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Intermediate representations in Computational Science for knowledge discovery

Grant number: 15/22308-2
Support type:Research Projects - Thematic Grants
Duration: November 01, 2017 - October 31, 2023
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
Principal researcher:Roberto Marcondes Cesar Junior
Grantee:Roberto Marcondes Cesar Junior
Home Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Pesquisadores principais:
Carlos Alberto Moreira Filho ; Luciano da Fontoura Costa ; Nina Sumiko Tomita Hirata ; Ronaldo Fumio Hashimoto
Assoc. researchers:Cesar Henrique Comin ; Edson Amaro Junior ; Fernanda Bernardi Bertonha ; Marcel Parolin Jackowski ; Maria da Graca Campos Pimentel ; Roberto Hirata Junior ; Ronaldo Fumio Hashimoto ; Silvia Yumi Bando Takahara ; Valeria Meirelles Carril Elui
Associated grant(s):20/06160-3 - Human leukocyte transcriptional response to SARS-CoV-2 infection, AP.R
18/17421-2 - 2018 IEEE International Conference on Image Processing, AR.EXT
Associated scholarship(s):21/09070-8 - Modeling, analysis, and inference of biological networks, BP.PD
21/07112-5 - Modeling knowledge by complex networks, BP.IC
20/13255-0 - Algorithms for the acquisition, formation and annotation of remote sensing images, BP.TT
+ associated scholarships 20/13275-1 - Projects cyberinfrastructure administrator, BP.TT
20/06744-5 - Deep learning and intermediate representations for pediatric image analysis, BP.PD
19/23343-7 - Temporal analysis of gene expression, BP.PD
19/01077-3 - Integrating computer vision and complex networks for urban analysis, BP.PD
19/06280-1 - Integration, transformation, dataset augmentation and quality control for intermediate representation, BP.PD
19/06254-0 - Structural pattern recognition and intermediate representations, BP.PD
19/04219-3 - Project cyberinfrasctruture administration, BP.TT
18/10489-0 - Transformations of complex networks and their implication in topology and dynamics of complex systems, BP.PD
18/00390-7 - QR code detection using deep learning models, BP.MS
18/00477-5 - Learning image-to-image transformations, BP.MS
18/07386-5 - Segmentation of neonatal magnetic resonance imaging: a structural approach, BP.MS - associated scholarships


This project focuses on a unified strategy for knowledge and emerging dynamics discovery in Computational Science using intermediate representations. The intended applications are in areas characterized by large volumes of data in which knowledge discovery implies the transition from raw data bases for intermediate representations (usually feature vectors and graphs), thus allowing for the subsequent use of different analytical methods. In this context, integration and transformation methods to be used in the generation of intermediate data should also ensure the quality and reliability of data generated for the intermediate representation. The results of the analysis phase may influence both experiments and the integration methods for generating new data by feedback mechanisms. This project has two general goals: 1) to develop methodologies to solve Computational Science problems based on a common approach of intermediate mathematical-computational representations; 2) to apply the developed methodologies to different scientific problems, thus creating specific solutions to each problem. This methodological strategy will be used to address specific problems in areas which our group has been working in recent years: intermediate representations in computer vision and urban informatics; study of biological networks dynamics to characterize the mechanisms of the health-disease transition; development of computational tools for processing of MRI images high field and their integration with biological data; development of new techniques for characterization and visualization of intermediate representations in complex dynamic networks, with applications in Systems Biology. (AU)

