bioRxiv Subject Collection: Neuroscience's Journal

Short Report: A Meta-Analysis of the Effects of Sleep Deprivation on the Cortical Transcriptome in Animal Models
Sleep deprivation (SD) causes large disturbances in mood and cognition. The molecular basis for these effects can be explored using transcriptional profiling to quantify brain gene expression. In the present report, we used a meta-analysis of public transcriptional profiling data to discover effects of SD on gene expression that are consistent across studies and paradigms. To conduct the meta-analysis, we used pre-specified search terms related to rodent SD paradigms to identify relevant studies within Gemma, a database containing >19,000 re-analyzed microarray and RNA-Seq datasets. Eight studies met our systematic inclusion/exclusion criteria, characterizing the effect of 18 SD interventions on gene expression in the mouse cerebral cortex (collective n=293). For each gene with sufficient data (n=16,290), we fit a random effects meta-analysis model to the SD effect sizes (log(2) fold changes). Our meta-analysis revealed 182 differentially expressed genes in response to SD (false discovery rate<0.05), 104 of which were upregulated and 78 downregulated. Gene-set enrichment analysis (fGSEA) revealed down-regulation in pathways related to stress response (e.g., glucocorticoid receptor, Nr3c1), cell death and neural cell differentiation, and upregulation related to hypoxia and inflammation. Exploratory analyses found that SD duration (ranging from 3-12 hrs) did not significantly influence differential expression. However, recovery sleep (RS: 2-18 hrs) was included in three studies, and reversed the impact of SD on four transcripts. Our meta-analysis illustrates the diverse molecular impact of SD on the rodent cerebral cortex, producing effects that occasionally parallel those seen in the periphery.

FMed-Diffusion Federated Learning on Medical Image Diffusion
Medical data is not available for public access due to privacy concerns of the patients and the stakeholders trustworthiness. However, Artificial Intelligence, especially all deeplearning models, is data hungry and fails to produce clinically relevant results without much data. Moreover, augmentation strategies are deployed to overcome the less data hurdle. The promising future in this direction is generative AI augmented data. The chatGPT and DALLE2 have become commercial products leveraging the generative AI in Natural Language Processing and Computer Vision. The diffusion models have started giving many promising results in the generative AI in computer vision. And in medical imaging, they can potentially create synthetic data to augment the scarce dataset. Diffusion models coupled with federated learning can create synthetic data on a large scale without the need to violate data privacy. This synthetic dataset could be used for further training of deeplearning models without the issues of patients identity theft from reverse engineering data. A Federated Learning paradigm of diffusion models has been proposed to overcome this hurdle and its related challenges. Our work focuses on diffusion models in federated learning settings. We named our novel model FMedDiffusion or Federated Learning on Medical Image Diffusion. We trained our model under distributed federated settings imitating real world clinical settings. We have achieved impressive results over three medical image datasets, APTOS 2019 Blindness Detection, Retinal OCT Detection, and COVID CT Detection in the federated setting on par with the traditional training. Our model FMedDiffusion has achieved an FID score of 7.1821 on the APTOS 2019 Blindness Detection dataset, an FID score of 8.8154 on the Retinal OCT Detection dataset and an FID score of 7.4486 on the COVID CT Detection dataset.reverse engineering data. A Federated Learning paradigm of diffusion models has been proposed to overcome this hurdle and its related challenges. Our work focuses on diffusion models in federated learning settings. We named our novel model FMedDiffusion or Federated Learning on Medical Image Diffusion. We trained our model under distributed federated settings imitating real world clinical settings. We have achieved impressive results over three medical image datasets, APTOS 2019 Blindness Detection, Retinal OCT Detection, and COVID CT Detection in the federated setting on par with the traditional training. Our model FMedDiffusion has achieved an FID score of 7.1821 on the APTOS 2019 Blindness Detection dataset, an FID score of 8.8154 on the Retinal OCT Detection dataset, and an FID score of 7.4486 on the COVID CT Detection dataset.reverse engineering data. A Federated Learning paradigm of diffusion models has been proposed to overcome this hurdle and its related challenges. Our work focuses on diffusion models in federated learning settings. We named our novel model FMedDiffusion or Federated Learning on Medical Image Diffusion. We trained our model under distributed federated settings imitating real world clinical settings. We have achieved impressive results over three medical image datasets, APTOS 2019 Blindness Detection, Retinal OCT Detection, and COVID CT Detection in the federated setting on par with the traditional training. Our model FMedDiffusion has achieved an FID score of 7.1821 on the APTOS 2019 Blindness Detection dataset, an FID score of 8.8154 on the Retinal OCT Detection dataset, and an FID score of 7.4486 on the COVID CT Detection dataset.

Attention induced perceptual traveling waves in binocular rivalry
Cortical traveling waves -smooth changes of phase over time across the cortical surface- have been proposed to modulate perception periodically as they travel through retinotopic cortex. Yet, little is known about the underlying computational principles. Here, we make use of binocular rivalry, a perceptual phenomenon in which perceptual (illusory) waves are perceived when a shift in dominance occurs between two rival images. First, we assessed these perceptual waves using psychophysics. Participants viewed a stimulus restricted to an annulus around fixation, with orthogonal orientations presented to each eye. The stimulus presented to one eye was of higher contrast thus generating perceptual dominance. When a patch of higher contrast was flashed briefly at one position in the other eye, it created a change in dominance that started at that location of the flash and expanded progressively, like a wave, as the previously suppressed stimulus became dominant. We found that the duration of the perceptual propagation increased with both distance traveled and eccentricity of the annulus. Diverting attention away from the annulus reduced drastically the occurrence and the speed of the wave. Second, we developed a computational model of traveling waves in which competition between the neural representations of the two stimuli is driven by both attentional modulation and mutual inhibition. We found that the model captured the key features of wave propagation dynamics. Together, these findings provide new insights into the functional relevance of cortical traveling waves and offer a framework for further experimental investigation into their role in perception.

