Identifying behavioral links to neural dynamics of multifiber photometry recordings in a mouse social behavior network.

Objective.Distributed hypothalamic-midbrain neural circuits help orchestrate complex behavioral responses during social interactions. Given rapid advances in optical imaging, it is a fundamental question how population-averaged neural activity measured by multi-fiber photometry (MFP) for calcium fluorescence signals correlates with social behaviors is a fundamental question. This paper aims to investigate the correspondence between MFP data and social behaviors.Approach:We propose a state-space analysis framework to characterize mouse MFP data based on dynamic latent variable models, which include a continuous-state linear dynamical system and a discrete-state hidden semi-Markov model. We validate these models on extensive MFP recordings during aggressive and mating behaviors in male-male and male-female interactions, respectively.Main results:Our results show that these models are capable of capturing both temporal behavioral structure and associated neural states, and produce interpretable latent states. Our approach is also validated in computer simulations in the presence of known ground truth.Significance:Overall, these analysis approaches provide a state-space framework to examine neural dynamics underlying social behaviors and reveals mechanistic insights into the relevant networks.

Large-scale foundation models and generative AI for BigData neuroscience.

Recent advances in machine learning have led to revolutionary breakthroughs in computer games, image and natural language understanding, and scientific discovery. Foundation models and large-scale language models (LLMs) have recently achieved human-like intelligence thanks to BigData. With the help of self-supervised learning (SSL) and transfer learning, these models may potentially reshape the landscapes of neuroscience research and make a significant impact on the future. Here we present a mini-review on recent advances in foundation models and generative AI models as well as their applications in neuroscience, including natural language and speech, semantic memory, brain-machine interfaces (BMIs), and data augmentation. We argue that this paradigm-shift framework will open new avenues for many neuroscience research directions and discuss the accompanying challenges and opportunities.

Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy.

High-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera (~2-3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.

Identifying behavioral links to neural dynamics of multifiber photometry recordings in a mouse social behavior network.

Distributed hypothalamic-midbrain neural circuits orchestrate complex behavioral responses during social interactions. How population-averaged neural activity measured by multi-fiber photometry (MFP) for calcium fluorescence signals correlates with social behaviors is a fundamental question. We propose a state-space analysis framework to characterize mouse MFP data based on dynamic latent variable models, which include continuous-state linear dynamical system (LDS) and discrete-state hidden semi-Markov model (HSMM). We validate these models on extensive MFP recordings during aggressive and mating behaviors in male-male and male-female interactions, respectively. Our results show that these models are capable of capturing both temporal behavioral structure and associated neural states. Overall, these analysis approaches provide an unbiased strategy to examine neural dynamics underlying social behaviors and reveals mechanistic insights into the relevant networks.

Changes in alpha, theta, and gamma oscillations in distinct cortical areas are associated with altered acute pain responses in chronic low back pain patients.

Introduction: Chronic pain negatively impacts a range of sensory and affective behaviors. Previous studies have shown that the presence of chronic pain not only causes hypersensitivity at the site of injury but may also be associated with pain-aversive experiences at anatomically unrelated sites. While animal studies have indicated that the cingulate and prefrontal cortices are involved in this generalized hyperalgesia, the mechanisms distinguishing increased sensitivity at the site of injury from a generalized site-nonspecific enhancement in the aversive response to nociceptive inputs are not well known. Methods: We compared measured pain responses to peripheral mechanical stimuli applied to a site of chronic pain and at a pain-free site in participants suffering from chronic lower back pain (n = 15) versus pain-free control participants (n = 15) by analyzing behavioral and electroencephalographic (EEG) data. Results: As expected, participants with chronic pain endorsed enhanced pain with mechanical stimuli in both back and hand. We further analyzed electroencephalographic (EEG) recordings during these evoked pain episodes. Brain oscillations in theta and alpha bands in the medial orbitofrontal cortex (mOFC) were associated with localized hypersensitivity, while increased gamma oscillations in the anterior cingulate cortex (ACC) and increased theta oscillations in the dorsolateral prefrontal cortex (dlPFC) were associated with generalized hyperalgesia. Discussion: These findings indicate that chronic pain may disrupt multiple cortical circuits to impact nociceptive processing.

