Alessandro Arena

• Signorelli, Letizia; Korchynska, Solomiia; Ortiz, Cantin; Arena, Alessandro; Wilhelm, Sophia Anna & Boccara, Charlotte (2026). Nyx: a flexible framework for sleep scoring across species, lifespan and modalities. bioRxiv - the preprint server for biology. doi: 10.64898/2026.07.24.740558. Full text in Research Archive Show summary

  Abstract Sleep is a key factor in almost every physiological process, yet scoring tools lag behind innovations in basic to clinical research. New automated algorithms are trained on narrow datasets, typically healthy adult mouse or human, and fail to generalise, leaving labs to fall back on slow, laborious, and often poorly reproducible manual scoring. Here we introduce Nyx, an unsupervised framework built on principal component analysis that flexibly clusters epochs into sleep states, akin to how spike-sorting algorithms cluster single-neuron activity. Validated on about 8,000 hours spanning 19 independent datasets, it generalises across species, lifespan, recording modalities, and altered sleep architectures, matching human inter-scorer agreement. Beyond this, Nyx opens new ground for modern sleep research: classifying NREM subtypes in rodents, revealing states that cut across canonical boundaries in non-mammalian species, and enabling real-time, closed-loop manipulation. Distributed as an open-source package with a graphical user interface, Nyx offers an accessible, explainable framework built to scale with the pace of innovation itself.

• Sanchez-Vives, Maria V; Manasanch, Arnau; Pigorini, Andrea; Arena, Alessandro; Camassa, Alessandra & Juel, Bjørn Erik [Show all 20 contributors for this article] (2026). Multiscale dynamical characterization of cortical brain states: from synchrony to asynchrony. eLIFE. doi: 10.7554/elife.108613.1. Full text in Research Archive Show summary

  The cerebral cortex spontaneously displays different patterns of activity that evolve over time according to the brain state. Sleep, wakefulness, resting states, and attention are examples of a wide spectrum of physiological states that can be sustained by the same structural network. Furthermore, additional states are generated by drugs (e.g., different levels of anesthesia) or by pathological conditions (e.g., brain lesions, disorders of consciousness). While the significance of understanding brain states in relation to brain dynamics and behavior has become increasingly evident over the past two decades, a unified definition of brain states remains elusive. In this review, we focus on two extremes of this spectrum: synchronous versus asynchronous states. These functional states predominantly underlie unconsciousness and consciousness, respectively, although exceptions exist. Our aim is to integrate data from different levels into a multiscale understanding, ranging from local circuits to whole-brain dynamics, including properties such as cortical complexity, functional connectivity, synchronization, wave propagation, and excitatory-inhibitory balance that vary across states and characterize them. Experimental and clinical data, as well as computational models (at micro-, meso-, and macrocortical levels) associated with the discussed brain states, are made available to readers.

• Destexhe, Alain; Goldman, Jennifer S; Tort-Colet, Nuria; Roques, Axel; Fousek, Jan & Petkoski, Spase [Show all 35 contributors for this article] (2025). State-dependent brain responsiveness, from local circuits to the whole brain. eLIFE. 14, p. 1–36. doi: 10.7554/elife.108768.1. Full text in Research Archive Show summary

  The objective of this paper is to review physiological and computational aspects of the responsiveness of the cerebral cortex to stimulation, and how responsiveness depends on the state of the system. This correspondence between brain state and brain responsiveness (statedependent responses) is outlined at different scales from the cellular and circuit level, to the mesoscale and macroscale level. At each scale, we review how quantitative methods can be used to characterize network states based on brain responses, such as the Perturbational Complexity Index (PCI). This description will compare data and models, systematically and at multiple scales, with a focus on the mechanisms that explain how brain responses depend on brain states.

