141 results on '"Amaral, Olavo"'
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102. Lost in translation?
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Amaral, Olavo B., primary
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- 2013
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103. Detection of higher-order G protein-coupled receptor oligomers by a combined BRET–BiFC technique
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Gandia, Jorge, Galino, Jorge, Amaral, Olavo B., Soriano, Aroa, Lluís, Carme, Franco, Rafael, and Ciruela, Francisco
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- 2008
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104. Rising Publication Delays Inflate Journal Impact Factors
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Tort, Adriano B. L., primary, Targino, Zé H., additional, and Amaral, Olavo B., additional
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- 2012
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105. A Mismatch-Based Model for Memory Reconsolidation and Extinction in Attractor Networks
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Osan, Remus, primary, Tort, Adriano B. L., additional, and Amaral, Olavo B., additional
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- 2011
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106. 37 years of scientific activity in a Biochemistry Department in Brazil: patterns of growth and factors leading to increased productivity
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Gomes, Urubatã E., primary, Oliveira, Diogo L. de, additional, Berti, Luciana C., additional, Amaral, Olavo, additional, Souza, Diogo O., additional, and Wofchuk, Susana T., additional
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- 2011
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107. Do biomarkers trump behavior?
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Amaral, Olavo B.
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Author(s): Olavo B Amaral [1] To the editor: The article entitled 'Biomarkers trump behavior in mental illness diagnosis' [1] seems to misinterpret the growing data on biomarkers in psychiatry in [...]
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- 2007
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108. A synaptic reinforcement‐based model for transient amnesia following disruptions of memory consolidation and reconsolidation
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Amaral, Olavo B., primary, Osan, Remus, additional, Roesler, Rafael, additional, and Tort, Adriano B.L., additional
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- 2008
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109. Transient Disruption of Fear-Related Memory by Post-Retrieval Inactivation of Gastrin-Releasing Peptide or N-Methyl-D-Aspartate Receptors in the Hippocampus
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Roesler, Rafael, primary, Luft, Tatiana, additional, Amaral, Olavo, additional, and Schwartsmann, Gilberto, additional
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- 2008
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110. Isolated central nervous system histoplasmosis in immunocompetent hosts: A series of 11 cases
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Schestatsky, Pedro, primary, Chedid, Marcio F., additional, Amaral, Olavo B., additional, Unis, Gisela, additional, Oliveira, Flávio M., additional, and Severo, Luiz Carlos, additional
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- 2006
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111. Serum S100B in Pregnancy-Related Hypertensive Disorders: A Case–Control Study
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Schmidt, Adriana P, primary, Tort, Adriano B L, primary, Amaral, Olavo B, primary, Schmidt, André P, primary, Walz, Roger, primary, Vettorazzi-Stuckzynski, Janete, primary, Martins-Costa, Sérgio H, primary, Ramos, José Geraldo L, primary, Souza, Diogo O, primary, and Portela, Luis V C, primary
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- 2004
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112. USE AND MISUSE OF BENZODIAZEPINES IN BRAZIL: A REVIEW
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Kapczinski, Flávio, primary, Amaral, Olavo B., additional, Madruga, Marcelo, additional, Quevedo, João, additional, Busnello, João V., additional, and de Lima, Maurício S., additional
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- 2001
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113. Evoked Potentials for the Evaluation of Latent Hepatic Encephalopathy in Pediatric Liver Transplant Candidates
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Nora, Daniel B., primary, Amaral, Olavo B., additional, Busnello, João V., additional, Quevedo, João, additional, Vieira, Sandra, additional, da Silveira, Themis R., additional, and Kapczinski, Flávio, additional
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- 2000
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114. MAPK and memory
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Walz, Roger, primary, Rockenbach, Isabel C, additional, Amaral, Olavo B, additional, Quevedo, João, additional, and Roesler, Rafael, additional
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- 1999
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115. Dose-dependent impairment of inhibitory avoidance retention in rats by immediate post-training infusion of a mitogen-activated protein kinase kinase inhibitor into cortical structures
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Walz, Roger, primary, Roesler, Rafael, additional, Quevedo, João, additional, Rockenbach, Isabel C, additional, Amaral, Olavo B, additional, Vianna, Mônica R.M, additional, Lenz, Guido, additional, Medina, Jorge H, additional, and Izquierdo, Iván, additional
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- 1999
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116. Flumazenil and hepatic encephalopathy
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Amaral, Olavo B., primary, Quevedo, Jo�o, additional, Walz, Roger, additional, and Kapczinski, Fl�vio, additional
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- 1999
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117. Patogênese da encefalopatia hepática
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Quevedo, João, primary, Amaral, Olavo B., additional, Walz, Roger, additional, and Kapczinski, Flávio, additional
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- 1999
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118. On the transdiagnostic nature of peripheral biomarkers in major psychiatric disorders: A systematic review.
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Pinto, Jairo Vinícius, Moulin, Thiago C., and Amaral, Olavo B.
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BIOMARKERS , *PATHOLOGICAL psychology , *SCHIZOPHRENIA , *BIOLOGICAL psychiatry , *PSYCHIATRIC treatment , *DIAGNOSIS - Abstract
The search for biomarkers has been a leading endeavor in biological psychiatry. To analyze its evolution over the years, we performed a systematic review to evaluate (a) the most studied peripheral molecular markers in major psychiatric disorders, (b) the main features of studies proposing them as biomarkers and (c) whether their patterns of variation are similar across disorders. Of the six molecules most commonly studied as plasmatic markers of schizophrenia, major depressive disorder or bipolar disorder, five (BDNF, TNF-alpha, IL-6, C-reactive protein and cortisol) were the same across diagnoses. An analysis of this literature showed that, while 66% of studies compared patients and controls, only 34% were longitudinal, and only 10% presented a measure of diagnostic or prognostic efficacy. Meta-analyses showed variation in the levels of these molecules to be robust across studies, but similar among disorders, suggesting them to reflect transdiagnostic systemic consequences of psychiatric illness. Based on this, we discuss how current publication practices have led to research fragmentation across diagnoses, and suggest approaches to face this issue. [ABSTRACT FROM AUTHOR]
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- 2017
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119. Transcriptional profiling of striatal neurons in response to single or concurrent activation of dopamine D2, adenosine A2A and metabotropic glutamate type 5 receptors: Focus on beta-synuclein expression
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Canela, Laia, Selga, Elisabet, García-Martínez, Juan Manuel, Amaral, Olavo B., Fernández-Dueñas, Víctor, Alberch, Jordi, Canela, Enric I., Franco, Rafael, Noé, Véronique, Lluís, Carme, Ciudad, Carlos J., and Ciruela, Francisco
