bioRxiv Subject Collection: Neuroscience's Journal

Spacetime concordance in the primate cortex
The expanding scale and complexity of functional brain image datasets require space-time analytics. Spacetime concordance (STC) meets this need through an adaptive and robust framework optimized for high-speed analysis. At the core of STC, the Regional Functional Affinity (RFA) metric quantifies functional diversity and uniformity in primate connectomes using wakeful fMRI. This data-driven optimization achieves considerably faster processing, becoming broadly relevant to comparative neuroscience applications. We validated this approach using large-scale datasets from the Human Connectome Project (HCP) (N = 1,003) and the NIH Marmoset Brain Mapping Project (N = 26). Results demonstrate striking correspondence between parcellation boundaries of HCP atlas and functional heterogeneity, with boundary lines consistently aligning with regions of low RFA values. In humans, higher-order association networks exhibited lower RFA values indicating functional diversity, while primary sensorimotor networks displayed higher RFA values reflecting uniformity. Cross-species analysis revealed evolutionary conservation of this organizational principle alongside species-specific adaptations. The RFA metric successfully bridges discrete parcellation schemes and continuous models of brain function, offering new insights into primate brain organization and evolution.

Beyond the straight path: high-density laminar recordings in the ventral hippocampus with curved microprobes
Brain function is governed by neural circuits distributed across an intricate, three-dimensional landscape of anatomically complex structures. Current methods for monitoring neural activity are limited to investigating structures that lie along a single, linear trajectory. While this approach is effective for columnar regions, such as dorsal cortical areas or the relatively planar dorsal hippocampus, it fails in deep or curved structures, like the ventral hippocampus, where a linear probe can only achieve with difficulty the combination of physical access and perpendicular orientation required for recordings across all layers. To overcome this limitation, we developed a multisite microelectrode array with a pre-formed curved geometry, engineered to align perpendicularly with neuronal layers in deep anatomical targets regardless of their orientation. This interface integrates a polymer-based array, featuring 16 PEDOT:BF4-coated microelectrodes for robust signal acquisition, with a dissolvable silk stiffener for precise surgical insertion. The resulting device exhibited excellent electrical properties (avg. impedance 18 k{Omega}) and enabled accurate placement across the distinct neuronal layers of the ventral hippocampus CA1 region. These capabilities allowed for successful recordings of both local field potentials and single-unit activity from this region, providing a powerful new tool to investigate the network dynamics of previously inaccessible neural circuits.

Flexible gaze reinstatement during working memory for natural scenes
Working memory (WM) representations may be more action-oriented and anatomically widespread than previously assumed. For instance, oculomotor signatures like gaze biases can reflect spatial WM content. However, the specificity and functional relevance of such signatures is unclear. Here, we tracked eye gaze during WM for naturalistic images, and manipulated which image features were most task-relevant (visual or semantic). In two experiments, we found that the eyes carried out item-specific spatiotemporal gaze sequences during WM maintenance, retracing the scanpath from stimulus encoding. Therefore, gaze patterns during WM track the identity of complex, natural images held in mind. Moreover, the degree of such WM gaze reinstatement was stronger when the task prioritized visual detail, and ramped up in anticipation of the test probe. Oculomotor WM signals are therefore malleable to when and how the content will be used, indicating that distributed WM representations are prospectively-oriented and functionally flexible to situational needs.

Disrupted Regional Dynamics of Structure-Function Connectivity Coupling in Euthymic Bipolar Disorder
Background: Bipolar disorder (BD) is characterized by persistent disturbances in emotional regulation and cognitive function, even during euthymia, yet its neural mechanisms remain unclear. Given evidence of structural and dynamic functional connectivity (dFC) abnormalities in BD, investigating dynamic structure-function connectivity coupling (SC-FC coupling) may provide insights into the pathophysiology of the disorder. Methods: Diffusion tensor imaging and resting-state fMRI data were collected from 61 euthymic BD-I patients and 54 healthy controls (HC). Structural connectivity was derived using probabilistic tractography, and dFC was estimated with a sliding-window approach. SC-FC coupling was quantified as the extent to which structural features predicted dFC using multivariate linear regression. Abnormal SC-FC coupling in BD was assessed at both the network and regional levels, relative to HC. Over time, SC-FC coupling was categorized into high- and low-coupling states, and dynamic state analyses of dwell time, occurrence rate, and transition probabilities were performed in the affected brain regions. Results: Network-level analyses indicated that BD exhibits lower SC-FC coupling in subcortical regions compared with HC. Regional analyses revealed significantly reduced dynamic SC-FC coupling in two thalamic subregions (medial posterior and rostral temporal) and in the right primary somatosensory cortex in BD compared to HC. Dynamic analyses further demonstrated thalamic instability: BD showed shorter dwell times in high-coupling states, increased occurrence of low-coupling states, and more frequent high-to-low coupling transitions than HC. These abnormalities suggest that BD is characterized by disrupted structure-function integration and unstable thalamocortical dynamics. Conclusion: Our findings reveal regional abnormalities in SC-FC coupling dynamics in BD, indicating persistent dysfunction of structure-function integration during euthymia. Dynamic coupling measures may provide preliminary insights into potential biomarkers for disease monitoring.

