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1. Communication Intervention Using Digital Technology to Facilitate Informed Choices at Childbirth in the Context of the COVID-19 Pandemic: Protocol for a Randomized Controlled Trial

Author

Diniz, Carmen Simone Grilo, Franzon, Ana Carolina Arruda, Fioretti-Foschi, Beatriz, Niy, Denise Yoshie, Pedrilio, Livia Sanches, Amaro Jr, Edson, and Sato, João Ricardo

Subjects
Medicine, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

BackgroundIn Brazil and other low- and middle-income countries, excess interventions in childbirth are associated with an increase in preterm and early-term births, contributing to stagnant morbidity and mortality of mothers and neonates. The fact that women often report a negative experience with vaginal childbirth, with physical pain and feelings of unsafety, neglect, or abuse, may explain the high acceptability of elective cesarean sections. The recognition of information needs and of the right to informed choice during childbirth can help change this reality. The internet has been the main source of health information, but its quality is highly variable. ObjectiveThis study aimed to develop and evaluate an information and communication strategy through a smartphone app with respect to childbirth, to facilitate informed choices for access to safer and evidence-based care in the context of the COVID-19 pandemic. MethodsA randomized controlled trial, with 2 arms (intervention and control) and a closed, blind, parallel design, will be conducted with a smartphone app designed for behavior and opinion research in Brazil, with women of reproductive age previously registered on the app. After completing an entry questionnaire to verify the eligibility criteria and obtaining ethical consent, approximately 20,000 participants will be randomly allocated to the intervention and control groups at a 1:1 ratio. Participants allocated to the intervention group will be invited to engage in a digital information and communication strategy, which is designed to expand evidence-based knowledge on the advantages and disadvantages of options for labor and childbirth and the safety of the care processes. The information is based on the guidelines of the Ministry of Health and the World Health Organization for a positive childbirth experience and has been updated to include the new challenges and disruptions in maternity care within the context of the COVID-19 pandemic. The control group will receive information regarding disposable and reusable diapers as a placebo intervention. The groups will be compared in their responses in generating the birth plan and the entry and exit questionnaires, regarding responses less or more aligned with the guidelines for a positive childbirth experience. A qualitative component to map information needs is included. ResultsThe digital trial started recruiting participants in late October 2020, and data collection has been projected to be complete by December 2020. ConclusionsThis study will evaluate an innovative intervention that has the potential to promote better communication between women and providers, such that they can make better choices using an approach suitable for use during the COVID-19 pandemic. Trial RegistrationThe Brazilian Clinical Trials Registry U1111-1255-8683; http://www.ensaiosclinicos.gov.br/rg/RBR-3g5f9f/ International Registered Report Identifier (IRRID)PRR1-10.2196/25016

Published
2021
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2. Transformer-based normative modelling for anomaly detection of early schizophrenia

Author

Da Costa, Pedro F, Dafflon, Jessica, Mendes, Sergio Leonardo, Sato, João Ricardo, Cardoso, M. Jorge, Leech, Robert, Jones, Emily JH, and Pinaya, Walter H. L.

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence
Abstract

Despite the impact of psychiatric disorders on clinical health, early-stage diagnosis remains a challenge. Machine learning studies have shown that classifiers tend to be overly narrow in the diagnosis prediction task. The overlap between conditions leads to high heterogeneity among participants that is not adequately captured by classification models. To address this issue, normative approaches have surged as an alternative method. By using a generative model to learn the distribution of healthy brain data patterns, we can identify the presence of pathologies as deviations or outliers from the distribution learned by the model. In particular, deep generative models showed great results as normative models to identify neurological lesions in the brain. However, unlike most neurological lesions, psychiatric disorders present subtle changes widespread in several brain regions, making these alterations challenging to identify. In this work, we evaluate the performance of transformer-based normative models to detect subtle brain changes expressed in adolescents and young adults. We trained our model on 3D MRI scans of neurotypical individuals (N=1,765). Then, we obtained the likelihood of neurotypical controls and psychiatric patients with early-stage schizophrenia from an independent dataset (N=93) from the Human Connectome Project. Using the predicted likelihood of the scans as a proxy for a normative score, we obtained an AUROC of 0.82 when assessing the difference between controls and individuals with early-stage schizophrenia. Our approach surpassed recent normative methods based on brain age and Gaussian Process, showing the promising use of deep generative models to help in individualised analyses., Comment: 10 pages, 2 figures, 2 tables, presented at NeurIPS22@PAI4MH

Published
2022

3. White matter diffusion estimates in obsessive-compulsive disorder across 1653 individuals: machine learning findings from the ENIGMA OCD Working Group