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GENETIC transcription , *NEURAL physiology , *DOPAMINE , *ADENOSINES , *NEOSTRIATUM , *GLUTAMATE receptors , *SYNUCLEINS , *G protein coupled receptors - Abstract
Abstract: G protein-coupled receptor oligomerization is a concept which is changing the understanding of classical pharmacology. Both, oligomerization and functional interaction between adenosine A2A, dopamine D2 and metabotropic glutamate type 5 receptors have been demonstrated in the striatum. However, the transcriptional consequences of receptors co-activation are still unexplored. We aim here to determine the changes in gene expression of striatal primary cultured neurons upon isolated or simultaneous receptor activation. Interestingly, we found that 95 genes of the total analyzed (15,866 transcripts and variants) changed their expression in response to simultaneous stimulation of all three receptors. Among these genes, we focused on the β-synuclein (β-Syn) gene (SCNB). Quantitative PCR verified the magnitude and direction of change in expression of SCNB. Since β-Syn belongs to the homologous synuclein family and may be considered a natural regulator of α-synuclein (α-Syn), it has been proposed that β-Syn might act protectively against α-Syn neuropathology. [Copyright &y& Elsevier]
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- 2012
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120. Reconsolidação e extinção de memórias: uma abordagem computacional
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Santiago, Rodrigo Marques de Melo, Rossato, Janine Inez, Amaral, Olavo Bohrer, and Tort, Adriano Bretanha Lopes
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Memória de medo ao contexto ,Consolidação ,Rede de atratores ,Modelo computacional ,Esquiva inibitória ,OUTROS::CIENCIAS: NEUROCIÊNCIAS [CNPQ] ,Extinção ,Hopfield ,Rede de ,Reconsolidação ,Condição limitante - Abstract
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) A reconsolidação e a extinção de memórias aversivas e suas condições limitantes têm sido estudadas exaustivamente a fim de se traçar melhores estratégias para o tratamento de desordens relacionadas ao medo e à ansiedade. Em 2011, Osan et al. desenvolveram um modelo computacional para a exploração de tais fenômenos baseado na dinâmica de atratores, na plasticidade hebbiana e na degradação sináptica induzida por erro de predição. Este modelo foi capaz de explicar em um formalismo único diversos achados experimentais relativos ao comportamento de congelamento (freezing) de roedores sujeitos a paradigmas de consolidação, reconsolidação e extinção de memórias de medo ao contexto. Em 2017, Radiske et al., a partir de experimentos em ratos submetidos a tarefa de esquiva inibitória, descobriram que o conhecimento prévio do atual contexto aversivo como nãoaversivo é uma condição limitante para a reconsolidação da memória do choque experienciado no contexto. No presente trabalho, visamos investigar se o formalismo introduzido por Osan et al. (2011) é suficientemente geral para explicar os resultados comportamentais descritos por Radiske et al. (2017). Para tanto, primeiro implementamos o modelo de Osan et al. (2011) em uma linguagem de programação aberta (Python) e o validamos através da replicação dos principais resultados reportados na publicação original referentes ao condicionamento de medo ao contexto. Em seguida, adaptamos o modelo para simular protocolos experimentais na tarefa de esquiva inibitória empregados por Radiske et al. (2017). Os resultados mostram que a condição limitante encontrada por Radiske et al. (2017) é compatível com a dinâmica de uma rede de atratores que suporta um sistema de labilização sináptica comum à reconsolidação e extinção. Por fim, através da varredura de parâmetros do modelo – como os níveis de síntese e degradação proteica –, fornecemos previsões comportamentais na tarefa de esquiva inibitória passíveis de serem testadas experimentalmente. The reconsolidation and extinction of aversive memories and their boundary conditions have been extensively studied in order to outline better strategies for the treatment of fear and anxiety related disorders. In 2011, Osan et al. developed a computational model for exploring such phenomena based on attractors dynamics, Hebbian plasticity and synaptic degradation induced by prediction error. This model was able to explain in a single formalism several experimental findings regarding the freezing behavior of rodents submitted to paradigms of contextual fear memory consolidation, reconsolidation and extinction. In 2017, Radiske et al., based on experiments in rats subjected to the inhibitory avoidance task, found that the previous knowledge of the current aversive context as non-aversive is a boundary condition for the reconsolidation of the shock memory experienced in that context. In the present work, we aimed to investigate whether the formalism introduced by Osan et al. (2011) is sufficiently general to explain the behavioral results described by Radiske et al. (2017). To do so, we first implemented Osan et al.'s (2011) model in an open programming language (Python) and validated it through the replication of the main results reported in the original publication regarding contextual fear conditioning. Then, we adapted the model to simulate experimental protocols in the inhibitory avoidance task employed by Radiske et al. (2017). The results show that the boundary condition found by Radiske et al. (2017) is compatible with the dynamics of an attractor network that supports a synaptic labilization system common to reconsolidation and extinction. Finally, by exploring some model parameters – such as the levels of protein synthesis and degradation –, we provide behavioral predictions in the inhibitory avoidance task that can be tested experimentally.
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- 2018
121. Desvendando oscilações hipocampais através de comodulações
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Teixeira, Robson Scheffer, Laplagne, Diego Andres, Maciel, Sergio Tulio Neuenschwander, Amaral, Olavo Bohrer, Durand, Pablo José Fuentealba, Ribeiro, Sidarta Tollendal Gomes, and Tort, Adriano Bretanha Lopes
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Acoplamento entre frequências ,Eletrofisiologia ,Hipocampo ,OUTROS::CIENCIAS: NEUROCIÊNCIAS [CNPQ] ,HFO ,CA1 ,Teta - Abstract
Análises espectrais de registros eletrofisiológicos extracelulares têm revelado que a atividade elétrica produzida pelo cérebro é comumente organizada em padrões rítmicos, conhecidos como oscilações neuronais. Mais recentemente, descobriu-se que as oscilações neuronais de frequências distintas não são independentes, mas podem interagir entre si. Ao longo das últimas duas décadas, diversas ferramentas de análises foram desenvolvidas, amadurecidas e incorporadas de outras áreas para se estudar os chamados acoplamentos entre frequências de oscilações neuronais observadas nestes registros. Oscilações neuronais são ditas acopladas se houver uma relação de dependência entre suas características, como fase, amplitude ou frequência instantâneas. Dentre elas, o acoplamento fase-amplitude é caracterizado por um aumento da amplitude instantânea de uma banda de frequência condicionado a uma fase instantânea de uma oscilação de outra banda, enquanto que o acoplamento fase-fase do tipo n:m é caracterizado pela relação fixa entre m ciclos de uma frequência em nciclos de outra. O hipocampo é uma região cerebral envolvida na formação de memórias e navegação espacial. Assim como em outras estruturas, as redes neuronais do hipocampo produzem diversos padrões oscilatórios, que variam de acordo com os estados do ciclo sono-vigília. Entre estes padrões, classicamente destacam-se os ritmos teta (4-12 Hz) e gama (30-100 Hz), que caracterizam estados comportamentais de locomoção e sono REM. No entanto, o estudo dos padrões de acoplamento oscilatório no hipocampo tem revelado subtipos oscilatórios distintos dentro da definição tradicional da banda gama. Mais ainda, trabalhos recentes têm mostrado a existência de oscilações acopladas ao ritmo teta em frequências mais altas (>100 Hz), embora haja uma divergência na literatura atual sobre até aonde estas oscilações de altas frequências representariam atividade oscilatória genuína de redes neuronais ou se seriam derivadas de efeitos espúrios oriundos de contaminações por resquícios de potencias de ação registrados extracelularmente. A presente tese de doutorado visa contribuir para o maior entendimento dos padrões oscilatórios produzidos por redes neuronais do hipocampo, com particular foco nas relações de acoplamento entre oscilações de diferentes frequências. Através de dados