Aberrant resting-state functional connectivity of the globus pallidus interna in first-episode schizophrenia.

BACKGROUND: The striatal-pallidal pathway plays an important role in cognitive control and modulation of behaviors. Globus pallidus interna (GPi), as a primary output structure, is crucial in modulating excitation and inhibition. Studies of GPi in psychiatric illnesses are lacking given the technical challenges of examining this small and functionally diverse subcortical structure. METHODS: 71 medication-naïve first episode schizophrenia (FES) participants and 73 healthy controls (HC) were recruited at the Shanghai Mental Health Center. Clinical symptoms and imaging data were collected at baseline and, in a subset of patients, 8 weeks after initiating treatment. Resting-state functional connectivity of sub-regions of the GP were assessed using a novel mask that combines two atlases to create 8 ROIs in the GP. RESULTS: Baseline imaging data from 63 FES patients and 55 HC met quality standards and were analyzed. FES patients exhibited less negative connectivity and increased positive connectivity between the right anterior GPi and several cortical and subcortical areas at baseline compared to HC (PFWE < 0.05). Positive functional connectivity between the right anterior GPi and several brain areas, including the right dorsal anterior cingulate gyrus, was associated with severity of positive symptoms (PFWE < 0.05) and predicted treatment response after 8 weeks (n = 28, adjusted R2 = 0.486, p < 0.001). CONCLUSIONS: Our results implicate striatal-pallidal-thalamic pathways in antipsychotic efficacy. If replicated, these findings may reflect failure of neurodevelopmental processes in adolescence and early adulthood that decrease functional connectivity as an index of failure of the limbic/associative GPi to appropriately inhibit irrelevant signals in psychosis.

Spiking Recurrent Neural Networks Represent Task-Relevant Neural Sequences in Rule-Dependent Computation.

Background: Prefrontal cortical neurons play essential roles in performing rule-dependent tasks and working memory-based decision making. Methods: Motivated by PFG recordings of task-performing mice, we developed an excitatory-inhibitory spiking recurrent neural network (SRNN) to perform a rule-dependent two-alternative forced choice (2AFC) task. We imposed several important biological constraints onto the SRNN, and adapted spike frequency adaptation (SFA) and SuperSpike gradient methods to train the SRNN efficiently. Results: The trained SRNN produced emergent rule-specific tunings in single-unit representations, showing rule-dependent population dynamics that resembled experimentally observed data. Under varying test conditions, we manipulated the SRNN parameters or configuration in computer simulations, and we investigated the impacts of rule-coding error, delay duration, recurrent weight connectivity and sparsity, and excitation/inhibition (E/I) balance on both task performance and neural representations. Conclusions: Overall, our modeling study provides a computational framework to understand neuronal representations at a fine timescale during working memory and cognitive control, and provides new experimentally testable hypotheses in future experiments.

Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy.

High-speed widefield fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio (SNR) at high frame rates, limiting their ability to detect faint fluorescent events. Here we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high SNR. In high-speed voltage imaging experiments, our image sensor significantly increases the output SNR compared to a low-noise scientific CMOS camera (~2-3 folds). This SNR gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our proposed camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.

In search of a composite biomarker for chronic pain by way of EEG and machine learning: where do we currently stand?

Machine learning is becoming an increasingly common component of routine data analyses in clinical research. The past decade in pain research has witnessed great advances in human neuroimaging and machine learning. With each finding, the pain research community takes one step closer to uncovering fundamental mechanisms underlying chronic pain and at the same time proposing neurophysiological biomarkers. However, it remains challenging to fully understand chronic pain due to its multidimensional representations within the brain. By utilizing cost-effective and non-invasive imaging techniques such as electroencephalography (EEG) and analyzing the resulting data with advanced analytic methods, we have the opportunity to better understand and identify specific neural mechanisms associated with the processing and perception of chronic pain. This narrative literature review summarizes studies from the last decade describing the utility of EEG as a potential biomarker for chronic pain by synergizing clinical and computational perspectives.

