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Foundations for an ontology of brain areas, circuits and functions

Bénédicte M Batrancourt
2013 BMC Neuroscience  
Foundations for an ontology of brain areas, circuits and functions Bénédicte Batrancourt This article describes a method for building the foundations for an ontology of brain areas, brain circuits and  ...  To cite this version:Bénédicte Batrancourt.  ... 
doi:10.1186/1471-2202-14-s1-p19 fatcat:iwng6ziqo5cfjfghjvohfq6ukm

A propositional representation model of anatomical and functional brain data

Pablo Maturana, Bénédicte Batrancourt
2011 Journal of Physiology - Paris  
A great number of natural systems can be represented by networks. Recent developments in the domain of networks have been transfered to the neurosciences. For example, the graph model has been used in neuroimaging research as a methodological tool to examine brain network organization, topology and complex dynamics, as well as as a framework to test the structure-function hypothesis. In the current work we propose a network of anatomical brain data and neuropsychological assessments linked to
more » ... e functions explored in these assessments, offering a platform to visualize, in a single graph-theoretic framework, anatomo-functional and neuropsychological information. We apply this framework to a database belonging to the Center of Cognitive Anatomy (CAC), which contains neuropsychological data of patients presenting sequels of focal brain damage. KEY WORDS Brain, Atlas, Graph, Neuropsychology, Ontology and Modelling.
doi:10.1016/j.jphysparis.2011.07.016 pmid:21854847 fatcat:kpclijhzsbfrvhngr7vryubwty

A Multilayer Ontology of Instruments for Neurological, Behavioral and Cognitive Assessments

Bénédicte Batrancourt, Michel Dojat, Bernard Gibaud, Gilles Kassel
2014 Neuroinformatics  
Advances in neuroscience are underpinned by large, multicenter studies and a mass of heterogeneous datasets. When investigating the relationships between brain anatomy and brain functions under normal and pathological conditions, measurements obtained from a broad range of brain imaging techniques are correlated with the information on each subject's neurologic states, cognitive assessments and behavioral scores derived from questionnaires and tests. The development of ontologies in
more » ... appears to be a valuable way of gathering and handling properly these heterogeneous dataparticularly through the use of federated architectures. We recently proposed a multilayer ontology for sharing brain images and regions of interest in neuroimaging. Here, we report on an extension of this ontology to the representation of instruments used to assess brain and cognitive functions and behavior in humans. This extension consists of a 'core' ontology that accounts for the properties shared by all instruments supplemented by 'domain' ontologies that conceptualize standard instruments. We also specify how this core ontology has been refined to build domain ontologies dedicated to widely used instruments and how various scores used in the neurosciences are represented. Lastly, we discuss our design choices, the ontology's limitations and planned extensions aimed at querying and reasoning across distributed data sources.
doi:10.1007/s12021-014-9244-3 pmid:25240319 pmcid:PMC4303739 fatcat:aguax7z46nbt5f4eged6bgdfle

Rostro-caudal Architecture of the Frontal Lobes in Humans

Michel Thiebaut de Schotten, Marika Urbanski, Benedicte Batrancourt, Richard Levy, Bruno Dubois, Leonardo Cerliani, Emmanuelle Volle
2016 Cerebral Cortex  
The nature of the inputs and outputs of a brain region defines its functional specialization. The frontal portion of the brain is essential for goal-directed behaviors, however, the biological basis for its functional organization is unknown. Here, exploring structural connectomic properties, we delineated 12 frontal areas, defined by the pattern of their white matter connections. This result was highly reproducible across neuroimaging centers, acquisition parameters, and participants. These
more » ... as corresponded to regions functionally engaged in specific tasks, organized along a rostro-caudal axis from the most complex high-order association areas to the simplest idiotopic areas. The rostro-caudal axis along which the 12 regions were organized also reflected a gradient of cortical thickness, myelination, and cell body density. Importantly, across the identified regions, this gradient of microstructural features was strongly associated with the varying degree of information processing complexity. These new anatomical signatures shed light onto the structural organization of the frontal lobes and could help strengthen the prediction or diagnosis of neurodevelopmental and neurodegenerative disorders.
doi:10.1093/cercor/bhw215 pmid:27461122 fatcat:h6yn7kqn4va4vf2qft2z6pmn7u

