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32,613 results on '"Castilho A"'

1. How Much Data is Enough Data? Fine-Tuning Large Language Models for In-House Translation: Performance Evaluation Across Multiple Dataset Sizes

Author

Vieira, Inacio, Allred, Will, Lankford, Séamus, Castilho, Sheila, and Way, Andy

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Decoder-only LLMs have shown impressive performance in MT due to their ability to learn from extensive datasets and generate high-quality translations. However, LLMs often struggle with the nuances and style required for organisation-specific translation. In this study, we explore the effectiveness of fine-tuning Large Language Models (LLMs), particularly Llama 3 8B Instruct, leveraging translation memories (TMs), as a valuable resource to enhance accuracy and efficiency. We investigate the impact of fine-tuning the Llama 3 model using TMs from a specific organisation in the software sector. Our experiments cover five translation directions across languages of varying resource levels (English to Brazilian Portuguese, Czech, German, Finnish, and Korean). We analyse diverse sizes of training datasets (1k to 207k segments) to evaluate their influence on translation quality. We fine-tune separate models for each training set and evaluate their performance based on automatic metrics, BLEU, chrF++, TER, and COMET. Our findings reveal improvement in translation performance with larger datasets across all metrics. On average, BLEU and COMET scores increase by 13 and 25 points, respectively, on the largest training set against the baseline model. Notably, there is a performance deterioration in comparison with the baseline model when fine-tuning on only 1k and 2k examples; however, we observe a substantial improvement as the training dataset size increases. The study highlights the potential of integrating TMs with LLMs to create bespoke translation models tailored to the specific needs of businesses, thus enhancing translation quality and reducing turn-around times. This approach offers a valuable insight for organisations seeking to leverage TMs and LLMs for optimal translation outcomes, especially in narrower domains.

Published
2024

2. On star-homogeneous-graded polynomial identities of upper triangular matrices over an arbitrary field

Author

de Mello, Thiago Castilho and Yasumura, Felipe Yukihide

Subjects
Mathematics - Rings and Algebras
Abstract

We study the graded polynomial identities with a homogeneous involution on the algebra of upper triangular matrices endowed with a fine group grading. We compute their polynomial identities and a basis of the relatively free algebra, considering an arbitrary base field. We obtain the asymptotic behaviour of the codimension sequence when the characteristic of the base field is zero. As a consequence, we compute the exponent and the second exponent of the same algebra endowed with any group grading and any homogeneous involution.

Published
2024

8. Long-Term Safety and Effectiveness of Rituximab Biosimilar RTXM83: A Retrospective Extension Study in Brazilian Patients with Diffuse Large B-Cell Lymphoma

Author

Delamain, Marcia Torresan, Cardoso, Ana Carolina Ferreira, Pericole, Fernando Vieira, da Silva Araújo, Sérgio Shusterschitz, Fogliatto, Laura, Higashi, Marcia, Pereira, Juliana, da Silva, Roberto Luiz, Werutsky, Gustavo, de Paulo Giacon Radtke, Patrícia, Salvino, Marco Aurélio, and Castilho, Vivienne

Published
2024
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16. State of the science and future directions for research on HIV and cancer: Summary of a joint workshop sponsored by IARC and NCI.

Author

Engels, Eric, Shiels, Meredith, Barnabas, Ruanne, Bohlius, Julia, Brennan, Paul, Castilho, Jessica, Chanock, Stephen, Clarke, Megan, Coghill, Anna, Combes, Jean-Damien, Dryden-Peterson, Scott, DSouza, Gypsyamber, Gopal, Satish, Jaquet, Antoine, Lurain, Kathryn, Makinson, Alain, Martin, Jeffrey, Muchengeti, Mazvita, Newton, Robert, Okuku, Fred, Orem, Jackson, Palefsky, Joel, Ramaswami, Ramya, Robbins, Hilary, Sigel, Keith, Silver, Sylvia, Suneja, Gita, Yarchoan, Robert, and Clifford, Gary

Subjects
cancer, epidemiology, human immunodeficiency virus, people living with HIV, prevention, United States, Humans, HIV, National Cancer Institute (U.S.), Neoplasms, HIV Infections, Anti-HIV Agents
Abstract

An estimated 38 million people live with human immunodeficiency virus (HIV) worldwide and are at excess risk for multiple cancer types. Elevated cancer risks in people living with HIV (PLWH) are driven primarily by increased exposure to carcinogens, most notably oncogenic viruses acquired through shared transmission routes, plus acceleration of viral carcinogenesis by HIV-related immunosuppression. In the era of widespread antiretroviral therapy (ART), life expectancy of PLWH has increased, with cancer now a leading cause of co-morbidity and death. Furthermore, the types of cancers occurring among PLWH are shifting over time and vary in their relative burden in different parts of the world. In this context, the International Agency for Research on Cancer (IARC) and the US National Cancer Institute (NCI) convened a meeting in September 2022 of multinational and multidisciplinary experts to focus on cancer in PLWH. This report summarizes the proceedings, including a review of the state of the science of cancer descriptive epidemiology, etiology, molecular tumor characterization, primary and secondary prevention, treatment disparities and survival in PLWH around the world. A consensus of key research priorities and recommendations in these domains is also presented.

