Publications using the ZIF-Clip

The ability to detect deviations from expected sensory input is fundamental for adaptive behavior. We recorded electrocorticographic activity from the auditory (AC) and prefrontal (PFC) cortices of behaving macaques during an auditory oddball task to probe the cortical dynamics of predictive processing. Repetition of standard stimuli evoked suppression and facilitation in AC and strong low-frequency (2 Hz) enhancement in PFC, accompanied by bidirectional delta-band GC-defined interactions indicative of a shared predictive state. Deviant stimuli triggered earlier AC responses followed by PFC activation and increased GC-defined directed interactions across theta, alpha, and conventional gamma bands. Behavioral engagement amplified both repetition-related and deviance-related ECoG responses, strengthening cortical network coordination. Together, these findings reveal behaviorally gated auditory–prefrontal dynamics that are consistent with hierarchical predictive-processing accounts, while also allowing for contributions from repetition-, novelty-, and salience-related mechanisms.

Brain function relies on coordinated activity across spatial and temporal scales. Single neurons integrate local and long-range connectivity and reflect activity across brain-wide networks. Understanding integrated brain function requires tools capable of recording from anatomically connected populations in distributed brain areas to bridge local and global dynamics. Here, we present high-density, micro-electrocorticography arrays that facilitate multi-scale studies of brain activity. The hybrid arrays integrate the desirable features of silicone elastomers and polyimide films: silicone provides optical transparency and permits repeated penetration with intracortical arrays, while polyimide enables fine photolithographic feature definition. This combination facilitates high-throughput functional mapping to identify targets and insertion of intracortical arrays for dense local sampling. We demonstrate functional mapping in rats, cats, and marmosets, showing how functional maps guide multi-area laminar recordings. Finally, we demonstrate local and feedforward optogenetic stimulation to investigate cortico-cortical interactions. These capabilities establish the hybrid μECoG as a compelling tool for systems neuroscience.

We describe properties and laminar organization of visual and auditory responses sampled with linear electrode arrays in and around the supplementary eye field of four macaque monkeys performing a visually guided task with a tone secondary reinforcer. Of pyramidal neurons in all layers and interneurons in L3 and L5/6, one-quarter were visually responsive, one-quarter, auditory, with 30% bimodal. Visual neurons were less common rostral, lateral, and medial to the supplementary eye field. Facilitated visual and auditory responses were much more common than suppressed. Pyramidal and interneurons responded to the stimulus in either hemifield with a weak bias for contralateral targets. Visual response latencies were comparable to values previously reported and later than auditory responses. Facilitated visual responses of interneurons preceded those of pyramidal neurons. Transient visual responses preceded sustained. Current-source density revealed visually evoked current sinks after auditory sinks that were transient for bright flashes and prolonged for the discrete task target. The earliest sink appeared at the L3 to L5 border and spread superficially and deeper with idiosyncratic variability across monkeys. These findings reveal new details about sensory processing in medial frontal cortex and complement our previous descriptions of the functional properties and laminar organization of neurons supporting cognitive control.

This work presents three open datasets featuring various levels of processing, containing neural recordings from the auditory cortex of rats. These recordings were obtained during experiments using the auditory oddball paradigm before, during and after the local microiontophoretic application of acetylcholine. The primary objective of these datasets is to investigate how the brain processes predictable versus unexpected auditory stimuli, and the role of cholinergic inputs during such processing. The data include multi-unit recordings of neuronal activity during the presentation of standard and deviant tones, classified by stimulus type and cortical sub-region. These resources enable quantitative investigations of deviance detection, stimulus-specific adaptation, cholinergic modulation and predictive-coding mechanisms at multiple temporal scales.

