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1.
iScience ; 27(4): 109370, 2024 Apr 19.
Artículo en Inglés | MEDLINE | ID: mdl-38523791

RESUMEN

The primary visual cortex is one of the most well understood regions supporting the processing involved in sensory computation. Following the popularization of high-density neural recordings, it has been observed that the activity of large neural populations is often constrained to low dimensional manifolds. In this work, we quantify the structure of such neural manifolds in the visual cortex. We do this by analyzing publicly available two-photon optical recordings of mouse primary visual cortex in response to visual stimuli with a densely sampled rotation angle. Using a geodesic metric along with persistent homology, we discover that population activity in response to such stimuli generates a circular manifold, encoding the angle of rotation. Furthermore, we observe that this circular manifold is expressed differently in subpopulations of neurons with differing orientation and direction selectivity. Finally, we discuss some of the obstacles to reliably retrieving the truthful topology generated by a neural population.

2.
bioRxiv ; 2024 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-38293236

RESUMEN

The local field potential (LFP), the low-frequency part of the extracellular potential, reflects transmembrane currents in the vicinity of the recording electrode. Thought mainly to stem from currents caused by synaptic input, it provides information about neural activity complementary to that of spikes, the output of neurons. However, the many neural sources contributing to the LFP, and likewise the derived current source density (CSD), can often make it challenging to interpret. Efforts to improve its interpretability have included the application of statistical decomposition tools like principal component analysis (PCA) and independent component analysis (ICA) to disentangle the contributions from different neural sources. However, their underlying assumptions of, respectively, orthogonality and statistical independence are not always valid for the various processes or pathways generating LFP. Here, we expand upon and validate a decomposition algorithm named Laminar Population Analysis (LPA), which is based on physiological rather than statistical assumptions. LPA utilizes the multiunit activity (MUA) and LFP jointly to uncover the contributions of different populations to the LFP. To perform the validation of LPA, we used data simulated with the large-scale, biophysically detailed model of mouse V1 developed by the Allen Institute. We find that LPA can identify laminar positions within V1 and the temporal profiles of laminar population firing rates from the MUA. We also find that LPA can estimate the salient current sinks and sources generated by feedforward input from the lateral geniculate nucleus (LGN), recurrent activity in V1, and feedback input from the lateromedial (LM) area of visual cortex. LPA identifies and distinguishes these contributions with a greater accuracy than the alternative statistical decomposition methods, PCA and ICA. Lastly, we also demonstrate the application of LPA on experimentally recorded MUA and LFP from 24 animals in the publicly available Visual Coding dataset. Our results suggest that LPA can be used both as a method to estimate positions of laminar populations and to uncover salient features in LFP/CSD contributions from different populations.

3.
bioRxiv ; 2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-37662298

RESUMEN

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.

4.
PLoS Comput Biol ; 19(11): e1011625, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-38032904

RESUMEN

In computational neuroscience, hypotheses are often formulated as bottom-up mechanistic models of the systems in question, consisting of differential equations that can be numerically integrated forward in time. Candidate models can then be validated by comparison against experimental data. The model outputs of neural network models depend on both neuron parameters, connectivity parameters and other model inputs. Successful model fitting requires sufficient exploration of the model parameter space, which can be computationally demanding. Additionally, identifying degeneracy in the parameters, i.e. different combinations of parameter values that produce similar outputs, is of interest, as they define the subset of parameter values consistent with the data. In this computational study, we apply metamodels to a two-population recurrent spiking network of point-neurons, the so-called Brunel network. Metamodels are data-driven approximations to more complex models with more desirable computational properties, which can be run considerably faster than the original model. Specifically, we apply and compare two different metamodelling techniques, masked autoregressive flows (MAF) and deep Gaussian process regression (DGPR), to estimate the power spectra of two different signals; the population spiking activities and the local field potential. We find that the metamodels are able to accurately model the power spectra in the asynchronous irregular regime, and that the DGPR metamodel provides a more accurate representation of the simulator compared to the MAF metamodel. Using the metamodels, we estimate the posterior probability distributions over parameters given observed simulator outputs separately for both LFP and population spiking activities. We find that these distributions correctly identify parameter combinations that give similar model outputs, and that some parameters are significantly more constrained by observing the LFP than by observing the population spiking activities.


