Biology subjects

Valente, M.

Publications and source records attributed to Valente, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Spontaneous slow waves index multiple dimensions of recovery in Disorders of Consciousness

Whether and how residual awareness is expressed in patients with Disorders of Consciousness (DoC) depends on the severity of brain damage and the transient functional state of the cortex at assessment. Classically, DoC are associated with electroencephalographic (EEG) slowing, marked by high-amplitude slow waves, even during the day. Yet, slow waves are also a hallmark of healthy sleep, where they are thought to serve restorative functions and to help maintain network homeostasis. Here, we asked whether slow waves in DoC can provide insights into the severity of cortical dysfunction or, conversely, into the preservation of residual awareness and recovery potential, by characterizing their spatial, temporal and morphological properties. We analyzed 256-channel EEG recorded during the Local-Global auditory paradigm in 236 DoC patients, including 123 in Unresponsive Wakefulness Syndrome (UWS), 62 in a Minimally Conscious State minus (MCS-) and 29 in MCS plus (MCS+). High-amplitude slow waves were detected as local events, and their density, amplitude and slopes were quantified scalp-wide and channel-wise, by mean level and temporal variability across the recording. Slow-wave features were related to concurrent (Coma Recovery Scale-Revised - CRS-R, Local-Global paradigm) and follow-up (one-year Glasgow Outcome Scale-Extended - GOS-E) assessments of consciousness and functional recovery. Associations with MRI-derived measures of cortical integrity and structural connectivity, and differences between anoxic and traumatic etiologies, were also examined. Slow waves were more frequent in less severe DoC patients (i.e., MCS) compared to UWS. Slow-wave slopes were also steeper frontally and increased at a faster rate in patients exhibiting higher levels of consciousness and/or markers of conscious access during the Local-Global paradigm. More frequent and steeper slow waves at baseline further predicted recovery of consciousness and of functional independence at one year. At the individual level, slow-wave features classified states of consciousness above chance (AUC = 0.62 and 0.71 for MCS- and MCS+ versus UWS), whereas outcome prediction remained modest (0.56-0.58). These clinical associations had a structural basis: slow-wave occurrence was greater after traumatic than anoxic injury and scaled with the integrity of subcortico-cortical projection fibers and consciousness-related cortical networks. Contrary to the classical view of delta activity as a non-specific marker of impaired consciousness, prominent spontaneous slow waves indexed behavioral and neurophysiological signs of awareness and better recovery. Beyond reflecting a propensity for pathological bistability, they may also signal the integrity of the networks required to generate them, together with their residual capacity for dynamic regulation.

neuroscience↗

bioRxiv2025

Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of Cryptosporidium parasites

Cryptosporidium is a globally endemic parasite genus with over 40 recognized species. While C. hominis and C. parvum are responsible for most human infections, human cases involving other species have also been reported. Furthermore, there is increasing evidence of simultaneous infections with multiple species. Therefore, we devised a new means to identify various species of Cryptosporidium in mixed infections by sequencing a 431 bp amplicon of the 18S rRNA gene encompassing two variable regions. Using the DADA2 pipeline, amplicons were first identified to a genus using the SILVA 132 reference database; then Cryptosporidium amplicons to a species using a custom database. This approach demonstrated sensitivity, successfully detecting and accurately identifying as little as 0.001 ng of C. parvum DNA in a complex stool background. Notably, we differentiated mixed infections and demonstrated the ability to identify potentially novel species of Cryptosporidium both in situ and in vitro. Using this method, we identified Cryptosporidium parvum in Egyptian rabbits with three samples showing minor mixed infections. By contrast, no mixed infections were detected in Egyptian children, who were primarily infected with C. hominis. Thus, this pipeline provides a sensitive tool for Cryptosporidium species-level identification, allowing for the detection and accurate identification of minor variants and mixed infections.

microbiology↗

bioRxiv2024

Dynamics of EEG Microstates Change Across the Spectrum of Disorders of Consciousness