A validated set of neural gene reporter mice and chemical tracers tools for mapping knee innervating neurons
Joint pain is an increasing concern for our aging population, as current therapies to slow joint disease progression or reduce pain are largely ineffective and often carry significant health and dependency risks. Age and joint disease induce changes to all tissues that make up the joint, including the dense neural network that innervates the joint. Several studies have correlated some joint innervation changes in joint diseases such as osteoarthritis or rheumatoid arthritis, but little is known about their respective functional consequences. In general, knee innervating neurons are classified as either non/peptidergic nociceptive or sympathetic neurons. How subtypes of these neurons affect individual pain experience remains relatively uncharacterized. The few studies typically focused on a single neural subtype due to the limited availability of validated tools to study joint innervation1-5. To better understand the relationship between aging, joint disease, and pain, systematic characterization of pain nociceptors and other neural subtypes that regulate joint homeostasis and pain signaling is urgently needed. The objective of this study was to establish a validated molecular and genetic toolbox for accurate mapping of the neuroarchitecture in the murine knee. We screened a panel of genetic reporter mice, consisting of Cre and Flp recombinase driver mouse lines that activate recombinase responsive reporter alleles in either peripheral nociceptors or post-ganglionic sympathetic neurons, for their specificity and accuracy in labeling their respective neural subtype in the dorsal root ganglion and knee joint. In addition, we compared the performance of a series of conventional retrograde tracers for effective tracking of primary afferent sensory and post-ganglionic sympathetic neurons from the knee joint. The validated molecular and genetic tools identified in this study will facilitate the creation of comprehensive joint innervation maps in physiological and pathological contexts, setting the stage for identifying the cellular and molecular changes responsible for mediating joint pain, a necessary goal for improved therapeutic interventions.

Target engagement in human motor cortex induced by constant sinusoidal and amplitude-modulated transcranial AC stimulation
Transcranial alternating current stimulation (tACS) is a noninvasive technique for modulating brain oscillations. While sinusoidal tACS (sin-tACS) delivers current at a constant amplitude, amplitude-modulated tACS (AM-tACS) uses a high-frequency carrier modulated by a low-frequency envelope. We systematically compared the acute effects of sin-tACS at theta (5 Hz), alpha (10 Hz), beta (20 Hz), and gamma (140 Hz) frequencies, and AM-tACS (140 Hz carrier frequency modulated at theta, alpha, or beta) on corticospinal excitability. Healthy participants received 2 mA peak-to-peak tACS to the primary motor hand area (M1HAND) via a bipolar montage (M1HAND-Pz). Each tACS block consisted of ten 30-second stimulation periods interleaved with 6-second pauses, followed by 11 minutes without stimulation. Corticospinal excitability was assessed during each block using single-pulse transcranial magnetic stimulation (TMS), delivered at the peak and trough of tACS. MEP amplitudes were generally larger at the trough. Only beta sin-tACS and theta AM-tACS significantly modulated corticospinal excitability. Beta sin-tACS increased MEP amplitudes in early stimulation epochs, while theta AM-tACS facilitated MEPs in later stimulation epochs and this facilitation persisted briefly after stimulation ended. Participants with stronger early responses to beta sin-tACS also tended to show greater delayed effects with theta AM-tACS. These excitability changes during tACS were not predicted by simulated electric field strength. A follow-up EEG experiment revealed that beta sin-tACS increased beta power over left sensorimotor cortex, while theta AM-tACS decreased beta power over midline parietal cortex. These EEG changes were restricted to tACS pauses. The results show that sin-tACS and AM-tACS can both modulate corticospinal excitability, but functional changes differ in temporal dynamics, frequency specificity, and cortical region engagement.

Computational modelling of novelty detection in the mismatch negativity protocols and its impairments in schizophrenia
The human auditory system rapidly distinguishes between novel and familiar sounds, a process reflected in mismatch neg- ativity (MMN), an EEG-based biomarker of auditory novelty detection. MMN is impaired in psychiatric conditions, most notably schizophrenia (SCZ), yet the neuronal mechanisms underlying this deficit remain unclear. Here, we combined com- putational modelling and genetic analyses to investigate how SCZ-associated cellular abnormalities affect auditory novelty detection. We developed an integrate-and-fire spiking network model capable of detecting four types of auditory novelty, including stimulus omission. Based on assumptions of short-term depressing synapses between the subpopulations of the net- work and the existence of neuronal inputs that are phase-locked to the rhythm of the recently experienced stimulus sequence, the model reliably reproduced MMN-like novelty detection and allowed systematic testing of SCZ-related cellular alterations. Simulations revealed that both reduced pyramidal cell excitability, linked to ion-channel dysfunction, and decreased spine density impaired novelty detection, with the latter producing stronger deficits. Our work provides a flexible spiking network model of auditory novelty detection that can link cellular-level abnormalities to measurable MMN deficits, improving their mechanistic interpretation and helping to explain the heterogeneity of SCZ.

