1,769 research outputs found
Centralized and distributed cognitive task processing in the human connectome
A key question in modern neuroscience is how cognitive changes in a human
brain can be quantified and captured by functional connectomes (FC) . A
systematic approach to measure pairwise functional distance at different brain
states is lacking. This would provide a straight-forward way to quantify
differences in cognitive processing across tasks; also, it would help in
relating these differences in task-based FCs to the underlying structural
network. Here we propose a framework, based on the concept of Jensen-Shannon
divergence, to map the task-rest connectivity distance between tasks and
resting-state FC. We show how this information theoretical measure allows for
quantifying connectivity changes in distributed and centralized processing in
functional networks. We study resting-state and seven tasks from the Human
Connectome Project dataset to obtain the most distant links across tasks. We
investigate how these changes are associated to different functional brain
networks, and use the proposed measure to infer changes in the information
processing regimes. Furthermore, we show how the FC distance from resting state
is shaped by structural connectivity, and to what extent this relationship
depends on the task. This framework provides a well grounded mathematical
quantification of connectivity changes associated to cognitive processing in
large-scale brain networks.Comment: 22 pages main, 6 pages supplementary, 6 figures, 5 supplementary
figures, 1 table, 1 supplementary table. arXiv admin note: text overlap with
arXiv:1710.0219
Graph analysis of functional brain networks: practical issues in translational neuroscience
The brain can be regarded as a network: a connected system where nodes, or
units, represent different specialized regions and links, or connections,
represent communication pathways. From a functional perspective communication
is coded by temporal dependence between the activities of different brain
areas. In the last decade, the abstract representation of the brain as a graph
has allowed to visualize functional brain networks and describe their
non-trivial topological properties in a compact and objective way. Nowadays,
the use of graph analysis in translational neuroscience has become essential to
quantify brain dysfunctions in terms of aberrant reconfiguration of functional
brain networks. Despite its evident impact, graph analysis of functional brain
networks is not a simple toolbox that can be blindly applied to brain signals.
On the one hand, it requires a know-how of all the methodological steps of the
processing pipeline that manipulates the input brain signals and extract the
functional network properties. On the other hand, a knowledge of the neural
phenomenon under study is required to perform physiological-relevant analysis.
The aim of this review is to provide practical indications to make sense of
brain network analysis and contrast counterproductive attitudes
Neuroelectronic interfacing with cultured multielectrode arrays toward a cultured probe
Efficient and selective electrical stimulation and recording of neural activity in peripheral, spinal, or central pathways requires multielectrode arrays at micrometer scale. ¿Cultured probe¿ devices are being developed, i.e., cell-cultured planar multielectrode arrays (MEAs). They may enhance efficiency and selectivity because neural cells have been grown over and around each electrode site as electrode-specific local networks. If, after implantation, collateral sprouts branch from a motor fiber (ventral horn area) and if they can be guided and contacted to each ¿host¿ network, a very selective and efficient interface will result. Four basic aspects of the design and development of a cultured probe, coated with rat cortical or dorsal root ganglion neurons, are described. First, the importance of optimization of the cell-electrode contact is presented. It turns out that impedance spectroscopy, and detailed modeling of the electrode-cell interface, is a very helpful technique, which shows whether a cell is covering an electrode and how strong the sealing is. Second, the dielectrophoretic trapping method directs cells efficiently to desired spots on the substrate, and cells remain viable after the treatment. The number of cells trapped is dependent on the electric field parameters and the occurrence of a secondary force, a fluid flow (as a result of field-induced heating). It was found that the viability of trapped cortical cells was not influenced by the electric field. Third, cells must adhere to the surface of the substrate and form networks, which are locally confined, to one electrode site. For that, chemical modification of the substrate and electrode areas with various coatings, such as polyethyleneimine (PEI) and fluorocarbon monolayers promotes or inhibits adhesion of cells. Finally, it is shown how PEI patterning, by a stamping technique, successfully guides outgrowth of collaterals from a neonatal rat lumbar spinal cord explant, after six days in cultur
Network-based brain computer interfaces: principles and applications
Brain-computer interfaces (BCIs) make possible to interact with the external
environment by decoding the mental intention of individuals. BCIs can therefore
be used to address basic neuroscience questions but also to unlock a variety of
applications from exoskeleton control to neurofeedback (NFB) rehabilitation. In
general, BCI usability critically depends on the ability to comprehensively
characterize brain functioning and correctly identify the user s mental state.
To this end, much of the efforts have focused on improving the classification
algorithms taking into account localized brain activities as input features.
