Biology subjects

Pavone, F. S.

Publications and source records attributed to Pavone, F. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Meditation Styles Are Highly Discriminable from EEG at the Subject Level With Limited Generalization Across the Population: A Machine-Learning Study

Meditation has been associated with improvements in attention, emotional regulation, and mental well-being, motivating increasing interest in objective methods for assessing meditative states. In this study, we investigate whether EEG-based machine learning can reliably distinguish between multiple meditation styles and mind-wandering states. EEG data were recorded from experienced meditators performing three meditation styles, Shamatha, Vipassana, and Metta, together with an eyes-closed mind-wandering condition. EEG signals were preprocessed to remove artifacts, and features were extracted from frequency, time-frequency, and time domains. Classification was evaluated using both intra-subject and inter-subject strategies with multiple machine learning classifiers. Results demonstrate high intra-subject classification accuracy across meditation-versus-mind-wandering and meditation-style comparisons, indicating strongly discriminative subject-specific neural signatures. In contrast, inter-subject performance decreased substantially, particularly for distinguishing meditation styles, suggesting considerable inter-individual variability in meditation-related EEG patterns. Furthermore, temporal analysis revealed that classification performance increase over time, indicating that the neural distinctions between meditation states become increasingly pronounced over time. Additionally, t-SNE visualization showed clear within-subject clustering but increased overlap across subjects, explaining the reduced inter-subject generalization. Overall, these findings highlight the potential of EEG-based machine learning for personalized assessment and monitoring of meditative states while emphasizing the challenges of developing subject-independent meditation classification systems.

neuroscience↗

bioRxiv2025

Ultrasensitive saliva-based detection of early Alzheimer's disease biomarkers via nanoparticle-enhanced evanescent scattering microscopy

Alzheimers disease (AD) is the most common neurodegenerative disease, yet early diagnosis remains a major challenge. Current cerebrospinal fluid (CSF) assays are invasive and unsuitable for large-scale or repeated screening. Blood-based biomarkers have achieved sensitivities above 90%, but still face challenges of standardization, cost, technical complexity, and the need for sophisticated instrumentation. Saliva offers an attractive, non-invasive solution; however, the low concentrations of AD biomarkers have thus far hindered its clinical applicability. Here, we introduce a saliva-based diagnostic platform that combines Total Internal Reflection Scattering (TIRS) microscopy with antibody-functionalized metallic nanoparticles (NPs), for ultrasensitive, real-time quantification of salivary amyloid-{beta} (A{beta}) proteins. Using two established AD mouse models (APPsl and 5xFAD), we found that salivary A{beta}2 levels robustly distinguish transgenic from wild-type animals and correlate with brain amyloid deposition. Pooled and stratified analyses suggest these associations are primarily driven by the transgenic-wild-type contrast rather than linear changes within groups. Predictive modeling further confirmed diagnostic utility: in APPsl, Logistic Regression and Support Vector Machine (SVM) classifiers both achieved 92% accuracy with balanced sensitivity and specificity, while in 5xFAD, SVM reached 88% accuracy with perfect specificity. These results establish the NPs-enhanced TIRS sensor as a rapid, accurate and non-invasive tool for AD detection via saliva. By addressing a critical unmet need in neurodegenerative disease screening, this platform has strong potential to transform early diagnosis, enable timely interventions, and support biomarker-guided clinical trials. Its simplicity, speed, and scalability, make it well-suited for point-of-care diagnostics and large-scale screening initiatives. One Sentence SummaryUltrasensitive saliva test detects early Alzheimers biomarkers using nanoparticle-enhanced scattering microscopy