• Nilsen, Andre Sevenius; Arena, Alessandro & Storm, Johan Frederik (2024). Exploring effects of anesthesia on complexity, differentiation, and integrated information in rat EEG. Neuroscience of Consciousness. 2024(1). doi: 10.1093/nc/niae021. Full text in Research Archive Show summary

  To investigate mechanisms underlying loss of consciousness, it is important to extend methods established in humans to rodents as well. Perturbational complexity index (PCI) is a promising metric of “capacity for consciousness” and is based on a perturbational approach that allows inferring a system’s capacity for causal integration and differentiation of information. These properties have been proposed as necessary for conscious systems. Measures based on spontaneous electroencephalography recordings, however, may be more practical for certain clinical purposes and may better reflect ongoing dynamics. Here, we compare PCI (using electrical stimulation for perturbing cortical activity) to several spontaneous electroencephalography-based measures of signal diversity and integrated information in rats undergoing propofol, sevoflurane, and ketamine anesthesia. We find that, along with PCI, the spontaneous electroencephalography-based measures, Lempel–Ziv complexity (LZ) and geometric integrated information (ΦG), were best able to distinguish between awake and propofol and sevoflurane anesthesia. However, PCI was anti-correlated with spontaneous measures of integrated information, which generally increased during propofol and sevoflurane anesthesia, contrary to expectations. Together with an observed divergence in network properties estimated from directed functional connectivity (current results) and effective connectivity (earlier results), the perturbation-based results seem to suggest that anesthesia disrupts global cortico-cortical information transfer, whereas spontaneous activity suggests the opposite. We speculate that these seemingly diverging results may be because of suppressed encoding specificity of information or driving subcortical projections from, e.g., the thalamus. We conclude that certain perturbation-based measures (PCI) and spontaneous measures (LZ and ΦG) may be complementary and mutually informative when studying altered states of consciousness.

• Hönigsperger, Christoph; Storm, Johan Frederik & Arena, Alessandro (2023). Laminar evoked responses in mouse somatosensory cortex suggest a special role for deep layers in cortical complexity. European Journal of Neuroscience. ISSN 0953-816X. p. 1–19. doi: 10.1111/ejn.16108. Full text in Research Archive Show summary

  Abstract It has been suggested that consciousness is closely related to the complexity of the brain. The perturbational complexity index (PCI) has been used in humans and rodents to distinguish conscious from unconscious states based on the global cortical responses (recorded by electroencephalography, EEG) to local cortical stimulation (CS). However, it is unclear how different cortical layers respond to CS and contribute to the resulting intra‐ and inter‐areal cortical connectivity and PCI. A detailed investigation of the local dynamics is needed to understand the basis for PCI. We hypothesized that the complexity level of global cortical responses (PCI) correlates with layer‐specific activity and connectivity. We tested this idea by measuring global cortical dynamics and layer‐specific activity in the somatosensory cortex (S1) of mice, combining cortical electrical stimulation in deep motor cortex, global electrocorticography (ECoG) and local laminar recordings from layers 1–6 in S1, during wakefulness and general anaesthesia (sevoflurane). We found that the transition from wake to sevoflurane anaesthesia correlated with a drop in both the global and local PCI (PCI st ) values (complexity). This was accompanied by a local decrease in neural firing rate, spike‐field coherence and long‐range functional connectivity specific to deep layers (L5, L6). Our results suggest that deep cortical layers are mechanistically important for changes in PCI and thereby for changes in the state of consciousness.

• Arena, Alessandro; Juel, Bjørn Erik; Comolatti, Renzo; Thon, Sarah & Storm, Johan Frederik (2021). Capacity for consciousness under ketamine anaesthesia is selectively associated with activity in posteromedial cortex in rats. Neuroscience of Consciousness. 2022(1), p. 1–15. doi: 10.1093/nc/niac004. Full text in Research Archive Show summary

  It remains unclear how specific cortical regions contribute to the brain’s overall capacity for consciousness. Clarifying this could help distinguish between theories of consciousness. Here, we investigate the association between markers of regionally specific (de)activation and the brain’s overall capacity for consciousness. We recorded electroencephalographic responses to cortical electrical stimulation in six rats and computed Perturbational Complexity Index state-transition (PCIST), which has been extensively validated as an index of the capacity for consciousness in humans. We also estimated the balance between activation and inhibition of specific cortical areas with the ratio between high and low frequency power from spontaneous electroencephalographic activity at each electrode. We repeated these measurements during wakefulness, and during two levels of ketamine anaesthesia: with the minimal dose needed to induce behavioural unresponsiveness and twice this dose. We found that PCIST was only slightly reduced from wakefulness to light ketamine anaesthesia, but dropped significantly with deeper anaesthesia. The high-dose effect was selectively associated with reduced high frequency/low frequency ratio in the posteromedial cortex, which strongly correlated with PCIST. Conversely, behavioural unresponsiveness induced by light ketamine anaesthesia was associated with similar spectral changes in frontal, but not posterior cortical regions. Thus, activity in the posteromedial cortex correlates with the capacity for consciousness, as assessed by PCIST, during different depths of ketamine anaesthesia, in rats, independently of behaviour. These results are discussed in relation to different theories of consciousness.

