bioRxiv Subject Collection: Neuroscience's Journal

TMEM145 is a key component in stereociliary link structures of outer hair cells
Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane-attachment crowns (TM-ACs), anchoring the tallest stereocilia to the tectorial membrane. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identified TMEM145, a transmembrane protein with a Golgi dynamics (GOLD) domain, as a crucial OHC stereocilia component. TMEM145 was expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibited profound hearing impairment at three weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy revealed the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacted with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 was undetectable in stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

Eye blinks synchronize with musical beats during music listening
Auditory-motor synchronization, the alignment of body movements with rhythmic patterns in music, is a universal human behavior, yet its full scope remains incompletely understood. Through four experiments with 123 young non-musicians, integrating eye-tracking, neurophysiological recordings, white matter structural imaging, and behavioral analysis, we reveal a previously unrecognized form of synchronization: spontaneous eye blinks synchronize with musical beats. Blinks robustly synchronized with beats across a range of tempi and independently of melodic cues. EEG recordings revealed a dynamic correspondence between blink timing and neural beat tracking. Individual differences in blink synchronization were linked to white matter microstructure variation in the left arcuate fasciculus, a key sensorimotor pathway. Additionally, the strength of blink synchronization reflected the modulation of dynamic auditory attention. These findings establish blink synchronization as a novel behavioral paradigm, expanding the auditory-motor synchronization repertoire and highlighting the intricate interplay between music rhythms and oculomotor activity. This discovery underscores a cross-modal active sensing mechanism, offering new insights into embodied music perception, rhythm processing, and their potential clinical applications.

Functional specialisation of multisensory temporal integration in the mouse superior colliculus
Our perception of the world depends on the brain's ability to integrate information from multiple senses, with temporal disparities providing a critical cue for binding or segregating cross-modal signals. The superior colliculus (SC) is a key site for integrating sensory modalities, but how cellular and network mechanisms in distinct anatomical regions within the SC contribute to multisensory integration remains poorly understood. Here, we recorded responses from over 5,000 neurons across the SC's anatomical axes of awake mice during presentations of spatially coincident audiovisual stimuli with varying temporal asynchronies. Our findings revealed that multisensory neurons reliably encoded audiovisual delays and exhibited nonlinear summation of auditory and visual inputs, with nonlinearities being more pronounced when visual stimuli preceded auditory stimuli, consistent with the natural statistics of light and sound propagation. Nonlinear summation was crucial for population-level decoding accuracy and precision of AV delay representation. Moreover, enhanced population decoding of audiovisual delays in the posterior-medial SC, facilitated temporal discriminability in the peripheral visual field. Cross-correlation analysis indicated higher connectivity in the medial SC and functional specific recurrent connectivity, with visual, auditory, and multisensory neurons preferentially connecting to other neurons of the same functional subclass, and multisensory neurons receiving approximately 50 percent of the total local input from other multisensory neurons. Our results highlight the interplay between single-neuron computations, network connectivity, and population coding in the SC, where nonlinear integration, distributed representations and regional functional specialisations enables robust sensory binding and supports the accurate encoding of temporal multisensory information. Our study provides new insights into how the brain leverages both single-neuron and network-level mechanisms to represent sensory features by adapting to the statistics of the natural world.

Motivational control is implemented by a cingulo-prefrontal pathway
The neuronal connections between the midcingulate cortex (MCC) and the dorsolateral prefrontal cortex (dlPFC) are associated with multiple cognitive functions, including rapid and long-term adaptive processes. Here we show that DREADD-mediated activation of MCC to dlPFC projection in macaques led to increased engagement in a foraging task, but did not alter their trial-to-trial adaptive strategy. We conclude that a critical role for MCC-dlPFC pathway is in the temporally extended control of behaviour rather than in rapid adaptation.

Connectome architecture favours within-module diffusion and between-module routing
Connectomes are the structural scaffold for signalling within nervous systems. While many network models have been proposed to describe connectome communication, current approaches assume that every pair of neural elements communicates according to the same principle. Connectomes, however, are heterogeneous networks, comprising elements with varied topological and neurobiological makeups. In this paper, we investigate how connectome architecture may facilitate different signalling regimes depending on the topological embedding of communicating neural elements. Specifically, we test the hypothesis that the modular structure of brain networks fosters a dual mode of communication balancing diffusion-passive signal broadcasting - and routing - selective transmission via efficient paths. To this end, we introduce the relative diffusion score (RDS), a measure to quantify the proportional capacity for network communication via diffusion versus routing. We examined the interplay between RDS and connectome architecture in 6 organisms spanning a wide range of spatial resolutions and connectivity mapping techniques - from the complete nervous system of the larval fly to the inter-areal human connectome. Our analyses establish multiple lines of evidence suggesting that connectomes may be universally organised to support within-module diffusion and between-module routing. Using a series of rewiring null models, we untangle the contributions of connectome topology and geometry to the relationship between routing, diffusion and modular architecture. In conclusion, our work puts forth a hybrid conceptualisation of neural communication, in which diffusion contributes to functional segregation by concentrating information within localised clusters, while specialised signal routes enable fast, long-range and cross-system functional integration.

Identifying Neurobiological Psychosis Biotypes Using Multi-Scale Functional Network Connectivity and its Latent Independent Subspace
Psychotic disorders present a great amount of biological heterogeneity. We explore this by leveraging multiscale functional network connectivity (msFNC) to identify distinct neurobiological psychosis biotypes. Resting-state fMRI data from 2103 B-SNIP 1&2 participants (1127 with psychosis, 350 relatives, 626 controls) were analyzed to obtain subject-specific multiscale intrinsic connectivity networks (msICNs) and compute msFNCs. A low-dimensional neurobiological subspace of multiscale connectivity features termed Latent Network Connectivity (LNC) was identified, consisting of three components (cognitive-related, typical, psychosis-related). Projections of psychosis participants' msFNC onto this subspace revealed three distinct biotypes through unsupervised learning. These biotypes, characterized by cognitive, clinical, and connectivity profiles, spanned all DSM diagnoses (Schizophrenia, Bipolar, Schizoaffective disorders), revealing their overlapping connectivity profiles. Biotype-1, the most cognitively impaired compared to other biotypes, showed Cerebellar-Subcortical and Visual-Sensorimotor hypoconnectivity, alongside Visual-Subcortical hyperconnectivity. Biotype-2 was most cognitively preserved and showed Visual-Subcortical, Subcortical-Sensorimotor, and Subcortical-Higher Cognition hypoconnectivity. Biotype-3 exhibited intermediate cognitive function, showing Cerebellar-Subcortical hypoconnectivity alongside Cerebellar-Sensorimotor and Subcortical-Sensorimotor hyperconnectivity. Notably, unaffected relatives displayed intermediate connectivity patterns, with 55% classified into the same biotype group as their affected family member--a significantly higher rate than random chance (p-valueRelatives-to-Biotype-1 < 0.001, p-valueRelatives-to-Biotype-2 < 0.05, p-valueRelatives-to-Biotype-3 < 0.001) compared to a non-significant 37% alignment using DSM-based diagnosis. Cognitive performance reliably aligns with distinct brain connectivity patterns, which are also evident in unaffected relatives, supporting their construct validity. These findings underscore the limitations of DSM-based classifications in capturing the biological complexity of psychotic disorders and highlight the potential of neurobiological biotypes to enhance our understanding of their spectrum.

