bioRxiv Preprints

{
  "doi": "10.64898/2026.07.23.740331",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.23.740331v3",
  "title": "A significant enrichment that is not: spatial nulls, co-expression, and the imaging transcriptomics of EEG alpha-power genetics",
  "source": "biorxiv",
  "authors": "Schenetti, J.",
  "version": "3",
  "abstract": "Background. Imaging transcriptomics routinely asks whether a trait-associated gene set is over-expressed in a region of interest, and the field standard is to guard that inference with a spatial-autocorrelation-preserving spin test. Electroencephalographic (EEG) oscillatory power is among the most heritable human neurophysiological traits, and the cortical generators of the alpha rhythm have been characterised independently from resting-state magnetoencephalography - making this a natural test bed both for asking whether trait genetics is regionally organised, and for asking what such a test actually establishes. Objective. To test whether alpha-associated genetic signal is spatially enriched in the cortical generators of the alpha rhythm, and to evaluate that inference against complementary null models. Methods. MAGMA gene-based analysis of ENIGMA-EEG summary statistics for six phenotypes: central and occipital alpha power, occipital alpha peak frequency, and theta, beta and delta power. Regional transcription was obtained from the Allen Human Brain Atlas (AHBA) with abagen in the Glasser HCP-MMP1.0 atlas, with Schaefer-100 and Yan-600 as sensitivity analyses. Enrichment in the 41",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Jacopo Schenetti",
  "journal_published_doi": null,
  "corresponding_institution": "University of Trento"
}

{
  "doi": "10.64898/2026.01.24.701491",
  "url": "https://www.biorxiv.org/content/10.64898/2026.01.24.701491v3",
  "title": "Which phonetic contrasts recover information lost to aggregate speech scoring in auditory nerve disorders: a computational framework",
  "source": "biorxiv",
  "authors": "Campi, M.; Partouche, E.; Gerenton, G.; Avan, P.; Gaultier, C.",
  "version": "3",
  "abstract": "Auditory nerve disorders, including auditory neuropathy spectrum disorders (ANSD), show distorted patterns of auditory nerve activity despite preserved spectral analysis of sound in the cochlea, producing impaired speech recognition despite normal auditory sensitivity. Distinct pathophysiological mechanisms affecting auditory-nerve activity have been identified in animal models, but current clinical speech tests were not designed to distinguish among them, because they average performance across phoneme categories, collapsing mechanism-specific confusion patterns into a single intelligibility score. Using computational modeling of auditory nerve responses, we simulated four candidate mechanisms and showed that their encoding disruptions cascade into systematic, phoneme-specific recognition failures: brief consonants were severely degraded while sustained vowels were preserved, and each mechanism produced a distinct confusion pattern. Models trained on ANSD-degraded signals developed compensation strategies that generalized to healthy signals, while the reverse did not, and noise training that benefited healthy models harmed ANSD models, mirroring real-world listening difficulty. Be",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Marta Campi",
  "journal_published_doi": null,
  "corresponding_institution": "University of Zurich"
}

{
  "doi": "10.1101/2025.11.21.689181",
  "url": "https://www.biorxiv.org/content/10.1101/2025.11.21.689181v3",
  "title": "High-amplitude oscillatory events coordinate large-scale cortical interactions during decision-making and attention allocation",
  "source": "biorxiv",
  "authors": "Siems, M.; Cao, Y.; Donner, T. H.; Tsetsos, K.; Engel, A. K.",
  "version": "3",
  "abstract": "How do large-scale functional brain networks dynamically emerge to enable cognition? Correlated oscillations, a mechanism for inter-areal interactions, can be expressed as phase coherence or correlated amplitude fluctuations. While the functional role of phase coherence has been addressed in the past, it remains unknown how large-scale amplitude coupling dynamically supports the rapid network reconfigurations necessary for adaptive behavior. Here, we demonstrate that cognitive processing relies on the temporal alignment of brief, high-amplitude oscillatory events across distant cortical regions, rather than sustained coupling of oscillations. Capitalizing on the spatio-temporal resolution of magnetoencephalography (MEG) during a task probing attention and decision-making, we show that oscillatory event coincidences form functionally relevant, transient networks: First, coincidences of high-amplitude oscillatory events in the alpha and beta frequency range increase prior to correct decisions within a parieto-frontal network. Second, transient theta/alpha oscillatory event coincidences within a medial parietal, temporo-parietal junction and lateral prefrontal network track the dynami",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Marcus Siems",
  "journal_published_doi": null,
  "corresponding_institution": "University Medical Center-Eppendorf, Hamburg"
}

