Dynamical principles in neuroscience

Dynamical modeling of neural systems and brain functions has a history of success over the last half century. This includes, for example, the explanation and prediction of some features of neural rhythmic behaviors. Many interesting dynamical models of learning and memory based on physiological experiments have been suggested over the last two decades. Dynamical models even of consciousness now exist. Usually these models and results are based on traditional approaches and paradigms of nonlinear dynamics including dynamical chaos. Neural systems are, however, an unusual subject for nonlinear dynamics for several reasons: (i) Even the simplest neural network, with only a few neurons and synaptic connections, has an enormous number of variables and control parameters. These make neural systems adaptive and flexible, and are critical to their biological function. (ii) In contrast to traditional physical systems described by well-known basic principles, first principles governing the dynamics of neural systems are unknown. (iii) Many different neural systems exhibit similar dynamics despite having different architectures and different levels of complexity. (iv) The network architecture and connection strengths are usually not known in detail and therefore the dynamical analysis must, in some sense, be probabilistic. (v) Since nervous systems are able to organize behavior based on sensory inputs, the dynamical modeling of these systems has to explain the transformation of temporal information into combinatorial or combinatorial-temporal codes, and vice versa, for memory and recognition. In this review these problems are discussed in the context of addressing the stimulating questions: What can neuroscience learn from nonlinear dynamics, and what can nonlinear dynamics learn from neuroscience?This work was supported by NSF Grant No. NSF/EIA-0130708, and Grant No. PHY 0414174; NIH Grant No. 1 R01 NS50945 and Grant No. NS40110; MEC BFI2003-07276, and Fundación BBVA

Theoretical and experimental approaches for the initiation and propagation of activity in spatially embedded neuronal cultures

[eng] Spatial embedding and inherited metric constraints are a fundamental trait of biological neuronal circuits. However their role in shaping connectivity and dynamics has been often disregarded, with models of neuronal networks paying much more attention to the distribution of connections in the quest for understanding network's behavior. In this thesis we aim at filling this gap by studying the importance of metric features in the complex connectivity- dynamics-noise interplay that shapes spontaneous neuronal activity. This thesis combines experiments in rat dissociated neuronal cultures with theoretical analyses to better comprehend the relevance of spatial embedding. We developed a new theoretical model grounded on Ising Models to assess metric effects in neuronal cultures' behavior, and in the context of percolation approaches. Once metric effects were settled, we illustrated their relevance in shaping spontaneous activity by perturbing the structural connectivity blueprint of neuronal cultures. This was achieved by patterning the substrate where neurons grow, and by using topographical molds that dictated the connectivity of the network. Next, and since the initiation of bursting activity is governed in great manner by a complex amplification mechanism that involves metric correlations and noise, we focused on the metric-driven amplification of spontaneous single-neuron noise to derive an analytical model that predicts the frequency of bursting events in neuronal cultures. We then further investigated in an experimental context the contribution of noise to the observed activity patterns, and by implementing a moderate electrical stimulation protocol that increases the level of activity noise in cultures. Finally, the latter study was completed with experiments regarding the specific role of inhibition in neuronal networks, to provide a wider understanding of the mechanisms that govern the initiation and propagation of activity fronts in cortical cultures.[cat] L'objectiu d'aquesta tesis és investigar els mecanismes que generen l'activitat espontània i estimulada en xarxes neuronals, més concretament en cultius corticals dissociats, i fent un especial èmfasi en l’efecte de les correlacions mètriques. En aquest marc, l’activitat col·lectiva consisteix en episodis esporàdics de dispars quasi sincronitzats entre totes les neurones del cultiu, anomenats “esclats de xarxa”. Tres elements principals en determinen les característiques: connectivitat entre neurones, dinàmica intrínseca neuronal, i soroll (activacions neuronals aleatòries). La investigació s’ha centrat en cinc línies de recerca: l’estudi de correlacions mètriques en cultius neuronals; el desenvolupament d’un model teòric per descriure i predir l’esclat de xarxa; l’anàlisi de la propagació dels fronts d’activitat experimentals sota pertorbacions estructurals de la connectivitat del cultiu; l’estudi de l’efecte de la inhibició en la iniciació i propagació dels esclats ‘in vitro’; i l’estudi de la resposta experimental dels cultius sota una estimulació elèctrica moderada de baixa freqüència. En la primera línia de recerca hem comprovat que les correlacions mètriques dominen el comportament dinàmic del cultiu, fins al punt d’emmascarar la contribució de la distribució del nombre de connexions. En la segona línia hem desenvolupat un model analític que prediu semi- quantitativament la freqüència dels esclats observada experimentalment. La tercera línia s’ha centrat en l’efecte de pertorbacions estructurals en la connectivitat; la dinàmica resultant ha mostrat una gran riquesa en patrons d’activitat, esclats de xarxa a diferents escales, i propagació altament específica de cada cultiu. La quarta línia de recerca ha demostrat que les xarxes sense inhibició disminueixen la seva freqüència d’esclat respecte a les xarxes control, que la velocitat de propagació de l’activitat incrementa lleugerament quan s’ha bloquejat la inhibició, i que els punts on s’inicien ens esclats varien respecte als controls. I, finalment, la cinquena línia de recerca ha constatat que l’aplicació d’un camp elèctric feble augmenta el soroll d’activitat de la xarxa, generant un increment en la freqüència dels esclats de xarxa