Despite considerable improvement BCI performance is still unstable and, as a
matter of fact, current features represent oversimplified descriptors of brain
functioning. In the last decade, growing evidence has shown that the brain
works as a networked system composed of multiple specialized and spatially
distributed areas that dynamically integrate information. While more complex,
looking at how remote brain regions functionally interact represents a grounded
alternative to better describe brain functioning. Thanks to recent advances in
network science, i.e. a modern field that draws on graph theory, statistical
mechanics, data mining and inferential modelling, scientists have now powerful
means to characterize complex brain networks derived from neuroimaging data.
Notably, summary features can be extracted from these networks to
quantitatively measure specific organizational properties across a variety of
topological scales. In this topical review, we aim to provide the
state-of-the-art supporting the development of a network theoretic approach as
a promising tool for understanding BCIs and improve usability
Deep convolutional networks for automated detection of posterior-element fractures on spine CT
Injuries of the spine, and its posterior elements in particular, are a common
occurrence in trauma patients, with potentially devastating consequences.
Computer-aided detection (CADe) could assist in the detection and
classification of spine fractures. Furthermore, CAD could help assess the
stability and chronicity of fractures, as well as facilitate research into
optimization of treatment paradigms.
In this work, we apply deep convolutional networks (ConvNets) for the
automated detection of posterior element fractures of the spine. First, the
vertebra bodies of the spine with its posterior elements are segmented in spine
CT using multi-atlas label fusion. Then, edge maps of the posterior elements
are computed. These edge maps serve as candidate regions for predicting a set
of probabilities for fractures along the image edges using ConvNets in a 2.5D
fashion (three orthogonal patches in axial, coronal and sagittal planes). We
explore three different methods for training the ConvNet using 2.5D patches
along the edge maps of 'positive', i.e. fractured posterior-elements and
'negative', i.e. non-fractured elements.
An experienced radiologist retrospectively marked the location of 55
displaced posterior-element fractures in 18 trauma patients. We randomly split
the data into training and testing cases. In testing, we achieve an
area-under-the-curve of 0.857. This corresponds to 71% or 81% sensitivities at
5 or 10 false-positives per patient, respectively. Analysis of our set of
trauma patients demonstrates the feasibility of detecting posterior-element
fractures in spine CT images using computer vision techniques such as deep
convolutional networks.Comment: To be presented at SPIE Medical Imaging, 2016, San Dieg
Neural reuse: A fundamental organizational principle of the brain
An emerging class of theories concerning the functional structure of the brain takes the reuse of neural circuitry for various cognitive purposes to be a central organizational principle. According to these theories, it is quite common for neural circuits established for one purpose to be exapted (exploited, recycled, redeployed) during evolution or normal development, and be put to different uses, often without losing their original functions. Neural reuse theories thus differ from the usual understanding of the role of neural plasticity (which is, after all, a kind of reuse) in brain organization along the following lines: According to neural reuse, circuits can continue to acquire new uses after an initial or original function is established; the acquisition of new uses need not involve unusual circumstances such as injury or loss of established function; and the acquisition of a new use need not involve (much) local change to circuit structure (e.g., it might involve only the establishment of functional connections to new neural partners). Thus, neural reuse theories offer a distinct perspective on several topics of general interest, such as: the evolution and development of the brain, including (for instance) the evolutionary-developmental pathway supporting primate tool use and human language; the degree of modularity in brain organization; the degree of localization of cognitive function; and the cortical parcellation problem and the prospects (and proper methods to employ) for function to structure mapping. The idea also has some practical implications in the areas of rehabilitative medicine and machine interface design
Resting-state functional brain netwoks in Parkinson's disease
The network approach is increasingly being applied to the investigation of normal brain function and its impairment. In the present review, we introduce the main methodological approaches employed for the analysis of resting-state neuroimaging data in Parkinson's disease studies. We then summarize the results of recent studies that used a functional network perspective to evaluate the changes underlying different manifestations of Parkinson's disease, with an emphasis on its cognitive symptoms. Despite the variability reported by many studies, these methods show promise as tools for shedding light on the pathophysiological substrates of different aspects of Parkinson's disease, as well as for differential diagnosis, treatment monitoring and establishment of imaging biomarkers for more severe clinical outcomes
Classification of Tactile and Motor Velocity-Evoked Hemodynamic Response in Primary Somatosensory and Motor Cortices as Measured by Functional Near-Infrared Spectroscopy