Asunto(s)
Redes Neurales de la Computación , Neuronas , Neuronas/fisiología
5.
bioRxiv ; 2023 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-37398070

RESUMEN

Schizophrenia phenotypes are suggestive of impaired cortical plasticity in the disease, but the mechanisms of these deficits are unknown. Genomic association studies have implicated a large number of genes that regulate neuromodulation and plasticity, indicating that the plasticity deficits have a genetic origin. Here, we used biochemically detailed computational modelling of post-synaptic plasticity to investigate how schizophrenia-associated genes regulate long-term potentiation (LTP) and depression (LTD). We combined our model with data from post-mortem mRNA expression studies (CommonMind gene-expression datasets) to assess the consequences of altered expression of plasticity-regulating genes for the amplitude of LTP and LTD. Our results show that the expression alterations observed post mortem, especially those in anterior cingulate cortex, lead to impaired PKA-pathway-mediated LTP in synapses containing GluR1 receptors. We validated these findings using a genotyped EEG dataset where polygenic risk scores for synaptic and ion channel-encoding genes as well as modulation of visual evoked potentials (VEP) were determined for 286 healthy controls. Our results provide a possible genetic mechanism for plasticity impairments in schizophrenia, which can lead to improved understanding and, ultimately, treatment of the disorder.

6.
Elife ; 122023 07 24.
Artículo en Inglés | MEDLINE | ID: mdl-37486105

RESUMEN

Local field potential (LFP) recordings reflect the dynamics of the current source density (CSD) in brain tissue. The synaptic, cellular, and circuit contributions to current sinks and sources are ill-understood. We investigated these in mouse primary visual cortex using public Neuropixels recordings and a detailed circuit model based on simulating the Hodgkin-Huxley dynamics of >50,000 neurons belonging to 17 cell types. The model simultaneously captured spiking and CSD responses and demonstrated a two-way dissociation: firing rates are altered with minor effects on the CSD pattern by adjusting synaptic weights, and CSD is altered with minor effects on firing rates by adjusting synaptic placement on the dendrites. We describe how thalamocortical inputs and recurrent connections sculpt specific sinks and sources early in the visual response, whereas cortical feedback crucially alters them in later stages. These results establish quantitative links between macroscopic brain measurements (LFP/CSD) and microscopic biophysics-based understanding of neuron dynamics and show that CSD analysis provides powerful constraints for modeling beyond those from considering spikes.


Asunto(s)
Neuronas , Corteza Visual Primaria , Animales , Ratones , Neuronas/fisiología , Encéfalo , Modelos Neurológicos
7.
J Comput Neurosci ; 51(2): 283-298, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-37058180

RESUMEN

The perineuronal nets (PNNs) are sugar coated protein structures that encapsulate certain neurons in the brain, such as parvalbumin positive (PV) inhibitory neurons. As PNNs are theorized to act as a barrier to ion transport, they may effectively increase the membrane charge-separation distance, thereby affecting the membrane capacitance. Tewari et al. (2018) found that degradation of PNNs induced a 25%-50% increase in membrane capacitance [Formula: see text] and a reduction in the firing rates of PV-cells. In the current work, we explore how changes in [Formula: see text] affects the firing rate in a selection of computational neuron models, ranging in complexity from a single compartment Hodgkin-Huxley model to morphologically detailed PV-neuron models. In all models, an increased [Formula: see text] lead to reduced firing, but the experimentally reported increase in [Formula: see text] was not alone sufficient to explain the experimentally reported reduction in firing rate. We therefore hypothesized that PNN degradation in the experiments affected not only [Formula: see text], but also ionic reversal potentials and ion channel conductances. In simulations, we explored how various model parameters affected the firing rate of the model neurons, and identified which parameter variations in addition to [Formula: see text] that are most likely candidates for explaining the experimentally reported reduction in firing rate.


