437 results on '"Caciagli P"'
Search Results
2. Human Learning of Hierarchical Graphs
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Xia, Xiaohuan, Klishin, Andrei A., Stiso, Jennifer, Lynn, Christopher W., Kahn, Ari E., Caciagli, Lorenzo, and Bassett, Dani S.
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Quantitative Biology - Neurons and Cognition ,Condensed Matter - Statistical Mechanics ,Physics - Biological Physics ,Physics - Physics and Society - Abstract
Humans are constantly exposed to sequences of events in the environment. Those sequences frequently evince statistical regularities, such as the probabilities with which one event transitions to another. Collectively, inter-event transition probabilities can be modeled as a graph or network. Many real-world networks are organized hierarchically and understanding how humans learn these networks is an ongoing aim of current investigations. While much is known about how humans learn basic transition graph topology, whether and to what degree humans can learn hierarchical structures in such graphs remains unknown. We investigate how humans learn hierarchical graphs of the Sierpi\'nski family using computer simulations and behavioral laboratory experiments. We probe the mental estimates of transition probabilities via the surprisal effect: a phenomenon in which humans react more slowly to less expected transitions, such as those between communities or modules in the network. Using mean-field predictions and numerical simulations, we show that surprisal effects are stronger for finer-level than coarser-level hierarchical transitions. Surprisal effects at coarser levels of the hierarchy are difficult to detect for limited learning times or in small samples. Using a serial response experiment with human participants (n=$100$), we replicate our predictions by detecting a surprisal effect at the finer-level of the hierarchy but not at the coarser-level of the hierarchy. To further explain our findings, we evaluate the presence of a trade-off in learning, whereby humans who learned the finer-level of the hierarchy better tended to learn the coarser-level worse, and vice versa. Our study elucidates the processes by which humans learn hierarchical sequential events. Our work charts a road map for future investigation of the neural underpinnings and behavioral manifestations of graph learning., Comment: 22 pages, 10 figures, 1 table
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- 2023
3. Exploring the effects of structure and melting on sweetness in additively manufactured chocolate
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Burkard, Johannes, Kohler, Lucas, Caciagli, Sophia, Herren, Nicolas, Kozamernik, Mark, Mantovani, Saskia, Windhab, Erich J., and Denkel, Christoph
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- 2024
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4. Dynamic Light Scattering based microrheology of End-functionalised triblock copolymer solutions
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Liu, Ren, Caciagli, Alessio, Yu, Jiaming, Tang, Xiaoying, Ghosh, Rini, and Eiser, Erika
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Condensed Matter - Soft Condensed Matter - Abstract
'Soft' patchy surfactant micelles have become an additional building tool in self-assembling systems. The triblock copolymer, Pluronic F108, forms spherical micelles in aqueous solutions upon heating leading to a simple phase diagram with a micellar crystalline solid at higher temperatures and concentrations. Here we report the strong influence of end-functionalising the chain ends either with an azide or azide-DNA complex on the systems' phase behaviour. We find that the azide(N3)- functionalisation renders the chain ends weakly hydrophobic at lower temperatures, causing them to self-assemble into flower-micelles. This hydrophobicity increases with increasing temperature and poses a competing self-assembling mechanism to the solvent induces hydrophobic interactions between the middle-blocks of F108 at higher temperatures and leads to a macroscopic phase separation that is absent in the pure F108 system. However, when we attached short, hydrophilic single-stranded (ss)DNA to the azide groups via click chemistry the chain ends became 'sticky' due to DNA hybridisation below the melting temperature of the complementary ssDNA ends while reverting to hydrophilic behaviour above. We characterise their structural and rheological properties via Dynamic Light Scattering (DLS) and DLS-based passive microrheology with an improved time-frequency domain inversion step. We present the structural behaviour of dilute and semi-dilute solutions of the original F108 system and compare the results with solutions containing either the F108- azide (F108-N3) or partially DNA-functionalised F108-azide chains. Our DLS and microrheology studies inform us on how the attachment of azide groups on F108 changes the mechanical and structural properties of micellar fluids pioneering further characterisation and design of these hybrid systems., Comment: Ready to submit to Polymers - open access journal of polymer science published semimonthly online by MDPI. 23 pages, 8 figures
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- 2022
5. Kinetically limited valence of colloidal particles with surface mobile DNA linkers
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Sánchez, Pedro A., Caciagli, Alessio, Kantorovich, Sofia S., and Eiser, Erika
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science ,Physics - Chemical Physics - Abstract
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between the main dynamic processes governing these systems and allows the simulation of the long time scales reached in experiments. The model is validated by direct comparison with available experimental results, showing an overall good agreement that includes measurements of the average effective valence and its probability distribution as a function of the density of DNA linkers on the particles surface. Finally, simulation results are used to evidence the opposite impact of particle density and characteristic DNA hybridization time on the effective valence., Comment: 10 pages, 6 figures
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- 2022
6. Macroscopic resting-state brain dynamics are best described by linear models
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Nozari, Erfan, Bertolero, Maxwell A., Stiso, Jennifer, Caciagli, Lorenzo, Cornblath, Eli J., He, Xiaosong, Mahadevan, Arun S., Pappas, George J., and Bassett, Dani S.
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- 2024
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7. Exploring the effects of structure and melting on sweetness in additively manufactured chocolate
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Johannes Burkard, Lucas Kohler, Sophia Caciagli, Nicolas Herren, Mark Kozamernik, Saskia Mantovani, Erich J. Windhab, and Christoph Denkel
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Medicine ,Science - Abstract
Abstract In view of the health concerns associated with high sugar intake, this study investigates methods to enhance sweetness perception in chocolate without increasing its sugar content. Using additive manufacturing, chocolate structures were created from masses with varying sugar and fat compositions, where hazelnut oil served as a partial cocoa butter replacement. The study found that while variations in sugar content minimally affected the physical properties of the chocolate masses, hazelnut oil significantly modified melting behavior and consumption time. Chocolate masses with higher hazelnut oil content but similar sugar content exhibited a 24% increase in sweetness perception, likely due to accelerated tastant (i.e., sucrose) release into saliva. Multiphase structures, designated as layered, cube-in-cube, and sandwich structures, exhibited less sensory differences compared to the homogeneous control. Nonetheless, structures with hazelnut oil-rich outer layers resulted in an 11% increase in sweetness perception, even without sugar gradients. This suggests that tastant release plays a more critical role than structural complexity in modifying sweetness perception. This research highlights the efficacy of simpler multiphase structures, such as sandwich designs, which offer sensory enhancements comparable to those of more complex designs but with reduced manufacturing effort, thus providing viable options for industrial-scale production.