Published
2024

17. Cardiovascular Risk Factors in Obese Children and Adolescents: A Systematic Review

Author

Azzini, Vitor Ohana Marques, primary, Lopes, Cristianne Confessor Castilho, additional, Beker, Natascha Szumsztajn, additional, Lopes, Eduardo Barbosa, additional, Lopes, Lucas Castilho, additional, Lopes, Maria Eduarda Castilho, additional, Pitanga, Fábio Herget, additional, Filho, Mushue Dayan Hampel Vieira, additional, and Guimarães, Larissa Silva, additional

Published
2024
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24. One sixth of Amazonian tree diversity is dependent on river floodplains

Author

Householder, John Ethan, Wittmann, Florian, Schöngart, Jochen, Piedade, Maria Teresa Fernandez, Junk, Wolfgang J., Latrubesse, Edgardo Manuel, Quaresma, Adriano Costa, Demarchi, Layon O., de S. Lobo, Guilherme, Aguiar, Daniel P. P. de, Assis, Rafael L., Lopes, Aline, Parolin, Pia, Leão do Amaral, Iêda, Coelho, Luiz de Souza, de Almeida Matos, Francisca Dionízia, Lima Filho, Diógenes de Andrade, Salomão, Rafael P., Castilho, Carolina V., Guevara-Andino, Juan Ernesto, Carim, Marcelo de Jesus Veiga, Phillips, Oliver L., Cárdenas López, Dairon, Magnusson, William E., Sabatier, Daniel, Revilla, Juan David Cardenas, Molino, Jean-François, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Ramos, José Ferreira, Rodrigues, Domingos de Jesus, Bánki, Olaf S., Peres, Carlos A., Pitman, Nigel C. A., Hawes, Joseph E., Almeida, Everton José, Barbosa, Luciane Ferreira, Cavalheiro, Larissa, dos Santos, Márcia Cléia Vilela, Luize, Bruno Garcia, Novo, Evlyn Márcia Moraes de Leão, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Costa, Flávia R. C., Honorio Coronado, Euridice N., Monteagudo Mendoza, Abel, Montero, Juan Carlos, Feldpausch, Ted R., Aymard C, Gerardo A., Baraloto, Chris, Castaño Arboleda, Nicolás, Engel, Julien, Petronelli, Pascal, Zartman, Charles Eugene, Killeen, Timothy J., Rincón, Lorena Maniguaje, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Schietti, Juliana, Sousa, Thaiane R., Vasquez, Rodolfo, Mostacedo, Bonifacio, Dantas do Amaral, Dário, Castellanos, Hernán, Medeiros, Marcelo Brilhante de, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, William F., Laurance, Susan G. W., Farias, Emanuelle de Sousa, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Mendonça Nascimento, Henrique Eduardo, Queiroz, Helder Lima de, Brienen, Roel, Stevenson, Pablo R., Araujo-Murakami, Alejandro, Baker, Tim R., Cintra, Bruno Barçante Ladvocat, Feitosa, Yuri Oliveira, Mogollón, Hugo F., Noronha, Janaína Costa, Barbosa, Flávia Rodrigues, de Sá Carpanedo, Rainiellen, Duivenvoorden, Joost F., Silman, Miles R., Ferreira, Leandro Valle, Levis, Carolina, Lozada, José Rafael, Comiskey, James A., Draper, Freddie C., Toledo, José Julio de, Damasco, Gabriel, Dávila, Nállarett, García-Villacorta, Roosevelt, Vicentini, Alberto, Cornejo Valverde, Fernando, Alonso, Alfonso, Arroyo, Luzmila, Dallmeier, Francisco, Gomes, Vitor H. F., Jimenez, Eliana M., Neill, David, Peñuela Mora, Maria Cristina, Carvalho, Fernanda Antunes, Coelho de Souza, Fernanda, Feeley, Kenneth J., Gribel, Rogerio, Pansonato, Marcelo Petratti, Ríos Paredes, Marcos, Barlow, Jos, Berenguer, Erika, Dexter, Kyle G., Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Huamantupa-Chuquimaco, Isau, Licona, Juan Carlos, Pennington, Toby, Villa Zegarra, Boris Eduardo, Vos, Vincent Antoine, Cerón, Carlos, Fonty, Émile, Henkel, Terry W., Maas, Paul, Pos, Edwin, Silveira, Marcos, Stropp, Juliana, Thomas, Raquel, Daly, Doug, Milliken, William, Pardo Molina, Guido, Vieira, Ima Célia Guimarães, Albuquerque, Bianca Weiss, Campelo, Wegliane, Emilio, Thaise, Fuentes, Alfredo, Klitgaard, Bente, Marcelo Pena, José Luis, Souza, Priscila F., Tello, J. Sebastián, Vriesendorp, Corine, Chave, Jerome, Di Fiore, Anthony, Hilário, Renato Richard, Pereira, Luciana de Oliveira, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Balee, William, Barbosa, Edelcilio Marques, Bonates, Luiz Carlos de Matos, Doza, Hilda Paulette Dávila, Gómez, Ricardo Zárate, Gonzales, Therany, Gonzales, George Pepe Gallardo, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, Miranda, Ires Paula de Andrade, Mozombite-Pinto, Linder Felipe, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Zent, Stanford, Zent, Egleé L., Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña, Maria Natalia, van der Heijden, Geertje, Vilanova Torre, Emilio, Ahuite Reategui, Manuel Augusto, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Parada, Germaine Alexander, Torres-Lezama, Armando, Urrego Giraldo, Ligia Estela, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., de Oliveira, Edmar Almeida, Garcia-Cabrera, Karina, Hernandez, Lionel, Palacios Cuenca, Walter, Pansini, Susamar, Pauletto, Daniela, Ramirez Arevalo, Freddy, Sampaio, Adeilza Felipe, Valderrama Sandoval, Elvis H., Valenzuela Gamarra, Luis, and ter Steege, Hans