próprios e compartilhados de terceiros de animais implantados cronicamente com matrizes de múltiplos eletrodos, obtivemos registros da atividade elétrica da região CA1 de ratos durante a exploração de ambientes familiares e períodos de sono. Investigamos a existência conjunta de distintos padrões oscilatórios do hipocampo em diferentes frequências através de marcadores eletrofisiológicos, anatômicos e comportamentais de cada oscilação neuronal que, quando combinados, levaram a um perfil único para cada banda de frequência. Nossos resultados mostram a existência de múltiplas bandas de frequência moduladas pelo ritmo teta hipocampal. As modulações são dotadas de diversos mecanismos separatórios, provavelmente de forma a minimizar interferências. Demonstramos ainda que padrões oscilatórios espúrios e genuínos podem co-existir numa mesma faixa de frequência, e que, ao contrário de trabalhos recentes, não há evidência para acoplamentos do tipo fase-fase n:m no hipocampo. A capacidade de uma oscilação neural interagir com outras oscilações, aparentemente independentes, levanta questionamentos naturais sobre sua significância biológica, que, apesar de diversos avanços na área, ainda permanece um mistério na sua essência. Spectral analysis of extracellular electrophysiological recordings revealed that the brain electrical activity is often organized in rhythmic patterns, known as neuronal oscillations. Recently, it was discovered that oscillations of distinct frequencies are not independent, but can interact to each other. In the last two decades, several analysis tools were developed or incorporated from other fields to study cross-frequency coupling between neural oscillations. Neural oscillations are said to be coupled if there is a dependency between their features, such as phase, amplitude or frequency. Among them, phase – amplitude coupling is characterized by an increase in the instantaneous amplitude of one frequency band conditioned to the instantaneous phase of another frequency band, whereas n:m phase – phase coupling is characterized by a fixed relation between m cycles of one frequency to n cycles of another one. The hippocampus is a brain region involved in memory formation and spatial navigation. As in other brain structures, hippocampal neural networks generate several oscillatory patterns, which vary according to the stage of the sleep-waking cycle. Among these patterns, theta (4 – 12 Hz) and gamma (30 – 100 Hz) oscillations are prominent during active waking and REM sleep. However, the study of coupling patterns in the hippocampus has revealed distinct sub-types of oscillatory activity inside the traditional gamma band. Moreover, recent studies have shown the existence of even faster oscillations coupled to theta in the hippocampus (> 100 Hz), although there is a current divergence in the literature about whether they represent genuine network activity or spurious by-products from incomplete filtering of extracellular spikes. This thesis investigates oscillatory patterns generated by hippocampal neural networks, focusing in the coupling relation among oscillations of different frequencies. Using our own data and shared third-party ones of chronically implanted animals with multisite electrodes, we recorded electrical activity in the CA1 region of rats while exploring a familiar environment and during sleep stages. We investigated the existence of simultaneous but distinct oscillatory patterns in the hippocampus separated by electrophysiological, anatomic and behavioral markers, which, once taken together, can lead to a unique profile for each frequency band. Our results point to the existence of several frequency bands coupled to the hippocampal theta rhythm. All modulations are found to be separated by mechanisms that can potentially avoid interferences. We also demonstrate that a spurious oscillatory patterns can emerge and co-exist in the same frequency band of genuine oscillations and, contrary to recent work, we show that there is lack of evidence for n:m phase – phase coupling in the hippocampus. The capacity of neural oscillations to interact with one another raises questions about the biological significance of such phenomenon; despite recent progress in the field, however, its essence remains a mystery.
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- 2016
122. Propriedade de membrana de neurônios do giro denteado em camundongos sem a enzima de reparo de DNA NEIL3
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Soares, Annara Yve Moura, Leão, Emelie Katarina Svahn, Amaral, Olavo Bohrer, and Leão, Richardson Naves
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CIENCIAS BIOLOGICAS: PSICOBIOLOGIA [CNPQ] ,Camundongo Neil3 knockout ,Giro denteado ,Propriedades neuronais ,Reparo de DNA ,Patch clamp - Abstract
Esse estudo objetiva avaliar se a expressão da enzima de reparo de DNA Neil3 é importante para o desenvolvimento funcional dos neurônios. Estudos previos tem demonstrado que Neil3 interfere tanto na neurogênese adulta como na fazer embrionaria. Eu utilizei whole cell patch clamp para estudar propriedades sinapticas e de membrana das células granulares do giro denteado. O giro denteado é uma das regiões com maior expressão de Neil3 no cérebro e estudos previos tem demonstrado que a neurogênese reativa em camundongos adultos é afetada pela ausencia da enzima de reparo Neil3. Eu encontrei que a maioria das propriedades de membrana nas células granulares de camundongos knockout para Neil3 são normais com exceção à resposta de membrana às correntes de hiperpolarização e pós-hiperpolarização. Diferentemente de neurônios imaturos, as células granulares do giro denteado de camundongos com ausência de Neil3, na qual as correntes de hiperpolarização ativadas são geralmente as ultimas a aparecerem durante o desenvolvimento. Além disso, correntes sinapticas excitatorias foram similar em amplitude mas apresentaram um decaimento ligeiramente mais rapido em células de camundongos knockout de Neil3. Esses resultados podem indicar um balanço diferente entre os receptores AMPA e NMDA em camundongos knockout. Analises morfologicas de neurônios preenchidos com biotina e reconstrução post hoc não apresentaram grandes diferenças na morfologia dendritica entre animais controle e knockout. Esse estudo mostra que, em relação diferenças entre animais controle, neurônios do giro denteado de animais knockout de Neil3 não podem ser classificados como imaturos. Eu encontrei diferenças pontuais na corrente de hiperpolarização e pequenas diferenças em propriedades sinapticas. Ainda devem ser avaliadas se essas diferenças podem ser responsáveis por alterações comportamentais encontradas em camundongos Neil3-knockout. Além disso, estudos futuros utilizando marcadores de neurônios recém-nascidos são necessários para analisar o efeito da eliminação da enzima Neil3 no desenvolvimento de neurônios. This study aims to assess whether the expression of the DNA repair enzyme Neil3 is important for the functional development of neurons. Previous studies have demonstrated that Neil3 interferes with both adult and embryonic neurogenesis. I have used whole cell patch clamp to study membrane and synaptic properties of granule cells of the dentate gyrus. The dentate gyrus is one of the regions with the highest expression of Neil3 in the brain, and previous studies have shown that reactive neurogenesis in adult mice is affected by Neil3 deletion. I found that most membrane properties of granule cells in Neil3-knockout mice are normal except from the membrane response to hyperpolarization currents and afterhyperpolarization currents. Different from immature neurons, granule cells of the dentate gyrus from Neil3-knockout mice, in which hyperpolarizing activated currents, are generally the last to appear during development. In addition, excitatory synaptic currents were similar in amplitude but showed a slightly faster decay in cells from Neil3-knockout mice. These results could indicate a different balance between AMPA and NMDA receptors in Neil3-knockout mice cells. Morphological analysis of neurons filled with biocytin and reconstructed post hoc showed no gross difference in dendritic morphology between dentate gyrus neurons of control and Neil3-knockout mice. This study shows that, while different from those of control littermates, dentate gyrus neurons of Neil3-knockout mice cannot be classified as ‘immature’. I found specific differences in hyperpolarizing activated currents and small differences in synaptic properties. Whether these differences may account for behavioral changes found in Neil3-knockout mice is yet to be assessed. In addition, future studies using markers of newly born neurons are necessary for analyzing the effect of Neil3 deletion in developing neurons.