• Arena, Alessandro; Comolatti, Renzo; Thon, Sarah Kriebel; Casali, Adenauer G. & Storm, Johan Frederik (2021). General Anesthesia Disrupts Complex Cortical Dynamics in Response to Intracranial Electrical Stimulation in Rats. eNeuro. 8(4). doi: 10.1523/ENEURO.0343-20.2021. Full text in Research Archive Show summary

  The capacity of human brain to sustain complex cortical dynamics appears to be strongly associated with conscious experience and consistently drops when consciousness fades. For example, several recent studies in humans found a remarkable reduction of the spatiotemporal complexity of cortical responses to local stimulation during dreamless sleep, general anesthesia, and coma. However, this perturbational complexity has never been directly estimated in non-human animals in vivo previously, and the mechanisms that prevent neocortical neurons to engage in complex interactions are still unclear. Here, we quantify the complexity of electroencephalographic (EEG) responses to intracranial electrical stimulation in rats, comparing wakefulness to propofol, sevoflurane, and ketamine anesthesia. The evoked activity changed from highly complex in wakefulness to far simpler with propofol and sevoflurane. The reduced complexity was associated with a suppression of high frequencies that preceded a reduced phase-locking, and disruption of functional connectivity and pattern diversity. We then showed how these parameters dissociate with ketamine and depend on intensity and site of stimulation. Our results support the idea that brief periods of activity-dependent neuronal silence can interrupt complex interactions in neocortical circuits, and open the way for further mechanistic investigations of the neuronal basis for consciousness and loss of consciousness across species.

• Arena, Alessandro; Juel, Bjørn Erik; Comolatti, Renzo; Thon, Sarah Kriebel & Storm, Johan (2021). Does the posteromedial cortex play a primary role for the capacity for consciousness in rats? BioRxiv. ISSN 0362-4331. doi: 10.1101/2021.01.22.427747. Full text in Research Archive Show summary

  It remains unclear how specific cortical regions contribute to the brain’s overall capacity for consciousness. Clarifying this could help distinguish between theories of consciousness. Here, we investigate the association between markers of regionally specific (de)activation and the brain’s overall capacity for consciousness. We recorded electroencephalographic (EEG) responses to cortical electrical stimulation in 6 rats, and computed Perturbational Complexity Index state-transition (PCIST), which has been extensively validated as an index of the capacity for consciousness in humans. We also estimated the balance between activation and inhibition of specific cortical areas with the ratio between high and low frequency power (HF/LF) from spontaneous EEG activity at each electrode. We repeated these measurements during wakefulness, and under the influence of ketamine anaesthesia at two doses: the minimal dose needed to induce behavioural unresponsiveness and twice this dose. We found that PCIST was only slightly reduced from wakefulness to light ketamine anaesthesia, but dropped significantly down with deeper anaesthesia. The high-dose effect was selectively associated with reduced HF/LF ratio in the posteromedial cortex, which strongly correlated with PCIST. Conversely, behavioural unresponsiveness induced by light ketamine anaesthesia, was associated with similar spectral changes in frontal, but not posterior cortical regions. These findings seem to support the claim that the posteromedial cortex may play a primary role for the capacity for consciousness. Such region-specific associations between cortical activation and the overall capacity for consciousness must be accounted for by theories of consciousness.