Author

Kim, Bo-Gyeom, Kim, Gakyung, Abe, Yoshinari, Alonso, Pino, Ameis, Stephanie, Anticevic, Alan, Arnold, Paul D., Balachander, Srinivas, Banaj, Nerisa, Bargalló, Nuria, Batistuzzo, Marcelo C., Benedetti, Francesco, Bertolín, Sara, Beucke, Jan Carl, Bollettini, Irene, Brem, Silvia, Brennan, Brian P., Buitelaar, Jan K., Calvo, Rosa, Castelo-Branco, Miguel, Cheng, Yuqi, Chhatkuli, Ritu Bhusal, Ciullo, Valentina, Coelho, Ana, Couto, Beatriz, Dallaspezia, Sara, Ely, Benjamin A., Ferreira, Sónia, Fontaine, Martine, Fouche, Jean-Paul, Grazioplene, Rachael, Gruner, Patricia, Hagen, Kristen, Hansen, Bjarne, Hanna, Gregory L., Hirano, Yoshiyuki, Höxter, Marcelo Q., Hough, Morgan, Hu, Hao, Huyser, Chaim, Ikuta, Toshikazu, Jahanshad, Neda, James, Anthony, Jaspers-Fayer, Fern, Kasprzak, Selina, Kathmann, Norbert, Kaufmann, Christian, Kim, Minah, Koch, Kathrin, Kvale, Gerd, Kwon, Jun Soo, Lazaro, Luisa, Lee, Junhee, Lochner, Christine, Lu, Jin, Manrique, Daniela Rodriguez, Martínez-Zalacaín, Ignacio, Masuda, Yoshitada, Matsumoto, Koji, Maziero, Maria Paula, Menchón, Jose M., Minuzzi, Luciano, Moreira, Pedro Silva, Morgado, Pedro, Narayanaswamy, Janardhanan C., Narumoto, Jin, Ortiz, Ana E., Ota, Junko, Pariente, Jose C., Perriello, Chris, Picó-Pérez, Maria, Pittenger, Christopher, Poletti, Sara, Real, Eva, Reddy, Y. C. Janardhan, van Rooij, Daan, Sakai, Yuki, Sato, João Ricardo, Segalas, Cinto, Shavitt, Roseli G., Shen, Zonglin, Shimizu, Eiji, Shivakumar, Venkataram, Soreni, Noam, Soriano-Mas, Carles, Sousa, Nuno, Sousa, Mafalda Machado, Spalletta, Gianfranco, Stern, Emily R., Stewart, S. Evelyn, Szeszko, Philip R., Thomas, Rajat, Thomopoulos, Sophia I., Vecchio, Daniela, Venkatasubramanian, Ganesan, Vriend, Chris, Walitza, Susanne, Wang, Zhen, Watanabe, Anri, Wolters, Lidewij, Xu, Jian, Yamada, Kei, Yun, Je-Yeon, Zarei, Mojtaba, Zhao, Qing, Zhu, Xi, Thompson, Paul M., Bruin, Willem B., van Wingen, Guido A., Piras, Federica, Piras, Fabrizio, Stein, Dan J., van den Heuvel, Odile A., Simpson, Helen Blair, Marsh, Rachel, and Cha, Jiook

Published
2024
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5. A magnetic resonance imaging-based morphometric and structural covariance network study of Brazilian adolescents stratified by depression risk

Author

Rohrsetzer, Fernanda, Balardin, Joana Bisol, Picon, Felipe, Sato, João Ricardo, Battel, Lucas, Viduani, Anna, Manfro, Pedro Henrique, Yoon, Leehyun, Kohrt, Brandon A, Fisher, Helen L, Mondelli, Valeria, Swartz, Johnna R, and Kieling, Christian

Subjects
Paediatrics, Biomedical and Clinical Sciences, Depression, Brain Disorders, Biomedical Imaging, Pediatric, Clinical Research, Mental Illness, Neurosciences, Mental Health, Mental health, adolescent, depression, risk factors, methods, neuroimaging/structural, Adolescent, Clinical Sciences, Psychiatry, Clinical sciences, Clinical and health psychology
Abstract

ObjectiveTo explore differences in regional cortical morphometric structure between adolescents at risk for depression or with current depression.MethodsWe analyzed cross-sectional structural neuroimaging data from a sample of 150 Brazilian adolescents classified as low-risk (n=50) or high-risk for depression (n=50) or with current depression (n=50) through a vertex-based approach with measurements of cortical volume, surface area and thickness. Differences between groups in subcortical volumes and in the organization of networks of structural covariance were also explored.ResultsNo significant differences in brain structure between groups were observed in whole-brain vertex-wise cortical volume, surface area or thickness. Also, no significant differences in subcortical volume were observed between risk groups. In relation to the structural covariance network, there was an indication of an increase in the hippocampus betweenness centrality index in the high-risk group network compared to the low-risk and current depression group networks. However, this result was only statistically significant when applying false discovery rate correction for nodes within the affective network.ConclusionIn an adolescent sample recruited using an empirically based composite risk score, no major differences in brain structure were detected according to the risk and presence of depression.