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- 2024
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8. Event‐based modeling in temporal lobe epilepsy demonstrates progressive atrophy from cross‐sectional data
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Lopez, Seymour M, Aksman, Leon M, Oxtoby, Neil P, Vos, Sjoerd B, Rao, Jun, Kaestner, Erik, Alhusaini, Saud, Alvim, Marina, Bender, Benjamin, Bernasconi, Andrea, Bernasconi, Neda, Bernhardt, Boris, Bonilha, Leonardo, Caciagli, Lorenzo, Caldairou, Benoit, Caligiuri, Maria Eugenia, Calvet, Angels, Cendes, Fernando, Concha, Luis, Conde‐Blanco, Estefania, Davoodi‐Bojd, Esmaeil, de Bézenac, Christophe, Delanty, Norman, Desmond, Patricia M, Devinsky, Orrin, Domin, Martin, Duncan, John S, Focke, Niels K, Foley, Sonya, Fortunato, Francesco, Galovic, Marian, Gambardella, Antonio, Gleichgerrcht, Ezequiel, Guerrini, Renzo, Hamandi, Khalid, Ives‐Deliperi, Victoria, Jackson, Graeme D, Jahanshad, Neda, Keller, Simon S, Kochunov, Peter, Kotikalapudi, Raviteja, Kreilkamp, Barbara AK, Labate, Angelo, Larivière, Sara, Lenge, Matteo, Lui, Elaine, Malpas, Charles, Martin, Pascal, Mascalchi, Mario, Medland, Sarah E, Meletti, Stefano, Morita‐Sherman, Marcia E, Owen, Thomas W, Richardson, Mark, Riva, Antonella, Rüber, Theodor, Sinclair, Ben, Soltanian‐Zadeh, Hamid, Stein, Dan J, Striano, Pasquale, Taylor, Peter N, Thomopoulos, Sophia I, Thompson, Paul M, Tondelli, Manuela, Vaudano, Anna Elisabetta, Vivash, Lucy, Wang, Yujiang, Weber, Bernd, Whelan, Christopher D, Wiest, Roland, Winston, Gavin P, Yasuda, Clarissa Lin, McDonald, Carrie R, Alexander, Daniel C, Sisodiya, Sanjay M, Altmann, Andre, Bargalló, Núria, Bartolini, Emanuele, O’Brien, Terence J, and Thomas, Rhys H
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Brain Disorders ,Epilepsy ,Neurodegenerative ,Neurosciences ,Clinical Research ,Biomedical Imaging ,Aetiology ,2.1 Biological and endogenous factors ,Neurological ,Good Health and Well Being ,Atrophy ,Biomarkers ,Cross-Sectional Studies ,Epilepsy ,Temporal Lobe ,Hippocampus ,Humans ,Magnetic Resonance Imaging ,Sclerosis ,disease progression ,duration of illness ,event-based model ,MTLE ,patient staging ,ENIGMA-Epilepsy Working Group ,Clinical Sciences ,Neurology & Neurosurgery - Abstract
ObjectiveRecent work has shown that people with common epilepsies have characteristic patterns of cortical thinning, and that these changes may be progressive over time. Leveraging a large multicenter cross-sectional cohort, we investigated whether regional morphometric changes occur in a sequential manner, and whether these changes in people with mesial temporal lobe epilepsy and hippocampal sclerosis (MTLE-HS) correlate with clinical features.MethodsWe extracted regional measures of cortical thickness, surface area, and subcortical brain volumes from T1-weighted (T1W) magnetic resonance imaging (MRI) scans collected by the ENIGMA-Epilepsy consortium, comprising 804 people with MTLE-HS and 1625 healthy controls from 25 centers. Features with a moderate case-control effect size (Cohen d ≥ .5) were used to train an event-based model (EBM), which estimates a sequence of disease-specific biomarker changes from cross-sectional data and assigns a biomarker-based fine-grained disease stage to individual patients. We tested for associations between EBM disease stage and duration of epilepsy, age at onset, and antiseizure medicine (ASM) resistance.ResultsIn MTLE-HS, decrease in ipsilateral hippocampal volume along with increased asymmetry in hippocampal volume was followed by reduced thickness in neocortical regions, reduction in ipsilateral thalamus volume, and finally, increase in ipsilateral lateral ventricle volume. EBM stage was correlated with duration of illness (Spearman ρ = .293, p = 7.03 × 10-16 ), age at onset (ρ = -.18, p = 9.82 × 10-7 ), and ASM resistance (area under the curve = .59, p = .043, Mann-Whitney U test). However, associations were driven by cases assigned to EBM Stage 0, which represents MTLE-HS with mild or nondetectable abnormality on T1W MRI.SignificanceFrom cross-sectional MRI, we reconstructed a disease progression model that highlights a sequence of MRI changes that aligns with previous longitudinal studies. This model could be used to stage MTLE-HS subjects in other cohorts and help establish connections between imaging-based progression staging and clinical features.
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- 2022
9. Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex
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Fotiadis, Panagiotis, Cieslak, Matthew, He, Xiaosong, Caciagli, Lorenzo, Ouellet, Mathieu, Satterthwaite, Theodore D., Shinohara, Russell T., and Bassett, Dani S.
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- 2023
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10. Dynamic network properties of the superior temporal gyrus mediate the impact of brain age gap on chronic aphasia severity
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Wilmskoetter, Janina, Busby, Natalie, He, Xiaosong, Caciagli, Lorenzo, Roth, Rebecca, Kristinsson, Sigfus, Davis, Kathryn A., Rorden, Chris, Bassett, Dani S., Fridriksson, Julius, and Bonilha, Leonardo
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- 2023
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11. Topographic divergence of atypical cortical asymmetry and atrophy patterns in temporal lobe epilepsy
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Park, Bo-yong, Larivière, Sara, Rodríguez-Cruces, Raul, Royer, Jessica, Tavakol, Shahin, Wang, Yezhou, Caciagli, Lorenzo, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Alvim, Marina KM, Yasuda, Clarissa, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Kreilkamp, Barbara AK, Domin, Martin, von Podewils, Felix, Langner, Soenke, Rummel, Christian, Rebsamen, Michael, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, Bender, Benjamin, O’Brien, Terence J, Law, Meng, Sinclair, Benjamin, Vivash, Lucy, Kwan, Patrick, Desmond, Patricia M, Malpas, Charles B, Lui, Elaine, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Lenge, Matteo, Guerrini, Renzo, Bartolini, Emanuele, Hamandi, Khalid, Foley, Sonya, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Parodi, Costanza, Tortora, Domenico, Hatton, Sean N, Vos, Sjoerd B, Duncan, John S, Galovic, Marian, Whelan, Christopher D, Bargalló, Núria, Pariente, Jose, Conde-Blanco, Estefania, Vaudano, Anna Elisabetta, Tondelli, Manuela, Meletti, Stefano, Kong, Xiang‐Zhen, Francks, Clyde, Fisher, Simon E, Caldairou, Benoit, Ryten, Mina, Labate, Angelo, Sisodiya, Sanjay M, Thompson, Paul M, McDonald, Carrie R, Bernasconi, Andrea, Bernasconi, Neda, and Bernhardt, Boris C
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Epilepsy ,Neurodegenerative ,Clinical Research ,Brain Disorders ,Neurosciences ,Aetiology ,2.1 Biological and endogenous factors ,Neurological ,Adult ,Atrophy ,Connectome ,Epilepsy ,Temporal Lobe ,Hippocampus ,Humans ,Magnetic Resonance Imaging ,temporal lobe epilepsy ,asymmetry ,cortical thickness ,multi-site ,gradients ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Temporal lobe epilepsy, a common drug-resistant epilepsy in adults, is primarily a limbic network disorder associated with predominant unilateral hippocampal pathology. Structural MRI has provided an in vivo window into whole-brain grey matter structural alterations in temporal lobe epilepsy relative to controls, by either mapping (i) atypical inter-hemispheric asymmetry; or (ii) regional atrophy. However, similarities and differences of both atypical asymmetry and regional atrophy measures have not been systematically investigated. Here, we addressed this gap using the multisite ENIGMA-Epilepsy dataset comprising MRI brain morphological measures in 732 temporal lobe epilepsy patients and 1418 healthy controls. We compared spatial distributions of grey matter asymmetry and atrophy in temporal lobe epilepsy, contextualized their topographies relative to spatial gradients in cortical microstructure and functional connectivity calculated using 207 healthy controls obtained from Human Connectome Project and an independent dataset containing 23 temporal lobe epilepsy patients and 53 healthy controls and examined clinical associations using machine learning. We identified a marked divergence in the spatial distribution of atypical inter-hemispheric asymmetry and regional atrophy mapping. The former revealed a temporo-limbic disease signature while the latter showed diffuse and bilateral patterns. Our findings were robust across individual sites and patients. Cortical atrophy was significantly correlated with disease duration and age at seizure onset, while degrees of asymmetry did not show a significant relationship to these clinical variables. Our findings highlight that the mapping of atypical inter-hemispheric asymmetry and regional atrophy tap into two complementary aspects of temporal lobe epilepsy-related pathology, with the former revealing primary substrates in ipsilateral limbic circuits and the latter capturing bilateral disease effects. These findings refine our notion of the neuropathology of temporal lobe epilepsy and may inform future discovery and validation of complementary MRI biomarkers in temporal lobe epilepsy.