biochemistry↗

bioRxiv2025

Anisotropic light propagation in human brain white matter

SignificanceAccurate modeling of light diffusion in the human brain is crucial for applications in optogenetics and spectroscopy diagnostic techniques. White matter tissue is composed of myelinated axon bundles, suggesting the occurrence of enhanced light diffusion along their local orientation direction, which however has never been characterized experimentally. Existing diffuse optics models assume isotropic properties, limiting their accuracy. AimWe aim to characterize the anisotropic scattering properties of human white matter tissue by directly measuring its tensor scattering components along different directions, and to correlate them with the local axon fiber orientation. ApproachUsing a time- and space-resolved setup, we image the transverse propagation of diffusely reflected light across two perpendicular directions in a ex vivo human brain sample. Local fiber orientation is independently determined using light sheet fluorescence microscopy (LSFM). ResultsThe directional dependence of light propagation in organized myelinated axon bundles is characterized via Monte Carlo (MC) simulations accounting for a tensor scattering coefficient, revealing a lower scattering rate parallel to the fiber orientation. The effects of white matter anisotropy are further assessed by simulating a typical time-domain near-infrared spectroscopy measurement in a four-layer human head model. ConclusionsThis study provides a first characterization of the anisotropic scattering properties in ex vivo human white matter, highlighting its direct correlation with axon fiber orientation, and opening to the realization of quantitatively accurate anisotropy-aware human head 3D meshes for diffuse optics applications.

neuroscience↗

bioRxiv2025

Myelinated fiber labeling and orientation mapping of the human brain with light-sheet fluorescence microscopy

The convoluted network of myelinated fibers that supports behavior, cognition, and sensory processing in the human brain is the source of its extraordinary complexity. Advancements in tissue optical clearing, 3D fluorescence microscopy, and automated image analysis have enabled unprecedented insights into the architecture of these networks. Here, we investigate the multiscale organization of myelinated fibers in human brain tissue from the brainstem, Brocas area, hippocampus, and primary visual cortex by exploiting a specific fiber staining method, light-sheet fluorescence microscopy (LSFM), and an advanced spatial orientation analysis tool. Using an optimized protocol that integrates tissue clearing with the lipophilic DiD probe to achieve uniform and deep myelinated fiber labeling, we generate micrometerresolution volumetric reconstructions of multiple brain regions through an inverted LSFM. Automated image processing, employing unsupervised 3D multiscale Frangi filters, provides orientation distribution functions and local orientation dispersion maps. This enables precise characterization of the directionality of white matter bundles, linking mesoscopic structural properties to orientation details computed at the native micrometric resolution of the LSFM apparatus. The presented workflow illustrates a robust platform for large-scale, high-resolution brain mapping, which may facilitate the investigation of pathological alterations with unparalleled spatial resolution and, furthermore, the validation of other neuroimaging modalities.

neuroscience↗

bioRxiv2024

Optogenetic inhibition quenches the integration of sensory input in the cortex

SignificanceWe designed a novel all-optical tool to simultaneously silence neuronal activity at arbitrary sites on the dorsal cortex, and monitor the consequences of the manipulation. Optogenetic inhibition of primary sensory regions determined short and long-term dampening of the sensory response across a distributed cortical network. IntroductionMany fundamental processes of brain computation, such as sensory perception and motor control, heavily rely on the mesoscopic dynamics of activity across the cerebral cortex. Manipulating mesoscale activity and observing its effects across multiple brain regions is crucial for understanding the causal link between cortical dynamics and behavior. ObjectiveThe goal of this study was to develop a novel all-optical system that allows inhibition of excitatory neurons while simultaneously monitoring cortical responses at arbitrary sites across the entire dorsal cortex of mice. MethodsWe combined wide-field imaging and optogenetics to create a mesoscale all-optical approach, enabling simultaneous monitoring and manipulation of cortical activity using light. Intravenous injection of two PHP.eB AAVs enabled the whole-brain co-expression of the red-shifted calcium indicator jRCaMP1b and the inhibitory actuator stGtACR2, with stable expression over several weeks. This system was calibrated, and the effects of inhibition on sensory responses were tested. ResultsIncreasing laser power progressively reduced spontaneous activity at the site of irradiation. A single 5-second pulse on the barrel field cortex significantly decreased the amplitude of sensory-evoked responses, not only in the stimulated region but across the entire stimulated hemisphere. ConclusionsThis novel all-optical system enables targeted inhibition while concurrently monitoring mesoscale cortical activity. It provides insights into the dynamics of cortical circuits and offers a milestone for investigating the causal links between neuronal activity and behavior. Future research can use this tool to address sensory responsiveness impairments in neurological and neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