Published
2023

6. Reduced gray matter volume in limbic and cortical areas is associated with anxiety and depression in alcohol use disorder patients

Author

Pereira-Rufino, Laís da Silva, Gobbo, Denise Ribeiro, Conte, Rafael, Sino, Raissa Mazzer de, Oliveira, Natan Nascimento de, Fidalgo, Thiago Marques, Sato, João Ricardo, Carrete Junior, Henrique, Souza-Formigoni, Maria Lucia Oliveira, Shi, Zhenhao, Vissoci, João Ricardo N., Wiers, Corinde E., and Céspedes, Isabel Cristina

Published
2025
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8. Optical imaging and spectroscopy for the study of the human brain: status report

Author

Ayaz, Hasan, Baker, Wesley B, Blaney, Giles, Boas, David A, Bortfeld, Heather, Brady, Kenneth, Brake, Joshua, Brigadoi, Sabrina, Buckley, Erin M, Carp, Stefan A, Cooper, Robert J, Cowdrick, Kyle R, Culver, Joseph P, Dan, Ippeita, Dehghani, Hamid, Devor, Anna, Durduran, Turgut, Eggebrecht, Adam T, Emberson, Lauren L, Fang, Qianqian, Fantini, Sergio, Franceschini, Maria Angela, Fischer, Jonas B, Gervain, Judit, Hirsch, Joy, Hong, Keum-Shik, Horstmeyer, Roarke, Kainerstorfer, Jana M, Ko, Tiffany S, Licht, Daniel J, Liebert, Adam, Luke, Robert, Lynch, Jennifer M, Mesquida, Jaume, Mesquita, Rickson C, Naseer, Noman, Novi, Sergio L, Orihuela-Espina, Felipe, O’Sullivan, Thomas D, Peterka, Darcy S, Pifferi, Antonio, Pollonini, Luca, Sassaroli, Angelo, Sato, João Ricardo, Scholkmann, Felix, Spinelli, Lorenzo, Srinivasan, Vivek J, St. Lawrence, Keith, Tachtsidis, Ilias, Tong, Yunjie, Torricelli, Alessandro, Urner, Tara, Wabnitz, Heidrun, Wolf, Martin, Wolf, Ursula, Xu, Shiqi, Yang, Changhuei, Yodh, Arjun G, Yücel, Meryem A, and Zhou, Wenjun

Subjects
Biomedical and Clinical Sciences, Engineering, Biomedical Engineering, Bioengineering, Neurosciences, Biomedical Imaging, Neurological, diffuse optics, optical spectroscopy, optical imaging, functional neuroscience, NIRS, DCS, Medical Biotechnology, Biomedical engineering
Abstract

This report is the second part of a comprehensive two-part series aimed at reviewing an extensive and diverse toolkit of novel methods to explore brain health and function. While the first report focused on neurophotonic tools mostly applicable to animal studies, here, we highlight optical spectroscopy and imaging methods relevant to noninvasive human brain studies. We outline current state-of-the-art technologies and software advances, explore the most recent impact of these technologies on neuroscience and clinical applications, identify the areas where innovation is needed, and provide an outlook for the future directions.

Published
2022

14. Correction: White matter diffusion estimates in obsessive-compulsive disorder across 1653 individuals: machine learning findings from the ENIGMA OCD Working Group