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- 2016
123. Ex Uno Plures: sobre o uso de camundongos transgênicos e optogenética para caracterizar populações de neurônios identificadas geneticamente
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Johann, Stéfano Pupe, Laplagne, Diego Andres, Cammarota, Martin Pablo, Amaral, Olavo Bohrer, Cota, Vinicius Rosa, Tort, Adriano Bretanha Lopes, Wallén-Mackenzie, Åsa, and Leão, Richardson Naves
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Neurociências ,Animais transgênicos ,Núcleo subtalâmico ,Optogenética ,Promotores genéticos ,Hipocampo ,OUTROS::CIENCIAS: NEUROCIÊNCIAS [CNPQ] ,Área tegmental ventral - Abstract
Os neurocientistas tem uma diversidade de perspectivas com as quais podem classificar diferentes partes do cérebro. Com o surgimento de técnicas baseadas na genética, como a optogenética, se torna cada vez mais importante identificar se um grupo de células, definidas através de morfologia, função ou posição anatômica possui um padrão característico de expressão de um ou mais promotores genéticos. Isso permitiria melhores formas de estudar essas populações de neurônios definidas geneticamente. Neste trabalho, eu apresento uma discussão teórica e três estudos experimentais nos quais essa foi a principal questão sendo abordada. O Estudo I discute as questões envolvidas em selecionar um promotor para estudar estruturas e subpopulações na Área Tegmental Ventral. O Estudo II caracteriza uma subpopulação de células na Área Tegmental Ventral que compartilha a expressão de um promotor, que é anatomicamente muito restrita, e que induz aversão quando estimulada. O Estudo II utiliza uma estratégia similar para investigar a subpopulação no núcleo subtalâmico que expressa PITX2 e VGLUT2 que, quando inativada, causa hiperlocomoção. O Estudo IV explora o fato de que um grupo de células previamente identificadas no Hipocampo Ventral expressa CHRNA2, e indica que essa subpopulação pode ser necessária e suficiente para o estabelecimento do ritmo teta (2-8 Hz) no Hipocampo Ventral de camundongos anestesiados. Todos esses estudos foram guiados pela mesma estratégia de identificar um promotor genético capaz de permitir o controle de uma população de neurônios identificada geneticamente, e eles demonstram as diferentes formas em que essa abordagem pode generar novas descobertas. Neuroscientists have a variety of perspectives with which to classify different parts of the brain. With the rise of genetic-based techniques such as optogenetics, it is increasingly important to identify whether a group of cells, defined by morphology, function or anatomical location possesses a distinct pattern of expression of one or more genetic promoters. This would allow for better ways to study of these genetically defined subpopulations of neurons. In this work, I present a theoretical discussion and threeexperimental studies in which this was the main question being addressed. Paper I discusses the issues involved in selecting a promoter to study structures and subpopulations in the Ventral Tegmental Area. Paper II characterizes a subpopulation of cells in the Ventral Tegmental Area that shares the expression of a promoter and is anatomically very restricted, and induces aversion when stimulated. Paper III utilizes a similar strategy to investigate a subpopulation in the subthalamic nucleus that expresses PITX2 and VGLUT2 which, when inactivated, causes hyperlocomotion. Paper IV exploits the fact that a previously identified group of cells in the ventral hippocampus expresses CHRNA2, and indicates that this population may be necessary and sufficient for the establishment of the theta rhythm (2-8 Hz) in the Local Field Potential of anesthetized mice. All of these studies were guided by the same strategy of characterizing and studying the role of a genetically defined subpopulation of cells, and they demonstrate the different ways in which this approach can generate new discoveries.
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- 2015
124. Characterization of hippocampal place cells and their relation to local field potential oscillations
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Souza, Bryan da Costa, Laplagne, Diego Andrés, Amaral, Olavo Bohrer, and Tort, Adriano Bretanha Lopes
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Campo receptivo de lugar ,Oscilações teta ,Células de lugar ,Hipocampo ,Oscilações gamma ,OUTROS::CIENCIAS: NEUROCIÊNCIAS [CNPQ] ,Córtex entorrinal - Abstract
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES As principais vias aferentes ao hipocampo vêm do córtex entorrinal e fazem parte de um loop que retorna ao entorrinal após passar pelo giro denteado, e pelas subareas do hipocampo CA3 e CA1. Desde a descoberta nos anos 50 de que o hipocampo está envolvido na formação de memórias, esta região vem sendo extensivamente estudada. Além desta função mnemônica, o hipocampo também está associado a navegação espacial. Em camundongos e ratos, células de lugar exibem um aumento da taxa de disparo relacionado à posição do animal. O local do ambiente onde uma determinada célula de lugar se ativa é chamado de campo de lugar. A taxa de disparo das células de lugar é máxima quando o animal está no centro do campo de lugar, e diminui a medida que ele se afasta desse ponto, sugerindo a existência de uma codificação espacial baseada em taxa de disparos. Entretanto, pesquisas prévias vêm mostrando a existência de oscilações hipocampais em múltiplas frequências e ligadas a diferentes estados comportamentais, e muitos acreditam que estas oscilações são importantes para uma codificação temporal. Em particular, oscilações teta (5-12 Hz) possuem uma relação espaço-temporal com as células de lugar conhecida como precessão de fase. Na precessão, a fase de disparos da célula de lugar muda gradualmente do pico de teta para o fundo e, posteriormente, para a fase ascendente, a medida que o animal atravessa o campo de lugar. Além disso, as teorias vigentes sugerem que CA1, a porta de saída do hipocampo, intermediaria a comunicação com o córtex entorrinal e CA3 através de oscilações em diferentes frequências chamadas, respectivamente, de gama alto (60-100 Hz; HG) e gama baixo (30-60 Hz; LG). Essas oscilações se relacionam com teta, estando aninhadas dentro de cada ciclo desta frequência mais lenta. Nesta dissertação, utilizamos dados disponibilizados online para fazer análises computacionais visando reproduzir resultados clássicos e recentes acerca da atividade das células de lugar no hipocampo de ratos em livre movimento. Em particular, nós revisitamos o debate sobre a relação da precessão de fase com variações na taxa de disparos e na posição do animal no campo de lugar. Concluímos que este fenômeno não pode ser explicado por nenhuma dessas variáveis sozinha, e sim pela interação entre elas. Nós também realizamos novas análises investigando as propriedades das células de lugar em relação às oscilações. Nós mostramos que o nível de modulação dos disparos por teta afeta apenas levemente a informação espacial contida nas células de lugar, enquanto a fase de disparo média não tem nenhuma influência na informação espacial. Também encontramos que as células de lugar estão moduladas por teta quando disparam fora do campo de lugar. Além disso, nossos resultados mostram que o disparo das células de lugar dentro do ciclo de teta segue os padrões de modulação de HG e LG por teta presentes nos potenciais de campo local de CA1 e córtex entorrinal. Por último, achamos um acoplamento fase-amplitude em CA1 associado apenas aos disparos dentro do campo de lugar na faixa de 40-80 Hz. Concluímos que o disparo de células de lugar está ligado a estados de rede refletidos no potencial de campo local e sugerimos que a atividade dessas células sejam interpretadas como um estado dinâmico ao invés de uma propriedade fixa da célula. The main inputs to the hippocampus arise from the entorhinal cortex (EC) and form a loop involving the dentate gyrus, CA3 and CA1 hippocampal subfields and then back to EC. Since the discovery that the hippocampus is involved in memory formation in the 50's, this region and its circuitry have been extensively studied. Beyond memory, the hippocampus has also been found to play an important role in spatial navigation. In rats and mice, place cells show a close relation between firing rate and the animal position in a restricted area of the environment, the so-called place field. The firing of place cells peaks at the center of the place field and decreases when the animal moves away from it, suggesting the existence of a rate code for space. Nevertheless, many have described the emergence of hippocampal network oscillations of multiple frequencies depending on behavioral state, which are believed to be important for temporal coding. In particular, theta oscillations (5-12 Hz) exhibit a spatio-temporal relation with place cells known as phase precession, in which place cells consistently change the theta phase of spiking as the animal traverses the place field. Moreover, current theories state that CA1, the main output stream of the hippocampus, would interplay inputs from EC and CA3 through network oscillations of different frequencies, namely high gamma (60-100 Hz; HG) and low gamma (30-50 Hz; LG), respectively, which tend to be nested in different phases of the theta cycle. In the present dissertation we use a freely available online dataset to make extensive computational analyses aimed at reproducing classical and recent results about the activity of place cells in the hippocampus of freely moving rats. In particular, we revisit the debate of whether phase precession is due to changes in firing frequency or space alone, and conclude that the phenomenon cannot be explained by either factor independently but by their joint influence. We also perform novel analyses investigating further characteristics of place cells in relation to network oscillations. We show that the strength of theta modulation of spikes only marginally affects the spatial information content of place cells, while the mean spiking theta phase has no influence on spatial information. Further analyses reveal that place cells are also modulated by theta when they fire outside the place field. Moreover, we find that the firing of place cells within the theta cycle is modulated by HG and LG amplitude in both CA1 and EC, matching cross-frequency coupling results found at the local field potential level. Additionally, the phase-amplitude coupling in CA1 associated with spikes inside the place field is characterized by amplitude modulation in the 40-80 Hz range. We conclude that place cell firing is embedded in large network states reflected in local field potential oscillations and suggest that their activity might be seen as a dynamic state rather than a fixed property of the cell.