Quantitative cytoarchitectural phenotyping of deparaffinized human brain tissues

Advanced 3D imaging techniques and image segmentation and classification methods can profoundly transform biomedical research by offering deep insights into the cytoarchitecture of the human brain in relation to pathological conditions. Here, we propose a comprehensive pipeline for performing 3D imaging and automated quantitative cellular phenotyping on Formalin-Fixed Paraffin-Embedded (FFPE) human brain specimens, a valuable yet underutilized resource. We exploited the versatility of our method by applying it to different human specimens from both adult and pediatric, normal and abnormal brain regions. Quantitative data on neuronal volume, ellipticity, local density, and spatial clustering level were obtained from a machine learning-based analysis of the 3D cytoarchitectural organization of cells identified by different molecular markers in two subjects with malformations of cortical development (MCD). This approach will grant access to a wide range of physiological and pathological paraffin-embedded clinical specimens, allowing for volumetric imaging and quantitative analysis of human brain samples at cellular resolution. Possible genotype-phenotype correlations can be unveiled, providing new insights into the pathogenesis of various brain diseases and enlarging treatment opportunities.

neuroscience↗

bioRxiv2024

A compact prism-based microscope for high sensitive measurements in fluid biopsy

The increasing demand for sensitive, portable, and cost-effective disease detection methods has raised significant interest in the development of biosensors for rapid and early-stage diagnosis, population mass-screening, and bedside monitoring. Although a certain number of sensing devices with high sensitivity has experienced considerable progress, their practical application has been hindered by challenges in replicating instrumental systems, obtaining rapid and multiplexed signals, and the high cost of manufacturing. In response, we present a streamlined prism-based Total Internal Reflection system which, in combination with surface functionalization techniques on gold nanoparticles, is capable of facilitating Evanescent Wave scattering for the highly sensitive and rapid detection of specific analytes in synthetic liquids and real human samples. The system achieves a remarkable limit of detection of 1 fg/mL concentration for the targeted pathological biomarker. Our innovative design addresses the limitations of existing technologies by reducing costs, minimising overall size, and ensuring swift biofluid analysis with remarkable sensitivity. To validate its efficacy, we conducted scattering experiments in synthetic and human serum samples, exploiting functionalized AuNPs to recognize bacterial lipopolysaccharides as biomarkers for sepsis disease. The cohesive integration of these techniques hopefully makes this biosensing setup a promising candidate for potential clinical deployment, meeting the pressing requirements for rapid personalised diagnosis, large-scale population screening and bed-monitoring.

biophysics↗

bioRxiv2024

Frequency-Dependent Inter-Brain Synchrony is Modulated by Social Interaction in Freely Moving Mice

Social interaction, a pivotal aspect of human and animal behavior, involves a dynamic exchange of information that shapes behavioral responses, emotional states, and cognitive processes. To gain insights into the neural mechanisms underlying these processes, it is necessary to simultaneously investigate the brain activity of socially interacting subjects. Commonly, the simultaneous study of behavior and brain activity during the execution of social tasks is conducted through Hyperscanning in humans which limits the availability of interventions. Here we describe a new experimental platform that combines the development of a new miniaturized optical system, the "MiCe-Scope", to monitor neural activity across the entire cortical mantle with a behavioral paradigm to perform a Hyperscanning study in freely moving mice engaged in social interaction. Our results revealed inter-brain synchrony across different frequency bands widespread over the entire cortical mantle, modulated by social behavior. This finding suggests that synchronization reflects the mutual prediction performed by the entire cortex in mice of interacting dyads. The presence of different synchronization maps in these frequency bands suggests a multiscale nature of interaction, extending the predictive nature of interaction to cortical areas beyond the medial prefrontal cortex. Our work provides an experimental framework to conduct Hyperscanning studies in an animal model that mirrors findings from human studies.

neuroscience↗

bioRxiv2024

Two-photon all-optical electrophysiology for the dissection of larval zebrafish brain functional connectivity

One of the most audacious goals of modern neuroscience is unraveling the complex web of causal relations underlying the activity of neuronal populations on a whole-brain scale. This endeavor, prohibitive just a couple of decades ago, has recently become within reach owing to the advancements in optical methods and the advent of genetically encoded indicators/actuators. These techniques, applied to the translucent larval zebrafish have enabled recording and manipulation of the activity of extensive neuronal populations spanning the entire vertebrate brain. Here, we present the conception of a custom two-photon optical system, coupling light-sheet imaging and 3D excitation with acousto-optic deflectors for simultaneous high-speed volumetric recording and optogenetic stimulation. By employing a zebrafish line with pan-neuronal expression of both the calcium reporter GCaMP6s and the red-shifted opsin ReaChR, we implemented a crosstalk-free, noninvasive all-optical approach and applied it to the reconstruction of the functional connectivity of the left habenula.