Mesoscale Imaging of Cortical Sensorimotor Integration in Huntington's Disease Mice During Reward-Guided Behaviour
Huntington's disease (HD) is a neurodegenerative disorder that affects numerous brain functions, yet how altered sensory processing contributes to behavioral and learning deficits remains poorly understood. Previous wide-field mesoscale imaging and electrophysiological recording from anesthetized HD mice revealed that sensory stimulation induced exaggerated, prolonged cortical activity across more brain regions compared to wildtype (WT) littermates. This suggests differences in sensory processing; as such, this study aimed to investigate the cortical activity in a cue-based sensory-guided learning task in a custom-built Raspberry Pi-controlled two-alternative forced choice (2AFC) rig. The rig reliably enabled head-fixed zQ175 knock-in HD mice and WT controls crossed with Thy1-GCaMP6s mice, to perform a cue-based visual discrimination task while mesoscale calcium imaging recorded activity across layer 2/3 of the cortex. Mice that successfully licked the reward spout displayed decreased global cortical activity before the reward presentation, with WT mice showing more spatially localized suppression than HD mice. HD mice exhibited exaggerated cortical responses to visual stimuli and prolonged motor-related activity during licking. While this is an exploratory pilot study with limited sample size, preventing definitive genotype-based comparisons, the custom behavioral system lays the groundwork for future studies into how sensory processing deficits contribute to cognitive impairments in HD. This work provides an important step toward understanding the interplay between cortical circuit dysfunction and behavioral outcomes in HD, offering a novel platform to investigate early sensorimotor integration learning impairments.

SYNAPTIC INTERACTIONS IN PRIMATE MOTOR CORTEX: RELATIONS BETWEEN CONNECTIVITY AND INTRACORTICAL LOCATION
To investigate intracortical microcircuits within primate motor cortical areas, we documented pairs of neurons whose synaptic interactions were identified by spike-triggered averaging (STA) of intracellularly recorded membrane potentials and whose relative location was histologically identified. Average synchronous excitation potentials (ASEPs) were the most commonly observed feature in STAs between neuron pairs in all cortical layers (about 70%). This synchrony spread broadly for distances of more than 4 mm, gradually decreasing in amplitude and probability with cell separation. Excitatory postsynaptic potentials (EPSPs) were observed among 9% of the neuron pairs, whose separation extended for distances of more than 4 mm. The peak amplitudes of EPSPs were inversely correlated with cell separation. Most source neurons were located in layer II-III or layer V, while the postsynaptic target neurons had wide laminar distribution. The probability of finding excitatory connections was not uniform within the cortical space. The connectivity between neuron pairs was relatively dense within 1.0 mm, and became sparse for distances between 1.0 and 2.0 mm, and showed a second peak for distance between 2.0 and 4.0 mm. Inhibitory postsynaptic potentials (IPSPs) and/or average synchronous inhibitory potentials (ASIPs) were observed for 10% of neuron pairs. Most of these were separated by less than 1.0 mm, suggesting that their influence was restricted within their own and neighboring columns. The major source neurons that provide these inhibitory effects were located within layer II-III. We conclude that excitatory synaptic effects (ASEPs and EPSPs) are widely distributed and omni-directional within primate motor cortex, while inhibitory connections (ASIPs and IPSPs) are restricted within columnar dimensions, and are predominantly directed from superficial to deeper layers. The appearance of independent zones that had no functional connectivity with neighboring columns indicates that primate motor cortical areas may not be organized in a uniform way. This would support the sparse coding theory and multiple representations of cortical output in the motor cortex.

Linking Oestradiol (E2) Timing and Tempo, Brain Development, and Mental Health in Adolescent Females
Background: Earlier timing and faster tempo of puberty have been associated with altered brain development and increased mental health symptoms in adolescents, particularly females. However, the role of oestradiol (E2) in these associations is unclear. Methods: Using longitudinal data from the US-based Adolescent Brain Cognitive Development Study SM (ABCD Study (R), we investigated whether, in females (N ~ 3k), E2 timing (at age 10) and tempo (rate of change from age 10 to 12) were prospectively associated with mental health symptoms at age 13 via structural brain development from age 10 to 12. Linear mixed-effects models and Bayesian mediation models were fitted to investigate the aims of the study. Results: Findings showed that E2 timing was not associated with mental health symptoms. However, earlier E2 timing was associated with a greater reduction in total cortical volume, total surface area, and surface area in the superior and middle temporal cortex over time. Further, a faster E2 tempo was associated with an increase in mental health symptoms, and this association was mediated by a faster reduction in total cortical volume and total surface area over time. Conclusion: Findings suggest that earlier E2 timing and faster E2 tempo contribute to accelerated development of gray matter structure in adolescent females, and for E2 tempo, such associated brain changes may partly contribute to increased mental health risk.

