Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression.

Brain activity during the resting state is widely used to examine brain organization, cognition and alterations in disease states. While it is known that neuromodulation and the state of alertness impact resting-state activity, neural mechanisms behind such modulation of resting-state activity are unknown. In this work, we used a computational model to demonstrate that change in excitability and recurrent connections, due to cholinergic modulation, impacts resting-state activity. The results of such modulation in the model match closely with experimental work on direct cholinergic modulation of Default Mode Network (DMN) in rodents. We further extended our study to the human connectome derived from diffusion-weighted MRI. In human resting-state simulations, an increase in cholinergic input resulted in a brain-wide reduction of functional connectivity. Furthermore, selective cholinergic modulation of DMN closely captured experimentally observed transitions between the baseline resting state and states with suppressed DMN fluctuations associated with attention to external tasks. Our study thus provides insight into potential neural mechanisms for the effects of cholinergic neuromodulation on resting-state activity and its dynamics.

Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain.

Slow-wave sleep (SWS), characterized by slow oscillations (SO, <1Hz) of alternating active and silent states in the thalamocortical network, is a primary brain state during Non-Rapid Eye Movement (NREM) sleep. In the last two decades, the traditional view of SWS as a global and uniform whole-brain state has been challenged by a growing body of evidence indicating that SO can be local and can coexist with wake-like activity. However, the understanding of how global and local SO emerges from micro-scale neuron dynamics and network connectivity remains unclear. We developed a multi-scale, biophysically realistic human whole-brain thalamocortical network model capable of transitioning between the awake state and slow-wave sleep, and we investigated the role of connectivity in the spatio-temporal dynamics of sleep SO. We found that the overall strength and a relative balance between long and short-range synaptic connections determined the network state. Importantly, for a range of synaptic strengths, the model demonstrated complex mixed SO states, where periods of synchronized global slow-wave activity were intermittent with the periods of asynchronous local slow-waves. Increase of the overall synaptic strength led to synchronized global SO, while decrease of synaptic connectivity produced only local slow-waves that would not propagate beyond local area. These results were compared to human data to validate probable models of biophysically realistic SO. The model producing mixed states provided the best match to the spatial coherence profile and the functional connectivity estimated from human subjects. These findings shed light on how the spatio-temporal properties of SO emerge from local and global cortical connectivity and provide a framework for further exploring the mechanisms and functions of SWS in health and disease.

The role of age-related sleep EEG changes in memory decline: experiments and computational modeling.

The slow oscillation (SO) observed during deep sleep is known to facilitate memory consolidation. However, the impact of age-related changes in sleep electroencephalography (EEG) oscillations and memory remains unknown. In this study, we aimed to investigate the contribution of age-related changes in sleep SO and its role in memory decline by combining EEG recordings and computational modeling. Based on the detected SO events, we found that older adults exhibit lower SO density, lower SO frequency, and longer Up and Down state durations during N3 sleep compared to young and middle-aged groups. Using a biophysically detailed thalamocortical network model, we simulated the "aged" brain as a partial loss of synaptic connections between neurons in the cortex. Our simulations showed that the changes in sleep SO properties in the "aged" brain, similar to those observed in older adults, resulting in impaired memory consolidation. Overall, this study provides mechanistic insights into how age-related changes modulate sleep SOs and memory decline.Clinical Relevance- This study contributes towards finding feasible biomarkers and target mechanism for designing therapy in older adults with memory deficits, such as Alzheimer's disease patients.

EMG-projected MEG High-Resolution Source Imaging of Human Motor Execution: Brain-Muscle Coupling above Movement Frequencies.