Published
2024
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25. Past and future climate effects on population structure and diversity of North Pacific surfgrasses

Author

Tavares, Ana I, Assis, Jorge, Anderson, Laura, Raimondi, Pete, Coelho, Nelson Castilho, Paulino, Cristina, Ladah, Lydia, Nakaoka, Masahiro, Pearson, Gareth A, and Serrao, Ester A

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Climate Action, climate change, genetic diversity, marine biogeography, range shifts, SDMs, seagrasses, Earth Sciences, Environmental Sciences, Biological sciences, Earth sciences, Environmental sciences
Abstract

Abstract: Aim: Understanding the impacts of past and future climate change on genetic diversity and structure is a current major research gap. We ask whether past range shifts explain the observed genetic diversity of surfgrass species and if future climate change projections anticipate genetic diversity losses. Our study aims to identify regions of long‐term climate suitability with higher and unique seagrass genetic diversity and predict future impacts of climate change on them. Location: Northeast Pacific. Time Period: Analyses considered a timeframe from the Last Glacial Maximum (LGM; 20 kybp) until one Representative Concentration Pathway (RCP) scenario of future climate changes (RCP 8.5; 2100). Major Taxa Studied: Two seagrass species belonging to the genus Phyllospadix. Methods: We estimated population genetic diversity and structure using 11 polymorphic microsatellite markers. We predicted the distribution of the species for the present, LGM, and near future (RCP 8.5, no climate mitigation) using Species Distribution Models (SDMs). Results: SDMs revealed southward range shifts during the LGM and potential poleward expansions in the future. Genetic diversity of Phyllospadix torreyi decreases from north to south, but in Phyllospadix scouleri the trend is variable. Phyllospadix scouleri displays signals of genome admixture at the southernmost and northernmost edges of its distribution. Main Conclusions: The genetic patterns observed in the present reveal the influence of climate‐driven range shifts in the past and suggest further consequences of climate change in the future, with potential loss of unique gene pools. This study also shows that investigating climate links to present genetic information at multiple timescales can establish a historical context for analyses of the future evolutionary history of populations.

Published
2024

28. Characterization of Critical Quality Attributes of an Anti-PCSK9 Monoclonal Antibody

Author

Thayana A. Cruz, Nicholas R. Larson, Yangjie Wei, Natalia Subelzu, Yaqi Wu, Christian Schöneich, Leda R. Castilho, and Charles Russell Middaugh

Subjects
anti-PCSK9 monoclonal antibody, evolocumab, Repatha, mAb characterization, critical quality attributes (CQAs), Biology (General), QH301-705.5
Abstract

During early development of biopharmaceuticals, suboptimal producing clones and production conditions can result in limited quantities of high-purity products. Here we describe a systematic approach, which requires minimal amounts of protein (~10 mg) to assess critical quality attributes of a monoclonal antibody (mAb). A commercial anti-PCSK9 IgG2 (evolocumab, Repatha®) and an early-stage biosimilar candidate were compared head-to-head using a range of high-throughput physicochemical and in-vitro binding analytical methods. Overall, both mAbs were shown to be highly pure and primarily monomeric, to share an identical primary structure, and to have similar higher-order structural integrity, apparent solubility, aggregation propensity, and physical stability profiles under temperature and pH stress conditions. Low levels of dimers were detected for the innovator (1.2%) and the biosimilar candidate mAb (0.3%), which also presented fragments (1.2%). Regarding charge heterogeneity, the amount of the main charge isoform was 53.6% for the innovator and 61.6% for the biosimilar candidate mAb. Acidic species were 38% for the innovator and 30% for the biosimilar candidate. Variations in the relative content of a few N-glycan species were found. The in-vitro binding affinity to PCSK9 was monitored, and no differences were detected. The mathematical approach called “error spectral difference” (ESD), proposed herein, enabled a quantitative comparison of the biophysical datasets. The workflow used in the present work to characterize CQAs at early stages is helpful in supporting the development of biosimilar mAb candidates.

