Nelson J. da Silva Júnior, Nelson W. Perioto, Neusa Hamada, Nicolas Degallier, Ning L. Chao, Noeli J. Ferla, Olaf H.H. Mielke, Olivia Evangelista, Oscar A. Shibatta, Otto M.P. Oliveira, Pablo C.L. Albornoz, Pablo M. Dellapé, Pablo R. Gonçalves, Paloma H.F. Shimabukuro, Paschoal Grossi, Patrícia E. da S. Rodrigues, Patricia O.V. Lima, Paul Velazco, Paula B. dos Santos, Paula B. Araújo, Paula K.R. Silva, Paula R. Riccardi, Paulo C. de A. Garcia, Paulo G.H. Passos, Paulo H.C. Corgosinho, Paulo Lucinda, Paulo M.S. Costa, Paulo P. Alves, Paulo R. de O. Roth, Paulo R.S. Coelho, Paulo R.M. Duarte, Pedro F. de Carvalho, Pedro Gnaspini, Pedro G.B. Souza-Dias, Pedro M. Linardi, Pedro R. Bartholomay, Peterson R. Demite, Petr Bulirsch, Piter K. Boll, Rachel M.M. Pereira, Rafael A.P.F. Silva, Rafael B. de Moura, Rafael Boldrini, Rafaela A. da Silva, Rafaela L. Falaschi, Ralf T.S. Cordeiro, Ramon J.C.L. Mello, Randal A. Singer, Ranyse B. Querino, Raphael A. Heleodoro, Raphael de C. Castilho, Reginaldo Constantino, Reinaldo C. Guedes, Renan Carrenho, Renata S. Gomes, Renato Gregorin, Renato J.P. Machado, Renato S. Bérnils, Renato S. Capellari, Ricardo B. Silva, Ricardo Kawada, Ricardo M. Dias, Ricardo Siewert, Ricaro Brugnera, Richard A.B. Leschen, Robert Constantin, Robert Robbins, Roberta R. Pinto, Roberto E. dos Reis, Robson T. da C. Ramos, Rodney R. Cavichioli, Rodolfo C. de Barros, Rodrigo A. Caires, Rodrigo B. Salvador, Rodrigo C. Marques, Rodrigo C. Araújo, Rodrigo de O. Araujo, Rodrigo de V.P. Dios, Rodrigo Johnsson, Rodrigo M. Feitosa, Roger W. Hutchings, Rogéria I.R. Lara, Rogério V. Rossi, Roland Gerstmeier, Ronald Ochoa, Rosa S.G. Hutchings, Rosaly Ale-Rocha, Rosana M. da Rocha, Rosana Tidon, Rosangela Brito, Roseli Pellens, Sabrina R. dos Santos, Sandra D. dos Santos, Sandra V. Paiva, Sandro Santos, Sarah S. de Oliveira, Sávio C. Costa, Scott L. Gardner, Sebastián A. Muñoz Leal, Sergio Aloquio, Sergio L.C. Bonecker, Sergio L. de S. Bueno, Sérgio M. de Almeida, Sérgio N. Stampar, Sérgio R. Andena, Sergio R. Posso, Sheila P. Lima, Sian de S. Gadelha, Silvana C. Thiengo, Simone C. Cohen, Simone N. Brandão, Simone P. Rosa, Síria L.B. Ribeiro, Sócrates D. Letana, Sonia B. dos Santos, Sonia C.S. Andrade, Stephane Dávila, Stéphanie Vaz, Stewart B. Peck, Susete W. Christo, Suzan B.Z. Cunha, Suzete R. Gomes, Tácio Duarte, Taís Madeira-Ott, Taísa Marques, Talita Roell, Tarcilla C. de Lima, Tatiana A. Sepulveda, Tatiana F. Maria, Tatiana P. Ruschel, Thaiana Rodrigues, Thais A. Marinho, Thaís M. de Almeida, Thaís P. Miranda, Thales R.O. Freitas, Thalles P.L. Pereira, Thamara Zacca, Thaynara L. Pacheco, Thiago F. Martins, Thiago M. Alvarenga, Thiago R. de Carvalho, Thiago T.S. Polizei, Thomas C. McElrath, Thomas Henry, Tiago G. Pikart, Tiago J. Porto, Tiago K. Krolow, Tiago P. Carvalho, Tito M. da C. Lotufo, Ulisses Caramaschi, Ulisses dos S. Pinheiro, Ulyses F.J. Pardiñas, Valéria C. Maia, Valeria Tavares, Valmir A. Costa, Vanessa S. do Amaral, Vera C. Silva, Vera R. dos S. Wolff, Verônica Slobodian, Vinícius B. da Silva, Vinicius C. Espíndola, Vinicius da Costa-Silva, Vinicius de A. Bertaco, Vinícius Padula, Vinicius S. Ferreira, Vitor C.P. da Silva, Vítor de Q. Piacentini, Vivian E. Sandoval-Gómez, Vivian Trevine, Viviane R. Sousa, Vivianne B. de Sant’Anna, Wayne N. Mathis, Wesley de O. Souza, Wesley D. Colombo, Wioletta Tomaszewska, Wolmar B. Wosiacki, Ximena M.C. Ovando, and Yuri L.R. Leite