Spatiotemporal dynamics of low frequency fluctuations in bold fMRI

Traditional fMRI utilizes blood oxygenation level dependent (BOLD) contrast to map brain activity. BOLD signal is sensitive to the hemodynamic changes associated with brain activity, and gives an indirect measure of brain activity. Low frequency fluctuations (LFFs) have been observed in the BOLD signal even in the absence of any anesthetic agent, and the correlations between the fluctuations from different brain regions has been used to map functional connectivity in the brain. Most studies involving spontaneous fluctuations in the BOLD signal extract connectivity patterns that show relationships between brain areas that are maintained over the length of the scanning session. The research presented in this document investigates the spatiotemporal dynamics of the BOLD fluctuations to identify common spatiotemporal patterns within a scan. First, the presence of a visually detectable spatiotemporal propagation pattern is demonstrated by utilizing single-slice data with high spatial and temporal resolution. The pattern consists of lateral-medial propagation of BOLD signal, demonstrating the presence of time-varying features in spontaneous BOLD fluctuations. Further, a novel pattern finding algorithm is developed for detecting repeated spatiotemporal patterns in BOLD fMRI data. The algorithm is applied to high temporal resolution T2*-weighted multislice images obtained from rats and humans in the absence of any task or stimulation. In rats, the primary pattern consists of waves of high signal intensity, propagating in a lateral-medial direction across the cortex, replicating the results obtained using visual observation. In humans, the most common spatiotemporal pattern consisted of an alteration between activation of areas comprising the "default-mode" (e.g., posterior cingulate and anterior medial prefrontal cortices) and the "task-positive" (e.g., superior parietal and premotor cortices) networks. Signal propagation from focal starting points is also observed. The pattern finding algorithm is shown to be reasonably insensitive to the variation in user-defined parameters, and the results are consistent within and between subjects. This novel approach for probing the spontaneous network activity of the brain has implications for the interpretation of conventional functional connectivity studies, and may increase the amount of information that can be obtained from neuroimaging data.Ph.D.Committee Chair: Keilholz, Shella; Committee Member: Hu, Xiaoping; Committee Member: Jaeger, Dieter; Committee Member: Sathian, Krish; Committee Member: Schumacher, Eri

VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

In vitro neuronal cultures on MEA: an engineering approach to study physiological and pathological brain networks

Reti neuronali accoppiate a matrici di microelettrodi: un metodo ingegneristico per studiare reti cerebrali in situazioni fisiologiche e patologich

Nonlinear brain dynamics as macroscopic manifestation of underlying many-body field dynamics