Computational models for state-dependent traveling waves in hippocampal formation.

Hippocampal theta (4-10 Hz) oscillations have been identified as traveling waves in both rodents and humans. In freely foraging rodents, the theta traveling wave is a planar wave propagating from the dorsal to ventral hippocampus along the septotemporal axis. Motivated from experimental findings, we develop a spiking neural network of excitatory and inhibitory neurons to generate state-dependent hippocampal traveling waves to improve current mechanistic understanding of propagating waves. Model simulations demonstrate the necessary conditions for generating wave propagation and characterize the traveling wave properties with respect to model parameters, running speed and brain state of the animal. Networks with long-range inhibitory connections are more suitable than networks with long-range excitatory connections. We further generalize the spiking neural network to model traveling waves in the medial entorhinal cortex (MEC) and predict that traveling theta waves in the hippocampus and entorhinal cortex are in sink.

Post-injury pain and behaviour: a control theory perspective.

Injuries of various types occur commonly in the lives of humans and other animals and lead to a pattern of persistent pain and recuperative behaviour that allows safe and effective recovery. In this Perspective, we propose a control-theoretic framework to explain the adaptive processes in the brain that drive physiological post-injury behaviour. We set out an evolutionary and ethological view on how animals respond to injury, illustrating how the behavioural state associated with persistent pain and recuperation may be just as important as phasic pain in ensuring survival. Adopting a normative approach, we suggest that the brain implements a continuous optimal inference of the current state of injury from diverse sensory and physiological signals. This drives the various effector control mechanisms of behavioural homeostasis, which span the modulation of ongoing motivation and perception to drive rest and hyper-protective behaviours. However, an inherent problem with this is that these protective behaviours may partially obscure information about whether injury has resolved. Such information restriction may seed a tendency to aberrantly or persistently infer injury, and may thus promote the transition to pathological chronic pain states.

Identification of atypical sleep microarchitecture biomarkers in children with autism spectrum disorder.

Importance: Sleep disorders are one of the most frequent comorbidities in children with autism spectrum disorder (ASD). However, the link between neurodevelopmental effects in ASD children with their underlying sleep microarchitecture is not well understood. An improved understanding of etiology of sleep difficulties and identification of sleep-associated biomarkers for children with ASD can improve the accuracy of clinical diagnosis. Objectives: To investigate whether machine learning models can identify biomarkers for children with ASD based on sleep EEG recordings. Design setting and participants: Sleep polysomnogram data were obtained from the Nationwide Children' Health (NCH) Sleep DataBank. Children (ages: 8-16 yrs) with 149 autism and 197 age-matched controls without neurodevelopmental diagnosis were selected for analysis. An additional independent age-matched control group (n = 79) selected from the Childhood Adenotonsillectomy Trial (CHAT) was also used to validate the models. Furthermore, an independent smaller NCH cohort of younger infants and toddlers (age: 0.5-3 yr.; 38 autism and 75 controls) was used for additional validation. Main outcomes and measures: We computed periodic and non-periodic characteristics from sleep EEG recordings: sleep stages, spectral power, sleep spindle characteristics, and aperiodic signals. Machine learning models including the Logistic Regression (LR) classifier, Support Vector Machine (SVM), and Random Forest (RF) model were trained using these features. We determined the autism class based on the prediction score of the classifier. The area under the receiver operating characteristics curve (AUC), accuracy, sensitivity, and specificity were used to evaluate the model performance. Results: In the NCH study, RF outperformed two other models with a 10-fold cross-validated median AUC of 0.95 (interquartile range [IQR], [0.93, 0.98]). The LR and SVM models performed comparably across multiple metrics, with median AUC 0.80 [0.78, 0.85] and 0.83 [0.79, 0.87], respectively. In the CHAT study, three tested models have comparable AUC results: LR: 0.83 [0.76, 0.92], SVM: 0.87 [0.75, 1.00], and RF: 0.85 [0.75, 1.00]. Sleep spindle density, amplitude, spindle-slow oscillation (SSO) coupling, aperiodic signal's spectral slope and intercept, as well as the percentage of REM sleep were found to be key discriminative features in the predictive models. Conclusion and relevance: Our results suggest that integration of EEG feature engineering and machine learning can identify sleep-based biomarkers for ASD children and produce good generalization in independent validation datasets. Microstructural EEG alterations may help reveal underlying pathophysiological mechanisms of autism that alter sleep quality and behaviors. Machine learning analysis may reveal new insight into the etiology and treatment of sleep difficulties in autism.

