The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Recording of fast activity at the onset of partial seizures: Depth EEG vs. scalp EEG.

International audienceRapid discharges (25-80Hz), a characteristic EEG pattern often recorded at seizure onset in partial epilepsies, are often considered as electrophysiological signatures of the epileptogenic zone. While the recording of rapid discharges from intracranial electrodes has long been established, their observation from the scalp is challenging. The prevailing view is that rapid discharges cannot be seen clearly (or at all) in scalp EEG because they have low signal-to-noise ratio. To date, however, no studies have investigated the 'observability' of rapid discharges, i.e. under what conditions and to what extent they can be visible in recorded EEG signals. Here, we used a model-based approach to examine the impact of several factors (distance to sources, skull conductivity, source area, source synchrony, and background activity) on the observability of rapid discharges in simultaneously simulated depth EEG and scalp EEG signals. In our simulations, the rapid discharge was clearly present in depth EEG signals but mostly almost not visible in scalp EEG signals. We identified some of the factors that may limit the observability of the rapid discharge on the scalp. Notably, surrounding background activity was found to be the most critical factor. The findings are discussed in relation to the presurgical evaluation of epilepsy

Localization of extended intracerebral current sources: Application to epilepsy.

International audienceWe propose a new method for localizing intracerebral current sources at the origin of epileptic spikes from non-invasive EEG/MEG data. This method was designed to account for three main constrains. First, most relevant spike generation models assume that sources are extended, i.e. spatially distributed over a focal or muti-focal area. Second, the background activity of the brain also contributes to EEG/MEG signals recorded during epileptic events. In this context, it can be seen as a penalizing Gaussian and spatially correlated noise. Third the array manifold is usually corrupted by errors due to the complexity of the conduction head volume. The proposed method is an adaptation of the well-established MUSIC method, that allows for the localization of Extended Sources (ExSo) assuming that all current dipoles comprised in the extended source are synchronous. In addition, we use Higher Order (HO) statistics, which are asymptotically insensitive to a Gaussian noise of unknown spatial coherence and which offer a greater robustness with respect to modeling errors. The method is called 2q-ExSo-MUSIC (q ges 2) as it combines the ExSo-MUSIC principle with the use of HO statistics. Using computer simulations of EEG signals, it is shown to highly increase the performance of classical MUSIC-like algorithms when physiologically relevant models for current sources and for volume conduction are considered

Fourth order approaches for localization of brain current sources.

International audienceTwo high resolution methods solving inverse problems potentially ill-posed, named 4-MUSIC and 4-RapMUSIC, are proposed. They allow for localization of brain current sources with unconstrained orientations from surface electro-or magneto-encephalographic data using spherical or realistic head geometries. The 4-MUSIC and 4-RapMUSIC methods are based on i) the separability of the data transfer matrix as a function of location and orientation parameters and ii) the fourth order (FO) virtual array theory. In addition, 4-RapMUSIC uses the deflation concept extended to FO statistics accounting for the presence of potentially but not totally coherent sources. Computer results display the superiority of the 4-RapMUSIC approach in different situations (two closed sources, additive Gaussian noise with unknown spatial covariance, ...) especially over classical algorithms

Computational modeling of simultaneously recorded scalp and depth EEG signals

ISBN : 978-2-9532965-0-1In epileptic patients candidate to surgery, the interpretation of electrophysiological signals recorded non-invasively (scalp EEG) and invasively (depth EEG) is a difficult but central question. Indeed, the localization of the epileptogenic zone, the determination of its organisation and the definition of subsequent therapeutic strategy is still largely based on the analysis of electrophysiological data. This issue is addressed in the present work through a realistic modeling of both scalp and depth EEG signals. The model is based on an anatomically and physiologically relevant description of the neuronal sources of brain electrical activity that combines a distributed dipole source model and a model of coupled neuronal populations. EEG signals are then simulated by solving the forward problem in the head volume conductor, simultaneously on scalp and depth electrodes. The model was used to study the influence, on simulated EEG signals, of source-related parameters (spatial extent, position, synchronization) leading to the generation of transient epileptic activity (interictal spikes). More generally, this modeling approach helps in the understanding of the relationship between the properties of signals collected by electrodes (scalp and depth) and the underlying spatio-temporal organization of the neuronal sources

The neuronal sources of EEG: Modeling of simultaneous scalp and intracerebral recordings in epilepsy.

International audienceIn many applications which make use of EEG to investigate brain functions, a central question is often to relate the recorded signals to the spatio-temporal organization of the underlying neuronal sources of activity. A modeling attempt to quantitatively investigate this imperfectly known relationship is reported. The proposed plausible model of EEG generation relies on an accurate representation of the neuronal sources of activity. It combines both an anatomically realistic description of the spatial features of the sources (convoluted dipole layer) and a physiologically relevant description of their temporal activities (coupled neuronal populations). The model was used in the particular context of epileptiform activity (interictal spikes) to interpret simultaneously generated scalp and intracerebral EEG. Its integrative properties allowed for the bridging between source-related parameters (spatial extent, location, synchronization) and the properties of resulting EEG signals (amplitude of spikes, amplitude gradient along intracerebral electrodes, topography over scalp electrodes). The sensitivity of both recording modalities to source-related parameters was also studied. The model confirmed that the cortical area involved in interictal spikes is rather large. Its relative location with respect to recording electrodes was found to strongly influence the properties of EEG signals as the source geometry is a critical parameter. The influence, on simulated signals, of the synchronization degree between neuronal populations within the epileptic source was also investigated. The model revealed that intracerebral EEG can reflect epileptic activities corresponding to weak synchronization between neuronal populations of the epileptic patch. These results, as well as the limitations of the model, are discussed

Computational modeling of epileptic activity: from cortical sources to EEG signals.

International audienceIn epileptic patients candidate to surgery, the interpretation of EEG signals recorded either within (depth EEG) or at the surface (scalp EEG) of the head is a crucial issue to determine epileptogenic brain regions and to define subsequent surgical strategy. This task remains difficult as there is no simple relationship between the spatiotemporal features of neuronal generators (convoluted cortical dipole layers) and the electric field potentials recorded by the electrodes. Indeed, this relationship depends on the complex interaction of several factors regarding involved cortical sources: location, area, geometry, and synchronization of neuronal activity. A computational model is proposed to address this issue. It relies on a neurophysiologically relevant model of EEG signals, which combines an accurate description of both the intracerebral sources of activity and the transfer function between dipole layers and recorded field potentials. The model is used, on the one hand, to quantitatively study the influence of source-related parameters on the properties of simulated signals, and on the other hand, to jointly analyze depth EEG and scalp EEG signals. In this article, the authors review some of the results obtained from the model with respect to the literature on the interpretation of EEG signals in the context of epilepsy