Magnetoencephalography (MEG) is a non-invasive functional imaging technique for pre-surgical mapping. However, movement-related MEG functional mapping of primary motor cortex (M1) has been challenging in presurgical patients with brain lesions and sensorimotor dysfunction due to the large numbers of trails needed to obtain adequate signal to noise. Moreover, it is not fully understood how effective the brain communication is with the muscles at frequencies above the movement frequency and its harmonics. We developed a novel Electromyography (EMG)-projected MEG source imaging technique for localizing M1 during ~1 minute recordings of left and right self-paced finger movements (~1 Hz). High-resolution MEG source images were obtained by projecting M1 activity towards the skin EMG signal without trial averaging. We studied delta (1-4 Hz), theta (4-7 Hz), alpha (8-12 Hz), beta (15-30 Hz), and gamma (30-90 Hz) bands in 13 healthy participants (26 datasets) and two presurgical patients with sensorimotor dysfunction. In healthy participants, EMG-projected MEG accurately localized M1 with high accuracy in delta (100.0%), theta (100.0%), and beta (76.9%) bands, but not alpha (34.6%) and gamma (0.0%) bands. Except for delta, all other frequency bands were above the movement frequency and its harmonics. In both presurgical patients, M1 activity in the affected hemisphere was also accurately localized, despite highly irregular EMG movement patterns in one patient. Altogether, our EMG-projected MEG imaging approach is highly accurate and feasible for M1 mapping in presurgical patients. The results also provide insight into movement related brain-muscle coupling above the movement frequency and its harmonics.

Sleep-like unsupervised replay reduces catastrophic forgetting in artificial neural networks.

Artificial neural networks are known to suffer from catastrophic forgetting: when learning multiple tasks sequentially, they perform well on the most recent task at the expense of previously learned tasks. In the brain, sleep is known to play an important role in incremental learning by replaying recent and old conflicting memory traces. Here we tested the hypothesis that implementing a sleep-like phase in artificial neural networks can protect old memories during new training and alleviate catastrophic forgetting. Sleep was implemented as off-line training with local unsupervised Hebbian plasticity rules and noisy input. In an incremental learning framework, sleep was able to recover old tasks that were otherwise forgotten. Previously learned memories were replayed spontaneously during sleep, forming unique representations for each class of inputs. Representational sparseness and neuronal activity corresponding to the old tasks increased while new task related activity decreased. The study suggests that spontaneous replay simulating sleep-like dynamics can alleviate catastrophic forgetting in artificial neural networks.

Satiety Associated with Calorie Restriction and Time-Restricted Feeding: Central Neuroendocrine Integration.

This review focuses on summarizing current knowledge on how time-restricted feeding (TRF) and continuous caloric restriction (CR) affect central neuroendocrine systems involved in regulating satiety. Several interconnected regions of the hypothalamus, brainstem, and cortical areas of the brain are involved in the regulation of satiety. Following CR and TRF, the increase in hunger and reduction in satiety signals of the melanocortin system [neuropeptide Y (NPY), proopiomelanocortin (POMC), and agouti-related peptide (AgRP)] appear similar between CR and TRF protocols, as do the dopaminergic responses in the mesocorticolimbic circuit. However, ghrelin and leptin signaling via the melanocortin system appears to improve energy balance signals and reduce hyperphagia following TRF, which has not been reported in CR. In addition to satiety systems, CR and TRF also influence circadian rhythms. CR influences the suprachiasmatic nucleus (SCN) or the primary circadian clock as seen by increased clock gene expression. In contrast, TRF appears to affect both the SCN and the peripheral clocks, as seen by phasic changes in the non-SCN (potentially the elusive food entrainable oscillator) and metabolic clocks. The peripheral clocks are influenced by the primary circadian clock but are also entrained by food timing, sleep timing, and other lifestyle parameters, which can supersede the metabolic processes that are regulated by the primary circadian clock. Taken together, TRF influences hunger/satiety, energy balance systems, and circadian rhythms, suggesting a role for adherence to CR in the long run if implemented using the TRF approach. However, these suggestions are based on only a few studies, and future investigations that use standardized protocols for the evaluation of the effect of these diet patterns (time, duration, meal composition, sufficiently powered) are necessary to verify these preliminary observations.

Satiety Associated with Calorie Restriction and Time-Restricted Feeding: Peripheral Hormones.