Foraging in the wild requires coordinated switching of critical functions, including goal-oriented navigation and context-appropriate action selection. Nevertheless, few studies have examined how different functions are represented in the brain during naturalistic foraging. To address this question, we recorded multiple single-unit activities from the medial prefrontal cortex (mPFC) of rats seeking a sucrose reward in the presence of an unpredictable attack posed by a robotic predator (Lobsterbot). Simultaneously recorded ensemble activities from neurons were analyzed in reference to various behavioral indices as the animal moved freely across the foraging area (F) between the nest (N) and the goal (E) area. An artificial neural network, trained with simultaneously recorded neural activity, estimated the rat’s current distance from the Lobsterbot. The accuracy of distance estimation was the highest in the middle F-zone in which the dominant behavior was active navigation. The spatial encoding persisted in the N-zone when non-navigational behaviors such as grooming, rearing, and sniffing were excluded. In contrast, the accuracy decreased as the animal approached the E-zone, when the activity of the same neuronal ensembles was more correlated with events related to dynamic decision-making between food procurement and Lobsterbot evasion. A population-wide analysis confirmed highly heterogeneous encoding by the region. To further assess the decision-related activity in the E-zone, a naive Bayesian classifier was trained to predict the success and failure of avoidance behavior. The classifier predicted the avoidance outcome as much as 6 s before the head withdrawal. In addition, two sub-populations of recorded units with distinct temporal dynamics contributed differently to the prediction. These findings suggest that an overlapping population of mPFC neurons may switch between two heterogeneous modes, encoding relevant locations for goal-directed navigation or an imminent situational challenge.

The non-rapid-eye movement (NREM) sleep power spectrum is composed of rhythmic and arrhythmic components, respectively associated with brain rhythms and scale-free dynamics. Both components are hypothesized to represent distinct processes underlying sleep-dependent memory consolidation as well as other brain complex processes. Recent advancements in spectral parametrization techniques and the use of multifractal models have enabled new insights into these components and their connection to brain networks. Aging impacts NREM sleep oscillations, but no animal studies considered the impact of age on rhythmic and arrhythmic components. In this study, we assessed the effects of age on the power spectrum and its two components using local field potential recordings in mice. We recorded across the cerebral cortex and within the hippocampus—a central brain hub involved in NREM sleep-dependent cognitive processing. Ten younger (7.6 months) and eleven older (15.7 months) C57BL/6 J male and female mice were continuously recorded over a 24-hour period. We extracted the NREM sleep standard and rhythmic spectra, controlled for scale-free activity, and estimated multifractal arrhythmic properties during NREM sleep using the Wavelet Leader and Bootstrap based MultiFractal analysis toolbox. Older mice showed specific alterations in both components compared to younger animals: reduced rhythmic gamma power in the anterior cortex, greater regional differentiation of scaling exponents, and higher multifractal dispersion of the arrhythmic component in the hippocampus. These findings demonstrate that aging alters rhythmic and arrhythmic properties of NREM sleep in distinct brain regions, suggesting that both contribute to age-related changes in sleep-dependent cognition.

Purpose: We aim to develop a robust method to improve the estimation accuracy of motor-evoked potential (MEP) recruitment curves (RCs), including motor threshold, in small-sample settings which typically involve fewer than 40 stimuli. Methods: We present a hierarchical Bayesian (HB) method to model MEP size as a rectified-logistic function of stimulation intensity. This method is designed to account for small samples, handle outliers without discarding data, quantify estimation uncertainty, and simulate synthetic data that closely matches real observations, useful for optimizing experimental design. We validate its performance on transcranial magnetic stimulation (TMS), epidural spinal cord stimulation (SCS), and synthetic TMS datasets, and provide an open-source library for Python, called hbMEP, for diverse applications. Results: The rectified-logistic outperformed sigmoidal functions in predictive accuracy on TMS and SCS datasets, as demonstrated through cross-validation. A mixture extension of the HB model improved robustness to outliers by further increasing its predictive accuracy. The HB model reduced threshold estimation error by up to 70% on sparse synthetic TMS data compared to non-hierarchical models. Bayesian estimation with the HB model reduced the required number of participants by at least 23% to detect a shift in threshold with 80% power, compared to frequentist testing. Empirical results on human SCS data further validated its applicability to real data. Conclusion: By improving accuracy on sparse data, our method minimizes the number of stimuli needed to probe each individual's neuromuscular parameters across multiple muscles simultaneously, thereby reducing session duration and the risk of inadvertent neuromodulation. Our approach provides a more statistically powerful and conclusive framework for inferring changes in threshold, and therefore corticospinal excitability. The hbMEP library streamlines and unifies the analysis of RCs across stimulation modalities and experimental paradigms.