PACS1 syndrome variant alters proteomic landscape of developing cortical organoids
PACS1 syndrome is a neurodevelopmental disorder resulting from a unique de novo p.R203W variant in Phosphofurin Acidic Cluster Sorting protein 1 (PACS1). PACS1 encodes a multifunctional sorting protein required for localizing furin to the trans-Golgi network. Although few studies have started to investigate the impact of the PACS1 p.R203W variant, the mechanisms by which the variant affects neurodevelopment are still poorly understood. In recent years, ASD patient-derived brain organoids have been increasingly used to identify pathogenic mechanisms and possible therapeutic targets. While most of these studies investigate the mechanisms by which ASD-risk genes affect the transcriptome, studies investigating the proteome are limited. Here, we investigated the effect of PACS1 p.R203W on the proteomic landscape of brain organoids using tandem mass tag (TMT) mass-spectrometry. Time series analysis between PACS1(+/+) and PACS1(+/R203W) organoids uncovered several proteins with dysregulated abundance or phosphorylation status, including known PACS1 interactors. Although we observed low overlap between proteins with altered expression and phosphorylation, the resulting dysregulated processes converged. The presence of PACS1 p.R203W variant putatively accelerated synaptogenesis and impaired vesicle loading and recycling, putatively leading to defective and/or incomplete synaptic function. Finally, the key dysregulated proteins observed in PACS1(+/R203W) organoids were also enriched in ASD-risk genes and have been associated with other neurological diseases. Our results highlight that proteomic analyses not only enhance our understanding of general NDD mechanisms by complementing transcriptomic studies, but also could uncover additional targets, facilitating therapy development.

Neuroanatomy Reflects Individual Variability In Impulsivity in Youth
Individual differences in neural circuits underlying emotional regulation, motivation, and decision-making are implicated in many psychiatric illnesses. Interindividual variability in these circuits may manifest, at least in part, as individual differences in impulsivity at both normative and clinically significant levels. Impulsivity reflects a tendency towards rapid, unplanned reactions to internal or external stimuli without considering potential negative consequences coupled with difficulty inhibiting responses. Here, we use multivariate brain-based predictive models to explore the neural bases of impulsivity across multiple behavioral scales, neuroanatomical features (cortical thickness, surface area, and gray matter volume), and sexes (females and males) in a large sample of youth from the Adolescent Brain Cognitive Development (ABCD) Study at baseline (n=9,099) and two-year follow-up (n=6,432). Impulsivity is significantly associated with neuroanatomical variability, and these associations vary across behavioral scales and neuroanatomical features. Impulsivity broadly maps onto cortical thickness in dispersed regions (e.g., inferior frontal, lateral occipital, superior frontal, entorhinal), as well as surface area and gray matter volume in specific medial (e.g., parahippocampal, cingulate) and polar (e.g., frontal and temporal) territories. Importantly, while many relationships are stable across sexes and time points, others are sex-specific and dynamic. These results highlight the complexity of the relationships between neuroanatomy and impulsivity across scales, features, sexes, and time points in youth. These findings suggest that neuroanatomy, in combination with other biological and environmental factors, reflects a key driver of individual differences in impulsivity in youth. As such, neuroanatomical markers may help identify youth at increased risk for developing impulsivity-related illnesses. Furthermore, this work emphasizes the importance of adopting a multidimensional and sex-specific approach in neuroimaging and behavioral research.

Developmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs in vivo
Appropriate development of long-range nervous system circuitry requires dynamic regulation of subcellular mRNA localization, but little is known about how specific neuron subtypes control this critical process in vivo. Here, we employ an integrated genetic and temporally controlled approach to investigate in vivo developmental mRNA dynamics in somata and axons of a prototypical cerebral cortex projection neuron subtype, callosal projection neurons (CPN), which connect the cortical hemispheres to integrate sensorimotor information, and regulate high-level associative cognition and behavior. We identify cis-regulatory elements that are associated with mRNA turnover in CPN somata, including specific 3' untranslated regions (UTRs), and elucidate distinct modes of axon transport in CPN axons for function-specific mRNA classes. Together, these findings elucidate how developing CPN control subcellular mRNA localization, and how dysregulation of these processes might lead to neurodevelopmental and/or neurodegenerative disorders. More broadly, this work identifies general mRNA localization mechanisms that likely function across projection neuron subtypes, and in other polarized cells.

Differential effects of neurodegenerative disorders on verbal creative idea generation and its cognitive cornerstones
Clinical research has documented a heterogeneous effect of neurodegenerative disorders on creativity. Some disorders are associated with impaired creative performance, while others may preserve, or even enhance, it. However, the underlying cognitive mechanisms that give rise to the heterogeneous behavioural manifestations remain poorly understood. From a theory-driven approach, we conducted a neuropsychological investigation to examine how frontotemporal lobar degeneration (FTLD), and Alzheimer's Disease (AD) differentially affected the cognitive mechanisms underlying creative thought (semantic cognition, episodic memory, executive control functions). In parallel, we assessed participants' verbal creative idea generation performance using the ideational fluency task (also known as the Alternate Uses Task). We analysed data from 24 individuals with FTLD [clinical consensus diagnosis corticobasal syndrome (CBS: n=20) or progressive supranuclear palsy (PSP: n=4)], 24 individuals with clinical consensus diagnosis AD, and 24 healthy individuals. We reached four major conclusions. First, while both disease groups exhibited deficits in controlled semantic retrieval and executive control functions, only participants with AD exhibited degradation in semantic representations and episodic memory. Second, both disease groups generated fewer responses in both typical and creative conditions across objects that were context-free - i.e., associated with multiple contexts (e.g., brick) and context-bound -i.e., associated with a dominant context (e.g., table knife). Third, when given a context-free object prompt, the ability to generate novel responses appeared to be preserved in participants with FTLD, which contrasted with an impaired ability when prompted to give creative uses for the context-bound object. Fourth, participants with AD produced similar levels of response novelty for both context-free and context-bound objects. From a clinical-cognitive neuroscience perspective, this study demonstrates that distinct cognitive profiles resulting from different neurodegenerative conditions yield differential effects on creative thought. As the first study to show that the contextual information of semantic stimuli can mediate the novelty of verbal responses, we suggest that future research should carefully examine how this factor influences creative task performance.