As a response to the environment and internal signals, brain networks reorganize on a sub-second scale. To capture this reorganization in patients with disorders of consciousness and understand their residual brain activity, we investigated the dynamics of electroencephalography (EEG) microstates. We analyze EEG microstate markers to quantify the periods of semi-stable topographies and the large-scale cortical networks they may reflect. To achieve this, EEG samples are clustered into four groups and then fit back into each time sample. We then obtain a time series of maps with different frequencies of occurrence and duration. One such occurrence of a map with a given duration is called a microstate. The goal of this work is to study the dynamics of these topographical patterns across patients with disorders of consciousness. Using the microstate time series, we calculate static and dynamic markers. In contrast to the static, the dynamic metrics depend on the specific temporal sequences of the maps. The static measure Ratio of Total Time covered (RTT) shows differences between healthy controls and patients, however, no differences were observed between the groups of patients. In contrast, some dynamic markers capture inter-patient group differences. The dynamic markers we investigated are Mean Microstate Durations (MMD), Microstate Duration Variances (MDV), Microstate Transition Matrices (MTM), and Entropy Production (EP). The MMD and MDV decrease with the state of consciousness, whereas the MTM non-diagonal transitions and EP increase. In other words, DoC patients have slower and closer to equilibrium (time-reversible) brain dynamics. In conclusion, static and dynamic EEG microstate metrics differ across consciousness levels, with the latter capturing the subtitler differences between groups of patients with disorders of consciousness. Abbreviated summaryThis study investigates EEG microstate dynamics in patients with disorders of consciousness (DoC) to understand residual brain activity and network reorganization. Entropy production, in addition to static markers, differs between patients and healthy controls, whereas the rest of the dynamic markers show differences across patient groups.

neuroscience↗

bioRxiv2024

Dissecting push/pull interactions in the rat subcortical auditory pathway

The role of subcortical structures in binaural integration is of great interest for auditory processing. The inferior colliculus (IC) is the main auditory midbrain center where ascending and descending auditory projections converge, which was suggested to encode auditory information via a push-pull mechanism between the two ICs. However, the origin of this push-pull mechanism in the brain and how it interacts with other upstream/downstream subcortical areas is still a matter of great debate. Here, we harness functional MRI (fMRI) in combination with IC lesions in the rat to dissect the push-pull interaction from a pathway-wide perspective. We find evidence for the push-pull mechanism in IC through negative/positive fMRI signals in the ipsilateral/contralateral ICs upon monaural stimulation. By unilaterally lesioning the corresponding contralateral IC, we demonstrate the necessity of collicular integrity and intercollicular interactions for the push-pull interaction. Using binaural stimulation and IC lesions, we show that the push-pull interaction is exerted also in binaural processing. Finally, we demonstrate that, at least at the population level revealed by fMRI, the main push-pull interactions occur first at the IC level, and not earlier, and that the outcome of the push-pull "calculation" is relayed downstream to MGB. This dissection of the push-pull interaction sheds light into subcortical auditory function.

neuroscience↗

bioRxiv2024

Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections

Plasmacytoid dendritic cells (pDCs) are major producers of type I/III interferons. As interferons are crucial for antiviral defense, pDCs are assumed to play an essential role in this process. However, robust evidence supporting this dogma is scarce. Genetic or pharmacological manipulations that eliminate pDC or disrupt their interferon production often affect other cells, confounding interpretation. To overcome this issue, we engineered pDC-less mice that are specifically and constitutively devoid of pDCs by expressing diphtheria toxin under coordinated control of the Siglech and Pacsin1 genes, uniquely co-expressed in pDCs. pDC-less mice mounted protective immunity against systemic infection with mouse Cytomegalovirus and showed higher survival and less lung immunopathology to intranasal infection with influenza virus and SARS-CoV2. Thus, contrary to the prevailing dogma, we revealed that pDCs and their interferons are dispensable or deleterious during several viral infections. pDC-less mice will enable rigorously reassessing the roles of pDCs in health and disease.