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- 2015
125. Indicadores de cálcio e de voltagem codificados geneticamente na detecção de potenciais de ação e inputs sinápticos em cultura de neurônios hipocampais
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Vieira, Hermany Munguba, Leão, Emelie Katarina Svahn, Amaral, Olavo Bohrer, and Leão, Richardson Naves
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Cultura neuronal. Patch-clamp. Imageamento de cálcio. Imageamento de voltagem ,Neuronal culture. patch-clamp. Calcium imaging. Voltage imaging ,OUTROS [CNPQ] - Abstract
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Recently, genetically encoded optical indicators have emerged as noninvasive tools of high spatial and temporal resolution utilized to monitor the activity of individual neurons and specific neuronal populations. The increasing number of new optogenetic indicators, together with the absence of comparisons under identical conditions, has generated difficulty in choosing the most appropriate protein, depending on the experimental design. Therefore, the purpose of our study was to compare three recently developed reporter proteins: the calcium indicators GCaMP3 and R-GECO1, and the voltage indicator VSFP butterfly1.2. These probes were expressed in hippocampal neurons in culture, which were subjected to patchclamp recordings and optical imaging. The three groups (each one expressing a protein) exhibited similar values of membrane potential (in mV, GCaMP3: -56 ±8.0, R-GECO1: -57 ±2.5; VSFP: -60 ±3.9, p = 0.86); however, the group of neurons expressing VSFP showed a lower average of input resistance than the other groups (in Mohms, GCaMP3: 161 ±18.3; GECO1-R: 128 ±15.3; VSFP: 94 ±14.0, p = 0.02). Each neuron was submitted to current injections at different frequencies (10 Hz, 5 Hz, 3 Hz, 1.5 Hz, and 0.7 Hz) and their fluorescence responses were recorded in time. In our study, only 26.7% (4/15) of the neurons expressing VSFP showed detectable fluorescence signal in response to action potentials (APs). The average signal-to-noise ratio (SNR) obtained in response to five spikes (at 10 Hz) was small (1.3 ± 0.21), however the rapid kinetics of the VSFP allowed discrimination of APs as individual peaks, with detection of 53% of the evoked APs. Frequencies below 5 Hz and subthreshold signals were undetectable due to high noise. On the other hand, calcium indicators showed the greatest change in fluorescence following the same protocol (five APs at 10 Hz). Among the GCaMP3 expressing neurons, 80% (8/10) exhibited signal, with an average SNR value of 21 ±6.69 (soma), while for the R-GECO1 neurons, 50% (2/4) of the neurons had signal, with a mean SNR value of 52 ±19.7 (soma). For protocols at 10 Hz, 54% of the evoked APs were detected with GCaMP3 and 85% with R-GECO1. APs were detectable in all the analyzed frequencies and fluorescence signals were detected from subthreshold depolarizations as well. Because GCaMP3 is the most likely to yield fluorescence signal and with high SNR, some experiments were performed only with this probe. We demonstrate that GCaMP3 is effective in detecting synaptic inputs (involving Ca2+ influx), with high spatial and temporal resolution. Differences were also observed between the SNR values resulting from evoked APs, compared to spontaneous APs. In recordings of groups of cells, GCaMP3 showed clear discrimination between activated and silent cells, and reveals itself as a potential tool in studies of neuronal synchronization. Thus, our results indicate that the presently available calcium indicators allow detailed studies on neuronal communication, ranging from individual dendritic spines to the investigation of events of synchrony in neuronal networks genetically defined. In contrast, studies employing VSFPs represent a promising technology for monitoring neural activity and, although still to be improved, they may become more appropriate than calcium indicators, since neurons work on a time scale faster than events of calcium may foresee Neurônios se comunicam por meio de sinapses, trocando mensagens capazes de modificar o potencial de membrana de outros neurônios. Demonstrar o papel desses sinais e decodificar essa linguagem elétrica representa o grande objetivo da neurociência moderna. Atualmente, a eletrofisiologia é o ramo da neurociência capaz de investigar esses recursos elétricos de neurônios - que vão desde registros de condutância e comportamento cinético de canais iônicos individuais até a demonstração de neurônios individuais implicados em comportamentos complexos. Nesse sentido, diferentes estados cerebrais e comportamentos implicam o recrutamento de grandes conjuntos de neurônios se comunicando em um estado coerente, dinâmico. Além disso, essas grandes populações são formadas por diversos subtipos neuronais cuja análise requer ténicas que possibilitem uma resolução temporal e espacial de células individuais e, prefencialmente, de subtipos específicos. Apenas recentemente, indicadores ópticos geneticamente codificados surgiram como ferramentas não invasivas de alta resolução espacial e temporal utilizados para monitorar a atividade de neurônios individuais e populações neuronais específicas. O número crescente de novos indicadores optogenéticos, juntamente com a ausência de comparações em condições idênticas, gerou dificuldade em escolher a mais adequada das proteínas, dependendo do desenho experimental. Portanto, o objetivo deste estudo foi comparar três proteínas repórter recentemente desenvolvidas: os indicadores de cálcio GCaMP3 e R-GECO1, e o indicador de voltagem VSFP butterfly1.2. Foram expressos em neurônios do hipocampo em cultura, os quais foram submetidos a registros de patch-clamp e de imageamento óptico. Os três grupos (cada um expressando uma proteína) exibiram valores semelhantes de potencial de membrana (em mV, GCaMP3: -56 ± 8,0; R-GECO1: -57 ± 2,5; VSFP: -60 ± 3,9; p = 0,86), no entanto, o grupo de neurônios que expressam VSFP mostrou uma média mais baixa de resistência de entrada do que os outros grupos (em Mohms, GCaMP3: 161 ± 18,3; GECO1-R: 128 ± 15,3; VSFP: 94 ± 14,0; p = 0,02). Cada neurônio foi submetido a injeções de correntes com frequências diferentes (10 Hz, 5 Hz, 3 Hz, 1,5 Hz, e 0,7 Hz) e as suas respostas de fluorescência foram registradas. Em nosso estudo, apenas 26,7% (4/15) dos neurônios que expressam VSFP mostraram sinal de fluorescência detectável em resposta a potenciais de ação. O valor médio de sinal-para-ruído (SNR), obtido em resposta a cinco potenciais de aҫão (a 10 Hz) foi pequeno (1,3 ± 0,21), no entanto a cinética rápida do VSFP permite a discriminação de disparos, como picos individuais, com detecção de 53% dos APs evocados. Freqüências abaixo de 5 Hz, assim como variaҫões no potencial de membrana subliminares, foram indetectáveis devido ao alto ruído do sinal de fluorescência. Por outro lado, os indicadores de cálcio mostraram maior alteração na fluorescência, seguindo o mesmo protocolo (cinco potenciais de aҫão a 10 Hz). Entre os neurônios expressando GCaMP3, 80% (8/10) exibiram sinal, com um valor médio de SNR de 21 ± 6,69 (soma), enquanto que para os neurônios expressando R-GECO1, 50% (2/4) dos neurônios demonstraram sinal com um valor médio SNR de 52 ± 19,7 (soma). Para protocolos de 10 Hz, 54% dos disparos foram detectados com evocado GCaMP3 e 85% com o R-GECO1. Disparos foram detectados em todas as frequências e os sinais de fluorescência foram também detectados a partir de despolarizações subliminares. Sendo GCaMP3 o indicador mais provável de produzir sinal de fluorescência e com alto SNR, alguns experimentos foram realizados somente com essa proteína. Observamos que GCaMP3 é eficaz na detecção de inputs sinápticas (envolvendo influxo de Ca2+), com alta resolução espacial e temporal. Também foram observadas diferenças entre os valores de SNR resultantes dos disparos evocados, em comparação com os disparos espontâneos. Em registros de grupos de células, GCaMP3 mostrou clara discriminação entre células ativadas e silêncio, revelando-se como uma ferramenta potencial em estudos de sincronização neuronal. Assim, nossos resultados sugerem que os indicadores de cálcio disponíveis atualmente permitem estudos detalhados sobre a comunicação neuronal, que vão desde dendritos individuais até a investigação de eventos de sincronia em redes neuronais geneticamente definidas. Em contraste, VSFPs representam uma tecnologia promissora para monitorar a atividade neural e, apesar de ainda requererem melhoramentos, podem se tornar mais apropriados do que os indicadores de cálcio, uma vez que os neurônios trabalham em uma escala de tempo mais rápida do que eventos de cálcio podem prever
