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Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data

Neymotin, Samuel A; Daniels, Dylan S; Caldwell, Blake; McDougal, Robert A; Carnevale, Nicholas T; Jas, Mainak; Moore, Christopher I; Hines, Michael L; Hämäläinen, Matti; Jones, Stephanie R
Magneto- and electro-encephalography (MEG/EEG) non-invasively record human brain activity with millisecond resolution providing reliable markers of healthy and disease states. Relating these macroscopic signals to underlying cellular- and circuit-level generators is a limitation that constrains using MEG/EEG to reveal novel principles of information processing or to translate findings into new therapies for neuropathology. To address this problem, we built Human Neocortical Neurosolver (HNN, software. HNN has a graphical user interface designed to help researchers and clinicians interpret the neural origins of MEG/EEG. HNN's core is a neocortical circuit model that accounts for biophysical origins of electrical currents generating MEG/EEG. Data can be directly compared to simulated signals and parameters easily manipulated to develop/test hypotheses on a signal's origin. Tutorials teach users to simulate commonly measured signals, including event related potentials and brain rhythms. HNN's ability to associate signals across scales makes it a unique tool for translational neuroscience research.
PMID: 31967544
ISSN: 2050-084x
CID: 4568162

Oscillatory Bursting as a Mechanism for Temporal Coupling and Information Coding

Tal, Idan; Neymotin, Samuel; Bickel, Stephan; Lakatos, Peter; Schroeder, Charles E
Even the simplest cognitive processes involve interactions between cortical regions. To study these processes, we usually rely on averaging across several repetitions of a task or across long segments of data to reach a statistically valid conclusion. Neuronal oscillations reflect synchronized excitability fluctuations in ensembles of neurons and can be observed in electrophysiological recordings in the presence or absence of an external stimulus. Oscillatory brain activity has been viewed as sustained increase in power at specific frequency bands. However, this perspective has been challenged in recent years by the notion that oscillations may occur as transient burst-like events that occur in individual trials and may only appear as sustained activity when multiple trials are averaged together. In this review, we examine the idea that oscillatory activity can manifest as a transient burst as well as a sustained increase in power. We discuss the technical challenges involved in the detection and characterization of transient events at the single trial level, the mechanisms that might generate them and the features that can be extracted from these events to study single-trial dynamics of neuronal ensemble activity.
PMID: 33071765
ISSN: 1662-5188
CID: 4637202

NetPyNE, a tool for data-driven multiscale modeling of brain circuits

Dura-Bernal, Salvador; Suter, Benjamin A; Gleeson, Padraig; Cantarelli, Matteo; Quintana, Adrian; Rodriguez, Facundo; Kedziora, David J; Chadderdon, George L; Kerr, Cliff C; Neymotin, Samuel A; McDougal, Robert A; Hines, Michael; Shepherd, Gordon Mg; Lytton, William W
Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool ( provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis - connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.
PMID: 31025934
ISSN: 2050-084x
CID: 4096952

Tau and amyloid-related pathologies in the entorhinal cortex have divergent effects in the hippocampal circuit

Angulo, S L; Orman, R; Neymotin, S A; Liu, L; Buitrago, L; Cepeda-Prado, E; Stefanov, D; Lytton, W W; Stewart, M; Small, S A; Duff, K E; Moreno, H
The entorhinal cortex (EC) is affected early in Alzheimer's disease, an illness defined by a co-occurrence of tau and amyloid-related pathologies. How the co-occurrence of these pathologies in the EC affects the hippocampal circuit remains unknown. Here we address this question by performing electrophysiological analyses of the EC circuit in mice that express mutant human amyloid precursor protein (hAPP) or tau (hTau), or both in the EC. We show that the alterations in the hippocampal circuit are divergent, with hAPP increasing but hTau decreasing neuronal/circuit excitability. Most importantly, mice co-expressing hAPP and hTau show that hTau has a dominant effect, dampening the excitatory effects of hAPP. Additionally, compensatory synaptic downscaling, in response to increased excitability in EC was observed in subicular neurons of hAPP mice. Based on simulations, we propose that EC interneuron pruning can account for both EC hyperexcitability and subicular synaptic downscaling found in mice expressing hAPP.
PMID: 28860088
ISSN: 1095-953x
CID: 4568132

Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis

Dura-Bernal, S; Neymotin, S A; Kerr, C C; Sivagnanam, S; Majumdar, A; Francis, J T; Lytton, W W
Biomimetic simulation permits neuroscientists to better understand the complex neuronal dynamics of the brain. Embedding a biomimetic simulation in a closed-loop neuroprosthesis, which can read and write signals from the brain, will permit applications for amelioration of motor, psychiatric, and memory-related brain disorders. Biomimetic neuroprostheses require real-time adaptation to changes in the external environment, thus constituting an example of a dynamic data-driven application system. As model fidelity increases, so does the number of parameters and the complexity of finding appropriate parameter configurations. Instead of adapting synaptic weights via machine learning, we employed major biological learning methods: spike-timing dependent plasticity and reinforcement learning. We optimized the learning metaparameters using evolutionary algorithms, which were implemented in parallel and which used an island model approach to obtain sufficient speed. We employed these methods to train a cortical spiking model to utilize macaque brain activity, indicating a selected target, to drive a virtual musculoskeletal arm with realistic anatomical and biomechanical properties to reach to that target. The optimized system was able to reproduce macaque data from a comparable experimental motor task. These techniques can be used to efficiently tune the parameters of multiscale systems, linking realistic neuronal dynamics to behavior, and thus providing a useful tool for neuroscience and neuroprosthetics.
PMID: 29200477
ISSN: 2151-8556
CID: 4568142

Tracking recurrence of correlation structure in neuronal recordings

Neymotin, Samuel A; Talbot, Zoe N; Jung, Jeeyune Q; Fenton, Andre A; Lytton, William W
BACKGROUND: Correlated neuronal activity in the brain is hypothesized to contribute to information representation, and is important for gauging brain dynamics in health and disease. Due to high dimensional neural datasets, it is difficult to study temporal variations in correlation structure. NEW METHOD: We developed a multiscale method, Population Coordination (PCo), to assess neural population structure in multiunit single neuron ensemble and multi-site local field potential (LFP) recordings. PCo utilizes population correlation (PCorr) vectors, consisting of pair-wise correlations between neural elements. The PCo matrix contains the correlations between all PCorr vectors occurring at different times. RESULTS: We used PCo to interpret dynamics of two electrophysiological datasets: multisite LFP and single unit ensemble. In the LFP dataset from an animal model of medial temporal lobe epilepsy, PCo isolated anomalous brain states, where particular brain regions broke off from the rest of the brain's activity. In a dataset of rat hippocampal single-unit recordings, PCo enabled visualizing neuronal ensemble correlation structure changes associated with changes of animal environment (place-cell remapping). COMPARISON WITH EXISTING METHOD(S): PCo allows directly visualizing high dimensional data. Dimensional reduction techniques could also be used to produce dynamical snippets that could be examined for recurrence. PCo allows intuitive, visual assessment of temporal recurrence in correlation structure directly in the high dimensionality dataset, allowing for immediate assessment of relevant dynamics at a single site. CONCLUSIONS: PCo can be used to investigate how neural correlation structure occurring at multiple temporal and spatial scales reflect underlying dynamical recurrence without intermediate reduction of dimensionality.
PMID: 27746231
ISSN: 1872-678x
CID: 2279762

Optimizing computer models of corticospinal neurons to replicate in vitro dynamics

Neymotin, Samuel A; Suter, Benjamin A; Dura-Bernal, Salvador; Shepherd, Gordon M G; Migliore, Michele; Lytton, William W
Corticospinal neurons (SPI), thick-tufted pyramidal neurons in motor cortex layer 5B that project caudally via the medullary pyramids, display distinct class-specific electrophysiological properties in vitro: strong sag with hyperpolarization, lack of adaptation, and a nearly linear frequency-current (F-I) relationship. We used our electrophysiological data to produce a pair of large archives of SPI neuron computer models in two model classes: 1) detailed models with full reconstruction; and 2) simplified models with six compartments. We used a PRAXIS and an evolutionary multiobjective optimization (EMO) in sequence to determine ion channel conductances. EMO selected good models from each of the two model classes to form the two model archives. Archived models showed tradeoffs across fitness functions. For example, parameters that produced excellent F-I fit produced a less-optimal fit for interspike voltage trajectory. Because of these tradeoffs, there was no single best model but rather models that would be best for particular usages for either single neuron or network explorations. Further exploration of exemplar models with strong F-I fit demonstrated that both the detailed and simple models produced excellent matches to the experimental data. Although dendritic ion identities and densities cannot yet be fully determined experimentally, we explored the consequences of a demonstrated proximal to distal density gradient of Ih, demonstrating that this would lead to a gradient of resonance properties with increased resonant frequencies more distally. We suggest that this dynamical feature could serve to make the cell particularly responsive to major frequency bands that differ by cortical layer.
PMID: 27760819
ISSN: 1522-1598
CID: 3092502