Subjects
Biodiversity, knowledge management, taxonomy, web services, zoology, Zoology, QL1-991
Abstract

ABSTRACT The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classifications. In this context, the Brazilian megadiverse fauna is no exception, and the Catálogo Taxonômico da Fauna do Brasil (CTFB) (http://fauna.jbrj.gov.br/), made public in 2015, represents a database on biodiversity anchored on a list of valid and expertly recognized scientific names of animals in Brazil. The CTFB is updated in near real time by a team of more than 800 specialists. By January 1, 2024, the CTFB compiled 133,691 nominal species, with 125,138 that were considered valid. Most of the valid species were arthropods (82.3%, with more than 102,000 species) and chordates (7.69%, with over 11,000 species). These taxa were followed by a cluster composed of Mollusca (3,567 species), Platyhelminthes (2,292 species), Annelida (1,833 species), and Nematoda (1,447 species). All remaining groups had less than 1,000 species reported in Brazil, with Cnidaria (831 species), Porifera (628 species), Rotifera (606 species), and Bryozoa (520 species) representing those with more than 500 species. Analysis of the CTFB database can facilitate and direct efforts towards the discovery of new species in Brazil, but it is also fundamental in providing the best available list of valid nominal species to users, including those in science, health, conservation efforts, and any initiative involving animals. The importance of the CTFB is evidenced by the elevated number of citations in the scientific literature in diverse areas of biology, law, anthropology, education, forensic science, and veterinary science, among others.

Published
2024
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31. A review on the diversity and distribution of athecate dinoflagellates in South Atlantic and in the Atlantic sector of the Southern Ocean: Research insights and gaps

Author

CHARIANE CAMILA WERLANG, MÁRCIO S. DE SOUZA, and CARLOS RAFAEL B. MENDES

Subjects
Antarctic, ecology, distribution, review, Science
Abstract

Abstract This review summarizes the state of knowledge on athecate dinoflagellates occurring within the South Atlantic Ocean and Atlantic sector of the Southern Ocean. We compiled data from 105 articles and selected 33 addressing any aspect of athecate dinoflagellate studies. Our aim is to discuss the patterns in athecate dinoflagellate distribution by building a thorough species list and an occurrence map based on species recorded in coastal and oceanic waters. We found 69 species totaling 141 occurrences in the entire South Atlantic Ocean basin. Contradicting global trends, most species distributed throughout this region are subtropical. We linked this trend to a higher local effort in dinoflagellate research instead of higher biodiversity, especially when compared to usual hotspots in biodiversity attributed to tropical oceans. The Subantarctic and Antarctic regions had a low number of occurrences, with 12 and 5, respectively. Except for the occurrence of Gyrodinium lachryma in the Antarctic Zone, all records are unique, poorly described and never recorded again for species such as Gymnodinium baccatum and Gymnodinium antarcticum. This demonstrates that the state of knowledge regarding athecate dinoflagellates in the South Atlantic and especially in the Antarctic region is still limited due to a lack of directed investigation.

Published
2024
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32. On the Evolution of A.I. and Machine Learning: Towards a Meta-level Measuring and Understanding Impact, Influence, and Leadership at Premier A.I. Conferences

Author

Audibert, Rafael B., Lemos, Henrique, Avelar, Pedro, Tavares, Anderson R., and Lamb, Luís C.