Calorie restriction (CR) is a common approach to inducing negative energy balance. Recently, time-restricted feeding (TRF), which involves consuming food within specific time windows during a 24-h day, has become popular owing to its relative ease of practice and potential to aid in achieving and maintaining a negative energy balance. TRF can be implemented intentionally with CR, or TRF might induce CR simply because of the time restriction. This review focuses on summarizing our current knowledge on how TRF and continuous CR affect gut peptides that influence satiety. Based on peer-reviewed studies, in response to CR there is an increase in the orexigenic hormone ghrelin and a reduction in fasting leptin and insulin. There is likely a reduction in glucagon-like peptide-1 (GLP-1), peptide YY (PYY), and cholecystokinin (CCK), albeit the evidence for this is weak. After TRF, unlike CR, fasting ghrelin decreased in some TRF studies, whereas it showed no change in several others. Further, a reduction in fasting leptin, insulin, and GLP-1 has been observed. In conclusion, when other determinants of food intake are held equal, the peripheral satiety systems appear to be somewhat similarly affected by CR and TRF with regard to leptin, insulin, and GLP-1. But unlike CR, TRF did not appear to robustly increase ghrelin, suggesting different influences on appetite with a potential decrease of hunger after TRF when compared with CR. However, there are several established and novel gut peptides that have not been measured within the context of CR and TRF, and studies that have evaluated effects of TRF are often short-term, with nonuniform study designs and highly varying temporal eating patterns. More evidence and studies addressing these aspects are needed to draw definitive conclusions.

Replay in Deep Learning: Current Approaches and Missing Biological Elements.

Replay is the reactivation of one or more neural patterns that are similar to the activation patterns experienced during past waking experiences. Replay was first observed in biological neural networks during sleep, and it is now thought to play a critical role in memory formation, retrieval, and consolidation. Replay-like mechanisms have been incorporated in deep artificial neural networks that learn over time to avoid catastrophic forgetting of previous knowledge. Replay algorithms have been successfully used in a wide range of deep learning methods within supervised, unsupervised, and reinforcement learning paradigms. In this letter, we provide the first comprehensive comparison between replay in the mammalian brain and replay in artificial neural networks. We identify multiple aspects of biological replay that are missing in deep learning systems and hypothesize how they could be used to improve artificial neural networks.

N-Glycosylation Network Construction and Analysis to Modify Glycans on the Spike (S) Glycoprotein of SARS-CoV-2.

Background: The N-glycan structure and composition of the spike (S) protein of SARS-CoV-2 are pertinent to vaccine development and efficacy. Methods: We reconstructed the glycosylation network based on previously published mass spectrometry data using GNAT, a glycosylation network analysis tool. Our compilation of the network tool had 26 glycosyltransferase and glucosidase enzymes and could infer the pathway of glycosylation machinery based on glycans in the virus spike protein. Once the glycan biosynthesis pathway was generated, we simulated the effect of blocking specific enzymes-swainsonine or deoxynojirimycin for blocking mannosidase-II and indolizidine for blocking alpha-1,6-fucosyltransferase-to see how they would affect the biosynthesis network and the glycans that were synthesized. Results: The N-glycan biosynthesis network of SARS-CoV-2 spike protein shows an elaborate enzymatic pathway with several intermediate glycans, along with the ones identified by mass spectrometric studies. Of the 26 enzymes, the following were involved-Man-Ia, MGAT1, MGAT2, MGAT4, MGAT5, B3GalT, B4GalT, Man-II, SiaT, ST3GalI, ST3GalVI, and FucT8. Blocking specific enzymes resulted in a substantially modified glycan profile of SARS-CoV-2. Conclusion: Variations in the final N-glycan profile of the virus, given its site-specific microheterogeneity, are factors in the host response to the infection, vaccines, and antibodies. Heterogeneity in the N-glycan profile of the spike (S) protein and its potential effect on vaccine efficacy or adverse reactions to the vaccines remain unexplored. Here, we provide all the resources we generated-the glycans in the glycoCT xml format and the biosynthesis network for future work.

Bidirectional Interaction of Hippocampal Ripples and Cortical Slow Waves Leads to Coordinated Spiking Activity During NREM Sleep.

