BrainCAT: a tool for automated and combined functional magnetic resonance imaging and diffusion tensor imaging brain connectivity analysis

Multimodal neuroimaging studies have recently become a trend in the neuroimaging field and are certainly a standard for the future. Brain connectivity studies combining functional activation patterns using resting-state or task-related functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) tractography have growing popularity. However, there is a scarcity of solutions to perform optimized, intuitive, and consistent multimodal fMRI/DTI studies. Here we propose a new tool, brain connectivity analysis tool (Brain CAT), for an automated and standard multimodal analysis of combined fMRI/DTI data, using freely available tools. With a friendly graphical user interface, BrainCAT aims to make data processing easier and faster, implementing a fully automated data processing pipeline and minimizing the need for user intervention, which hopefully will expand the use of combined fMRI/DTI studies. Its validity was tested in an aging study of the default mode network (DMN) white matter connectivity. The results evidenced the cingulum bundle as the structural connector of the precuneus/posterior cingulate cortex and the medial frontal cortex, regions of the DMN. Moreover, mean fractional anisotropy (FA) values along the cingulum extracted with BrainCAT showed a strong correlation with FA values from the manual selection of the same bundle. Taken together, these results provide evidence that BrainCAT is suitable for these analyses.The authors thank the developers of all the software tools used by BrainCAT, namely, MRIcron, FSL, Diffusion Toolkit, and TrackVis. This work was supported by SwitchBox-FP7-HEALTH-2010-grant 259772-2

Conetividade cerebral : ferramenta de processamento automático combinado de Ressonância Magnética Funcional e Tensor de Difusão

Dissertação de mestrado integrado em Engenharia BiomédicaOs estudos de conetividade cerebral têm-se revelado extremamente importantes no âmbito científico e clínico. Contudo, a realização destes estudos através da conjugação de análises de conetividade funcional via Ressonância Magnética funcional (RMf) e análises de conetividade estrutural via imagem por tensor de difusão (Diffusion Tensor Imaging – DTI), não é uma tarefa fácil. A quantidade de procedimentos e conhecimentos técnicos necessários em estudos de RMf e DTI, associados à quase inexistência de procedimentos padrão para o processamento dos dados e à multitude de soluções de software que é necessário utilizar são alguns dos maiores entraves. Assim, o objetivo principal deste trabalho consistiu em conceber um fluxo de processamento que possa servir de padrão ao processamento e conjugação dos resultados das análises de RMf e DTI. A concretização aplicacional da automatização fluxo concebido foi conseguida através do desenvolvimento de uma aplicação informática. O fluxo de processamento desenvolvido inclui as etapas mais relevantes para a conjugação dos resultados da análise de componentes independentes aos dados de RMf e da tratografia a partir dos dados de DTI. Os testes realizados indicam que a aplicação desenvolvida constitui uma ferramenta simples e de fácil utilização. Além disso, os resultados das análises de conetividade cerebral demonstraram ser consistentes com estudos anteriores e o tempo despendido pelo utilizador na manipulação dos dados de RMf e DTI foi reduzido significativamente.Studies of brain connectivity have proved extremely important in the scientific and clinical fields. However, these studies, through the combination of analysis of functional connectivity by functional Magnetic Resonance Imaging (fMRI) and structural connectivity analysis based on Diffusion Tensor Imaging (DTI) are not an easy task. The amount of procedures and technical expertise needed, associated with the virtual absence of standard procedures for processing the data and the multitude of software solutions that need to be used are some of the biggest barriers. Thus, the goal of this study was to devise a pipeline that could be used as a standard to process the data and combine the results of combined analysis of fMRI and DTI. The practical implementation of the automated processing pipeline was achieved by the development of a computer application. The conceived processing pipeline includes the most important steps used in the combination of the results from independent component analysis of fMRI data and tractography from DTI data. Tests indicate that the developed application is a simple and easy to use tool. Moreover, the results of brain connectivity analysis proved to be consistent with previous studies and the time spent by the user in data manipulation was significantly reduced