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computers and Society, Computer Science - Machine Learning, I.2.0, I.2.6, K.1, K.2, K.4
Abstract

Artificial Intelligence is now recognized as a general-purpose technology with ample impact on human life. This work aims at understanding the evolution of AI and, in particular Machine learning, from the perspective of researchers' contributions to the field. In order to do so, we present several measures allowing the analyses of AI and machine learning researchers' impact, influence, and leadership over the last decades. This work also contributes, to a certain extent, to shed new light on the history and evolution of AI by exploring the dynamics involved in the field's evolution by looking at papers published at the flagship AI and machine learning conferences since the first International Joint Conference on Artificial Intelligence (IJCAI) held in 1969. AI development and evolution have led to increasing research output, reflected in the number of articles published over the last sixty years. We construct comprehensive citation collaboration and paper-author datasets and compute corresponding centrality measures to carry out our analyses. These analyses allow a better understanding of how AI has reached its current state of affairs in research. Throughout the process, we correlate these datasets with the work of the ACM Turing Award winners and the so-called two AI winters the field has gone through. We also look at self-citation trends and new authors' behaviors. Finally, we present a novel way to infer the country of affiliation of a paper from its organization. Therefore, this work provides a deep analysis of Artificial Intelligence history from information gathered and analysed from large technical venues datasets and suggests novel insights that can contribute to understanding and measuring AI's evolution., Comment: 125 pages, 57 figures, 11 tables. Published in The Journal of Applied Logics - IFCoLog Journal of Logics and their Applications

Published
2022

33. The Brazilian Data at Risk in the Age of AI?

Author

Teixeira, Raoni F. da S., Januzi, Rafael B., and Faria, Fabio A.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Cryptography and Security
Abstract

Advances in image processing and analysis as well as machine learning techniques have contributed to the use of biometric recognition systems in daily people tasks. These tasks range from simple access to mobile devices to tagging friends in photos shared on social networks and complex financial operations on self-service devices for banking transactions. In China, the use of these systems goes beyond personal use becoming a country's government policy with the objective of monitoring the behavior of its population. On July 05th 2021, the Brazilian government announced acquisition of a biometric recognition system to be used nationwide. In the opposite direction to China, Europe and some American cities have already started the discussion about the legality of using biometric systems in public places, even banning this practice in their territory. In order to open a deeper discussion about the risks and legality of using these systems, this work exposes the vulnerabilities of biometric recognition systems, focusing its efforts on the face modality. Furthermore, it shows how it is possible to fool a biometric system through a well-known presentation attack approach in the literature called morphing. Finally, a list of ten concerns was created to start the discussion about the security of citizen data and data privacy law in the Age of Artificial Intelligence (AI)., Comment: 8 pages in Portuguese and 5 figures, Top 3 among the best papers at the ENIAC 2022

Published
2022

34. Logical coherence in Bayesian simultaneous three-way hypothesis tests

Author

Reimann, Bernardo F., Izbicki, Rafael, Stern, Julio M., Stern, Rafael B., and Esteves, Luis G.

Subjects
Mathematics - Statistics Theory, 62C10
Abstract

This paper studies whether Bayesian simultaneous three-way hypothesis tests can be logically coherent. Two types of results are obtained. First, under the standard error-wise constant loss, only for a limited set of models can a Bayes simultaneous test be logically coherent. Second, if more general loss functions are used, then it is possible to obtain Bayes simultaneous tests that are always logically coherent. An explicit example of such a loss function is provided., Comment: 19 pages, 1 figure

Published
2022

35. Ecosystem restoration job creation potential in Brazil

Author

Brancalion, Pedro HS, de Siqueira, Ludmila Pugliese, Amazonas, Nino T, Rizek, Mayte B, Mendes, Alex F, Santiami, Edson L, Rodrigues, Ricardo Ribeiro, Calmon, Miguel, Benini, Rubens, Tymus, Julio RC, Holl, Karen D, and Chaves, Rafael B

Subjects
Environmental Sciences, Environmental Management, Behavioral and Social Science, Decent Work and Economic Growth, ecological restoration, forest restoration, green economy, green jobs, large-scale restoration, restoration economy, restoration socioeconomics, sustainable development
Abstract