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- 2022
12. Resting-state background features demonstrate multidien cycles in long-term EEG device recordings
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William K.S. Ojemann, Brittany H. Scheid, Sofia Mouchtaris, Alfredo Lucas, Joshua J. LaRocque, Carlos Aguila, Arian Ashourvan, Lorenzo Caciagli, Kathryn A. Davis, Erin C. Conrad, and Brian Litt
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Neurostimulation ,Epilepsy ,RNS ,Biomarkers ,Interictal ,Spikes ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Background: Longitudinal EEG recorded by implanted devices is critical for understanding and managing epilepsy. Recent research reports patient-specific, multi-day cycles in device-detected epileptiform events that coincide with increased likelihood of clinical seizures. Understanding these cycles could elucidate mechanisms generating seizures and advance drug and neurostimulation therapies. Objective/hypothesis: We hypothesize that seizure-correlated cycles are present in background neural activity, independent of interictal epileptiform spikes, and that neurostimulation may temporarily interrupt these cycles. Methods: We analyzed regularly-recorded seizure-free data epochs from 20 patients implanted with a responsive neurostimulation (RNS) device for at least 1.5 years, to explore the relationship between cycles in device-detected interictal epileptiform activity (dIEA), clinician-validated interictal spikes, background EEG features, and neurostimulation. Results: Background EEG features tracked the cycle phase of dIEA in all patients (AUC: 0.63 [0.56–0.67]) with a greater effect size compared to clinically annotated spike rate alone (AUC: 0.55 [0.53–0.61], p
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- 2023
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13. Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex
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Panagiotis Fotiadis, Matthew Cieslak, Xiaosong He, Lorenzo Caciagli, Mathieu Ouellet, Theodore D. Satterthwaite, Russell T. Shinohara, and Dani S. Bassett
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Science - Abstract
Abstract Recent work has demonstrated that the relationship between structural and functional connectivity varies regionally across the human brain, with reduced coupling emerging along the sensory-association cortical hierarchy. The biological underpinnings driving this expression, however, remain largely unknown. Here, we postulate that intracortical myelination and excitation-inhibition (EI) balance mediate the heterogeneous expression of structure-function coupling (SFC) and its temporal variance across the cortical hierarchy. We employ atlas- and voxel-based connectivity approaches to analyze neuroimaging data acquired from two groups of healthy participants. Our findings are consistent across six complementary processing pipelines: 1) SFC and its temporal variance respectively decrease and increase across the unimodal-transmodal and granular-agranular gradients; 2) increased myelination and lower EI-ratio are associated with more rigid SFC and restricted moment-to-moment SFC fluctuations; 3) a gradual shift from EI-ratio to myelination as the principal predictor of SFC occurs when traversing from granular to agranular cortical regions. Collectively, our work delivers a framework to conceptualize structure-function relationships in the human brain, paving the way for an improved understanding of how demyelination and/or EI-imbalances induce reorganization in brain disorders.
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- 2023
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14. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression
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Larivière, Sara, Royer, Jessica, Rodríguez-Cruces, Raúl, Paquola, Casey, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Yasuda, Clarissa L, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Domin, Martin, von Podewills, Felix, Langner, Soenke, Rummel, Christian, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, O’Brien, Terence J, Sinclair, Benjamin, Vivash, Lucy, Desmond, Patricia M, Lui, Elaine, Vaudano, Anna Elisabetta, Meletti, Stefano, Tondelli, Manuela, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Winston, Gavin P, Griffin, Aoife, Singh, Aditi, Tiwari, Vijay K, Kreilkamp, Barbara AK, Lenge, Matteo, Guerrini, Renzo, Hamandi, Khalid, Foley, Sonya, Rüber, Theodor, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Tortora, Domenico, Kaestner, Erik, Hatton, Sean N, Vos, Sjoerd B, Caciagli, Lorenzo, Duncan, John S, Whelan, Christopher D, Thompson, Paul M, Sisodiya, Sanjay M, Bernasconi, Andrea, Labate, Angelo, McDonald, Carrie R, Bernasconi, Neda, and Bernhardt, Boris C
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Neurodegenerative ,Genetics ,Neurosciences ,Brain Disorders ,Epilepsy ,Aetiology ,2.1 Biological and endogenous factors ,Neurological ,Adult ,Connectome ,Epilepsy ,Generalized ,Epilepsy ,Temporal Lobe ,Gene Expression ,Humans ,Immunoglobulin E ,Magnetic Resonance Imaging ,Nerve Net - Abstract
Epilepsy is associated with genetic risk factors and cortico-subcortical network alterations, but associations between neurobiological mechanisms and macroscale connectomics remain unclear. This multisite ENIGMA-Epilepsy study examined whole-brain structural covariance networks in patients with epilepsy and related findings to postmortem epilepsy risk gene expression patterns. Brain network analysis included 578 adults with temporal lobe epilepsy (TLE), 288 adults with idiopathic generalized epilepsy (IGE), and 1328 healthy controls from 18 centres worldwide. Graph theoretical analysis of structural covariance networks revealed increased clustering and path length in orbitofrontal and temporal regions in TLE, suggesting a shift towards network regularization. Conversely, people with IGE showed decreased clustering and path length in fronto-temporo-parietal cortices, indicating a random network configuration. Syndrome-specific topological alterations reflected expression patterns of risk genes for hippocampal sclerosis in TLE and for generalized epilepsy in IGE. These imaging-transcriptomic signatures could potentially guide diagnosis or tailor therapeutic approaches to specific epilepsy syndromes.
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- 2022
15. Is the brain macroscopically linear? A system identification of resting state dynamics
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Nozari, Erfan, Bertolero, Maxwell A., Stiso, Jennifer, Caciagli, Lorenzo, Cornblath, Eli J., He, Xiaosong, Mahadevan, Arun S., Pappas, George J., and Bassett, Dani Smith
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Quantitative Biology - Neurons and Cognition ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Signal Processing ,Mathematics - Dynamical Systems ,Mathematics - Optimization and Control - Abstract
A central challenge in the computational modeling of neural dynamics is the trade-off between accuracy and simplicity. At the level of individual neurons, nonlinear dynamics are both experimentally established and essential for neuronal functioning. An implicit assumption has thus formed that an accurate computational model of whole-brain dynamics must also be highly nonlinear, whereas linear models may provide a first-order approximation. Here, we provide a rigorous and data-driven investigation of this hypothesis at the level of whole-brain blood-oxygen-level-dependent (BOLD) and macroscopic field potential dynamics by leveraging the theory of system identification. Using functional MRI (fMRI) and intracranial EEG (iEEG), we model the resting state activity of 700 subjects in the Human Connectome Project (HCP) and 122 subjects from the Restoring Active Memory (RAM) project using state-of-the-art linear and nonlinear model families. We assess relative model fit using predictive power, computational complexity, and the extent of residual dynamics unexplained by the model. Contrary to our expectations, linear auto-regressive models achieve the best measures across all three metrics, eliminating the trade-off between accuracy and simplicity. To understand and explain this linearity, we highlight four properties of macroscopic neurodynamics which can counteract or mask microscopic nonlinear dynamics: averaging over space, averaging over time, observation noise, and limited data samples. Whereas the latter two are technological limitations and can improve in the future, the former two are inherent to aggregated macroscopic brain activity. Our results, together with the unparalleled interpretability of linear models, can greatly facilitate our understanding of macroscopic neural dynamics and the principled design of model-based interventions for the treatment of neuropsychiatric disorders.
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- 2020
16. Dynamic network properties of the superior temporal gyrus mediate the impact of brain age gap on chronic aphasia severity
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Janina Wilmskoetter, Natalie Busby, Xiaosong He, Lorenzo Caciagli, Rebecca Roth, Sigfus Kristinsson, Kathryn A. Davis, Chris Rorden, Dani S. Bassett, Julius Fridriksson, and Leonardo Bonilha
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Biology (General) ,QH301-705.5 - Abstract
Abstract Brain structure deteriorates with aging and predisposes an individual to more severe language impairments (aphasia) after a stroke. However, the underlying mechanisms of this relation are not well understood. Here we use an approach to model brain network properties outside the stroke lesion, network controllability, to investigate relations among individualized structural brain connections, brain age, and aphasia severity in 93 participants with chronic post-stroke aphasia. Controlling for the stroke lesion size, we observe that lower average controllability of the posterior superior temporal gyrus (STG) mediates the relation between advanced brain aging and aphasia severity. Lower controllability of the left posterior STG signifies that activity in the left posterior STG is less likely to yield a response in other brain regions due to the topological properties of the structural brain networks. These results indicate that advanced brain aging among individuals with post-stroke aphasia is associated with disruption of dynamic properties of a critical language-related area, the STG, which contributes to worse aphasic symptoms. Because brain aging is variable among individuals with aphasia, our results provide further insight into the mechanisms underlying the variance in clinical trajectories in post-stroke aphasia.