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- 2013
126. Caracterização dos acoplamentos fase-amplitude na região CA1 do hopocampo
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Teixeira, Robson Scheffer, Araújo, Dráulio Barros de, Amaral, Olavo Bohrer, Ribeiro, Sidarta Tollendal Gomes, and Tort, Adriano Bretanha Lopes
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Potencial de campo local ,Acoplamento entre frequências ,Oscilações hipocampais ,Local field potential ,Gama ,Hippocampal oscillations ,Modulação de amplitude ,Gamma ,Cross-frequency coupling ,Theta ,Teta ,Amplitude modulation ,OUTROS [CNPQ] - Abstract
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Brain oscillation are not completely independent, but able to interact with each other through cross-frequency coupling (CFC) in at least four different ways: power-to-power, phase-to-phase, phase-to-frequency and phase-to-power. Recent evidence suggests that not only the rhythms per se, but also their interactions are involved in the execution of cognitive tasks, mainly those requiring selective attention, information flow and memory consolidation. It was recently proposed that fast gamma oscillations (60 150 Hz) convey spatial information from the medial entorhinal cortex to the CA1 region of the hippocampus by means of theta (4-12 Hz) phase coupling. Despite these findings, however, little is known about general characteristics of CFCs in several brain regions. In this work we recorded local field potentials using multielectrode arrays aimed at the CA1 region of the dorsal hippocampus for chronic recording. Cross-frequency coupling was evaluated by using comodulogram analysis, a CFC tool recently developted (Tort et al. 2008, Tort et al. 2010). All data analyses were performed using MATLAB (MathWorks Inc). Here we describe two functionally distinct oscillations within the fast gamma frequency range, both coupled to the theta rhythm during active exploration and REM sleep: an oscillation with peak activity at ~80 Hz, and a faster oscillation centered at ~140 Hz. The two oscillations are differentially modulated by the phase of theta depending on the CA1 layer; theta-80 Hz coupling is strongest at stratum lacunosum-moleculare, while theta-140 Hz coupling is strongest at stratum oriens-alveus. This laminar profile suggests that the ~80 Hz oscillation originates from entorhinal cortex inputs to deeper CA1 layers, while the ~140 Hz oscillation reflects CA1 activity in superficial layers. We further show that the ~140 Hz oscillation differs from sharp-wave associated ripple oscillations in several key characteristics. Our results demonstrate the existence of novel theta-associated high-frequency oscillations, and suggest a redefinition of fast gamma oscillations As oscilações cerebrais não são completamente independentes, mas capazes de interagir umas com as outras através de acoplamentos entre frequências (cross-frequency coupling, doravante CFC) em pelo menos quatro diferentes modalidades: amplitudeamplitude, fase-fase (coerência), fase-frequência e fase-amplitude. Evidências recentes sugerem que não somente os ritmos per se, mas também as interações entre eles estão envolvidas na execução de tarefas cognitivas, principalmente aquelas que requerem atenção seletiva, transmissão de informações e consolidação de memórias. Estudos recentes propõem que oscilações gama alto (60 150 Hz) transferem informações espaciais do córtex entorrinal medial para a região CA1 do hipocampo através do acoplamento com a fase de teta (4 12 Hz). Apesar destas descobertas, entretanto, pouco se sabe sobre as características gerais dos CFCs em diversas regiões cerebrais. Neste trabalho, registramos potenciais de campo local usando matrizes de multieletrodos implantadas no hipocampo dorsal para registro neural crônico. O acoplamento fase-amplitude foi avaliado por meio da análise de comodulogramas, uma ferramenta de CFC desenvolvida recentemente (Tort et al. 2008, Tort et al. 2010). Todas as análises de dados foram realizadas em MATLAB (MathWorks Inc). Descrevemos duas oscilações funcionalmente distintas dentro da faixa de frequência de gama, ambas acopladas ao ritmo teta durante exploração ativa e sono REM: uma oscilação com um pico de atividade em ~80 Hz e uma mais rápida centrada em ~140 Hz. As duas oscilações são diferencialmente moduladas pela fase de teta conforme a camada de CA1; o acoplamento teta-80 Hz é mais forte no stratum lacunosum-moleculare, enquanto que o acoplamento teta-140 Hz é mais forte no stratum oriens-alveus. Este perfil laminar sugere que a oscilação de 80 Hz origina-se das entradas do córtex entorrinal para as camadas profundas de CA1, e que a oscilação de 140 Hz reflete a atividade de CA1 em camadas superficiais. Ademais, nós mostramos que a oscilação de 140 Hz difere-se das oscilações ripples associadas com sharp-waves em diversos aspectos chave. Nossos resultados demonstram a existência de novas oscilações de alta frequência associadas à teta e sugerem uma redefinição das oscilações gama alto
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- 2011
127. Academic impact and scientific quality should not be conflated.
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Amaral OB
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- 2024
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128. Estimating the replicability of highly cited clinical research (2004-2018).
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da Costa GG, Neves K, and Amaral O
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- Reproducibility of Results, Humans, Journal Impact Factor, Biomedical Research
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Introduction: Previous studies about the replicability of clinical research based on the published literature have suggested that highly cited articles are often contradicted or found to have inflated effects. Nevertheless, there are no recent updates of such efforts, and this situation may have changed over time., Methods: We searched the Web of Science database for articles studying medical interventions with more than 2000 citations, published between 2004 and 2018 in high-impact medical journals. We then searched for replications of these studies in PubMed using the PICO (Population, Intervention, Comparator and Outcome) framework. Replication success was evaluated by the presence of a statistically significant effect in the same direction and by overlap of the replication's effect size confidence interval (CIs) with that of the original study. Evidence of effect size inflation and potential predictors of replicability were also analyzed., Results: A total of 89 eligible studies, of which 24 had valid replications (17 meta-analyses and 7 primary studies) were found. Of these, 21 (88%) had effect sizes with overlapping CIs. Of 15 highly cited studies with a statistically significant difference in the primary outcome, 13 (87%) had a significant effect in the replication as well. When both criteria were considered together, the replicability rate in our sample was of 20 out of 24 (83%). There was no evidence of systematic inflation in these highly cited studies, with a mean effect size ratio of 1.03 [95% CI (0.88, 1.21)] between initial and subsequent effects. Due to the small number of contradicted results, our analysis had low statistical power to detect predictors of replicability., Conclusion: Although most studies did not have eligible replications, the replicability rate of highly cited clinical studies in our sample was higher than in previous estimates, with little evidence of systematic effect size inflation. This estimate is based on a very select sample of studies and may not be generalizable to clinical research in general., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 da Costa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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129. Open Science 2.0: Towards a truly collaborative research ecosystem.