Author

Kim, Bo-Gyeom, Kim, Gakyung, Abe, Yoshinari, Alonso, Pino, Ameis, Stephanie, Anticevic, Alan, Arnold, Paul D., Balachander, Srinivas, Banaj, Nerisa, Bargalló, Nuria, Batistuzzo, Marcelo C., Benedetti, Francesco, Bertolín, Sara, Beucke, Jan Carl, Bollettini, Irene, Brem, Silvia, Brennan, Brian P., Buitelaar, Jan K., Calvo, Rosa, Castelo-Branco, Miguel, Cheng, Yuqi, Chhatkuli, Ritu Bhusal, Ciullo, Valentina, Coelho, Ana, Couto, Beatriz, Dallaspezia, Sara, Ely, Benjamin A., Ferreira, Sónia, Fontaine, Martine, Fouche, Jean-Paul, Grazioplene, Rachael, Gruner, Patricia, Hagen, Kristen, Hansen, Bjarne, Hanna, Gregory L., Hirano, Yoshiyuki, Höxter, Marcelo Q., Hough, Morgan, Hu, Hao, Huyser, Chaim, Ikuta, Toshikazu, Jahanshad, Neda, James, Anthony, Jaspers-Fayer, Fern, Kasprzak, Selina, Kathmann, Norbert, Kaufmann, Christian, Kim, Minah, Koch, Kathrin, Kvale, Gerd, Kwon, Jun Soo, Lazaro, Luisa, Lee, Junhee, Lochner, Christine, Lu, Jin, Manrique, Daniela Rodriguez, Martínez-Zalacaín, Ignacio, Masuda, Yoshitada, Matsumoto, Koji, Maziero, Maria Paula, Menchón, Jose M., Minuzzi, Luciano, Moreira, Pedro Silva, Morgado, Pedro, Narayanaswamy, Janardhanan C., Narumoto, Jin, Ortiz, Ana E., Ota, Junko, Pariente, Jose C., Perriello, Chris, Picó-Pérez, Maria, Pittenger, Christopher, Poletti, Sara, Real, Eva, Reddy, Y. C. Janardhan, van Rooij, Daan, Sakai, Yuki, Sato, João Ricardo, Segalas, Cinto, Shavitt, Roseli G., Shen, Zonglin, Shimizu, Eiji, Shivakumar, Venkataram, Soreni, Noam, Soriano-Mas, Carles, Sousa, Nuno, Sousa, Mafalda Machado, Spalletta, Gianfranco, Stern, Emily R., Stewart, S. Evelyn, Szeszko, Philip R., Thomas, Rajat, Thomopoulos, Sophia I., Vecchio, Daniela, Venkatasubramanian, Ganesan, Vriend, Chris, Walitza, Susanne, Wang, Zhen, Watanabe, Anri, Wolters, Lidewij, Xu, Jian, Yamada, Kei, Yun, Je-Yeon, Zarei, Mojtaba, Zhao, Qing, Zhu, Xi, Thompson, Paul M., Bruin, Willem B., van Wingen, Guido A., Piras, Federica, Piras, Fabrizio, Stein, Dan J., van den Heuvel, Odile A., Simpson, Helen Blair, Marsh, Rachel, and Cha, Jiook

Published
2024
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15. GeoSES -- um \'Indice Socioecon\^omico para Estudos de Sa\'ude no Brasil

Author

Barrozo, Ligia Vizeu, Fornaciali, Michel, de André, Carmen Diva Saldiva, Morais, Guilherme Augusto Zimeo, Mansur, Giselle, Cabral-Miranda, William, Sato, João Ricardo, and Júnior, Edson Amaro

Subjects
Computer Science - Other Computer Science, Statistics - Applications
Abstract

Objective: to define an index that summarizes the main dimensions of the socioeconomic context for research purposes, evaluation and monitoring health inequalities. Methods: the index was created from the 2010 Brazilian Demographic Census, whose variables selection was guided by theoretical references for health studies, including seven socioeconomic dimensions: education, mobility, poverty, wealth, income, segregation and deprivation of resources and services. The index was developed using principal component analysis, and was evaluated for its construct, content and applicability components. Results: GeoSES-BR dimensions showed good association with HDI-M (above 0.85). The model with the poverty dimension best explained the relative risk of avoidable cause mortality in Brazil. In the intraurban scale, the model with GeoSES-IM was the one that best explained the relative risk of mortality from circulatory system diseases. Conclusion: GeoSES showed significant explanatory potential in the studied scales., Comment: in Portuguese

Published
2019

19. Efficacy and safety of HD-tDCS and respiratory rehabilitation for critically ill patients with COVID-19 The HD-RECOVERY randomized clinical trial

Author

Andrade, Suellen Marinho, Cecília de Araújo Silvestre, Maria, Tenório de França, Eduardo Ériko, Bezerra Sales Queiroz, Maria Heloísa, de Jesus Santana, Kelly, Lima Holmes Madruga, Marcela Lais, Torres Teixeira Mendes, Cristina Katya, Araújo de Oliveira, Eliane, Bezerra, João Felipe, Barreto, Renata Gomes, Alves Fernandes da Silva, Silmara Maria, Alves de Sousa, Thais, Medeiros de Sousa, Wendy Chrystyan, Patrícia da Silva, Mariana, Cintra Ribeiro, Vanessa Meira, Lucena, Paulo, Beltrammi, Daniel, Catharino, Rodrigo Ramos, Caparelli-Dáquer, Egas, Hampstead, Benjamin M., Datta, Abhishek, Teixeira, Antonio Lucio, Fernández-Calvo, Bernardino, Sato, João Ricardo, and Bikson, Marom

Published
2022
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20. Integrating Students' Real-Time Gaze in Teacher–Student Interactions: Case Studies on the Benefits and Challenges of Eye Tracking in Primary Education.