ELECTROPHYSIOLOGICAL CORRELATES OF CONSCIOUS EXPERIENCES DURING SLEEP: LUCID DREAMS, SLEEP PARALYSIS, OUT-OF-BODY EXPERIENCES, AND FALSE AWAKENINGS
Consciousness does not always fade during sleep. Instead, it can re-emerge, giving rise to lucid dreams (LDs), sleep paralysis (SP), out-of-body experiences (OBEs), and false awakenings (FAs). While some of these states have been studied phenomenologically, their neurophysiological underpinnings remain unclear. Here, we investigate their electrophysiological correlates and distinguish them from standard sleep stages. We conducted overnight polysomnography in frequent experiencers, capturing 10 episodes (3 LDs, 2 SP, 2 OBEs, 3 FAs). Eye movement markers identified periods of lucidity. Relative spectral power was analyzed using principal component analysis (PCA) and permutation-based multivariate analysis of variance (PERMANOVA). Our results indicate that these conscious sleep states are distinct from wakefulness, yet share features with both stage 1 (S1) and rapid eye movement (REM) sleep. Notably, we provide the first documented eye movement markers during FAs and OBEs.

The NIH BRAIN Initiative's Experiment in Team Research
The NIH BRAIN Initiative is aimed at revolutionizing our understanding of the human brain. Presented here is an impact analysis of the BRAIN Initiative Team-Research BRAIN Circuits Program as an experiment in supporting team research in Neuroscience.

Hemispherotomy: a cortical island of sleep-like activity in awake humans
Hemispherotomy is a neurosurgical procedure for treating refractory epilepsy, which entails disconnecting a significant portion of the cortex, potentially encompassing an entire hemisphere, from its cortical and subcortical connections. While this intervention prevents the spread of seizures, it raises important questions. Given the complete isolation from sensory-motor pathways, it remains unclear whether the disconnected cortex retains any form of inaccessible awareness. More broadly, the activity patterns that large portions of the deafferented cortex can sustain in awake humans remain poorly understood. We address these questions by exploring for the first time the electrophysiological state of the isolated cortex before and after surgery in ten awake pediatric patients. Post-surgery, the isolated cortex exhibited prominent slow oscillations (<2 Hz) and a broad-band shift in power spectral density from high to low frequencies. This resulted in a marked decrease of the spectral exponent, a validated consciousness marker, indicating broad-band slowing characteristic of unconscious states. When compared with a reference pediatric sample across the sleep-wake cycle, the spectral exponent of the contralateral cortex aligned with wakefulness, whereas that of the isolated cortex was consistent with deep NREM sleep. However, spindles did not emerge in the isolated cortex due to the lack of subcortical inputs, constituting a fundamental difference from physiological sleep. These findings demonstrate a unihemispheric sleep-like state during wakefulness, challenging the possibility that hemispherotomy might lead to inaccessible "islands of awareness." Moreover, the persistence of sleep-like patterns years after disconnection provides unique insights into the electrophysiological effects of disconnections in the human brain.

Investigating the Role of Onchocerca ochengi in Epilepsy Development: A Gerbil Model Study
Background Onchocerca volvulus infection is linked to onchocerciasis-associated epilepsy (OAE) in humans, but the role of Onchocerca ochengi in epilepsy development remains unexplored. This study aimed to investigate whether O. ochengi infection contributes to epilepsy development. Methodology/Principal Findings Gerbils were implanted with O. ochengi worm masses (test group) or underwent sham surgery (control group). Behavioral and physical assessments were performed between days 15-19 using multiple tests, including the elevated plus maze, open-field, object recognition, and hanging wire tests. On day 21, gerbils were sacrificed, and body/organ weights were recorded, along with worm mass survival. Implantation of 15 worm masses resulted in 100% mortality in the test group, while implantation of 10 worm masses resulted in 53.3% mortality, with all control animals surviving. At day 21, worm mass survival averaged 1.4 out of 10, with a viability score of 93.3%. Test animals showed significant reductions in body weight and increased spleen weight compared to controls, but no significant behavioral differences were observed. Conclusions/Significance While O. ochengi infection caused notable physical effects, including high mortality and changes in body/organ weights, no behavioral evidence of epilepsy was observed. The high mortality rate and limited observation period restrict the interpretation of these findings. Further studies with larger cohorts and longer observation periods are needed to assess the potential role of Onchocerca spp. in epilepsy development. To the best of our knowledge, this study represents the first attempt to establish an animal model for OAE.

Identification of V0g propriospinal neurons and their role in locomotor control
Propriospinal neurons relay sensory and motor information across the spinal cord and are critical components of the circuits coordinating body movements. Their diversity and roles in motor control are not clearly defined yet. In this study, by combining anatomical, molecular, and functional analyses in mice, we identified and characterized an ascending subtype of propriospinal neurons belonging to the Pitx2+ V0 family of spinal neurons. We found that Pitx2+ ascending neurons are integrated in spinal sensorimotor circuits and their function is important for the execution of precise limb movements required for effectively moving in challenging environments, like walking on a horizontal ladder or a balance beam. This work advances our understanding of the functional organization of propriospinal and V0 neurons, highlighting a previously unappreciated role in adjusting body movements to the more demanding needs of skilled locomotor tasks.

Virus-against-virus dominant-negative interference strategy targeting a viral CC chemokine prevents cytomegalovirus-related neurodevelopmental pathogenesis
Background: Congenital cytomegalovirus (CMV) infections are one leading cause of human neurodevelopmental disorders. Increasing evidence for the pathogenic involvement of brain immune alterations was obtained in the recent years. Host and virus-encoded chemokines might play important roles in CMV-related neuropathogenesis by regulating leukocyte trafficking and microglia recruitment in the CMV-infected brains, and by interfering with key neurodevelopmental steps. In a rat model of CMV infection of the fetal brain in utero that leads to detrimental neurologic and other severe phenotypes postnatally, we reported on the early alteration of microglia and on the infiltration of the infected brains by lymphoid and myeloid cells. Particularly, expression of the r129 gene encoding the viral chemokine RCK3 was detected as early as 24h post-infection; together with the previously reported chemotaxis properties exerted by RCK3 on lymphocytes and on macrophages in vitro, this suggested that RCK3 might be involved in the brain immune cell alterations seen in the CMV-infected developing brains, and in the related neuropathogenesis. Methods: Infection of the rat fetal brain was done by intracerebroventricular injections in utero of either rat CMV encoding wild-type (wt) RCK3 (RCMV-wt), or a mutant CMV counterpart encoding RCK3 with a deletion in its chemokine domain (RCMV-r129{triangleup}NT). As RCMV-r129{triangleup}NT had shown dominant-negative effects on the chemotaxis properties of RCK3 in vitro, simultaneous and successive co-infection rescue assays were also performed. The detrimental postnatal phenotypes in vivo and the epileptiform activity ex vivo usually detected after infection of the rat developing brain with RCMV-wt were monitored in the RCMV-r129{triangleup}NT condition and in co-infection assays. Results: In sharp contrast with RCMV-wt whose infection of the fetal brain led to decreased postnatal survival, impaired sensorimotor development, hindlimb hyperextension and epileptic seizures in neonatal pups, RCMV-r129{triangleup}NT infection was not associated with any severe postnatal phenotype in vivo. Consistently, the epileptiform activity recorded in most neocortical slices from RCMV-wt-infected pups was not detected in any slice from RCMV-r129{triangleup}NT-infected pups. Simultaneous co-infection assays led to dramatic prevention against the postnatal phenotypes in vivo and the altered network activity ex vivo, revealing a dose-dependent rescuing effect exerted by RCMV-r129{triangleup}NT on RCMV-wt. Importantly, successful rescue was also obtained when the mutant RCMV-r129{triangleup}NT was inoculated in the fetal brains either before or after infection with RCMV-wt. Significance: Our data demonstrate the crucial neuropathogenic role of RCK3 CMV chemokine in vivo. The dramatic success and apparent safety of the dominant-negative RCK3 rescue assays in vivo provide a proof-of-principle for the beneficial use of a virus-against-virus approach against CMV-related pathogenesis.

