Biology subjects

Vernet, M.

Publications and source records attributed to Vernet, M..

15 recordsLinked to original sources

bioRxiv2026

Detecting movement preparation with HYDRE: a hybrid model of temporal and spectral brain signals

Previous research on brain-computer interfaces (BCIs) has demonstrated the feasibility of decoding different movements. However, less attention has been given to detecting motor preparation (i.e., decoding from brain signals whether or not a participant is about to perform a given movement). In this study, we wanted to assess the performance of a new model, rooted in motor preparation physiology, in detecting an upcoming movement across the period preceding a voluntary action. Participants (n=18, including 7 females) performed a simple self-paced motor task where they either pressed a button to change an image shown on screen, or let the computer change the image. Participants' brain activity was recorded using magnetoencephalography and submitted to a newly developed linear ensemble classifier that relies on features extracted using PCA from the temporal, spectral and Riemannian domain. We then compared its performance against other classifiers used in BCIs. Our HYbrid Domain Riemannian Ensemble (HYDRE) classifier emerged as the best-performing method, achieving average above-chance decoding up to 1400ms before the action, with a maximum ROC score of 76% at the time of the button press. Moreover, decoding performance in the temporal and Riemannian domains was respectively predictive of Readiness Field and Event-Related Desynchronization magnitudes, two well-known motor preparation markers. Combining features from the temporal, spectral, and Riemannian domains significantly improved motor preparation decoding compared to single-domain approaches. By leveraging the most discriminative features from each domain, HYDRE yielded consistent performance gains across participants with varying baseline decoding performance, effectively addressing inter-individual variability in motor preparation markers.

neuroscience↗

bioRxiv2025

The sense of agency in near and far space: where do we stand?

Modern technology frequently places the consequences of our actions at a distance (e.g., remote surgery, smart-home control, virtual reality). Does spatial distance between an action and its outcome weaken the sense of agency (SoA) - the feeling of control over ones actions and consequences? Two recent studies answered "yes", reporting stronger temporal binding (TB) in near than far space and interpreting this as greater implicit agency (Jenkins & Obhi, 2021; Mariano et al., 2024). A third study - our own work with a similar paradigm - found no distance effect (Kong et al., 2024). Here we (i) provide a rigorous side-by-side methodological comparison of the three studies, (ii) argue why a direct test to establish a distance modulation of TB (the Near - Far difference of the Active - Passive delta) should be performed in order to reach meaningful conclusions, and (iii) report new re-analyses of our data and direct tests on the two target studies. Overall, current evidence does not support a distance effect on SoA. Our reassessment provides alternative explanations that converge with available evidence suggesting that distance may influence temporal interval perception, but that effect is independent of action intention and therefore of agency. Public Significance StatementIn our increasingly connected world, we often interact with devices and influence events that are physically distant from us - like controlling smart appliances remotely or engaging in virtual reality experiences. Does the distance between us and the effects of our actions change how much we feel in control of the outcomes of our actions? Recent studies have suggested that we feel less responsible when action outcomes appear in far space compared to near space. However, methodological limitations in these studies, as well as our own results with a similar paradigm, challenge the validity of this claim. We aim to contribute to the crucial debate on the role of spatial distance on humans feeling of responsibility by providing a respectful though critical analysis of recent findings and offering recommendations for future research.

neuroscience↗

bioRxiv2025

No evidence of neural feature-specific pre-activation during the prediction of an upcoming stimulus

Our brains constantly make predictions about upcoming events based on prior knowledge of the environment. Although several neural mechanisms have been proposed to support this capacity, it is not yet clear how the brain makes such predictions. A compelling hypothesis is that the brain preactivates a sensory template of a predictable stimulus before it appears. In a recent study, Demarchi et al. had participants listen to sequences of sounds with different levels of predictability. For some sequences, participants could anticipate the next sound (in regular sequences), for others not (in random sequences). Using magnetoencephalography recordings and machine-learning methods to decode sounds from brain signals, Demarchi et al. concluded that auditory predictions pre-activate tone-specific neural templates before the sound onset. In our reanalysis of their data, we demonstrate that their results can be fully explained by a bias induced by the structure of the sequences: because the most likely stimulus also happens to be physically close to the previous one, spurious higher-than-chance decoding performance arises before the sound onset. We provide general criteria to assess whether a study is affected by this confound and requires a reexamination. We conclude that there is no evidence of anticipatory predictive perception in the Demarchi et al. dataset, and that existing evidence for feature-specific pre-activation during prediction in humans remains inconclusive.

