bioRxiv Subject Collection: Neuroscience's Journal

Same bi-directional modulation of contrast appearance for voluntary presaccadic attention and involuntary exogenous attention
Different types of attention alter subjective visual perception in fundamentally distinct ways. Previous studies have focused on covert attention without concurrent eye movements, showing that covert exogenous (involuntary) attention enhances contrast appearance of low-contrast stimuli while diminishing that of high-contrast stimuli, whereas covert endogenous (voluntary) attention uniformly enhances contrast appearance. However, the attentional effect preceding saccadic eye movements, a critical component of natural vision, remain understudied. Here, we found that when participants voluntarily initiated saccades, presaccadic attention enhanced the appearance of low-contrast stimuli while attenuating the appearance of high-contrast stimuli (Experiment 1, N = 29 adults). This pattern is surprisingly similar to exogenous attention but distinct from endogenous attention. Notably, the presaccadic attentional attenuation effect accumulated gradually during saccade preparation and remained positively correlated with the exogenous attentional effect (Experiment 2, N = 24 adults). These findings suggest a shared mechanism between presaccadic and exogenous attention in shaping visual perception.

Bilingualism Modulates Executive Function Development in Pre-School Aged Children: A Preliminary Study
This preliminary study was conducted to explore the effects of bilingualism on executive function development in children ages 3 to 5 years old. Two groups (bilinguals and monolinguals) were recruited across various sites in Southern Alberta. Children were assessed through parent rated executive function using the Behaviour Rating Inventory of Executive Function Preschool version, a standardized assessment of executive function in children aged 2 years, 0 months through 5 years, 11 months. The questionnaire contains 63 items measuring 5 aspects of executive functioning, inhibit, shift, emotional control, working memory, and plan/organize. Children were also assessed using a battery of executive function tasks, which include the reverse categorization, pictorial Stroop, Dimensional Change Card Sort, backward digit span, and dyadic social play. Results show that bilingual children outperform monolinguals on the emotional control scale, dimensional change card sort and dyadic social play. Despite the controversial literature surrounding bilingualisms impact on executive function, the study reveals support for second language use to improve areas of executive function among young children.

Aperiodic neural excitation of the prefrontal cortex offsets age-related decrease in hippocampal theta activity for spatial memory maintenance
Currently, there is a critical gap in age-related electrophysiological changes in the human brain and how they are correlated with individual decline and maintenance of spatial cognitive function. To characterize these complex neurocognitive changes using direct intracranial recordings, we isolated periodic band power from the aperiodic spectral slope from iEEG power spectra of 69 presurgical epilepsy patients between 19 and 61 years of age while they performed a virtual spatial navigation task. We found a flattening of aperiodic spectral slope in the prefrontal cortex, but also observed a steepening in the hippocampus, suggestive of region-specific changes in excitatory/inhibitory balance across aging. The hippocampus showed pronounced changes in periodic (oscillatory) activity, including a decrease in theta power that correlated with impaired spatial memory, potentially due to changes in the cholinergic system. Interestingly, individuals with the flatter spectral slope in DLPFC showed preserved performance despite lower hippocampal theta, indicating a potential compensatory mechanism for cognitive maintenance. These findings provide new evidence that individual age-related cognitive decline can be predicted by changes in hippocampal theta oscillation, in combination with concomitant prefrontal compensatory mechanisms.

Autophagy, the Ubiquitin proteasome system, and the MAPK pathway control the temperature dependence of synaptic growth.
There is clear evidence that Earth's temperature is rising at an unprecedented rate. While consequences on ecosystems are being extensively studied, little is known about the consequences of temperature on the nervous system of ectothermic animals. Here we used the Drosophila model NMJ to assess the effect of temperature on the synaptic growth of a phasic, and a tonic, motoneuron. We find that the tonic neuron's synaptic size is not affected by temperature, however we do observe a temperature-dependent synaptic growth in the phasic neuron, which might be related to the increased motility observed previously at higher temperatures. We find that the level of autophagy activity changes with temperature and that autophagy genes are responsible for the temperature dependence of synaptic growth. We present evidence that this regulation could occur through the major synaptic growth regulator and ubiquitin ligase Highwire, and a pathway involving the Mitogen-Activated Protein Kinases. We present a new function for the MAPKKK, Wallenda and the MAPK P38b in directing the additional synaptic growth that takes place between 25{degrees}C and 29{degrees}C. This illustrates that temperature has different effects on a diverse population of neurons and that distinct genetic pathways are involved in regulating temperature driven changes.

Contextual Neural Dynamics During Time Perception in Primate Ventral Premotor Cortex
Understanding how time perception adapts to cognitive demands remains a significant challenge. In some contexts, the brain encodes time categorically (as long or short), while in others, it encodes precise time intervals on a continuous scale. Although the ventral premotor cortex (VPC) is known for its role in complex temporal processes, such as speech, its specific involvement in time estimation remains underexplored. In this study, we investigated how the VPC processes temporal information during a time interval comparison task (TICT) and a time interval categorization task (TCT) in primates. We found a notable heterogeneity in neuronal responses associated with time perception across both tasks. While most neurons responded during time interval presentation, a smaller subset retained this information during the working memory periods. Population-level analysis revealed distinct dynamics between tasks: in TICT, population activity exhibited a linear and parametric relationship with interval duration, whereas in TCT, neuronal activity diverged into two distinct dynamics corresponding to the interval categories. During delay periods, these categorical or parametric representations remained consistent within each task context. This contextual shift underscores the VPC's adaptive role in interval estimation and highlights how temporal representations are modulated by cognitive demands.

Generating brain-wide connectome using synthetic axonal morphologies
Recent experimental advancements, including electron microscopy reconstructions, have produced detailed connectivity data for local brain regions. On the other hand, large-scale imaging techniques such as MRI provide insights into inter-regional connectivity. However, understanding the links between local and long-range connectivity is essential to studying the healthy and pathological conditions of the brain. Leveraging a novel dataset of whole-brain axonal reconstructions, we present a technique to predict whole-brain connectivity at single cell level by generating detailed whole-brain axonal morphologies from sparse experimental data. The computationally generated axons accurately reproduce the local and global morphological properties of experimental reconstructions. Furthermore, the computationally synthesized axons generate large-scale inter-regional connectivity, defining the projectome and the connectome of the brain, thereby enabling the in-silico experimentation of large brain regions.