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- 2023
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17. Crowd Control in Plazas Constrained to Social Distancing
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García, Álvaro González, R., James L. Martín, and Caciagli, Alessio
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Physics - Physics and Society ,Condensed Matter - Soft Condensed Matter - Abstract
We present a simple and versatile method for calculating the maximum capacity of public spaces constrained to social distancing, following the recommended measures of the WHO due to the COVID-19 pandemic outbreak. This method assumes a minimum required distance of two meters between persons and is tested in four actual plazas. Additionally, we estimate public space capacity in case of public events, such as markets or concerts. We believe our method will directly provide guidelines for crowd control in the so-called "new normality", serving as a first step for future and more accurate developments., Comment: 11 pages, 3 figures
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- 2020
18. Controlled Optofluidic Crystallization of Colloids Tethered at Interfaces
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Caciagli, Alessio, Singh, Rajesh, Joshi, Darshana, Adhikari, R., and Eiser, Erika
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
We report experiments that show rapid crystallization of colloids tethered to an oil-water interface in response to laser illumination. This light-induced transition is due to a combination of long-ranged thermophoretic pumping and local optical binding. We show that the flow-induced force on the colloids can be described as the gradient of a potential. The nonequilibrium steady state due to local heating thus admits an effective equilibrium description. The optofluidic manipulation explored in this work opens novel ways to manipulate and assemble colloidal particles, Comment: Published version
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- 2020
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19. Retraction Note: Modulation of the TGF-β1-induced epithelial to mesenchymal transition (EMT) mediated by P1 and P2 purine receptors in MDCK cells
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Zuccarini, Mariachiara, Giuliani, Patricia, Buccella, Silvana, Di Liberto, Valentina, Mudò, Giuseppa, Belluardo, Natale, Carluccio, Marzia, Rossini, Margherita, Condorelli, Daniele Filippo, Rathbone, Michel Piers, Caciagli, Francesco, Ciccarelli, Renata, and Di Iorio, Patrizia
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- 2023
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20. On the Role of Flexibility in Linker-Mediated DNA Hydrogels
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Stoev, Iliya D., Cao, Tianyang, Caciagli, Alessio, Yu, Jiaming, Ness, Christopher, Liu, Ren, Ghosh, Rini, O'Neill, Thomas, Liu, Dongsheng, and Eiser, Erika
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Physics - Biological Physics ,Condensed Matter - Soft Condensed Matter - Abstract
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters., Comment: 14 pages, 9 figures, 2 tables
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- 2019
21. Cytomegalovirus blood reactivation in COVID-19 critically ill patients: risk factors and impact on mortality
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Gatto, Ilenia, Biagioni, Emanuela, Coloretti, Irene, Farinelli, Carlotta, Avoni, Camilla, Caciagli, Valeria, Busani, Stefano, Sarti, Mario, Pecorari, Monica, Gennari, William, Guaraldi, Giovanni, Franceschini, Erica, Meschiari, Marianna, Mussini, Cristina, Tonelli, Roberto, Clini, Enrico, Cossarizza, Andrea, and Girardis, Massimo
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- 2022
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22. Tunable colloidal photonic crystals
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Erdem, Talha, Zupkauskas, Mykolas, ONeill, Thomas, Caciagli, Alessio, Xu, Peicheng, Lan, Yang, Boesecke, Peter, and Eiser, Erika
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Physics - Optics ,Physics - Applied Physics - Abstract
Spherical colloids arranged in a crystalline order are known to produce structural colors. The intensity and brilliance of such photonic crystals require high size-monodispersity of the colloids, a low number of lattice defects and disorder, as well as a relatively large refractive index contrast between the scattering colloids and the continuous background. Here we present the unexpected photonic properties of aqueous suspensions of charge-stabilized, 186 nm large, fluorinated colloids with a refractive index of 1.37. Employing reflectivity, optical observation, small angle x-ray scattering measurements and reflectivity modeling, we demonstrate that these suspensions become partially transparent while showing strong, almost angle-independent color in reflection despite the very small refractive index difference. Under certain conditions, additional sharp Bragg reflections are observed. We were able to tune the observed structural colors continuously across the entire visible range by simply changing the volume fraction of these colloidal suspensions, which show a white appearance when dilute, structural color and Bragg peaks when concentrated enough to form Wiegner crystal, and angle-independent color when very concentrated and in a glassy phase.
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- 2018
23. Inducing transparency in the films of highly scattering particles
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Erdem, Talha, Yang, Lan, Xu, Peicheng, Altintas, Yemliha, ONeil, Thomas, Caciagli, Alessio, Ducati, Caterina, Mutlugun, Evren, Scherman, Oren A., and Eiser, Erika
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Physics - Applied Physics ,Physics - Optics - Abstract
Today colloids are employed in various products from creams and coatings to electronics. The ability to control their chemical, optical, or electronic features by controlling their size and shape explains why these materials are so widely employed. Nevertheless, altering some of these properties may also lead to some undesired side effects, one of which is an increase in optical scattering upon concentration. Here, we address this strong scattering issue in films made of colloids with high surface roughness. We focus on raspberry type polymeric particles made of a spherical polystyrene core decorated by small hemispherical domains of acrylate. Owing to their surface charge and model roughness, aqueous dispersions of these particles display an unusual stability against aggregation. Under certain angles, their solid films display a brilliant red color due to Bragg scattering but otherwise appear completely white on account of`strong scattering. To suppress the scattering and induce transparency, we prepared films by hybridizing them either with oppositely-charged PS-particles that fit the length-scale of the raspberry roughness or with quantum dots. We report that the smaller PS-particles prevent raspberry particle aggregation in solid films and suppress scattering by decreasing the spatial variation of the refractive index. We believe that the results presented here provide a simple strategy to suppress strong scattering of rough particles and allow for their utilization in optical coatings, cosmetics, or photonics.
- Published
- 2018
24. Microrheology of DNA Hydrogels
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Xing, Zhongyang, Caciagli, Alessio, Cao, Tianyang, Stoev, Iliya, Zupkauskas, Mykolas, O'Neill, Thomas, Wenzel, Tobias, Lamboll, Robin, Liu, Dongsheg, and Eiser, Erika
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Condensed Matter - Soft Condensed Matter - Abstract
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing-wave spectroscopy (DWS) to investigate the viscoelastic behavior of a hydrogel made of Y-shaped DNA nano-stars over a wide range of frequencies and temperatures. Results show a clear liquid-to-equilibrium-gel transition as the temperature cycles up and down across the melting-temperature region for which the Y-DNA bind to each other. These first measurements reveal the crossover of the elastic G'({\omega}) and loss modulus G'({\omega}) when the DNA-hydrogel formed at low temperatures is heated to a fluid phase of DNA nano-stars well above the melt temperature Tm. We show that the crossover relates to the life-time of the DNA-bond and also that percolation coincides with the systems' Tm. The approach demonstrated here can be easily extended to more complicated DNA hydrogel systems and provides guidance for the future design of such transient, semi-flexible networks that can be adapted to the application of molecular sensing and controlled release.
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- 2017
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25. WONOEP appraisal: Network concept from an imaging perspective
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Wykes, Robert C, Khoo, Hui Ming, Caciagli, Lorenzo, Blumenfeld, Hal, Golshani, Peyman, Kapur, Jaideep, Stern, John M, Bernasconi, Andrea, Dedeurwaerdere, Stefanie, and Bernasconi, Neda
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Biomedical and Clinical Sciences ,Neurosciences ,Clinical Sciences ,Biomedical Imaging ,Epilepsy ,Brain Disorders ,Neurodegenerative ,Neurological ,Animals ,Brain ,Drug Resistant Epilepsy ,Education ,Epilepsy ,Temporal Lobe ,Functional Neuroimaging ,Humans ,calcium imaging ,epileptic networks ,fMRI ,graph theory ,neuroimaging ,Neurology & Neurosurgery ,Clinical sciences - Abstract
Neuroimaging techniques applied to a variety of organisms-from zebrafish, to rodents to humans-can offer valuable insights into neuronal network properties and their dysfunction in epilepsy. A wide range of imaging methods used to monitor neuronal circuits and networks during evoked seizures in animal models and advances in functional magnetic resonance imaging (fMRI) applied to patients with epilepsy were discussed during the XIV Workshop on Neurobiology of Epilepsy (XIV WONOEP) organized in 2017 by the Neurobiology Commission of the International League Against Epilepsy (ILAE). We review the growing number of technological approaches developed, as well as the current state of knowledge gained from studies applying these advanced imaging approaches to epilepsy research.