Gpnmb Defines a Phagocytic State of Microglia Linked to Neuronal Loss in Prion Disease
The reaction of different cell types to prion infections is highly heterogeneous. While neurons experience spine retraction and eventually death, astrocytes and microglia undergo strong activation and proliferation. Here we analyzed the cell-type specific responses to prion diseases by establishing a spatiotemporal transcriptomic atlas of mice infected with RML prion strain. Brain areas with severe neuronal loss, such as thalamus and cerebellum, experienced intense microgliosis. Starting from 30 weeks post-inoculation, we observed the accumulation of a novel microglial subpopulation characterized by strong expression of Gpnmb in these brain regions. The molecular profile of Gpnmb+ microglia reflected a state of enhanced phagocytic activity with upregulation of genes associated with lysosomal function and degradation, including vacuolar ATPase V0 domain subunit d2 (Atp6v0d2) and Galectin-3 (Lgals3). In murine BV2 cells, Gpnmb upregulation was induced by soluble find-me signals released during apoptosis, but not by apoptotic bodies or prion accumulation. Gpnmb ablation in BV2 cells impaired their ability to phagocytose apoptotic cells, underscoring its essential role in maintaining microglial phagocytosis. Our findings define Gpnmb microglia as a distinct, apoptosis-driven phagocytic state, linking neuronal loss to microglial activation in prion disease. The upregulation of GPNMB in sCJD patients, along with its role in apoptotic clearance and lysosomal function, positions it as both a key regulator of microglial responses and a potential biomarker of disease progression.

Presaccadic modulation of lateral interactions
Lateral interactions are pervasive in early visual processing, contributing directly to processes such as object grouping and segregation. This study examines whether saccade preparation - known to affect visual perception - modulates lateral interactions. In a psychophysical task, participants were instructed to detect a Gabor target flanked by two adjacent Gabors, while they either prepared a saccade to the target or maintained central fixation. Flanker gratings could be iso- or orthogonally oriented to the target and were positioned at three different distances (4{lambda}, 8{lambda}, and 16{lambda}). Contrast thresholds for target detection were estimated in each condition using a 3-down/1-up staircase procedure. The results showed that in both presaccadic and fixation conditions, the target was suppressed at the shortest flanker distance (4{lambda}), revealed by markedly higher thresholds in iso-oriented compared to orthogonal flanker configurations. Lateral interaction effects were completely abolished at their largest separation (16{lambda}). Interestingly, at the intermediate flanker distance (8{lambda}), we observed an increase in suppression of targets presented during the presaccadic period, but not in the fixation condition. This result suggests that saccade preparation can modulate lateral interactions, promoting suppressive effects over larger distances. These findings are consistent with the visual remapping phenomenon observed before saccade execution, especially the convergent remapping of receptive fields in oculomotor and visual areas. Finally, this presaccadic expansion of inhibitory lateral interactions could assist target selection by suppressing homogeneous peripheral signals - such as iso-oriented collinear patterns - while prioritizing the processing of more salient visual information.

Time-to-onset and temporal dynamics of EEG during breath-watching meditation
Introduction: Mind-body practices, such as meditation, enhance mental well-being. Research studies consistently demonstrate improved brain function and psychological well-being in meditation practitioners. A substantial body of neuroscientific evidence highlights changes in alpha and theta frequency bands during meditation among practitioners. Neurophysiological effects of meditation are reported as average power changes from resting to meditative states. However, there is a notable gap in research concerning the time-to-onset and temporal dynamics of these changes during meditation. Method: Our study addresses this gap by recording high-density 128-channel EEG data during breath-watching meditation in three groups: meditation-naive controls (n = 28), novice meditators (n = 33), and advanced meditators (n = 42). Meditators were trained in the Isha Yoga tradition. Real-time changes in brain power across different frequency bands were analyzed by segmenting the EEG data into 1-minute intervals. Using the first 30 seconds of breath-watching as the baseline, we calculated within-group power differences between this baseline and successive 1-minute segments (non-overlapping, non-sliding windows). For between-group comparisons, we assessed power differences among the three groups at 0.5, 3, 6, and 9 minutes. Results: Our results indicate that time-to-onset of statistically significant increases in alpha, theta, and beta1 power, as well as decreases in delta and gamma1 power, occur around the 2-3 minute mark, with effects starting to peak between 7- and 10-minutes duration across all three groups. Statistically significant differences were observed between groups in the magnitude of these changes: advanced practitioners exhibited higher theta and theta-alpha power at all time points compared to the other groups. Conclusion: Our findings suggest that neurophysiological changes begin around 2-3 minutes after starting meditation and peak around 7-10 minutes across all three groups. However, the magnitude of these effects is greater in the advanced meditator group. As long as meditation retreats are not possible for many individuals, brief meditation practices of 7 minutes or more, delivered through digital platforms, could offer accessible, effective, and scalable solutions to improve mental well-being. This suggests a broader application of meditation practices in daily life, encouraging even those with tight schedules to incorporate such beneficial practices.

The Influence of Spatial Frequencies, Orientation and Familiarity on Face Stimuli Integration
When we observe an object, our visual system identifies its shape and integrates it with specific details to form a coherent representation. This coarse-to-fine approach involves rapid processing of low spatial frequency (LSF) content to generate a basic template, which aids the integration of the more detailed high spatial frequency (HSF) information. Here we explore with two experiments how the contribution of LSF and HSF integration extends to face processing. To do so, we leveraged the face inversion effect, whereby inverted faces are more difficult to recognize than upright ones. In Experiment 1, ten participants matched two familiar faces displayed in rapid succession (template and probe face, respectively). The template and the probe shared either the same SF (congruent) or had complementary SF (incongruent). In congruent conditions, HSF templates yielded better matching accuracy than LSF templates. However, in incongruent conditions, mapping LSF probes onto HSF templates was more effective, but only for upright faces. We propose that, depending on the task, holistic processing may be facilitated by detailed information. In Experiment 2, twelve participants performed the same task with both familiar and unfamiliar faces. While for familiar faces the effects were the same as Experiment 1, for unfamiliar faces the overall accuracy was better for congruent than incongruent conditions, and, crucially, it was independent of the template SF. Our results challenge the view that LSF content provides a foundational template for integrating HSF information, and instead suggest a flexible encoding of SF information, that depends on image contingencies.

Incorporation of complex narratives into dreaming
Reactivation of waking neuronal activity during sleep holds a functional role in memory consolidation. Reprocessing of daytime memory in dreams might aid later memory performance in a similar way. Numerous findings hint at a link between dreaming and sleep-dependent memory processing, however, studies investigating day-residue incorporation in dreaming led to mixed results so far. In this study, we used a naturalistic learning paradigm aimed at biasing dream content by manipulating pre-sleep experience. Participants listened to one of four different audiobooks while falling asleep and were awoken several times during the night to report their dreams. Afterwards, we tested how well they remembered the content of the audiobook. We then asked three blind raters to guess, based solely on anonymized dream reports, which audiobook someone had listened to before experiencing a dream. Our findings show that dreams across the whole night and from both NREM and REM awakenings contain specific information about the content of narratives studied before sleep. Moreover, if participants dreamt of the audiobook, they retained the content better across the sleep period. Finally, memory performance was lower when the experimental situation was incorporated into dreams, regardless of the presence of audiobook content, suggesting competitive reprocessing between audiobook and experimental memory representations.