Conflict neurons in cingulate cortex of macaques
Conflict, the magnitude of co-activation of mutually incompatible response processes, was proposed to explain how cognitive control is invoked (Botvinick et al. 2001) and continues to engage debate (Becker et al. 2024). Original observations consistent with this construct emphasized the primary contribution of cingulate cortex (CC) based on human functional imaging (Botvinick et al., 1999; Carter et al., 2000) and electroencephalogram (Yeung, Botvinick, & Cohen, 2004). In countermanding tasks conflict arises through co-activation of competing GO and STOP processes (Boucher et al. 2007; Schall & Boucher 2007; Sajad et al. 2022). Single neuron activity representing conflict has been described in the supplementary motor cortex of human epilepsy patients (Fu et al., 2019; Sheth et al., 2012) and of macaque monkeys (Sajad, Errington, & Schall, 2022; Stuphorn, Taylor, & Schall, 2000) and in human cingulate cortex (Fu et al., 2019; Sheth et al., 2012) but not in monkey cingulate cortex (Ebitz & Platt, 2015; Ito, Stuphorn, Brown, & Schall, 2003; Nakamura, Roesch, & Olson, 2005). This lack of homology generated debate about the utility of macaques for investigation of cognitive control (Cole et al. 2009; Schall & Emeric 2010). With higher-resolution, less-biased samples, we re-examined the presence of a conflict signal in cingulate cortex of monkeys. Neurons modulating specifically when response conflict was maximal were found in cingulate cortex, more commonly in the dorsal than the ventral bank. However, such neurons were much more common in supplementary motor cortex. These data confirm the presence of a conflict signal in medial frontal cortex and demonstrate that it can be found in a small fraction of neurons in cingulate cortex. Further research is needed to determine if the weak response conflict signal in cingulate cortex is sufficient or negligible.

Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in a mouse model of Down syndrome
Down syndrome (DS) has been linked with deficits in hippocampal dependent cognitive tasks and adult neurogenesis, yet treatment options are still very limited. We and others previously showed that a non-invasive multisensory gamma stimulation using light and sound at 40 Hz ameliorated Alzheimers disease pathology and symptoms in mouse models. In this study, we tested the effects of 40 Hz multisensory stimulation in the Ts65Dn mice, a mouse model of DS. For three weeks, mice were exposed daily to one hour of stimulation or one hour of ambient light and sound. Mice receiving the stimulation showed improved object recognition and spatial working memory. Using single nuclei RNA-seq and experimental validations in mouse hippocampal samples, we identified underlying expression changes in gene regulatory networks and demonstrated increased adult neurogenesis and reorganization of synapses as potential mechanisms for these improved cognitive phenotypes. Together, our data reveal a novel effect of multisensory gamma stimulation on adult neurogenesis and beneficial effects of 40 Hz treatment on cognitive function in DS model mice.

Parallel neuroinflammatory pathways to cerebrovascular injury and amyloid-beta in Alzheimer's disease
Importance: While the hallmark pathologies of amyloid-beta and tau in Alzheimer's disease (AD) are well documented and even part of the definition, upstream neuroinflammation is thought to play an important role but remains poorly understood. Objectives: We tested whether two distinct neuroinflammatory markers are associated with cerebrovascular injury and amyloid-beta, and whether these markers are associated with plasma phosphorylated tau (pTau) concentration, medial temporal lobe (MTL) cortical and hippocampal atrophy, and memory deficits. We examined neuroinflammatory markers plasma YKL-40 and GFAP, due to previous conflicting evidence relating YKL-40 and GFAP to AD pathogenic markers. Design: Cross-sectional data from a community observational study (Biomarker Exploration in Aging, Cognition, and Neurodegeneration - BEACoN) were included. Setting: All participants were enrolled in a single site, at University of California, Irvine. Participants: 126 participants were included if they had at least one of the following measures available: neuropsychological data, MRI, amyloid-PET, or plasma. Exposures: Plasma YKL-40 and plasma glial fibrillary acidic protein (GFAP) levels. Main outcomes and measures: White matter hyperintensity (WMH) volume, 18F-florbetapir (FBP) PET mean SUVR, plasma phosphorylated tau (pTau-217) concentration, MTL cortical thickness, hippocampal volume, and memory function assessed by Rey Auditory Verbal Learning Test. Using path analysis, we tested whether higher plasma YKL-40 and GFAP are associated with WMH and amyloid-beta, and whether these converge to downstream markers of tauopathy, MTL neurodegeneration, and memory deficits. Results: In older adults without dementia (N=126, age=70.60+6.29, 62% women), we found that higher plasma YKL-40 concentration was associated with greater WMH volume, while higher plasma GFAP concentration was related to increased FBP SUVR. Further, higher plasma GFAP, WMH and FBP SUVR were independently associated with increased pTau-217. In turn, plasma pTau-217 was associated with reduced MTL cortical thickness and hippocampal volume. Subsequently, only reduced hippocampal volume was related to lower memory function. Conclusions and Relevance: Neuroinflammatory markers contribute to parallel pathways of cerebrovascular injury and amyloid-beta, which converge to tau-associated neurodegeneration and memory deficits in older adults. These observations underscore the need for a more comprehensive approach to developing an AD framework and treatment strategies.

An electrophysiological study about the pharmacological manipulation of the immediate consequences of a spinal trauma reveals a crucial role for TRPV4 antagonism.
A physical trauma to the spinal cord produces an immediate massive depolarizing injury potential accompanied both by a transient episode of spinal hypoxia, and an extensive cell loss at the level of injury, which interrupts conduction of longitudinal input along white matter tracts. Afterwards, the transient hypotonia and areflexia characterize the following spinal shock phase. The relationship between the extent of injury potentials and spinal cord injury (SCI) progression, as well as the potential pharmacological modulation of the immediate consequences of a trauma, have not yet been explored. To limit the peak of injury potentials and speed up recovery of reflex motor responses, we serially applied selective neurochemicals in the exact moment of an experimental physical trauma delivered through a calibrated device impacting the mid-thoracic cord of an entire CNS preparation of neonatal rats. Continuous lumbar root recordings monitored baseline DC-levels and reflex responses elicited by trains of electric pulses applied to sacrocaudal afferents. In uninjured preparations, each agent showed distinct effects on baseline polarization, modulation of synaptic responses, and appearance of bursting activity. Interestingly, neurochemicals acting on glutamatergic-, adenosinergic-, glycinergic- or GABAergic receptors, did not affect the monitored outcome when each parameter was normalized against pre-injury values. Conversely, the selective TRPV4 antagonist, RN1734, unlike the TRPA1 antagonist, AP18, reduced peak of injury potentials and speeded up full recovery of reflex responses within 1 min from trauma. Similarly, blockage of gap junctions quickly, yet partially, restored motor reflexes, while antagonism of GABAA receptors restored full reflexes, though slightly later. The current study indicates that both mechanosensitive TRPV4 receptors and GABAergic transmission reduce the immediate pathological consequences of a trauma when applied at the moment of impact, envisaging a clinical translation for preventing accidental spinal lesions during the most delicate spinal surgeries.