Published
2024
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29. Breast cancer and cervical cancer: a comparison of the period before and during the COVID-19 pandemic

Author

Kely Paviani Stevanato, Lander dos Santos, Fernando Castilho Pelloso, Deise Helena Pelloso Borghesan, Marcia Edilaine Lopes Consolaro, Rosane de Almeida, Isabela Morais Tavares Huber, Paulo Egger, Ana Carolina Jacinto Alarcão, Rebeca Rosa de Souza, Helena Fiats Ribeiro, Camila Wohlenberg Camparoto, Mariá Romanio Bitencourt, Pedro Beraldo Borba, Lincoln Luis Silva, Maria Dalva de Barros Carvalho, and Sandra Marisa Pelloso

Subjects
Cervical cancer, Breast cancer, COVID-19, Gynecology and obstetrics, RG1-991, Public aspects of medicine, RA1-1270
Abstract

Abstract Background The coronavirus 2019 (COVID-19) pandemic impacted cancer health care in several countries, with delays in the detection and treatment of breast and cervical cancer. The objective of this study is to analyze and compare the screening, diagnosis and treatment of breast and cervical cancer in the pre-COVID period and during the COVID-19 period. Methods Cross-sectional study with secondary data collected from the Mortality Information System (SIM), Hospital Information System (SIH), Ambulatory Information System (SIA) and the Oncology Panel (PO) of breast cancer notifications with ICD C50.0 to C50.9 and cervix ICD C53.0 to C53.9, The analyzed period before the pandemic was from March 1 to October 1, 2019, and during the pandemic from March 1 to October 1, 2020. The period from 2013 to 2022 was also analyzed with the same information, including the number of diagnoses, treatments, and deaths from breast cancer and cervical cancer. The study population consisted of Brazilian women aged 25 to 70 years. In order to compare categorical variables between periods, the Chi-Square or Fisher’s Exact tests, and Mann-Whitney U tests were applied, and the Poisson Regression model was applied to model the number of reported cases of COVID-19 and the amount of procedures. Results There was a decrease in the number of mammograms and cytopathological exams during COVID-19, as well as a decrease in cases of breast and cervical cancer. The Poisson regression showed that the increase in the number of COVID-19 cases caused a decrease in the number of breast cytopathological examinations, cervical-vaginal cytopathological examinations/microflora and screening, diagnosis, initiation of treatment for breast cancer and deaths from this disease. Meanwhile, in some regions of Brazil, as the number of Covid-19 increased, there was a significantly increase in the number of mammograms performed and cervical cancer diagnoses. Conclusions The COVID-19 period in 2020 significantly impacted screening, diagnosis, treatment for breast and cervical cancer.

Published
2024
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30. Feed Restriction in Angus Steers Impacts Ruminal Bacteria, Its Metabolites, and Causes Epithelial Inflammation

Author

Qianming Jiang, Matheus Castilho Galvão, Abdulrahman S. Alharthi, Ibrahim A. Alhidary, Mateus P. Gionbelli, Joshua C. McCann, and Juan J. Loor

Subjects
beef cattle, immune response, microbiota, rumen function, Nutrition. Foods and food supply, TX341-641
Abstract

We identified alterations in the ruminal microbiome, metabolome, and epithelial inflammatory response due to moderate feed restriction (FR). Ruminal digesta and epithelial biopsies from seven ruminally cannulated Angus steers were initially collected during ad libitum access to feed (PRE). After a 10 day recovery, steers underwent a 3-day FR period (FRP) at 25% intake of PRE followed by a 15 day recovery (POST) phase with ad libitum access to feed. At the end of FRP and POST, ruminal digesta and epithelial biopsies were collected again for microbial DNA and tissue RNA extraction. RT-qPCR was applied for relative microbial abundance and RNA extraction. Metabolite profiling of digesta was performed via GC-MS. The abundance of Succinivibrio dextrinosolvens, Streptococcus bovis, and Bifidobacteria spp. (N124) was higher (p < 0.05) during FRP than PRE and POST, while Lactobacillus spp. (C25), Escherichia coli (EC42405), Fibrobacter succinogenes, and Megaspheara elsdenii abundances were lower in FRP than PRE (p < 0.05). The TNF and TLR2 mRNA abundance was greater in FRP than PRE (p < 0.05). Among 15 detected amino acids, glutamine, isoleucine, lysine, phenylalanine, threonine, and valine were lower (p < 0.05) in FRP than PRE. Metabolite pathway analysis revealed alterations in amino acid, fatty acid, vitamin, and energy metabolism during FRP (p < 0.05). The mRNA of the proinflammatory genes TNF and TLR2 in the epithelium peaked (p < 0.05) at FRP and remained higher at POST. Results indicated that a short FR influenced ruminal bacteria, reduced concentrations of most metabolites, and triggered an inflammatory response.