NeuroLOG: sharing neuroimaging data using an ontology-based federated approach

Bernard Gibaud, Gilles Kassel, Michel Dojat, Bénédicte Batrancourt, Franck Michel, Alban Gaignard, Johan Montagnat
2011 AMIA Annual Symposium Proceedings  
This paper describes the design of the NeuroLOG middleware data management layer, which provides a platform to share heterogeneous and distributed neuroimaging data using a federated approach. The semantics of shared information is captured through a multi-layer application ontology and a derived Federated Schema used to align the heterogeneous database schemata from different legacy repositories. The system also provides a facility to translate the relational data into a semantic
more » ... that can be queried using a semantic search engine thus enabling the exploitation of knowledge embedded in the ontology. This work shows the relevance of the distributed approach for neurosciences data management. Although more complex than a centralized approach, it is also more realistic when considering the federation of large data sets, and open strong perspectives to implement multi-centric neurosciences studies.
pmid:22195101 pmcid:PMC3243145 fatcat:klhgfosejbcpbmw6i7pqdcbd2m

Exploration Deficits Under Ecological Conditions as a Marker of Apathy in Frontotemporal Dementia

Bénédicte Batrancourt, Karen Lecouturier, Johan Ferrand-Verdejo, Vincent Guillemot, Carole Azuar, David Bendetowicz, Raffaella Migliaccio, Armelle Rametti-Lacroux, Bruno Dubois, Richard Levy
2019 Frontiers in Neurology  
Apathy is one of the six clinical criteria for the behavioral variant of frontotemporal dementia (bvFTD), and it is almost universal in this disease. Although its consequences in everyday life are debilitating, its underlying mechanisms are poorly known, its assessment is biased by subjectivity and its care management is very limited. In this context, we have developed "ECOCAPTURE," a method aimed at providing quantifiable and objective signature(s) of apathy in order to assess it and identify
more » ... ts precise underlying mechanisms. ECOCAPTURE consists of the observation and recording of the patient's behavior when the participant is being submitted to a multiple-phase scenario reproducing a brief real-life situation. It is performed in a functional exploration platform transformed into a fully furnished waiting room equipped with a video and sensor-based data acquisition system. This multimodal method allowed video-based behavior analyses according to predefined behavioral categories (exploration behavior, sustained activities or inactivity) and actigraphy analyses from a 3D accelerometer. The data obtained were also correlated with behavioral/cognitive tests and scales assessing global cognitive efficiency, apathy, cognitive disinhibition, frontal syndrome, depression and anxiety. Here, bvFTD patients (n = 14) were compared to healthy participants (n = 14) during the very first minutes of the scenario, when the participants discovered the room and were encouraged to explore it. We showed that, in the context of facing a new environment, healthy participants first explored it and then engaged in sustained activities. By contrast, bvFTD patients were mostly inactive and eventually explored this new place, but in a more irregular and less efficient mode than normal subjects. This exploration deficit was correlated with apathy, disinhibition and cognitive and behavioral dysexecutive syndromes. These findings led us to discuss the presumed underlying mechanisms responsible for the exploration deficit (an inability to self-initiate actions, to integrate reward valuation and to inhibit involuntary behavior). Altogether, these results pave the way for simple and objective assessment of behavioral changes that represents a critical step for the evaluation of disease progression and efficacy of treatment in bvFTD.
doi:10.3389/fneur.2019.00941 pmid:31551908 pmcid:PMC6736613 fatcat:xg6pxxdsojckneramb47ytxcbq

Integrated multimedia electronic patient record and graph-based image information for cerebral tumors

John Puentes, Bénédicte Batrancourt, Jamal Atif, Elsa Angelini, Laurent Lecornu, Abdelhamid Zemirline, Isabelle Bloch, Gouenou Coatrieux, Christian Roux
2008 Computers in Biology and Medicine  
Current electronic patient record (EPR) implementations do not incorporate medical images, nor structural information extracted from them, despite images increasing role for diagnosis. This paper presents an integration framework into EPRs of anatomical and pathological knowledge extracted from segmented magnetic resonance imaging (MRI), applying a graph of representation for anatomical and functional information for individual patients. Focusing on cerebral tumors examination and patient
more » ... -up, multimedia EPRs were created and evaluated through a 3D navigation application, developed with open-source libraries and standards. Results suggest that the enhanced clinical information scheme could lead to original changes in the way medical experts utilize image-based information. ᭧
doi:10.1016/j.compbiomed.2008.01.009 pmid:18325489 fatcat:g6myzzjtr5byzkv2z7fxw7etoq

ECOCAPTURE@HOME: Protocol for the Remote Assessment of Apathy and Its Everyday-Life Consequences

Valérie Godefroy, Richard Levy, Arabella Bouzigues, Armelle Rametti-Lacroux, Raffaella Migliaccio, Bénédicte Batrancourt
2021 International Journal of Environmental Research and Public Health  
the behavioural markers of apathy in a laboratory context reproducing a closeto-real-life situation (wait comfortably in a waiting room), using an acquisition system combining video and sensors (see Batrancourt  ... 
doi:10.3390/ijerph18157824 pmid:34360133 pmcid:PMC8345445 fatcat:e4hj62txnzfbpi2yjgfxcxgesq

