Biology subjects

Schubert, J.

Publications and source records attributed to Schubert, J..

11 recordsLinked to original sources

bioRxiv2026

The dynamic relationship between pupil dilation and neural surprise in natural language comprehension

Predictive processing accounts hold that the brain continuously generates predictions and updates internal models from error signals, but it remains unclear whether prediction representation and model-updating reflect a single graded computation or computationally distinct operations implemented in dissociable systems. We recorded magnetoencephalography (MEG) and pupillometry while participants listened to continuous natural speech, quantifying word-by-word lexical surprise and semantic prediction error with a GPT-2 model. Broadly speaking, lexical surprise was tracked in a predominantly graded fashion, whereas the response to semantic error was better captured by a rectified linear (ReLU) gating function - i.e., that responds only when the error exceeds a recent contextual baseline. There were also some interesting dissociations in the strength of these relative effects. The auditory cortex tracked lexical surprise in a graded, continuous manner, with later cortical stages reflecting semantic error. By contrast, tonic pupil diameter and source-localised brainstem responses were predominantly captured by a gated response to semantic error. A pupil-coupling analysis confirmed that this gating signature was statistically shared between pupil-linked arousal and brainstem-localised, but not cortical, responses. Together, these findings reveal a division of labour in which the cortex maintains a continuous, high-fidelity map of predictive information while a pupil-linked model-update system acts as a selective gate, engaged specifically by meaning-disrupting events that have crossed a threshold level of error. This asymmetry suggests that signals serving continuous parsing of prediction error and signals serving model revision may be computationally dissociated, with a range of implications for our understanding of the intrinsic interactions between mechanisms serving perception and learning.

neuroscience↗

bioRxiv2026

From Head to Toe: Efficient Somatosensory Mapping with Fast Stimulation and Multivariate Pattern Analysis

BackgroundSomatosensory evoked potentials (SEPs) measured with electroencephalography (EEG) are widely used to study cortical responses to touch but most research has limited the focus on few body parts, typically a finger, and applied time-consuming testing protocols. Multivariate pattern analysis (MVPA) provides a complementary approach that may increase sensitivity and allow faster stimulation, yet its relationship to classical SEP analysis in somatosensory research remains largely unexplored. MethodsFifteen participants received vibrotactile stimulation on the finger, hand, cheek, and foot while EEG was recorded. We compared a traditional "slow" stimulation protocol (800-1200 ms inter-stimulus intervals) with a "fast" protocol (300-500 ms). We compared temporal and topographical aspects between SEP and MVPA. ResultsBoth stimulation protocols produced highly similar SEP components (P100, N140, P200), topographies, and classification results, while the fast protocol reduced testing time by about 60%. SEPs revealed systematic body-part differences, with earlier components for cheek stimulation and delayed responses for the foot. Multivariate classification distinguished body parts with accuracies up to [~]50-55% (chance: 25%), peaking around 100 ms after stimulus onset. Classifier weight maps closely matched SEP topographies over centroparietal electrodes, indicating that classification relied on physiologically meaningful somatosensory signals. Classification accuracy peaked around 100 ms after stimulus onset, coinciding with the SEP P100 component, but declined gradually thereafter, suggesting that early somatosensory responses contain particularly informative multivariate patterns that generalize over time. ConclusionsFaster stimulation protocols substantially increase efficiency without compromising interpretability. Combining classical SEP analysis with multivariate classification provides complementary insights and offers a powerful framework for mapping somatosensory representations across the body.

neuroscience↗

bioRxiv2025

Linker Histones Enhance Robustness in Diurnal Transcription Dynamics.

Linker histone H1 is crucial for chromatin organization and gene expression in Arabidopsis thaliana, influencing development and stress responses. To explore its role in diurnal gene regulation, we examined H1-deficient plants and found that H1 is essential for maintaining rhythmic gene expression. Genes losing synchronization often contained NAC transcription factor binding sites, indicating H1 may affect their accessibility. Nuclear imaging revealed that H1 subtly modulates nuclear size and chromatin distribution across the photoperiod. Epigenetic analysis showed typical diurnal changes--declines in H3K4me3 and active RNA Pol II in the evening and increases in H3K27me3. In H1 mutants, these patterns persisted but with elevated H3K4me3 and RNA Pol II (Ser2P) levels at night and in the morning. These results suggest that H1 fine-tunes chromatin and transcriptional rhythms, contributing to the temporal coordination of gene activity in response to environmental and developmental signals.

plant biology↗

bioRxiv2025

A citrullination-ubiquitination pathway controls pre-meiotic H1 eviction and is essential for gametogenesis in Arabidopsis