Induction of Chimera States in Hindmarsh-Rose Neurons through Astrocytic Modulation: Implications for Learning Mechanisms
Chimera states, a form of partial synchronization in neural networks, are characterized by the coexistence of synchronized and asynchronous regions. These states are crucial for various cognitive functions, such as learning and information processing. Conversely, abnormal synchronization often referred to as hyper synchronization can lead to pathological conditions such as epilepsy and Parkinson disease. Understanding the mechanisms underlying synchronization can provide valuable insights for developing effective therapeutic strategies for these disorders. Astrocyte, a primary type of glial cell, plays a pivotal role in modulating neural synchrony. They influence the synchronization threshold of neurons by providing feedback through the release of gliotransmitters, promoting group firing of neurons within the domain of astrocyte. This research aims to explore how astrocytes can facilitate the conversion of hyper-synchronized states into healthy chimera states within neural networks. This process is vital for maintaining normal brain function and may be critical to advancing treatments for neurological conditions. We analyzed how astrocytes can induce chimera states in nonlocally two-dimensional Hindmarsh-Rose neurons, which serve as realistic models of neuronal ensembles. Our findings demonstrate that astrocytes can effectively transition unhealthy hyper synchronization states into healthy chimera states. Furthermore, by analyzing time spans, spatiotemporal patterns, inter spike interval distributions (ISI), and phase plane diagrams of 2D HR neurons, we validated our hypothesis about the crucial role of astrocytes in the development of chimera states. The outcomes may pave the way for innovative therapeutic approaches to restore normal neural activity patterns, ultimately improving patient outcomes in conditions such as epilepsy and Parkinson disease.

Rearing conditions bidirectionally modulate cognitive abilities and AP-1 signaling in hippocampal neurons in a cell type-specific manner.
Environmental conditions profoundly influence cognitive development, particularly during early life. Transcriptional and epigenetic mechanisms may serve as molecular substrates for the lasting effects of environmental enrichment (EE) and impoverishment (IE) on cognitive abilities and hippocampal function. However, the specific gene programs driving these changes remain largely unknown. In this study, EE and IE modulated the cognitive abilities of mice in opposing directions. By combining hippocampal microdissection and genetic tagging of neuronal nuclei with genome-wide analyses of gene expression, chromatin accessibility, histone acetylation, and DNA methylation, we uncovered profound differences in the transcriptional and epigenetic profiles of CA1 pyramidal neurons and dentate gyrus (DG) granule neurons. These analyses revealed cell type-specific genomic changes induced by EE and IE, highlighting distinct patterns of neuroadaptation within each population. This multiomic screen pinpointed the activity-regulated transcription factor AP-1 as a crucial mediator of neuroadaptation to conditions during early life in both cell types, albeit through distinct downstream mechanisms. Conditional deletion of Fos, a core AP-1 subunit, in excitatory neurons hampered EE-induced cognitive enhancement, further underscoring the pivotal role of this transcription factor in neuroadaptation.

Effects of treadmill exercise on retinal vascular morphology, function, and circulating immune factors in a mouse model of retinal degeneration
Purpose: Exercise is neuroprotective in rodents undergoing retinal degeneration (RD). However, the effects of exercise on retinal vasculature remain unexplored. Here, we investigate whether treadmill exercise influences retinal vascular morphology, function, gene expression, and circulating factors in a light-induced retinal degeneration (LIRD) mouse model. Methods: 6-week-old female BALB/c mice were assigned to inactive+dim, active+dim, inactive+LIRD and active+LIRD groups (n=20 per group). Active mice were treadmill exercised (1hr/d 10m/min) for two weeks, then LIRD was induced (5000 lux/4hrs). Inactive mice were placed on a static treadmill. Retinal neurovascular coupling was measured with functional hyperemia (FH) and vascular morphology using OCT-A. Vascular gene expression was quantified from isolated retinal endothelial cells using ddPCR five days following LIRD. Serum was collected for circulating cytokine and chemokine analyses. Data were analyzed using 2-way ANOVA. Results: Retinal vessel vasodilation was significantly increased in active+LIRD mice compared to inactive+LIRD mice. Superficial and intermediate/deep vascular plexi from inactive+LIRD mice had significantly decreased vessel density and total vessel length, with increased numbers of end points and lacunarity compared to active groups. Isolated retinal endothelial cell gene expression varied among groups. Most notably, Active+LIRD mice had a distinct immune response profile, with increased expression of IL-6, KC, and VEGF-A. Conclusions: Treadmill exercise maintained retinal vascular morphology and function, modestly altered endothelial gene expression, and is associated with a specific circulating immune response profile in a LIRD mouse model. These data indicate therapeutic effects of exercise on retinal vasculature in RD.

Mapping Anhedonia-Related Damage Network: Insights for TMS Treatment
Background: Many studies have explored anhedonia-related functional connectivity (FC), but the findings remain inconsistent. There is a gap in identifying a consistent anhedonia-related damage network and applying it to TMS treatment. Methods: We systematically reviewed studies on anhedonia-related functional connectivity and identified anhedonia-related brain damage locations. Using a novel functional connectivity network mapping approach applied to a large normative connectome dataset, we mapped these damage locations to anhedonia-related damage networks. Subsequently, transcriptomic analysis was conducted to uncover underlying molecular mechanisms. Additionally, we investigated the application of the anhedonia-related damage network in transcranial magnetic stimulation (TMS) treatment, focusing on changes in FC within this network following TMS treatment and its association with anhedonia improvement, as well as predicting TMS treatment efficacy based on baseline FC within the anhedonia-related damage network. Results: A total of eight experiments from seven studies using the nucleus accumbens (NAc) as the seed were eligible for functional connectivity network mapping analysis. This study identified an anhedonia-related damage network, primarily characterized by disrupted functional connectivity between the NAc and the default mode network. Transcriptomic analysis revealed gene enrichment associated with synaptic signaling, neuronal development, ion transport, and actin cytoskeleton regulation. TMS treatment increased NAc functional connectivity within the anhedonia-related damage network in the response group, with these changes correlating with improvements in anhedonia. Furthermore, baseline NAc FC within this network demonstrated predictive potential for TMS treatment efficacy. Conclusion: The anhedonia-related damage network was identified, emphasizing its underlying mechanisms and predictive value for TMS in treating anhedonia.