- Published
- 2019
26. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression
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Sara Larivière, Jessica Royer, Raúl Rodríguez-Cruces, Casey Paquola, Maria Eugenia Caligiuri, Antonio Gambardella, Luis Concha, Simon S. Keller, Fernando Cendes, Clarissa L. Yasuda, Leonardo Bonilha, Ezequiel Gleichgerrcht, Niels K. Focke, Martin Domin, Felix von Podewills, Soenke Langner, Christian Rummel, Roland Wiest, Pascal Martin, Raviteja Kotikalapudi, Terence J. O’Brien, Benjamin Sinclair, Lucy Vivash, Patricia M. Desmond, Elaine Lui, Anna Elisabetta Vaudano, Stefano Meletti, Manuela Tondelli, Saud Alhusaini, Colin P. Doherty, Gianpiero L. Cavalleri, Norman Delanty, Reetta Kälviäinen, Graeme D. Jackson, Magdalena Kowalczyk, Mario Mascalchi, Mira Semmelroch, Rhys H. Thomas, Hamid Soltanian-Zadeh, Esmaeil Davoodi-Bojd, Junsong Zhang, Gavin P. Winston, Aoife Griffin, Aditi Singh, Vijay K. Tiwari, Barbara A. K. Kreilkamp, Matteo Lenge, Renzo Guerrini, Khalid Hamandi, Sonya Foley, Theodor Rüber, Bernd Weber, Chantal Depondt, Julie Absil, Sarah J. A. Carr, Eugenio Abela, Mark P. Richardson, Orrin Devinsky, Mariasavina Severino, Pasquale Striano, Domenico Tortora, Erik Kaestner, Sean N. Hatton, Sjoerd B. Vos, Lorenzo Caciagli, John S. Duncan, Christopher D. Whelan, Paul M. Thompson, Sanjay M. Sisodiya, Andrea Bernasconi, Angelo Labate, Carrie R. McDonald, Neda Bernasconi, and Boris C. Bernhardt
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Science - Abstract
Epilepsy is a brain network disorder with associated genetic risk factors. Here, the authors show that spatial patterns of transcriptomic vulnerability co-vary with structural brain network alterations in focal and generalized epilepsy.
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- 2022
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27. DNA-coated Functional Oil Droplets
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Caciagli, Alessio, Zupkauskas, Mykolas, Levin, Aviad, Knowles, Tuomas P. J., Mugemana, Clément, Bruns, Nico, O'Neill, Thomas, Frith, William J., and Eiser, Erika
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Condensed Matter - Soft Condensed Matter - Abstract
Many industrial soft materials often include oil-in-water (O/W) emulsions at the core of their formulations. By using tuneable interface stabilizing agents, such emulsions can self-assemble into complex structures. DNA has been used for decades as a thermoresponsive highly specific binding agent between hard and, recently, soft colloids. Up until now, emulsion droplets functionalized with DNA had relatively low coating densities and were expensive to scale up. Here a general O/W DNA-coating method using functional non-ionic amphiphilic block copolymers, both diblock and triblock, is presented. The hydrophilic polyethylene glycol ends of the surfactants are functionalized with azides, allowing for efficient, dense and controlled coupling of dibenzocyclooctane functionalized DNA to the polymers through a strain-promoted alkyne-azide click reaction. The protocol is readily scalable due to the triblock's commercial availability. Different production methods (ultrasonication, microfluidics and membrane emulsification) are used with different oils (hexadecane and silicone oil) to produce functional droplets in various size ranges (sub-micron, $\sim 20\,\mathrm{\mu m}$ and $> 50\,\mathrm{\mu m}$), showcasing the generality of the protocol. Thermoreversible sub-micron emulsion gels, hierarchical "raspberry" droplets and controlled droplet release from a flat DNA-coated surface are demonstrated. The emulsion stability and polydispersity is evaluated using dynamic light scattering and optical microscopy. The generality and simplicity of the method opens up new applications in soft matter and biotechnological research and industrial advances., Comment: 7 pages, 2 figures, 1 table
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- 2017
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28. Optical trapping of colloids at a liquid-liquid interface
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Caciagli, Alessio, Joshi, Darshana, Kotar, Jurij, and Eiser, Erika
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Condensed Matter - Soft Condensed Matter - Abstract
We demonstrate the realization of (laterally) optically bounded colloidal structures on a liquid-liquid interface of an emulsion droplet. We use DNA tethers to graft the particles to the droplet surface, effectively confining them to a quasi-2D plane with minimum constraints on the lateral movement even when optically trapped in a common single-beam configuration. We show that relatively weak interactions such as depletion can be measured in the optically bounded crystals by video-microscopy imaging and analysis. This illustrates the possible use of our system as template to study optically controlled quasi two-dimensional colloidal assembly on liquid-liquid interfaces., Comment: 10 pages, 4 figures
- Published
- 2017
29. Association between Pulmonary Aspergillosis and Cytomegalovirus Reactivation in Critically Ill COVID-19 Patients: A Prospective Observational Cohort Study
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Valeria Caciagli, Irene Coloretti, Marta Talamonti, Carlotta Farinelli, Ilenia Gatto, Emanuela Biagioni, Mario Sarti, Erica Franceschini, Marianna Meschiari, Cristina Mussini, Roberto Tonelli, Enrico Clini, Massimo Girardis, Stefano Busani, and Modena COVID-19 Working Group
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COVID-19 ,invasive pulmonary aspergillosis ,critically ill ,cytomegalovirus ,ards ,Microbiology ,QR1-502 - Abstract
COVID-19-associated invasive pulmonary aspergillosis (CAPA) is common and is associated with poor outcomes in critically ill patients. This prospective observational study aimed to explore the association between CAPA development and the incidence and prognosis of cytomegalovirus (CMV) reactivation in critically ill COVID-19 patients. We included all consecutive critically ill adult patients with confirmed COVID-19 infection who were admitted to three COVID-19 intensive care units (ICUs) in an Italian hospital from 25 February 2020 to 8 May 2022. A standardized procedure was employed for early detection of CAPA. Risk factors associated with CAPA and CMV reactivation and the association between CMV recurrence and mortality were estimated using adjusted Cox proportional hazard regression models. CAPA occurred in 96 patients (16.6%) of the 579 patients analyzed. Among the CAPA population, 40 (41.7%) patients developed CMV blood reactivation with a median time of 18 days (IQR 7–27). The CAPA+CMV group did not exhibit a significantly higher 90-day mortality rate (62.5% vs. 48.2%) than the CAPA alone group (p = 0.166). The CAPA+CMV group had a longer ICU stay, fewer ventilation-free days, and a higher rate of secondary bacterial infections than the control group of CAPA alone. In the CAPA population, prior immunosuppression was the only independent risk factor for CMV reactivation (HR 2.33, 95% C.I. 1.21–4.48, p = 0.011). In critically ill COVID-19 patients, CMV reactivation is common in those with a previous CAPA diagnosis. Basal immunosuppression before COVID-19 appeared to be the primary independent variable affecting CMV reactivation in patients with CAPA. Furthermore, the association of CAPA+CMV versus CAPA alone appears to impact ICU length of stay and secondary bacterial infections but not mortality.
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- 2023
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30. Editorial: Advances in neuroimaging of epilepsy
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Emanuele Bartolini, Lorenzo Caciagli, Sara Larivière, and Karin Trimmel
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seizures ,brain morphometry ,functional connectivity ,quantitative imaging ,MRI ,Neurology. Diseases of the nervous system ,RC346-429 - Published
- 2023
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31. The impact of temporal lobe epilepsy surgery on picture naming and its relationship to network metric change
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Lawrence Peter Binding, Peter Neal Taylor, Aidan G. O'Keeffe, Davide Giampiccolo, Marine Fleury, Fenglai Xiao, Lorenzo Caciagli, Jane de Tisi, Gavin P. Winston, Anna Miserocchi, Andrew McEvoy, John S. Duncan, and Sjoerd B. Vos
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White Matter ,Anterior Temporal Lobe Resection ,Picture Naming Decline ,Graph Theory ,Machine Learning ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Background: Anterior temporal lobe resection (ATLR) is a successful treatment for medically-refractory temporal lobe epilepsy (TLE). In the language-dominant hemisphere, 30%- 50% of individuals experience a naming decline which can impact upon daily life. Measures of structural networks are associated with language performance pre-operatively. It is unclear if analysis of network measures may predict post-operative decline. Methods: White matter fibre tractography was performed on preoperative diffusion MRI of 44 left lateralised and left resection individuals with TLE to reconstruct the preoperative structural network. Resection masks, drawn on co-registered pre- and post-operative T1-weighted MRI scans, were used as exclusion regions on pre-operative tractography to estimate the post-operative network. Changes in graph theory metrics, cortical strength, betweenness centrality, and clustering coefficient were generated by comparing the estimated pre- and post-operative networks. These were thresholded based on the presence of the connection in each patient, ranging from 75% to 100% in steps of 5%. The average graph theory metric across thresholds was taken.We incorporated leave-one-out cross-validation with smoothly clipped absolute deviation (SCAD) least absolute shrinkage and selection operator (LASSO) feature selection and a support vector classifier to assess graph theory metrics on picture naming decline. Picture naming was assessed via the Graded Naming Test preoperatively and at 3 and 12 months post-operatively and the outcome was classified using the reliable change index (RCI) to identify clinically significant decline. The best feature combination and model was selected using the area under the curve (AUC). The sensitivity, specificity and F1-score were also reported. Permutation testing was performed to assess the machine learning model and selected regions difference significance. Results: A combination of clinical and graph theory metrics were able to classify outcome of picture naming at 3 months with an AUC of 0.84. At 12 months, change in strength to cortical regions was best able to correctly classify outcome with an AUC of 0.86. Longitudinal analysis revealed that betweenness centrality was the best metric to identify patients who declined at 3 months, who will then continue to experience decline from 3 to 12 months. Both models were significantly higher AUC values than a random classifier. Conclusion: Our results suggest that inferred changes of network integrity were able to correctly classify picture naming decline after ATLR. These measures may be used to prospectively to identify patients who are at risk of picture naming decline after surgery and could potentially be utilised to assist tailoring the resection in order to prevent this decline.