Autism is an early‐onset neurodevelopmental disorder characterized by restricted, repetitive behaviors and atypical patterns of social communication and interaction. A considerable proportion of autistic individuals experience divergent auditory perception, which can interfere with their ability to navigate everyday sound environments. Auditory brainstem responses are electrophysiological potentials elicited by auditory stimuli that evaluate neural activity along the auditory nerve and brainstem. Importantly, the auditory brainstem response varies by sex, with females typically showing higher amplitudes and shorter latencies than males. This sex‐specific neurophysiological profile is especially relevant in autism research, where the male‐to‐female diagnosis ratio is approximately 3:1. Thus, exploring the neurobiological mechanisms underlying sex‐specific variations in autistic traits is essential. Furthermore, autism sensory profiles may vary based on the independent and mutual effects of environmental and genetic factors. To deepen this understanding, we examined auditory brainstem responses in two rat models of autism: the GRIN2B rare mutation model and the prenatal valproic acid induction model, alongside control animals. We assessed peak amplitudes and latencies (Waves I through V), inter‐peak intervals (I–III, I–V, and III–V), and amplitude ratios (III:I, V:I, and V:III). Female rats generally exhibited greater amplitudes and longer latencies across waveforms. Regarding rat models, control animals consistently showed larger amplitudes and shorter latencies compared to autism‐like models. Exploratory analyses further suggested pairwise interactions between sex and rat model, indicating modulation of auditory phenotypes linked to autism. Thus, our findings reveal key insights into the effects of sex and rat model, as well as their interactions.

Most spinal cord injuries (SCI) spare descending and sublesional circuits that can be targeted through motor cortex and spinal cord stimulation to mitigate locomotor deficits. However, the potential synergy between cortical and spinal stimulation remains unknown. Here, we first investigated the phase-locked electrical stimulation of the motor cortex and lumbar spinal cord at 40 Hz in a rat model of unilateral SCI. Combining cortical and lumbar stimulation around the anticipated lift synergistically enhanced leg movements. When integrated into rehabilitation training, cortical stimulation proved essential for the recovery of skilled locomotion. We next investigated the effects of high-frequency (330 Hz) lumbar and sacral stimulation combined with cortical stimulation. Timely integration during the swing phase showed that cortical and lumbar stimulations enhance the initial and mid-swing phases, while sacral stimulation improves extension velocity in the late swing. These findings indicate that supraspinal and sublesional neuromodulation offer complementary neuroprosthetic effects in targeted SCI gait rehabilitation.

Long-term robust intracortical microelectrode (IME) neural recording quality is negatively affected by the neuroinflammatory response following microelectrode insertion. This adversely impacts brain-machine interface (BMI) performance for patients with neurological disorders or amputations. Recent studies suggest that the leakage of blood-brain barrier (BBB) and microhemorrhage caused by IME insertions contribute to increased neuroinflammation and reduced neural recording performance. Here, we evaluated dexamethasone sodium phosphate-loaded platelet-inspired nanoparticles (DEXSPPIN) to simultaneously augment local hemostasis and serve as an implant-site targeted drug-delivery vehicle. Weekly systemic treatment or control therapy was provided to rats for 8 weeks following IME implantation, while evaluating extracellular single-unit recording performance. End-point immunohistochemistry was performed to further assess the local tissue response to the IMEs. Treatment with DEXSPPIN significantly increased the recording capabilities of IMEs compared to controls over the 8-week observation period. Immunohistochemical analyses of neuron density, activated microglia/macrophage density, astrocyte density, and BBB permeability suggested that the improved neural recording performance may be attributed to reduced neuron degeneration and neuroinflammation. Overall, we found that DEXSPPIN treatment promoted an anti-inflammatory environment that improved neuronal density and enhanced IME recording performance.

Brain-computer interfaces (BCIs) enable direct communication between the brain and computers. However, their long-term functionality remains limited due to signal degradation caused by acute insertion trauma, chronic foreign body reaction (FBR), and biofouling at the device-tissue interface. To address these challenges, we introduce a multifunctional surface modification strategy called targeting-specific interaction and blocking nonspecific adhesion (TAB) coating for flexible fiber, achieving a synergistic integration of mechanical compliance and biochemical stability. The coating combines brain-derived neurotrophic factor (BDNF) conjugation and a lubricant-infused surface. This dual-functional design enables selective interaction with neurons and astrocytes while preventing nonspecific adhesion. Notably, high-quality single-unit neural signals were stably recorded for more than 12 months after implantation, demonstrating exceptional long-term recording performance. Integrating mechanical compatibility, antifouling properties, and selective neural cell interaction, the TAB-coated multifunctional fiber represents a transformative approach for neural implants, bridging biological systems with computational systems.