Cognitive Graphs of Latent Structure in Rostral Anterior Cingulate Cortex
Mental maps of environmental structure enable the flexibility that defines intelligent behavior. We describe a striking internal representation in rat prefrontal cortex that exhibits hallmarks of a workspace for constructing goal-specific, cognitive graphs for sequences of abstract states that animals must traverse through their actions. As rats uncover - unguided - complex sequential patterns, neural ensemble activity in rostral Anterior Cingulate Cortex develops a highly structured yet compact, scalable representation anchored in states at the start and end of self-organized sequences. Graphs are organized to reflect relational similarities across contexts, and individually, permit flexible refinement of component states. The representation's crystalline organization permits instantaneous inference of the animal's current state within self-generated sequences, offering insights into the algorithmic and representational principles underlying unguided parsing of open-ended problems.

Neuronal Hyperexcitability: A Key to Unravelling Hippocampal Synaptic Dysfunctions in Lafora Disease
Lafora disease (LD) is a rare progressive disorder caused by mutations in the EPM2A or EPM2B genes, characterized by the accumulation of Lafora bodies, drug-resistant epilepsy, and cognitive decline. To investigate the early molecular mechanisms of LD, we studied electrophysiological changes in the dentate gyrus (DG) of the Epm2aR240X knock-in mouse model at various ages. Electrophysiological recordings measured neuronal membrane properties, epileptic-like activity, epileptic thresholds, and synaptic plasticity in Epm2aR240X mice at 1, 3, and 12 months. We also employed PAS diastase staining, immunofluorescence, and Western blotting to detect Lafora bodies, amyloid beta deposition, and glutamate receptor subunit expression. Epileptic-like activity began at 1 month and intensified with age. Aberrant long-term potentiation (LTP) appeared at 3 months and worsened by 12 months. Notably, cannabidiol (CBD) treatment reduced excitability and restored LTP in older mice, suggesting its potential therapeutic value. These findings indicate that network hyperexcitability is an early event in LD, highlighting a therapeutic window for interventions like CBD.

Iron deposition and functional connectivity alterations in the right substantia nigra of adult males with autism
The substantia nigra (SN) is a midbrain nucleus implicated not only in motor control and reward processing but also in higher-order cognitive functions. Iron homeostasis in this region is essential for neurotransmitter synthesis, especially for dopamine, and thus, iron dysregulation may contribute to the symptomatology of autism spectrum disorder (ASD). However, iron deposition and functional circuits of the SN in the autistic brain remain underexplored. This study investigated iron deposition and functional connectivity (FC) of the SN in 53 adult males with ASD and 99 typically developing controls using quantitative susceptibility mapping and resting-state fMRI. Compared to controls, the ASD group exhibited higher magnetic susceptibility in the right SN, suggesting elevated iron deposition. Within the ASD group, higher iron deposition was associated with more severe socio-communicative deficits and reduced sensory-seeking behavior. Seed-based FC analyses further revealed that the ASD group exhibited stronger FC between the right SN and bilateral visual cortices and reduced FC with the right superior frontal gyrus. These results highlight the critical role of SN in the autistic brain and indicate that altered iron homeostasis in the SN may contribute to disruptions in the dopaminergic system that underlie the core symptoms of ASD.

Neural oscillatory dynamics in joint action: distinct contributions of entrainment and beta modulation to self/other integration
Temporal coordination plays a pivotal role in human activities, enabling effective communication and collaboration. Yet, the neural mechanisms supporting this ability remain poorly understood. Recent research suggests that synchronized beta modulation across individual brains, as measured via EEG hyperscanning, may reflect a shared sensorimotor framework underpinning interpersonal synchronization. Building on the idea that self/other integration is a key mechanism in this process, behavioral studies have shown that adopting a partner's first person visual perspective (1P) enhances interpersonal coordination, as opposed to the natural second person perspective (2P). Here, we used the body swap illusion in immersive virtual reality to directly manipulate embodied perspective and investigate its neural consequences. Specifically, we examined how this illusion modulates beta activity and neural entrainment during joint rhythmic action. Forty participants (N=40), randomly paired into twenty dyads, performed a joint finger-tapping task while wearing head mounted displays for immersive virtual environments. In coupled conditions, the visual scene was manipulated so that participants viewed their partner's hand from a 1P perspective, as if it belonged to their own body, or from a natural 2P perspective. In uncoupled control conditions, participants saw their own hand in 1P and 2P, without perceiving any information about their partner's tapping. EEG hyperscanning revealed that both neural entrainment (measured as the convergence of low frequency oscillations) and beta modulation (changes in ~20 Hz power linked to partner-generated movements) occurred in 1P and 2P visually coupled conditions. However, only beta modulation was selectively enhanced when participants experienced their partner's hand from a 1P perspective. These findings suggest that while neural entrainment reflects a general mechanism for tracking a partner's rhythmic behavior, beta modulation specifically supports the integration of the other's effector into one's bodily representation.