Abstract: The central motivation to restore ecosystems at a planetary scale has been to reverse degradation and provide multiple environmental benefits, but key global players like governments may be more interested in social outcomes from undertaking restoration, such as job creation. Assessing the job opportunities stemming from ongoing restoration programmes can leverage additional investments for their implementation and support their long‐term maintenance. Here, we aimed to understand and quantify current and potential ecosystem restoration jobs in Brazil, based on a widely distributed online survey performed in 2020 and led by the main restoration networks in the country. We explored the structure, job distribution and outputs of the national restoration supply chain. At the beginning of 2020, 4713 temporary and 3510 permanent jobs were created, nearly 60% of which were generated by organizations specialized in restoration, mainly from the non‐profit (48%) and private (37%) sectors. Restoration jobs were concentrated in organizations working in one (58%) or two (28%) biomes, and the vast majority were in the Atlantic Forest (85%). Similarly, most restoration jobs were concentrated in the southeast region (61%), with one‐third in the state of São Paulo. This geographical distribution was more strongly associated with the states' GDP than with the legal deficit of native vegetation area. Nearly 20% of the restoration jobs were terminated during the COVID‐19 pandemic in 2020. We estimate that restoration activities can generate 0.42 jobs per hectare undergoing restoration, which could potentially create 1.0–2.5 million direct jobs through the implementation of Brazil's target of restoring 12 million hectares. We conclude by reinforcing the value of ecosystem restoration in promoting economic development and job creation, which can be crucial to promote countries' effective engagement in the UN Decade on Ecosystem Restoration. We also highlight the critical role of grassroots organizations to maximize restoration opportunities for socioeconomic development during the post‐pandemic economic recovery. Read the free Plain Language Summary for this article on the Journal blog.

Published
2022

39. Subcutaneous vs intravenous abatacept in rheumatoid arthritis-interstitial lung disease. National multicentre study of 397 patients

Author

López-Maraver, Marta, Serrano-Combarro, Ana, Atienza-Mateo, Belén, del Val, Natividad, Casafont-Solé, Ivette, Melero-Gonzalez, Rafael B., Pérez-Linaza, Alba, Calvo Gutiérrez, Jerusalem, Mena-Vázquez, Natalia, Vegas-Revenga, Nuria, Domínguez-Casas, Lucía, Loarce Martos, Jesús, Peralta Ginés, Cilia Amparo, Diez Morrondo, Carolina, Pérez Albaladejo, Lorena, López Sánchez, Rubén, Manzano Canabal, Mª Guadalupe, Brandy-García, Anahy Mª, López Viejo, Patricia, Bonilla, Gema, Maiz-Alonso, Olga, Carrasco-Cubero, Carmen, Garijo Bufort, Marta, Moreno, Mireia, Urruticoechea-Arana, Ana, Ordóñez-Palau, Sergio, González-Montagut, Carmen, Giner Serret, Emilio, De Dios Jiménez De Aberasturi, Juan Ramón, Lozano Morillo, Fernando, Vázquez Rodríguez, Tomás, Carreira, Patricia E, Blanco Madrigal, Juan María, Miguel Ibáñez, Belén, Rodríguez López, Marina, Fernández-Díaz, Carlos, Loricera, Javier, Ferraz-Amaro, Iván, Ferrer-Pargada, Diego, Castañeda, Santos, and Blanco, Ricardo

Published
2024
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43. Tame sets in homogeneous spaces

Author

Andrist, Rafael B. and Ugolini, Riccardo

Subjects
Mathematics - Complex Variables, Mathematics - Algebraic Geometry, 32M05, 32Q56
Abstract

We prove the existence of strongly tame sets in affine algebraic homogenenous spaces of linear algebraic Lie groups. We also show that $(\mathbb{C}^n,A)$ for a discrete tame set enjoy the relative density property, and we provide examples of Stein manifolds admitting non-equivalent tame sets.

Published
2022
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44. Virtual vs. Reality: External Validation of COVID-19 Classifiers using XCAT Phantoms for Chest Computed Tomography

Author

Tushar, Fakrul Islam, Abadi, Ehsan, Sotoudeh-Paima, Saman, Fricks, Rafael B., Mazurowski, Maciej A., Segars, W. Paul, Samei, Ehsan, and Lo, Joseph Y.