The locus coeruleus–norepinephrine (LC-NE) system regulates arousal and awakening; however, it remains unclear whether the LC does this in a global or circuit-specific manner. We hypothesized that sensory-evoked awakenings are predominantly regulated by specific LC-NE efferent pathways. Anatomical, physiological, and functional modularities of LC-NE pathways involving the mouse basal forebrain (BF) and pontine reticular nucleus (PRN) were tested. We found partial anatomical segregation between the LC → PRN and LC → BF circuits. Extracellular NE dynamics in BF and PRN exhibited distinct sound-evoked activation during sleep, including a fast sound-evoked NE peak specific to PRN. Causal optogenetic interrogation of LC efferent pathways, by retro-channelrhodopsin (ChR2) activation or Platynereis dumerilii ciliary opsin (PdCO) silencing of synapses in target regions, revealed a role for early LC → PRN activity in driving arousal and sound-evoked awakenings. Together, our results uncover a role for early LC-NE PRN activity in connecting sensory and arousal pathways and establish LC heterogeneity in regulating arousal.

The ability to detect deviations from expected sensory input is fundamental for adaptive behavior. We recorded electrocorticographic activity from the auditory (AC) and prefrontal (PFC) cortices of behaving macaques during an auditory oddball task to probe the cortical dynamics of predictive processing. Repetition of standard stimuli evoked suppression and facilitation in AC and strong low-frequency (2 Hz) enhancement in PFC, accompanied by bidirectional delta-band coupling indicative of a shared predictive state. Deviant stimuli triggered early AC responses followed by PFC activation and increased feedforward and feedback connectivity across delta, theta, and gamma bands. Behavioral engagement amplified both prediction and prediction error signals, strengthening cortical network coordination. Together, these findings reveal a hierarchical predictive network in which the AC encodes sensory regularities and violations, while the PFC integrates predictive context in a behaviorally dependent manner.

Intracortical microelectrodes are used for recording activity from individual neurons, providing both a valuable neuroscience tool and an enabling medical technology for individuals with motor disabilities. Standard neural probes carrying the microelectrodes are rigid silicon-based structures that can penetrate the brain parenchyma to interface with the targeted neurons. Unfortunately, within weeks after implantation, neural recording quality from microelectrodes degrades, owing largely to a neuroinflammatory response. Key contributors to the neuroinflammatory response include mechanical mismatch at the device-tissue interface and oxidative stress. We developed a mechanically-adaptive, resveratrol-eluting (MARE) neural probe to mitigate both mechanical mismatch and oxidative stress and thereby promote improved neural recording quality and longevity. In this work, we demonstrate that compared to rigid silicon controls, highly-flexible MARE probes exhibit improved recording performance, more stable impedance, and a healing tissue response. With further optimization, MARE probes can serve as long-term, robust neural probes for brain-machine interface applications.

Advancements in the field of implantable neurotechnologies have enabled the integration of hundreds of microelectrodes on ultra-thin and flexible substrates. Besides implantable components, also connectors, headstages and cables have to comply with the high-count demand, resulting in a complex and compact chain with reduced line spacing and smaller safety margins. Here, we show that epicortical recordings acquired from anesthetized rat brains with a state-of-art neural acquisition system are undoubtedly compromised by crosstalk, with signal coherence maps exhibiting a strong dependency to the routing layout. A crosstalk back-correction algorithm is developed, allowing to infer on how signals would look like under a zero-crosstalk scenario. We found that signal coherence between closely routed channels effectively drops after correction, corroborating crosstalk contamination. Our work stresses the importance of validating recorded data against the routing layout as a crucial step of data quality control, helping to come closer to ground truth data.

The hippocampus (HPC) supports spatial working memory (SWM) through its interactions with the prefrontal cortex (PFC). However, it is not clear whether and how the dorsal (dHPC) and ventral (vHPC) poles of the HPC make distinct contributions to SWM and whether they differentially influence the PFC. To address this question, we optogenetically silenced the dHPC or the vHPC while simultaneously recording from the PFC of mice performing a SWM task. We found that whereas both HPC subregions were necessary during the encoding phase of the task, only the dHPC was necessary during the choice phase. Unexpectedly, silencing of either subregion did not affect PFC neurons’ ability to represent the animal’s position, but did alter how it was represented. In contrast, only silencing of the vHPC affected their coding of spatial goals. These results thus reveal distinct contributions of the dorsal and ventral HPC poles to SWM and the coding of behaviorally relevant spatial information by PFC neurons.