Author

Soares Jr., Raimundo da Silva, Pinheiro, Eneyse Dayane, Oku, Amanda Yumi Ambriola, Rizzo, Marilia Biscaia, Vieira, Carolinne das Neves, and Sato, João Ricardo

Subjects
EYE tracking, DATA privacy, LEARNING, TEACHER training, STUDENT financial aid
Abstract

Integrating neuroscience techniques, such as eye tracking, into educational practices has opened new avenues for understanding the cognitive processes underlying learning. This study investigates the feasibility and practicality of using eye tracking as a supportive tool for educators in primary school settings. By taking into account eye-tracking features in lesson plans and instruction, this study explores the benefits and challenges of this technology from teachers' perspective. The findings reveal that eye tracking can enhance interactivity, maintain student attention, and provide immediate feedback, thereby aiding in identifying student difficulties that may otherwise go unnoticed. However, the study also highlights concerns related to technical complexities, data privacy, and the need for teacher training to utilize and interpret eye-tracking data effectively. These insights contribute to a nuanced understanding of how eye-tracking technology can be implemented in educational settings, offering potential pathways for personalized teaching and improved learning outcomes. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Correlation between graphs with an application to brain networks analysis

Author

Fujita, André, Takahashi, Daniel Yasumasa, Balardin, Joana Bisol, and Sato, João Ricardo

Subjects
Statistics - Methodology, Quantitative Biology - Neurons and Cognition
Abstract

The global functional brain network (graph) is more suitable for characterizing brain states than local analysis of the connectivity of brain regions. Therefore, graph-theoretic approaches are the natural methods to study the brain. However, conventional graph theoretical analyses are limited due to the lack of formal statistical methods for estimation and inference for random graphs. For example, the concept of correlation between two vectors of graphs is yet not defined. The aim of this article to introduce a notion of correlation between graphs. In order to develop a framework to infer correlation between graphs, we assume that they are generated by mathematical models and that the parameters of the models are our random variables. Then, we define that two vectors of graphs are independent whether their parameters are independent. The problem is that, in real world, the model is rarely known, and consequently, the parameters cannot be estimated. By analyzing the graph spectrum, we showed that the spectral radius is highly associated with the parameters of the graph model. Based on it, we constructed a framework for correlation inference between graphs and illustrate our approach in a functional magnetic resonance imaging data composed of 814 subjects comprising 529 controls and 285 individuals diagnosed with autism spectrum disorder (ASD). Results show that correlations between default-mode and control, default-mode and somatomotor, and default-mode and visual sub-networks are higher ($p<0.05$) in ASD than in controls.

Published
2015

28. Quantitative assessment of pilot-endured workloads during helicopter flying emergencies: an analysis of physiological parameters during an autorotation

Author

Scarpari, José Ricardo Silva, Ribeiro, Mauricio Watanabe, Deolindo, Camila Sardeto, Aratanha, Maria Adelia Albano, de Andrade, Donizeti, Forster, Carlos Henrique Quartucci, Figueira, José Márcio Pereira, Corrêa, Fernando Lucas Soares, Lacerda, Shirley Silva, Machado, Birajara Soares, Amaro Júnior, Edson, Sato, João Ricardo, Kozasa, Elisa Harumi, and Annes da Silva, Roberto Gil

Published
2021
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29. Association between spontaneous activity of the default mode network hubs and leukocyte telomere length in late childhood and early adolescence

Author

Rebello, Keila, Moura, Luciana M., Xavier, Gabriela, Spindola, Leticia M., Carvalho, Carolina Muniz, Hoexter, Marcelo Queiroz, Gadelha, Ary, Picon, Felipe, Pan, Pedro Mario, Zugman, André, Grassi-Oliveira, Rodrigo, Brietzke, Elisa, Belangero, Sintia I., Salum, Giovanni Abrahão, Rohde, Luis Augusto, Miguel, Eurípedes Constantino, Bressan, Rodrigo, Jackowski, Andrea, and Sato, João Ricardo

Published
2019
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30. Genetic risk for Alzheimer's disease and functional brain connectivity in children and adolescents

Author

Axelrud, Luiza Kvitko, Sato, João Ricardo, Santoro, Marcos Leite, Talarico, Fernanda, Pine, Daniel Samuel, Rohde, Luis Augusto, Zugman, Andre, Junior, Edson Amaro, Bressan, Rodrigo Affonseca, Grassi-Oliveira, Rodrigo, Pan, Pedro Mario, Hoffmann, Maurício Scopel, Simioni, Andre Rafael, Guinjoan, Salvador Martin, Hakonarson, Hakon, Brietzke, Elisa, Gadelha, Ary, Pellegrino da Silva, Renata, Hoexter, Marcelo Queiroz, Miguel, Euripedes Constantino, Belangero, Sintia Iole, and Salum, Giovanni Abrahão

