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2. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion.

Author

Maini Rekdal, Vayu, Villalobos-Escobedo, José, Rodriguez-Valeron, Nabila, Olaizola Garcia, Mikel, Prado Vásquez, Diego, Rosales, Alexander, Sörensen, Pia, Baidoo, Edward, Calheiros de Carvalho, Ana, Riley, Robert, Lipzen, Anna, He, Guifen, Yan, Mi, Haridas, Sajeet, Daum, Christopher, Yoshinaga, Yuko, Ng, Vivian, Grigoriev, Igor, Munk, Rasmus, Wijaya, Christofora, Nuraida, Lilis, Damayanti, Isty, Cruz-Morales, Pablo, and Keasling, Jay

Subjects
Fermentation, Fermented Foods, Neurospora, Phylogeny, Indonesia, Food Microbiology, Metagenomics, Humans, Metabolomics
Abstract

Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.

Published
2024

5. MYCOLICIBACTERIUM FORTUITUM INFECTION IN EX SITU EMERALD TREE BOA (Corallus batesii)

Author

Gonzaga, Cássia Regina Ramos, Matos, Flora Nogueira, Caiaffa, Mayara Grego, Silva, Maraya Lincoln, Teixeira, Rodrigo Hidalgo Friciello, Ferreira-Machado, Eduardo, Ervedosa, Ticiana Brasil, Navas-Suárez, Pedro Enrique, Ressio, Rodrigo Albergaria, dos Santos Cirqueira, Cinthya, Figueiredo, Ketlyn Bolsachini, de Carvalho, Ana Carolina Souza Ramos, Guerra, Juliana Mariotti, de Azevedo Fernandes, Natália Coelho Couto, and da Costa, André Luiz Mota

Published
2024
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7. Index

Author

Carvalho, Ana M., Orozco, Rafael, and Shin, Naomi Lapidus

Published
2015

8. Contributors

Author

Carvalho, Ana M., Orozco, Rafael, and Shin, Naomi Lapidus

Published
2015

24. Preface

Author

Carvalho, Ana M., Orozco, Rafael, and Shin, Naomi Lapidus

Published
2015

25. Retinal Dystrophies Associated With Peripherin-2: Genetic Spectrum and Novel Clinical Observations in 241 Patients.

Author

Heath Jeffery, Rachael, Thompson, Jennifer, Lo, Johnny, Chelva, Enid, Armstrong, Sean, Pulido, Jose, Procopio, Rebecca, Vincent, Andrea, Bianco, Lorenzo, Battaglia Parodi, Maurizio, Ziccardi, Lucia, Antonelli, Giulio, Barbano, Lucilla, Marques, João, Geada, Sara, Carvalho, Ana, Tang, Wei, Chan, Choi, Boon, Camiel, Hensman, Jonathan, Chen, Ta-Ching, Lin, Chien-Yu, Chen, Pei-Lung, Vincent, Ajoy, Tumber, Anupreet, Heon, Elise, Grigg, John, Jamieson, Robyn, Cornish, Elisa, Nash, Benjamin, Borooah, Shyamanga, Ayton, Lauren, Britten-Jones, Alexis, Edwards, Thomas, Ruddle, Jonathan, Sharma, Abhishek, Porter, Rowan, Lamey, Tina, McLaren, Terri, McLenachan, Samuel, Roshandel, Danial, and Chen, Fred

Subjects
Humans, Peripherins, Middle Aged, Adult, Male, Female, Adolescent, Retinal Dystrophies, Aged, Visual Acuity, Child, Young Adult, Electroretinography, Child, Preschool, Phenotype, Tomography, Optical Coherence, Mutation, Fluorescein Angiography, Genetic Association Studies, Retrospective Studies, DNA Mutational Analysis, DNA, Pedigree
Abstract