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Scientific publications (55)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
COMIN, CESAR H.; TAYLOR, GAVIN J.; COSTA, LUCIANO DA F.. Quantifying the regularity of a 3D set of points on the surface of an ellipsoidal object. PATTERN RECOGNITION LETTERS, v. 133, p. 1-7, . (15/22308-2, 11/50761-2, 18/09125-4)
PORTES, MARIA TERESA; DAMINELI, DANIEL S. C.; FEIJO, JOSE A.. Spatiotemporal Quantification of Cytosolic pH in Arabidopsis Pollen Tubes. BIO-PROTOCOL, v. 11, n. 14, . (19/26129-6, 19/23343-7, 15/22308-2, 21/05363-0)
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S.. Low-Complexity Feature Stochastic Gradient Algorithm for Block-Lowpass Systems. IEEE ACCESS, v. 7, p. 141587-141593, . (15/22308-2, 19/06280-1)
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S.. Improved simple set-membership affine projection algorithm for sparse system modelling: Analysis and implementation. IET SIGNAL PROCESSING, v. 14, n. 2, p. 81-88, . (15/22308-2, 19/06280-1)
RODRIGUEZ, MAYRA Z.; COMIN, CESAR H.; CASANOVA, DALCIMAR; BRUNO, ODEMIR M.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.; RODRIGUES, FRANCISCO A.. Clustering algorithms: A comparative approach. PLoS One, v. 14, n. 1, . (16/19069-9, 14/20830-0, 15/18942-8, 15/22308-2, 14/08026-1, 18/09125-4, 11/50761-2)
BENATTI, ALEXANDRE; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI NASCIMENTO; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Opinion diversity and social bubbles in adaptive Sznajd networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. 2020, n. 2, . (15/22308-2, 11/50761-2, 18/09125-4, 18/10489-0)
DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Problem-solving using complex networks. European Physical Journal B, v. 92, n. 6, . (13/07375-0, 15/22308-2, 11/50761-2, 18/09125-4)
VIEIRA, SANDRA E.; BANDO, SILVIA Y.; DE PAULIS, MILENA; OLIVEIRA, DANIELLE B. L.; THOMAZELLI, LUCIANO M.; DURIGON, EDISON L.; MARTINEZ, MARINA B.; MOREIRA-FILHO, CARLOS ALBERTO. Distinct transcriptional modules in the peripheral blood mononuclear cells response to human respiratory syncytial virus or to human rhinovirus in hospitalized infants with bronchiolitis. PLoS One, v. 14, n. 3, . (15/22308-2, 12/22854-9)
CHAMORRO MARTINEZ, JORGE A.; OLIVEIRA, HUGO; DOS SANTOS, JEFERSSON A.; FEITOSA, RAUL QUEIROZ. Open Set Semantic Segmentation for Multitemporal Crop Recognition. IEEE Geoscience and Remote Sensing Letters, v. 19, . (17/50236-1, 20/06744-5, 15/22308-2)
BRITO, ANA C. M.; SILVA, FILIPI N.; DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. lassification of abrupt changes along viewing profiles of scientific article. Journal of Informetrics, v. 15, n. 2, . (18/10489-0, 19/16223-5, 15/08003-4, 16/19069-9, 18/09125-4, 15/22308-2)
LIMA, THALES S.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. The dynamics of knowledge acquisition via self-learning in complex networks. Chaos, v. 28, n. 8, . (16/19069-9, 17/09280-7, 15/22308-2, 11/50761-2, 17/13464-6, 15/08003-4, 15/18942-8)
DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; LIMA, THALES S.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. An image analysis approach to text analytics based on complex networks. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 510, p. 110-120, . (16/19069-9, 15/22308-2, 15/05676-8, 11/50761-2)
DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. How integrated are theoretical and applied physics?. SCIENTOMETRICS, v. 116, n. 2, p. 1113-1121, . (15/18942-8, 15/22308-2, 11/50761-2)
SANDRA ELISABETE VIEIRA; SILVIA YUMI BANDO; GERHARD DA PAZ LAUTERBACH; CARLOS ALBERTO MOREIRA-FILHO. Human Leukocyte Transcriptional Response to SARS-CoV-2 Infection. Clinics, v. 75, . (20/06160-3, 15/22308-2)
DE RESENDE, BRUNO MESSIAS F.; COSTA, LUCIANO DA F.. Characterization and comparison of large directed networks through the spectra of the magnetic Laplacian. Chaos, v. 30, n. 7, . (13/07375-0, 15/22308-2)
KHAKHKI, MOHSEN KAZEMNIA; MOGHADDAM, PEYMAN POOR; YAZDANPANAH, HAMED; MANSUR, WEBE J.. High-resolution time-frequency hilbert transform using sparsity-aware weighting function. EARTH SCIENCE INFORMATICS, . (15/22308-2)
BANDO, SILVIA YUMI; BERTONHA, FERNANDA BERNARDI; PIMENTEL-SILVA, LUCIANA RAMALHO; MANSANO DE OLIVEIRA, JOAO GABRIEL; DUARTE CARNEIRO, MARCO ANTONIO; MANOEL OKU, MARIANA HIROMI; WEN, HUNG-TZU; MARTINS CASTRO, LUIZ HENRIQUE; MOREIRA-FILHO, CARLOS ALBERTO. Hippocampal CA3 transcriptional modules associated with granule cell alterations and cognitive impairment in refractory mesial temporal lobe epilepsy patients. SCIENTIFIC REPORTS, v. 11, n. 1, . (15/22308-2, 05/56446-0)
MENDES, RODRIGO DE P.; YUAN, XIN; GENEGA, ELIZABETH M.; XU, XIAOYIN; COSTA, LUCIANO DA F.; COMIN, CESAR H.. Gland context networks: A novel approach for improving prostate cancer identification. Computerized Medical Imaging and Graphics, v. 94, . (21/12354-8, 18/09125-4, 15/22308-2)
MEDINA-RODRIGUEZ, ROSARIO; BELTRAN-CASTANON, CESAR; HASHIMOTO, RONALDO FUMIO. An Approach to Growth Delimitation of Straight Line Segment Classifiers Based on a Minimum Bounding Box. Entropy, v. 23, n. 11, . (15/22308-2)
TOKUDA, ERIC K.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Revisiting agglomerative clustering. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 585, . (19/01077-3, 15/22308-2, 18/09125-4)
COSTA, LUCIANO DA FONTOURA; DE ARRUDA, HENRIQUE FERRAZ. Syntonets: toward a harmony-inspired general model of complex networks. European Physical Journal B, v. 93, n. 12, . (18/10489-0, 15/22308-2, 19/16223-5)
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S.. Feature Adaptive Filtering: Exploiting Hidden Sparsity. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-REGULAR PAPERS, v. 67, n. 7, p. 2358-2371, . (15/22308-2, 19/06280-1)
BORDELEAU, MAUDE; COMIN, CESAR H.; DE COSSIO, LOURDES FERNANDEZ; LACABANNE, CHLOE; FREITAS-ANDRADE, MOISES; IBANEZ, FERNANDO GONZALEZ; RAMAN-NAIR, JOANNA; WAKEM, MICHAEL; CHAKRAVARTY, MALLAR; COSTA, LUCIANO DA F.; et al. aternal high-fat diet in mice induces cerebrovascular, microglial and long-term behavioural alterations in offsprin. COMMUNICATIONS BIOLOGY, v. 5, n. 1, . (15/22308-2, 18/09125-4)
VEGA-OLIVEROS, DIDIER A.; COSTA, LUCIANO DA FONTOURA; RODRIGUES, FRANCISCO APARECIDO. Influence maximization by rumor spreading on correlated networks through community identification. COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION, v. 83, . (15/22308-2, 11/50761-2, 15/50122-0, 13/07375-0, 16/23698-1, 18/24260-5)
TOKUDA, ERIC K.; LOCKERMAN, YITZCHAK; FERREIRA, GABRIEL B. A.; SORRELGREEN, ETHAN; BOYLE, DAVID; CESAR-JR, ROBERTO M.; SILVA, CLAUDIO T.. A New Approach for Pedestrian Density Estimation Using Moving Sensors and Computer Vision Sensing the city. ACM TRANSACTIONS ON SPATIAL ALGORITHMS AND SYSTEMS, v. 6, n. 4, . (14/24918-0, 15/22308-2)