The dialogue between cortex and hippocampus is known to be crucial for sleep-dependent memory consolidation. During slow wave sleep, memory replay depends on slow oscillation (SO) and spindles in the (neo)cortex and sharp wave-ripples (SWRs) in the hippocampus. The mechanisms underlying interaction of these rhythms are poorly understood. We examined the interaction between cortical SO and hippocampal SWRs in a model of the hippocampo-cortico-thalamic network and compared the results with human intracranial recordings during sleep. We observed that ripple occurrence peaked following the onset of an Up-state of SO and that cortical input to hippocampus was crucial to maintain this relationship. A small fraction of ripples occurred during the Down-state and controlled initiation of the next Up-state. We observed that the effect of ripple depends on its precise timing, which supports the idea that ripples occurring at different phases of SO might serve different functions, particularly in the context of encoding the new and reactivation of the old memories during memory consolidation. The study revealed complex bidirectional interaction of SWRs and SO in which early hippocampal ripples influence transitions to Up-state, while cortical Up-states control occurrence of the later ripples, which in turn influence transition to Down-state.

Differential Covariance: A New Method to Estimate Functional Connectivity in fMRI.

Measuring functional connectivity from fMRI recordings is important in understanding processing in cortical networks. However, because the brain's connection pattern is complex, currently used methods are prone to producing false functional connections. We introduce differential covariance analysis, a new method that uses derivatives of the signal for estimating functional connectivity. We generated neural activities from dynamical causal modeling and a neural network of Hodgkin-Huxley neurons and then converted them to hemodynamic signals using the forward balloon model. The simulated fMRI signals, together with the ground-truth connectivity pattern, were used to benchmark our method with other commonly used methods. Differential covariance achieved better results in complex network simulations. This new method opens an alternative way to estimate functional connectivity.

Can sleep protect memories from catastrophic forgetting?

Continual learning remains an unsolved problem in artificial neural networks. The brain has evolved mechanisms to prevent catastrophic forgetting of old knowledge during new training. Building upon data suggesting the importance of sleep in learning and memory, we tested a hypothesis that sleep protects old memories from being forgotten after new learning. In the thalamocortical model, training a new memory interfered with previously learned old memories leading to degradation and forgetting of the old memory traces. Simulating sleep after new learning reversed the damage and enhanced old and new memories. We found that when a new memory competed for previously allocated neuronal/synaptic resources, sleep replay changed the synaptic footprint of the old memory to allow overlapping neuronal populations to store multiple memories. Our study predicts that memory storage is dynamic, and sleep enables continual learning by combining consolidation of new memory traces with reconsolidation of old memory traces to minimize interference.

Stimulation Augments Spike Sequence Replay and Memory Consolidation during Slow-Wave Sleep.

Newly acquired memory traces are spontaneously reactivated during slow-wave sleep (SWS), leading to the consolidation of recent memories. Empirical studies found that sensory stimulation during SWS can selectively enhance memory consolidation with the effect depending on the phase of stimulation. In this new study, we aimed to understand the mechanisms behind the role of sensory stimulation on memory consolidation using computational models implementing effects of neuromodulators to simulate transitions between awake and SWS sleep, and synaptic plasticity to allow the change of synaptic connections due to the training in awake or replay during sleep. We found that when closed-loop stimulation was applied during the Down states of sleep slow oscillation, particularly right before the transition from Down to Up state, it significantly affected the spatiotemporal pattern of the slow waves and maximized memory replay. In contrast, when the stimulation was presented during the Up states, it did not have a significant impact on the slow waves or memory performance after sleep. For multiple memories trained in awake, presenting stimulation cues associated with specific memory trace could selectively augment replay and enhance consolidation of that memory and interfere with consolidation of the others (particularly weak) memories. Our study proposes a synaptic-level mechanism of how memory consolidation is affected by sensory stimulation during sleep.SIGNIFICANCE STATEMENT Stimulation, such as training-associated cues or auditory stimulation, during sleep can augment consolidation of the newly encoded memories. In this study, we used a computational model of the thalamocortical system to describe the mechanisms behind the role of stimulation in memory consolidation during slow-wave sleep. Our study suggests that stimulation preferentially strengthens memory traces when delivered at a specific phase of the slow oscillation, just before the Down to Up state transition when it makes the largest impact on the spatiotemporal pattern of sleep slow waves. In the presence of multiple memories, presenting sensory cues during sleep could selectively strengthen selected memories. Our study proposes a synaptic-level mechanism of how memory consolidation is affected by sensory stimulation during sleep.

Phenotyping Women Based on Dietary Macronutrients, Physical Activity, and Body Weight Using Machine Learning Tools.