Published
2019
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32. Discriminating different classes of biological networks by analyzing the graphs spectra distribution

Author

Takahashi, Daniel Yasumasa, Sato, João Ricardo, Ferreira, Carlos Eduardo, and Fujita, André

Subjects
Statistics - Methodology, Computer Science - Social and Information Networks, Physics - Physics and Society, Quantitative Biology - Quantitative Methods
Abstract

The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world topology. Recent studies indicate that some pathologies present topological network alterations relative to norms seen in the general population. Therefore, methods to discriminate the processes that generate the different classes of networks (e.g., normal and disease) might be crucial for the diagnosis, prognosis, and treatment of the disease. It is known that several topological properties of a network (graph) can be described by the distribution of the spectrum of its adjacency matrix. Moreover, large networks generated by the same random process have the same spectrum distribution, allowing us to use it as a "fingerprint". Based on this relationship, we introduce and propose the entropy of a graph spectrum to measure the "uncertainty" of a random graph and the Kullback-Leibler and Jensen-Shannon divergences between graph spectra to compare networks. We also introduce general methods for model selection and network model parameter estimation, as well as a statistical procedure to test the nullity of divergence between two classes of complex networks. Finally, we demonstrate the usefulness of the proposed methods by applying them on (1) protein-protein interaction networks of different species and (2) on networks derived from children diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and typically developing children. We conclude that scale-free networks best describe all the protein-protein interactions. Also, we show that our proposed measures succeeded in the identification of topological changes in the network while other commonly used measures (number of edges, clustering coefficient, average path length) failed.

Published
2012

33. Identification and quantification of Granger causality between gene sets

Author

Fujita, Andre, Sato, Joao Ricardo, Kojima, Kaname, Gomes, Luciana Rodrigues, Nagasaki, Masao, Sogayar, Mari Cleide, and Miyano, Satoru

Subjects
Statistics - Methodology
Abstract

Wiener and Granger have introduced an intuitive concept of causality between two variables which is based on the idea that an effect never occurs before its cause. Later, Geweke has generalized this concept to a multivariate Granger causality, i.e., n variables Granger-cause another variable. Although Granger causality is not "effective causality", this concept is useful to infer directionality and information flow in observational data. Granger causality is usually identified by using VAR models due to their simplicity. In the last few years, several VAR-based models were presented in order to model gene regulatory networks. Here, we generalize the multivariate Granger causality concept in order to identify Granger causalities between sets of gene expressions, i.e., whether a set of n genes Granger-causes another set of m genes, aiming at identifying and quantifying the flow of information between gene networks (or pathways). The concept of Granger causality for sets of variables is presented. Moreover, a method for its identification with a bootstrap test is proposed. This method is applied in simulated and also in actual biological gene expression data in order to model regulatory networks. This concept may be useful to understand the complete information flow from one network or pathway to the other, mainly in regulatory networks. Linking this concept to graph theory, sink and source can be generalized to node sets. Moreover, hub and centrality for sets of genes can be defined based on total information flow. Another application is in annotation, when the functionality of a set of genes is unknown, but this set is Granger caused by another set of genes which is well studied. Therefore, this information may be useful to infer or construct some hypothesis about the unknown set of genes.

Published
2009

36. Effect of male-specific childhood trauma on telomere length

Author

Xavier, Gabriela, Spindola, Letícia M., Ota, Vanessa K., Carvalho, Carolina M., Maurya, Pawan Kumar, Tempaku, Priscila F., Moretti, Patricia N., Mazotti, Diego R., Sato, João Ricardo, Brietzke, Elisa, Miguel, Euripedes Constantino, Grassi-Oliveira, Rodrigo, Mari, Jair, Bressan, Rodrigo A., Gadelha, Ary, Pan, Pedro M., and Belangero, Sintia Iole

Published
2018
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39. Effects of the brain-derived neurotropic factor variant Val66Met on cortical structure in late childhood and early adolescence

Author

de Araujo, Celia Maria, Zugman, Andre, Swardfager, Walter, Belangero, Sintia Iole Nogueira, Ota, Vanessa Kiyomi, Spindola, Leticia Maria, Hakonarson, Hakon, Pellegrino, Renata, Gadelha, Ary, Salum, Giovanni Abrahão, Pan, Pedro Mario, de Moura, Luciana Monteiro, Del Aquilla, Marco, Picon, Felipe Almeida, Amaro, Edson, Jr., Sato, João Ricardo, Brietzke, Elisa, Grassi-Oliveira, Rodrigo, Rohde, Luis Augusto P., Miguel, Euripedes Constantino, Bressan, Rodrigo A., and Jackowski, Andrea Parolin