• Arena, Alessandro; Thon, Sarah; Casali, Adenauer Girardi & Storm, Johan Frederik (2020). General anaesthesia disrupts complex cortical dynamics in response to intracranial electrical stimulation in rats. BioRxiv. ISSN 0362-4331. doi: 10.1101/2020.02.25.964056. Full text in Research Archive
• Ferro, Mattia; Lamanna, Jacopo; Ripamonti, Maddalena; Racchetti, Gabriella; Arena, Alessandro & Spadini, Sara [Show all 10 contributors for this article] (2017). Functional mapping of brain synapses by the enriching activity-marker SynaptoZip. Nature Communications. 8(1). doi: 10.1038/s41467-017-01335-4. Full text in Research Archive Show summary

  Ideally, elucidating the role of specific brain circuits in animal behavior would require the ability to measure activity at all involved synapses, possibly with unrestricted field of view, thus even at those boutons deeply located into the brain. Here, we introduce and validate an efficient scheme reporting synaptic vesicle cycling in vivo. This is based on SynaptoZip, a genetically encoded molecule deploying in the vesicular lumen a bait moiety designed to capture upon exocytosis a labeled alien peptide, Synbond. The resulting signal is cumulative and stores the number of cycling events occurring at individual synapses. Since this functional signal is enduring and measurable both online and ex post, SynaptoZip provides a unique method for the analysis of the history of synaptic activity in regions several millimeters below the brain surface. We show its broad applicability by reporting stimulus-evoked and spontaneous circuit activity in wide cortical fields, in anesthetized and freely moving animals.

• Arena, Alessandro; Lamanna, Jacopo; Gemma, Marco; Ripamonti, Maddalena; Ravasio, Giuliano & Zimarino, Vincenzo [Show all 9 contributors for this article] (2016). Linear transformation of the encoding mechanism for light intensity underlies the paradoxical enhancement of cortical visual responses by sevoflurane. Journal of Physiology. ISSN 0022-3751. 595(1), p. 339–339. doi: 10.1113/jp272215. Full text in Research Archive Show summary

  Key points The mechanisms of action of anaesthetics on the living brain are still poorly understood. In this respect, the analysis of the differential effects of anaesthetics on spontaneous and sensory‐evoked cortical activity might provide important and novel cues. Here we show that the anaesthetic sevoflurane strongly silences the brain but potentiates in a dose‐ and frequency‐dependent manner the cortical visual response. Such enhancement arises from a linear scaling by sevoflurane of the power‐law relation between light intensity and the cortical response. The fingerprint of sevoflurane action suggests that circuit silencing can boost linearly synaptic responsiveness presumably by scaling the number of responding units and/or their correlation following a sensory stimulation. Abstract General anaesthetics, which are expected to silence brain activity, often spare sensory responses. To evaluate differential effects of anaesthetics on spontaneous and sensory‐evoked cortical activity, we characterized their modulation by sevoflurane and propofol. Power spectra and the bust‐suppression ratio from EEG data were used to evaluate anaesthesia depth. ON and OFF cortical responses were elicited by light pulses of variable intensity, duration and frequency, during light and deep states of anaesthesia. Both anaesthetics reduced spontaneous cortical activity but sevoflurane greatly enhanced while propofol diminished the ON visual response. Interestingly, the large potentiation of the ON visual response by sevoflurane was found to represent a linear scaling of the encoding mechanism for light intensity. To the contrary, the OFF cortical visual response was depressed by both anaesthetics. The selective depression of the OFF component by sevoflurane could be converted into a robust potentiation by the pharmacological blockade of the ON pathway, suggesting that the temporal order of ON and OFF responses leads to a depression of the latter. This hypothesis agrees with the finding that the enhancement of the ON response was converted into a depression by increasing the frequency of light‐pulse stimulation from 0.1 to 1 Hz. Overall, our results support the view that inactivity‐dependent modulation of cortical circuits produces an increase in their responsiveness. Among the implications of our findings, the silencing of cortical circuits can boost linearly the cortical responsiveness but with negative impact on their frequency transfer and with a loss of the information content of the sensory signal.