Identifying functional subdivisions in the medial frontal cortex

[Excerpt] The medial frontal cortex (MFC) is thought to be involved in numerous sensorimotor, cognitive, and affective processes. This region is commonly divided into separate subregions, including the anterior cingulate cortex, supplementary motor area (SMA), and the pre-SMA, orbitofrontal cortex, and anterior frontal poles (Amodio and Frith, 2006). The activity of the MFC is highly heterogeneous. Activation of the MFC is reported in many fMRI studies, and it is associated with a variety of processes, including action monitoring (Bonini et al., 2014), response conflict (Gehring and Fencsik, 2001), reward (Taylor et al., 2006), and decision-making (Kahnt et al., 2011). This creates uncertainty in the identification of specific psychological states associated with patterns of activity in the MFC, referred as the reverse inference problem. (...)P. S. M. was supported by PhD-iHES Program FCT Fellowship Grant PDE/BDE/113601/2015. R.M. was supported by PhD-iHES Program FCT Fellowship Grant PDE/BDE/113604/2015. P.M. was supported by Fundação Calouste Gulbenkian Contract Grant P-139977 (“Better mental health during ageing based on temporal prediction of individual brain ageing trajectories”)

The impact of normalization and segmentation on resting state brain networks

Graph theory has recently received a lot of attention from the neuroscience community as a method to represent and characterize brain networks. Still, there is a lack of a gold standard for the methods that should be employed for the preprocessing of the data and the construction of the networks, as well as a lack of knowledge on how different methodologies can affect the metrics reported. We used graph theory analysis applied to resting-state functional Magnetic Resonance Imaging (rs-fMRI) to investigate the influence of different node-defining strategies and the effect of normalizing the functional acquisition on several commonly reported metrics used to characterize brain networks. The nodes of the network were defined using either the individual FreeSurfer segmentation of each subject or the FreeSurfer segmented MNI (Montreal National Institute) 152 template, using the Destrieux and sub-cortical atlas. The functional acquisition was either kept on the functional native space or normalized into MNI standard space. The comparisons were done at three levels: on the connections, on the edge properties and on the network properties levels. Our results reveal that different registration and brain parcellation strategies have a strong impact on all the levels of analysis, possibly favoring the use of individual segmentation strategies and conservative registration approaches. In conclusion, several technical aspects must be considered so that graph theoretical analysis of connectivity MRI data can provide a framework to understand brain pathologies.(undefined

Central autonomic nervous system response to autonomic challenges is altered in patients with a previous episode of Takotsubo Cardiomyopathy

Aims: Takotsubo cardiomyopathy is an intriguing disease characterized by acute transient left ventricular dysfunction usually triggered by an episode of severe stress. The excessive levels of catecholamines and the overactivation of the sympathetic system are believed to be the main pathophysiologic mechanisms of Takotsubo cardiomyopathy, but it is unclear whether there is a structural or functional signature of the disease. In this sense, our aim was to characterize the central autonomic system response to autonomic challenges in patients with a previous episode of Takotsubo cardiomyopathy when compared with a control group of healthy volunteers. Methods and results: Functional magnetic resonance imaging (fMRI) was performed in four patients with a previous episode of Takotsubo cardiomyopathy (average age of 6712 years) and in eight healthy volunteers (average age of 66 +/- 5 years) while being submitted to different autonomic challenges (cold exposure and Valsalva manoeuvre). The fMRI analysis revealed a significant variation of the blood oxygen level dependent signal triggered by the Valsalva manoeuvre in specific areas of the brain involved in the cortical control of the autonomic system and significant differences in the pattern of activation of the insular cortex, amygdala and the right hippocampus between patients with Takotsubo cardiomyopathy and controls, even though these regions did not present significant volumetric changes. Conclusion: The central autonomic response to autonomic challenges is altered in patients with Takotsubo cardiomyopathy, thus suggesting a dysregulation of the central autonomic nervous system network. Subsequent studies are needed to unveil whether these alterations are causal or predisposing factors to Takotsubo cardiomyopathy.The work was supported by the European Commission (FP7): ‘SwitchBox’ (Contract HEALTH-F2-2010-259772) and ‘MyHealth’ project (Contract DoIT-13853), and by Fundação para a Ciência e Tecnologia (project FCT-ANR/NEU-OSD/0258/2012 Portuguese North Regional Operational Program (ON.2 – O Novo Norte)) under the National Strategic Reference Framework (QREN), through the European Regional Development Fund (FEDER). PM is supported by a ‘SwitchBox’ fellowship and RM by a FCT-ANR/NEU-OSD/0258/2012 fellowship

Safinamide: a new hope for Parkinson's disease?