Bilateral Symmetry and Asymmetry in the C. elegans Connectome: A Graph-Theoretic Analysis based on Redundancy Measures
Understanding the balance between symmetry and asymmetry in animal nervous systems is crucial for unraveling the complexities of neural architectures and their functions. Previous studies have primarily focused on morphological symmetry, such as neuron placement, leaving the symmetry in the functional architecture largely unexplored. The current study investigates this aspect within the Caenorhabditis elegans connectomes by introducing a graph-theoretic approach. By defining a 'mirror-symmetry index,' we quantitatively assess the symmetry in these connectomes, revealing a significant level of bilateral symmetry alongside notable asymmetry. Our approach also incorporates measures including connectivity similarity, motif-fingerprint differences, and path-compensation index to evaluate the network's functional redundancy and its capacity to compensate for unilateral disturbances. Here we show the C. elegans connectomes' robust bilateral symmetry, which not only facilitates similar functions across neuron pairs but also ensures resilience against disruptions. This redundancy is not confined to symmetrical connections; it also includes asymmetric ones, adding to the neural network's complexity. An in-depth analysis into different neuron types shows varied redundancy levels: high in interneurons, moderate in motor neurons, and low in sensory neurons. This pattern suggests a strategic neural design where diverse inputs from sensory neurons, coupled with the stable integration by interneurons, lead to coordinated actions through motor neurons. This study advances our understanding of neural connectomes, offering insights into the intricate balance of symmetry and asymmetry in neural systems and their implications for complex, adaptive behaviors.

Spatial and network principles behind neural generation of locomotion
Generation of locomotion is a fundamental function of the spinal cord, yet the underlying principles remain unclear. In particular, the relationship between neuronal cell types, networks and function has been difficult to establish. Here, we propose principles by which functions arise primarily from spatial features of the cord. First, we suggest that distinct cell types with dissimilar length of projection constitute an asymmetrical "Mexican hat" topology, i.e. local excitation and surrounding inhibition, along the rostro-caudal axis. Second, the transversal segregation of cell types conveniently allows synapses to form with appropriate targets. We demonstrate these principles in a model of the mouse spinal cord, where networks are constructed by probabilistic sampling of synaptic connections from cell-specific projection patterns, which are gleaned from literature. The cell-type distributions are derived from single-cell RNA sequencing combined with spatial transcriptomics. We find that essential aspects of locomotion are recapitulated and easily controlled, and several experimental observations can now be explained mechanistically. Further, two main features are predicted: propagating bumps of neural activity and asymmetric neuronal projections with local excitation and wider inhibition. Besides linking cell types, structure and function, our approach provides a unifying framework for understanding motor activity across limbed and undulatory species.

Regulation of REM Sleep Onset and Homeostasis by Preoptic Glutamatergic Neurons
The preoptic area of the hypothalamus is key for the control of sleep onset and sleep homeostasis. Although traditionally considered exclusively somnogenic, recent studies identified a group of preoptic glutamatergic neurons that promote wakefulness. Specifically, our previous investigations demonstrated that chemogenetic stimulation of glutamatergic neurons within the medial-lateral preoptic area (MLPO_VGLUT2) promotes wakefulness, fragments non-rapid eye movement sleep (NREMs), and suppresses REM sleep (REMs). This evidence is further supported by recent work showing that preoptic glutamatergic neurons are activated during microarousals that fragment sleep in response to stress, and optogenetic stimulation of these neurons promotes microarousals and wakefulness. Thus, while the wake-promoting function of MLPO_VGLUT2 is clear, their role in sleep homeostasis has not been assessed. We tested the hypothesis that MLPO_VGLUT2 are wake-active, and their activation will increase wakefulness and disrupt sleep homeostasis via projections to arousal-promoting systems. Using fiber photometry, we found that MLPO_VGLUT2 were highly active during REMs, wakefulness and brief arousals, and remained minimally active during NREMs. Chemogenetic stimulation of MLPO_VGLUT2 inhibited REMs onset and suppressed the REMs homeostatic response after total sleep deprivation. Chemogenetic inhibition of MLPO_VGLUT2 increased REMs time (during the light phase only) but did not influence REMs and NREMs homeostasis. Anterograde projection mapping revealed that MLPO_VGLUT2 innervate central regions that promote wakefulness and inhibit REMs. We conclude that MLPO_VGLUT2 powerfully suppress REMs and that exogenous (and possibly pathologic) activation of these neurons disrupts REMs recovery, presumably by directly or indirectly activating REMs-inhibitory mechanisms.

Finding Agreement: fMRI-hyperscanning reveals that dyads explore in mental state space to align opinions.
Many prize synchrony as the ingredient that turns a conversation from a debate into a delightful duet. Yet, learning from other people's diverging opinions can also foster understanding and agreement, satisfy curiosity, and spur imagination. Using fMRI hyperscanning and natural language processing we tested how two debaters navigate conflictual conversations to find agreement. Dyads (N=60) discussed pressing societal problems while being instructed to either persuade their partner or compromise with each other. Our analysis uncovered three key insights: First, individuals instructed to compromise rather than persuade tended to agree more at the end of the session. Second, hyperscanning and linguistic analyses revealed that encouraging compromise resulted in increased exploration during conversations; dyads given compromise instructions traversed more diverse mental states and topics. Third, heightened exploration was linked to greater eventual agreement. Notably, the effect of the compromise instruction on agreement was entirely mediated by the degree of exploration. Together, these results suggest that trying to find agreement may be spurred by exploration, something that happens when people are motivated to compromise but not persuade.