Despite being evolutionary distant, plants and animals share a common phenomenon at the somatic-to-reproductive cell fate transition with extensive structural and compositional changes in chromatin. Such chromatin reprogramming occurs in the plant SMCs (Spore Mother Cells) and animal PGCs (primordial germ cells) and is initiated by the loss of linker histones (H1). H1 loss is essential to establish pluripotency in animal PGCs but its role is not known in plants. Here, we identified two regulatory pathways involving a citrullinase and an E3-ubiquitin ligase that contribute H1.1 loss in female SMC in Arabidopsis. We also identified roles for two specific residues: an arginine, whose positive charge contributes to H1.1 destabilization from chromatin, and a lysine in the globular domain that is essential for H1.1 degradation. Ovules with impaired H1.1 loss in the SMC proceed through sporogenesis but fail to complete gametogenesis. We propose a citrullination-ubiquitination pathway governing pre-meiotic H1 depletion as a critical mechanism for establishing post-meiotic competence in the Arabidopsis germline.

plant biology↗

bioRxiv2024

The "Ocular Response Function" for encoding and decoding oculomotor related neural activity

Oculomotor activity provides critical insights into cognition and health, with growing evidence demonstrating its involvement in various cognitive functions such as attention, memory, and sensory processing, and that it is a significant indicator of psychopathologies and neurological disorders. Despite its crucial importance across domains, the neural mechanisms supporting oculomotion have been underexplored, largely because eye movements are typically treated as artefacts to be removed from the neural signal. While useful for data cleaning, this approach risks discarding valuable information about oculomotor control, and there has been recent interest in modelling these signals instead to understand them. Using time-resolved regression methods with magnetoencephalography (MEG) and eye tracking during the resting state, we thus here sought to model Ocular Response Functions (ORFs), that characterise the neural signatures of distinct oculomotor events, specifically saccades, blinks, and pupil dilation. We demonstrate the relationships between ocular action and neural activity (encoding), revealing a range of sensory cortical, cerebellar and frontal signatures preceding and following such ocular events. We conversely show how we can reconstruct ocular events from brain activity, and further apply resting-state derived ORFs to a passive listening task - demonstrating how some neural markers interpreted as directly related to sensation may in principle indirectly result from oculomotor contributions to task-related neural processing. By providing an accessible framework for examining the interplay between eye movements and neural processes, we offer a range of insights with potential applications across cognitive and clinical neuroscience.

neuroscience↗

bioRxiv2023

Prediction tendency, eye movements, and attention in a unified framework of neural speech tracking

Auditory speech comprehension is a multi-faceted process in which attention, prediction, and sensorimotor integration (via active sensing) interact with or complement each other. Although different conceptual models that focus on one of these aspects exist, we still lack a unified understanding of their role in speech processing. Here, we first replicated two recently published studies from our lab, confirming 1) a positive relationship between individual prediction tendencies and neural speech tracking, and 2) the phenomenon of ocular speech tracking - the tracking of attended speech by eye movements - and its shared contribution with neural activity to speech processing. In addition, we extended these findings with complementary analyses and investigated these phenomena in relation to each other in a multi-speaker paradigm with continuous, narrative speech. Importantly, prediction tendency and ocular speech tracking seem to be unrelated. In contrast to the shared contributions of oculomotor and neural activity to speech processing over a distributed set of brain regions that are critical for attention, individual prediction tendency and its relation to neural speech tracking seem to be largely independent of attention. Based on these findings, we propose a framework that aims to bridge the gaps between attention, prediction, and active (ocular) sensing in order to contribute to a holistic understanding of neural speech processing. In this speculative framework for listening, auditory inflow is, on a basic level, temporally modulated via active ocular sensing, and incoming information is interpreted based on probabilistic assumptions.

neuroscience↗

bioRxiv2023

Individual prediction tendencies are related but not the same across modalities

Predictive processing theories, which model the brain as a "prediction machine", explain a wide range of cognitive functions, including learning, perception and action. Furthermore, it is increasingly accepted that aberrant prediction tendencies play a crucial role in psychiatric disorders. Given this explanatory value for clinical psychiatry, prediction tendencies are often implicitly conceptualised as individual traits or as tendencies that generalise across situations. As this has not yet explicitly been shown, in the current study, we quantify to what extent the individual tendency to anticipate sensory features of high probability generalises across modalities. Using magnetoencephalography (MEG), we recorded brain activity while participants were presented a sequence of four different (either visual or auditory) stimuli, which changed according to predefined transitional probabilities of two entropy levels: ordered vs. random. Our results show that, on a group-level, under conditions of low entropy, stimulus features of high probability are preactivated in the auditory but not in the visual modality. Crucially, the magnitude of the individual tendency to predict sensory events seems not to correlate between the two modalities. Furthermore, reliability statistics indicate poor internal consistency, suggesting that the measures from the different modalities are unlikely to reflect a single, common cognitive process. In sum, our findings suggest that quantification and interpretation of individual prediction tendencies cannot be generalised across modalities.