Nutritional phenotyping can help achieve personalized nutrition, and machine learning tools may offer novel means to achieve phenotyping. The primary aim of this study was to use energy balance components, namely input (dietary energy intake and macronutrient composition) and output (physical activity) to predict energy stores (body weight) as a way to evaluate their ability to identify potential phenotypes based on these parameters. From the Women's Health Initiative Observational Study (WHI OS), carbohydrates, proteins, fats, fibers, sugars, and physical activity variables, namely energy expended from mild, moderate, and vigorous intensity activity, were used to predict current body weight (both as body weight in kilograms and as a body mass index (BMI) category). Several machine learning tools were used for this prediction. Finally, cluster analysis was used to identify putative phenotypes. For the numerical predictions, the support vector machine (SVM), neural network, and k-nearest neighbor (kNN) algorithms performed modestly, with mean approximate errors (MAEs) of 6.70 kg, 6.98 kg, and 6.90 kg, respectively. For categorical prediction, SVM performed the best (54.5% accuracy), followed closely by the bagged tree ensemble and kNN algorithms. K-means cluster analysis improved prediction using numerical data, identified 10 clusters suggestive of phenotypes, with a minimum MAE of ~1.1 kg. A classifier was used to phenotype subjects into the identified clusters, with MAEs <5 kg for 15% of the test set (n = ~2000). This study highlights the challenges, limitations, and successes in using machine learning tools on self-reported data to identify determinants of energy balance.

Ionic and synaptic mechanisms of seizure generation and epileptogenesis.

The biophysical mechanisms underlying epileptogenesis and the generation of seizures remain to be better understood. Among many factors triggering epileptogenesis are traumatic brain injury breaking normal synaptic homeostasis and genetic mutations disrupting ionic concentration homeostasis. Impairments in these mechanisms, as seen in various brain diseases, may push the brain network to a pathological state characterized by increased susceptibility to unprovoked seizures. Here, we review recent computational studies exploring the roles of ionic concentration dynamics in the generation, maintenance, and termination of seizures. We further discuss how ionic and synaptic homeostatic mechanisms may give rise to conditions which prime brain networks to exhibit recurrent spontaneous seizures and epilepsy.

Timing between Cortical Slow Oscillations and Heart Rate Bursts during Sleep Predicts Temporal Processing Speed, but Not Offline Consolidation.

Central and autonomic nervous system activities are coupled during sleep. Cortical slow oscillations (SOs; <1 Hz) coincide with brief bursts in heart rate (HR), but the functional consequence of this coupling in cognition remains elusive. We measured SO-HR temporal coupling (i.e., the peak-to-peak interval between downstate of SO event and HR burst) during a daytime nap and asked whether this SO-HR timing measure was associated with temporal processing speed and learning on a texture discrimination task by testing participants before and after a nap. The coherence of SO-HR events during sleep strongly correlated with an individual's temporal processing speed in the morning and evening test sessions, but not with their change in performance after the nap (i.e., consolidation). We confirmed this result in two additional experimental visits and also discovered that this association was visit-specific, indicating a state (not trait) marker. Thus, we introduce a novel physiological index that may be a useful marker of state-dependent processing speed of an individual.

Coupling of autonomic and central events during sleep benefits declarative memory consolidation.

While anatomical pathways between forebrain cognitive and brainstem autonomic nervous centers are well-defined, autonomic-central interactions during sleep and their contribution to waking performance are not understood. Here, we analyzed simultaneous central activity via electroencephalography (EEG) and autonomic heart beat-to-beat intervals (RR intervals) from electrocardiography (ECG) during wake and daytime sleep. We identified bursts of ECG activity that lasted 4-5 s and predominated in non-rapid-eye-movement sleep (NREM). Using event-based analysis of NREM sleep, we found an increase in delta (0.5-4 Hz) and sigma (12-15 Hz) power and an elevated density of slow oscillations (0.5-1 Hz) about 5 s prior to peak of the heart rate burst, as well as a surge in vagal activity, assessed by high-frequency (HF) component of RR intervals. Using regression framework, we show that these Autonomic/Central Events (ACE) positively predicted post-nap improvement in a declarative memory task after controlling for the effects of spindles and slow oscillations from sleep periods without ACE. No such relation was found between memory performance and a control nap. Additionally, NREM ACE negatively correlated with REM sleep and learning in a non-declarative memory task. These results provide the first evidence that coordinated autonomic and central events play a significant role in declarative memory consolidation.