Asunto(s)
Interneuronas , Modelos Neurológicos , Matriz Extracelular/metabolismo , Neuronas , Encéfalo
8.
PLoS Biol ; 20(10): e3001440, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36301995

RESUMEN

The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase-the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and applied this method to estimate baseline CMRO2 in awake mice across cortical layers. To our surprise, our results revealed a decrease in baseline CMRO2 from layer I to layer IV. This decrease of CMRO2 with cortical depth was paralleled by an increase in tissue oxygenation. Higher baseline oxygenation and cytochrome density in layer IV may serve as an O2 reserve during surges of neuronal activity or certain metabolically active brain states rather than reflecting baseline energy needs. Our study provides to our knowledge the first quantification of microscopically resolved CMRO2 across cortical layers as a step towards better understanding of brain energy metabolism.


Asunto(s)
Complejo IV de Transporte de Electrones , Consumo de Oxígeno , Animales , Ratones , Complejo IV de Transporte de Electrones/metabolismo , Consumo de Oxígeno/fisiología , Oxígeno/metabolismo , Corteza Cerebral/metabolismo , Encéfalo/fisiología , Circulación Cerebrovascular
9.
Acta Physiol (Oxf) ; 236(2): e13865, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-35959512

RESUMEN

Mathematical models of the cardiovascular system have come a long way since they were first introduced in the early 19th century. Driven by a rapid development of experimental techniques, numerical methods, and computer hardware, detailed models that describe physical scales from the molecular level up to organs and organ systems have been derived and used for physiological research. Mathematical and computational models can be seen as condensed and quantitative formulations of extensive physiological knowledge and are used for formulating and testing hypotheses, interpreting and directing experimental research, and have contributed substantially to our understanding of cardiovascular physiology. However, in spite of the strengths of mathematics to precisely describe complex relationships and the obvious need for the mathematical and computational models to be informed by experimental data, there still exist considerable barriers between experimental and computational physiological research. In this review, we present a historical overview of the development of mathematical and computational models in cardiovascular physiology, including the current state of the art. We further argue why a tighter integration is needed between experimental and computational scientists in physiology, and point out important obstacles and challenges that must be overcome in order to fully realize the synergy of experimental and computational physiological research.


Asunto(s)
Fenómenos Fisiológicos Cardiovasculares , Modelos Teóricos , Modelos Biológicos , Proyectos de Investigación
10.
PLoS Comput Biol ; 18(8): e1010353, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35960767

RESUMEN

Simulations of neural activity at different levels of detail are ubiquitous in modern neurosciences, aiding the interpretation of experimental data and underlying neural mechanisms at the level of cells and circuits. Extracellular measurements of brain signals reflecting transmembrane currents throughout the neural tissue remain commonplace. The lower frequencies (≲ 300Hz) of measured signals generally stem from synaptic activity driven by recurrent interactions among neural populations and computational models should also incorporate accurate predictions of such signals. Due to limited computational resources, large-scale neuronal network models (≳ 106 neurons or so) often require reducing the level of biophysical detail and account mainly for times of action potentials ('spikes') or spike rates. Corresponding extracellular signal predictions have thus poorly accounted for their biophysical origin. Here we propose a computational framework for predicting spatiotemporal filter kernels for such extracellular signals stemming from synaptic activity, accounting for the biophysics of neurons, populations, and recurrent connections. Signals are obtained by convolving population spike rates by appropriate kernels for each connection pathway and summing the contributions. Our main results are that kernels derived via linearized synapse and membrane dynamics, distributions of cells, conduction delay, and volume conductor model allow for accurately capturing the spatiotemporal dynamics of ground truth extracellular signals from conductance-based multicompartment neuron networks. One particular observation is that changes in the effective membrane time constants caused by persistent synapse activation must be accounted for. The work also constitutes a major advance in computational efficiency of accurate, biophysics-based signal predictions from large-scale spike and rate-based neuron network models drastically reducing signal prediction times compared to biophysically detailed network models. This work also provides insight into how experimentally recorded low-frequency extracellular signals of neuronal activity may be approximately linearly dependent on spiking activity. A new software tool LFPykernels serves as a reference implementation of the framework.