immunology↗

bioRxiv2024

Evidence for a push-pull interaction between superior colliculi in monocular dynamic vision mode

Visual perception can operate in two distinct vision modes - static and dynamic - that have been associated with different neural activity regimes in the superior colliculus (SC). The static vision mode (low flashing frequencies) is associated with strong SC activation modulated by cortical gain and inhibitory intertectal effects, while the dynamic vision mode (high flashing frequencies) evokes the continuity illusion, with associated suppression of SC neural activity. However, the pathway-wide mechanisms underpinning the dynamic vision mode remain poorly understood, especially in terms of corticotectal and tectotectal feedback. Here, we harness rat functional MRI combined with brain lesions to investigate whole-pathway interactions in the dynamic vision mode. In the SC, we find contralateral suppression of activity opposing positive ipsilateral neural activation upon monocular visual stimulation in the dynamic vision mode. A cortical amplification effect was confirmed for both static and dynamic vision modes through cortical lesions, while further lesioning ipsilateral SC led to a boost in the contralateral negative signals, suggesting an active push-pull interaction between ipsilateral and contralateral SCs during the dynamic vision mode regime. This push-pull interaction is specific to the dynamic vision mode; in the static vision mode, both SCs show similar response polarities. These results highlight hitherto unreported frequency-dependent modulations in the tectotectal pathway and further challenge the contemporary notion that intertectal connections solely serve as reciprocal inhibitory mechanisms for avoiding visual blur during saccade occurrence. One Sentence SummaryOpposing signals between superior colliculi in the dynamic vision mode suggest an active push-pull interaction within the tectotectal commissural pathway.

neuroscience↗

bioRxiv2023

Ensembling Unets, sparse representation and low dimensional visualization for rare chromosomal aberration detection in light microscopy images

AO_SCPLOWBSTRACTC_SCPLOWIn biological dosimetry, a radiation dose is estimated using the average number of chromosomal aberration per peripheral blood lymphocytes. To achieve an adequate precision in the estimation of this average, hundreds of cells must be analyzed in 2D microscopy images. Currently, this analysis is performed manually, as conventional computer vision techniques struggle with the wide variety of shapes showcased by chromosomes. The false discovery rate of current automated detection systems is high and variable, depending on small variations in data quality (chromosome spread, illumination variations ...), which makes using it in a fully automated fashion impossible. Automating chromosomal aberration is needed to reduce diagnosis time. Furthermore, an automated system can process more images, which improves confidence intervals around the estimated radiation dose. We build an object detection model to automate chromosomal aberration detection using recent advances in deep convolutional neural networks and statistical learning. We formulated the problem of rare aberration detection as a heatmap regression problem requiring the minimization of a sparsity-promoting loss to reduce the false alarm rate. Our Unet-based approach is analoguous to a one-stage object detector, and keeps the number of hyperparameters to a minimum. Finally, we demonstrate large performance improvements using an ensemble of checkpoints collected during a single run of training. A PCA-based strategy is used to provide cues for interpretation of our deep neural network-based model. The methodology is demonstrated on real, large, and challenging datasets depicting rare chromosomal aberrations and is favorably compared to a reference dosimetry technique.

bioinformatics↗

bioRxiv2022

Activation/suppression balances in rat Superior Colliculus encode the visual continuity illusion