neuroscience↗

bioRxiv2025

Learning Amidst Noise: The Complementary Roles of Neural Predictive Activity and Representational Changes

The ability to extract structured sensory patterns from a noisy environment is fundamental to cognition, yet how the brain learns complex regularities remains unclear. Using magnetoencephalography during a visuomotor task, we tracked the neural dynamics as humans learned non-adjacent temporal dependencies embedded in noise. We reveal that learning is supported by two temporally dissociable mechanisms. Neural predictive activity emerged rapidly, with stimulus-specific patterns appearing before stimulus onset and preceding measurable behavioral improvements. This is followed by a slower build-up of representational change, characterized by an increased neural pattern similarity between statistically dependent, non-adjacent elements. Both processes are supported by a distributed consortium of networks, with the sensorimotor and dorsal attentional networks playing a central role. These findings suggest that both neural predictive activity and representational changes contribute to learning regularities, revealing a temporal hierarchy in which neural predictive activity precedes behavioral improvement and is followed by neural representational changes, possibly facilitating the gradual consolidation of knowledge into stable neural representations.

neuroscience↗

bioRxiv2025

Spatial distance and temporal attentional focus modulate voluntary action preparation and awareness

Peripersonal space (PPS)--the immediate space surrounding the body--modulates perception and motor control. However, its impact on how voluntary actions are initiated and subjectively experienced remains underexplored. Similarly, how directing attention to different phases of an action, such as intention formation versus execution, and anticipating outcomes of an action, modulates the neural readiness for movement, has yet to be fully examined. This study investigates whether spatial proximity, attentional focus, and anticipated action outcomes influence action preparation and action awareness, using a virtual reality adaptation of the Libet clock paradigm during EEG recordings. Neural results reveal that attentional focus and anticipated action outcomes modulate different phases of motor preparation, as indexed by the readiness potential (RP)--a gradual buildup of neural activity preceding voluntary movement. Focusing on decision timing (without subsequent action outcomes) enhances early RP amplitude and decreases the late RP slope, suggesting increased preparatory neural engagement during intention formation. In contrast, focusing on action execution leads to a steeper late RP slope, indicating later and faster motor activity buildup when attention is directed toward movement onset. Anticipating action outcomes increased late RP slope, which was accompanied by the temporal binding effect: when a tone followed the action, both decision and action estimates shifted toward it. Spatial proximity also modulates early RP slope, with a steeper buildup in near versus far space, suggesting facilitated motor preparation within PPS. It further enhances the late RP amplitude when participants focused on their intention to act. Behavioural results show that actions are perceived as occurring earlier when the clock is displayed near compared to far, indicating that PPS influences the temporal perception of action timing. Overall, these findings highlight the dynamic interplay among external spatial context and internal cognitive processes in shaping motor preparation and action awareness. Importantly, a temporal internal attentional focus on intention to act modulates early RP--traditionally considered an unconscious stage of neural readiness. These results contribute to a deeper understanding of how PPS and the locus of attention on specific action phases affect action preparation and awareness, with potential implications for future research on the sense of agency and voluntary action decision making.

neuroscience↗

bioRxiv2024

EEMtoolbox: A user-friendly R package for flexible ensemble ecosystem modeling

O_LIForecasting ecosystem changes due to disturbances or conservation interventions is essential to improve ecosystem management and anticipate unintended consequences of conservation decisions. Mathematical models allow practitioners to understand the potential effects and unintended consequences via simulation. However, calibrating these models is often challenging due to a paucity of appropriate ecological data. C_LIO_LIEnsemble ecosystem modelling (EEM) is a quantitative method used to parameterize models from theoretical ecosystem features rather than data. Two approaches have been considered to find parameter values satisfying those features: a standard accept-reject algorithm, appropriate for small ecosystem networks; and a sequential Monte Carlo (SMC) algorithm, that is more computationally efficient for larger networks. In practice, using SMC for EEM generation requires advanced statistical and mathematical knowledge, as well as strong programming skills, which might limit its uptake. In addition, current EEM approaches have been developed for only one model structure (generalized Lotka-Volterra). C_LIO_LITo facilitate the usage of EEM methods we introduce EEMtoolbox, an R package for calibrating quantitative ecosystem models. Our package allows the generation of parameter sets satisfying ecosystem features, by using either the standard accept-reject algorithm or the novel SMC procedure. Our package extends the existing EEM methodology, originally developed for the generalized Lotka-Volterra model, to two additional model structures (the multi-species Gompertz, and the Bimler-Baker model), and additionally allows users to define their own model structures. C_LIO_LIWe demonstrate the usage of EEMtoolbox by modelling the introduction of sihek (extinct-in-the-wild) on Palmyra Atoll in the Pacific Ocean. With its simple interface, our package facilitates straightforward generation of EEM parameter sets, thus unlocks advanced statistical methods supporting conservation decisions using ecosystem network models. C_LI

ecology↗

bioRxiv2024

Increase of tropical seabirds (Sula) in the California Current Ecosystem with warmer ocean conditions