Asunto(s)
Modelos Neurológicos , Neuronas , Potenciales de Acción/fisiología , Encéfalo/fisiología , Simulación por Computador , Neuronas/fisiología
11.
Adv Exp Med Biol ; 1359: 179-199, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35471540

RESUMEN

Measurements of electric potentials from neural activity have played a key role in neuroscience for almost a century, and simulations of neural activity is an important tool for understanding such measurements. Volume conductor (VC) theory is used to compute extracellular electric potentials stemming from neural activity, such as extracellular spikes, multi-unit activity (MUA), local field potentials (LFP), electrocorticography (ECoG), and electroencephalography (EEG). Further, VC theory is also used inversely to reconstruct neuronal current source distributions from recorded potentials through current source density methods. In this book chapter, we show how VC theory can be derived from a detailed electrodiffusive theory for ion concentration dynamics in the extracellular medium, and we show what assumptions must be introduced to get the VC theory on the simplified form that is commonly used by neuroscientists. Furthermore, we provide examples of how the theory is applied to compute spikes, LFP signals, and EEG signals generated by neurons and neuronal populations.


Asunto(s)
Electroencefalografía , Neuronas , Neuronas/fisiología
12.
Nat Neurosci ; 24(12): 1711-1720, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34764474

RESUMEN

En route from the retina to the cortex, visual information passes through the dorsolateral geniculate nucleus (dLGN) of the thalamus, where extensive corticothalamic (CT) feedback has been suggested to modulate spatial processing. How this modulation arises from direct excitatory and indirect inhibitory CT feedback pathways remains enigmatic. Here, we show that in awake mice, retinotopically organized cortical feedback sharpens receptive fields (RFs) and increases surround suppression in the dLGN. Guided by a network model indicating that widespread inhibitory CT feedback is necessary to reproduce these effects, we targeted the visual sector of the thalamic reticular nucleus (visTRN) for recordings. We found that visTRN neurons have large RFs, show little surround suppression and exhibit strong feedback-dependent responses to large stimuli. These features make them an ideal candidate for mediating feedback-enhanced surround suppression in the dLGN. We conclude that cortical feedback sculpts spatial integration in the dLGN, likely via recruitment of neurons in the visTRN.


Asunto(s)
Cuerpos Geniculados , Núcleos Talámicos , Animales , Retroalimentación , Cuerpos Geniculados/fisiología , Ratones , Neuronas/fisiología , Tálamo , Vías Visuales/fisiología
13.
PLoS Comput Biol ; 17(7): e1008143, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34270543

RESUMEN

Within the computational neuroscience community, there has been a focus on simulating the electrical activity of neurons, while other components of brain tissue, such as glia cells and the extracellular space, are often neglected. Standard models of extracellular potentials are based on a combination of multicompartmental models describing neural electrodynamics and volume conductor theory. Such models cannot be used to simulate the slow components of extracellular potentials, which depend on ion concentration dynamics, and the effect that this has on extracellular diffusion potentials and glial buffering currents. We here present the electrodiffusive neuron-extracellular-glia (edNEG) model, which we believe is the first model to combine compartmental neuron modeling with an electrodiffusive framework for intra- and extracellular ion concentration dynamics in a local piece of neuro-glial brain tissue. The edNEG model (i) keeps track of all intraneuronal, intraglial, and extracellular ion concentrations and electrical potentials, (ii) accounts for action potentials and dendritic calcium spikes in neurons, (iii) contains a neuronal and glial homeostatic machinery that gives physiologically realistic ion concentration dynamics, (iv) accounts for electrodiffusive transmembrane, intracellular, and extracellular ionic movements, and (v) accounts for glial and neuronal swelling caused by osmotic transmembrane pressure gradients. The edNEG model accounts for the concentration-dependent effects on ECS potentials that the standard models neglect. Using the edNEG model, we analyze these effects by splitting the extracellular potential into three components: one due to neural sink/source configurations, one due to glial sink/source configurations, and one due to extracellular diffusive currents. Through a series of simulations, we analyze the roles played by the various components and how they interact in generating the total slow potential. We conclude that the three components are of comparable magnitude and that the stimulus conditions determine which of the components that dominate.


