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Foundations for an ontology of brain areas, circuits and functions
2013
BMC Neuroscience
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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
2011
Journal of Physiology - Paris
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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
doi:10.1016/j.jphysparis.2011.07.016
pmid:21854847
fatcat:kpclijhzsbfrvhngr7vryubwty
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... 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.
A Multilayer Ontology of Instruments for Neurological, Behavioral and Cognitive Assessments
2014
Neuroinformatics
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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
doi:10.1007/s12021-014-9244-3
pmid:25240319
pmcid:PMC4303739
fatcat:aguax7z46nbt5f4eged6bgdfle
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... 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.
Rostro-caudal Architecture of the Frontal Lobes in Humans
2016
Cerebral Cortex
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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
doi:10.1093/cercor/bhw215
pmid:27461122
fatcat:h6yn7kqn4va4vf2qft2z6pmn7u
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... 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.
NeuroLOG: sharing neuroimaging data using an ontology-based federated approach
2011
AMIA Annual Symposium Proceedings
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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
pmid:22195101
pmcid:PMC3243145
fatcat:klhgfosejbcpbmw6i7pqdcbd2m
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... 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.
Exploration Deficits Under Ecological Conditions as a Marker of Apathy in Frontotemporal Dementia
2019
Frontiers in Neurology
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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
doi:10.3389/fneur.2019.00941
pmid:31551908
pmcid:PMC6736613
fatcat:xg6pxxdsojckneramb47ytxcbq
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... 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.
Integrated multimedia electronic patient record and graph-based image information for cerebral tumors
2008
Computers in Biology and Medicine
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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
doi:10.1016/j.compbiomed.2008.01.009
pmid:18325489
fatcat:g6myzzjtr5byzkv2z7fxw7etoq
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... -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. ᭧
ECOCAPTURE@HOME: Protocol for the Remote Assessment of Apathy and Its Everyday-Life Consequences
2021
International Journal of Environmental Research and Public Health
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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
2021
Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring
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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
2010
Studies in Health Technology and Informatics
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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.
pmid:20543431
pmcid:PMC2938713
fatcat:upx43zpnpjfolku2cwtghguko4
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... 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.
CATI: A Large Distributed Infrastructure for the Neuroimaging of Cohorts
2016
Neuroinformatics
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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
doi:10.1007/s12021-016-9295-8
pmid:27066973
fatcat:i6mgcfwcpndtfctmv4ws4uuyai
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... 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.
White matter lesional predictors of chronic visual neglect: a longitudinal study
2015
Brain
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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
2020
Human Brain Mapping
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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