PURPOSE: To describe the clinical, electrophysiological and genetic spectrum of inherited retinal diseases associated with variants in the PRPH2 gene. METHODS: A total of 241 patients from 168 families across 15 sites in 9 countries with pathogenic or likely pathogenic variants in PRPH2 were included. Records were reviewed for age at symptom onset, visual acuity, full-field ERG, fundus colour photography, fundus autofluorescence (FAF), and SD-OCT. Images were graded into six phenotypes. Statistical analyses were performed to determine genotype-phenotype correlations. RESULTS: The median age at symptom onset was 40 years (range, 4-78 years). FAF phenotypes included normal (5%), butterfly pattern dystrophy, or vitelliform macular dystrophy (11%), central areolar choroidal dystrophy (28%), pseudo-Stargardt pattern dystrophy (41%), and retinitis pigmentosa (25%). Symptom onset was earlier in retinitis pigmentosa as compared with pseudo-Stargardt pattern dystrophy (34 vs 44 years; P = 0.004). The median visual acuity was 0.18 logMAR (interquartile range, 0-0.54 logMAR) and 0.18 logMAR (interquartile range 0-0.42 logMAR) in the right and left eyes, respectively. ERG showed a significantly reduced amplitude across all components (P < 0.001) and a peak time delay in the light-adapted 30-Hz flicker and single-flash b-wave (P < 0.001). Twenty-two variants were novel. The central areolar choroidal dystrophy phenotype was associated with 13 missense variants. The remaining variants showed marked phenotypic variability. CONCLUSIONS: We described six distinct FAF phenotypes associated with variants in the PRPH2 gene. One FAF phenotype may have multiple ERG phenotypes, demonstrating a discordance between structure and function. Given the vast spectrum of PRPH2 disease our findings are useful for future clinical trials.

Published
2024

26. Microfibrillated celluloses produced from kraft pulp of coffee parchment

Author

Coura, Marcela Ribeiro, Demuner, Antonio Jacinto, Ribeiro, Robisnea Adriana, Demuner, Iara Fontes, de Cristo Figueiredo, Júlia, Gomes, Fernando José Borges, de Paula Barbosa, Verônica Oliveira, Firmino, Maria José Magalhães, Carvalho, Ana Márcia Macedo Ladeira, Blank, Daiane Einhardt, and dos Santos, Marcelo Henrique

Published
2024
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29. Genetic profile of syndromic retinitis pigmentosa in Portugal

Author

Cortinhal, Telmo, Santos, Cristina, Vaz-Pereira, Sara, Marta, Ana, Duarte, Lilianne, Miranda, Vitor, Costa, José, Sousa, Ana Berta, Peter, Virginie G., Kaminska, Karolina, Rivolta, Carlo, Carvalho, Ana Luísa, Saraiva, Jorge, Soares, Célia Azevedo, Silva, Rufino, Murta, Joaquim, Santos, Luísa Coutinho, and Marques, João Pedro

Published
2024
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30. Constraining LLTB models with galaxy cluster counts from next generation surveys

Author

Sakr, Ziad, Carvalho, Ana, Da Silva, Antonio, Bellido, Juan Garcia, Mimoso, Jose P., Camarena, David, Nesseris, Savvas, Martins, Carlos J. A. P., Nunes, Nelson J., and Sapone, Domenico

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Universe's assumed homogeneity and isotropy is known as the cosmological principle. It is one of the assumptions that lead to the Friedmann-Lema\^{\i}tre-Robertson-Walker (FLRW) metric and it is a cornerstone of modern cosmology, because the metric plays a crucial role into the determination of the cosmological observables. Thus, it is of paramount importance to question this principle and perform observational tests that may falsify this hypothesis. Here we explore the use of galaxy cluster counts as a probe of a large-scale inhomogeneity, which is a novel approach for the study of inhomogeneous models, and to determine the precision with which future galaxy cluster surveys will be able to test the cosmological principle. We present forecast constraints on the inhomogeneous Lema\^{\i}tre-Tolman-Bondi (LTB) model with a cosmological constant and cold dark matter, from a combination of simulated data according to a compilation of `Stage-IV' galaxy surveys following a methodology that involves the use of a mass function correction from numerical $N$-body simulations of an LTB cosmology. When considering the \lcdm fiducial model as a baseline for constructing our mock catalogs, we find that our combination of the forthcoming cluster surveys, will improve the constraints on the cosmological principle parameters as well on the FLRW parameters by about $50\%$ with respect to previous similar forecasts performed using geometrical and linear growth of structure probes, with $\pm20\%$ variations depending on the level of knowledge of systematic effects.These results indicate that galaxy cluster abundances are sensitive probes of inhomogeneity, and that next-generation galaxy cluster surveys, will thoroughly test homogeneity at cosmological scales, tightening the constraints on possible violations of the cosmological principle in the framework of $\Lambda$LTB scenarios. (Abridged), Comment: 9 pages, 5 figure, accepted as is and published in A&A journal after adding Fig. 1 for illustrative purposes