Midbrain organoids with an SNCA gene triplication display dopamine-dependent alterations in network activity
Human midbrain organoids (hMOs) show promise as a patient-derived model for the study of Parkinson's disease (PD). Yet, much remains unknown about how accurately hMOs recapitulate key features of PD in the human brain. In both PD patients and animal models, disease progression leads to characteristic changes in neural activity throughout the basal ganglia. Here we demonstrate that patient-derived induced pluripotent stem cell (iPSC) hMOs harboring a triplication in the SNCA gene, encoding -synuclein, a key protein in PD pathogenesis, can recapitulate PD-associated changes in neural activity. Namely, we observe hyperactive network activity in SNCA triplication hMOs, but not in isogenic, CRISPR-corrected iPSC hMOs. These changes are characterized by an increase in the number of bursts and network-wide bursts. Moreover, SNCA triplication hMOs exhibit an increase in network synchrony and burst/network burst strength similar to observations in animal and human PD brains. Subsequently, we show that the observed changes in neuronal activity are attributed to dopamine D2 receptor hypoactivity due to dopamine depletion, which could be reversed by the D2 receptor agonist quinpirole. Thus, hMOs faithfully model network wide electrophysiological changes associated with PD progression and serve as a promising tool for PD research and personalized medicine.

Sleep firing rate homeostasis is disrupted in mild parkinsonism
Sleep-associated downscaling of neuronal firing, i.e. firing rate homeostasis (FRH), is essential for restorative sleep. Sleep dysfunction is common in Parkinson's disease (PD), but FRH has not been investigated. Here, using a within-subject design in the nonhuman primate model of PD, we report that thalamocortical FRH is disrupted in parkinsonism. These findings can inform therapeutic approaches tailored towards normalizing FRH to reestablish restorative sleep in PD.

Evidence of elemental encoding at the olfactory periphery
How complex, multifaceted perceptual odor qualities of volatile chemicals are encoded by the olfactory system is poorly understood. We explore the receptive fields of individual odorant receptors and show how potent agonists share a consistent perceptual quality despite chemical diversity. This supports the idea that the olfactory neural connectome maintains peripheral information like odor quality through the distinct layers of the system, akin to a labeled line regime present in other sensory structures. We further observe that simple combinatorial activation of odorant receptors can generate a perceptual sum. Human olfaction may thus be shaped by the orthogonal and elemental encoding of olfactory features detected by receptor selectivity and activity. These results provide novel insights into how the brain processes olfactory information and more broadly into neural encoding during sensory processing.

Maturation of GABAergic signalling times the opening of a critical period in Drosophila melanogaster
The occurrence of critical periods during the development of neural networks is widely documented. Activity manipulation when these periods are open can lead to permanent, and often debilitating, effects to the mature neural network. Detailed understanding of the specific contribution of critical periods to network development, however, remains elusive. This is partly because identified critical periods in mammals are present in complex sensory networks (e.g., visual and auditory) that make focused experimental manipulation challenging. It is significant, therefore, that critical periods have been identified in simpler model systems. A critical period occurs during the development of the embryonic locomotor network in the fruit fly, Drosophila melanogaster. Perturbation of neuronal activity during this period is sufficient to permanently destabilise the mature larval locomotor network: leaving it prone to induced seizures. Given a clear role of {gamma}-aminobutyric acid (GABA) in the timing of the mammalian critical period of ocular dominance, we sought to establish whether this neurotransmitter also regulates the opening of the Drosophila locomotor critical period. Utilising GABA agonists, antagonists, and genetics, we manipulated the embryonic GABAergic system and, at the end of larval life, measured an induced seizure phenotype in mature third-instar larvae. We found that potentiating GABAergic signalling, via embryonic exposure to diazepam or overexpression of the GABAA receptor rdl, induced precocious opening of the critical period. By contrast, exposure to the GABA antagonist gabazine, or knockdown of the GABA-synthetic enzyme Gad1, delayed opening. Thus, we show that critical period timing within the Drosophila CNS is dictated by GABAergic signalling, indicating a phylogenetically conserved role.

Lipid Mediated Formation of Antiparallel Aggregates in Cerebral Amyloid Angiopathy
Cerebral amyloid angiopathy (CAA) is a cerebrovascular disorder marked by amyloid-{beta} (A{beta}) deposition in blood vessel walls, leading to hemorrhage and recurring stroke. Despite significant overlap with Alzheimer's disease (AD) through shared A{beta} pathology, the specific structural characteristics of A{beta} aggregates in CAA and their variations between stages of disease severity are yet to be fully understood. Traditional approaches relying on brain-derived fibrils can potentially overlook the polymorphic heterogeneity and chemical associations within vascular amyloids. This study utilizes sub-diffraction, label-free mid-infrared photothermal (MIP) spectroscopic imaging to directly probe the chemical structure and heterogeneity of vascular amyloid aggregates within human brain tissues across different CAA stages. Our results demonstrate a clear increase in {beta}-sheet content within vascular A{beta} deposits corresponding to disease progression. Crucially, we identify a significant presence of antiparallel {beta}-sheet structures, particularly prevalent in moderate/severe CAA. The abundance of antiparallel structures correlates strongly with co-localized lipids, implicating a lipid-mediated aggregation mechanism. We substantiate the ex-vivo observations using nanoscale AFM-IR spectroscopy and demonstrate that A{beta}40 aggregated in vitro with brain-derived lipids adopts antiparallel structural distributions mirroring those found in CAA vascular lesions. This work provides critical insights into the structural distributions of A{beta} aggregates in CAA, highlighting the presence of polymorphs typically associated with transient intermediates, which may lead to alternate mechanisms for neurotoxicity.