Early Postnatal Dysfunction of mPFC PV Interneurons in Shank3B-/- Mice
Medial prefrontal cortex (mPFC) dysfunction is associated with cognitive and sensory abnormalities in individuals with autism spectrum disorder (ASD), yet the trajectory of mPFC circuit development in these conditions remains poorly understood. In this study, we investigated the postnatal maturation of glutamatergic connectivity and neuronal excitability in pyramidal neurons (PYR) and parvalbumin-positive interneurons (PVIN) in the mPFC of mice harboring deletions in SHANK3, a well-established genetic cause of autism associated with severe cognitive impairments and seizures. Our findings reveal early deficits in PVIN excitability that precede changes in the synaptic and intrinsic properties of PYR, resulting in impaired feedforward inhibition. In vivo calcium imaging demonstrated hypoactivity of PVIN in dorsal mPFC circuits during early postnatal development, characterized by reduced calcium transients in PVIN. By adulthood, these excitability phenotypes were reversed, with PVIN becoming hyperexcitable and PYR hypoexcitable. These results suggest that early PVIN dysfunction in Shank3B-/- mice emerges during postnatal development and may represent a key pathogenic mechanism and potential therapeutic target in SHANK3-related disorders.

Modulation of sweet preference by neurosteroid-sensitive, δ-GABAA receptors in adult mouse gustatory insular cortex
Taste preference is a fundamental driver of feeding behavior influencing dietary choices and eating patterns. Extensive experimental evidence indicates that the gustatory cortex (GC) is engaged in taste perception, palatability and preference. However, our knowledge of the neural and neurochemical signals regulating taste preference is rather limited. Neuromodulators can affect preferences, though their effects on neural circuits for taste are incompletely understood. Neurosteroids are of particular interest in view of reports that systemic administration of the neurosteroid allopregnanolone, a potent modulator of tonic GABAergic inhibition, induces hyperphagia and increases intake of energy rich food in human and animal subjects. Tonic inhibition is a powerful modulator of circuit excitability and is primarily mediated by extrasynaptic GABAA receptors containing the delta subunit ({delta}-GABAARs). These receptors are widely distributed in the brain, but information regarding the expression of {delta}-GABAARs within gustatory circuits is lacking, and their role in taste preference has not been investigated. Here, we focused on GC to investigate whether activation of {delta}-GABAARs affects sweet taste preference in adult mice. Our data reveal that {delta}-GABAARs are expressed in multiple cell types within GC. These receptors mediate an allopregnanolone-sensitive tonic current and decrease sweet taste preference by altering the behavioral sensitivity to sucrose concentration in a cell type-specific manner. Our findings demonstrate that taste sensitivity and preference in the adult mammalian brain are modulated by tonic inhibition mediated by neurosteroid-activated {delta}-GABAARs in GC.

Test-retest reliability of perturbation-evoked cortical activity reflects stable individual differences in reactive balance control
There is a growing interest in measuring cortical activity during balance control for understanding mechanisms of impaired balance with aging and neurological dysfunction. The most well-characterized electrophysiological signal elicited by a balance disturbance is the perturbation-evoked N1 potential that peaks 100-200 msec post-perturbation and is thought to reflect error processing. We previously found associations between the N1 and individual differences in balance ability, suggesting it may be a potential biomarker of balance health. However, a potential biomarker of balance function will be limited by its reliability and clinical feasibility, which has yet to be established. Here, we characterized the reliability of the N1 elicited by standing balance perturbations within and between sessions over a one-week interval in 10 younger and 14 older adults. A subset of older adults (n=12) completed a session approximately one year prior to the main experiment. We extracted N1 amplitude and latency from the Cz electrode using an advanced, computationally-intensive approach that relies on large amounts of data (e.g., 64 channels, many trials), Test-retest reliability was assessed using the intra-class correlation coefficient (ICC). Internal consistency was quantified by split-half reliability using the Spearman correlation coefficient. N1s varied across individuals (amplitude:12-82V, latency: 142-282ms), yet within individuals, the N1 showed excellent test-retest reliability (ICC>0.9) across a one-week and one-year time span. N1 amplitude reached excellent internal reliability for each session and group (r>0.9), that generally plateaued within 6 trials, while more trials were needed to reliably measure N1 latency. Similar results were obtained when quantifying N1s using a minimal approach performed with only three electrodes and simple preprocessing. Overall, the N1 is stable within and across sessions, and is largely independent of approach suggesting it could be a clinically-feasible biomarker of balance function. Characterizing reliability in populations with neurologic dysfunction and in different environmental contexts will be necessary to enhance our understanding of the N1, optimize experimental design, and determine its predictive validity of clinical outcomes (e.g., falls risk).

Discovering Temporally Compositional Neural Manifolds with Switching Infinite GPFA
Gaussian Process Factor Analysis (GPFA) is a powerful latent variable model for extracting low-dimensional manifolds underlying population neural activities. However, one limitation of standard GPFA models is that the number of latent factors needs to be pre-specified or selected through heuristic-based processes, and that all factors contribute at all times. We propose the infinite GPFA model, a fully Bayesian non-parametric extension of the classical GPFA by incorporating an Indian Buffet Process (IBP) prior over the factor loading process, such that it is possible to infer a potentially infinite set of latent factors, and the identity of those factors that contribute to neural firings in a compositional manner at each time point. Learning and inference in the infinite GPFA model is performed through variational expectation-maximisation, and we additionally propose scalable extensions based on sparse variational Gaussian Process methods. We empirically demonstrate that the infinite GPFA model correctly infers dynamically changing activations of latent factors on a synthetic dataset. By fitting the infinite GPFA model to population activities of hippocampal place cells during spatial navigation, we identify non-trivial and behaviourally meaningful dynamics in the neural encoding process.

Motor Imagery Enhances Performance Beyond the Imagined Action
Motor imagery is frequently utilized to improve the performance of specific target movements in sports and rehabilitation. In this study, we show that motor imagery can facilitate learning of not only the imagined target movements but also sequentially linked overt movements. Hybrid sequences comprising imagined and physically executed segments allowed participants to learn specific movement characteristics of the executed segments when they were consistently associated with specific imagined segments. Electrophysiological recordings revealed that the degree of event-related synchronization in the alpha and beta bands during a basic motor imagery task was correlated with imagery-evoked motor learning. Thus, both behavioral and neural evidence indicate that motor imagery's benefits extend beyond the imagined movements, improving performance in linked overt movements. This provides new evidence for the functional equivalence of imagined and overt movements and suggests new applications for imagery in sports and rehabilitation.