High density probes reveal medullary seizure and rapid medullary shutdown in a model of fatal apnea in seizure
Objective: Sudden unexpected death in epilepsy (SUDEP) is suggested to be a cardiorespiratory collapse that occurs shortly after a seizure. Prior work in rats suggests that reflexive apneas (produced by stimulation of trigeminal or vagal peripheral sensory targets) is highly fatal during seizure but well tolerated otherwise. These reflexes share network connectivity in the medulla, particularly the caudal solitary nucleus (NTS) and ventral respiratory column (VRC), and possibly other intermediate structures. We sought to observe the electrographic activity in these regions. Methods: We use urethane anesthetized long evans rats. We utilized either 125 m silver wire in the caudal NTS or a Neuropixel 1.0 probe along a dorsoventral trajectory that spanned the caudal NTS to the VRC. We additionally recorded cardiorespiratory activity via several methods. We induced a reflexive apnea - the diving reflex - by nasal irrigation of cold water for several seconds, which produces a period of apnea, then gasping, and then a gradual return to eupnea. We repeated several trials while the animal was healthy and subsequently induced continuous seizure activity with kainate and repeated the reflexes, which are ultimately fatal during seizure. Results: Seizure activity confounds many established methods of analyzing high-density single unit data such as provided by Neuropixels probes, and so our analyses focus on averaging responses over larger anatomical regions (120 m) covering small populations of neurons. Seizure produces broad increases in neuronal activity across the medullary tract, which by itself is not dangerous. Ictal reflexive apneas were broadly more inhibitory (producing a reduction in firing rate) than they were preictally, and fatal ictal responses resulted in a very rapid shutdown of all medullary activity. We only rarely observed ictal central apneas (apneas with no apparent stimuli), but when we did they were apparently safe, always survived, and produced no significant change in network activity (neither increase nor decrease). Conclusions: These data support the theory that central apnea events in seizure are relatively safe as we observed they produce little change in the medullary tract network, while stimuli-induced-reflexive-apneas are dangerous because they produce profound quieting across respiratory centers. Our data suggest that seizure spreads to this medullary tract at approximately the same rate and intensity as forebrain, as previously described in this model. These data are supportive of SUDEP mechanisms involving brainstem inhibition as a primary cause, such as spreading depolarization waves. These findings likely extend beyond nasal irrigation to any sensory reflexive apnea caused by airway irritation of any kind, and may bear relevance to similar deaths seen in infants.

Dynamic nanoscale architecture of synaptic vesicle fusion in mouse hippocampal neurons
During neurotransmission, presynaptic action potentials trigger synaptic vesicle fusion with the plasma membrane within milliseconds. To visualize membrane dynamics before, during, and right after vesicle fusion at central synapses under near-native conditions, we developed an experimental strategy for time-resolved in situ cryo-electron tomography with millisecond temporal resolution. We coupled optogenetic stimulation with cryofixation and confirmed the stimulation-induced release of neurotransmitters via cryo-confocal microscopy of a fluorescent glutamate sensor. Our morphometric analysis of tomograms from stimulated and control synapses allowed us to characterize five states of vesicle fusion intermediates ranging from stalk formation to the formation, opening, and collapsing of a fusion pore. Based on these measurements, we generated a coarse-grained simulation of a synaptic vesicle approaching the active zone membrane. Both, our morphofunctional and computational analyses, support a model in which calcium-triggered fusion is initiated from synaptic vesicles in close proximity to the active zone membrane, whereby neither tight docking nor an induction of membrane curvature at the active zone are favorable. Numbers of filamentous tethers closely correlated to the distance between vesicle and membrane, but not to their respective fusion readiness, indicating that the formation of multiple tethers is required for synaptic vesicle recruitment preceding fusion.

A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations
Retinal ganglion cells (RGCs) transmit visual information from the eye to the brain. In mice, several RGC subtypes show nonuniform spatial distributions, potentially mediating specific visual functions. However, the full extent of RGC specialization remains unknown. Here, we used en-face cryosectioning, spatial transcriptomics, and machine learning to map the spatial distribution of all RGC subtypes identified in previous single-cell studies. While two-thirds of RGC subtypes were evenly distributed, others showed strong biases toward ventral or dorso-temporal regions associated with sky vision and the area retinae temporalis (ART), the predicted homolog of the area centralis. Additionally, we observed unexpected spatial variation in gene expression within several subtypes along the dorso-ventral axis or within vs. outside the ART, independent of RGC density profiles. Finally, we found limited correlations between the gene profiles of the ART and the primate macula, suggesting divergent specialization between the mouse and primate central vision.

Exposure to rotenone triggers redox driven systemwide lipidome alterations and metabolic tradeoffs linked to Parkinsons disease
With the global rise in aging populations, the increasing incidence of neurodegenerative diseases underscores concerns about brain health, with pesticides like rotenone, emerging as key environmental hazardous. The precise mechanism by which chronic environmental concentration of rotenone exposure causes Parkinson-like phenotype is not understood. Previous studies showed that rotenone induces depletion of dopaminergic neurons by influencing mitochondrial functions. Mitochondrial dysfunction alters lipid homeostasis; therefore, brain lipids can be potential targets for the early risk assessment and prognosis of Parkinsons disease (PD). However, the specific lipidome changes and associated biomarkers of chronic rotenone in vivo exposure causing PD are largely unknown. This study investigates the lipid profile disruptions and biomarkers induced by environmentally relevant concentrations of chronic rotenone exposure using the neuro-model Drosophila melanogaster. An untargeted LC-HRAMS-based lipidomics identified that lipid classes, GP, SP, FA and GL were significantly altered. Furthermore, system-wide loss of cross talk of mitochondrial and peroxisome lipids by altering their redox homeostasis causing PD was observed. Additionally, lipid oxidative stress markers, and behavior abnormalities correlated with altered lipids linked to PD. The findings highlight the rotenone induced complex metabolic trade-offs, prioritizing brains neural integrity at the expense of peripheral lipid levels, leading to PD.

Too little and too much: medial prefrontal functional inhibition impairs early acquisition of operant reversal learning, whereas medial prefrontal disinhibition impairs established serial-reversal performance in rats
Schizophrenia has been linked to hypofrontality (reduced prefrontal activation) and neural disinhibition (reduced GABAergic inhibition) within the dorsolateral prefrontal cortex (dlPFC), as well as reversal learning deficits. Interestingly, whilst reversal learning has been strongly linked to the orbitofrontal cortex, research suggests that the primate dlPFC - or its rodent analogue, the medial PFC (mPFC) - is less important for this process. Nevertheless, we hypothesized that the mPFC may be required for reversal learning if the reversal is particularly demanding. Furthermore, even if the mPFC is not required, mPFC disinhibition may impair reversals, because it may disrupt processing in mPFC projection sites. To test this, we induced mPFC functional inhibition and disinhibition in rats, using microinfusions of the GABA-A receptor agonist muscimol or antagonist picrotoxin, respectively, and examined the impact on early and serial reversals on a food-reinforced two-lever discrimination task. Using classical performance measures and Bayesian trial-by-trial strategy analysis, we found that mPFC functional inhibition impaired early, but not serial, reversals by increasing perseveration and impairing exploratory (lose-shift) behavior. In contrast, disinhibition impaired serial reversals, which was associated with reduction in both exploratory (lose-shift) and exploitative (win-stay) behavior. These findings suggest that mPFC hypoactivation and disinhibition disrupt distinct aspects of reversal learning by different mechanisms.

Ankyrins are essential for synaptic integrity of photoreceptors in the mouse outer retina
The mammalian visual system consists of two distinct pathways: rod- and cone-driven vision. The rod pathway is responsible for dim light vision whereas the cone pathway mediates daylight vision and color perception. The distinct processing of visual information begins at the first synapse of rod and cone photoreceptors. The unique composition and organization of the rod and cone synapse is what allows information to be parsed into the different visual pathways. Although this is a critical process for vision, little is known about the key molecules responsible for establishing and maintaining the distinct synaptic architecture of the rod and cone synapse. In the present study, we uncovered a new role for Ankyrins in maintaining the synaptic integrity of the rod and cone synapse. Loss of Ankyrin-B and Ankyrin-G results in connectivity defects between photoreceptors and their synaptic partners. Ultrastructure analysis of the rod and cone synapse revealed impaired synaptic innervation, abnormal terminal morphology, and disruption of synaptic connections. Consistent with these findings, functional studies revealed impaired in vivo retinal responses in animals with loss of Ankyrin-B and Ankyrin-G. Taken together, our data supports a new role for Ankyrins in maintaining synaptic integrity and organization of photoreceptor synapses in the mouse outer retina.