Asunto(s)
Potenciales de Acción/fisiología , Estimulación Eléctrica , Modelos Neurológicos , Neuroglía/fisiología , Neuronas/fisiología , Animales , Encéfalo/citología , Encéfalo/fisiología , Biología Computacional , Espacio Extracelular/fisiología
14.
Front Cell Neurosci ; 15: 671549, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34122014

RESUMEN

Voltage imaging and "all-optical electrophysiology" in human induced pluripotent stem cell (hiPSC)-derived neurons have opened unprecedented opportunities for high-throughput phenotyping of activity in neurons possessing unique genetic backgrounds of individual patients. While prior all-optical electrophysiology studies relied on genetically encoded voltage indicators, here, we demonstrate an alternative protocol using a synthetic voltage sensor and genetically encoded optogenetic actuator that generate robust and reproducible results. We demonstrate the functionality of this method by measuring spontaneous and evoked activity in three independent hiPSC-derived neuronal cell lines with distinct genetic backgrounds.

15.
Schizophr Bull ; 47(6): 1751-1760, 2021 10 21.
Artículo en Inglés | MEDLINE | ID: mdl-33963856

RESUMEN

Several lines of research suggest that impairments in long-term potentiation (LTP)-like synaptic plasticity might be a key pathophysiological mechanism in schizophrenia (SZ) and bipolar disorder type I (BDI) and II (BDII). Using modulations of visually evoked potentials (VEP) of the electroencephalogram, impaired LTP-like visual cortical plasticity has been implicated in patients with BDII, while there has been conflicting evidence in SZ, a lack of research in BDI, and mixed results regarding associations with symptom severity, mood states, and medication. We measured the VEP of patients with SZ spectrum disorders (n = 31), BDI (n = 34), BDII (n = 33), and other BD spectrum disorders (n = 2), and age-matched healthy control (HC) participants (n = 200) before and after prolonged visual stimulation. Compared to HCs, modulation of VEP component N1b, but not C1 or P1, was impaired both in patients within the SZ spectrum (χ 2 = 35.1, P = 3.1 × 10-9) and BD spectrum (χ 2 = 7.0, P = 8.2 × 10-3), including BDI (χ 2 = 6.4, P = .012), but not BDII (χ 2 = 2.2, P = .14). N1b modulation was also more severely impaired in SZ spectrum than BD spectrum patients (χ 2 = 14.2, P = 1.7 × 10-4). N1b modulation was not significantly associated with Positive and Negative Syndrome Scale (PANSS) negative or positive symptoms scores, number of psychotic episodes, Montgomery and Åsberg Depression Rating Scale (MADRS) scores, or Young Mania Rating Scale (YMRS) scores after multiple comparison correction, although a nominal association was observed between N1b modulation and PANSS negative symptoms scores among SZ spectrum patients. These results suggest that LTP-like plasticity is impaired in SZ and BD. Adding to previous genetic, pharmacological, and electrophysiological evidence, these results implicate aberrant synaptic plasticity as a mechanism underlying SZ and BD.


Asunto(s)
Trastorno Bipolar/fisiopatología , Trastorno Ciclotímico/fisiopatología , Potenciales Evocados Visuales/fisiología , Plasticidad Neuronal/fisiología , Trastornos Psicóticos/fisiopatología , Esquizofrenia/fisiopatología , Corteza Visual/fisiopatología , Adolescente , Adulto , Anciano , Anticonvulsivantes/farmacología , Antipsicóticos/farmacología , Trastorno Bipolar/tratamiento farmacológico , Trastorno Ciclotímico/tratamiento farmacológico , Electroencefalografía , Potenciales Evocados Visuales/efectos de los fármacos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Plasticidad Neuronal/efectos de los fármacos , Trastornos Psicóticos/tratamiento farmacológico , Esquizofrenia/tratamiento farmacológico , Corteza Visual/efectos de los fármacos , Adulto Joven
16.
PLoS Comput Biol ; 17(4): e1008893, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33798190