YAZDANPANAH, HAMED; APOLINARIO JR, JOSE A.. The Extended Feature LMS Algorithm: Exploiting Hidden Sparsity for Systems with Unknown Spectrum. CIRCUITS SYSTEMS AND SIGNAL PROCESSING, v. 40, n. 1, . (15/22308-2, 19/06280-1)
OUELLETTE, JULIE; TOUSSAY, XAVIER; COMIN, CESAR H.; COSTA, LUCIANO DA F.; HO, MIRABELLE; LACALLE-AURIOLES, MARIA; FREITAS-ANDRADE, MOISES; LIU, QING YAN; LECLERC, SONIA; PAN, YOULIAN; et al. Vascular contributions to 16p11.2 deletion autism syndrome modeled in mice. NATURE NEUROSCIENCE, v. 23, n. 9, . (15/18942-8, 15/22308-2, 11/50761-2)
PERON, THOMAS; DE RESENDE, BRUNO MESSIAS F.; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F.; MENDEZ-BERMUDEZ, J. A.. Spacing ratio characterization of the spectra of directed random networks. Physical Review E, v. 102, n. 6, . (15/22308-2, 19/06931-2, 13/07375-0, 16/23827-6, 16/25682-5)
LOURENCO, JOSE; BARROS, SILVIA C.; ZE-ZE, LIBIA; DAMINELI, DANIEL S. C.; GIOVANETTI, MARTA; OSORIO, HUGO C.; AMARO, FATIMA; HENRIQUES, ANA M.; RAMOS, FERNANDA; LUIS, TIAGO; et al. est Nile virus transmission potential in Portuga. COMMUNICATIONS BIOLOGY, v. 5, n. 1, . (15/22308-2, 19/23343-7, 20/06160-3)
RAMOS, P. L.; COSTA, L. F.; LOUZADA, F.; RODRIGUES, F. A.. Power laws in the Roman Empire: a survival analysis. ROYAL SOCIETY OPEN SCIENCE, v. 8, n. 7, . (15/22308-2, 13/07375-0, 17/25971-0)
COMIN, CESAR H.; PERON, THOMAS; SILVA, FILIPI N.; AMANCIO, DIEGO R.; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F.. Complex systems: Features, similarity and connectivity. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, v. 861, p. 1-41, . (15/22308-2, 15/08003-4, 16/23827-6, 18/09125-4, 16/19069-9, 14/20830-0, 13/26416-9)
DOMINGUES, G. S.; SILVA, F. N.; COMIN, C. H.; COSTA, L. DA F.. Topological characterization of world cities. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, . (17/09280-7, 15/22308-2, 11/50761-2, 15/08003-4, 15/18942-8)
DAZZI, ESTEPHAN; DE CAMPOS, TEOFILO; HILTON, ADRIAN; CESAR JR, ROBERTO M.. Scalable object instance recognition based on keygraph matching. PATTERN RECOGNITION LETTERS, v. 114, n. SI, p. 53-62, . (14/50769-1, 15/22308-2, 11/50761-2)
SOUZA, PAULO J. P.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Topology and dynamics in complex networks: The role of edge reciprocity. EPL, v. 122, n. 2, . (15/18942-8, 15/22308-2, 11/50761-2)
CERVANTES, EVELYN PEREZ; COMIN, CESAR HENRIQUE; CESAR JUNIOR, ROBERTO MARCONDES; COSTA, LUCIANO DA FONTOURA. Morphological Neuron Classification Based on Dendritic Tree Hierarchy. NEUROINFORMATICS, v. 17, n. 1, p. 147-161, . (15/18942-8, 15/22308-2)
DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R.. Paragraph-based representation of texts: A complex networks approach. INFORMATION PROCESSING & MANAGEMENT, v. 56, n. 3, p. 479-494, . (16/19069-9, 15/22308-2, 11/50761-2, 17/13464-6, 15/05676-8)
RODRIGUES, FRANCISCO C. M.; ESPADOTO, MATEUS; HIRATA JR, ROBERTO; TELEA, ALEXANDRU C.. Constructing and Visualizing High-Quality Classifier Decision Boundary Maps dagger. INFORMATION, v. 10, n. 9, . (15/22308-2, 15/24485-9, 15/01587-0)
FERREIRA, GUSTAVO RODRIGUES; NAKAYA, HELDER IMOTO; COSTA, LUCIANO DA FONTOURA. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs. Physical Review E, v. 97, n. 4, . (14/19323-7, 12/19278-6, 15/22308-2)
BANDO, SILVIA YUMI; IAMASHITA, PRISCILA; GUTH, BEATRIZ E.; DOS SANTOS, LUIS F.; FUJITA, ANDRE; ABE, CECILIA M.; FERREIRA, LEANDRO R.; MOREIRA-FILHO, CARLOS ALBERTO. A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells. PLoS One, v. 12, n. 12, . (15/22308-2, 11/50761-2)