neuroscience↗

bioRxiv2023

Segmentation of supragranular and infragranular layers in ultra-high resolution 7T ex vivo MRI of the human cerebral cortex

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Lever-aging recent advancements in ultra-high resolution ex vivo MRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers in ex vivo MRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphere ex vivo scans at 120 {micro}m, we propose a multi-resolution U-Nets framework (MUS) that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation, while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Cortical mapping of the sensory response reveals strong brain-state dependence of the late component

Sensory information must be integrated across a distributed brain network for stimulus processing and perception. Recent studies have revealed specific spatiotemporal patterns of cortical activation for the early and late components of sensory-evoked responses, which are associated with stimulus features and perception, respectively. However, our understanding of how the brain state influences the sensory-evoked activation across the mouse cortex remains limited. In this study, we utilized isoflurane to modulate the brain state and conducted wide-field calcium imaging of Thy1-GCaMP6f mice to monitor the distributed activation evoked by multi-whisker stimulation. Our findings reveal that the level of anesthesia strongly shapes the spatiotemporal features and the functional connectivity of the sensory-activated network. As anesthesia levels decrease, we observe increasingly complex responses, accompanied by the emergence of the late component within the sensory-evoked response. The persistence of the late component under anesthesia raises new questions regarding the potential existence of perception during unconscious states.

neuroscience↗

bioRxiv2023

Microplastics reach the brain and interfere with honey bee cognition

Scientific research exploring the impact of microplastics (MPs) in terrestrial systems is still at an early stage but has already confirmed that exposure to plastics leads to various detrimental health effects in several organisms. Although recent studies have shown the toxicological effects of single MP polymers on honey bees, the effects of different polymer combinations and their consequences on cognitive and behavioural performance remain unknown. To fill this knowledge gap, we investigated the effects of MPs, both individually and in combination, on the cognitive abilities of the honey bee Apis mellifera. We evaluated the acute oral toxicity of Polystyrene (PS) and Plexiglass (PMMA) MPs, as well as a combination of the two (MIX), at three different concentrations (0.5, 5 and 50 mg/L-1) and analysed their effects on sucrose responsiveness and appetitive olfactory learning and memory. We also explored whether these MPs could reach and accumulate in the insect brain using Two-Photon Fluorescence Microscopy (TPFM) in combination with an optimized version of the DISCO clearing technique. The results revealed that PS reduced the responsiveness of foragers to sucrose, whereas PMMA had no significant impact; however, the combination of PMMA and PS had a pronounced negative effect on sucrose responsiveness. In addition, both PMMA and PS, as well as MIX, impaired bee learning formation and memory retrieval, with PS exhibiting the most severe effects. Regarding our brain imaging analysis performed with TFPM, we found that after only three days of oral exposure, MPs could penetrate and accumulate in the brain. These results raise concerns about the potential mechanical, cellular, and biochemical damage that MPs may cause to the central nervous system.

animal behavior and cognition↗

bioRxiv2023

Optimization of highly inclined Illumination for diffraction-limited and super-resolution microscopy

In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single-molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and how this impact on the image quality complicates setting HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the impact of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 m). Based on this, we present a simple optical solution to reduce the inclined beam thickness down to 2.6 m while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.

biophysics↗

bioRxiv2022

Fiber enhancement and 3D orientation analysis inlabel-free two-photon fluorescence microscopy

3D fluorescence microscopy can be profitably used in combination with tissue clearing and myelin labeling techniques for investigating the human brain myeloarchitectonics with sub-micrometric resolution, and for providing detailed histological reference data for the validation of diffusion magnetic resonance imaging (dMRI) tractography. Differently from state-of-the-art polarimetry-based neuroimaging modalities such as 3D polarized light imaging and 3D polarized-sensitive optical coherence tomography, the quantitative histological analysis of cortical and white matter fiber architectures from fluorescence microscopy images requires the estimation of fiber orientations via image processing techniques, as Fourier or structure tensor analysis. However, these can be error-prone as they are not able to detect myelinated fibers in surrounding brain tissue. Here we present a novel image processing pipeline built around a 3D Frangi filter able to enhance fiber structures of varying diameters in tiled brain section reconstructions of arbitrary size, and to produce accurate 3D fiber orientation maps in both grey and white matter regions, while preserving the native resolution of the employed microscopy system. The developed software tool also features the estimation of fiber orientation distribution functions which, in view of their widespread use in the neuroimaging community, may favor a multimodal comparison with brain connectivity data obtained from the aforementioned label-free optical modalities, and the validation of modern dMRI-based tractography. The proposed image processing pipeline was applied to brain samples treated according to a novel label-free preparation technique capable of enhancing the autofluorescence of myelinated fiber axons, thus demonstrating the feasibility of single fiber orientation analyses in fluorescence microscopy without the need for exogenous staining.