{
  "doi": "10.1101/2025.08.08.668418",
  "url": "https://www.biorxiv.org/content/10.1101/2025.08.08.668418v2",
  "title": "Calcium-dependent cytoskeletal collapse and recovery of axons after partial laser ablation",
  "source": "biorxiv",
  "authors": "Mishra, A.; Joshi, P.; Ashraf, M. A.; Pullarkat, P. A.",
  "version": "2",
  "abstract": "Traumatic stretch or crush injury to axons causes widespread and often irreversible damage to the axonal cytoskeleton, in which calcium-mediated breakdown is known to play a central role. Unlike complete transection, where recovery must proceed through formation of a new growth cone, milder injury can disrupt the axonal cytoskeleton while leaving the plasma membrane intact. How the cytoskeleton fails, and how it can recover, under these conditions remains unclear. Here we address this using a partial laser-ablation method that damages the cytoskeleton and evokes a calcium transient while preserving membrane continuity. We show that the ensuing cytoskeletal retraction is set by a mechanical balance between acto-myosin contractility and microtubule stability: stabilizing microtubules or inhibiting acto-myosin contractility suppresses retraction. Moreover, chelating extracellular calcium mitigates degeneration and, in a subset of axons, permits complete recovery. We also show that microtubules and actin filaments show distinct loss and recovery dynamics and provide a hypothesis for the \"burning-fuse\" -like depolymerization of the microtubule bundle. These findings provide insights int",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Pramod A Pullarkat",
  "journal_published_doi": null,
  "corresponding_institution": "Raman Research Institute"
}

{
  "doi": "10.1101/2023.10.17.562748",
  "url": "https://www.biorxiv.org/content/10.1101/2023.10.17.562748v2",
  "title": "Biomolecular Resolution as a Quantification of Structural Information Content",
  "source": "biorxiv",
  "authors": "Kinz-Thompson, C. D.; Ray, K. K.",
  "version": "2",
  "abstract": "Resolution is a poorly defined, ad hoc concept in structural biology, and multiple, seemingly conflicting definitions exist. In part, this ambiguity is because the structural information describing a biomolecule manifests in different ways depending upon the length scale being considered, while typical approaches to resolution just consider a single length scale. To address this shortcoming, here we develop a definition of resolution as a measure of how effectively those different manifestations of biomolecular structural information are embedded in experimental data across different length scales. We show how biomolecular structures can be decomposed into a hierarchy of structural elements, and combinations of those structural elements yield representations of the biomolecule with different degrees of spatial detail. A probabilistic measure, which we call \"hierarchical resolution,\" can then be calculated to determine the statistically optimal representation of a biomolecule in an experiment. Hierarchical resolution is a local, detection-sensitive resolution measure capable of quantifying the biomolecular structural content of an experiment. Altogether, these advances comprise a te",
  "category": "biophysics",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Colin D Kinz-Thompson",
  "journal_published_doi": null,
  "corresponding_institution": "Rutgers University-Newark"
}

{
  "doi": "10.64898/2026.01.28.702352",
  "url": "https://www.biorxiv.org/content/10.64898/2026.01.28.702352v3",
  "title": "PLCβs are recruited to the plasma membrane in macrophages by both Gβγ and Gαq",
  "source": "biorxiv",
  "authors": "Falzone, M.; Banerjee, P.; MacKinnon, R.",
  "version": "3",
  "abstract": "PLC{beta} enzymes cleave PIP2 from the plasma membrane, producing IP3 and DAG, which regulate intracellular Ca2+ levels and protein kinase C activity, respectively. They are regulated by GPCR signaling through the G proteins G{beta}{gamma} and Gq and have been shown to function as coincidence detectors for dual stimulation of Gq and Gi-coupled receptors via these G proteins. PLC{beta}s are aqueous-soluble enzymes, but partition onto the membrane surface to access their lipid substrate. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie G{beta}{gamma}-dependent regulation of PLC{beta} enzymes. Using macrophages as a model system, where PLC{beta} signaling is essential for responses to infection and tissue injury, we investigated the contribution of G{beta}{gamma}-dependent regulation and membrane recruitment of PLC{beta} in the context of endogenous signaling. By measuring Ca2+ mobilization, we demonstrate that both Gi and Gq-coupled receptors independently stimulate PLC{beta} activity, illustrating that G{beta}{gamma} alone is sufficient to activate PLC{beta} in certain contexts. Using total internal reflectio",
  "category": "biophysics",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Roderick MacKinnon",
  "journal_published_doi": null,
  "corresponding_institution": "Rockefeller University"
}

{
  "doi": "10.1101/2025.08.17.670701",
  "url": "https://www.biorxiv.org/content/10.1101/2025.08.17.670701v3",
  "title": "Cortical GABAergic dynamics around hippocampal sharp-wave ripples",
  "source": "biorxiv",
  "authors": "Rezaei, E.; Tohidi, S.; Nazari, M.; McNaughton, B. L.; Mohajerani, M. H.",
  "version": "3",
  "abstract": "Hippocampal sharp wave ripples (SWRs) coordinate hippocampal and neocortical interactions for memory consolidation, yet how cortical GABA signaling is organized around SWRs remains unclear. Here we approach this problem by combining wide-field mesoscale imaging of extracellular GABA using iGABASnFR2 with simultaneous dorsal CA1 electrophysiology and sleep state monitoring in mice, enabling GABA dynamics to be mapped across 17 cortical regions during natural sleep and wakefulness. Using ripple triggered activity mapping and singular value decomposition, we identified a cortex wide GABA response consisting of a dominant global component and regionally structured components that were reconfigured across brain states. Across cortical subnetworks, SWRs were associated with a reduction in GABA signaling followed by widespread activation, with both components enhanced during NREM sleep. During NREM sleep, GABA responses emerged earliest and most strongly in the retrosplenial and other medial cortical regions before progressing laterally. During wakefulness, responses were faster, preferentially recruited lateral sensory regions and progressed towards medial cortex. Transitions between NRE",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Edris Rezaei",
  "journal_published_doi": null,
  "corresponding_institution": "University of Lethbridge"
}