Restoring upper limb function is critical in individuals with central paralysis, and hand control is a priority in patients with neurological impairments. Functional electrical stimulation with implantable electrodes targeting the peripheral nervous system has the potential to selectively recruit hand muscles and generate multiple functional hand movements. However, the implantation of electrodes in the forearm or elbow areas requires multiple incisions for surgery, and elbow joint movements cannot be performed. In this study, we designed and implanted two epineural cuffs on the median and radial nerves in the distal brachial plexus of a single Japanese macaque ( Macaca fuscata ) monkey. The cuffs were successfully placed via an axillary approach using a single incision. Electrical stimuli were applied to innervate the contraction patterns of the hand, forearm, and triceps muscles relevant to the median and radial nerves. The evoked potentials of the target muscles electrically stimulated the distal brachial plexus to reliably and selectively innervate the upper limb muscles at the functional group level. Our results demonstrated that the distal brachial plexus can be a useful stimulation site for upper limb muscle contraction and that the axillary approach enables electrode placement to peripheral nerves required for upper limb control.

Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.

The ability of the brain to process auditory information across multiple temporal scales is crucial for perception. This study introduces an innovative experimental approach using nonlinguistic structured stimuli composed of click trains that alternate at different rates to investigate auditory processing across 3 distinct temporal scales: individual clicks (tens of milliseconds), click trains forming auditory objects (hundreds of milliseconds), and higher-order click trains in neuronal novelty detection (seconds) in both rhesus monkeys and humans. Electrocorticography recordings in the auditory cortex of rhesus monkeys unveil the primate brain’s remarkable ability to process intricate auditory temporal patterns at timescales of tens and hundreds of milliseconds. Furthermore, extracellular recordings in monkeys demonstrate pronounced responsiveness to deviant click trains at longer temporal scales in the primary auditory cortex (A1), accompanied by synchronization with both individual clicks and click trains. By contrast, neurons in the auditory thalamus prefer individual clicks only. Notably, neurons in A1 exhibit the ability to synchronize with individual clicks while simultaneously integrating these clicks into cohesive train objects, a phenomenon we term “temporal integration during synchronization”. Additional human electroencephalography recordings complement and support these findings, highlighting the paradigm’s potential for clinical applications. Our research offers novel insights into the neural mechanisms underpinning auditory information processing across various temporal scales at the neuronal level.

Alcohol use disorder (AUD) is a chronic relapsing brain disorder characterized by an impaired ability to stop or control alcohol consumption despite adverse social, occupational, or health consequences. AUD affects nearly one-third of adults at some point during their lives, with an associated cost of approximately $249 billion annually in the U.S. alone. The effects of alcohol consumption are expected to increase significantly during the COVID-19 pandemic, with alcohol sales increasing by approximately 54%, potentially exacerbating health concerns and risk-taking behaviors. Unfortunately, existing pharmacological and behavioral therapies for AUD are associated with poor success rates, with approximately 40% of individuals relapsing within three years of treatment.Pre-clinical studies have shown that chronic alcohol consumption leads to significant changes in synaptic function within the dorsal medial striatum (DMS), one of the brain regions associated with AUD and responsible for mediating goal-directed behavior. Specifically, chronic alcohol consumption has been associated with hyperactivity of dopamine receptor 1 (D1) medium spiny neurons (MSN) and hypoactivity of dopamine receptor 2 (D1) MSNs within the DMS. Optogenetic, chemogenetic, and transgenic approaches have demonstrated that reducing the D1/D2 MSN signaling imbalance decreases alcohol self-administration in rodent models of AUD.Here, we present an electrical stimulation approach that uses ultra-low (≤ 1 Hz) frequency (ULF) spike-timing-dependent plasticity (STDP) in mouse models of AUD to reduce DMS D1/D2 MSN signaling imbalances by stimulating D1-MSN afferents into the GPi and ACC glutamatergic projections to the DMS in a time-locked stimulation sequence. Our data suggest that GPi/ACC ULF-STDP selectively decreases DMS D1-MSN hyperactivity leading to reduced alcohol consumption without evoking undesired affective behaviors using electrical stimulation rather than approaches requiring genetic modification. This work represents a step towards fulfilling the unmet need for a reliable method of treating severe AUD through cell-type-specific control with clinically available neuromodulation tools.