bioengineering↗

bioRxiv2022

BRAin-wide Neuron quantification Tool reveals strong sexual dimorphism in the evolution of fear memory

Fear responses are functionally adaptive behaviors that are strengthened as memories. Indeed, a detailed knowledge of the neural circuitry modulating fear and fear memory could be the turning point for the comprehension of this emotion and its pathological states. A comprehensive understading of the neural circuits mediating memory encoding, consolidation, and retrieval over time presents the fundamental technological challenge of analyzing activity in the entire brain with single-neuron resolution. In this context, we developed the BRAin-wide Neuron quantification Toolkit (BRANT) for mapping whole-brain neuronal activation at micron-scale resolution, combining tissue clearing, high-resolution light-sheet microscopy, and automated 3D image analysis. The robustness and scalability of this method allowed us to quantify the evolution of neuronal activation patterns across multiple phases of memory in mice. This approach highlighted a strong sexual dimorphism in the circuits recruited during memory recall, which had no counterpart in the behaviour. The methodology presented here paves the way for a comprehensive functional characterization of the evolution of fear memory.

neuroscience↗

bioRxiv2021

Particle localization using local gradients and its application to nanometer stabilization of a microscope

Accurate localization of single particles plays an increasingly important role in a range of biological techniques, including single molecule tracking and localization-based superresolution microscopy. Such techniques require fast and accurate particle localization algorithms as well as nanometer-scale stability of the microscope. Here, we present a universal method for three-dimensional localization of single labeled and unlabeled particles based on local gradient calculation of microscopy images. The method outperforms current techniques in high noise conditions, and it is capable of nanometer accuracy localization of nano- and micro-particles with sub-ms calculation time. By localizing a fixed particle as fiducial mark and running a feedback loop, we demonstrate its applicability for active drift correction in sensitive nanomechanical measurements such as optical trapping and superresolution imaging. A multiplatform open software package comprising a set of tools for local gradient calculation in brightfield and fluorescence microscopy is shared to the scientific community.

biophysics↗

bioRxiv2021

A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex

Cells are not uniformly distributed in the human cerebral cortex. Rather, they are arranged in a regional and laminar fashion that span a range of scales. Here we demonstrate an innovative imaging and analysis pipeline to construct a reliable cell census across the human cerebral cortex. Magnetic resonance imaging (MRI) is used to establish a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with both traditional immunohistochemistry, to provide a stereological gold-standard, and with a custom-made inverted confocal light-sheet fluorescence microscope (LSFM) for 3D imaging at cellular resolution. Finally, mesoscale optical coherence tomography (OCT) enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system.

neuroscience↗

bioRxiv2021

Exploring the human cerebral cortex using confocal microscopy

Cover-all mapping of the distribution of neurons in the human brain would have a significant impact on the deep understanding of brain function. Therefore, complete knowledge of the structural organization of different human brain regions at the cellular level would allow understanding their role in the functions of specific neural networks. Recent advances in tissue clearing techniques have allowed important advances towards this goal. These methods use specific chemicals capable of dissolving lipids, making the tissue completely transparent by homogenizing the refractive index. However, labeling and clearing human brain samples is still challenging. Here, we present an approach to perform the cellular mapping of the human cerebral cortex coupling immunostaining with SWITCH/TDE clearing and confocal microscopy. A specific evaluation of the contributions of the autofluorescence signals generated from the tissue fixation is provided as well as an assessment of lipofuscin pigments interference. Our evaluation demonstrates the possibility of obtaining an efficient clearing and labeling process of parts of adult human brain slices, making it an excellent method for morphological classification and antibody validation of neuronal and non-neuronal markers.

neuroscience↗