Leveraging clinical sleep data across multiple pediatric cohorts for insights into neurodevelopment: the Retrospective Analysis of Sleep in Pediatric (RASP) cohorts study
Sleep disturbances are prominent across neurodevelopmental disorders (NDDs) and may reflect specific abnormalities in brain development and function. Overnight polysomnography (PSG) allows for detailed investigation of sleep architecture, offering a unique window into neurocircuit function. A better understanding of sleep in NDDs compared to typically developing children could therefore define mechanisms underlying abnormal development in NDDs and provide avenues for the development of therapeutic interventions to improve sleep quality and developmental outcomes. Here, we introduce and characterize a collection of 1527 pediatric overnight PSGs across five different sites. We first developed an automated stager trained on independent pediatric sleep data, which yielded better performance compared to a stager trained on adults. Using consistent staging across cohorts, we derived a panel of EEG micro-architectural features. This unbiased approach replicated broad trajectories previously described in typically developing sleep architecture. Further, we found sleep architecture disruptions in children with Down's Syndrome (DS) that were consistent across independent cohorts. Finally, we built and evaluated a model to predict age from sleep EEG metrics, which recapitulated our previous findings of younger predicted brain age in children with DS. Altogether, by creating a resource pooled from existing clinical data we expanded the available datasets and computational resources to study sleep in pediatric populations, specifically towards a better understanding of sleep in NDDs. This Retrospective Analysis of Sleep in Pediatric (RASP) cohorts dataset, including staging annotation derived from our automated stager, will be deposited at https://sleepdata.org.

ASSESSMENT OF THE IMPACT OF SLEEP DEPRIVATION AND DIET ON GROWTH, COGNITION, INFLAMMATION, OXIDATIVE STRESS, AND TISSUE HISTOLOGY
This study explores the interplay encompassing amino acids' roles, metabolic processes, growth, and the intricate relationships between sleep patterns, amino acid-deficient diet, and caffeine consumption, with emphasis on the vital connections between diet, oxidative stress, and cognitive health while investigating the essential role of quality sleep in maintaining cognitive function. This study investigates the intricate connections among amino acids, metabolic processes, growth, sleep patterns, amino acid-deficient diets, and caffeine consumption. Emphasizing the crucial links between diet, oxidative stress, and cognitive health, the research underscores the essential role of quality sleep in maintaining cognitive function. The bidirectional relationship between disrupted sleep and cognitive health, as well as the impact of caffeine on cognitive function, is explored. The study involved adult male Wistar rats divided into 10 groups A - J based on cage conditions and diet. Group A-E were kept in a normal cage with diets containing varying levels of tryptophan and other essential amino acids, while Group F-J underwent sleep deprivation using a disk-over-water method and received diets with varying tryptophan and other essential amino acid levels, in addition to caffeine. The experiment spanned 2 weeks, blood samples were collected on days 1,4,7, and 13 for relevant biochemical serum analyses, and the rats were sacrificed on the fourteenth day for blood sample collection, biochemical assays, and brain histology. The 2-week experiment revealed a linear decrease in melatonin and serotonin levels across all caffeine-administered groups, possibly due to stress and anxiety as compared with the reduction in these parameters observed in control rats, suggesting melatonin and serotonin as potential sleep deprivation biomarkers. Testosterone and insulin-like growth hormone assays showed a significant decrease in sleep-deprived rats with caffeine, impacting secondary sex characteristics and growth. Elevated TNF- and interleukin-1b levels in the caffeine-administered, sleep-deprived group suggest potential health risks associated with sleep deprivation and caffeine. Serum assays for antioxidant enzymes indicated heightened oxidative stress in sleep-deprived rats with caffeine. Histopathological studies revealed cellular abnormalities in the sleep-deprived group, indicating increased cellular metabolism and potential pathological conditions. This study elucidates the complex relationships among sleep, dietary factors, and hormonal and inflammatory responses. It underscores the potential neurotoxic effects associated with caffeine consumption when coupled with sleep deprivation. These results underscore the urgent need for further investigation into dietary strategies that could alleviate these adverse effects and promote better health. Keywords: Sleep deprivation, Amino acid deficiency, Oxidative stress, Cognitive health, Caffeine

Mammalian chemosensory bile acid detection supports species and gut microbiome evaluation
The rodent accessory olfactory system (AOS) detects environmental chemosignals and guides social and survival-oriented behaviors. Fecal bile acids activate neurons in the AOS, potentially serving as mammalian pheromones and kairomones, but few molecules in this large class have been evaluated thus far. We used live volumetric Ca2+ imaging to screen naturally occurring bile acids for their capacity to activate peripheral vomeronasal sensory neurons (VSNs). We found that taurine-conjugated bile acids (tauro-BAs), including taurine-conjugates of cholic acid, deoxycholic acid, lithocholic acid, and chenodeoxycholic acid (TCA, TDCA, TLCA, TCDCA, respectively) activate large populations of VSNs at sub-micromolar concentrations. Tauro-BA-sensitive VSNs rarely responded to unconjugated (CA, CDCA, DCA, LCA), glycine-conjugated (GCA, GDCA, GLCA, GCDCA), or keto-conjugated (7-keto DCA, 12-keto DCA, 7-keto LCA) bile acids. Tauro-BA-sensitive VSNs were also insensitive to well-studied sulfated steroids, suggesting tauro-BAs activate vomeronasal receptors that have not yet been de-orphaned. Among the tauro-BAs, TDCA displayed particularly strong potency, activating many VSNs at sub-micromolar concentrations. Tauro-BAs were not detectable in mouse fecal extracts by mass spectrometry, but were found in reptile fecal extracts and germ-free mouse fecal extracts. VSN responses to germ-free and conventional mouse fecal extracts, conjugated bile acids, and tauro-BAs revealed that non-overlapping populations of VSNs respond to germ-free and conventional mouse feces. A subset of VSNs that were activated by germ-free mouse fecal extracts responded to tauro-BAs, whereas VSNs responsive to conventionally fecal extracts responded to unconjugated bile acids. In vivo exposure to TDCA alone, and to mouse fecal extracts spiked with TDCA, elicited mild aversion and stress-associated behaviors in a non-social context (avoidance, digging, grooming, etc.). These studies establish tauro-BAs as a novel class of aversive vomeronasal ligands that vary in feces across species and gut microbiomes.