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- 2023
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32. Subcortical functional connectivity gradients in temporal lobe epilepsy
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Alfredo Lucas, Sofia Mouchtaris, Eli J. Cornblath, Nishant Sinha, Lorenzo Caciagli, Peter Hadar, James J. Gugger, Sandhitsu Das, Joel M. Stein, and Kathryn A. Davis
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Subcortex ,Focal epilepsy ,Dimensionality ,Connectome ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Background and Motivation: Functional gradients have been used to study differences in connectivity between healthy and diseased brain states, however this work has largely focused on the cortex. Because the subcortex plays a key role in seizure initiation in temporal lobe epilepsy (TLE), subcortical functional-connectivity gradients may help further elucidate differences between healthy brains and TLE, as well as differences between left (L)-TLE and right (R)-TLE. Methods: In this work, we calculated subcortical functional-connectivity gradients (SFGs) from resting-state functional MRI (rs-fMRI) by measuring the similarity in connectivity profiles of subcortical voxels to cortical gray matter voxels. We performed this analysis in 24 R-TLE patients and 31 L-TLE patients (who were otherwise matched for age, gender, disease specific characteristics, and other clinical variables), and 16 controls. To measure differences in SFGs between L-TLE and R-TLE, we quantified deviations in the average functional gradient distributions, as well as their variance, across subcortical structures. Results: We found an expansion, measured by increased variance, in the principal SFG of TLE relative to controls. When comparing the gradient across subcortical structures between L-TLE and R-TLE, we found that abnormalities in the ipsilateral hippocampal gradient distributions were significantly different between L-TLE and R-TLE. Conclusion: Our results suggest that expansion of the SFG is characteristic of TLE. Subcortical functional gradient differences exist between left and right TLE and are driven by connectivity changes in the hippocampus ipsilateral to the seizure onset zone.
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- 2023
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33. Kinetic control of the coverage of oil droplets by DNA-functionalised colloids
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Joshi, Darshana, Bargteil, Dylan, Caciagli, Alessio, Burelbach, Jerome, Xing, Zhongyang, Nunes, André S., Pinto, Diogo E. P., Araújo, Nuno A. M., Bruijc, Jasna, and Eiser, Erika
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
We report a study of reversible adsorption of DNA-coated colloids on complementary functionalized oil droplets. We show that it is possible to control the surface coverage of oil droplets by colloidal particles, by exploiting the fact that during slow adsorption, compositional arrest takes place well before structural arrest occurs. As a consequence, we can prepare colloid-coated oil droplets with a `frozen' degree of loading, but with fully ergodic colloidal dynamics on the droplets. We illustrate the equilibrium nature of the adsorbed colloidal phase by exploring the quasi two-dimensional (2d) phase behaviour of the adsorbed colloids under the influence of depletion interactions. We present simulations of a simple model that illustrates the nature of the compositional arrest and the structural ergodicity., Comment: 9 pages, 4 figures
- Published
- 2016
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34. Guanine inhibits the growth of human glioma and melanoma cell lines by interacting with GPR23
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Roberta Garozzo, Mariachiara Zuccarini, Patricia Giuliani, Valentina Di Liberto, Giuseppa Mudò, Francesco Caciagli, Renata Ciccarelli, Francisco Ciruela, Patrizia Di Iorio, and Daniele F. Condorelli
- Subjects
guanine-based purines (GBPs) ,guanine (GUA) ,purine nucleoside phosphorylase (PNP) ,antiproliferative effects ,G protein-coupled receptor 23 (GPR23) ,glioma cell lines ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Guanine-based purines (GBPs) exert numerous biological effects at the central nervous system through putative membrane receptors, the existence of which is still elusive. To shed light on this question, we screened orphan and poorly characterized G protein-coupled receptors (GPRs), selecting those that showed a high purinoreceptor similarity and were expressed in glioma cells, where GBPs exerted a powerful antiproliferative effect. Of the GPRs chosen, only the silencing of GPR23, also known as lysophosphatidic acid (LPA) 4 receptor, counteracted GBP-induced growth inhibition in U87 cells. Guanine (GUA) was the most potent compound behind the GPR23-mediated effect, acting as the endpoint effector of GBP antiproliferative effects. Accordingly, cells stably expressing GPR23 showed increased sensitivity to GUA. Furthermore, while GPR23 expression was low in a hypoxanthine-guanine phosphoribosyl-transferase (HGPRT)-mutated melanoma cell line showing poor sensitivity to GBPs, and in HGPRT-silenced glioma cells, GPR23-induced expression in both cell types rescued GUA-mediated cell growth inhibition. Finally, binding experiments using [3H]-GUA and U87 cell membranes revealed the existence of a selective GUA binding (KD = 29.44 ± 4.07 nM; Bmax 1.007 ± 0.035 pmol/mg prot) likely to GPR23. Overall, these data suggest GPR23 involvement in modulating responses to GUA in tumor cell lines, although further research needs to verify whether this receptor mediates other GUA effects.
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- 2022
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35. Timber Structures of Florence Cathedral: Wood Species Identification, Technological Implications and Their Forest Origin
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Nicola Macchioni, Marco Degl’Innocenti, Francesca Mannucci, Ilaria Stefani, Simona Lazzeri, and Samuele Caciagli
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historic timber structures ,wood identification ,forest source ,Florence Cathedral ,Plant ecology ,QK900-989 - Abstract
The Cathedral of Florence is one of the largest churches in the world and is known for one of the most famous domes ever, which characterizes the skyline of the city. The dimensions of the building mean that the dimensions of the roof are equally large and so are the wooden structures that support it. The roof of the cathedral is organized on two levels: the roof of the large central nave and, at a lower level, those of the two lateral naves. The purpose of this paper is the identification of the wood species of which the structures are made. The sampling method of the 408 samples that have been identified is then described, the methods followed to reach a reliable identification and finally the results. The timbers most represented among the structural elements are those of silver fir, chestnut and elm. Other timbers are then found in the other components less directly linked to the main structural parts that make up the trusses. The paper then discusses the technological implications on the use of those woods within the wooden covering structures of the cathedral and the main sources of timber that the builders had available, in particular the Casentino forests that the Municipality of Florence had donated to the structure that managed the construction of the cathedral (Opera di Santa Maria del Fiore—OPA). OPA still exists today and is responsible for the maintenance of the cathedral and other annexed buildings.
- Published
- 2023
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36. Contemporary Urban Commons. Rebuilding the Analytical Framework
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Carlotta Caciagli and Chiara Milan
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contemporary cities ,contentious politics ,institutionalization ,urban commons ,urban politics ,Political science (General) ,JA1-92 - Abstract
The article contributes to the understanding of contemporary urban commons by developing a renewed analytical framework which approaches them as dynamic configurations. By investigating different types of urban commons in Italy, the article disentangles the notion of urban commons along two axes that take into account their relationship with both local institutions and the surrounding environment. The combination of these two axes produces four possible configurations that allow to grasp the complexity of urban commons, accounting for their multifaceted and at times controversial nature. Moreover, this article identifies three functions that urban commons can perform in the contemporary European cities: as resilient spaces, as reclaimed spaces incorporated into capitalistic models of urban development, or contentious and transformative spaces that combine social reproduction with anti-capitalistic politics. The article is based on qualitative research and participant observation grounded on extensive fieldwork in various urban commons across Italy between 2016 and 2019.