Oxytocin promotes prefrontal population activity via the PVN-PFC pathway to regulate pain.

Neurons in the prefrontal cortex (PFC) can provide top-down regulation of sensory-affective experiences such as pain. Bottom-up modulation of sensory coding in the PFC, however, remains poorly understood. Here, we examined how oxytocin (OT) signaling from the hypothalamus regulates nociceptive coding in the PFC. In vivo time-lapse endoscopic calcium imaging in freely behaving rats showed that OT selectively enhanced population activity in the prelimbic PFC in response to nociceptive inputs. This population response resulted from the reduction of evoked GABAergic inhibition and manifested as elevated functional connectivity involving pain-responsive neurons. Direct inputs from OT-releasing neurons in the paraventricular nucleus (PVN) of the hypothalamus are crucial to maintaining this prefrontal nociceptive response. Activation of the prelimbic PFC by OT or direct optogenetic stimulation of oxytocinergic PVN projections reduced acute and chronic pain. These results suggest that oxytocinergic signaling in the PVN-PFC circuit constitutes a key mechanism to regulate cortical sensory processing.

Hierarchical predictive coding in distributed pain circuits.

Predictive coding is a computational theory on describing how the brain perceives and acts, which has been widely adopted in sensory processing and motor control. Nociceptive and pain processing involves a large and distributed network of circuits. However, it is still unknown whether this distributed network is completely decentralized or requires networkwide coordination. Multiple lines of evidence from human and animal studies have suggested that the cingulate cortex and insula cortex (cingulate-insula network) are two major hubs in mediating information from sensory afferents and spinothalamic inputs, whereas subregions of cingulate and insula cortices have distinct projections and functional roles. In this mini-review, we propose an updated hierarchical predictive coding framework for pain perception and discuss its related computational, algorithmic, and implementation issues. We suggest active inference as a generalized predictive coding algorithm, and hierarchically organized traveling waves of independent neural oscillations as a plausible brain mechanism to integrate bottom-up and top-down information across distributed pain circuits.

How our understanding of memory replay evolves.

Memory reactivations and replay, widely reported in the hippocampus and cortex across species, have been implicated in memory consolidation, planning, and spatial and skill learning. Technological advances in electrophysiology, calcium imaging, and human neuroimaging techniques have enabled neuroscientists to measure large-scale neural activity with increasing spatiotemporal resolution and have provided opportunities for developing robust analytic methods to identify memory replay. In this article, we first review a large body of historically important and representative memory replay studies from the animal and human literature. We then discuss our current understanding of memory replay functions in learning, planning, and memory consolidation and further discuss the progress in computational modeling that has contributed to these improvements. Next, we review past and present analytic methods for replay analyses and discuss their limitations and challenges. Finally, looking ahead, we discuss some promising analytic methods for detecting nonstereotypical, behaviorally nondecodable structures from large-scale neural recordings. We argue that seamless integration of multisite recordings, real-time replay decoding, and closed-loop manipulation experiments will be essential for delineating the role of memory replay in a wide range of cognitive and motor functions.

Temporal pain processing in the primary somatosensory cortex and anterior cingulate cortex.

Pain is known to have sensory and affective components. The sensory pain component is encoded by neurons in the primary somatosensory cortex (S1), whereas the emotional or affective pain experience is in large part processed by neural activities in the anterior cingulate cortex (ACC). The timing of how a mechanical or thermal noxious stimulus triggers activation of peripheral pain fibers is well-known. However, the temporal processing of nociceptive inputs in the cortex remains little studied. Here, we took two approaches to examine how nociceptive inputs are processed by the S1 and ACC. We simultaneously recorded local field potentials in both regions, during the application of a brain-computer interface (BCI). First, we compared event related potentials in the S1 and ACC. Next, we used an algorithmic pain decoder enabled by machine-learning to detect the onset of pain which was used during the implementation of the BCI to automatically treat pain. We found that whereas mechanical pain triggered neural activity changes first in the S1, the S1 and ACC processed thermal pain with a reasonably similar time course. These results indicate that the temporal processing of nociceptive information in different regions of the cortex is likely important for the overall pain experience.