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Computer Science - Neural and Evolutionary Computing
Abstract

Research studies of artificial intelligence models in medical imaging have been hampered by poor generalization. This problem has been especially concerning over the last year with numerous applications of deep learning for COVID-19 diagnosis. Virtual imaging trials (VITs) could provide a solution for objective evaluation of these models. In this work utilizing the VITs, we created the CVIT-COVID dataset including 180 virtually imaged computed tomography (CT) images from simulated COVID-19 and normal phantom models under different COVID-19 morphology and imaging properties. We evaluated the performance of an open-source, deep-learning model from the University of Waterloo trained with multi-institutional data and an in-house model trained with the open clinical dataset called MosMed. We further validated the model's performance against open clinical data of 305 CT images to understand virtual vs. real clinical data performance. The open-source model was published with nearly perfect performance on the original Waterloo dataset but showed a consistent performance drop in external testing on another clinical dataset (AUC=0.77) and our simulated CVIT-COVID dataset (AUC=0.55). The in-house model achieved an AUC of 0.87 while testing on the internal test set (MosMed test set). However, performance dropped to an AUC of 0.65 and 0.69 when evaluated on clinical and our simulated CVIT-COVID dataset. The VIT framework offered control over imaging conditions, allowing us to show there was no change in performance as CT exposure was changed from 28.5 to 57 mAs. The VIT framework also provided voxel-level ground truth, revealing that performance of in-house model was much higher at AUC=0.87 for diffuse COVID-19 infection size >2.65% lung volume versus AUC=0.52 for focal disease with <2.65% volume. The virtual imaging framework enabled these uniquely rigorous analyses of model performance., Comment: 7 pages, 5 figures, 2 tables, presented at the Medical Imaging 2022: Computer-Aided Diagnosis, 2022

Published
2022

45. Hierarchical clustering: visualization, feature importance and model selection

Author

Cabezas, Luben M. C., Izbicki, Rafael, and Stern, Rafael B.

Subjects
Statistics - Methodology, Computer Science - Machine Learning, I.5.3
Abstract

We propose methods for the analysis of hierarchical clustering that fully use the multi-resolution structure provided by a dendrogram. Specifically, we propose a loss for choosing between clustering methods, a feature importance score and a graphical tool for visualizing the segmentation of features in a dendrogram. Current approaches to these tasks lead to loss of information since they require the user to generate a single partition of the instances by cutting the dendrogram at a specified level. Our proposed methods, instead, use the full structure of the dendrogram. The key insight behind the proposed methods is to view a dendrogram as a phylogeny. This analogy permits the assignment of a feature value to each internal node of a tree through an evolutionary model. Real and simulated datasets provide evidence that our proposed framework has desirable outcomes and gives more insights than state-of-art approaches. We provide an R package that implements our methods., Comment: 29 pages, 9 figures, 3 tables

Published
2021

47. The experience of pregnant women and their families who were infected with covid-19 before vaccination: A qualitative approach within a multicenter study in Brazil

Author

Metelus, Sherly, Castro, Lester, Pabon, Stephanie, Silva, Amanda D, Junior, Paulo S R, Sardinha, Thais G, Japenga, Rodolfo R, Urquiza, Erica R F, Machado, Maíra R, Simões, Marcela Maria, Solda, Larissa M, Yazaki-Sun, Sue, Mota, Priscilla, Soares, Arimaza C, Machado, Ellen, Bergmann, Anne, Raupp dos Santos, Gustavo, Peres, Patrícia B, Arbeli, Cristiane L, Quevedo, Rafael M, Yamashita, Carolina F, Corradin, Julia D, Bergamini, Isabella, Ramos, José Geraldo L, Oppermann, Maria Lúcia R, Quadro, Laisa S, Marins, Lina, Paniz, Érika V, Xavier, Thaís Vicentini, Parreira, Bruna E, Tosetto, Aline, Savazoni, Sabrina, Costa, Aline C, Almeida, Marina HL, Moura, Bruna FV, França, Lidiane R, Vieira, Hanna, Aquino, Rafael B, Leite, Débora F, Monteiro, Isabella, Nakamura-Pereira, Marcos, Guerra, Bruna O, Gorga, Gabriela, Pinheiro, Daisy, Cordeiro, Denise, Miná, Priscila L, Dornellas, Carol, Oliveira, Kevin FA, Makyama, Mariana Emi Varicoda, Leal, Caio, Amana, Rayra, Santos, Cristiane O, dos Santos, Marina M, Neto, Carlos, Gomes, Thiago, Pereira, Isabela R, Salustrino, Clélia Andrade, Pontes, Valéria B, Franco, Roberto Allen da Silva, Bilibio, João Paolo, Brito, Gislânia P F, Pinto, Hana Paula C, de Oliveira, Danielle Leal, Guerra, Andrezza A, Moura, Andrea O, Pantoja, Natasha, David, Fernanda, Silva, Alina, Bacha, Angela M, Borovac-Pinheiro, Anderson, Pereira, Belmiro G, Amaral, Eliana M, Ferreira, Elton, Milanez, Helaine MBPM, Caldas, Jamil P S, Baccaro, Luiz F, Nomura, Marcelo, Rehder, Patrícia M, Simone, Renata Z, Passini, Renato, Jr, Torrezan, Cristiano, Modena, João L P, Nunes dos Santos, Magnun N, Marba, Sergio T M, Zumpano dos Santos, Tábata R, Soeiro, Rachel E, Souza, Renato T, Bento, Silvana F, Cecatti, Jose G, Surita, Fernanda G, Freitas-Jesus, Juliana Vasconcellos, Pacagnella, Rodolfo C, Ribeiro-Do-Valle, Carolina C, Luz, Adriana G, Lajos, Giuliane J, Nobrega, Guilherme M, Griggio, Thayna B, Charles, Charles M, Silveira, Carla, Miele, Maria J, Tedesco, Ricardo P, Fernandes, Karayna G, Martins-Costa, Sérgio HA, Peret, Frederico JA, Feitosa, Francisco E, Traina, Evelyn, Cunha Filho, Edson V, Vettorazzi, Janete, Haddad, Samira M, Andreucci, Carla B, Guida, José P, Correa Junior, Mario D, Dias, Marcos AB, Oliveira, Leandro G, Melo Junior, Elias F, Luz, Marília GQ DA, and Costa, Maria Laura