Monosynaptic ventral tegmental area glutamate projections to the locus coeruleus enhance aversive processing
Distinct excitatory synaptic inputs to the locus coeruleus (LC), the primary source of norepinephrine for the central nervous system, modulate behavioral flexibility. Here we identify a novel monosynaptic glutamatergic input to the LC from the ventral tegmental area (VTA). We show VTA glutamatergic axons project robustly to the dorsal pons and provide direct glutamatergic transmission onto LC neurons. Despite weak summation of this synaptic input, optogenetic activation of these axons in LC enhances tonic firing and facilitates real-time and conditioned aversive behavior. We hypothesized this VTA-LC glutamatergic projection may provide modulatory synaptic integration with other excitatory inputs. To test this notion, we used coincident photostimulation of VTA-LC axons and local electrical stimulation and demonstrate enhanced burst induction in the LC. To determine whether this integration also occurs in vivo, we took an analogous approach using the Punishment Risk Task to measure the reward-seeking behavior during unpredictable probabilistic punishment. Here, optogenetic activation of the VTA-LC glutamatergic projections with a concurrent noxious stimulus did not delay the reward-seeking behavior, but increased the probability of task failure. Together, our findings identify a novel VTA-LC glutamatergic projection that drives concurrent synaptic summation during salient stimuli to promote behavioral avoidance.

Brain-like neural dynamics for behavioral control develop through reinforcement learning
During development, neural circuits are shaped continuously as we learn to control our bodies. The ultimate goal of this process is to produce neural dynamics that enable the rich repertoire of behaviors we perform with our limbs. What begins as a series of "babbles" coalesces into skilled motor output as the brain rapidly learns to control the body. However, the nature of the teaching signal underlying this normative learning process remains elusive. Here, we test two well-established and biologically plausible theories-supervised learning (SL) and reinforcement learning (RL)-that could explain how neural circuits develop the capacity for skilled movements. We trained recurrent neural networks to control a biomechanical model of a primate arm using either SL or RL and compared the resulting neural dynamics to populations of neurons recorded from the motor cortex of monkeys performing the same movements. Intriguingly, only RL-trained networks produced neural activity that matched their biological counterparts in terms of both the geometry and dynamics of population activity. We show that the similarity between RL-trained networks and biological brains depends critically on matching biomechanical properties of the limb. We then demonstrated that monkeys and RL-trained networks, but not SL-trained networks, show a strikingly similar capacity for robust short-term behavioral adaptation to a movement perturbation, indicating a fundamental and general commonality in the neural control policy. Together, our results support the hypothesis that neural dynamics for behavioral control emerge through a process akin to reinforcement learning. The resulting neural circuits offer numerous advantages for adaptable behavioral control over simpler and more efficient learning rules and expand our understanding of how developmental processes shape neural dynamics.

Subcortical Hubs of Brain Networks Sustaining Human Consciousness
Neuromodulation of subcortical network hubs by pharmacologic, electrical, or ultrasonic stimulation is a promising therapeutic strategy for patients with disorders of consciousness (DoC). However, optimal subcortical targets for therapeutic stimulation are not well established. Here, we leveraged 7 Tesla resting-state functional MRI (rs-fMRI) data from 168 healthy subjects from the Human Connectome Project to map the subcortical connectivity of six canonical cortical networks that modulate higher-order cognition and function: the default mode, executive control, salience, dorsal attention, visual, and somatomotor networks. Based on spatiotemporally overlapped networks generated by the Nadam-Accelerated SCAlable and Robust (NASCAR) tensor decomposition method, our goal was to identify subcortical hubs that are functionally connected to multiple cortical networks. We found that the ventral tegmental area (VTA) in the midbrain and the central lateral (CL) and parafascicular (Pf) nuclei of the thalamus - regions that have historically been targeted by neuromodulatory therapies to restore consciousness - are subcortical hubs widely connected to multiple cortical networks. Further, we identified a subcortical hub in the pontomesencephalic tegmentum that overlapped with multiple reticular and extrareticular arousal nuclei and that encompassed a well-established "hot spot" for coma-causing brainstem lesions. Multiple hubs within the brainstem arousal nuclei and thalamic intralaminar nuclei were functionally connected to both the DMN and SN, emphasizing the importance of these cortical networks in integrative subcortico-cortical signaling. Additional subcortical connectivity hubs were observed within the caudate head, putamen, amygdala, hippocampus, and bed nucleus of the stria terminalis, regions classically associated with modulation of cognition, behavior, and sensorimotor function. Collectively, these results suggest that multiple subcortical hubs in the brainstem tegmentum, thalamus, basal ganglia, and medial temporal lobe modulate cortical function in the human brain. Our findings strengthen the evidence for targeting subcortical hubs in the ventral tegmental area, central lateral thalamus, and pontomesencephalic tegmentum to restore consciousness in patients with DoC. We release all subcortical connectivity maps to support ongoing efforts at therapeutic neuromodulation of consciousness.

Representation of Verbal Thought in Motor Cortex and Implications for Speech Neuroprostheses
Speech brain-computer interfaces show great promise in restoring communication for people who can no longer speak, but have also raised privacy concerns regarding their potential to decode private verbal thought. Using multi-unit recordings in three participants with dysarthria, we studied the representation of inner speech in the motor cortex. We found a robust neural encoding of inner speech, such that individual words and continuously imagined sentences could be decoded in real-time This neural representation was highly correlated with overt and perceived speech. We investigated the possibility of "eavesdropping" on private verbal thought, and demonstrated that verbal memory can be decoded during a non-speech task. Nevertheless, we found a neural "overtness" dimension that can help to avoid any unintentional decoding. Together, these results demonstrate the strong representation of verbal thought in the motor cortex, and highlight important design considerations and risks that must be addressed as speech neuroprostheses become more widespread.