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Thibault RT, Amaral OB, Argolo F, Bandrowski AE, Davidson AR, and Drude NI
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- Information Dissemination, Scholarly Communication, Ecosystem, Communication
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Conversations about open science have reached the mainstream, yet many open science practices such as data sharing remain uncommon. Our efforts towards openness therefore need to increase in scale and aim for a more ambitious target. We need an ecosystem not only where research outputs are openly shared but also in which transparency permeates the research process from the start and lends itself to more rigorous and collaborative research. To support this vision, this Essay provides an overview of a selection of open science initiatives from the past 2 decades, focusing on methods transparency, scholarly communication, team science, and research culture, and speculates about what the future of open science could look like. It then draws on these examples to provide recommendations for how funders, institutions, journals, regulators, and other stakeholders can create an environment that is ripe for improvement., Competing Interests: AB is an Academic Editor for PLOS Biology. AB is a founder of SciCrunch Inc, a company that works with publishers to improve the representation of research resources in scientific literature. She is also a member of the board, and serves as the CEO. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. OBA is a member of the eLife Global South Advisory Committee and co-founder of the Brazilian Reproducibility Network. N.D. is an external consultant and animal welfare officer at Medizinisches Kompetenzzentrum c/o HCx Consulting, Brandenburg, Germany. All other authors declare no conflict of interest., (Copyright: © 2023 Thibault et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2023
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130. Characterization of Comments About bioRxiv and medRxiv Preprints.
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Carneiro CFD, da Costa GG, Neves K, Abreu MB, Tan PB, Rayêe D, Boos FZ, Andrejew R, Lubiana T, Malicki M, and Amaral OB
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- Humans, Cross-Sectional Studies, Data Collection, Software, Peer Review, Research Design
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Importance: Preprints have been increasingly used in biomedical science, and a key feature of many platforms is public commenting. The content of these comments, however, has not been well studied, and it is unclear whether they resemble those found in journal peer review., Objective: To describe the content of comments on the bioRxiv and medRxiv preprint platforms., Design, Setting, and Participants: In this cross-sectional study, preprints posted on the bioRxiv and medRxiv platforms in 2020 were accessed through each platform's application programming interface on March 29, 2021, and a random sample of preprints containing between 1 and 20 comments was evaluated independently by 3 evaluators using an instrument to assess their features and general content., Main Outcome and Measures: The numbers and percentages of comments from authors or nonauthors were assessed, and the comments from nonauthors were assessed for content. These nonauthor comments were assessed to determine whether they included compliments, criticisms, corrections, suggestions, or questions, as well as their topics (eg, relevance, interpretation, and methods). Nonauthor comments were also analyzed to determine whether they included references, provided a summary of the findings, or questioned the preprint's conclusions., Results: Of 52 736 preprints, 3850 (7.3%) received at least 1 comment (mean [SD] follow-up, 7.5 [3.6] months), and the 1921 assessed comments (from 1037 preprints) had a median length of 43 words (range, 1-3172 words). The criticisms, corrections, or suggestions present in 694 of 1125 comments (61.7%) were the most prevalent content, followed by compliments (n = 428 [38.0%]) and questions (n = 393 [35.0%]). Criticisms usually regarded interpretation (n = 286), methodological design (n = 267), and data collection (n = 238), while compliments were mainly about relevance (n = 111) and implications (n = 72)., Conclusions and Relevance: In this cross-sectional study of preprint comments, topics commonly associated with journal peer review were frequent. However, only a small percentage of preprints posted on the bioRxiv and medRxiv platforms in 2020 received comments on these platforms. A clearer taxonomy of peer review roles would help to describe whether postpublication peer review fulfills them.
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- 2023
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131. Are most published research findings false in a continuous universe?
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Neves K, Tan PB, and Amaral OB
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- Reproducibility of Results, Computer Simulation, Publication Bias, Bias, Research Design
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Diagnostic screening models for the interpretation of null hypothesis significance test (NHST) results have been influential in highlighting the effect of selective publication on the reproducibility of the published literature, leading to John Ioannidis' much-cited claim that most published research findings are false. These models, however, are typically based on the assumption that hypotheses are dichotomously true or false, without considering that effect sizes for different hypotheses are not the same. To address this limitation, we develop a simulation model that overcomes this by modeling effect sizes explicitly using different continuous distributions, while retaining other aspects of previous models such as publication bias and the pursuit of statistical significance. Our results show that the combination of selective publication, bias, low statistical power and unlikely hypotheses consistently leads to high proportions of false positives, irrespective of the effect size distribution assumed. Using continuous effect sizes also allows us to evaluate the degree of effect size overestimation and prevalence of estimates with the wrong sign in the literature, showing that the same factors that drive false-positive results also lead to errors in estimating effect size direction and magnitude. Nevertheless, the relative influence of these factors on different metrics varies depending on the distribution assumed for effect sizes. The model is made available as an R ShinyApp interface, allowing one to explore features of the literature in various scenarios., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Neves et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2022
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132. To fix peer review, break it into stages.
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Amaral OB
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- Peer Review, Research methods, Peer Review, Research standards, Peer Review, Research trends
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- 2022
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133. Memory destabilization during reconsolidation: a consequence of homeostatic plasticity?
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Amorim FE, Chapot RL, Moulin TC, Lee JLC, and Amaral OB
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- Brain, Mental Recall, Neuronal Plasticity, Memory, Memory Consolidation
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Remembering is not a static process: When retrieved, a memory can be destabilized and become prone to modifications. This phenomenon has been demonstrated in a number of brain regions, but the neuronal mechanisms that rule memory destabilization and its boundary conditions remain elusive. Using two distinct computational models that combine Hebbian plasticity and synaptic downscaling, we show that homeostatic plasticity can function as a destabilization mechanism, accounting for behavioral results of protein synthesis inhibition upon reactivation with different re-exposure times. Furthermore, by performing systematic reviews, we identify a series of overlapping molecular mechanisms between memory destabilization and synaptic downscaling, although direct experimental links between both phenomena remain scarce. In light of these results, we propose a theoretical framework where memory destabilization can emerge as an epiphenomenon of homeostatic adaptations prompted by memory retrieval., (© 2021 Amorim et al.; Published by Cold Spring Harbor Laboratory Press.)
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- 2021
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134. Reproducibility: expect less of the scientific paper.
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Amaral OB and Neves K
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- Animals, Brazil, Cooperative Behavior, Humans, Mice, Multicenter Studies as Topic, Reproducibility of Results, Research organization & administration, Research standards, Research Design, Research Report standards
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- 2021
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135. Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature.
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Carneiro CFD, Queiroz VGS, Moulin TC, Carvalho CAM, Haas CB, Rayêe D, Henshall DE, De-Souza EA, Amorim FE, Boos FZ, Guercio GD, Costa IR, Hajdu KL, van Egmond L, Modrák M, Tan PB, Abdill RJ, Burgess SJ, Guerra SFS, Bortoluzzi VT, and Amaral OB
- Abstract
Background: Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader's ability to independently interpret data and reproduce findings., Methods: In this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals., Results: Peer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication., Conclusions: Our results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.
- Published
- 2020
- Full Text
- View/download PDF
136. Two years into the Brazilian Reproducibility Initiative: reflections on conducting a large-scale replication of Brazilian biomedical science.