Published
2023

32. Effects of mixed nuts as part of a Brazilian Cardioprotective diet on LDL-cholesterol in adult patients after myocardial infarction: a multicenter randomized controlled clinical trial

Author

Bersch-Ferreira, Ângela Cristine, Weschenfelder, Camila, Vieira Machado, Rachel Helena, Nakagawa Santos, Renato Hideo, Riley, Terrence M., da Silva, Lucas Ribeiro, Miyada, Debora Harumi Kodama, Sady, Erica Regina Ribeiro, de Abreu-Silva, Erlon Oliveira, Laranjeira, Ligia Nasi, de Quadros, Alexandre Schaan, dos Santos, Júlia Lorenzon, Souza, Gabriela Corrêa, Parahiba, Suena Medeiros, Fayh, Ana Paula Trussardi, Bezerra, Danielle Soares, Carvalho, Ana Paula Perillo Ferreira, Machado, Malaine Morais Alves, Vasconcelos, Sandra Mary Lima, Santos, Mayranne Victórya Rocha, de Figueiredo Neto, José Albuquerque, Dias, Luciana Pereira Pinto, Zaina Nagano, Francisca Eugenia, de Almeida, Cássia Cristina Paes, Moreira, Annie Seixas Bello, de Oliveira, Rodrigo Damasceno, Rogero, Marcelo Macedo, Sampaio, Geni Rodrigues, da Silva Torres, Elizabeth Aparecida Ferraz, Weber, Bernardete, Cavalcanti, Alexandre Biasi, and Marcadenti, Aline

Published
2024
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37. Geographic variation of mutagenic exposures in kidney cancer genomes

Author

Senkin, Sergey, Moody, Sarah, Díaz-Gay, Marcos, Abedi-Ardekani, Behnoush, Cattiaux, Thomas, Ferreiro-Iglesias, Aida, Wang, Jingwei, Fitzgerald, Stephen, Kazachkova, Mariya, Vangara, Raviteja, Le, Anh Phuong, Bergstrom, Erik N., Khandekar, Azhar, Otlu, Burçak, Cheema, Saamin, Latimer, Calli, Thomas, Emily, Atkins, Joshua Ronald, Smith-Byrne, Karl, Cortez Cardoso Penha, Ricardo, Carreira, Christine, Chopard, Priscilia, Gaborieau, Valérie, Keski-Rahkonen, Pekka, Jones, David, Teague, Jon W., Ferlicot, Sophie, Asgari, Mojgan, Sangkhathat, Surasak, Attawettayanon, Worapat, Świątkowska, Beata, Jarmalaite, Sonata, Sabaliauskaite, Rasa, Shibata, Tatsuhiro, Fukagawa, Akihiko, Mates, Dana, Jinga, Viorel, Rascu, Stefan, Mijuskovic, Mirjana, Savic, Slavisa, Milosavljevic, Sasa, Bartlett, John M. S., Albert, Monique, Phouthavongsy, Larry, Ashton-Prolla, Patricia, Botton, Mariana R., Silva Neto, Brasil, Bezerra, Stephania Martins, Curado, Maria Paula, Zequi, Stênio de Cássio, Reis, Rui Manuel, Faria, Eliney Ferreira, de Menezes, Nei Soares, Ferrari, Renata Spagnoli, Banks, Rosamonde E., Vasudev, Naveen S., Zaridze, David, Mukeriya, Anush, Shangina, Oxana, Matveev, Vsevolod, Foretova, Lenka, Navratilova, Marie, Holcatova, Ivana, Hornakova, Anna, Janout, Vladimir, Purdue, Mark P., Rothman, Nathaniel, Chanock, Stephen J., Ueland, Per Magne, Johansson, Mattias, McKay, James, Scelo, Ghislaine, Chanudet, Estelle, Humphreys, Laura, de Carvalho, Ana Carolina, Perdomo, Sandra, Alexandrov, Ludmil B., Stratton, Michael R., and Brennan, Paul