Frontotemporal dementia subtypes based on behavioral inhibition deficits

Valérie Godefroy, Delphine Tanguy, Arabella Bouzigues, Idil Sezer, Johan Ferrand‐Verdejo, Carole Azuar, David Bendetowicz, Guilhem Carle, Armelle Rametti‐Lacroux, Stéphanie Bombois, Emmanuel Cognat, Pierre Jannin (+5 others)
2021 Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring  
As described in Batrancourt et al., 9 participants followed a multiplephase scenario, starting with a first freely moving phase (7 minutes) when participants entered and discovered the room.  ... 
doi:10.1002/dad2.12178 pmid:33851004 pmcid:PMC8022767 fatcat:x746jep5evbgpevsaxlmc4hkde

Grid-wide neuroimaging data federation in the context of the NeuroLOG project

Franck Michel, Alban Gaignard, Farooq Ahmad, Christian Barillot, Bénédicte Batrancourt, Michel Dojat, Bernard Gibaud, Pascal Girard, David Godard, Gilles Kassel, Diane Lingrand, Grégoire Malandain (+5 others)
2010 Studies in Health Technology and Informatics  
Grid technologies are appealing to deal with the challenges raised by computational neurosciences and support multi-centric brain studies. However, core grids middleware hardly cope with the complex neuroimaging data representation and multi-layer data federation needs. Moreover, legacy neuroscience environments need to be preserved and cannot be simply superseded by grid services. This paper describes the NeuroLOG platform design and implementation, shedding light on its Data Management Layer.
more » ... It addresses the integration of brain image files, associated relational metadata and neuroscience semantic data in a heterogeneous distributed environment, integrating legacy data managers through a mediation layer.
pmid:20543431 pmcid:PMC2938713 fatcat:upx43zpnpjfolku2cwtghguko4

CATI: A Large Distributed Infrastructure for the Neuroimaging of Cohorts

Grégory Operto, Marie Chupin, Bénédicte Batrancourt, Marie-Odile Habert, Olivier Colliot, Habib Benali, Cyril Poupon, Catherine Champseix, Christine Delmaire, Sullivan Marie, Denis Rivière, Mélanie Pélégrini-Issac (+24 others)
2016 Neuroinformatics  
This paper provides an overview of CATI, a platform dedicated to multicenter neuroimaging. Initiated by the French Alzheimer's plan (2008)(2009)(2010)(2011)(2012), CATI is a research project called on to provide service to other projects like an industrial partner. Its core mission is to support the neuroimaging of large populations, providing concrete solutions to the increasing complexity involved in such projects by bringing together a service infrastructure, the know-how of its expert
more » ... ic teams and a large-scale, harmonized network of imaging facilities. CATI aims to make data sharing across studies easier and promotes sharing as much as possible. In the last four years, CATI has assisted the clinical community by taking charge of 35 projects so far and has emerged as a recognized actor at the national and international levels.
doi:10.1007/s12021-016-9295-8 pmid:27066973 fatcat:i6mgcfwcpndtfctmv4ws4uuyai

White matter lesional predictors of chronic visual neglect: a longitudinal study

Marine Lunven, Michel Thiebaut De Schotten, Clémence Bourlon, Christophe Duret, Raffaella Migliaccio, Gilles Rode, Paolo Bartolomeo
2015 Brain  
Acknowledgements We thank Bénédicte Batrancourt for help with MRI acquisition within the framework of the MRI database for the Centre for Cognitive Anatomy (CAC; http://bit.ly/ 1nJC6Er).  ... 
doi:10.1093/brain/awu389 pmid:25609686 pmcid:PMC4339774 fatcat:2usdubxidvaijbi6hhp32hkcra

Game theoretical mapping of white matter contributions to visuospatial attention in stroke patients with hemineglect

Monica N. Toba, Melissa Zavaglia, Caroline Malherbe, Tristan Moreau, Federica Rastelli, Anna Kaglik, Romain Valabrègue, Pascale Pradat-Diehl, Claus C. Hilgetag, Antoni Valero-Cabré
2020 Human Brain Mapping  
Bénédicte Batrancourt for managing the CAC database, and Dr. Paolo Bartolomeo for advice with the selection and scoring approaches of neuropsychological neglect tests.  ... 
doi:10.1002/hbm.24987 pmid:32243676 pmcid:PMC7336155 fatcat:kv6yvzrjdzfvbgpiequkzrn2hi