The loss of dopaminergic neurons (DAn) and reduced dopamine (DA) production underlies the reasoning behind the gold standard treatment for Parkinson's disease (PD) using levodopa (L-DOPA). Recently licensed by the European Medicine Agency (EMA) and US Food and Drug Administration (FDA), safinamide [a monoamine oxidase B (MOA-B) inhibitor] is an alternative to L-DOPA; as we discuss here, it enhances dopaminergic transmission with decreased secondary effects compared with L-DOPA. In addition, nondopaminergic actions (neuroprotective effects) have been reported, with safinamide inhibiting glutamate release and sodium/calcium channels, reducing the excitotoxic input to dopaminergic neuronal death. Effects of safinamide have been correlated with the amelioration of non-motor symptoms (NMS), although these remain under discussion. Overall, safinamide can be considered to have potential antidyskinetic and neuroprotective effects and future trials and/or studies should be performed to provide further evidence for its potential as an anti-PD drug.The authors acknowledge funding from the Portuguese Foundation for Science and Technology (IF development grant IF/ 00111/2013 to A.J.S.) and a postdoctoral fellowship to F.G.T. (SFRH/BPD/118408/2016). This work was funded by FEDER funds, through the Competitiveness Factors Operational Programme (COMPETE), and by national funds, through the Foundation for Science and Technology (FCT), under the scope of the project POCI-01-0145-FEDER-007038. This article has also been developed under the scope of the project NORTE-01-0145-FEDER-000023, supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)

VÍDEOS EDUCATIVOS EM PROL DA PRESERVAÇÃO DE DOCUMENTOS ESCOLARES NO CONTEXTO DE UMA CULTURA DIGITAL

Este artigo foca o processo de ensino e de aprendizagem por meio das Tecnologias Digitais da Informação e Comunicação (TDIC) e descreve a criação e a utilização dos vídeos educativos como instrumentos de mediação pedagógica no contexto da Educação Matemática. O referido estudo de cunho exploratório-descritivo aborda também a necessidade de pensar em novos rumos para a formação inicial e continuada de professores. São apresentados análises e resultados da investigação desenvolvida, em contexto universitário, considerando as possibilidades de criação e do uso dos vídeos para disseminar informação e auxiliar a prática docente em sala de aula. Esses vídeos, com um caráter didático, foram produzidos pelo grupo de pesquisa GEPHEM (Grupo de Estudo e Pesquisa em História do Ensino da Matemática) e têm sido referência para conscientização dos universitários e da comunidade em geral a respeito da preservação e restauração de documentos escolares em suporte papel, vinculando entre outras, a potencialidade do uso dos vídeos nas aulas tanto nos cursos de licenciatura quanto nos cursos de formação continuada. Nos resultados da investigação infere-se que o vídeo, como instrumento didático educativo, oferece possibilidades de utilização e motivação nas práticas educativas, apontando para a possibilidade de que tal recurso venha a ser utilizado para ampliar as oportunidades de aprendizagem em sala de aula. As conclusões apontam para mudança na escola no que diz respeito ao uso das TDIC decorrente do quadro complexo em que se dá a educação escolar, e para se pensar os novos rumos para a formação de professores