Differential roles of sleep spindles and sleep slow oscillations in memory consolidation.

Sleep plays an important role in the consolidation of recent memories. However, the cellular and synaptic mechanisms of consolidation during sleep remain poorly understood. In this study, using a realistic computational model of the thalamocortical network, we tested the role of Non-Rapid Eye Movement (NREM) sleep in memory consolidation. We found that sleep spindles (the hallmark of N2 stage sleep) and slow oscillations (the hallmark of N3 stage sleep) both promote replay of the spike sequences learned in the awake state and replay was localized at the trained network locations. Memory performance improved after a period of NREM sleep but not after the same time period in awake. When multiple memories were trained, the local nature of the spike sequence replay during spindles allowed replay of the distinct memory traces independently, while slow oscillations promoted competition that could prevent replay of the weak memories in a presence of the stronger memory traces. This could lead to extinction of the weak memories unless when sleep spindles (N2 sleep) preceded slow oscillations (N3 sleep), as observed during the natural sleep cycle. Our study presents a mechanistic explanation for the role of sleep rhythms in memory consolidation and proposes a testable hypothesis how the natural structure of sleep stages provides an optimal environment to consolidate memories.

Origin of slow spontaneous resting-state neuronal fluctuations in brain networks.

Resting- or baseline-state low-frequency (0.01-0.2 Hz) brain activity is observed in fMRI, EEG, and local field potential recordings. These fluctuations were found to be correlated across brain regions and are thought to reflect neuronal activity fluctuations between functionally connected areas of the brain. However, the origin of these infra-slow resting-state fluctuations remains unknown. Here, using a detailed computational model of the brain network, we show that spontaneous infra-slow (<0.05 Hz) activity could originate due to the ion concentration dynamics. The computational model implemented dynamics for intra- and extracellular K+ and Na+ and intracellular Cl- ions, Na+/K+ exchange pump, and KCC2 cotransporter. In the network model simulating resting awake-like brain state, we observed infra-slow fluctuations in the extracellular K+ concentration, Na+/K+ pump activation, firing rate of neurons, and local field potentials. Holding K+ concentration constant prevented generation of the infra-slow fluctuations. The amplitude and peak frequency of this activity were modulated by the Na+/K+ pump, AMPA/GABA synaptic currents, and glial properties. Further, in a large-scale network with long-range connections based on CoCoMac connectivity data, the infra-slow fluctuations became synchronized among remote clusters similar to the resting-state activity observed in vivo. Overall, our study proposes that ion concentration dynamics mediated by neuronal and glial activity may contribute to the generation of very slow spontaneous fluctuations of brain activity that are reported as the resting-state fluctuations in fMRI and EEG recordings.

Thalamocortical and intracortical laminar connectivity determines sleep spindle properties.

Sleep spindles are brief oscillatory events during non-rapid eye movement (NREM) sleep. Spindle density and synchronization properties are different in MEG versus EEG recordings in humans and also vary with learning performance, suggesting spindle involvement in memory consolidation. Here, using computational models, we identified network mechanisms that may explain differences in spindle properties across cortical structures. First, we report that differences in spindle occurrence between MEG and EEG data may arise from the contrasting properties of the core and matrix thalamocortical systems. The matrix system, projecting superficially, has wider thalamocortical fanout compared to the core system, which projects to middle layers, and requires the recruitment of a larger population of neurons to initiate a spindle. This property was sufficient to explain lower spindle density and higher spatial synchrony of spindles in the superficial cortical layers, as observed in the EEG signal. In contrast, spindles in the core system occurred more frequently but less synchronously, as observed in the MEG recordings. Furthermore, consistent with human recordings, in the model, spindles occurred independently in the core system but the matrix system spindles commonly co-occurred with core spindles. We also found that the intracortical excitatory connections from layer III/IV to layer V promote spindle propagation from the core to the matrix system, leading to widespread spindle activity. Our study predicts that plasticity of intra- and inter-cortical connectivity can potentially be a mechanism for increased spindle density as has been observed during learning.