Contralateral-Ipsilateral Segregation as a Conserved Principle of the Visual Corpus Callosum
How the corpus callosum (CC) integrates the left and right visual fields to create a unified perceptual experience is a fundamental unresolved question. It remains unresolved whether the CC transmits this information via segregated parallel channels or through mixed, integrated pathways. Here, we resolve this by creating a multimodal functional blueprint of the forceps major (FMA), the principal component of the visual callosum, in humans and mice. By combining ultra-high-field 7T fMRI with Bayesian population receptive field (pRF) modeling in humans, we directly test the competing hypotheses: segregated streams should manifest as voxels dominated by single pRFs, whereas integrated signals would produce voxels with multiple pRFs. Our results reveal a functionally segregated architecture dominated by single pRFs (expected probability 0.92), forming parallel streams that represent the contralateral (87.7%) and distinct ipsilateral (12.3%) visual field. In contrast, integrative dual pRFs are sparse and localized to the cortical boundary, reflecting the localized convergence of bilateral axons. This organizational principle is anatomically corroborated at the mesoscale in the mouse, where dual-color neuronal viral tracing and whole-brain light sheet microscopy imaging reveal a complementary laminar segregation of callosal fibers. Collectively, these findings establish that the visual callosum operates as a set of parallel, segregated information conduits, providing a new framework for understanding unified visual perception and for investigating callosal disruptions in neurological disorders.

Impact of Connectivity Granularity: A Comparison of ROI and Network-Level Approaches for Early Schizophrenia Classification
While schizophrenia diagnosis relies on clinical interviews, there is growing interest in neuroimaging-based computational tools to aid classification. In particular, resting-state fMRI-derived functional connectivity has been explored as a potential biomarker, with applications not only in supporting clinical assessment but also in research contexts such as patient stratification and probing disease mechanisms. Here, we compare two common approaches to computing functional connectivity - region of interest (ROI)-level and brain network-level - and evaluate their predictive power for classifying first-episode schizophrenia patients, in contrast to most prior work focusing on chronic patients. We show that ROI-level features consistently outperform network-level features. Despite the simplicity of our classification models, we achieved accuracies up to 83.15% using the AAL90 atlas. We also found that non-lagged functional connectivity generally outperforms lagged variants, suggesting that added temporal complexity may introduce noise rather than improve predictive power. Overall, our findings highlight region-based connectivity from a medium-resolution atlas as a promising representation for early-stage schizophrenia classification, while emphasising the need for validation on independent datasets to confirm generalisability.

Effects of combined prenatal exposure to air pollution and maternal stress on immune and dopaminergic gene expression in the gut-brain axis
Air pollution and maternal stress during pregnancy are both risk factors for neurodevelopmental disorders and often converge on the same communities. Epidemiological and animal studies suggest that maternal psychosocial stress may worsen the effects of air pollutants on neurodevelopmental outcomes. Previous work utilizing a mouse model of combined prenatal exposure to diesel exhaust particles (DEP) and maternal stress (MS) has found numerous sex-specific effects of DEP/MS exposure on neuroimmune outcomes, dopamine receptors, the gut-brain axis, and social behavior. However, it is unclear how broadly the immune landscape is shifted in the brain and intestinal epithelium following DEP/MS. Here, we analyzed immune gene expression in 5 brain regions important for social behavior and in 3 regions of the intestinal epithelium in both male and female offspring following either DEP/MS or control exposure. We found several interesting overall patterns. First, changes in expression of immune genes such as CD11b and Tlr4 were concentrated in the nucleus accumbens and hippocampus. Tlr4 and Il-17ra mRNA also increased in the jejunum and colon following DEP/MS, but only in females. Second, in the nucleus accumbens, catecholamine-O-methyltransferase (Comt) and dopamine transporter 1 (Slc6a3) gene expression were increased following DEP/MS indicating increased dopamine degradation at and reuptake from the synapse, respectively. Additionally, Drd2 mRNA was decreased following DEP/MS in males. Finally, we observed numerous sex differences in immune gene expression regardless of treatment in both the brain and gut. Together, these findings suggest the nucleus accumbens is a key site for neuroimmune and dopaminergic changes following DEP/MS exposure and indicate persistent female-specific changes in intestinal immunity following these prenatal exposures.