{
  "doi": "10.64898/2026.03.03.709421",
  "url": "https://www.biorxiv.org/content/10.64898/2026.03.03.709421v2",
  "title": "No evidence for sleep-dependent memory generalization in a large online sample",
  "source": "biorxiv",
  "authors": "Lu, T.; Ji, Z.; Tompary, A.; Schechtman, E.",
  "version": "2",
  "abstract": "Memory generalization allows individuals to extract and apply information from prior experiences to novel situations, supporting flexible learning and efficient decision-making. Theoretical models suggest that sleep should facilitate generalization, yet the literature examining its role in promoting generalization is mixed. We recruited 137 participants via Prolific to complete an image-location memory task over two sessions spaced 12 hours apart. Participants were randomly assigned to the Wake group (learning in the morning) or the Sleep group (learning in the evening). In Session 1, participants learned the location of stimuli on the screen and were tested on their memory five minutes later. Twelve hours later, in Session 2, they were tested on their memory again. Stimuli consisted of 160 images from eight semantic categories and were strategically positioned on-screen to test the effects of generalization on retrieval (i.e., category-based memory distortions and biases). After the delay, retrieval was less accurate and demonstrated more generalization. However, these effects were mostly independent of Group, with some evidence for enhanced generalization following a period of wa",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Eitan Schechtman",
  "journal_published_doi": null,
  "corresponding_institution": "University of California Irvine"
}

{
  "doi": "10.64898/2026.07.08.737182",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.08.737182v2",
  "title": "Longitudinal Subject Pairing in Cross-Sectional Neonatal Data Reveals Asynchronous Structural and Functional Brain Maturation",
  "source": "biorxiv",
  "authors": "Namiranian, R.; Sadeghi, M.; Abrishami Moghaddam, H.",
  "version": "2",
  "abstract": "The asynchronous development of structural and functional brain networks in early childhood remains largely unexamined, primarily due to the scarcity of longitudinal neuroimaging data. Resolving this temporal dimension is critical, as it promises to reshape our understanding of structural-functional (S-F) coupling, revealing not only whether brain architecture supports function, but also when and over what timescale its influence emerges. However, while rapid neonatal brain maturation and logistical constraints continue to hinder longitudinal data collection, large-scale cross-sectional multimodal datasets are currently available to bridge this gap. Here, we propose a longitudinal subject-pairing framework that reconstructs developmental trajectories from cross-sectional data. It pairs the infants with a predefined age gap while maximizing their similarity in both structural and functional features, thereby approximating the longitudinal trajectory of functional changes in relation to structural maturation. As a case study, we applied this framework to the perisylvian region in a subset of 505 neonates from the multimodal dHCP brain dataset. The myelination index was derived as a s",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Hamid Abrishami Moghaddam",
  "journal_published_doi": null,
  "corresponding_institution": "K.N. Toosi University of Technology"
}

{
  "doi": "10.64898/2026.03.16.712233",
  "url": "https://www.biorxiv.org/content/10.64898/2026.03.16.712233v4",
  "title": "EEG-based classification models reveal differential neural processing of words and images",
  "source": "biorxiv",
  "authors": "Morakabati, N. R.; Thiha, A. S.; Schechtman, E.",
  "version": "4",
  "abstract": "Background: Machine learning methods employing neuroimaging data are useful for monitoring the activation of neural representations. Specifically, they can be used to discern the brain networks engaged in processing specific categories of items. This approach has been employed on neuroimaging data, including functional magnetic resonance imaging data and electroencephalography (EEG) data. New method: Here, we present a task and an analytical pipeline for investigating category representations using EEG. Participants (N = 30) viewed a series of images and words of objects belonging to five categories (Animals, Tools, Food, Scenes, and Vehicles) and responded when items from the same category were presented consecutively. Results: We trained support vector machines on EEG data within participants and found that both image trials and word trials yielded significant category classification accuracy, with image trials achieving higher accuracy than word trials. When comparing categories in a pair-wise fashion, all pairs were statistically distinguishable for image trials, whereas only one pair was distinguishable for word trials. Parietal and Left Temporal electrodes contributed more to",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Eitan Schechtman",
  "journal_published_doi": null,
  "corresponding_institution": "University of California Irvine"
}