Published
2024
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40. Enablers and Difficulties in the Implementation of Gamification: A Case Study with Teachers

Author

Araújo, Inês and Carvalho, Ana Amélia

Abstract

Although there is ample evidence that gamification can engage students in learning, it is less used than one would expect. This raises the question of the difficulties teachers face in planning and implementing gamification in their classes. What enables teachers' implementation of gamification? These questions were addressed through a case study, and data were collected along the four phases of a teachers' training course. The first phase approached the gamification concept, the Octalysis Framework, the types of gamification, and digital tools. The second phase focused on planning the gamification activity, the third one on implementing it with their students in school, and the fourth phase on sharing and reflecting on their experience. It was possible to identify enablers and difficulties that influenced the planning, such as personal background, time available, and technical conditions in the classroom. Most teachers opted for a platform with digital tools that allowed them to apply all the desired features to their gamified activities. The most complex gamified activities were related to the teacher's gaming experience, use of digital tools, and risk-taking.

Published
2022

41. Solving graph problems with single-photons and linear optics

Author

Mezher, Rawad, Carvalho, Ana Filipa, and Mansfield, Shane

Subjects
Quantum Physics
Abstract

An important challenge for current and near-term quantum devices is finding useful tasks that can be preformed on them. We first show how to efficiently encode a bounded $n \times n$ matrix $A$ into a linear optical circuit with $2n$ modes. We then apply this encoding to the case where $A$ is a matrix containing information about a graph $G$. We show that a photonic quantum processor consisting of single-photon sources, a linear optical circuit encoding $A$, and single-photon detectors can solve a range of graph problems including finding the number of perfect matchings of bipartite graphs, computing permanental polynomials, determining whether two graphs are isomorphic, and the $k$-densest subgraph problem. We also propose pre-processing methods to boost the probabilities of observing the relevant detection events and thus improve performance. Finally we present both numerical simulations and implementations on Quandela's Ascella photonic quantum processor to validate our findings., Comment: 9 pages + 9 pages appendix. To appear in Phys.Rev. A. Part of numerics section moved from appendix to main text. New experiments on photonic quantum hardware (Quandela's Ascella) added

Published
2023

42. OCUPAÇÃO DE LEITOS DE TERAPIA INTENSIVA NA PANDEMIA DA COVID-19: PERSPECTIVAS GERENCIAIS DA ENFERMAGEM ONCOLÓGICA

Author

Mazzoni, Vivian Gomes, primary, Marcellini, Paulo Sergio, additional, Carvalho, Eloá Carneiro, additional, Muzi, Camila Drumond, additional, Mello, Lucas Rodrigo Garcia de, additional, Marins, Ana Lucia Cascardo, additional, Carvalho, Ana Fátima Coelho, additional, Mesquita, Ayla Maria Farias de, additional, Stipp, Marluci Andrade Conceição, additional, and Andrade, Karla Biancha Silva de, additional

Published
2024
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44. CONDIÇÕES DE SAÚDE BUCAL DE UMA COMUNIDADE RURAL COMO EXPRESSÃO SÓCIOECONÔMICA