RESUMEN

The electroencephalogram (EEG) is a major tool for non-invasively studying brain function and dysfunction. Comparing experimentally recorded EEGs with neural network models is important to better interpret EEGs in terms of neural mechanisms. Most current neural network models use networks of simple point neurons. They capture important properties of cortical dynamics, and are numerically or analytically tractable. However, point neurons cannot generate an EEG, as EEG generation requires spatially separated transmembrane currents. Here, we explored how to compute an accurate approximation of a rodent's EEG with quantities defined in point-neuron network models. We constructed different approximations (or proxies) of the EEG signal that can be computed from networks of leaky integrate-and-fire (LIF) point neurons, such as firing rates, membrane potentials, and combinations of synaptic currents. We then evaluated how well each proxy reconstructed a ground-truth EEG obtained when the synaptic currents of the LIF model network were fed into a three-dimensional network model of multicompartmental neurons with realistic morphologies. Proxies based on linear combinations of AMPA and GABA currents performed better than proxies based on firing rates or membrane potentials. A new class of proxies, based on an optimized linear combination of time-shifted AMPA and GABA currents, provided the most accurate estimate of the EEG over a wide range of network states. The new linear proxies explained 85-95% of the variance of the ground-truth EEG for a wide range of network configurations including different cell morphologies, distributions of presynaptic inputs, positions of the recording electrode, and spatial extensions of the network. Non-linear EEG proxies using a convolutional neural network (CNN) on synaptic currents increased proxy performance by a further 2-8%. Our proxies can be used to easily calculate a biologically realistic EEG signal directly from point-neuron simulations thus facilitating a quantitative comparison between computational models and experimental EEG recordings.


Asunto(s)
Encéfalo/fisiología , Electroencefalografía/métodos , Modelos Neurológicos , Neuronas/fisiología , Encéfalo/citología , Electrodos , Humanos , Neuronas/metabolismo , Ácido alfa-Amino-3-hidroxi-5-metil-4-isoxazol Propiónico/metabolismo , Ácido gamma-Aminobutírico/metabolismo
17.
Neuroinformatics ; 19(3): 493-514, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33394388

RESUMEN

Hippocampal sharp wave ripples (SPW-R) have been identified as key bio-markers of important brain functions such as memory consolidation and decision making. Understanding their underlying mechanisms in healthy and pathological brain function and behaviour rely on accurate SPW-R detection. In this multidisciplinary study, we propose a novel, self-improving artificial intelligence (AI) detection method in the form of deep Recurrent Neural Networks (RNN) with Long Short-Term memory (LSTM) layers that can learn features of SPW-R events from raw, labeled input data. The approach contrasts conventional routines that typically relies on hand-crafted, heuristic feature extraction and often laborious manual curation. The algorithm is trained using supervised learning on hand-curated data sets with SPW-R events obtained under controlled conditions. The input to the algorithm is the local field potential (LFP), the low-frequency part of extracellularly recorded electric potentials from the CA1 region of the hippocampus. Its output predictions can be interpreted as time-varying probabilities of SPW-R events for the duration of the inputs. A simple thresholding applied to the output probabilities is found to identify times of SPW-R events with high precision. The non-causal, or bidirectional variant of the proposed algorithm demonstrates consistently better accuracy compared to the causal, or unidirectional counterpart. Reference implementations of the algorithm, named 'RippleNet', are open source, freely available, and implemented using a common open-source framework for neural networks (tensorflow.keras) and can be easily incorporated into existing data analysis workflows for processing experimental data.