Menstrual cycle phase alters corticospinal excitability and spike-timing-dependent plasticity in healthy females
The known fluctuations in ovarian hormone concentrations across the eumenorrheic menstrual cycle contribute to modulations in cortical excitability and inhibition. However, how such changes affect spike-timing-dependent plasticity (STDP) has not been systematically studied. This research aimed to determine the effect of the menstrual cycle on corticospinal excitability and STDP. Twelve eumenorrheic female participants (age: 25 {+/-} 5 years), visited the lab in three menstrual cycle phases: early follicular (EF), late follicular (LF), and mid-luteal (ML). Visits comprised of corticospinal excitability (motor evoked potential [MEP]/Mmax), short-intracortical inhibition (SICI), and intracortical facilitation (ICF) measures, recorded in the resting first dorsal interosseous. Followed by a paired associative stimulation (PAS) protocol, utilising ulnar nerve and transcranial magnetic stimulation (25 ms interstimulus interval) to elicit neuroplasticity. To assess the time course of STDP, measurements were repeated at 15 and 30-minutes post PAS. Corticospinal excitability (MEP/Mmax) was greater in the LF phase (p [≤]0.002) compared to EF and ML, with no phase effects observed for SICI or ICF (p[≥]0.112). PAS elicited an increase in MEP/Mmax across all phases at 15-minutes (112 {+/-} 5, 115 {+/-} 5, and 113 {+/-} 7% baseline, p[≤]0.010), whereas at 30-minutes only ML was facilitated (126 {+/-} 7% baseline, p=0.029). The present data demonstrates facilitatory STDP can be induced with PAS across the tested menstrual cycle phases, but responses are prolonged and potentiated in the ML phase. Additionally, increased corticospinal excitability in the LF phase is likely due to intrinsic changes within the descending tract, as no changes in intracortical neurotransmission were observed.

Exploring Single-Cell Gene Regulatory Dynamics in Rett Syndrome
Rett syndrome is a monogenic disorder with an incidence of 95% in women, characterized by the complexity of studying the associated phenotype due to the heterogeneity in patient tissues from the stochastic silencing of the affected X chromosome. Furthermore, we are largely unaware of the cascade of alterations that occur in neurons due to transcriptional changes induced by the affected MECP2 gene. To address these challenges, an in-depth network analysis was implemented using organoid single-cell transcriptomic data derived from human patients. We performed a Weighted correlation network analysis and trajectory analysis to understand the differences in the developmental processes between samples, we followed by the generation of gene regulatory networks for each relevant cell developmental pathways to assess the master regulator that are involved in this process with potential therapeutic implications which we identified by integration with SFARI and Genes4Epi. The results were adapted into dynamic Boolean models from fitted with the transcriptomic data for validation in which we evaluated the attractor field from each reachable state . These approaches allowed us to explore differences in regulatory behavior in the developmental pathways. Our study provides an insight that pinpoints the cellular stages on which the regulation and compensatory mechanism activate and regulate Rett syndrome. We identified 19 Master regulators for the Dopaminergic developmental trajectory, as well as 34 Master regulator genes for the Gabaergic developmental trajectory. Dynamic Boolean modeling of this systems showcased a comprehensive understanding of the disrupted developmental pathways of Rett syndrome, highlighting the transitional states of potential within maturation trajectories as the key point of divergence in regulation for Rett syndrome. After complementing with enrichment and clinical relevant variant analysis, we identify the key actors in this system as NR2F1 and TCF4, with TCF4 suggesting a symmetrical compensatory relationship with MeCP2, and NR2F1 as possible link with wider developmental conditions, this concluded with highlighting the possibility of regulation in this condition being affected by the MAPK-ERK pathway of transcriptional regulation in this condition being affected by the MAPK-ERK pathway of transcriptional regulation, offering a novel angle for targeted research.

Cerebral Bases and Neural Dynamics of Audiovisual Temporal Binding Window: a TMS study
The temporal binding window (TBW) refers to the time interval within which two stimuli, typically visual and auditory, are perceived as synchronous. Neural bases underlying this process consistently implicate a large-scale network with superior temporal sulcus (STS) as a central hub, alongside contributions from primary auditory and visual cortices and higher-order areas including prefrontal and posterior parietal cortex. This study aimed to provide causal evidence for the involvement of superior temporal gyrus (STG) and intraparietal sulcus (IPS) in the simultaneity judgment (SJ) task using MRI-guided transcranial magnetic stimulation (TMS). In particular, we aimed to clarify temporal dynamics of these regions in audiovisual synchrony perception. Forty adults performed an SJ task in which they had to determine whether stimuli were synchronous or asynchronous. Single-pulse TMS was applied over bilateral IPS, STG, or the vertex at different delays following stimulus offset. Early stimulation of left IPS and right STG increased the proportion of "synchronous" responses. In contrast, later stimulation of bilateral STG was associated with reduced synchrony perception. These findings provide causal evidence for a dynamic interplay between parietal and temporal regions in audiovisual temporal integration. Early IPS and STG involvement facilitates temporal integration, while later STG activity promotes perceptual segregation.

LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD
The long interspersed element-1 (LINE1) retrotransposon RNAs are abnormally elevated in various neurodegenerative disorders, but their pathogenic roles remain unclear. Here we investigated the mechanism of LINE1 RNA accumulation and its function in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) associated with C9ORF72 repeat expansion and TDP-43 loss-of-function, the leading causes of familial and sporadic forms of these neurodegenerative diseases. We show that LINE1 RNA is dysregulated due to an impaired nuclear exosome targeting (NEXT) degradation pathway. Its elevation epigenetically increases chromatin accessibility, enhancing global transcription via a retrotransposon-independent mechanism. Reducing LINE1 RNA mitigates chromosomal abnormalities and improves the survival of disease-relevant neurons. These findings uncover an essential noncoding RNA function and regulatory mechanism of LINE1 in neurons, providing insights into disease pathogenesis and highlighting potential therapeutic targets for neurodegenerative diseases.

Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons
Neurons in the central nervous system (CNS) display a high capacity for axon growth during early development but lose this ability at a pivotal differentiation stage marked by synaptic maturation, circuit integration, and a profound shift in gene transcription. Once mature, most CNS neurons fail to reverse this transcriptional switch after axon injury, fundamentally constraining their intrinsic capacity for axon regeneration. Here, we show with single-nucleus RNA sequencing that forced expression of the transcription factor Sox11 in mature corticospinal tract (CST) neurons produces large-scale and stable changes in gene expression that are highly enriched for growth-relevant processes, and which strongly resemble those of pre-synaptic embryonic stages. Moreover, Sox11 is equally effective when delivered to chronically injured CST neurons. These data reveal the ability of Sox11 to reverse a critical step of neuronal maturation even in otherwise unperturbed neurons, clarifying the transcriptional underpinnings and highlighting the potential of Sox11 to act as a pro-regenerative stimulus.

Human brain organoids record the passage of time over multiple years in culture
The human brain develops and matures over an exceptionally prolonged period of time that spans nearly two decades of life. Processes that govern species-specific aspects of human postnatal brain development are difficult to study in animal models. While human brain organoids offer a promising in vitro model, they have thus far been shown to largely mimic early stages of brain development. Here, we developed human brain organoids for an unprecedented 5 years in culture, optimizing growth conditions able to extend excitatory neuron viability beyond previously-known limits. Using module scores of maturation-associated genes derived from a time course of endogenous human brain maturation, we show that brain organoids transcriptionally age with cell type-specificity through these many years in culture. Whole-genome methylation profiling reveals that the predicted epigenomic age of organoids sampled between 3 months and 5 years correlates precisely with time spent in vitro, and parallels epigenomic aging in vivo. Notably, we show that in chimeric organoids generated by mixing neural progenitors derived from 'old' organoids with progenitors from 'young' organoids, old progenitors rapidly produce late neuronal fates, skipping the production of earlier neuronal progeny that are instead produced by their young counterparts in the same co-cultures. The data indicate that human brain organoids can mature and record the passage of time over many years in culture. Progenitors that age in organoids retain a memory of the time spent in culture reflected in their ability to execute age-appropriate, late developmental programs.

Subsequent memory effect in the inferior frontal gyrus revealed by fNIRS
A central finding in memory research is the subsequent memory effect, which describes consistent neural differences during encoding between events that are later remembered versus those that are forgotten, which has been reliably replicated with both EEG and fMRI for the past decades. Replicating the subsequent memory effect using fNIRS could enable research opportunities that are difficult to pursue with other methods, including studies with children, patient populations, or experiments in highly naturalistic settings. Therefore, our study investigated whether the prefrontal cortex is differentially involved in subsequently remembered versus subsequently forgotten stimuli using fNIRS. Our results showed that in particular channels mapping onto the inferior frontal gyrus showed more activation during encoding of subsequently remembered events compared to subsequently forgotten events. These results demonstrate that fNIRS can reliably capture the subsequent memory effect, providing new opportunities to study memory mechanisms across diverse populations and real-world contexts.

Vividness of mental imagery is a broad trait measure of internally generated visual experiences
Research on mental visual imagery typically relies on vividness ratings. However, vividness is ill-defined as it lacks an objective reference. Here, we present survey results that suggest vividness is nevertheless a robust trait. It explains individual differences of a broad range of subjective experiences, from the detail of mental imagery, the propensity to report having other internally generated visual experiences, and the vividness of visual dreams. Critically, simple vividness ratings can replace the protracted questionnaires commonly used for this purpose and reduce methodological issues with these instruments. We further find that vividness is closely linked with the experience of "seeing" mental images or projecting them into the external world. People who report seeing mental images with their eyes shut are also more likely to experience externally projected imagery. Nevertheless, many people report having mental depictions but without seeing. Overall, our results indicate we should redefine visual aphantasia to distinguish individuals with faint or unseen visual images from those completely lacking a pictorial representation.

From rest to focus: Pharmacological modulation of the relationship between resting state dynamics and task-based brain activation
Dynamic resting-state brain activity provides insight into intrinsic neural function and holds promise for predicting individual responses to cognitive demands and pharmacological interventions. This research could ultimately guide medication selection, yet links between network dynamics and medication effects on cognitive function require further validation. Here, we examined whether dynamic activity of an attentional network at rest relates to task-evoked brain activation on the Multi Source Interference Task (MSIT) following administration of methylphenidate (20mg) and haloperidol (2mg), which have opposing effects on attention and catecholaminergic function. Fifty-nine healthy adults completed resting-state and task-based fMRI on three separate days on which they received methylphenidate, haloperidol, or placebo in a double-blind placebo-controlled design. Coactivation pattern analysis determined time spent in the dorsal attention network (DAN) under placebo at rest. Linear mixed-effects modelling assessing the relationship between MSIT task activation under drug and time spent in DAN at rest under placebo and MSIT task activation under drug identified a significant interaction in the dorsolateral prefrontal cortex (dlPFC; p<0.001). Post-hoc analyses indicated that more time in the DAN at rest under placebo was associated with decreased MSIT dlPFC activation under methylphenidate and increased dlPFC activation under haloperidol. Findings demonstrate that resting dynamics of an attentional network are linked to task-related brain responses under different drug conditions within a region implicated in attentional control and sensitive to catecholaminergic variance. Resting-state dynamics may predict pharmacological modulation of goal-directed cognition, highlighting the potential clinical utility of resting-state dynamics in predicting medication response and supporting individualized treatment.