Identifying Networks within an fMRI Multivariate Searchlight Analysis
There is great interest in understanding how different brain regions represent information across space and time. Information-based searchlight analyses systematically examine the information encoded within clusters of functional magnetic resonance imaging (fMRI) voxels across the brain. Significant searchlights contain information that can be used to decode conditions of interest, but significant discriminability can be achieved in a variety of ways. We have developed and report on a new analysis method that can identify sub-networks of searchlights. Notably, unlike methods that collapse trials by condition, such as Representational Similarity Analysis, our method groups searchlights based on them having similar temporal changes in information. We present this method and apply it to fMRI data collected as participants viewed words, faces, shapes, and numbers. After running a searchlight analysis with a 4-way Gaussian Naive Bayes (GNB) classifier, the accuracy vector was submitted to a multi-subject Independent Component Analysis (ICA) to group searchlights based on their decoding timeseries. The ICA identified seven components (sub-networks) of searchlights. These networks identified sets of brain areas that have been commonly associated with the processing of faces, words, shapes and numbers. For instance, two of the components drew strongly on the face-processing network, including fusiform cortex. Switching the classification scheme to faces versus non-faces reconfigured the observed network to reflected face-related systems. These results demonstrate that this method can divide searchlight maps into meaningful components.

Temporal Synchronization Analysis: A Model-Free Method for Detecting Robust and Nonlinear Brain Activation in fMRI Data
The sluggishness of the fMRI blood oxygenation level dependent (BOLD) signal has motivated the use of block or trial-based experimental designs that rely on the assumption of linearity, typically modeled using the General Linear Model (GLM). But many non-sensory brain regions and subcortical areas do not correspond to such linearities. We introduce a model-free estimation method called Temporal Synchronization Analysis (TSA) which detects significant brain activations across trials and subjects at an individual time point. We validate it across multiple cognitive tasks (combined n=1600). In constrained task stimuli like visual checkerboard paradigms, we discovered novel nonlinearities not reported previously. In model-free task paradigms like listening to naturalistic auditory stimuli, TSA can detect unique stimuli linked quasi-temporal activations across default mode and language networks. Our user-friendly Python toolkit enables cognitive neuroscience researchers to identify stable and robust brain activation across various cognitive paradigms that are challenging to model with current methods.

TDP-43 toxic gain of function links ALS/FTLD-TDP and Alzheimer's Disease through splicing
Loss of nuclear TDP-43 splicing activity is a common feature across neurodegenerative diseases, but its relevance to Alzheimer's disease (AD) remains unclear. Here, we show that TDP-43 pathology in AD is broadly associated with splicing abnormalities, including aberrant splicing of amyloid precursor protein (APP). We demonstrate that TDP-43 drives the formation of elongated APP isoforms, APP751 and APP770. Thus, TDP-43 dysregulation disrupts APP695/751/770 alternative splicing across ALS/FTLD-TDP and AD, providing a compelling mechanism for a 37-year-old observation of APP isoform dysregulation. We further establish a mechanistic link between TDP-43 pathology, APP splicing, and A{beta} pathology. Unexpectedly, this effect is mediated by a toxic gain of cytoplasmic TDP-43 function, rather than loss of its nuclear role. Using proximity proteomics and base editing in human iPSC-derived neurons, we show that TDP-43 pathology causes cytoplasmic co-sequestration of splicing regulators SCAF11, SRSF5, and TIAL1, which are involved in APP mis-splicing, but not in the regulation of other TDP-43 targets such as STMN2 or UNC13A. Together, our findings suggest that TDP-43-mediated splicing dysfunction upstream of APP contributes to the pathogenesis of seemingly disparate neurodegenerative diseases, uniting AD and ALS/FTLD-TDP through a shared molecular mechanism.

Aperiodic neural timescales in prefrontal cortex dilate with increased task abstraction
Navigating everyday environments requires that the brain perform information processing at multiple different timescales. For example, while watching a movie we use sensory information from every video frame to construct the current movie scene, which itself is continuously integrated into the narrative arc of the film. This critical function is supported by sensory inputs propagating from dynamic sensory cortices to association cortices, where neural activity remains more stable over time. The hierarchical organization of cortex is therefore reflected in a gradient of neural timescales. While this propagation of inputs up the cortical hierarchy is facilitated by both rhythmic (oscillatory) and non-rhythmic (aperiodic) neural activity, traditional measures of oscillations are often confounded by the influence of aperiodic signals. The reverse is also true: traditional measures of aperiodic neural timescales are influenced by oscillations. This makes it difficult to distinguish between oscillatory and timescale effects in cognition. Here, we analyzed electroencephalography (EEG) data from participants performing a cognitive control task that manipulated the amount of task-relevant contextual information, called task abstraction. Critically, we separated aperiodic neural timescales from the confounding influence of oscillatory power. We hypothesized that neural timescales would increase during the task, and more so in high-abstraction conditions. We found that task abstraction dilated the aperiodic neural timescale, as estimated from the autocorrelation function, over prefrontal cortical regions. Our findings suggests that neural timescales are a dynamic feature of the cerebral cortex that change to meet task demands.