Global dynamics of selective attention and its lapses in primary auditory cortex

Lakatos, Peter; Barczak, Annamaria; Neymotin, Samuel A; McGinnis, Tammy; Ross, Deborah; Javitt, Daniel C; O'Connell, Monica Noelle
Previous research demonstrated that while selectively attending to relevant aspects of the external world, the brain extracts pertinent information by aligning its neuronal oscillations to key time points of stimuli or their sampling by sensory organs. This alignment mechanism is termed oscillatory entrainment. We investigated the global, long-timescale dynamics of this mechanism in the primary auditory cortex of nonhuman primates, and hypothesized that lapses of entrainment would correspond to lapses of attention. By examining electrophysiological and behavioral measures, we observed that besides the lack of entrainment by external stimuli, attentional lapses were also characterized by high-amplitude alpha oscillations, with alpha frequency structuring of neuronal ensemble and single-unit operations. Entrainment and alpha-oscillation-dominated periods were strongly anticorrelated and fluctuated rhythmically at an ultra-slow rate. Our results indicate that these two distinct brain states represent externally versus internally oriented computational resources engaged by large-scale task-positive and task-negative functional networks.
PMID: 27618311
ISSN: 1546-1726
CID: 2246872

Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex

Neymotin, S A; McDougal, R A; Bulanova, A S; Zeki, M; Lakatos, P; Terman, D; Hines, M L; Lytton, W W
Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium (Ca(2+)) regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. The network contained 776 compartmental neurons arranged in the cortical layers, connected using synapses containing AMPA/NMDA/GABAA/GABAB receptors. Metabotropic glutamate receptors (mGluR) produced inositol triphosphate (IP3) which caused the release of Ca(2+) from endoplasmic reticulum (ER) stores, with reuptake by sarco/ER Ca(2+)-ATP-ase pumps (SERCA), and influence on HCN channels. Stimulus-induced depolarization led to Ca(2+) influx via NMDA and voltage-gated Ca(2+) channels (VGCCs). After a delay, mGluR activation led to ER Ca(2+) release via IP3 receptors. These factors increased HCN channel conductance and produced firing lasting for ∼1min. The model displayed inter-scale synergies among synaptic weights, excitation/inhibition balance, firing rates, membrane depolarization, Ca(2+) levels, regulation of HCN channels, and induction of persistent activity. The interaction between inhibition and Ca(2+) at the HCN channel nexus determined a limited range of inhibition strengths for which intracellular Ca(2+) could prepare population-specific persistent activity. Interactions between metabotropic and ionotropic inputs to the neuron demonstrated how multiple pathways could contribute in a complementary manner to persistent activity. Such redundancy and complementarity via multiple pathways is a critical feature of biological systems. Mediation of activation at different time scales, and through different pathways, would be expected to protect against disruption, in this case providing stability for persistent activity.
PMID: 26746357
ISSN: 1873-7544
CID: 4568112

Restoring Behavior via Inverse Neurocontroller in a Lesioned Cortical Spiking Model Driving a Virtual Arm

Dura-Bernal, Salvador; Li, Kan; Neymotin, Samuel A; Francis, Joseph T; Principe, Jose C; Lytton, William W
Neural stimulation can be used as a tool to elicit natural sensations or behaviors by modulating neural activity. This can be potentially used to mitigate the damage of brain lesions or neural disorders. However, in order to obtain the optimal stimulation sequences, it is necessary to develop neural control methods, for example by constructing an inverse model of the target system. For real brains, this can be very challenging, and often unfeasible, as it requires repeatedly stimulating the neural system to obtain enough probing data, and depends on an unwarranted assumption of stationarity. By contrast, detailed brain simulations may provide an alternative testbed for understanding the interactions between ongoing neural activity and external stimulation. Unlike real brains, the artificial system can be probed extensively and precisely, and detailed output information is readily available. Here we employed a spiking network model of sensorimotor cortex trained to drive a realistic virtual musculoskeletal arm to reach a target. The network was then perturbed, in order to simulate a lesion, by either silencing neurons or removing synaptic connections. All lesions led to significant behvaioral impairments during the reaching task. The remaining cells were then systematically probed with a set of single and multiple-cell stimulations, and results were used to build an inverse model of the neural system. The inverse model was constructed using a kernel adaptive filtering method, and was used to predict the neural stimulation pattern required to recover the pre-lesion neural activity. Applying the derived neurostimulation to the lesioned network improved the reaching behavior performance. This work proposes a novel neurocontrol method, and provides theoretical groundwork on the use biomimetic brain models to develop and evaluate neurocontrollers that restore the function of damaged brain regions and the corresponding motor behaviors.
PMID: 26903796
ISSN: 1662-4548
CID: 2136962