Spike sorting AI agent
Spike sorting is a fundamental process for decoding neural activity, involving preprocessing, spike detection, feature extraction, clustering, and validation. However, conventional spike sorting methods are highly fragmented, labor-intensive, and heavily reliant on expert manual curation, limiting their scalability and reproducibility. This challenge has become more pressing with advances in neural recording technology, such as high-density Neuropixels for large-scale neural recording or flexible electrodes for long-term stable recording over months to years. The volume and complexity of these datasets make manual curation infeasible, requiring an automated and scalable solution. Here, we introduce SpikeAgent, a multimodal large language model (LLM)-based AI agent that automates and standardizes the entire spike sorting pipeline. Unlike traditional approaches, SpikeAgent integrates multiple LLM backends, coding functions, and established algorithms, autonomously performing spike sorting with reasoning-based decision-making and real-time interaction with intermediate results. It generates interpretable reports, providing transparent justifications for each sorting decision, enhancing transparency and reliability. We benchmarked SpikeAgent against human experts across various neural recording technology, demonstrating its versatility and ability to achieve curation consistency that are equal to, or even higher than human experts. It also drastically reduces the expertise barrier and accelerates the curation and validation time by orders of magnitude. Moreover, it enables automated interpretability of the neural spiking data, which cannot be achieved by any conventional methods. SpikeAgent presents a paradigm shift in processing signals for neuroscience and brain-computer interfaces, while laying the ground for AI agent-augmented science across various domains.

Axonal Mechanotransduction Drives Cytoskeletal Responses to Physiological Mechanical Forces
Axons experience strong mechanical forces due to animal movement. While these forces serve as sensory cues in mechanosensory neurons, their impact on other neuron types remains poorly defined. Here, we uncover signaling that controls an axonal cytoskeletal response to external physiological forces and plays a key role in axonal integrity. Live imaging of microtubules at single-polymer resolution in a C. elegans motor neuron reveals local oscillatory movements that fine-tune polymer positioning. Combining cell-specific chemogenetic silencing with targeted degradation alleles to distinguish neuron-intrinsic from extrinsic regulators of these movements, we find that they are driven by muscle contractions and require the mechanosensitive protein Talin, the small GTPase RhoA, and actomyosin activity in the axon. Genetic perturbation of the axon's ability to buffer tension by disrupting the spectrin-based membrane-associated skeleton leads to RhoA hyperactivation, actomyosin relocalization to foci at microtubule ends, and converts local oscillations into processive bidirectional movements. This results in large gaps between microtubules, disrupting coverage of the axon and leading to its breakage and degeneration. Notably, hyperpolarizing muscle or degrading components of the mechanotransduction signaling pathway in the axon rescues cytoskeletal defects in spectrin-deficient axons. These results identify mechanisms of an axonal cytoskeletal response to physiological forces and highlight the importance of force-buffering and mechanotransduction signaling for axonal integrity.

Enhanced Neural Plasticity of the Primary Visual Cortex in Visual Snow Syndrome: Evidence from MEG Gamma Oscillations
Visual Snow Syndrome (VSS) is a neurological disorder characterized by persistent visual disturbances and associated symptoms. Although the neural basis of VSS remains poorly understood, it may involve increased neuronal excitability and/or altered neuroplasticity in the visual cortex, which could, in turn, affect visual gamma oscillations. An altered excitation-inhibition (E-I) balance is hypothesized to alter the modulation of gamma power and frequency by stimulation intensity, while maladaptive neuroplasticity may impact time-dependent changes in gamma power during repeated stimulation. To investigate potential alterations in E-I balance and neuroplasticity in VSS, we magnetoencephalography to record visual gamma oscillations in 26 VSS patients and 27 healthy controls. Participants were exposed to repeatedly presented high-contrast annular gratings, which were either static or drifting at varying speeds to systematically manipulate stimulation intensity. We also measured heart rate variability (HRV) during rest and repetitive visual stimulation to explore the relationship between time-dependent gamma changes and parasympathetic activation, which is known to promote activity-dependent plasticity. Our results showed no significant group differences in gamma power or frequency, nor in their modulation by drift rate, suggesting that the excitation-inhibition (E-I) balance in the primary visual cortex remains largely intact in VSS. Both groups exhibited an initial brief decrease in gamma power followed by a sustained linear increase with stimulus repetition, likely reflecting activity-dependent plasticity. HRV parameters were comparable across groups, with the parasympathetic-sympathetic balance index correlating with repetition-related increase in gamma power, further supporting the link between time-dependent gamma changes and neuroplasticity. Notably, VSS patients exhibited a steeper repetition-related increase in gamma power, indicating atypically heightened activity-dependent plasticity in this group. These findings provide the first experimental evidence suggesting that altered activity-dependent neuroplasticity plays a role in the pathophysiology of VSS. Furthermore, they identify repetition-related increases in gamma power as a potential biomarker of aberrant neuroplasticity, offering novel insights into VSS pathophysiology and potential avenues for targeted therapeutic interventions.

Humans can learn bimodal priors in complex sensorimotor behaviour
Extensive research suggests that humans integrate sensory information and prior expectations in a Bayesian manner to reduce uncertainty in perception and action. However, while Bayesian integration provides a powerful explanatory framework, the question remains as to what extent it explains human behaviour in naturalistic situations, including more complex movements and distributions. Here, we examine whether humans can learn bimodal priors in a complex sensorimotor task: returning tennis serves. Participants returned serves in an immersive virtual reality setup with realistic movements and spatiotemporal task demands matching those in real tennis. The location of the opponent's serves followed a bimodal distribution. We manipulated visual uncertainty through three levels of ball speeds: slow, moderate, and fast. After extensive exposure to the opponent's serves, participants' movements were biased by the bimodal prior distribution. As predicted by Bayesian theory, the magnitude of the bias depends on visual uncertainty. Additionally, our data indicate that participants' movements in this complex task were not only biased by prior expectations but also by biomechanical constraints and associated motor costs. Intriguingly, an explicit knowledge test after the experiment revealed that, despite incorporating prior knowledge of the opponent's serve distribution into their behaviour, participants were not explicitly aware of the pattern. Our results show that humans can implicitly learn and utilise bimodal priors in complex sensorimotor behaviour.