A model of rhythm production and rhythmic auditory stimulation in healthy and Parkinsonian basal ganglia
In fMRI experiments, the basal ganglia is consistently activated by rhythmic action and sensorimotor synchronization to a metronome, and conditions like Parkinsons Disease that affect basal ganglia and its dopaminergic modulation are experimentally seen to affect performance on both types of task. However, it is not clear what role this circuit or dopaminergic modulation play during rhythm production and synchronization tasks. Here, we propose that the basal ganglia may specify, maintain, and adapt the tempo with which rhythmic action (e.g. finger tapping or walking) is performed. We build a model based on previous "action selection" models of the cortico-basal-ganglia loop, altered such that cortico-basal-ganglia loops correspond not to distinct actions but to a continuum of possible action tempi. During rhythm production, an initial tempo is selected by cortical input, and rhythmic action can be automatized to continue in the absence of cortical input if tonic dopamine levels in striatum are sufficiently high. When striatal dopamine is reduced, our model reproduces two key features of dopamine deprivation in Parkinsons disease: freezing of gait, and increased variation in produced intertap intervals during rhythmic tapping. By reanalyzing data from a recent experiment with Parkinsonian patients, we confirm the models prediction that increased interval variability should be largely attributable to increased tempo drift (rather than, e.g., increased timekeeper noise). This model of rhythm production is the first to invoke specific features of basal ganglia circuitry. It augments existing models of action selection in basal ganglia with the addition of continuous action parameters, and in doing so provides a starting point for further modeling of action timing and rhythm in the motor system. It offers a new model of the mechanism by which rhythmic auditory stimulation supports gait in Parkinsons patients, and makes a new, testable prediction about sensorimotor synchronization under conditions of low tonic dopamine.

White Matter Microstructure Fingerprint of Cerebral Small Vessel Disease
There is much controversy about the spatial heterogeneity and microstructural characterisation of white matter hyperintensities (WMHs), the neuroimaging hallmark of cerebral small vessel disease. To address this knowledge gap, we analysed relaxometry and diffusion-weighted magnetic resonance imaging (MRI) together with cardiovascular risk data in a community-dwelling adult cohort (202 participants, mean age: 69.2 years, range: 53.3-85.4 years, 110 females). Following automated WMH detection, we compared MRI-derived metrics of tissue myelination, iron content, axonal density, and extracellular water, between WMH and normal-appearing white matter (NAWM). Principal component analysis demonstrated a pattern of demyelination, axonal loss, and extracellular fluid accumulation, particularly pronounced in periventricular regions. The layer-specific profiles of theWMHs revealed a centrifugal gradient of white matter vulnerability, with myelin loss and extracellular water accumulation, interpreted as oedema, at the core, and ongoing axonal reorganization and demyelination in the surrounding tissue. The obtained signatures of white matter pathology were intimately linked to the aging-related increase in cardiovascular risk. High blood pressure and impaired glucose regulation, together with reduced cholesterol and hemoglobin levels, emerged as key contributors. Our findings suggest that WMHs represent the radiologically visible endpoint of a more widespread white matter damage in cerebral small vessel disease. This underscores the pressing need for early detection and consequent treatment of cardiovascular risk factors.

AGO1 in neural progenitor cells orchestrates brain development and sociability via LIN28A-REELIN axis
AGO1, an essential RNA binding protein (RBP) in RNA interference, is associated with autism spectrum disorder (ASD). However, the precise functions of AGO1 in brain development and related disorders remain largely unexplored. Here, we report the critical roles of AGO1 in neural progenitor cells (NPCs) in shaping the structure of the developing brain and promoting sociability. In human forebrain organoids, AGO1 KO disrupts the formation of ventricle-like structures and delays cortical layer development. We discovered that AGO1 KO results in a loss of polarity in NPCs, which subsequently reduces neuronal development. These AGO1 KO phenotypes originate from the failure to suppress LIN28A in NPCs. AGO1 is primarily localized in the nucleus within NPCs and binds to the LIN28A promoter region, thereby inhibiting LIN28A transcription. We found that increased LIN28A in AGO1 KO NPCs alters the expression of endoplasmic reticulum (ER)-associated genes. The aberrant polarity phenotype in AGO1 KO NPCs was successfully ameliorated by either LIN28A knockdown or supplementing critical candidate effectors. We observed the impaired cortical structure and hyposociability and an increased repetitive behavior in Ago1 knockout (KO) mouse, characteristic symptoms of ASD. Collectively, our findings elucidate the intricate molecular mechanisms orchestrated by nuclear AGO1 in NPCs and underscores its pivotal roles in brain development, providing significant insights into ASD.

