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In the brain, spiking patterns live in a high-dimensional space of neurons and time. Thus, determining the intrinsic structure of this space presents a theoretical and experimental challenge. To address this challenge, we introduce a new framework for applying topological data analysis (TDA) to spike train data and use it to determine the geometry of spiking patterns in the visual cortex. Key to our approach is a parametrized family of distances based on the timing of spikes that quantifies the dissimilarity between neuronal responses. We applied TDA to visually driven single-unit and multiple single-unit spiking activity in macaque V1 and V2. TDA across timescales reveals a common geometry for spiking patterns in V1 and V2 which, among simple models, is most similar to that of a low-dimensional space endowed with Euclidean or hyperbolic geometry with modest curvature. Remarkably, the inferred geometry depends on timescale and is clearest for the timescales that are important for encoding contrast, orientation and spatial correlations., NIH grants number EY09314 and EY07977 from the National Eye Institute of the NIH. NIH grants no. EY034150 from the National Eye Institute and NS111019 from the National Institute of Neurological Disorders and Stroke. Ikerbasque. Wallenberg AI, Autonomous Systems and Software Program (WASP) funded by the Knut and Alice Wallenberg Foundation. Inria Associated Team "NeuroTransSF".

Background: Unravelling the mystery of Alzheimer's disease (AD) requires urgent resolution given the worldwide increase of the aging population. There is a growing concern that the current leading AD hypothesis, the amyloid cascade hypothesis, does not stand up to validation with respect to emerging new data. Indeed, several paradoxes are being discussed in the literature, for instance, both the deposition of the amyloid-β peptide (Aβ) and the intracellular neurofibrillary tangles could occur within the brain without any cognitive pathology. Thus, these paradoxes suggest that something more fundamental is at play in the onset of the disease and other key and related pathomechanisms must be investigated. Objective: The present study follows our previous investigations on the infectious hypothesis, which posits that some pathogens are linked to late onset AD. Our studies also build upon the finding that Aβ is a powerful antimicrobial agent, produced by neurons in response to viral infection, capable of inhibiting pathogens as observed in in vitro experiments. Herein, we ask what are the molecular mechanisms in play when Aβ neutralizes infectious pathogens? Methods: To answer this question, we probed at nanoscale lengths with FRET (Förster Resonance Energy Transfer), the interaction between Aβ peptides and glycoprotein B (responsible of virus-cell binding) within the HSV-1 virion Results: The experiments show an energy transfer between Aβ peptides and glycoprotein B when membrane is intact. No energy transfer occurs after membrane disruption or treatment with blocking antibody. Conclusion: We concluded that Aβ insert into viral membrane, close to glycoprotein B, and participate in virus neutralization., Ikerbasque GV-AI-HEALTH Inria Associated Team "NeuroTransSF"

We propose a minimalist phenomenological model for the ‘interfacial water’ phenomenon that occurs near hydrophilic polymeric surfaces. We achieve this by combining a Ginzburg–Landau approach with Maxwell’s equations which leads us to a well-posed model providing a macroscopic interpretation of experimental observations. From the derived governing equations, we estimate the unknown parameters using experimental measurements from the literature. The resulting profiles of the polarization and electric potential show exponential decay near the surface, in qualitative agreement with experiments. Furthermore, the model’s quantitative prediction of the electric potential at the hydrophilic surface is in excellent agreement with experiments. The proposed model is a first step towards a more complete parsimonious macroscopic model that will, for example, help to elucidate the effects of interfacial water on cells (e.g. neuronal excitability), the effects of infrared neural stimulation or the effects of drugs mediated by interfacial water., Ikerbasque (The Basque Foundation for Science) Inria Associated Team "NeuroTransSF"

Metastability refers to the fact that the state of a dynamical system spends a large amount of time in a restricted region of its available phase space before a transition takes place, bringing the system into another state from where it might recur into the previous one. Beim Graben and Hutt suggested to use the recurrence plot (RP) technique introduced by Eckmann et al. for the segmentation of system’s trajectories into metastable states using recurrence grammars. Here, we apply this recurrence structure analysis (RSA) for the first time to resting-state brain dynamics obtained from functional magnetic resonance imaging (fMRI). Brain regions are defined according to the brain hierarchical atlas (BHA) developed by Diez et al., and as a consequence, regions present high-connectivity in both structure (obtained from diffusion tensor imaging) and function (from the blood-level dependent-oxygenation —BOLD— signal). Remarkably, regions observed by Diez et al. were completely time-invariant. Here, in order to compare this static picture with the metastable systems dynamics obtained from the RSA segmentation, we determine the number of metastable states as a measure of complexity for all subjects and for region numbers varying from 3 to 100. We find RSA convergence towards an optimal segmentation of 40 metastable states for normalized BOLD signals, averaged over BHA modules. Next, we build a bistable dynamics at population level by pooling 30 subjects after Hausdorff clustering. In link with this finding, we reflect on the different modeling frameworks that can allow for such scenarios: heteroclinic dynamics, dynamics with riddled basins of attraction, multiple-timescale dynamics. Finally, we characterize the metastable states both functionally and structurally, using templates for resting state networks (RSNs) and the automated anatomical labeling (AAL) atlas, respectively., Ikerbasque, FEDER grant DPI2016-79874-R, Elkartek Program KK-2018/00032