- Published
- 2021
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37. Rhamnolipid coating reduces microbial biofilm formation on titanium implants: an in vitro study
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Erica Tambone, Emiliana Bonomi, Paolo Ghensi, Devid Maniglio, Chiara Ceresa, Francesca Agostinacchio, Patrizio Caciagli, Giandomenico Nollo, Federico Piccoli, Iole Caola, Letizia Fracchia, and Francesco Tessarolo
- Subjects
Dental implants ,Biofilm ,Titanium ,Biosurfactant ,Staphylococcus spp ,Dentistry ,RK1-715 - Abstract
Abstract Background Peri-implant mucositis and peri-implantitis are biofilm-related diseases causing major concern in oral implantology, requiring complex anti-infective procedures or implant removal. Microbial biosurfactants emerged as new anti-biofilm agents for coating implantable devices preserving biocompatibility. This study aimed to assess the efficacy of rhamnolipid biosurfactant R89 (R89BS) to reduce Staphylococcus aureus and Staphylococcus epidermidis biofilm formation on titanium. Methods R89BS was physically adsorbed on titanium discs (TDs). Cytotoxicity of coated TDs was evaluated on normal lung fibroblasts (MRC5) using a lactate dehydrogenase assay. The ability of coated TDs to inhibit biofilm formation was evaluated by quantifying biofilm biomass and cell metabolic activity, at different time-points, with respect to uncoated controls. A qualitative analysis of sessile bacteria was also performed by scanning electron microscopy. Results R89BS-coated discs showed no cytotoxic effects. TDs coated with 4 mg/mL R89BS inhibited the biofilm biomass of S. aureus by 99%, 47% and 7% and of S. epidermidis by 54%, 29%, and 10% at 24, 48 and 72 h respectively. A significant reduction of the biofilm metabolic activity was also documented. The same coating applied on three commercial implant surfaces resulted in a biomass inhibition higher than 90% for S. aureus, and up to 78% for S. epidermidis at 24 h. Conclusions R89BS-coating was effective in reducing Staphylococcus biofilm formation at the titanium implant surface. The anti-biofilm action can be obtained on several different commercially available implant surfaces, independently of their surface morphology.
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- 2021
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38. Transparent Colloidal Crystals With Structural Colours
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Talha Erdem, Thomas O’Neill, Mykolas Zupkauskas, Alessio Caciagli, Peicheng Xu, Yang Lan, Peter Bösecke, and Erika Eiser
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colloid ,structural color ,SAXS (small-angle X-ray scattering) ,latex particle ,photonic crystals ,Physics ,QC1-999 - Abstract
Spatially ordered arrangements of spherical colloids are known to exhibit structural colours. The intensity and brilliance of these structural colours typically improve with colloidal monodispersity, low concentrations of point and line defects and with increasing refractive index contrast between the colloids and the embedding medium. Here we show that suspensions of charge stabilised, fluorinated latex particles with low refractive-index contrast to their aqueous background form Wigner crystals with FCC symmetry for volume fractions between 13 and 40%. In reflection they exhibit both strong, almost angle-independent structural colours and sharp, more brilliant Bragg peaks despite the particle polydispersity and bimodal distribution. Simultaneously, these suspensions appear transparent in transmission. Furthermore, binary AB, A2B and A13B type mixtures of these fluorinated and similarly sized polystyrene particles appeared predominantly white but with clear Bragg peaks indicating a CsCl-like BCC structure and more complex crystals. We characterised the suspensions using a combination of reflectivity measurements and small-angle x-ray scattering, complemented by reflectivity modelling.
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- 2022
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39. Impaired naming performance in temporal lobe epilepsy: language fMRI responses are modulated by disease characteristics
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Trimmel, Karin, Caciagli, Lorenzo, Xiao, Fenglai, van Graan, Louis A., Koepp, Matthias J., Thompson, Pamela J., and Duncan, John S.
- Published
- 2021
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40. Effect of Anti-seizure Medications on Functional Anatomy of Language: A Perspective From Language Functional Magnetic Resonance Imaging
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Fenglai Xiao, Lorenzo Caciagli, Britta Wandschneider, Bhavini Joshi, Sjoerd B. Vos, Andrea Hill, Marian Galovic, Lili Long, Daichi Sone, Karin Trimmel, Josemir W. Sander, Dong Zhou, Pamela J. Thompson, Sallie Baxendale, John S. Duncan, and Matthias J. Koepp
- Subjects
epilepsy ,language functional MRI ,drug load ,cognitive effect ,polytherapy ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
BackgroundIn epilepsy, cognitive difficulties are common, partly a consequence of anti-seizure medications (ASM), and cognitive side-effects are often considered to be more disabling than seizures and significantly affect quality of life. Functional MRI during verbal fluency tasks demonstrated impaired frontal activation patterns and failed default mode network deactivation in people taking ASM with unfavourable cognitive profiles. The cognitive effect of ASMs given at different dosages in monotherapy, or in different combinations, remains to be determined.MethodsHere, we compared the effects of different drug loads on verbal fluency functional MRI (fMRI) in people (i) taking dual therapy of ASMs either considered to be associated with moderate (levetiracetam, lamotrigine, lacosamide, carbamazepine/oxcarbazepine, eslicarbazepine, valproic acid; n = 119, 56 females) or severe (topiramate, zonisamide) side-effects; n = 119, 56 females), (ii) taking moderate ASMs in either mono-, dual- or triple-therapy (60 subjects in each group), or (iii) taking different dosages of ASMs with moderate side-effect profiles (n = 180). “Drug load” was defined as a composite value of numbers and dosages of medications, normalised to account for the highest and lowest dose of each specific prescribed medication.ResultsIn people taking “moderate” ASMs (n = 119), we observed higher verbal-fluency related to left inferior frontal gyrus and right inferior parietal fMRI activations than in people taking “severe” ASMs (n = 119). Irrespective of the specific ASM, people on monotherapy (n = 60), showed greater frontal activations than people taking two (n = 60), or three ASMs (n = 60). People on two ASMs showed less default mode (precuneus) deactivation than those on monotherapy. In people treated with “moderate” ASMs (n = 180), increased drug load correlated with reduced activation of language-related regions and the right piriform cortex.ConclusionOur study delineates the effects of polytherapy and high doses of ASMs when given in monotherapy on the functional anatomy of language. Irrespective of the cognitive profile of individual ASMs, each additional ASM results in additional alterations of cognitive activation patterns. Selection of ASMs with moderate cognitive side effects, and low doses of ASMs when given in polytherapy, could reduce the cognitive effect.
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- 2022
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41. Dynamic Light Scattering Based Microrheology of End-Functionalised Triblock Copolymer Solutions
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Ren Liu, Alessio Caciagli, Jiaming Yu, Xiaoying Tang, Rini Ghosh, and Erika Eiser
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competing self-assembly ,triblock-copolymer ,DNA ,dynamic light scattering ,microrheology ,transient hydrogels ,Organic chemistry ,QD241-441 - Abstract
Nano-sized particles functionalised with short single-stranded (ss)DNAs can act as detectors of complementary DNA strands. Here we consider tri-block-copolymer-based, self-assembling DNA-coated nanoparticles. The copolymers are chemically linked to the DNA strands via azide (N3) groups. The micelles aggregate when they are linked with complementary ssDNA. The advantage of such block-copolymer-based systems is that they are easy to make. Here we show that DNA functionalisation results in inter-micellar attraction, but that N3-groups that have not reacted with the DNA detector strands also change the phase behaviour of the tri-block polymer solution. We studied the triblock copolymer, Pluronic® F108, which forms spherical micelles in aqueous solutions upon heating. We find that the triblock chains ending with either an N3 or N3-DNA complex show a dramatic change in phase behaviour. In particular, the N3-functionalisation causes the chain ends to cluster below the critical micelle temperature (CMT) of pure F108, forming flower-micelles with the N3-groups at the core, while the PPO groups are exposed to the solvent. Above the CMT, we see an inversion with the PPO chains forming the micellar core, while the N3-groups are now aggregating on the periphery, inducing an attraction between the micelles. Our results demonstrate that, due to the two competing self-assembling mechanisms, the system can form transient hydrogels.
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- 2023
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42. Rhamnolipid coating reduces microbial biofilm formation on titanium implants: an in vitro study
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Tambone, Erica, Bonomi, Emiliana, Ghensi, Paolo, Maniglio, Devid, Ceresa, Chiara, Agostinacchio, Francesca, Caciagli, Patrizio, Nollo, Giandomenico, Piccoli, Federico, Caola, Iole, Fracchia, Letizia, and Tessarolo, Francesco
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- 2021
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43. Adult mesenchymal stem cells: is there a role for purine receptors in their osteogenic differentiation?