Published
2024
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31. Enhancing volumetric muscle loss (VML) recovery in a rat model using super durable hydrogels derived from bacteria

Author

Seyyed Vahid Niknezhad, Mehdi Mehrali, Farinaz Riyahi Khorasgani, Reza Heidari, Firoz Babu Kadumudi, Nasim Golafshan, Miguel Castilho, Cristian Pablo Pennisi, Masoud Hasany, Mohammadjavad Jahanshahi, Mohammad Mehrali, Younes Ghasemi, Negar Azarpira, Thomas L. Andresen, and Alireza Dolatshahi-Pirouz

Subjects
Materials of engineering and construction. Mechanics of materials, TA401-492, Biology (General), QH301-705.5
Abstract

Bacteria can be programmed to deliver natural materials with defined biological and mechanical properties for controlling cell growth and differentiation. Here, we present an elastic, resilient and bioactive polysaccharide derived from the extracellular matrix of Pantoea sp. BCCS 001. Specifically, it was methacrylated to generate a new photo crosslinkable hydrogel that we coined Pantoan Methacrylate or put simply PAMA. We have used it for the first time as a tissue engineering hydrogel to treat VML injuries in rats. The crosslinked PAMA hydrogel was super elastic with a recovery nearing 100 %, while mimicking the mechanical stiffness of native muscle. After inclusion of thiolated gelatin via a Michaelis reaction with acrylate groups on PAMA we could also guide muscle progenitor cells into fused and aligned tubes – something reminiscent of mature muscle cells. These results were complemented by sarcomeric alpha-actinin immunostaining studies. Importantly, the implanted hydrogels exhibited almost 2-fold more muscle formation and 50 % less fibrous tissue formation compared to untreated rat groups. In vivo inflammation and toxicity assays likewise gave rise to positive results confirming the biocompatibility of this new biomaterial system. Overall, our results demonstrate that programmable polysaccharides derived from bacteria can be used to further advance the field of tissue engineering. In greater detail, they could in the foreseeable future be used in practical therapies against VML.

Published
2024
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32. The Forms of Self-Criticising & Self-Reassuring Scale - Short Form for Adolescents: Psychometric Properties in Clinical and Non-Clinical Portuguese Samples

Author

Marina Cunha, Ana Xavier, Maria Céu Salvador, and Paula Castilho

Abstract

Self-criticism is a psychological process largely studied as a vulnerability factor for several psychological difficulties in the adult population and, to a lower extent, in adolescent samples. Thus, the availability of instruments to effectively capture this construct is important, especially for younger populations. This study examined the factor structure, measurement invariance to group samples, and psychometric properties of the short version of the Forms of Self-criticism and Self-reassuring Scale (FSCRS-SF) in Portuguese adolescents in non-clinical and clinical samples. Two non-clinical samples (N = 1224 and N = 140) and a clinical sample (N = 103) were used. Participants' ages ranged between 12 and 18 years old for both genders. Participants voluntarily completed a set of self-report questionnaires in the classroom. 418 adolescents completed the FSCRS 6-weeks after the first administration. Confirmatory factor analyses showed that the factor structure of the FSCRS-SF was similar to the one found in the adults' version, with three factors (inadequate self, hated self, and reassured self). The measurement invariance was established for both samples. The FSCRS-SF revealed adequate to good construct validity, reliability, and temporal stability. Gender differences were found for the three subscales. Similarly, adolescents from the clinical sample reported higher levels of inadequate self and hated self and lower levels of reassured self in comparison with the non-clinical sample, as expected. The FSCRS-SF was revealed to be a valid and reliable measure of self-criticism and self-reassurance for adolescents and seems to be a useful tool for research and clinical purposes.

Published
2024
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38. Analyzing Dataset Annotation Quality Management in the Wild

Author

Klie, Jan-Christoph, de Castilho, Richard Eckart, and Gurevych, Iryna

Subjects
Computer Science - Computation and Language
Abstract

Data quality is crucial for training accurate, unbiased, and trustworthy machine learning models as well as for their correct evaluation. Recent works, however, have shown that even popular datasets used to train and evaluate state-of-the-art models contain a non-negligible amount of erroneous annotations, biases, or artifacts. While practices and guidelines regarding dataset creation projects exist, to our knowledge, large-scale analysis has yet to be performed on how quality management is conducted when creating natural language datasets and whether these recommendations are followed. Therefore, we first survey and summarize recommended quality management practices for dataset creation as described in the literature and provide suggestions for applying them. Then, we compile a corpus of 591 scientific publications introducing text datasets and annotate it for quality-related aspects, such as annotator management, agreement, adjudication, or data validation. Using these annotations, we then analyze how quality management is conducted in practice. A majority of the annotated publications apply good or excellent quality management. However, we deem the effort of 30\% of the works as only subpar. Our analysis also shows common errors, especially when using inter-annotator agreement and computing annotation error rates.

Published
2023

39. Reanalysis of neutron-capture elements in the benchmark r-rich star CS 31082-001

Author

Ernandes, H., Castro, M. J., Barbuy, B., Spite, M., Hill, V., Castilho, B., and Evans, C. J.