Climate change is impacting marine ecosystems in the California Current Ecosystem (CCE) through physical changes (e.g., an increase in the frequency and intensity of marine heatwaves) that manifest biologically at all trophic levels. We investigated range expansion into the CCE and correlations with environment for a group of tropical/sub-tropical seabirds. We assessed changes in the abundance (2002-2022) of five species from the genus, Sula (Cocos, Blue-footed, Red-footed, Masked, and Nazca Boobies), using a novel compilation of four data sources (at-sea surveys, n=82 observations, records from Southeast Farallon Island, n=600, the California Rare Birds Committee, n=593, and eBird -a citizen science mobile application, n= 20,529), and looked for relationships with the environment, including broad temporal and spatial scale dynamics (El Nino Southern Oscillation), local conditions where the bird was reported, and potential source conditions from Baja California Sur and the Gulf of California. All five species increased in abundance, and all, with the exception of Blue-footed, exhibited a northward range expansion by as much as 6.8 degrees latitude and increased range area of between 235-1013% within the CCE. There was increased abundance during warmer conditions (El Nino and warm SST) for Cocos, Red-footed, Masked, and Nazca Boobies, and all species increased by 692-3015% after the extreme marine heatwaves that began in late 2013. Our results document a tropical shift in seabirds of the CCE, which may present future challenges to resident species. As marine heatwaves are projected to increase in frequency and intensity, in addition to long-term warming, we hypothesize that these species will continue to expand their range northward in the CCE.

ecology↗

bioRxiv2023

Humans progressively feel agency over events triggered before their actions

Artificial Intelligence (AI) has become increasingly efficient in anticipating our behavior. Will this impact, in the near future, how much we feel control over events generated with AI-assistance? This would in turn influence our decisions, actions, mental health and sense of responsibility. In everyday life, our sense of agency over events occurring at various delays after our actions has adapted to accommodate these delays. Here, we investigate whether our sense of agency can also adapt to an unusual situation where a consequence precedes an action. We used an online game in which players aimed to beat the computer at finding and clicking on a target to trigger an animation, while, in fact, an algorithm triggered the animation before the players click. The animation was not randomly controlled by the algorithm, but rather based on the history of the players past movements and on the beginning of their current movement. We used correlational, machine learning decoding, and modelling approaches to capture how players compute their reported sense of agency over the animation. We found evidence that, in less than an hour, players implicitly learned that the timing of the animation was related to their own actions, and adapted their sense of agency accordingly. Such findings may help us to anticipate how humans will integrate AI-assistance to guide their behavior.

neuroscience↗

bioRxiv2023

No evidence in favour of the existence of 'intentional' binding

Intentional binding refers to the subjective temporal compression between a voluntary action and its sensory outcome. Despite some studies having challenged the link between temporal compression and intentional action, the intentional binding is still widely used as an implicit measure for the sense of agency. The debate remains unsettled primarily because the experimental conditions used in previous studies were confounded with various alternative causes for temporal compression, and action intention has not yet been tested comprehensively against all potential alternative causes in a single study. Here, we solve this puzzle by jointly comparing participants estimates of the interval between three types of triggering events with comparable predictability - voluntary movement, passive movement, external sensory event - and an external sensory outcome (auditory or visual across experiments). Results failed to show intentional binding, i.e., no shorter interval estimation for the voluntary than the passive movement conditions. Instead, we observed temporal (but not intentional) binding when comparing both movement conditions to the external sensory condition. Thus, temporal binding seems to originate from sensory integration and temporal prediction, not from action intention. As such, these findings underscore the need to reconsider the use of "intentional binding" as a reliable proxy of the sense of agency. Public Significance StatementWhen we press a light switch and observe a bulb lightening, we experience a sense of agency, a feeling of control over these events. We also estimate the temporal interval between our voluntary action and its consequence shorter than the same interval between two events in which we are not involved. Such temporal binding has thus been taken as a measure of the sense of agency. However, our study reveals that voluntary actions are neither necessary, nor sufficient for temporal binding. Instead, temporal binding relies on predicting and integrating information. The sense of agency can be disturbed in various psychiatric disorders and its brain mechanisms are currently actively explored. Our study urges amending how it is measured.