Retro Nasal blockade reduces the Neural Processing of Sucrose in the Human Brain
Traditionally, taste perception is understood to occur through taste receptors located in the oral cavity, particularly on the tongue. Recent findings suggest that taste compounds, when aerosolized, can reach the retro nasal olfactory region and be perceived. However, the neural mechanisms by which the human brain interprets taste stimuli via retro nasal pathways remain unclear. Healthy adults (N=34, Mean age 25 yrs.) were recruited. We examined neural activity during the tasting of sucrose with a nose clip on (to block retro nasal sensation) compared to when there was no nose clip. We examined whole brain data and ROIs involved in taste (insula, postcentral gyrus, amygdala), smell (olfactory cortex, piriform cortex) odour attention (sgACC) and multi-modal flavour processing (OFC) and reward (pgACC and nucleus accumbens). We also examined subjective ratings of pleasantness and fullness of the sucrose with and without the nose clip. We found that the nose clip condition reduced neural activity in primary taste and olfaction regions and regions involved in attention to odours, and food reward. When examining the whole brain activity, we also found reduced activity in the rolandic operculum, lingual gyrus and precuneus. The olfactory cortex and prefrontal cortex ROIs tracked the sucrose subjective fullness ratings, but this effect was not present with the nose clip on. In conclusion, our findings are the first to demonstrate that blocking retro nasal sensation with a nose clip significantly reduces the subjective and objective neural responses to sucrose taste. These findings support the idea that retro nasal sensations could play a role in the perception of sucrose taste. This study suggests that developing more satisfying low-sugar foods could be achieved by enhancing the perception of sweetness through aroma modulation.

The role of symmetry breaking in connectivity and neurodegeneracy in the brain's resting state dynamics
The functioning of brain networks can be broadly categorized as an interplay of two main contributors, namely the neurological processes dictating the local dynamics and the patterns of anatomical connections that enable the interactions between the various local processes, resulting in a global emergent behavior. Using Brain Network Modeling we describe the constraints of the anatomical structure upon the resting state dynamics of the human brain. We identify a low-dimensional representation of the brain states, the Resting State Manifold (RSM), and leveraging network degeneracy and its relationship to structural properties, we identify dynamic patterns supported by the RSM. Noise driven dynamics of the BNM are used to explore the manifold and validate the contours of degeneracy. We demonstrate that the patterns of degeneracy regulate the dynamics of the broader system in the presence of external and/or internal perturbations, revealing the productive relationship between emergent network processes and their constituent network entities.

The Relationship Between Visual Motion Detection Thresholds and Visual Sensitivity to Medial/Lateral Balance Control
The ability to differentiate between self-motion and motion in the environment is an important factor for maintaining upright balance control. Visual motion can elicit the sensation of a fall by cueing a false position sense. While there is evidence supporting the role of central vision and fall risk, including measures of contrast sensitivity, depth perception, and size of the visual field, the relationship between motion detection thresholds and balance control remains unknown. The aim of this study is to explore the relationship between visual motion detection thresholds (VMDTs) of the environment and measures of visual sensitivity to balance disturbances in the environment while walking. Thirty young adults (18-35 years) and thirty older adults (55-79 years) participated in a counter-balanced study where they 1) walked on a self-paced treadmill within a virtual environment that delivered frontal plane multi-sine visual disturbances at three amplitudes (6{degrees}, 10{degrees}, and 15{degrees}), and 2) performed 100 trials of a two-alternative forced choice (2AFC) task in which they discriminated between a counterclockwise (left) and clockwise (right) rotation of a visual scene under three conditions (standing, standing with optic flow, and walking). Visual sensitivity was measured using frequency response functions of the center of mass displacement relative to the screen tilt (cm/deg) while VMDTs were measured by fitting a psychometric curve to the responses of the 2AFC task. We found significant positive correlations between measures of visual sensitivity and VMDTs for 7 out of the 9 conditions in young adults, and nonsignificant positive correlations between the two measures in older adults. VMDTs were overall higher in older adults, although not significantly in the standing condition, indicating more motion in the environment is required for older adults to consciously perceive it. VMDTs also tended to increase from standing, standing with optic flow, and walking, although not significantly between the standing and standing with optic flow conditions for both populations. We interpret the positive correlations between the two measures as an indication that individuals with lower motion detection thresholds can more accurately differentiate between self-motion and motion in the environment, resulting in lower responses from visual disturbances in the environment.

Ketamine Alters Tuning of Neural and Behavioral Spatial Working Memory Precision
Deficits in working memory (WM) are a hallmark of neuropsychiatric disorders such as schizophrenia, yet their neurobiological basis remains poorly understood. Glutamate N-methyl-D-aspartate receptors (NMDARs) are critical for spatial WM (sWM), with NMDAR antagonist ketamine known to attenuate task-evoked activation and reduce sWM accuracy. Cortical microcircuit models hypothesize that NMDAR antagonism impairs sWM by broadening neural spatial tuning, but this mechanism has not been directly tested in humans. Using a pharmacological fMRI approach, we showed how ketamine broadened neural spatial tuning, attenuated activation across visual, parietal, and frontal areas, and worsened sWM performance in healthy humans. Ketamine-induced changes in tuning were more consistent across individuals and brain regions than changes in overall activation and correlated with individual differences in sWM performance. These findings provide empirical evidence linking NMDAR antagonism to disruptions in cortical microcircuit dynamics, the resulting neural tuning alterations, and sWM impairments, advancing frameworks for therapeutic development.

Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer's Disease
Single-cell multiomic technologies have allowed unprecedented access to gene profiles of individual cells across species and organ systems, including >1000 papers focused on brain cell types alone. The Allen Institute has created foundational atlases characterizing mammalian brain cell types in the adult mouse brain and the neocortex of aged humans with and without Alzheimer's disease (AD). With so many public cell type classifications (or 'taxonomies') available and many groups choosing to define their own, linking cell types and associated knowledge between studies remains a major challenge. Here, we introduce Annotation Comparison Explorer (ACE), a web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). ACE allows filtering of cells and includes an interactive set of tools for comparing two or more taxonomy annotations alongside collected knowledge (e.g., increased abundance in disease conditions, cell type aliases, or other information about a specific cell type). We present three primary use cases for ACE. First, we demonstrate how a user can assign cell type labels from the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) taxonomy to cells from their own study and compare these cell type mappings to existing cell type assignments and cell metadata. Second, we extend this approach to ten published human AD studies which we previously reprocessed through a common data analysis pipeline. This allowed us to compare brain taxonomies across otherwise incomparable studies and identify congruent cell type abundance changes in AD, including a decrease in abundance of subsets of somatostatin interneurons. Finally, ACE includes translation tables between different mouse and human brain cell type taxonomies publicly accessible on Allen Brain Map, from initial studies in individual neocortical areas to more recent studies spanning the whole brain. ACE can be freely and publicly accessed as a web application (https://sea-ad.shinyapps.io/ACEapp/) and on GitHub (github.com/AllenInstitute/ACE).

Astrocytic PI3Kα controls synaptic plasticity and cognitive function via serine metabolism
Astrocytes are known to modulate neuronal activity by gliotransmission and through metabolic regulation. However, the connection between these two processes is still poorly defined. In this work we show that the p110 isoform of the phosphatidylinositol 3-kinase (PI3K) in astrocytes is required for long-term potentiation (LTP) and has an impact on learning and memory. Using a specific deletion of p110 from hippocampal astrocytes in adult mice, we found that LTP depends on astrocytic p110 to sustain D-serine levels for the activation of NMDA receptors during LTP induction. This requirement is based on the L-serine biosynthetic pathway of the astrocyte, which is defective in the absence of p110 because of a reduced glycolytic flux. Accordingly, the behavioral impairment in mice lacking p110 can be rescued by in vivo administration of L-serine. These results link for the first time the function of PI3K in astrocytes to cerebral metabolism and its influence in synaptic plasticity and cognition.