COSTA, LUCIANO DA F.; SILVA, FILIPI N.; COMIN, CESAR H.. A pattern recognition approach to transistor array parameter variance. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 499, p. 176-185, . (15/18942-8, 15/22308-2, 15/08003-4, 11/50761-2)
CERIBELI, CAROLINE; FERRAZ DE ARRUDA, HENRIQUE; DA FONTOURA COSTA, LUCIANO. How coupled are capillary electrophoresis and mass spectrometry?. SCIENTOMETRICS, v. 126, n. 5, p. 3841-3851, . (13/07375-0, 15/22308-2, 19/16223-5, 18/10489-0, 11/50761-2)
LIM, MARKUS V. S.; DINIZ, PAULO S. R.; YAZDANPANAH, HAMED. Set-Membership Constrained Frequency-Domain Algorithm. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS, v. 68, n. 2, p. 797-801, . (19/06280-1, 15/22308-2)
COMIN, CESAR H.; TSIRUKIS, I, DEMETRIOS; SUN, YE; XU, XIAOYIN. Quantification of retinal blood leakage in fundus fluorescein angiography in a retinal angiogenesis model. SCIENTIFIC REPORTS, v. 11, n. 1, . (15/22308-2, 18/09125-4)
LI, SIYUAN; REN, WENQI; WANG, FENG; ARAUJO, IAGO BRENO; TOKUDA, ERIC K.; JUNIOR, ROBERTO HIRATA; CESAR-JR., ROBERTO M.; WANG, ZHANGYANG; CAO, XIAOCHUN. A Comprehensive Benchmark Analysis of Single Image Deraining: Current Challenges and Future Perspectives. INTERNATIONAL JOURNAL OF COMPUTER VISION, v. 129, n. 4, p. 1301-1322, . (15/22308-2)
HIRATA, NINA S. T.; PAPAKOSTAS, GEORGE A.. On Machine-Learning Morphological Image Operators. MATHEMATICS, v. 9, n. 16, . (17/25835-9, 15/22308-2)
ALMEIDA DE MACEDO OLIVEIRA, ARTUR ANDRE; HIRATA JR, ROBERTO. INACITY - INvestigate and Analyze a CITY. SOFTWAREX, v. 15, . (18/10767-0, 15/22308-2, 15/24485-9)
BANDO, SILVIA Y.; IAMASHITA, PRISCILA; SILVA, FILIPI N.; COSTA, LUCIANO DA F.; ABE, CECILIA M.; BERTONHA, FERNANDA B.; GUTH, BEATRIZ E. C.; FUJITA, ANDRE; MOREIRA-FILHO, CARLOS A.. Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic-Uremic Syndrome. MICROORGANISMS, v. 7, n. 7, . (15/22308-2, 11/50761-2)
SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, . (15/22308-2, 15/08003-4, 17/09280-7, 15/18942-8, 13/07375-0, 18/09125-4, 11/50761-2)
CIBA, MANUEL; BESTEL, ROBERT; NICK, CHRISTOPH; DE ARRUDA, GUILHERME FERRAZ; PERON, THOMAS; HENRIQUE, COMIN CESAR; COSTA, LUCIANO DA FONTOURA; RODRIGUES, FRANCISCO APARECIDO; THIELEMANN, CHRISTIANE. Comparison of Different Spike Train Synchrony Measures Regarding Their Robustness to Erroneous Data From Bicuculline-Induced Epileptiform Activity. NEURAL COMPUTATION, v. 32, n. 5, p. 887-911, . (15/22308-2, 16/23827-6, 18/09125-4, 13/26416-9, 12/51301-8, 12/25219-2)
TOKUDA, ERIC K.; DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; JR, ROBERTO M. CESAR; SILVA, CLAUDIO T.; COSTA, LUCIANO DA F.. Spatial distribution of graffiti types: a complex network approach. European Physical Journal B, v. 94, n. 9, . (19/01077-3, 19/16223-5, 18/09125-4, 15/22308-2, 18/10489-0)
NAKAZONO, L.; DE OLIVEIRA, C. MENDES; HIRATA, N. S. T.; JERAM, S.; QUEIROZ, C.; EIKENBERRY, STEPHEN S.; GONZALEZ, A. H.; ABRAMO, R.; OVERZIER, R.; ESPADOTO, M.; et al. On the discovery of stars, quasars, and galaxies in the Southern Hemisphere with S-PLUS DR2. Monthly Notices of the Royal Astronomical Society, v. 507, n. 4, p. 5847-5868, . (18/09165-6, 19/06766-1, 19/10923-5, 15/22308-2, 19/26492-3, 18/20977-2, 14/10566-4, 19/01312-2, 18/25671-9, 19/23388-0, 17/25835-9, 15/11442-0, 16/12331-0)
GEWERS, FELIPE L.; FERREIRA, GUSTAVO R.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. Principal Component Analysis: A Natural Approach to Data Exploration. ACM COMPUTING SURVEYS, v. 54, n. 4, . (16/19069-9, 15/22308-2, 11/50761-2, 17/13464-6, 18/10489-0, 18/09125-4, 19/16223-5)

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