neuroscience↗

bioRxiv2022

A proton pump enhancing photosynthesis links phagocytosis to marine phytoplankton symbiogenesis

Diatoms, dinoflagellates, and coccolithophorids are the dominant groups of marine eukaryotic phytoplankton collectively responsible for the majority of primary production in the ocean1. These phytoplankton contain additional intracellular membranes around their chloroplasts derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary endosymbiosis2. This symbiogenesis hypothesis for the origin of modern secondary endosymbiotic phytoplankton is supported by a wealth of palaeontologic, morphologic, and genomic evidence3-6. However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton are unknown. We report that the proton-pumping enzyme V-type H+-ATPase (VHA), ubiquitously used in eukaryotic intercellular digestion, is localized around the chloroplasts of centric diatoms and that VHA-activity significantly enhances photosynthesis over a wide range of oceanic irradiances. Similar results in pennate diatoms, dinoflagellates, and coccolithophorids, but not green or red microalgae, imply a mechanism resulting from the co-option of phagocytic VHA activity into a carbon concentrating mechanism that is common to secondary endosymbiotic phytoplankton. Furthermore, analogous VHA-dependent mechanisms in extant photosymbiotic marine invertebrates7-9 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Our results suggest that VHA-dependent enhancement of photosynthesis contributes at least 7% of primary production in the ocean, providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.

evolutionary biology↗

bioRxiv2020

Statistical learning occurs during practice while high-order rule learning during rest period

Knowing when the brain learns is crucial for both the comprehension of memory formation and consolidation, and for developing new training and neurorehabilitation strategies in healthy and patient populations. Recently, a rapid form of offline learning developing during short rest periods has been shown to account for most of procedural learning, leading to the hypothesis that the brain mainly learns during rest between practice periods. Nonetheless, procedural learning has several subcomponents not disentangled in previous studies investigating learning dynamics, such as acquiring the statistical regularities of the task, or else the high-order rules that regulate its organization. Here, we analyzed 506 behavioral sessions of implicit visuomotor deterministic and probabilistic sequence learning tasks, allowing the distinction between general skill learning, statistical learning and high-order rule learning. Our results show that the temporal dynamics of apparently simultaneous learning processes differ. While general skill and high-order rule learning are acquired offline, statistical learning is evidenced online. These findings open new avenues on the short-scale temporal dynamics of learning and memory consolidation and reveal a fundamental distinction between statistical and high-order rule learning, the former benefiting from online evidence accumulation and the latter requiring short rest periods for rapid consolidation.

neuroscience↗

bioRxiv2020

Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance

Despite the ubiquity and ecological importance of diatoms, much remains to be understood about their physiology and metabolism, including their carotenoid biosynthesis pathway. Early carotenoid biosynthesis steps are well-conserved, while the identity of the enzymes that catalyze the later steps and their order remain unclear. Those steps lead to the biosynthesis of the final pathway products: the main accessory light-harvesting pigment fucoxanthin (Fx) and the main photoprotective pigment pool comprised of diadinoxanthin (Ddx) and its reversibly de-epoxidized form diatoxanthin (Dtx). We used sequence comparison to known carotenoid biosynthesis enzymes to identify novel candidates in the diatom Thalassiosira pseudonana. Microarray and RNA-seq data was used to select candidates with transcriptomic responses similar to known carotenoid biosynthesis genes and to create full-length gene models, and we focused on those that encode proteins predicted to be chloroplast-localized. We identified a violaxanthin de-epoxidase-like gene (Thaps3_11707, VDL2) that when overexpressed results in increased Fx abundance while stoichiometrically reducing Ddx+Dtx. Based on transcriptomics, we hypothesize that Thaps3_10233 may also contribute to Fx biosynthesis, in addition to VDL2. Separately using antisense RNA to target VDL2, VDL1, and both LUT1-like copies (hypothesized to catalyze an earlier step in the pathway) simultaneously, reduced the overall cellular photosynthetic pigment content, including chlorophylls, suggesting destabilization of light-harvesting complexes by Fx deficiency. Based on transcriptomic and physiological data, we hypothesize that the two predicted T. pseudonana zeaxanthin epoxidases have distinct functions and that different copies of phytoene synthase and phytoene desaturase may serve to initiate carotenoid biosynthesis in response to different cellular needs. Finally, nine carotene cis/trans isomerase (CRTISO) candidates identified based on sequence identity to known CRTISO proteins were narrowed to two most likely to be part of the T. pseudonana carotenoid biosynthesis pathway based on transcriptomic responses and predicted chloroplast targeting.