The Link to Oxidative Metabolism Varies across rs-fMRI Metrics: A Whole-Brain Assessment Using Macrovascular Correction
One of the major obstacles to the clinical application of resting-state functional magnetic resonance imaging (rs-fMRI) is the complex nature of its measurements, which limits interpretability. An approach to enhance the interpretability of the rs-fMRI metrics is to link them to more fundamental brain physiology, especially cerebral metabolism. Previous studies have established associations between glucose metabolism (CMRglu) and rs-fMRI measurements. In spite of this, oxidative metabolism (CMRO2) is more closely related to cerebral blood flow (CBF) and thus the BOLD signal, and its relationship with CMRglu is complex. Additionally, most currently published rs-fMRI metrics are uncorrected for macrovascular contribution, which may obscure the neuronal contributions. In this study, we measured resting CMRO2 (along with the oxygen extraction fraction, OEF and cerebral blood flow, CBF) using gas-free calibrated fMRI. We used linear mixed-effects (LME) models to examine associations between CMRO2 and various rs-fMRI metrics before and after macrovascular correction. We found that: 1) significant associations exist between CMRO2 and multiple rs-fMRI metrics, with the strongest association found for the global functional density (gFCD) and the weakest for seed-based functional connectivity (FC); 2) associations with rs-fMRI metrics also varied for OEF and CBF; 3) significant sex differences were observed in the above associations; 4) the use of macrovascular correction substantially strengthened the goodness fit of all LME models examined. This latter improvement further validates the use of macrovascular correction in rs-fMRI. These results provide a framework for linking rs-fMRI metrics to fundamental brain physiology, thus improving interpretability of rs-fMRI measurements. This is the first study to formally link whole-brain MRI-based baseline CMRO2 and rs-fMRI metrics, and helps to push the envelope for rs-fMRI in future clinical applications.

Wearable MEG data recorded during human stepping
Non-invasive spatiotemporal imaging of brain activity during large-scale, whole body movement is a significant methodological challenge for the field of movement neuroscience. Here, we present a dataset recorded using a new imaging modality, optically-pumped magnetoencephalography (OP-MEG), to record brain activity during human stepping. Participants (n=3) performed a visually guided stepping task requiring precise foot placement while dual-axis and triaxial OP-MEG and leg muscle activity (electromyography, EMG) were recorded. The dataset also includes a structural MRI for each participant and foot kinematics. We validate the fidelity of the OPM data by showing movement-related beta band desynchronization source localised to the primary motor cortex. This multimodal dataset offers a resource for methodological development and testing for OPM data (e.g., movement-related interference rejection), within-subject analyses, and exploratory analyses to generate hypotheses for further work on the neural control of human stepping.

Semiparametric Confidence Sets for Arbitrary Effect Sizes in Longitudinal Neuroimaging
The majority of neuroimaging inference focuses on hypothesis testing rather than effect estimation. With concerns about replicability, there is growing interest in reporting standardized effect sizes from neuroimaging group-level analyses. Confidence sets are a recently developed approach to perform inference for effect sizes in neuroimaging but are restricted to univariate effect sizes and cross-sectional data. Thus, existing methods exclude increasingly common multigroup or nonlinear longitudinal associations of biological brain measurements with inter- and intra-individual variations in diagnosis, development, or symptoms. We broadly generalize the confidence set approach by developing a method for arbitrary effect sizes in longitudinal studies. Our method involves robust estimation of the effect size image and spatial and temporal covariance function based on generalized estimating equations. We obtain more efficient effect size estimates by concurrently estimating the exchangeable working covariance and using a nonparametric bootstrap to determine the joint distribution of effect size across voxels used to construct confidence sets. These confidence sets identify regions of the image where the lower or upper simultaneous confidence interval is above or below a given threshold with high probability. We evaluate the coverage and simultaneous confidence interval width of the proposed procedures using realistic simulations and perform longitudinal analyses of aging and diagnostic differences of cortical thickness in Alzheimer's disease and diagnostic differences of resting-state hippocampal activity in psychosis. This comprehensive approach along with the visualization functions integrated into the pbj R package offers a robust tool for analyzing repeated neuroimaging measurements.

Tissue damage-induced axon injury-associated responses in sensory neurons - requirements, prevention, and potential role in persistent post-surgical pain
Pain resulting from tissue damage, including surgical incision, is often only partially responsive to standard treatments focusing on inflammation, suggesting additional mechanisms are involved. Tissue damage leads to expression in dorsal root ganglion (DRG) sensory neurons of genes associated with axonal injury and regeneration, most notably activating transcription factor 3 (ATF3) and GAP-43. ATF3 expression is associated with sensitization of cellular physiology and enhanced amplitude/duration of a nociceptive reflex. It is unclear how tissue damage leads to these changes in the sensory neurons, but it could include direct damage to the tissue-innervating axons and inflammation-associated retrograde biochemical signalling. Using the CTM reflex to map innervation fields, we examined the necessity and sufficiency of incision, inflammation, and axonal conduction for induction of ATF3 in response to skin incision. Incision outside the innervation field, but close enough to induce inflammation inside the innervation field, was not sufficient to induce ATF3 expression in the field-innervating DRG. Incision inside the innervation field led to strong expression of ATF3. Anti-inflammatory treatments did not prevent this induction of ATF3. In rodent models of repeated injury - a major etiological factor for chronic pain - ATF3 expression was synergistically-increased and the threshold for paw-withdrawal to mechanical stimulation was significantly decreased for an extended duration. Together, these results suggest that actual damage to axons innervating the skin is both necessary and sufficient for induction of ATF3, expression of which appears additionally increased by repeated injury. Further, pre-treatment of the nerves innervating the incised skin with bupivacaine, a local anesthetic commonly used to reduce surgical pain, did not prevent induction of ATF3, indicating that conduction of action potentials is not necessary for induction of ATF3. We also determined that closure of incision with surgical glue significantly reduced incision-induced expression of GAP-43. Intriguingly, treatment with polyethylene glycol (PEG), known to enhance membrane integrity after injury among other effects, reduced incision-associated ATF3 expression and electrophysiological changes. These results suggest that pain resulting from tissue damage may arise from a mix of ATF3-/axonal-damage-associated mechanism as well as ATF3-independent inflammation-related mechanisms and therefore require a mix of approaches to achieve more complete control.

Fast adaptation in invertebrate looming-sensitive descending neurons
Motion vision plays a crucial role in guiding dynamic behaviors, such as determining when to escape from predators, pursue prey, navigate obstacles, or adjust flight patterns during migration. Adaptation to repetitive motion stimuli is a crucial aspect of this process, allowing animals to efficiently process new stimuli while avoiding sensory overload. This helps animals remain responsive to novel or important stimuli, ensuring appropriate behavioral reactions. Adaptation to looming stimuli, which often signal an approaching threat through the rapid expansion of an object's image on the retina, allows animals to distinguish harmless from harmful stimuli. While neural adaptation has been extensively studied in the fly's optic lobes, less is known about how descending neurons, which link the optic lobes to the motor centers in the thoracic ganglia, adapt. To address this gap, we investigate adaptation in looming-sensitive descending neurons in the hoverfly Eristalis tenax. Using intracellular recordings, we show that these descending neurons adapt to looming stimuli with inter-stimulus intervals of 1-3 s. We show that the level of adaptation depends on the ISI, with shorter intervals leading to greater adaptation. Specifically, we find that adaptation leads to decreased response duration, with a pronounced delayed response onset. We identified descending neurons that responded to looming stimuli either unilaterally or bilaterally and used this to show that most of the adaptation takes place within the neuron itself, rather than its pre-synaptic inputs. Finally, we found that the wing beat amplitude of tethered hoverflies did not appear to adapt to repetitive looming stimuli.