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

We revisit the abundances of neutron-capture elements in the metal-poor ([Fe/H]=-2.9) r-process-rich halo star CS 31082-001. Partly motivated by the development of the new near-ultraviolet Cassegrain U-band Efficient Spectrograph for the Very Large Telescope, we compiled an expanded line list for heavy elements over the range 3000-4000 {\AA}, including hyperfine structure for several elements. Combining archival near-ultraviolet spectra of CS 31082-001 from the Hubble Space Telescope and the Very Large Telescope, we investigate the abundances and nucleosynthesis of 35 heavy elements (Ge, Sr, Y, Zr, Nb, Mo, Ru, Rh, Pd, Ag, Cd, Sn, Ba, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Os, Ir, Pt, Pb, Bi, Th, and U). Our analysis includes the first abundance estimates for tin, holmium, and ytterbium from these data, and the first for lutetium from ground-based data, enabling a more complete view of the abundance pattern of this important reference star. In general, the r-process dominated elements are as enhanced as those in the Sun, particularly for elements with Z $\ge$ 56 (Ba and heavier). However, the abundances for the lighter elements in our sample, from Ge to Sn (31 $\le$ Z $\le$ 50), do not scale with the solar abundance pattern. Moreover, the Ge abundance is deficient relative to solar, indicating that it is dominantly an iron-peak rather than neutron-capture element. Our results (or upper limits) on Sn, Pt, Au, Pb and Bi all pose further questions, prompting further study on the origin and evolution of the known r-rich and actinide-rich, metal-poor stars.

Published
2023
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40. Sensitivity of South American tropical forests to an extreme climate anomaly

Author

Bennett, Amy C, Rodrigues de Sousa, Thaiane, Monteagudo-Mendoza, Abel, Esquivel-Muelbert, Adriane, Morandi, Paulo S, Coelho de Souza, Fernanda, Castro, Wendeson, Duque, Luisa Fernanda, Flores Llampazo, Gerardo, Manoel dos Santos, Rubens, Ramos, Eliana, Vilanova Torre, Emilio, Alvarez-Davila, Esteban, Baker, Timothy R, Costa, Flávia RC, Lewis, Simon L, Marimon, Beatriz S, Schietti, Juliana, Burban, Benoît, Berenguer, Erika, Araujo-Murakami, Alejandro, Restrepo Correa, Zorayda, Lopez, Wilmar, Delgado Santana, Flávia, Viscarra, Laura Jessica, Elias, Fernando, Vasquez Martinez, Rodolfo, Marimon-Junior, Ben Hur, Galbraith, David, Sullivan, Martin JP, Emilio, Thaise, Prestes, Nayane CCS, Barlow, Jos, Alencar Fagundes, Nathalle Cristine, Almeida de Oliveira, Edmar, Alvarez Loayza, Patricia, Alves, Luciana F, Aparecida Vieira, Simone, Andrade Maia, Vinícius, Aragão, Luiz EOC, Arets, Eric JMM, Arroyo, Luzmila, Bánki, Olaf, Baraloto, Christopher, Barbosa Camargo, Plínio, Barroso, Jorcely, Bento da Silva, Wilder, Bonal, Damien, Borges Miranda Santos, Alisson, Brienen, Roel JW, Brown, Foster, Castilho, Carolina V, Cerruto Ribeiro, Sabina, Chama Moscoso, Victor, Chavez, Ezequiel, Comiskey, James A, Cornejo Valverde, Fernando, Dávila Cardozo, Nállarett, de Aguiar-Campos, Natália, de Oliveira Melo, Lia, del Aguila Pasquel, Jhon, Derroire, Géraldine, Disney, Mathias, do Socorro, Maria, Dourdain, Aurélie, Feldpausch, Ted R, Ferreira, Joice, Forni Martins, Valeria, Gardner, Toby, Gloor, Emanuel, Gutierrez Sibauty, Gloria, Guillen, René, Hase, Eduardo, Hérault, Bruno, Honorio Coronado, Eurídice N, Huaraca Huasco, Walter, Janovec, John P, Jimenez-Rojas, Eliana, Joly, Carlos, Kalamandeen, Michelle, Killeen, Timothy J, Lais Farrapo, Camila, Levesley, Aurora, Lizon Romano, Leon, Lopez Gonzalez, Gabriela, Maës dos Santos, Flavio Antonio, Magnusson, William E, Malhi, Yadvinder, Matias de Almeida Reis, Simone, Melgaço, Karina, Melo Cruz, Omar A, Mendoza Polo, Irina, Montañez, Tatiana, Morel, Jean Daniel, Núñez Vargas, M Percy, Oliveira de Araújo, Raimunda, Pallqui Camacho, Nadir C, Parada Gutierrez, Alexander, Pennington, Toby, and Pickavance, Georgia C

Subjects
Agricultural, Veterinary and Food Sciences, Climate Change Impacts and Adaptation, Biological Sciences, Ecology, Environmental Sciences, Forestry Sciences, Climate Action, Life on Land, Atmospheric Sciences, Physical Geography and Environmental Geoscience, Environmental Science and Management
Abstract

Abstract: The tropical forest carbon sink is known to be drought sensitive, but it is unclear which forests are the most vulnerable to extreme events. Forests with hotter and drier baseline conditions may be protected by prior adaptation, or more vulnerable because they operate closer to physiological limits. Here we report that forests in drier South American climates experienced the greatest impacts of the 2015–2016 El Niño, indicating greater vulnerability to extreme temperatures and drought. The long-term, ground-measured tree-by-tree responses of 123 forest plots across tropical South America show that the biomass carbon sink ceased during the event with carbon balance becoming indistinguishable from zero (−0.02 ± 0.37 Mg C ha−1 per year). However, intact tropical South American forests overall were no more sensitive to the extreme 2015–2016 El Niño than to previous less intense events, remaining a key defence against climate change as long as they are protected.