Functional near-infrared spectroscopy (fNIRS) is an emerging technique in studying cerebral hemodynamics; however, consensus on the analysis methods and the clinical applications has yet to be established. In this study, we demonstrate the results of a pilot fNIRS study of cerebral hemodynamic response (HR) evoked by pneumotactile and sensorimotor stimuli on the dominant hand. Our goal is to find the optimal stimulus parameters to maximally evoke HR in the primary somatosensory and motor cortices. We use a pulsatile pneumatic array of 14 tactile cells that were attached to the glabrous surface of the dominant hand, with a patterned stimulus that resembles saltation at three distinct traverse velocities [10, 25, and 45 cm/s]. NIRS optodes (16 sources; 20 detectors) are bilaterally and symmetrically placed over the pre-and post-central gyri (M1 and S1). Our objective is to identify the extent to which cerebral HR can encode the velocity of the somatosensory and/or motor stimuli. We use common spatial pattern for feature extraction and regularized-discriminant analysis for classifying the fNIRS time series into velocity classes. The classification results demonstrate discriminatory features of the fNIRS signal from each distinct stimulus velocity. The results are inconclusive regarding the velocity which evokes the highest intensity of hemodynamic response
Deploying and Optimizing Embodied Simulations of Large-Scale Spiking Neural Networks on HPC Infrastructure
Simulating the brain-body-environment trinity in closed loop is an attractive proposal
to investigate how perception, motor activity and interactions with the environment
shape brain activity, and vice versa. The relevance of this embodied approach, however,
hinges entirely on the modeled complexity of the various simulated phenomena. In this
article, we introduce a software framework that is capable of simulating large-scale,
biologically realistic networks of spiking neurons embodied in a biomechanically accurate
musculoskeletal system that interacts with a physically realistic virtual environment. We
deploy this framework on the high performance computing resources of the EBRAINS
research infrastructure and we investigate the scaling performance by distributing
computation across an increasing number of interconnected compute nodes. Our
architecture is based on requested compute nodes as well as persistent virtualmachines;
this provides a high-performance simulation environment that is accessible to multidomain
users without expert knowledge, with a view to enable users to instantiate
and control simulations at custom scale via a web-based graphical user interface. Our
simulation environment, entirely open source, is based on the Neurorobotics Platform
developed in the context of the Human Brain Project, and the NEST simulator. We
characterize the capabilities of our parallelized architecture for large-scale embodied
brain simulations through two benchmark experiments, by investigating the effects of
scaling compute resources on performance defined in terms of experiment runtime, brain instantiation and simulation time. The first benchmark is based on a largescale
balanced network, while the second one is a multi-region embodied brain
simulation consisting of more than a million neurons and a billion synapses. Both
benchmarks clearly show how scaling compute resources improves the aforementioned
performance metrics in a near-linear fashion. The second benchmark in particular is
indicative of both the potential and limitations of a highly distributed simulation in
terms of a trade-off between computation speed and resource cost. Our simulation
architecture is being prepared to be accessible for everyone as an EBRAINS service,
thereby offering a community-wide tool with a unique workflow that should provide
momentum to the investigation of closed-loop embodiment within the computational
neuroscience community.European Union’s Horizon
2020 Framework Programme 785907 945539European Union’s Horizon
2020 800858MEXT (hp200139, hp210169) MEXT KAKENHI grant
no. 17H06310
Deploying and Optimizing Embodied Simulations of Large-Scale Spiking Neural Networks on HPC Infrastructure
Simulating the brain-body-environment trinity in closed loop is an attractive proposal to investigate how perception, motor activity and interactions with the environment shape brain activity, and vice versa. The relevance of this embodied approach, however, hinges entirely on the modeled complexity of the various simulated phenomena. In this article, we introduce a software framework that is capable of simulating large-scale, biologically realistic networks of spiking neurons embodied in a biomechanically accurate musculoskeletal system that interacts with a physically realistic virtual environment. We deploy this framework on the high performance computing resources of the EBRAINS research infrastructure and we investigate the scaling performance by distributing computation across an increasing number of interconnected compute nodes. Our architecture is based on requested compute nodes as well as persistent virtual machines; this provides a high-performance simulation environment that is accessible to multi-domain users without expert knowledge, with a view to enable users to instantiate and control simulations at custom scale via a web-based graphical user interface. Our simulation environment, entirely open source, is based on the Neurorobotics Platform developed in the context of the Human Brain Project, and the NEST simulator. We characterize the capabilities of our parallelized architecture for large-scale embodied brain simulations through two benchmark experiments, by investigating the effects of scaling compute resources on performance defined in terms of experiment runtime, brain instantiation and simulation time. The first benchmark is based on a large-scale balanced network, while the second one is a multi-region embodied brain simulation consisting of more than a million neurons and a billion synapses. Both benchmarks clearly show how scaling compute resources improves the aforementioned performance metrics in a near-linear fashion. The second benchmark in particular is indicative of both the potential and limitations of a highly distributed simulation in terms of a trade-off between computation speed and resource cost. Our simulation architecture is being prepared to be accessible for everyone as an EBRAINS service, thereby offering a community-wide tool with a unique workflow that should provide momentum to the investigation of closed-loop embodiment within the computational neuroscience community.journal articl
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