The C. elegans gustatory receptor homolog LITE-1 is a chemoreceptor required for diacetyl avoidance
The nematode C. elegans does not have eyes but can respond to aversive UV and blue light stimulation and even distinguish colours. The gustatory receptor homolog LITE-1 was identified in forward genetic screens for worms that failed to respond to blue light stimulation. When LITE-1 is expressed in body-wall muscles, it causes contraction in response to blue light suggesting that LITE-1 is both necessary and sufficient for blue light response. Here we show that in addition to light avoidance, LITE-1 is also required for worms' avoidance of high concentrations of diacetyl, an odorant that is attractive at low concentrations. Like blue light, diacetyl causes muscle contraction in transgenic worms engineered to express LITE-1 in body-wall muscles. These data are consistent with a direct chemoreceptor function for LITE-1 which would make it a multimodal sensor of aversive stimuli.

FGF21 signals through KLB-expressing glutamatergic neurons in the hindbrain to mediate the effects of dietary protein restriction
Animals adaptively respond to protein restriction by altering both behavior and metabolism. Previous work demonstrated that the metabolic hormone FGF21 acted in the brain to coordinate these adaptive responses, but the exact site of action remains unclear. Here, we identify a discrete population of glutamatergic, Klb-expressing neurons in the nucleus of the solitary tract (NTS), demonstrating that these neurons are key to mediating FGF21 action during protein restriction. Using a novel Klb-Flp mouse line combined with intersectional genetics, we demonstrate that these neurons are directly activated by FGF21. While previous work implicated the SCN, PVN, and VMH in FGF21 action, we find that these areas do not impact the response to protein restriction. Instead, selective ablation of NTS-KLB neurons prevents metabolic adaptations to protein restriction (food intake, food choice, and energy expenditure), while their chemogenetic activation is sufficient to drive these responses. These findings establish NTS-KLB neurons as a critical node for detecting protein status and coordinating whole-body metabolic responses, providing new insight into how the brain monitors and maintains protein homeostasis.

Translatome profiling reveals opposing alterations in inhibitory and excitatory neurons of Fragile X mice and identifies EPAC2 as a therapeutic target.
Symptoms of Fragile X Syndrome (FXS), the leading monogenic cause of intellectual disability and autism, are thought to arise from an excitation/inhibition (E/I) imbalance. Here, we leverage cell type specific mRNA sequencing to profile molecular alterations of cortical excitatory and inhibitory neurons in Fmr1 knockout (KO) mice, integrating transcriptomic results with circuit and behavioral readouts to prioritize novel therapeutic targets. Differentially expressed genes (DEG) were largely upregulated in Camk2a expressing excitatory neurons but downregulated in Pvalb-expressing inhibitory neurons, and the underlying signaling pathways were often altered in opposite directions. Among the 184 DEGs that were concordantly dysregulated across both cell types, only Rapgef4 (Epac2) was also an FMRP target, an ASD risk gene and brain enriched. EPAC2 has been implicated in synaptic maturation and plasticity. Systemic administration of an EPAC2 antagonist restored cortical circuit function in Fmr1 KO mice and ameliorated sensory behavioral phenotypes. EPAC2 is a potential target for therapy in FXS.

T cell responses towards PINK1 and α-synuclein are elevated in prodromal Parkinson's disease
A role of the immune system in Parkinsons disease (PD) progression has long been suspected due to the increased frequency of activated glial cells and infiltrating T cells into the substantia nigra. It was previously reported that PD donors have increased T cell responses towards PINK1 and -synuclein (-syn), two Lewy body-associated proteins. Further, T cell reactivity towards -syn was highest closer to disease onset, highlighting that autoreactive T cells might play a role in PD pathogenesis. However, whether T cell autoreactivity is present during prodromal PD is unknown. Here, we investigated T cell responses towards PINK1 and -syn in donors at high risk of developing PD (i.e. prodromal PD: genetic risk, hyposmia, and or REM sleep behavior disorder), in comparison to PD and healthy control donors. T cell reactivity to these two autoantigens was detected in prodromal PD at levels comparable to those detected in individuals with clinically diagnosed PD. Aligned with the increased incidence of PD in males, we found that males with PD, but not females, had elevated T cell reactivity compared to healthy controls. However, among prodromal PD donors, males and females had elevated T cell responses. These differing trends in reactivity highlights the need for further studies of the impact of biological sex on neuroinflammation and PD progression.

Behavioral deficits and exacerbated hemodynamics during lifespan of a mouse model of late onset Alzheimer's disease expressing humanized APOEϵ4 and Trem2*R47H
Alzheimers Disease (AD) poses a significant global health challenge, being the most prominent cause of dementia with prevalence increasing as the population ages. While the majority of AD cases are late-onset (LOAD), current animal models predominantly represent the more aggressive, faster progressing early-onset AD (EOAD), limiting their ability in assessing early biomarkers and gaining deeper understanding of LOAD progression. This study explores a promising translatable model, the APOE4.TREM2 mouse, which combines the APOE4 allele and the Trem2 p.R47H mutation, both linked to increased AD risk in the human population. We performed behavioral phenotyping and measured hemodynamics in dorsal olfactory bulbs (dOB) during odor stimulation of the APOE4.TREM2 mouse line. Experimental evidence of olfactory dysfunction prior to clinical symptoms suggests the opportunity of utilizing smell testing and fMRI as tools for screening of AD, both for preclinical and clinical studies. Here we assess and confirm the translatability of the APOE4.TREM2 mouse LOAD model, reporting exacerbated anxiety, deficits in odor-based foraging and spatial memory, and exacerbated odor-evoked dOB intrinsic responses in an age-dependent manner.

Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to α-synuclein
Parkinson's disease (PD) is a complex neurodegenerative disease with a largely unknown etiology. Although the loss of dopaminergic neurons in the substantia nigra pars compacta is the pathological hallmark of PD, neuroinflammation also plays a fundamental role in PD pathology. We have previously reported that PD patients have increased frequencies of T cell reactive to peptides from -synuclein (-syn). However, not all PD participants respond to -syn. Furthermore, we have previously found that CD4 T cells from PD participants responding to -syn (PD_R) are transcriptionally distinct from PD participants not responding to -syn (PD_NR). To gain further insight into the pathology of PD_R participants, we investigated surface protein expression of 11 proteins whose genes had previously been found to be differentially expressed when comparing PD_R and healthy control participants not responding to -syn (HC_NR). We found that Cadherin EGF LAG seven-pass G-type receptor 2 (CELSR2) was expressed on a significantly higher proportion of CD4 effector memory T cells (TEM) in PD_R compared to HC_NR. Single-cell RNA sequencing analysis of cells expressing or not expressing CELSR2 revealed that PD_R participants have elevated frequencies of activated TEM subsets and an almost complete loss of cytotoxic TEM cells. Flow cytometry analyses confirmed that Granulysin+ CD4 cytotoxic TEM cells are reduced in PD_R. Taken together, these results provide further insight into the perturbation of T cell subsets in PD_R, and highlights the need for further investigation into the role of Granulysin+ CD4 cytotoxic TEM in PD pathology.

The influence of similarity, sensitivity and bias on letter identification
Previous studies have demonstrated that bias, sensitivity and similarity between letters are causes of errors in letter identification. However, these factors and their relative contribution in letter identification have not been investigated extensively. Our previous model (noisy template model) was devised to calculate the effect of bias and sensitivity in letter identification task. In the current study, we used the method of constant stimuli to measure letter acuity for Sloan letters at an eccentricity of 7 deg from fixation (temporal visual field). Similar to our previous work, we devised an tested a variety of models to estimate the joint role of bias and sensitivity, but extended our model to also incorporate the similarity between letters.

Modelling results showed that bias is the major factor in determining the pattern of total, correct and incorrect responses in letter identification. Furthermore, the joint effect of similarity and bias was found to be higher than the joint effect of either bias and sensitivity or similarity and sensitivity in shaping the pattern of overall responses in letter identification. Incorporating the similarity factor to the noisy template model improved our understanding of the simultaneous contribution of the bias, sensitivity and similarity between letters in the letter identification task.

Dissociating stimulus encoding and task demands in ECoG responses from human visual cortex
Brain responses to sensory stimuli depend on the specific task performed by the observer. Previously, fMRI measurements in ventral temporal cortex (VTC) showed that BOLD responses to words and faces scale with the difficulty of a categorization task compared to responses observed during a fixation task (Kay and Yeatman, 2017). This scaling of BOLD responses is thought to be driven by the engagement of cognitive functions during image categorization. To understand how these cognitive task demands change dynamically over time and influence neural activity in VTC, we measured electrocorticography (ECoG) data in two human participants during the same experimental tasks. The ECoG high frequency broadband activity (>70 Hz) showed that local neuronal responses increased with image contrast (as expected for sensory encoding) and were scaled by task demands 0.2 seconds after stimulus onset. In contrast, ECoG low frequency activity in the alpha/beta range (8-28 Hz) was insensitive to image contrast and showed larger suppression with increasing task demands. These results indicate that high frequencies in VTC reflect both the encoding of sensory inputs and task demands, similar to prior BOLD response measurements, whereas low frequency oscillations represent task demands, not sensory inputs per se. In line with the interpretation that low frequency oscillations reflect pulsed inhibition, we speculate that suppression of low frequency oscillations amplifies neural activity in VTC in support of visual task demands.

Structural insights into allosteric mechanism of glycine transporter-mediated analgesia
Chronic neuropathic pain, caused by nerve damage or disease, affects 10% of the population with rising incidence. The burden is exacerbated by ineffective treatments and overreliance on opioids. Neuronal glycine transporter, GlyT2, represents a promising target to restore disrupted inhibitory glycinergic neurotransmission in neuropathic pain. However, most GlyT2 inhibitors have not progressed to clinical use because of significant side effects, partly from irreversible inhibition at analgesic doses. Here, we report cryo-EM structures of human GlyT2 bound to the potent pseudo-irreversible inhibitor ORG25543, a reversible analogue RPI-GLYT2-82, and in substrate-free state. Both inhibitors bind an extracellular allosteric site, locking the transporter in an outward-open conformation, whereas the substrate-free GlyT2 adopts an inward-open conformation. We demonstrate that RPI-GLYT2-82 has a faster off-rate, providing analgesia in mouse neuropathic pain models, with no observed mechanism-based side-effects or addiction liability. Our data provide a model for allosteric inhibition, enabling structure-based design of new non-opioid analgesics.