Published
2023

42. Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil

Author

Castilho, Marcia da Costa, de Filippis, Ana Maria Bispo, Machado, Lais Ceschini, de Lima Calvanti, Thaise Yasmine Vasconcelos, Lima, Morganna Costa, Fonseca, Vagner, Giovanetti, Marta, Docena, Cassia, Neto, Armando Menezes, Botto-Menezes, Camila Helena Aguiar, Kara, Edna Oliveira, de La Barrera, Rafael, Modjarrad, Kayvon, Giozza, Silvana Pereira, Pereira, Gerson Fernando, Alcantara, Luiz Carlos Junior, Broutet, Nathalie Jeanne Nicole, Calvet, Guilherme Amaral, Wallau, Gabriel Luz, and Franca, Rafael Freitas Oliveira

Subjects
Genomics -- Analysis -- Health aspects, Viral antibodies -- Health aspects -- Analysis, Genomes -- Analysis -- Health aspects, Phylogeny -- Health aspects -- Analysis, Antibodies -- Health aspects -- Analysis, Health, World Health Organization
Abstract

Zika virus (ZIKV) is an arthropodborne virus belonging to the Flaviviridae family. Virions are enveloped for a single-stranded positive-sense RNA genome of [approximately equal to]10.8-kb (1). ZIKV is transmitted through [...]

Published
2024
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43. Comparing Master-Slave Topologies for Time Signal Distribution

Author

Piqueira, José Roberto Castilho, Abarbanel, Henry D. I., Series Editor, Braha, Dan, Series Editor, Érdi, Péter, Series Editor, Friston, Karl J., Series Editor, Grillner, Sten, Series Editor, Haken, Hermann, Series Editor, Jirsa, Viktor, Series Editor, Kacprzyk, Janusz, Series Editor, Kaneko, Kunihiko, Series Editor, Kelso, Scott, Founding Editor, Kirkilionis, Markus, Series Editor, Menezes, Ronaldo, Series Editor, Kurths, Jürgen, Series Editor, Nowak, Andrzej, Series Editor, Qudrat-Ullah, Hassan, Series Editor, Reichl, Linda, Series Editor, Schuster, Peter, Series Editor, Schweitzer, Frank, Series Editor, Sornette, Didier, Series Editor, Thurner, Stefan, Series Editor, Castilho Piqueira, José Roberto, editor, Nigro Mazzilli, Carlos Eduardo, editor, Pesce, Celso Pupo, editor, and Franzini, Guilherme Rosa, editor

Published
2024
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44. The biogeography of the Amazonian tree flora