Published
2024
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49. Impact of quality and transparency in scientific writing on the reduction of animal usage in experimental protocols: a review based in pertinent literature

Author

Matheus M. Neves, Sandra G. Klein, Ray C. Silva, Lucas M. M. Bernardes, Serena M. Malta, Thiago N. Vieira, Rafael B. Rosa, Isabela L. Lima, Flávia B. Ferreira, and Murilo V. Silva

Subjects
laboratory animal science, data reproducibility, 3R’s, scientific writing, animal models, Veterinary medicine, SF600-1100
Abstract

The irreproducibility in scientific research has become a critical issue. Despite the essential role of rigorous methodology in constructing a scientific article, more than half of publications, on average, are considered non-reproducible. The implications of this irreproducibility extend to reliability problems, hindering progress in technological production and resulting in substantial financial losses. In the context of laboratory animal research, this work emphasizes the importance of choosing an appropriate experimental model within the 3R’s principle (Refine, Reduce, Replace). This study specifically addresses a deficiency in data specification in scientific articles, revealing inadequacies in the description of crucial details, such as environmental conditions, diet, and experimental procedures. For this purpose, 124 articles from journals with relevant impact factors were analyzed, conducting a survey of data considered important for the reproducibility of studies. Important flaws in the presentation of data were identified in most of the articles evaluated. The results of this study highlight the need to improve the description of essential information, standardizing studies, and ensuring the reproducibility of experiments in areas such as metabolism, immunity, hormones, stress, among others, to enhance the reliability and reproduction of experimental results, aligning with international guidelines such as ARRIVE and PREPARE.

Published
2024
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50. Distribution pattern in the rupiculous genus Orthophytum (Bromelioideae/Bromeliaceae) reveals high microendemicity in different types of rocky outcrops

Author

SWAMI L. COSTA, RAFAEL B. LOUZADA, SILMARA CECÍLIA NEPOMUCENO, JOILSON V. ALVES, and MARIA TERESA BURIL

Subjects
Bromelioideae, Areas of Endemism, Rocky outcrops, Microendemism, PAE, Poales, Science
Abstract

Abstract This study aimed to recognize the biogeographic patterns, richness, and diversity levels of the Brazilian endemic genus Orthophytum and identify their biotic components through a parsimony analysis of endemicity (PAE), to better understand the evolutionary history of this group and develop strategies for the conservation of its species. We prepared a database for the 54 currently known species of Orthophytum, including their geographical locations as obtained from digital databases of the principal herbaria of Brazil, Europe, and the USA. A parsimony analysis of endemicity (PAE) was used to delimit the areas of endemism based on two grids’ sizes (1º x 1º and 2º × 2º). The majority rule consensus tree resulting from the PAE indicated three areas of endemism with high bootstrap, diversity, and richness indices: the northern portion of the Espinhaço Range, the southern portion of the Espinhaço Range, and the central portion of the Atlantic Forest. The recognition of those distribution patterns reveals a high number of microendemic species, which is discussed here.

Published
2024
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