- Author
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Neves K, Carneiro CF, Wasilewska-Sampaio AP, Abreu M, Valério-Gomes B, Tan PB, and Amaral OB
- Subjects
- Brazil, Reproducibility of Results, Biomedical Research trends, Research Design
- Abstract
Scientists have increasingly recognised that low methodological and analytical rigour combined with publish-or-perish incentives can make the published scientific literature unreliable. As a response to this, large-scale systematic replications of the literature have emerged as a way to assess the problem empirically. The Brazilian Reproducibility Initiative is one such effort, aimed at estimating the reproducibility of Brazilian biomedical research. Its goal is to perform multicentre replications of a quasi-random sample of at least 60 experiments from Brazilian articles published over a 20-year period, using a set of common laboratory methods. In this article, we describe the challenges of managing a multicentre project with collaborating teams across the country, as well as its successes and failures over the first two years. We end with a brief discussion of the Initiative's current status and its possible future contributions after the project is concluded in 2021.
- Published
- 2020
- Full Text
- View/download PDF
137. Using collaboration networks to identify authorship dependence in meta-analysis results.
- Author
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Moulin TC and Amaral OB
- Subjects
- Algorithms, Bias, Cluster Analysis, Eye Movement Desensitization Reprocessing, Humans, Programming Languages, Reproducibility of Results, Research Design, Sample Size, Software, Stress Disorders, Post-Traumatic therapy, Meta-Analysis as Topic, Publications
- Abstract
Meta-analytic methods are powerful resources to summarize the existing evidence concerning a given research question and are widely used in many academic fields. Meta-analyzes can also be used to study sources of heterogeneity and bias among results, which should be considered to avoid inaccuracies. Many of these sources can be related to study authorship, as both methodological heterogeneity and researcher bias may lead to deviations in results between different research groups. In this work, we describe a method to objectively attribute study authorship within a given meta-analysis to different research groups by using graph cluster analysis of collaboration networks. We then provide empirical examples of how the research group of origin can impact effect size in distinct types of meta-analyzes, demonstrating how non-independence between within-group results can bias effect size estimates if uncorrected. Finally, we show that multilevel random-effects models using research group as a level of analysis can be a simple tool for correcting for authorship dependence in results., (© 2020 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd.)
- Published
- 2020
- Full Text
- View/download PDF
138. On the transition from reconsolidation to extinction of contextual fear memories.
- Author
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Cassini LF, Flavell CR, Amaral OB, and Lee JLC
- Subjects
- Analysis of Variance, Animals, Dizocilpine Maleate pharmacology, Excitatory Amino Acid Antagonists pharmacology, Extinction, Psychological drug effects, Fear drug effects, Freezing Reaction, Cataleptic drug effects, Male, Maze Learning drug effects, Memory drug effects, Rats, Conditioning, Psychological, Extinction, Psychological physiology, Fear physiology, Freezing Reaction, Cataleptic physiology, Memory physiology
- Abstract
Retrieval of an associative memory can lead to different phenomena. Brief reexposure sessions tend to trigger reconsolidation, whereas more extended ones trigger extinction. In appetitive and fear cued Pavlovian memories, an intermediate "null point" period has been observed where neither process seems to be engaged. Here we investigated whether this phenomenon extends to contextual fear memory. Adult rats were subjected to a contextual fear conditioning paradigm, reexposed to the context 2 d later for 3, 5, 10, 20, or 30 min, with immediate injections of MK-801 or saline following reexposure, and tested on the following day. We observed a significant effect of MK-801 with the 3- and 30-min sessions, impairing reconsolidation and extinction, respectively. However, it did not have significant effects with 5-, 10-, or 20-min sessions, even though freezing decreased from reexposure to test. Further analyses indicated that this is not likely to be due to a variable transition point at the population level. In conclusion, the results show that in contextual fear memories there is a genuine "null point" between the parameters that induce reconsolidation and extinction, as defined by the effects of MK-801, although NMDA receptor-independent decreases in freezing can still occur in these conditions., (© 2017 Cassini et al.; Published by Cold Spring Harbor Laboratory Press.)
- Published
- 2017
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- View/download PDF
139. Protocol for a Systematic Review of Effect Sizes and Statistical Power in the Rodent Fear Conditioning Literature.
- Author
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Moulin TC, Carneiro CFD, Macleod MR, and Amaral OB
- Abstract
The concepts of effect size and statistical power are often disregarded in basic neuroscience, and most articles in the field draw their conclusions solely based on the arbitrary significance thresholds of statistical inference tests. Moreover, studies are often underpowered, making conclusions from significance tests less reliable. With this in mind, we present the protocol of a systematic review to study the distribution of effect sizes and statistical power in the rodent fear conditioning literature, and to analyze how these factors influence the description and publication of results. To do this we will conduct a search in PubMed for "fear conditioning" AND ("mouse" OR "mice" OR "rat" OR "rats") and obtain all articles published online in 2013. Experiments will be included if they: (a) describe the effect(s) of a single intervention on fear conditioning acquisition or consolidation; (b) have a control group to which the experimental group is compared; (c) use freezing as a measure of conditioned fear; and (d) have available data on mean freezing, standard deviation and sample size of each group and on the statistical significance of the comparison. We will use the extracted data to calculate the distribution of effect sizes in these experiments, as well as the distribution of statistical power curves for detecting a range of differences at a threshold of α=0.05. We will assess correlations between these variables and (a) the chances of a result being statistically significant, (b) the way the result is described in the article text, (c) measures to reduce risk of bias in the article and (d) the impact factor of the journal and the number of citations of the article. We will also perform analyses to see whether effect sizes vary systematically across species, gender, conditioning protocols or intervention types., Competing Interests: Conflicts of Interest: The authors report no conflicts of interest
- Published
- 2016
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- View/download PDF
140. Signet-ring cell hilar cholangiocarcinoma: case report.
- Author
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Chedid MF, Lucas ET, Cerski CT, Lopes MF, Amaral OB, and Chedid AD
- Subjects
- Aged, Female, Humans, Bile Duct Neoplasms pathology, Bile Duct Neoplasms surgery, Carcinoma, Signet Ring Cell pathology, Carcinoma, Signet Ring Cell surgery, Klatskin Tumor pathology, Klatskin Tumor surgery
- Published
- 2015
- Full Text
- View/download PDF
141. Memory labilization in reconsolidation and extinction--evidence for a common plasticity system?
- Author
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Almeida-Corrêa S and Amaral OB
- Subjects
- Animals, Humans, Reinforcement, Psychology, Extinction, Psychological physiology, Memory physiology, Neuronal Plasticity physiology
- Abstract
Reconsolidation and extinction are two processes occurring upon memory retrieval that have received great attention in memory research over the last decade, partly due to their purported potential in the treatment of anxiety disorders. Due to their opposite behavioral effects, the two phenomena have usually been considered as separate entities, with few attempts to build a unified view of how both could be produced by similar mechanisms. Based on computational modeling, we have previously proposed that reconsolidation and extinction are behavioral outcomes of the same set of plasticity systems, albeit working at different synapses. One of these systems seems to be pharmacologically similar to the one involved in initial memory consolidation, and likely involves traditional Hebbian plasticity, while the second seems to be more involved with the labilization of existing memories and/or synaptic changes. In this article, we review the evidence for the existence of a plasticity system specifically involved in memory labilization, as well as its possible molecular requirements, anatomical substrates, synaptic mechanisms and physiological roles. Based on these data, we propose that the field of memory updating might ultimately benefit from a paradigm shift in which reconsolidation and extinction are viewed not as separate processes but as different instantiations of plasticity systems responsible for reinforcement and labilization of synaptic changes., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
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