Dynamic Models of Neural Population Dynamics
The recent developments in artificial intelligence (AI) increase the hope that AI can provide a powerful tool to facilitate scientific discovery and to generate and validate new ideas for scientific research autonomously. Large Language Models (LLMs), such as ChatGPT4 have demonstrated remarkable capabilities in understanding and generating human-like text. Their potential extends beyond simple language tasks, offering transformative possibilities in scientific research of all fields. By leveraging vast amounts of data and advanced computational power, LLMs can assist researchers in generating novel ideas, automating routine tasks, and fostering interdisciplinary collaborations. On September 12, 2024, OpenAI released their updated generative artificial intelligence system called ChatGPTo1. This new AI system, built upon chain-of-thought and reinforcement learning, has greatly enhanced logical reasoning abilities and can effectively solve various complex problems from elementary-level mathematical problems to modern scientific research issues in physics, chemistry, and biology. Unlike previous LLMs in which logical reasoning and data analysis abilities are developed through training on actual data, ChatGPTo1 logical reasoning ability and capacity to generate new scientific ideas are primarily acquired through chain-of-thought processes and reinforcement learning rather than pre-training. To examine this, we specifically tested ChatGPTo1 current reasoning and scientific discovery capabilities by developing theoretically complex and quantitatively challenging scientific equations in various fields of neuroscience, such as dynamical systems, nonlinear dynamical systems, dynamical systems on differential manifolds, neural field theory, nonlinear divergence theorems, nonlinear heat conduction equations and Laplace equations and their extensions on differential manifolds, nonlinear statistical analysis methods, deep learning, and other topics involving multiple fields. The current large language models may illustrate a certain degree of general intelligence, even if fundamentally it may be different from human intelligence. However, it does not mean the current LLMs can fully apply such ability in practical applications or that their reasoning potential can be fully tapped. It is essential to explore specific pathways and methods to cultivate their potential for scientific discovery. To accomplish this, we consider how to integrate them with common search engines (such as Google) capabilities and ChatGPT4o cross-modal abilities to better understand new disciplines and scientific discoveries. To this point, the major shortcoming of ChatGPTo1 is that it is not an end-to-end scientific discovery method and lacks the ability to achieve full automation. It also lacks methods for image analysis and full-scale data analysis, making it difficult to use simulation and data analysis to evaluate and test proposed new theories and methods.

Automated, Stress-Free, and Precise Measurement of Songbird Weight in Neuroscience Experiments
Monitoring the health and well-being of research animals is essential for both ethical and scientific purposes. In songbirds, body weight is one of the main indicators for their overall condition, yet traditional weighing methods can be intrusive and stress-inducing, which could decrease their song rate. We developed a novel, automated system designed to continuously monitor the weight of untethered and tethered birds without disrupting their natural behavior in neuroscience experiments. We used the system to track weight fluctuations in six canaries over several weeks, revealing physiological patterns such as overnight weight loss, with one bird losing approximately 5.17% of its body weight during a 9.5-hour period of inactivity. Our system's high sensitivity detected weight changes below 1% of body mass, validating its reliability for long-term studies. Control experiments confirmed that weight fluctuations observed were physiological rather than due to equipment deviations. By eliminating the need for manual handling, this system offers a non-invasive, hands-free approach that reduces stress and improves the accuracy of health assessments. This study demonstrates the system's potential for expanding research on how environmental factors, diet, and other variables influence bird physiology and behavior. Future applications could integrate additional health metrics, providing a more comprehensive understanding of animal welfare in neuroscience and behavioral studies.

Heterogeneous distribution of inhibitory inputs among motor units as a key mechanism for motor adaptations to pain
Pain significantly influences movement, yet the precise neural mechanisms underlying the wide range of observed motor adaptations remain unclear. This study combined experimental data and in silico models to investigate the contribution of inhibitory and neuromodulatory inputs to motor unit behaviour during submaximal contractions performed in the presence of pain. Specifically, we aimed to unravel the distribution pattern of inhibitory inputs to the motor unit pool. Seventeen participants performed isometric knee extension tasks under three conditions: Control, Pain (induced by injecting hypertonic saline into the infra-patellar fat pad), and Washout. We identified large samples of motor units in the vastus lateralis (up to 53/participant) from high-density electromyographic signals, which led to three key observations. First, while motor unit discharge rates significantly decreased during Pain, a substantial proportion of motor units (14.8-24.8%) did not show this decrease and, in some cases, even exhibited an increase. Second, using complementary approaches we showed that pain did not alter the amplification and prolongation effects of persistent inward currents on motor unit discharge, providing evidence that neuromodulatory drive to motor neurons remained unchanged. Third, we observed a significant reduction in the proportion of common inputs to motor units during Pain. To explore potential neurophysiological mechanisms underlying these experimental results, we simulated the behaviour of motor unit pools with varying distribution patterns of inhibitory inputs. Our simulation supports the hypothesis of a non-homogeneous distribution of inhibitory inputs, independent of motor unit size, as a key neural mechanism underlying motor adaptations to experimental pain.

A preprocessing toolbox for 2-photon subcellular calcium imaging
Recording the spiking activity from subcellular compartments of neurons such as axons and dendrites during behavior with 2-photon calcium imaging is increasingly common yet remains challenging due to low signal-to-noise, inaccurate region-of-interest (ROI) identification, movement artifacts, and difficulty in grouping ROIs from the same neuron. To address these issues, we present a computationally efficient pre-processing pipeline for subcellular signal detection, movement artifact identification, and ROI grouping. For subcellular signal detection, we capture the frequency profile of calcium transient dynamics by applying Fast Fourier Transform (FFT) on smoothed time-series calcium traces collected from axon ROIs. We then apply band-pass filtering methods (e.g. 0.05 to 0.12 Hz) to select ROIs that contain frequencies that match the power band of transients. To remove motion artifacts from z-plane movement, we apply Principal Component Analysis on all calcium traces and use a Bottom-Up Segmentation change-point detection model on the first principal component. After removing movement artifacts, we further identify calcium transients from noise by analyzing their prominence and duration. Finally, ROIs with high activity correlation are grouped using hierarchical or k-means clustering. Using axon ROIs in the CA1 region, we confirm that both clustering methods effectively determine the optimal number of clusters in pairwise correlation matrices, yielding similar groupings to "ground truth" data. Our approach provides a guideline for standardizing the extraction of physiological signals from subcellular compartments during behavior with 2-photon calcium imaging.