When visual stimuli are presented at a sufficiently high temporal frequency, visual perception shifts from the static to dynamic vision mode, thereby facilitating a continuity illusion which is key for correctly identifying continuous and moving objects and placing them in the context of the surrounding environment. However, how this continuity illusion is encoded along the entire visual pathway remains poorly understood, with disparate Flicker Fusion Frequency (FFF) thresholds measured at retinal, cortical, and behavioural levels. Here, we hypothesized that these disparities may suggest that other brain areas may be involved in encoding the shift from static to dynamic vision modes. We employ a comprehensive approach encompassing behavioural measurements, whole brain activation mapping with high fidelity functional MRI (fMRI), and local electrophysiological validation for studying the mechanisms underlying the shift from static to dynamic vision modes in the rat. Our behavioural measurements reported an FFF threshold proxy of 18{+/-}2 Hz. At the network level, functional MRI revealed that the superior colliculus (SC) exhibits marked signal transitions from positive to negative fMRI signal regimes at the behaviourally measured FFF threshold surrogates, with a strong linear correlation between fMRI signal and behaviour, while thalamic and cortical visual areas displayed a significantly poorer correlation with the behaviour. fMRI-driven neurometric curves approximated the behavioural psychometric curve in SC but not in the other visual areas. Electrophysiological recordings in SC suggested that these fMRI signals transitions arise from strong neural activation/suppression at low/high frequency regimes, respectively, and that a transition between these regimes occurs around the measured FFF threshold proxies. Lesions in V1 further reinforced that these transitions originate in SC. Combined, our data suggests a critical role for SC in encoding temporal frequency discriminations, in particular the shifts from the static to the dynamic vision modes.

neuroscience↗

bioRxiv2022

Immunofilaments Provide a Nanoscale Platform for In Vivo T Cell Expansion and Cancer Immunotherapy

Adoptive T cell therapy has successfully been implemented for the treatment of cancer. Nevertheless, the precarious ex vivo expansion of T cells by artificial antigen-presenting cells (aAPCs) remains cumbersome and can compromise T cell functionality, thereby limiting their therapeutic potential. Here, we propose a radically different approach aiming at direct expansion of T cells in vivo, thereby omitting the need for large-scale ex vivo T cell production. We engineered nanosized immunofilaments (IFs), consisting of a soluble semiflexible polyisocyanopeptide polymer backbone that presents peptide-loaded major histocompatibility complexes and co-stimulatory molecules in a multivalent fashion. We demonstrate that IFs readily activate and expand antigen-specific T cells in a manner highly similar to natural APCs, as evidenced by transcriptomic analyses of T cells. Upon intravenous injection, IFs reach lymphoid organs including spleen and lymph nodes and induce antigen-specific T cell responses in vivo. Moreover, IFs display remarkable anti-tumor efficacy resulting in inhibition of melanoma metastases formation and reduction of primary tumor growth in synergy with immune checkpoint blockade. In conclusion, nanosized IFs represent a powerful new type of aAPC that provide a modular platform for direct activation and expansion of antigen-specific T cells in vivo, which can greatly contribute to cancer immunotherapy.

immunology↗

bioRxiv2022

Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins

Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 38 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.

biophysics↗

bioRxiv2022

A novel mouse model based on intersectional genetics enables unambiguous in vivo discrimination between plasmacytoid and other dendritic cells and their comparative characterization

Plasmacytoid dendritic cells (pDC) were identified about 20 years ago, based on their unique ability to rapidly produce copious amounts of all subsets of type I and type III interferon (IFN-I/III) upon virus sensing, while being refractory to infection. Yet, the identity and physiological functions of pDC are still a matter of debate, in a large part due to their lack of specific expression of any single cell surface marker or gene that would allow to track them in tissues and to target them in vivo with high specificity and penetrance. Indeed, recent studies showed that previous methods that were used to identify or deplete pDC also targeted other cell types, including pDC-like cells and transitional DC (tDC) that were proposed to be responsible for all the antigen presentation ability previously attributed to steady state pDC. Hence, improving our understanding of the nature and in vivo choreography of pDC physiological functions requires the development of novel tools to unambiguously identify and track these cells, including in comparison to pDC-like cells and tDC. Here, we report successful generation of a pDC-reporter mouse model, by using an intersectional genetic strategy based on the unique co-expression of Siglech and Pacsin1 in pDC. This pDC-Tomato mouse strain allows specific ex vivo and in situ detection of pDC. Breeding them with Zbtb46GFP mice allowed side-by-side purification and transcriptional profiling by single cell RNA sequencing of bona fide pDC, pDC-like cells and tDC, in comparison to type 1 and 2 conventional DC (cDC1 and cDC2), both at steady state and during a viral infection, revealing diverging activation patterns of pDC-like cells and tDC. Finally, by breeding pDC-Tomato mice with Ifnb1EYFP mice, we determined the choreography of pDC recruitment to the micro-anatomical sites of viral replication in the spleen, with initially similar but later divergent behaviors of the pDC that engaged or not into IFN-I production. Our novel pDC-Tomato mouse model, and newly identified gene modules specific to combinations of DC types and activations states, will constitute valuable resources for a deeper understanding of the functional division of labor between DC types and its molecular regulation at homeostasis and during viral infections.