microbiology↗

bioRxiv2019

Causal modulation of right fronto-parietal phase synchrony with Transcranial Magnetic Stimulation during a conscious visual detection task

Correlational evidence in non-human primates has reported evidence of increased frontoparietal high-beta band (22-30 Hz) synchrony during the endogenous allocation of visuospatial attention. But may the engagement of inter-regional synchrony at this specific frequency band provide the causal mechanism by which top-down processes are engaged and they facilitate visual perception in humans? Here we further analyzed electroencephalographic (EEG) signals from a group of healthy human participants who performed a conscious visual detection task, under the influence of brief rhythmic (30 Hz) or random bursts of Transcranial Magnetic Stimulation (TMS), with an identical number of pulses and duration, delivered to the right Frontal Eye Field (FEF) prior to the onset of a lateralized near-threshold target. We report increases of inter-regional synchronization in the high-beta band (25-35 Hz) between the electrode closest to the stimulated region (right FEF) and parietal leads, and increases of local inter-trial coherence in the same frequency band over parietal contacts, both driven by rhythmic but not random TMS patterns. Importantly, such increases were accompained by increases of visual sensitivity for left visual targets (contralateral to the stimulation) in the rhythmic but not the random TMS condition at the group level. These outcomes suggest that human high-beta synchrony between right frontal and parietal regions can be modulated non-invasively and that high-beta oscillatory activity across the right dorsal fronto-parietal network may contribute to the facilitation of conscious visual detection. Our study also supports future applications of non-invasive brain stimulation technologies for the manipulation of inter-regional synchrony, which could be administered to improve visual behaviors in healthy humans or neurological patients.

neuroscience↗

bioRxiv2019

Entrainment of local synchrony reveals a causal role for high-beta right frontal oscillations in human visual consciousness

Prior evidence supports the critical role of oscillatory activity in cognitive function, but are cerebral oscillations simply correlated or causally linked to specific aspects of visual cognition? Here, EEG signals were recorded on humans performing a conscious visual detection task, while they received brief rhythmic or random noninvasive stimulation patterns delivered to the right Frontal Eye Field prior to the onset of a lateralized target. Compared to random patterns, rhythmic high-beta patterns led to greater entrainment of local oscillations (i.e., increased power and phase alignment at the stimulation frequency), and to higher conscious detection of contralateral targets. When stimulation succeeded in enhancing visual detection, the magnitude of oscillation entrainment correlated with visual performance increases. Our study demonstrates a causal link between high-beta oscillatory activity in the Frontal Eye Field and conscious visual perception. Furthermore, it supports future applications of brain stimulation to manipulate local synchrony and improve or restore impaired visual behaviors.

neuroscience↗

bioRxiv2017

The ventral stream receives spatial information from the dorsal stream during configural face processing

Configural face processing is considered to be vital for face perception. If configural face processing requires an evaluation of spatial information, might this process involve interactions between ventral stream face-processing regions and dorsal stream visuospatial-processing regions? We explored this possibility using thetaburst stimulation (TBS) with fMRI in humans. Participants were shown two faces that differed in either the shape (featural differences) or the spatial configuration (configural differences) of their features. TBS applied on dorsal location-processing regions: 1) reduced fMRI activity within ventral stream face-processing regions during configural but not featural face processing; and 2) reduced functional connectivity between these face regions significantly more for configural than featural face processing. No changes occurred when TBS was delivered on the vertex control site for either face task. We conclude that ventral stream face-processing regions receive visuospatial information from dorsal stream location-processing regions during configural face processing.\n\nSignificance statementFace perception is thought to be mediated exclusively by neural substrates within the ventral visual pathway. However, by using non-invasive brain stimulation (thetabust transcranial magnetic stimulation) in healthy human adults, we demonstrate that the face-processing regions of the ventral visual pathway receive information from visuospatial-processing regions of the dorsal visual pathway during configural face processing, a vital function in face perception. Our findings thus indicate that veridical face perception may depend on both the ventral and dorsal visual pathways.

neuroscience↗