Neural activity patterns related to behavior occur at many scales in time and space from the atomic and molecular to the whole brain. Here we explore the feasibility of interpreting neurophysiological data in the context of many-body physics by using tools that physicists have devised to analyze comparable hierarchies in other fields of science. We focus on a mesoscopic level that offers a multi-step pathway between the microscopic functions of neurons and the macroscopic functions of brain systems revealed by hemodynamic imaging. We use electroencephalographic (EEG) records collected from high-density electrode arrays fixed on the epidural surfaces of primary sensory and limbic areas in rabbits and cats trained to discriminate conditioned stimuli (CS) in the various modalities. High temporal resolution of EEG signals with the Hilbert transform gives evidence for diverse intermittent spatial patterns of amplitude (AM) and phase modulations (PM) of carrier waves that repeatedly re-synchronize in the beta and gamma ranges at near zero time lags over long distances. The dominant mechanism for neural interactions by axodendritic synaptic transmission should impose distance-dependent delays on the EEG oscillations owing to finite propagation velocities. It does not. EEGs instead show evidence for anomalous dispersion: the existence in neural populations of a low velocity range of information and energy transfers, and a high velocity range of the spread of phase transitions. This distinction labels the phenomenon but does not explain it. In this report we explore the analysis of these phenomena using concepts of energy dissipation, the maintenance by cortex of multiple ground states corresponding to AM patterns, and the exclusive selection by spontaneous breakdown of symmetry (SBS) of single states in sequences.Comment: 31 page

Oscillator-based neuronal modeling for seizure progression investigation and seizure control strategy

The coupled oscillator model has previously been used for the simulation of neuronal activities in in vitro rat hippocampal slice seizure data and the evaluation of seizure suppression algorithms. Each model unit can be described as either an oscillator which can generate action potential spike trains without inputs, or a threshold-based unit. With the change of only one parameter, each unit can either be an oscillator or a threshold-based spiking unit. This would eliminate the need for a new set of equations for each type of unit. Previous analysis has suggested that long kernel duration and imbalance of inhibitory feedback can cause the system to intermittently transition into and out of ictal activities. The state transitions of seizure-like events were investigated here; specifically, how the system excitability may change when the system undergoes transitions in the preictal and postictal processes. Analysis showed that the area of the excitation kernel is positively correlated with the mean firing rate of the ictal activity. The kernel duration is also correlated to the amount of ictal activity. The transition into ictal activity involved the escape from the saddle point foci in the state space trajectory identified by using Newton\u27s method. The ability to accurately anticipate and suppress seizures is an important endeavor that has tremendous impact on improving the quality of lives for epileptic patients. The stimulation studies have suggested that an electrical stimulation strategy that uses the intrinsic high complexity dynamics of the biological system may be more effective in reducing the duration of seizure-like activities in the computer model. In this research, we evaluate this strategy on an in vitro rat hippocampal slice magnesium-free model. Simulated postictal field potential data generated by an oscillator-based hippocampal network model was applied to the CA1 region of the rat hippocampal slices through a multi-electrode array (MEA) system. It was found to suppress and delay the onset of future seizures temporarily. The average inter-seizure time was found to be significantly prolonged after postictal stimulation when compared to the negative control trials and bipolar square wave signals. The result suggests that neural signal-based stimulation related to resetting may be suitable for seizure control in the clinical environment

SLEEPING WHILE AWAKE: A NEUROPHYSIOLOGICAL INVESTIGATION ON SLEEP DURING WAKEFULNESS.