Author

DE ARAÚJO MENDES CARDOSO, SARAH, primary, CARDOSO DE ARAÚJO, CAROLINA, additional, WESLLEN MACEDO DA COSTA, OUSANAS, additional, GABRIEL DE CARVALHO LIMA, NICOLLAS, additional, LUZIA SOARES MORAIS, ULHIANA, additional, ABREU VILELA DE MACÊDO, MAYARA, additional, COSME SANTOS DA SILVA, FLAVIO, additional, CLARA DE SOUSA CARVALHO, ANA, additional, BRÍGIDA GUIMARÃES DE MACÊDO, ANA, additional, RIBEIRO DA SILVA, BEATRIZ, additional, VIEIRA DE CARVALHO, VICTORIA, additional, MARIA RODRIGUES DA SILVA, PAULA, additional, REGINA DA SILVA MEDEIROS, LAÍS, additional, and LUA VIEIRA DE ABREU COSTA, MARINA, additional

Published
2024
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46. The ECFA Early Career Researcher's Panel: composition, structure, and activities, 2021 -- 2022

Author

Panel, ECFA Early-Career Researcher, Geanta, Andrei Alexandru, Amendola, Chiara, Apolinario, Liliana, Arling, Jan-Hendrik, Ashkenazi, Adi, Augsten, Kamil, Bagnaschi, Emanuele, Bakos, Evelin, Barak, Liron, Bastos, Diogo, Benato, Giovanni, Bilin, Bugra, Kraljevic, Neven Blaskovic, Brenner, Lydia, Brizioli, Francesco, Camper, Antoine, Camplani, Alessandra, Vidal, Xabier Cid, Dag, Hüseyin, Dias, Flavia de Almeida, Degens, Jordy, Diociaiuti, Eleonora, Dufour, Laurent, Dunne, Katherine, Erhardt, Filip, Ghinescu, Stefan-Alexandru, Gouskos, Loukas, Herzan, Andrej, Hinger, Viktoria, Hiti, Bojan, Ilg, Armin, Irles, Adrián, Jarkovská, Kateřina, Jovicevic, Jelena, Keszeghova, Lucia, Kirschenmann, Henning, Klaver, Suzanne, Konstantinou, Sotiroulla, Kuich, Magdalena, Kumari, Neelam, Gajdošová, Katarína Křížková, Lelek, Aleksandra, Lorenz, Jeanette, Carvalho, Ana Luisa, Major, Péter, Malczewski, Jakub, Mancini, Giada, Martikainen, Laura, Maurice, Émilie, Mee, Seán, Milosevic, Vukasin, Moravcova, Zuzana, Valero, Laura Moreno, Moureaux, Louis, Mäntysaari, Heikki, Nikiforou, Nikiforos, Otarid, Younes, Pitt, Michael, Placinta, Vlad-Mihai, Räuber, Géraldine, Ripellino, Giulia, Roberts, Bryn, Šantelj, Luka, Schramm, Steven, Shopova, Mariana, Skovpen, Kirill, Smolkovič, Aleks, Sokmen, Gamze, Sznajder, Paweł, Gomez, Lourdes Urda, Waldron, Abigail Victoria, Williams, Sarah, Zaccolo, Valentina, Zardoshti, Nima, and Zeyen, Manuel

Subjects
Physics - Accelerator Physics, Physics - Physics and Society
Abstract

The European Committee for Future Accelerators (ECFA) Early Career Researcher's (ECR) panel, which represents the interests of the ECR community to ECFA, officially began its activities in January 2021. In the first two years, the panel has defined its own internal structure, responded to ECFA requests for feedback, and launched its own initiatives to better understand and support the diverse interests of early career researchers. This report summarises the panel composition and structure, as well as the different activities the panel has been involved with during the first two years of its existence., Comment: Editors: Jan-Hendrik Arling, Emanuele Bagnaschi, Xabier Cid Vidal, Katherine Dunne, Viktoria Hinger, Armin Ilg, Henning Kirschenmann, Steven Schramm, Pawe{\l} Sznajder, Sarah Williams, Valentina Zaccolo