Metabolism-weighted brain connectome reveals synaptic integration and vulnerability to neurodegeneration
The remarkable abilities of the human brain arise from its specialized regions, which process and integrate information through complex connectivity patterns. While network science has developed various metrics to assess the degree of connectivity between these regions, it has not yet considered the level of activity within each region. Consequently, a highly connected region might be classified as a hub in the brain's connectome, even if it is weakly active or linked primarily to less active areas. Conversely, a region that is highly active but has only a few connections may be undervalued. To address this issue, we present a fully-weighted brain graph in which both edges (representing connectivity) and nodes (indicating metabolic activity) contribute to the importance, or centrality, of each region. In this model, the metabolism-weighted centrality (MwC) of each brain region integrates both connectivity and metabolic activity, using three datasets from simultaneously acquired functional MRI and metabolic FDG-PET data. We found that our fully-weighted brain graph demonstrates a greater ability to explain quantitative imaging data of signaling metabolism and its association with cognitive domains than a classical, edge-weighted graph. Additionally, regions with relatively high MwC exhibited increased synaptic and metabolic activity, as indicated by transcriptomic data. Furthermore, these regions showed higher susceptibility to neurodegenerative disorders. This framework of a fully-weighted brain graph represents a paradigm shift from connectivity-based metrics to an activity-aware brain graph. It offers a more biologically informed representation of brain network dynamics, connecting metabolic activity levels to higher cognitive functions as well as neurodegeneration.

The inhibition of the JNK2-Syntaxin-1A interaction neuroprotects against retinal degeneration
Retinal diseases (RDs) involve the degeneration of retinal cells, particularly retinal ganglion cells (RGCs), often driven by glutamate imbalance and aberrant signaling. We previously identified a presynaptic self-amplifying mechanism of glutamate overflow, where NMDA overstimulation activates JNK2-mediated phosphorylation of STX1A. To block this mechanism, a cell-permeable peptide, called JGRi1, was previously developed to disrupt the JNK2-STX1A interaction. Here, we investigated whether inhibition of this pathway by JGRi1 could provide neuroprotection in retinal degeneration. Here we showed that JGRi1 efficiently reached the mouse retina upon topical administration as eye drops and granted retinal protection. Using an ex vivo optic nerve cut (evONC) model, we demonstrated that JGRi1 preserved RGC viability, reduced phosphorylation of JNK and STX1A, and lowered glutamate release. In retinal wholemounts, JGRi1 similarly preserved RGC survival. Furthermore, in an NMDA-induced degeneration model, JGRi1 protected RGCs, reduced glutamate levels, disrupted the JNK2-STX1A interaction, and limited microglial infiltration. Collectively, our findings highlight the central role of the JNK2-STX1A pathway in retinal degeneration and identify JGRi1 as a promising neuroprotective tool.

Gut microbiota as a modulator of circadian neural development in the honey bee model.
Disruption in gut microbiota during the early postnatal period can disrupt normal neural development and result in long-term behavioral alterations (1). Similar to other neural systems, the circadian clock mechanism continues to mature after birth (2), yet how microbial disturbances in the early period influence the onset of circadian rhythms and the development of central clock mechanisms remains poorly understood. Here we studied whether early life gut dysbiosis affects the ontogeny of behavioral circadian rhythms and the maturation of clock neurons using the honey bee (Apis mellifera), a model organism that shares features of postnatal development of behavioral circadian rhythm and clock system (3,5) with humans (6). Our findings demonstrate that antibiotic-treated and gnotobiotic-reared bees display reduced rhythmicity compared to controls. These treatments also impair the development of the circadian pacemaker, marked by fewer Pigment-Dispersing Factor (PDF)-expressing neurons. Additionally, antibiotic exposure increased the expression of the Insulin-like Growth Factor Binding Protein Acid Labile Subunit (IGFALS) in early ages, which stabilizes the IGF-1/27, a hormone important for neurodevelopmental processes42. Together, these results identify gut microbiota as a modulator of circadian development. Our work provides an understanding of how early-life microbial disruptions influence the development of circadian rhythms, providing information that may extend to other animals, including humans.

Hypoxia preconditioned neural xenografts promote repair of brain tissue after stroke
Stroke is a leading cause of long-term disability, yet no effective regenerative therapies exist. While cell-based therapies have shown promise in preclinical animal models, their clinical application remains limited due to poor survival of transplanted cells in the ischemic stroke environment. Hypoxic preconditioning has emerged as a strategy to potentially enhance graft survival, but the cellular mechanisms and translational relevance in human iPSC-derived neural progenitor cells (NPCs) are not fully understood. Here, we tested whether hypoxic preconditioning of NPCs affects their molecular and functional properties including proliferation and survival in vitro and after transplantation into a stroke mouse model. Hypoxic preconditioning enhanced proliferation and glial differentiation in vitro, improved cell survival post-transplantation, and enhanced regeneration-associated tissue responses such as vascular remodeling in the peri-infarct brain. These findings suggest that hypoxic preconditioning is a clinically translatable approach to increase the NPC graft survival in the post-stroke brain.