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Carluccio, Marzia, Ziberi, Sihana, Zuccarini, Mariachiara, Giuliani, Patricia, Caciagli, Francesco, Di Iorio, Patrizia, and Ciccarelli, Renata
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- 2020
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44. Clientelismo, corruzione e criminalità organizzata. Comparare per distinguere
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Mario Caciagli
- Subjects
Comparative political analysis ,clientelism ,corruption ,organised crime ,Sociology (General) ,HM401-1281 - Abstract
This article focuses on the similarities and the differences of three degenerations of the political system. The author proposes the cultural political approach to define and to sign the boundaries between clientelism and corruption, clientelism and criminality, corruption and criminality. Clientelism and criminality are into a political culture; corruption on the contrary is out of a culture.
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- 2021
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45. Editorial: 'Purinergic Signaling 2020: The State-of-The-Art Commented by the Members of the Italian Purine Club'
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Francisco Ciruela, Kjell Fuxe, Peter Illes, Henning Ulrich, and Francesco Caciagli
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purines ,purinergic signaling ,purinergic enzymes ,purinergic receptor ,purinergic receptor signaling ,Therapeutics. Pharmacology ,RM1-950 - Published
- 2021
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46. Naming fMRI predicts the effect of temporal lobe resection on language decline
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Karin Trimmel, Louis A. vanGraan, Gloria G. Gonzálvez, Anja Haag, Lorenzo Caciagli, Sjoerd B. Vos, Silvia Bonelli, Meneka Sidhu, Pamela J. Thompson, Matthias J. Koepp, and John S. Duncan
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Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Objective To develop language functional MRI (fMRI) methods that accurately predict postsurgical naming decline in temporal lobe epilepsy (TLE). Methods Forty‐six patients with TLE (25 left) and 19 controls underwent two overt fMRI paradigms (auditory naming and picture naming, both with active baseline conditions) and one covert task (verbal fluency). Clinical naming performance was assessed preoperatively and 4 months following anterior temporal lobe resection. Preoperative fMRI activations were correlated with postoperative naming decline. Individual laterality indices (LI) were calculated for temporal (auditory and picture naming) and frontal regions (verbal fluency) and were considered as predictors of naming decline in multiple regression models, along with other clinical variables (age at onset of seizures, preoperative naming scores, hippocampal volume, age). Results In left TLE patients, activation of the left posterior inferior temporal gyrus during auditory naming and activation of left fusiform gyrus during picture naming were related to greater postoperative naming decline. Activation LI were the best individual predictors of naming decline in a multivariate regression model. For picture naming, an LI of higher than 0.34 gave 100% sensitivity and 92% specificity (positive predictive value (PPV) 91.6%). For auditory naming, a temporal lobe LI higher than 0.18 identified all patients with a clinically significant naming decline with 100% sensitivity and 58% specificity (PPV: 58.3%). No effect was seen for verbal fluency. Interpretation Auditory and picture naming fMRI are clinically applicable to predict postoperative naming decline after left temporal lobe resection in individual patients, with picture naming being more specific.
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- 2019
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47. Labour Activism and Social Movement Unionism in the Gig Economy. Food Delivery Workers Struggles in Italy
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Riccardo Emilio Chesta, Lorenzo Zamponi, and Carlotta Caciagli
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food delivery workers ,gig economy ,labour activism ,platform capitalism ,social movement unionism ,Political science (General) ,JA1-92 - Abstract
This article aims to explore the forms of collective actions that are emerging in new sectors of digital capitalism. In particular, it enquires into the mobilisation of food delivery workers that has been developing since 2016 in four Italian cities: Milan, Turin, Bologna and Florence. Despite the high level of precarisation and atomisation that characterise this subset of gig economy jobs, the so-called riders were able to organise into self-organised workers' collectives, which not only gave rise to many protest events, but also drew the attention of the institutions and the media. What are the conditions and the strategies that made this possible? And, more broadly, what does this case tell us about the possibility of labour activism in gig economy work? We argue that the high level of activation of food delivery workers is to be related to their capability to provide resources for reconstructing social ties among workers and, in turn, for translating them into political engagement and contentious action. This is realised through the combination of three factors that will be scrutinised in the paper. The analysis points out that although precarisation creates significant obstacles to organisation and mobilisation, collective action does actually take place also in the gig economy, in certain conditions.
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- 2019
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48. Surface ruptures following the 26 December 2018, Mw 4.9, Mt. Etna earthquake, Sicily (Italy): EMERGEO Working Group (Etna 2018)
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Riccardo Civico, Stefano Pucci, Rosa Nappi, Raffaele Azzaro, Fabio Villani, Daniela Pantosti, Francesca R. Cinti, Luca Pizzimenti, Stefano Branca, Carlo Alberto Brunori, Marco Caciagli, Massimo Cantarero, Luigi Cucci, Salvatore D’Amico, Emanuela De Beni, Paolo Marco De Martini, Maria Teresa Mariucci, Paola Montone, Rosella Nave, Tullio Ricci, Vincenzo Sapia, Alessandra Smedile, Gabriele Tarabusi, Roberto Vallone, and Alessandra Venuti
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surface faulting ,coseismic ruptures ,geological prompt survey ,earthquake ,2018 mt. etna volcano seismic sequence ,southern italy ,Maps ,G3180-9980 - Abstract
We present a 1:10,000 scale map of the coseismic surface ruptures following the 26 December 2018 Mw 4.9 earthquake that struck the eastern flank of Mt. Etna volcano (southern Italy). Detailed rupture mapping is based on extensive field surveys in the epicentral region. Despite the small size of the event, we were able to document surface faulting for about 8 km along the trace of the NNW-trending active Fiandaca Fault, belonging to the Timpe tectonic system in the eastern flank of the volcano. The mapped ruptures are characterized in most cases by perceivable opening and by a dominant right-oblique sense of slip, with an average slip of about 0.09 m and a peak value of 0.35 m. It is also noteworthy that the ruptures vary significantly in their kinematic expression, denoting locally high degree of complexity of the surface faulting.
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- 2019
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49. Purinergic Signaling in Oral Tissues
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Mariachiara Zuccarini, Patricia Giuliani, Maurizio Ronci, Francesco Caciagli, Vanni Caruso, Renata Ciccarelli, and Patrizia Di Iorio
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purines ,purine receptors ,purine enzymes ,salivary glands ,taste buds ,dental structures ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The role of the purinergic signal has been extensively investigated in many tissues and related organs, including the central and peripheral nervous systems as well as the gastrointestinal, cardiovascular, respiratory, renal, and immune systems. Less attention has been paid to the influence of purines in the oral cavity, which is the first part of the digestive apparatus and also acts as the body’s first antimicrobial barrier. In this review, evidence is provided of the presence and possible physiological role of the purinergic system in the different structures forming the oral cavity including teeth, tongue, hard palate, and soft palate with their annexes such as taste buds, salivary glands, and nervous fibers innervating the oral structures. We also report findings on the involvement of the purinergic signal in pathological conditions affecting the oral apparatus such as Sjögren’s syndrome or following irradiation for the treatment of head and neck cancer, and the use of experimental drugs interfering with the purine system to improve bone healing after damage. Further investigations are required to translate the results obtained so far into the clinical setting in order to pave the way for a wider application of purine-based treatments in oral diseases.
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- 2022
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50. The assessment of high sensitivity cardiac troponin in patients with COVID-19: A multicenter study
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Marco Alfonso Perrone, Federica Spolaore, Massimiliano Ammirabile, Francesco Romeo, Patrizio Caciagli, Ferruccio Ceriotti, and Sergio Bernardini
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COVID-19 ,Cardiac troponin ,Myocardial injury ,Myocarditis ,SARS-CoV-2 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background: Recent studies have shown that patients diagnosed with coronarivus disease 2019 (COVID-19) and also with previous cardiovascular diseases have a higher mortality due to worsening heart disease. At the same time, patients without previous cardiovascular disease may also have cardiac complications. The aim of this multicenter study was to assess high sensitivity cardiac troponin T (hs-cTnT) in patients with COVID-19 and to evaluate the incidence of myocardial injury. Methods: In this multicenter study we enrolled 543 patients, 57.8% males, median age 63 years (range 18–99) from three selected hospitals: University Hospital Tor Vergata in Rome, Fondazione IRCCS Ca 'Granda Ospedale Maggiore Policlinico, in Milan, S Chiara Hospital in Trento. We measured hs-cTnT in all patients to assess myocardial injury and correlations with patient’s age, symptoms and disease course. Results: The data showed that, among the 543 patients studied, 257 patients (47.3%) had hs-cTnT values higher than the upper reference limit (URL) of 14 ng/L. Patients with high hs-cTnT had more frequently fever (p
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- 2021
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