Asunto(s)
Inteligencia Artificial , Hipocampo , Potenciales de Acción , Redes Neurales de la Computación
18.
Neuroimage ; 225: 117467, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33075556

RESUMEN

Electroencephalography (EEG) and magnetoencephalography (MEG) are among the most important techniques for non-invasively studying cognition and disease in the human brain. These signals are known to originate from cortical neural activity, typically described in terms of current dipoles. While the link between cortical current dipoles and EEG/MEG signals is relatively well understood, surprisingly little is known about the link between different kinds of neural activity and the current dipoles themselves. Detailed biophysical modeling has played an important role in exploring the neural origin of intracranial electric signals, like extracellular spikes and local field potentials. However, this approach has not yet been taken full advantage of in the context of exploring the neural origin of the cortical current dipoles that are causing EEG/MEG signals. Here, we present a method for reducing arbitrary simulated neural activity to single current dipoles. We find that the method is applicable for calculating extracranial signals, but less suited for calculating intracranial electrocorticography (ECoG) signals. We demonstrate that this approach can serve as a powerful tool for investigating the neural origin of EEG/MEG signals. This is done through example studies of the single-neuron EEG contribution, the putative EEG contribution from calcium spikes, and from calculating EEG signals from large-scale neural network simulations. We also demonstrate how the simulated current dipoles can be used directly in combination with detailed head models, allowing for simulated EEG signals with an unprecedented level of biophysical details. In conclusion, this paper presents a framework for biophysically detailed modeling of EEG and MEG signals, which can be used to better our understanding of non-inasively measured neural activity in humans.


Asunto(s)
Electroencefalografía/métodos , Magnetoencefalografía/métodos , Modelos Neurológicos , Algoritmos , Fenómenos Biofísicos , Encéfalo/fisiología , Mapeo Encefálico/métodos , Simulación por Computador , Humanos , Neuronas
19.
PLoS Comput Biol ; 16(11): e1008386, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-33253147

RESUMEN

Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic integration of data into realistic, multiscale models. Here we describe the Brain Modeling ToolKit (BMTK), a software suite for building models and performing simulations at multiple levels of resolution, from biophysically detailed multi-compartmental, to point-neuron, to population-statistical approaches. Leveraging the SONATA file format and existing software such as NEURON, NEST, and others, BMTK offers a consistent user experience across multiple levels of resolution. It permits highly sophisticated simulations to be set up with little coding required, thus lowering entry barriers to new users. We illustrate successful applications of BMTK to large-scale simulations of a cortical area. BMTK is an open-source package provided as a resource supporting modeling-based discovery in the community.


Asunto(s)
Mapeo Encefálico/métodos , Encéfalo/fisiología , Biología Computacional , Programas Informáticos , Potenciales de Acción , Fenómenos Biofísicos , Humanos , Red Nerviosa
20.
Neuroimage ; 223: 117302, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-32828930

RESUMEN

Experience-dependent modulation of the visual evoked potential (VEP) is a promising proxy measure of synaptic plasticity in the cerebral cortex. However, existing studies are limited by small to moderate sample sizes as well as by considerable variability in how VEP modulation is quantified. In the present study, we used a large sample (n = 415) of healthy volunteers to compare different quantifications of VEP modulation with regards to effect sizes and retention of the modulation effect over time. We observed significant modulation for VEP components C1 (Cohen's d = 0.53), P1 (d = 0.66), N1 (d=-0.27), N1b (d=-0.66), but not P2 (d = 0.08), and in three clusters of total power modulation, 2-4 min after 2 Hz prolonged visual stimulation. For components N1 (d=-0.21) and N1b (d=-0.38), as well for the total power clusters, this effect was retained after 54-56 min, by which time also the P2 component had gained modulation (d = 0.54). Moderate to high correlations (0.39≤ρ≤0.69) between modulation at different postintervention blocks revealed a relatively high temporal stability in the modulation effect for each VEP component. However, different VEP components also showed markedly different temporal retention patterns. Finally, participant age correlated negatively with C1 (χ2=30.4), and positively with P1 modulation (χ2=13.4), whereas P2 modulation was larger for female participants (χ2=15.4). There were no effects of either age or sex on N1 and N1b potentiation. These results provide strong support for VEP modulation, and especially N1b modulation, as a robust measure of synaptic plasticity, but underscore the need to differentiate between components, and to control for demographic confounders.


Asunto(s)
Encéfalo/fisiología , Potenciales Evocados Visuales , Plasticidad Neuronal , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Electroencefalografía , Potenciales Evocados , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estimulación Luminosa , Adulto Joven
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