Individual differences in the pharmacokinetic profiling of {triangleup}9-THC may be associated with differential motivational effects of {triangleup}9-THC on cognitive performance.
Cannabis is the most widely used illicit substance in the United States, and its use is increasing with the recent push for legalization and decriminalization, as well as the growing use for medicinal purposes. While cannabis can have positive effects in some individuals, there are potential negative consequences including dependence, psychosis, and cognitive impairments. The top reported reasoning for using cannabis is to alleviate stress, however, whether cannabis differentially induces positive or negative effects under stress has not been studied. The current study investigates whether stress affects working memory, and if THC can exacerbate or ameliorate its effect. An additional aim is to determine if plasma THC concentrations are associated with cognitive performance. Adult male and female Sprague Dawley rats performed a delay-match-to-sample working memory task. Rats assigned to the stress group were exposed to acute restraint stress prior to administration of either vehicle, 0.5,1, or 3 mg/kg THC. Blood samples were collected 5, 25, 60, and 120 minutes after administration. Acute restraint stress and THC did not impact working memory. However, acute administration of 3mg/kg THC disrupted motivation-related engagement in the task in a subset of rats. These non-responders exhibited greater plasma THC and metabolite concentrations compared to rats who maintained baseline response rates after 3mg/kg THC administration. Individual differences in the pharmacokinetic/metabolic profile of THC may be associated with differential sensitivity to cognitive/motivational effects of THC and highlight one potential mechanism for the diversity of reported adverse versus positive outcomes after THC exposure.

Chronic Ethanol Drinking Alters Medial Prefrontal Cortex and Nucleus Accumbens Astrocyte Translatome and Extracellular Matrix Glycosaminoglycans
Alcohol Use Disorder is a leading preventable cause of morbidity and mortality, yet knowledge of mechanisms driving ethanol-related neuroplasticity remains incomplete. While research has traditionally focused on neuronal signaling, emerging evidence implicates astrocytes in addiction-related adaptations. Here, we investigated the astrocyte-specific molecular consequences of chronic ethanol consumption in the prefrontal cortex and nucleus accumbens, two brain regions critical for executive control and reward processing. Using Translating Ribosome Affinity Purification RNA-seq and bulk RNA-seq in Aldh1l1-EGFP/Rpl10a mice, expressing an EGFP tag on astrocyte ribosomes, we identified hundreds of differentially translated astrocytic genes following chronic continuous two-bottle choice ethanol drinking. Sex-specific analyses revealed greater astrocytic changes in the female PFC and male NAc. Pathway enrichment highlighted extracellular matrix remodeling, synaptic signaling, mitochondrial function, and immune-related pathways. Analyses of individual drinking levels further demonstrated distinct correlations between ethanol intake and astrocytic translation. The major components of the brain extracellular matrix are chondroitin sulfate proteoglycans, produced primarily by astrocytes and covalently bound to chondroitin sulfate glycosaminoglycan chains. Complementary mass spectrometry/liquid chromatography analyses of chondroitin sulfate, heparan sulfate, and hyaluronic acid glycosaminoglycan disaccharides revealed ethanol-induced alterations in chondroitin sulfate glycosaminoglycan sulfation patterns, with additional baseline differences identified between selectively bred high- and low-ethanol preference lines. Together, these findings indicate that astrocytes undergo profound sex- and region-specific adaptations to chronic ethanol, implicating extracellular matrix and glycosaminoglycan remodeling as key risk-factors for and mediators of chronic ethanol-related neuroplasticity.

MACS: Multi-Domain Adaptation Enables Accurate Connectomics Segmentation
Connectomics aims to map the neural wiring of brain by segmenting cellular structures from high-resolution electron microscopy (EM) images. Manual labeling and proofreading remain a major bottleneck for accurate extraction of microstructures. While computational models have advanced automated segmentation, they typically require training from scratch on each dataset, demanding substantial annotated data. Domain adaptation methods address this by transferring knowledge from a labeled source to a less-annotated tar get. However, existing approaches are limited to adaptation from a single source domain. This overlooks the potential benefits of integrating information from multiple diverse domains, motivating the development of multi domain adaptation. To address this, we propose MACS, the first known multi domain adaptation framework that combines knowledge from multiple heterogeneous source domains to learn segmentation in the target domain, and employs active learning to efficiently select the most informative target samples for annotation. MACS uses information-theoretic weighting to com bine source domains, and introduces a novel and efficient Bayesian Laplace approximation for uncertainty estimation. Our extensive experiments across nine connectomics datasets demonstrate that MACS consistently and sub stantially outperforms state-of-the art models, even under limited annotation budgets, with a mean improvement of 5.89% at the lowest annotation bud get and 27.72% at the highest annotation budget. In-depth analyses further reveal that MACS offers mechanistic interpretability by quantifying and ex plicitly upweighting the most transferable source domains for each target. The preprocessed datasets and the source code of MACS are publicly avail able at http://github.com/abrarrahmanabir/MACS.