Pain, from perception to action: A computational perspective.

Pain is driven by sensation and emotion, and in turn, it motivates decisions and actions. To fully appreciate the multidimensional nature of pain, we formulate the study of pain within a closed-loop framework of sensory-motor prediction. In this closed-loop cycle, prediction plays an important role, as the interaction between prediction and actual sensory experience shapes pain perception and subsequently, action. In this Perspective, we describe the roles of two prominent computational theories-Bayesian inference and reinforcement learning-in modeling adaptive pain behaviors. We show that prediction serves as a common theme between these two theories, and that each of these theories can explain unique aspects of the pain perception-action cycle. We discuss how these computational theories and models can improve our mechanistic understandings of pain-centered processes such as anticipation, attention, placebo hypoalgesia, and pain chronification.

Excitatory-inhibitory recurrent dynamics produce robust visual grids and stable attractors.

Spatially modulated grid cells have been recently found in the rat secondary visual cortex (V2) during active navigation. However, the computational mechanism and functional significance of V2 grid cells remain unknown. To address the knowledge gap, we train a biologically inspired excitatory-inhibitory recurrent neural network to perform a two-dimensional spatial navigation task with multisensory input. We find grid-like responses in both excitatory and inhibitory RNN units, which are robust with respect to spatial cues, dimensionality of visual input, and activation function. Population responses reveal a low-dimensional, torus-like manifold and attractor. We find a link between functional grid clusters with similar receptive fields and structured excitatory-to-excitatory connections. Additionally, multistable torus-like attractors emerged with increasing sparsity in inter- and intra-subnetwork connectivity. Finally, irregular grid patterns are found in recurrent neural network (RNN) units during a visual sequence recognition task. Together, our results suggest common computational mechanisms of V2 grid cells for spatial and non-spatial tasks.

Modern views of machine learning for precision psychiatry.

In light of the National Institute of Mental Health (NIMH)'s Research Domain Criteria (RDoC), the advent of functional neuroimaging, novel technologies and methods provide new opportunities to develop precise and personalized prognosis and diagnosis of mental disorders. Machine learning (ML) and artificial intelligence (AI) technologies are playing an increasingly critical role in the new era of precision psychiatry. Combining ML/AI with neuromodulation technologies can potentially provide explainable solutions in clinical practice and effective therapeutic treatment. Advanced wearable and mobile technologies also call for the new role of ML/AI for digital phenotyping in mobile mental health. In this review, we provide a comprehensive review of ML methodologies and applications by combining neuroimaging, neuromodulation, and advanced mobile technologies in psychiatry practice. We further review the role of ML in molecular phenotyping and cross-species biomarker identification in precision psychiatry. We also discuss explainable AI (XAI) and neuromodulation in a closed human-in-the-loop manner and highlight the ML potential in multi-media information extraction and multi-modal data fusion. Finally, we discuss conceptual and practical challenges in precision psychiatry and highlight ML opportunities in future research.

Are Grid-Like Representations a Component of All Perception and Cognition?

Grid cells or grid-like responses have been reported in the rodent, bat and human brains during various spatial and non-spatial tasks. However, the functions of grid-like representations beyond the classical hippocampal formation remain elusive. Based on accumulating evidence from recent rodent recordings and human fMRI data, we make speculative accounts regarding the mechanisms and functional significance of the sensory cortical grid cells and further make theory-driven predictions. We argue and reason the rationale why grid responses may be universal in the brain for a wide range of perceptual and cognitive tasks that involve locomotion and mental navigation. Computational modeling may provide an alternative and complementary means to investigate the grid code or grid-like map. We hope that the new discussion will lead to experimentally testable hypotheses and drive future experimental data collection.