Investigation of cellular and molecular changes linked with neuropathic pain in healthy and injured human trigeminal nerves
Injuries to the trigeminal nerve, responsible for sensory innervation to the face, may occur during routine dental procedures, resulting in the formation of a neuroma accompanied by loss of sensation and/or symptoms of pain. In order to gain insight into the molecular mechanisms underpinning the sensory changes, single nuclei RNA sequencing and spatial transcriptomics were employed to profile the transcriptional landscape at single cell resolution of human trigeminal nerves and neuromas. Cellular and transcriptional changes were identified that correlated with the presence of pain, including an expansion of endothelial cells with a pro-inflammatory phenotype and over-expression of HLA-A, CXCL2 and CXCL8. Interactome analysis highlighted signalling changes linked with the presence of pain. HLA-A protein expression was confirmed in neuromas and positively correlated with symptoms of pain. The atlas generated represents a valuable resource for pain research, highlighting the role of inflammation, endothelial cell dysfunction and chemokine signalling in neuropathic pain.

Impact of Optogenetic Activation of the Thalamic Reticular Nucleus on Sleep Architecture in Mice
Alzheimer's disease (AD) is a progressive neurodegenerative disorder affecting millions worldwide and is often accompanied by significant sleep disturbances, such as sleep fragmentation, early awakenings, decreased sleep efficiency, and insomnia. It has been suggested that the alterations in activity of the thalamic reticular nucleus (TRN) are closely associated with sleep disruptions in AD. Evidence suggests that activating neurons expressing gamma-aminobutyric acid (GABA) within the TRN may enhance sleep quality and potentially ameliorate neuropathology associated with AD. However, the precise mechanisms through which TRN influences sleep disruptions and AD pathophysiology remain poorly understood. In this study, we investigated whether activating GABAergic TRN neurons could alter sleep architecture in wild-type mice. Utilizing optogenetic stimulation, we observed that activation of these neurons did not significantly alter sleep state durations or delta wave power, a key indicator of Slow Wave Sleep (SWS). Furthermore, the application of a two-virus strategy inadvertently led to non-specific opsin expression beyond the targeted TRN area. We discuss the potential factors that contributed to these outcomes, providing directions for future investigations to better delineate the role of the TRN in sleep and AD.

Superior colliculus projections drive dopamine neuron activity and movement but not value
To navigate complex environments, animals must rapidly integrate sensory information and respond appropriately to gather rewards and avoid threats. It is well established that dopamine neurons in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) are key for creating and maintaining associations between environmental stimuli (i.e., cues) and the outcomes they predict, through Pavlovian learning. However, it remains unclear how relevant sensory information is integrated into dopamine (DA) pathways to guide exploration and learning. The superior colliculus (SC) receives direct visual input and is anatomically positioned as a relay for rapid sensory augmentation of dopamine neurons, which could underlie the formation of Pavlovian associations. Here, we characterize the anatomical organization and functional impact of SC projections to the VTA and SNc in rats. First, using anatomical tracing techniques, we show that neurons in the intermediate and deep layers of SC synapse densely throughout the ventral midbrain, interfacing directly with neurons projecting to the striatum and ventral pallidum. Using fiber photometry, we find that these SC projections excite both dopamine and GABA neurons in the VTA and dopamine neurons in the SNc in vivo. Despite this, cues predicting SC terminal stimulation did not reliably evoke behavior on their own in an optogenetic Pavlovian conditioning paradigm. Further, optogenetic activation of SC terminals in the VTA/SNc did not support primary reinforcement or produce place preference or avoidance. Instead, we find that stimulation of SC terminals in the VTA and SNc reliably evoked head turning behavior. This body reorientation increased in intensity with repeated stimulations, suggesting that strengthening this circuit could underlie sensorimotor learning related to exploration and attentional bias. Together our results show that collicular neurons contribute to cue-guided learning by controlling pose adjustments through interaction with dopamine systems.

Antisense oligonucleotide targeting pathogenic sense repeat RNA in C9ORF72 suppresses production of antisense-dependent dipeptide repeat proteins implicated in ALS/FTD
A six nucleotide repeat expansion in intron-1 of the C9ORF72 gene is the most common genetic mutation affecting individuals with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Bi-directional transcription of the repeat expansion generates sense and antisense repeat RNAs that can then be translated in all reading frames to produce six distinct dipeptide repeat (DPR) proteins with unique termini. The precise site of translation initiation of these proteins within the C9ORF72 repeat expansion remains elusive. We used CRISPR-Cas9 genome editing and steric-blocking antisense oligonucleotides (ASOs) to investigate the contribution of different AUG codons in the antisense repeat RNA to the production of DPR proteins, poly(GP) and poly(PR) in C9ORF72 expansion carrier motor neurons and lymphoblast cells. We then utilized ASOs targeting C9ORF72 sense repeat RNA to examine whether sense or antisense RNA is the major source of the poly(GP) protein - a question for which conflicting evidence exists. We found that these ASOs reduced the intended sense RNA target, but also the antisense RNA, thus preventing the production of poly(PR). Our data highlights the importance of the sequences preceding the antisense CCCCGG repeat expansion for the synthesis of antisense DPR proteins and supports the use of sense C9ORF72 ASOs to prevent the accumulation of both sense- and antisense-dependent DPR proteins in C9ORF72 ALS/FTD.

Early auditory and adult mating experiences interact with singer identity to shape neural responses to song in female zebra finches
Social and sensory experiences across the lifespan can shape social interactions, however, experience-dependent plasticity is widely studied within discrete life stages. In the socially monogamous zebra finch, in which females use learned vocal signals to identify individuals and form long-lasting pair bonds, developmental exposure to song is key for females to show species-typical song perception and preferences. While adult mating experience can still lead to pair-bonding and song preference learning even in birds with limited previous song exposure ("song-naive"), whether similarities in adult behavioral plasticity between normally-reared and song-naive females reflect convergent patterns of neural activity is unknown. We investigated this using expression of a marker of neural activity and plasticity (phosphorylated S6) in mated normally-reared and song-naive females in response to song from either their mate, a neighbor, or an unfamiliar male. We found that in portions of a secondary auditory region (the caudomedial nidopallium NCM) and in dopaminergic neurons of the caudal ventral tegmental area hearing the mate's song significantly increased pS6 expression in females from both rearing conditions. In contrast, within other NCM subregions, song-identity drove different patterns of pS6 expression depending on the rearing condition. These data suggest that developmental experiences can have long-lasting impacts on the neural signatures of behaviors acquired in adulthood and that socially-driven behavioral plasticity in adults may arise through both shared and divergent neural circuits depending on an individual's developmental experiences.