immunology↗

bioRxiv2021

Hypoxia promotes a perinatal-like progenitor state in the adult murine epicardium

The epicardium is a reservoir of progenitors that give rise to coronary vasculature and stroma during development and mediates cardiac vascular repair in lower vertebrates. However, its role as a source of progenitors in the adult mammalian heart remains unclear due to lack of clear lineage markers and single-cell culture systems to elucidate epicardial progeny cell fate. We found that in vivo exposure of mice to physiological hypoxia induced adult epicardial cells to re-enter the cell cycle and to express a subset of developmental genes. Multiplex transcriptional profiling revealed a lineage relationship between epicardial cells and smooth muscle, stromal, and endothelial fates, and that physiological hypoxia promoted an endothelial cell fate. In vitro analyses of purified epicardial cells showed that cell growth and subsequent differentiation is dependent upon hypoxia, and that resident epicardial cells retain progenitor identity in the adult mammalian heart with self-renewal and multilineage differentiation potential. These results point to a source of progenitor cells in the adult heart that can promote heart revascularization, providing an invaluable in vitro model for further studies.

cell biology↗

bioRxiv2021

Fibroadipogenic Progenitors contribute to microvascular repair during skeletal muscle regeneration

Skeletal muscle injury results in a disruption of the muscle bed vascular network. A local source of vascular progenitors during muscle regeneration has not been clearly identified. Fibroadipogenic progenitors (FAPs) are required for proper regeneration, however they can also directly contribute to fibrotic and fatty infiltration in response to chronic muscle injury and muscle disease. We show here that acute muscle injury leads to hypoxia and glucose deprivation, triggering FAP proliferation and differentiation into endothelial cells in vitro and in vivo. In response to glucose deprivation, FAPs down regulate fibrotic and fat associated genes and acquire an endothelial cell fate, which is dependent upon mTORC2-HIF2-eNOS pathway. These findings bring new insights into the mechanisms of vascular regeneration during muscle regeneration and define a highly plastic resident progenitor population that responds to oxygen/glucose-deprivation induced cell stress by promoting an endothelial cell fate.

cell biology↗

bioRxiv2020

Remodeling and activation mechanisms of outer arm dynein revealed by cryo-electron microscopy

Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryoelectron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with molecular dynamics simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.

cell biology↗

bioRxiv2020

Conscious processing of narrative stimuli synchronizes heart rate between individuals

Heart rate has natural fluctuations that are typically ascribed to autonomic function. Recent evidence suggests that conscious processing can affect the timing of the heartbeat. We hypothesized that heart rate is modulated by conscious processing and therefore dependent on attentional focus. To test this, we leverage the observation that neural processes can be synchronized between subjects by presenting an identical narrative stimulus. As predicted, we find significant inter-subject correlation of the heartbeat (ISC-HR) when subjects are presented with an auditory or audiovisual narrative. Consistent with the conscious processing hypothesis, we find that ISC-HR is reduced when subjects are distracted from the narrative, and that higher heart rate synchronization predicts better recall of the narrative. Finally, patients with disorders of consciousness who are listening to a story have lower ISC-HR, as compared to healthy individuals, and that individual ISC-HR might predict a patients prognosis.. We conclude that heart rate fluctuations are partially driven by conscious processing, depend on attentional state, and may represent a simple metric to assess conscious state in unresponsive patients.