Il sonno e la veglia vengono comunemente considerati come due stati distinti. L\u2019alternanza tra essi, la cui presenza \ue8 stata dimostrata in ogni specie animale studiata fino ad oggi, sembra essere una delle caratteristiche che definisce la nostra vita. Allo stesso tempo, per\uf2, le scoperte portate alla luce negli ultimi decenni hanno offuscato i confini tra questi due stati. I meccanismi del sonno hanno sempre affascinato i neurofisiologi, che infatti, nell\u2019ultimo secolo, li hanno caratterizzati in dettaglio: ora sappiamo che all\u2019attivit\ue0 del sonno sottost\ue0 una specifica attivit\ue0 neuronale chiamata slow oscillation. La slow oscillation, che \ue8 costituita da (ancora una volta) un\u2019alternanza tra periodi di attivit\ue0 e periodi di iperpolarizzazione e silenzio neuronale (OFF-periods), \ue8 la modalit\ue0 base di attivazione del cervello dormiente. Questa alternanza \ue8 dovuta alla tendenza dei neuroni surante lo stato di sonno, di passare ad un periodo silente dopo un\u2019attivazione iniziale, una tendenza a cui viene dato il nome di bistabilit\ue0 neuronale. Molti studi hanno dimostrato come la bistabilit\ue0 neuronale tipica del sonno ed i relativi OFF-periods, possano accadere anche durante la veglia in particolari condizioni patologiche, nelle transizioni del sonno e durante le deprivazioni di sonno. Per questo motivo, se accettassimo che la bistabilit\ue0 neuronale e gli OFF-periods rappresentino una caratteristica fondamentale del sonno, allora dovremmo ammettere che stiamo assistendo ad un cambio di paradigma: da una prospettiva neurofisiologica il sonno pu\uf2 intrudere nella veglia. In questa tesi ho analizzato i nuovi -fluidi- confini tra sonno e veglia e le possibili implicazioni di questi nel problema della persistenza personale attraverso il tempo. Inoltre, ho studiato le implicazioni cliniche dell\u2019intrusione di sonno nella veglia in pazienti con lesioni cerebrali focali di natura ischemica. In particolare, i miei obiettivi sono stati: 1) Dimostrare come la bistabilit\ue0 neuronale possa essere responsabile della perdita di funzione nei pazienti affetti da ischemia cerebrale e come questo potrebbe avere implicazioni nello studio della patofisiologia dell\u2019ischemia cerebrale e nella sua terapia; 2) Stabilire le basi per un modello di sonno locale presente nella vita di tutti i giorni: la sensazione di sonnolenza. Infatti, essa potrebbe riflettere la presenza di porzioni di corteccia in stato di sonno, ma durante lo stato di veglia; 3) Difendere il criterio biologico di identit\ue0, che troverebbe nell\u2019attivit\ue0 cerebrale la continuit\ue0 necessaria al mantenimento della nostra identit\ue0 nel tempo.Sleep and wakefulness are considered two mutually exclusive states. The alternation between those two states seems to be a defining characteristic of our life, a ubiquitous phenomenon demonstrated in every animal species investigated so far. However, during the last decade, advances in neurophysiology have blurred the boundaries between those states. The mechanisms of sleep have always intrigued neurophysiologists and great advances have been made over the last century in understanding them: we now know that the defining characteristic underlying sleep activity is a specific pattern of neuronal activity, namely the slow oscillation. The slow oscillation, which is characterized by the periodic alternation between periods of activity (ON-periods) and periods of hyperpolarization and neuronal silence (OFF-periods) is the default mode of activity of the sleeping cortex. This alternation is due to the tendency of neurons to fall into a silent period after an initial activation; such tendency is known as \u201cbistability\u201d. There is accumulating evidence that sleep-like bistability, and the ensuing OFF-periods, may occur locally in the awake human brain in some pathological conditions, in sleep transition, as well as after sleep deprivation. Therefore, to the extent that bistability and OFF periods represents the basic neuronal features of sleep, a paradigm shift is in place: from a neurophysiological perspective sleep can intrude into wakefulness. In this thesis, I explore the fluid boundaries between sleep and wakefulness and investigate their possible implications on the problem of personal persistence over time. Moreover, I study the clinical implications of the intrusion of sleep into wakefulness in patients with focal brain injury due to stroke. Specifically, I aim to: 1) show how the sleep-like bistability can be responsible for the loss of function in stroke patients. This may have implications for understanding the pathophysiology of stroke and helping to foster recovery; 2) establish the basis for a model of local sleep that might be present in the everyday life, id est the sensation of sleepiness. Indeed, sleepiness could reflect islands of sleep during wakefulness; 3) advocate the biological criterion of identity, in which the continuity necessary for maintaining ourselves over time could be represented by never resting activity in the brain