EFEITO RESIDUAL DE HERBICIDAS AUXÍNICOS EM SOJA

The control of weeds in pastures is essential to improve the productivity indexes of agricultural activity and the correct and conscious use of herbicides is very important to reduce the problems caused by the residual effect in subsequent culture. Thus, this study evaluated the residual effect of the auxinic herbicides 2,4-D, picloram and 2,4-D + picloram on the initial development of soybean seedlings. The work was carried out in a greenhouse in a completely randomized design, in a 7 x 3 factorial scheme, with four replications. The first factor was composed of the percentages of the recommended doses of herbicides (100%, 50%, 25%, 12.50%, 6.25%, 3.12% and 0.00%) in which the highest dose (100% ) was equivalent to 2 L ha-1. The second factor was composed of the herbicides: 2,4-D, Picloram + 2,4-D and Picloram. The number of plants emerged for each treatment at 10 DAS, plant height and accumulation of fresh and dry mass at 40 DAS were evaluated. The herbicide picloram negatively affects the variables number and height of plants from the dose 3.12% and fresh and dry mass from the dose 6.25% and the herbicide picloram + 2,4-D negatively affects the variables number of plants from 3.12% dose, height plant from 6.25% dose and fresh and dry mass from 12.5% dose. Soy showed high sensitivity to picloram residues in the soil. The 25% and 50% doses, respectively, of the herbicides picloram + 2,4-D and picloram, limited the seedling emergence and the 100% dose prevented the germination of soybean seeds. No residual effect was observed for the herbicide 2,4-D in soybean seedlings in any of the studied doses.O controle das plantas daninhas em pastagens é indispensável para melhoria dos índices de produtividade da atividade agropecuária e a utilização correta e consciente dos herbicidas é muito importante para reduzir os problemas ocasionados pelo efeito residual em culturas subsequentes. Portanto, avaliou-se com este estudo o efeito residual dos herbicidas auxínicos 2,4-D, picloram e 2,4-D + picloram no desenvolvimento inicial de plântulas de soja. O trabalho foi conduzido em casa de vegetação no delineamento inteiramente casualizado, em esquema fatorial 7 x 3, com quatro repetições. O primeiro fator foi composto pelas porcentagens das doses recomendadas de herbicidas (100%, 50%, 25%, 12,50%, 6,25%, 3,12% e 0,00%) na qual a maior dose (100%) foi equivalente a 2 L ha-1. O segundo fator foi composto pelos herbicidas: 2,4-D, picloram + 2,4-D e picloram. Foram avaliados o número de plantas emergidas para cada tratamento aos 10 DAS, altura de plantas e acúmulo de massa fresca e seca aos 40 DAS. O herbicida picloram afeta negativamente as variáveis número e altura de plantas a partir da dose 3,12% e massa fresca e seca a partir da dose 6,25% e o herbicida picloram + 2,4-D afeta negativamente as variáveis número de plantas a partir da dose 3,12%, altura de plantas a partir da dose 6,25% e massa fresca e seca a partir da dose 12,5%. A soja demonstrou alta sensibilidade aos resíduos de picloram no solo. As doses 25% e 50% respectivamente, dos herbicidas picloram + 2,4-D e picloram, limitaram a emergência das plântulas e a dose 100% impediu a germinação das sementes de soja. Não foi observado efeito residual para o herbicida 2,4-D em plântulas de soja em quaisquer das doses estudadas

The dynamics of stress: a longitudinal MRI study of rat brain structure and connectome

Stress is a well-established trigger for a number of neuropsychiatric disorders, as it alters both structure and function of several brain regions and its networks. Herein, we conduct a longitudinal neuroimaging study to assess how a chronic unpredictable stress protocol impacts the structure of the rat brain and its functional connectome in both high and low responders to stress. Our results reveal the changes that stress triggers in the brain, with structural atrophy affecting key regions such as the prelimbic, cingulate, insular and retrosplenial, somatosensory, motor, auditory and perirhinal/entorhinal cortices, the hippocampus, the dorsomedial striatum, nucleus accumbens, the septum, the bed nucleus of the stria terminalis, the thalamus and several brain stem nuclei. These structural changes are associated with increasing functional connectivity within a network composed by these regions. Moreover, using a clustering based on endocrine and behavioural outcomes, animals were classified as high and low responders to stress. We reveal that susceptible animals (high responders) develop local atrophy of the ventral tegmental area and an increase in functional connectivity between this area and the thalamus, further spreading to other areas that link the cognitive system with the fight-or-flight system. Through a longitudinal approach we were able to establish two distinct patterns, with functional changes occurring during the exposure to stress, but with an inflection point after the first week of stress when more prominent changes were seen. Finally, our study revealed differences in functional connectivity in a brainstem-limbic network that distinguishes resistant and susceptible responders before any exposure to stress, providing the first potential imaging-based predictive biomarkers of an individual's resilience/vulnerability to stressful conditions.This work is part of the Sigma project with the reference FCT-ANR/NEU-OSD/ 0258/2012 co-financed by the French public funding agency ANR (Agence National pour la Recherche, APP Blanc International II 2012), the Portuguese FCT (Fundação para a Ciência e Tecnologia) and by the Portuguese North Regional Operational Program (ON.2 – O Novo Norte) under the National Strategic Reference Framework (QREN), through the European Regional Development Fund (FEDER) as well as the Projecto Estratégico co-funded by FCT (PEst-C/SAU/LA0026-/2013) and the European Regional Development Fund COMPETE (FCOMP-01-0124-FEDER-037298). DAB and AN were funded by grants from FCT-ANR/NEU-OSD/0258/2012. RM is supported by the FCT fellowship grant with the reference PDE/BDE/113604/2015 from the PhDiHES program; AC was supported by a grant from the foundation NRJ. PM was funded by Fundação Calouste Gulbenkian (Portugal; ‘Better mental health during ageing based on temporal prediction of individual brain ageing trajectories (TEMPO)’), Grant Number P-139977. We thank Drs Patrício Costa and Pedro Moreira for support on the various statistical analyses.info:eu-repo/semantics/publishedVersio