neuroscience↗

bioRxiv2020

Transient disruption of the inferior parietal lobule impairs the ability to attribute intention to action

Although it is well established that fronto-parietal regions are active during action observation, whether they play a causal role in the ability to infer others intentions from visual kinematics remains undetermined. In experiments reported here, we combined offline continuous theta-burst stimulation (cTBS) with computational modeling to reveal single-trial computations in the inferior parietal lobule (IPL) and inferior frontal gyrus (IFG). Participants received cTBS over the left anterior IPL and the left IFG pars orbitalis, in separate sessions, before completing an intention discrimination task (discriminate intention of observed reach-to-grasp acts) or a kinematic discrimination task (discriminate peak wrist height of the same acts) unrelated to intention. We targeted intentions-sensitive regions whose fMRI-measured activity accurately discriminated intention from the same action stimuli. We found that transient disruption of activity of the left IPL, but not the IFG, impaired the observers ability to judge intention from movement kinematics. Kinematic discrimination unrelated to intention, in contrast, was largely unaffected. Computational analyses revealed that IPL cTBS did not impair the ability to see changes in movement kinematics, nor did it alter the weight given to informative versus non-informative kinematic features. Rather, it selectively impaired the ability to link variations in informative features to the correct intention. These results provide the first causal evidence that left anterior IPL maps kinematics to intentions.

neuroscience↗

bioRxiv2020

Correlations enhance the behavioral readout of neural population activity in association cortex

The spatiotemporal structure of activity in populations of neurons is critical for accurate perception and behavior. Experimental and theoretical studies have focused on "noise" correlations - trial-to-trial covariations in neural activity for a given stimulus - as a key feature of population activity structure. Much work has shown that these correlations limit the stimulus information encoded by a population of neurons, leading to the widely-held prediction that correlations are detrimental for perceptual discrimination behaviors. However, this prediction relies on an untested assumption: that the neural mechanisms that read out sensory information to inform behavior depend only on a populations total stimulus information independently of how correlations constrain this information across neurons or time. Here we make the critical advance of simultaneously studying how correlations affect both the encoding and the readout of sensory information. We analyzed calcium imaging data from mouse posterior parietal cortex during two perceptual discrimination tasks. Correlations limited the ability to encode stimulus information, but (seemingly paradoxically) correlations were higher when mice made correct choices than when they made errors. On a single-trial basis, a mouses behavioral choice depended not only on the stimulus information in the activity of the population as a whole, but unexpectedly also on the consistency of information across neurons and time. Because correlations increased information consistency, sensory information was more efficiently converted into a behavioral choice in the presence of correlations. Given this enhanced-by-consistency readout, we estimated that correlations produced a behavioral benefit that compensated or overcame their detrimental information-limiting effects. These results call for a re-evaluation of the role of correlated neural activity, and suggest that correlations in association cortex can benefit task performance even if they decrease sensory information.

neuroscience↗

bioRxiv2019

Transient disruption of the inferior parietal lobule impairs action mindreading

Although it is well established that fronto-parietal regions are active during action observation, whether they play a causal role in the ability to "mindread" others actions remains controversial. In experiments reported here, we combined offline continuous theta-burst stimulation (cTBS) with computational modeling to reveal single-trial computations in the inferior parietal lobule (IPL) and inferior frontal gyrus (IFG). Participants received cTBS over the left IPL and IFG, in separate sessions, before completing an intention discrimination task or a kinematic discrimination task unrelated to intention. We found that transient disruption of activity of the IPL, but not the IFG, specifically impaired the observers ability to judge intention from movement kinematics. Kinematic discrimination unrelated to intention, in contrast, was largely unaffected. Computational analyses revealed that IPL cTBS did not impair the ability to see changes in movement kinematics, nor did it alter the weight given to informative versus non-informative kinematic features. Rather, it selectively impaired the ability to link variations in informative features to the correct intention. These results provide the first causal evidence that IPL maps kinematics to intentions.

neuroscience↗