neuroscience↗

bioRxiv2023

Eye movements track prioritized auditory features in selective attention to natural speech

Over the last decades, cognitive neuroscience has identified a distributed set of brain regions that are critical for attention - one of the key principles of adaptive behavior. A strong anatomical overlap with brain regions critical for oculomotor processes suggests a joint network for attention and eye movements. However, the role of this shared network in complex, naturalistic environments remains understudied. Here, we investigated eye movements in relation to (un)attended sentences of natural speech in simultaneously recorded eye tracking and magnetoencephalographic (MEG) data. Using temporal response functions (TRF), we show that eye gaze tracks acoustic features (envelope and acoustic onsets) of attended speech, a phenomenon we termed ocular speech tracking. Ocular speech envelope tracking even differentiates a target from a distractor in a multi speaker context and is further related to intelligibility. Moreover, we provide evidence for its contribution to neural differences in speech processing, emphasizing the necessity to consider oculomotor activity in future research and in the interpretation of neural differences in auditory cognition. Our results extend previous findings of a joint network of attention and eye movement control as well as motor theories of speech. They provide valuable new directions for research into the neurobiological mechanisms of the phenomenon, its dependence on learning and plasticity, and its functional implications in social communication.

neuroscience↗

bioRxiv2022

Individual prediction tendencies facilitate cortical speech tracking

Listening can be conceptualized as a process of active inference, in which the brain forms internal models to predict and integrate auditory information in a complex interaction of bottom-up and top-down processes. Whether inter-individual "prediction tendencies" shape listening experiences of real-world stimuli such as speech is, however, unknown. In the current study, we used a passive paradigm presenting tone sequences of varying entropy level, to independently quantify auditory prediction tendency (as the tendency to anticipate low-level acoustic features according to their contextual probability) for each individual. This measure was then used to predict the magnitude of cortical speech (envelope) tracking in a multi speaker listening task, where participants listened to audiobooks narrated by a target speaker in isolation or interfered by 1 or 2 distractors. Furthermore, rare semantic violations were introduced into the story, enabling us to also examine effects of word surprisal during continuous speech processing. Our results show that individual prediction tendency facilitates cortical speech tracking. Furthermore, we find interactions between individual prediction tendency and background noise as well as word surprisal in disparate brain regions. In sum, our findings suggest that individual prediction tendencies are generalizable across different listening situations and may serve as a valuable element to explain interindividual differences in natural listening experience.

neuroscience↗

bioRxiv2021

Assessing the impact of fire on spider abundance through a global comparative analysis

In many regions fire regimes are changing due to anthropogenic factors. Understanding the responses of species to fire can help to develop predictive models and inform fire management decisions. Spiders are a diverse and ubiquitous group and can offer important insights into the impacts of fire on invertebrates and whether these depend on environmental factors, phylogenetic history, or functional traits. We conducted phylogenetic comparative analyses of data from studies investigating the impacts of fire on spiders. We investigated whether fire affects spider abundance or presence and whether ecologically relevant traits or site-specific factors influence species responses to fire. Although difficult to make broad generalisations about the impacts of fire due to variation in site- and fire-specific factors, we find evidence that short fire intervals may be a threat to some spiders, and that fire affects abundance and species compositions in forests relative to other vegetation types. Orb and sheet web weavers were also more likely to be absent after fire than ambush hunters, ground hunters, and other hunters suggesting functional traits may affect responses. Finally, we show that analyses of published data can be used to detect broad scale patterns and provide an alternative to traditional meta-analytical approaches.

ecology↗

bioRxiv2018

Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis

Chromatin in eukaryotes provides a tunable platform to control gene expression and convey an epigenetic memory throughout cell divisions. H1 linker histones are abundant components with an intrinsic potential in influencing chromatin structure and function. We detail the impact of H1 depletion in Arabidopsis on fine-scale chromatin organization, transcription and development. While required for chromocenter assembly, H1s are dispensable for transposable element (TE) silencing and peripheral positioning of heterochromatin. In euchromatin, H1 regulates nucleosome density, mobility, and regular distribution of nanoscale chromatin domains. While necessary to maintain epigenetic patterns, H1 only moderately affects transcription. Its depletion is associated with failures in transitional fate changes such as lateral root initiation, root hair production, stomata patterning but also flowering and dormancy regulation. Therefore, Arabidopsis H1 variants are chromatin architects mediating nano- and microscale levels-of-organization operating downstream of epigenetic and transcriptional establishment processes and contribute to epigenetic reorientations in developmental transitions.

molecular biology↗