Published
2022

47. ASMA NA INFÂNCIA: DO DIAGNÓSTICO AO TRATAMENTO

Author

GONÇALVES DE ALMEIDA, LARISSA, primary, BARRETO DO NASCIMENTO FILHO, THIAGO, additional, VICTÓRIA RODRIGUES DE MENEZES, MARIA, additional, VICTOR RODRIGUES DE MENEZES, JOSÉ, additional, LUIZA MENDONÇA FARIAS DE CARVALHO, ANA, additional, CORREIA FREIRE, NATHAN, additional, COSTA ARAGÃO, RAFAELA, additional, CAROLINA RIBEIRO CARVALHO, ANA, additional, MENEZES DE JESUS SANTOS, YASMYN, additional, BARBOSA LUCENA, LARISSA, additional, DE MELO RIBEIRO, FREDERIC, additional, VITÓRIA SILVA BOMFIM, KAMILE, additional, GONÇALVES EVANGELISTA, CARISSA, additional, BATISTA SOUZA, ALEXANDRE, additional, and RABÊLO JEREMIAS GUIMARÃES, RAFAEL, additional

Published
2023
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48. Age at the diagnosis and in the beginning of intervention from hearing impaired children, in a public Brazilian hearing health service

Author

Pinto, Meliane Melina, Raimundo, Jeziela Cristina, Carvalho, Ana Claudia Martinho de, Samelli, Alessandra Giannella, Matas, Carla Gentile, Ferrari, Gisele Munhoes dos Santos, Garbi, Sérgio, Bento, Ricardo Ferreira, and Gândara, Mara

Subjects
hearing, auxiliary of hearing, children, hearing loss, Medicine, Otorhinolaryngology, RF1-547
Abstract

Introduction: The earlier the diagnosis and the intervention from the hearing impairment less will be the impact for the development of cognitive abilities, hearing and of speech from the child. Objective: Characterize the age in the diagnosis and the beginning of intervention of the hearing loss and the accompaniment of the assisted children in a public Brazillian hearing health service - Espaço Reouvir from the Clinicas Hospital from the Medical School from the University of São Paulo. Method: Retrospective study with information from 166 medical records from children regarding the: gender; etiology, type, degree and laterality of the hearing impairment; age in the diagnosis and adaptation of the Hearing aids (HA) and accompaniment in the service. Results: The sample was composed by 56% men and 44% women. The prevailing etiology was from multifactorial origin. The hearing loss from the neurosensory type occurred in 88,6% of the cases. The degree of moderate hearing loss was the most frequent (30,7%), symmetry in both ears was found in 69,9% of the cases and unilateral hearing loss in 2,4%. The average age in the diagnosis was of 5,46 years and in the intervention was of 6,86 years. A total of 96,98% of children had already completed the process of adaptation and 78,32% still remained in the accompaniment. Conclusion: The program Reouvir-HCFMUSP still receives children, both for diagnosis and or intervention in a late manner. However, still is possible the realization of the accompaniment of a significant number of users of the hearing aids, enabling a process of adaptation more effective.

Published
2012

50. Product Mix Optimization of a Footwear Company Using Activity-Based Costing Information

Author

Carvalho, Ana, Costa e Silva, Eliana, Silva, Rui, Chaari, Fakher, Series Editor, Gherardini, Francesco, Series Editor, Ivanov, Vitalii, Series Editor, Haddar, Mohamed, Series Editor, Cavas-Martínez, Francisco, Editorial Board Member, di Mare, Francesca, Editorial Board Member, Kwon, Young W., Editorial Board Member, Tolio, Tullio A. M., Editorial Board Member, Trojanowska, Justyna, Editorial Board Member, Schmitt, Robert, Editorial Board Member, Xu, Jinyang, Editorial Board Member, Machado, Jose, editor, Soares, Filomena, editor, Antosz, Katarzyna, editor, Cagáňová, Dagmar, editor, Manupati, Vijaya Kumar, editor, and Pereira, Alejandro, editor

Published
2024
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