Author

Luize, Bruno Garcia, Tuomisto, Hanna, Ekelschot, Robin, Dexter, Kyle G., Amaral, Iêda L. do, Coelho, Luiz de Souza, Matos, Francisca Dionízia de Almeida, Lima Filho, Diógenes de Andrade, Salomão, Rafael P., Wittmann, Florian, Castilho, Carolina V., Carim, Marcelo de Jesus Veiga, Guevara, Juan Ernesto, Phillips, Oliver L., Magnusson, William E., Sabatier, Daniel, Cardenas Revilla, Juan David, Molino, Jean-François, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Ramos, José Ferreira, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Cárdenas López, Dairon, Pitman, Nigel C. A., Demarchi, Layon O., Schöngart, Jochen, de Leão Novo, Evlyn Márcia Moraes, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Honorio Coronado, Euridice N., Mendoza, Abel Monteagudo, Montero, Juan Carlos, Costa, Flávia R. C., Feldpausch, Ted R., Quaresma, Adriano Costa, Castaño Arboleda, Nicolás, Zartman, Charles Eugene, Killeen, Timothy J., Marimon, Beatriz S., Marimon, Ben Hur, Vasquez, Rodolfo, Mostacedo, Bonifacio, Assis, Rafael L., Baraloto, Chris, do Amaral, Dário Dantas, Engel, Julien, Petronelli, Pascal, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, William F., Laurance, Susan G. W., Rincón, Lorena Maniguaje, Schietti, Juliana, Sousa, Thaiane R., Mori, Gisele Biem, Farias, Emanuelle de Sousa, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Nascimento, Henrique Eduardo Mendonça, de Queiroz, Helder Lima, Vasconcelos, Caroline C., Aymard C, Gerardo A., Brienen, Roel, Stevenson, Pablo R., Araujo-Murakami, Alejandro, Cintra, Bruno Barçante Ladvocat, Baker, Tim R., Feitosa, Yuri Oliveira, Mogollón, Hugo F., Duivenvoorden, Joost F., Peres, Carlos A., Silman, Miles R., Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A., de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Draper, Freddie C., García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Valverde, Fernando Cornejo, Alonso, Alfonso, Arroyo, Luzmila, Dallmeier, Francisco, Gomes, Vitor H. F., Jimenez, Eliana M., Neill, David, Peñuela Mora, Maria Cristina, Noronha, Janaína Costa, de Aguiar, Daniel P. P., Barbosa, Flávia Rodrigues, Bredin, Yennie K., Carpanedo, Rainiellen de Sá, Carvalho, Fernanda Antunes, Souza, Fernanda Coelho de, Feeley, Kenneth J., Gribel, Rogerio, Haugaasen, Torbjørn, Hawes, Joseph E., Pansonato, Marcelo Petratti, Pipoly, III, John J., Paredes, Marcos Ríos, Rodrigues, Domingos de Jesus, Barlow, Jos, Berenguer, Erika, da Silva, Izaias Brasil, Ferreira, Maria Julia, Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Levis, Carolina, Licona, Juan Carlos, Villa Zegarra, Boris Eduardo, Vos, Vincent Antoine, Cerón, Carlos, Durgante, Flávia Machado, Fonty, Émile, Henkel, Terry W., Householder, John Ethan, Huamantupa-Chuquimaco, Isau, Silveira, Marcos, Stropp, Juliana, Thomas, Raquel, Daly, Doug, Milliken, William, Molina, Guido Pardo, Pennington, Toby, Vieira, Ima Célia Guimarães, Albuquerque, Bianca Weiss, Campelo, Wegliane, Fuentes, Alfredo, Klitgaard, Bente, Pena, José Luis Marcelo, Tello, J. Sebastián, Vriesendorp, Corine, Chave, Jerome, Di Fiore, Anthony, Hilário, Renato Richard, Pereira, Luciana de Oliveira, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Balee, William, Barbosa, Edelcilio Marques, Bonates, Luiz Carlos de Matos, Dávila Doza, Hilda Paulette, Zárate Gómez, Ricardo, Gonzales, Therany, Gallardo Gonzales, George Pepe, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, Miranda, Ires Paula de Andrade, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Zent, Stanford, Zent, Egleé L., Endara, María José, Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Monteiro Flores, Bernardo, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Lobo, Guilherme, Torres Montenegro, Luis, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Pombo, Maihyra Marina, Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Umaña, Maria Natalia, van der Heijden, Geertje, Vilanova Torre, Emilio, Vargas, Tony Mori, Ahuite Reategui, Manuel Augusto, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Parada, Germaine Alexander, Torres-Lezama, Armando, Urrego Giraldo, Ligia Estela, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., de Oliveira, Edmar Almeida, Fortier, Riley P., Garcia-Cabrera, Karina, Hernandez, Lionel, Palacios Cuenca, Walter, Pansini, Susamar, Pauletto, Daniela, Ramirez Arevalo, Freddy, Sampaio, Adeilza Felipe, Valderrama Sandoval, Elvis H., Valenzuela Gamarra, Luis, Hirota, Marina, Palma-Silva, Clarisse, and ter Steege, Hans

Published
2024
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45. Building a Portuguese coalition for biodiversity genomics

Author

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

Published
2024
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46. Breast cancer and cervical cancer: a comparison of the period before and during the COVID-19 pandemic

Author

Stevanato, Kely Paviani, Santos, Lander dos, Pelloso, Fernando Castilho, Borghesan, Deise Helena Pelloso, Consolaro, Marcia Edilaine Lopes, de Almeida, Rosane, Huber, Isabela Morais Tavares, Egger, Paulo, Alarcão, Ana Carolina Jacinto, de Souza, Rebeca Rosa, Ribeiro, Helena Fiats, Camparoto, Camila Wohlenberg, Bitencourt, Mariá Romanio, Borba, Pedro Beraldo, Silva, Lincoln Luis, de Barros Carvalho, Maria Dalva, and Pelloso, Sandra Marisa

Published
2024
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48. Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis

Author

de Carvalho Araujo, Andreina, Cho, Andrew Yong, Silva, Laura Morais Nascimento, Corrêa, Thais Camilo, de Souza, Gabriela Cristini, Albuquerque, Adriana Silva, Macagnan, Eduardo, Kolesnikvoas, Cristiane K. M., Meurer, Rafael, Vieira, Jenyffer Vierheller, Lemos, Giulia Gaglianone, Barreto, André Silva, Dick, Jeferson Luis, Groch, Karina Rejane, de Castilho, Pedro Volkmer, Amgarten, Deyvid, Malta, Fernanda, Miller, Michael, Dorlass, Erick G., Palameta, Soledad, Lee, Sun-Hak, Arns, Clarice Weis, Durigon, Edison L., Pinho, João Renato R., Lee, Dong-Hun, and Ferreira, Helena Lage

Published
2024
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