Published
2018
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42. Brain Imaging and neurostimulation in health and disorders: status report

Author

Baptista, Abrahão Fontes, primary, Casali, Adenauer Girardi, additional, Oda, Adriana Leico, additional, Okano, Alexandre Hideki, additional, Moreira, Alexandre, additional, Santos, Ana Lúcia Yaeko da Silva, additional, Fernandes, Ana Mércia, additional, Fontana, Ana Paula, additional, Brunoni, André, additional, Fonseca, André, additional, Gosling, Artur Padão, additional, Boffino, Catarina Costa, additional, Tanaka, Clarice, additional, De Oliveira, Claudia Eunice Neves, additional, Caparelli-Dáquer, Egas, additional, De Angelis, Elisabete Carrara, additional, Rodrigues, Erika de Carvalho, additional, Fraga, Francisco, additional, Hazime, Fuad Ahmad, additional, Santana, Jamille Evelyn, additional, Sato, João Ricardo, additional, Da Silva, Josie Resende Torres, additional, Goulardins, Juliana Barbosa, additional, Valente, Julie Azevedo Araújo, additional, Monte-Silva, Katia Karina, additional, Sá, Katia Nunes, additional, Valiengo, Leandro, additional, Trambaiolli, Lucas Remoaldo, additional, Maia, Maércio, additional, Da Silva, Marcelo Lourenço, additional, Santana, Marcus Vinícius, additional, Carthery-Goulart, Maria Teresa, additional, Muszkat, Mauro, additional, Lee, Michael, additional, Parizotto, Nivaldo Antonio, additional, Montoya, Pedro, additional, Baptista, Rachel Fontes, additional, Duarte-Moreira, Rafael Jardim, additional, Brito, Rodrigo de Mattos, additional, De Oliveira, Rogério Adas Ayres, additional, Cury, Rubens, additional, Shinjo, Samuel Katsuyuki, additional, Lopes, Tiago da Silva, additional, and Zana, Yossi, additional

Published
2023
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43. Gene expression in blood of children and adolescents: Mediation between childhood maltreatment and major depressive disorder

Author

Spindola, Leticia Maria, Pan, Pedro Mario, Moretti, Patricia Natalia, Ota, Vanessa Kiyomi, Santoro, Marcos Leite, Cogo-Moreira, Hugo, Gadelha, Ary, Salum, Giovanni, Manfro, Gisele Gus, Mari, Jair Jesus, Brentani, Helena, Grassi-Oliveira, Rodrigo, Brietzke, Elisa, Miguel, Euripedes Constantino, Rohde, Luis Augusto, Sato, João Ricardo, Bressan, Rodrigo Affonseca, and Belangero, Sintia Iole

Published
2017
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50. Contributors