• Montesano, Giovanni; Belfiore, Marcello; Ripamonti, Maddalena; Arena, Alessandro; Lamanna, Jacopo & Ferro, Mattia [Show all 9 contributors for this article] (2015). Effects of the Concomitant Activation of ON and OFF Retinal Ganglion Cells on the Visual Thalamus: Evidence for an Enhanced Recruitment of GABAergic Cells. Frontiers in Neural Circuits. 9. doi: 10.3389/fncir.2015.00077. Full text in Research Archive

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• Signorelli, Letizia; Korchynska, Solomiia; Ortiz, Cantin; Arena, Alessandro; Wilhelm, Sophia Anna & Boccara, Charlotte (2026). Sleep scoring with Nyx: a generalisable framework across species, ages and recording Methods. Full text in Research Archive Show summary

  Background and aims: Sleep scoring is essential for the characterisation of sleep architecture and supports most analyses in sleep research, yet it remains a time-consuming task. While automated sleep scoring has the potential to reduce manual workload and inter-rater variability, its adoption remains limited. Most existing tools are tailored to specific datasets, reducing their generalisability, and function as black-box algorithms, limiting interpretability and undermining researchers' trust. To address these challenges, we present Nyx, a generalisable, explainable, and accessible sleep scoring framework, based on Principal Component Analysis (PCA) for transparent feature extraction and flexible stage clustering. We demonstrate its application across species, lifespan, and recording modalities, and release it as an open-source tool with a graphical user interface (GUI) for non-technical users. Methods: Nyx was first validated on rodent polysomnographic (PSG) data from 17 datasets (10 baseline and 7 experimental manipulations; rats and mice; ~7,937 h of recordings). Then generalisation was evaluated across three dimensions: species (rodents, humans and additional species), developmental stage (juvenile, adolescent and adult), and recording modality, including acquisition setup (wired, wireless and telemetric) and signal combinations (electroencephalography (EEG) with electromyography (EMG), EEG with video or accelerometry, and EEG-only). Agreement with human scorers and established automated tools was quantified using Cohen's κ and F1 score. Preliminary evaluation of real-time sleep classification was also conducted to explore the framework's potential for closed-loop applications. Results: Nyx achieved performance comparable to inter-rater human agreement across all rodent baseline and experimental datasets (κ ≥ 0.80, F1 ≥ 0.85). The framework generalised across species and developmental stages, accurately differentiating human sleep stages (4-stage: κ ≥ 0.70, F1 ≥ 0.80; 5-stage: κ ≥ 0.65, F1 ≥ 0.75), while maintaining consistent performance across age groups. Real-time classification performance indicates suitability for closed-loop experimental applications. Conclusions: Nyx provides a reproducible, generalisable and accessible framework for sleep scoring across species, developmental stages and recording modalities. Its transparent architecture based on PCA addresses a key barrier to the adoption of automated scoring approaches. By enabling consistent analysis across diverse datasets and acquisition methods, Nyx facilitates more standardised sleep research and the exploration of cross-species, lifespan and cross-modality insights.

• Arena, Alessandro; Comolatti, Renzo; Casali, Adenauer G. & Storm, Johan F. (2018). Cortical complexity and cause‐effect power are reduced by general anesthesia compared to wakefulness in rats. Full text in Research Archive
• Pigorini, Andrea; Arena, Alessandro; Castillo, A. Barbero; Wolff, A.; Galluzzi, A. & Raimondo, F. [Show all 18 contributors for this article] (2018). Consciousness and brain complexity: a multi-scale exploration across species and model. Full text in Research Archive
• Arena, Alessandro (2018). Conscious vs. unconscious brain states in rodents. Full text in Research Archive
• Arena, Alessandro; Comolatti, Renzo; Casali, Adenauer G. & Storm, Johan F. (2018). A New Approach For Assessing Perturbational Complexity In Rats. Full text in Research Archive
• Arena, Alessandro & Storm, Johan Frederik (2017). TOWARD THE EXPLORATION OF COMPLEXITY IN RATS. Full text in Research Archive
• Arena, Alessandro (2017). Toward exploration of cortical complexity in rats. Full text in Research Archive
• Nilsen, Andre Sevenius; Arena, Alessandro; Juel, Bjørn Erik; Storm, Johan Frederik; Murphy, Ricardo & Hu, Hua [Show all 7 contributors for this article] (2017). Forsknigstorget: Hvordan kan hjernen skape bevissthet. Full text in Research Archive

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