Author

Almqvist, Jessica, primary, Asadi, Amir, additional, Aziz, Qasim, additional, Balardin, Joana Bisol, additional, Ballester, Pedro, additional, Barbeiro, Hermes Vieira, additional, Barbeiro, Denise Frediani, additional, Bekri, Soumeya, additional, Belfort, Rubens, additional, Bergero, Miguel A., additional, Bester, Adri, additional, Bhattacharjee, Gargi, additional, Biazoli, Claudinei Eduardo, additional, Billeci, Lucia, additional, Biude da Silva Duarte, Graziela, additional, Blair, Alex B., additional, Braddick, Darren, additional, Brant, Rodrigo, additional, Britton, Robert A., additional, Burkhart, Richard A., additional, Byrne, J.A., additional, Cabral, Joaquim M.S., additional, Cabral, Thiago, additional, Câmara, José S., additional, Campillo-Artero, Carlos, additional, Castro Guzman, Grover Enrique, additional, Catela Ivkovic, Tina, additional, Cayún, Juan P., additional, Charoo, Naseem A., additional, Chen, Y., additional, Codari, Marina, additional, Correa, Graciely G., additional, Coto-Llerena, Mairene, additional, Couzigou, Patrice, additional, Cozetto, Daniel A., additional, Currie, Gemma, additional, Dalla-Pozza, L., additional, de Jesus, Victor N., additional, de Lara, Zabalo Manrique, additional, Delles, Christian, additional, de Miguel Beriain, Iñigo, additional, de Moura, Juliana, additional, de Paiva, Cintia S., additional, de Souza, Rodrigo G., additional, Detti, Paolo, additional, Díaz, Romina, additional, Ehrenfeld, Jesse M., additional, Faintuch, Bluma Linkowski, additional, Faintuch, Joel, additional, Faintuch, Jacob J., additional, Faintuch, Salomao, additional, Faraldo Corrêa, Telma A., additional, Farmer, Adam D., additional, Freire, Paulo J.C., additional, Fujita, Andre, additional, Garrido, Daniel, additional, Gayatri, Athalye-Jape, additional, Gohil, Nisarg, additional, Gómez de Cedrón, Marta, additional, Gonzalez Moron, Dolores, additional, Ishii, Tetsuya, additional, J. Pirtle, Claude, additional, Jain, Abhishek, additional, Jamieson, R.V., additional, Jiramongkolchai, Kim, additional, Kaiser, Thomas, additional, Kamel Boulos, Maged N., additional, Kanuri, Sri Harsha, additional, Kauffman, Marcelo A., additional, Khambhati, Khushal, additional, Khan, Mansoor A., additional, Kreutz, Rolf P., additional, Kuttolamadom, Mathew, additional, Lal, Hitesh, additional, Lima de Carvalho, Jose Ronaldo, additional, Lins, Milca R.C.R., additional, López-Campos, José Luis, additional, Louis Gehlbach, Peter, additional, Lumbreras, Blanca, additional, Mahajan, Vinit B., additional, Maia, Mauricio, additional, Mani, Indra, additional, Martinez, J. Alfredo, additional, Martinez, Pablo F., additional, Mary, Sheon, additional, Mathur, Tanmay, additional, Miranda, Cláudia C., additional, Mirnezami, Reza, additional, Ng, Charlotte K.Y., additional, Palau, Francesc, additional, Panchasara, Happy, additional, Pandian, Navaneeth K.R., additional, Park, Karen Sophia, additional, Passos, Ives Cavalcante, additional, Pastor-Valero, Maria, additional, Patella, Francesca, additional, Patralekh, Mohit Kumar, additional, Patusco, Lucas Mohr, additional, Pedrolli, Danielle B., additional, Pereira, Jorge A.M., additional, Pesapane, Filippo, additional, Pincelli, João Vitor, additional, Piscuoglio, Salvatore, additional, Ponce-Lorenzo, Jose J., additional, Porto-Figueira, Priscilla, additional, Priyadharshini, V.S., additional, Pushparaj, Peter Natesan, additional, Quiñones, Luis A., additional, Quintanilha, Bruna Jardim, additional, Rahman, Ziyaur, additional, Ramírez de Molina, Ana, additional, Ramos-Lopez, Omar, additional, Ramos, Kenneth S., additional, Rapole, Srikanth, additional, Rebello Pinho, João Renato, additional, Reis, Bruna Zavarize, additional, Rey-Lopez, Juan Pablo, additional, Ribeiro, Nathan V., additional, Rogero, Marcelo Macedo, additional, Roizenblatt, Marina, additional, Roizenblatt, Jaime, additional, Roza, Thiago Henrique, additional, Rozich, Noah S., additional, Ruffle, James K., additional, Sanjay, Patole, additional, Saraiva, Fábio P., additional, Sardanelli, Francesco, additional, Sato, João Ricardo, additional, Schutte, Aletta E., additional, Schwerdtfeger, Luke A., additional, Selahi, Amirali, additional, Sharma, Prakash Chand, additional, Shripada, Rao, additional, Silva, Patrick J., additional, Singh, Vijai, additional, Slaby, Ondrej, additional, Soares, Bruno Araujo, additional, Soriano, Francisco Garcia, additional, Souckova, Kamila, additional, Squizato, Patrick N., additional, Stabellini, Nickolas, additional, Staley, Christopher, additional, Stanke Scandelari, João Paulo, additional, Suter, Matteo B., additional, Sylvester, D.E., additional, Taware, Ravindra, additional, Tebani, Abdellah, additional, Teran, Luis M., additional, Terracciano, Luigi M., additional, Tis, Taleb Ba, additional, Tobet, Stuart A., additional, Tonacci, Alessandro, additional, Toribio-Mateas, Miguel, additional, Tsang, Stephen H., additional, Tsivaka, Dimitra, additional, Tsougos, Ioannis, additional, Vamvakas, Alexandros, additional, Varanini, Maurizio, additional, Vassiou, Katerina, additional, Vatti, Giampaolo, additional, Verma, Renu, additional, Verma, Kalyani, additional, Vittorelli, Luiz Otávio, additional, Volonté, Caterina, additional, von Flüe, Markus, additional, Wafi, Arsalan, additional, Wagatuma Bottolo, Bruna Mayumi, additional, Wei, Qingshan, additional, Zhang, Peng, additional, Zhang, Shengwei, additional, Zhu, Zhigang, additional, and Zimerman, Aline, additional

Published
2020
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