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2. Network Inference and Reconstruction in Bioinformatics

Author

Petti, Manuela, primary, Punzi, Clara, additional, Alfano, Caterina, additional, Farina, Lorenzo, additional, Astolfi, Laura, additional, Paci, Paola, additional, Guzzi, Pietro H., additional, Castiglione, Filippo, additional, and Tieri, Paolo, additional

Published
2024
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4. Identification of psychiatric disorder subtypes from functional connectivity patterns in resting-state electroencephalography

Author

Zhang, Yu, Wu, Wei, Toll, Russell T, Naparstek, Sharon, Maron-Katz, Adi, Watts, Mallissa, Gordon, Joseph, Jeong, Jisoo, Astolfi, Laura, Shpigel, Emmanuel, Longwell, Parker, Sarhadi, Kamron, El-Said, Dawlat, Li, Yuanqing, Cooper, Crystal, Chin-Fatt, Cherise, Arns, Martijn, Goodkind, Madeleine S, Trivedi, Madhukar H, Marmar, Charles R, and Etkin, Amit

Subjects
Neurosciences, Brain Disorders, Post-Traumatic Stress Disorder (PTSD), Depression, Mental Health, Serious Mental Illness, Major Depressive Disorder, Anxiety Disorders, Mental health, Good Health and Well Being, Adult, Antidepressive Agents, Brain, Case-Control Studies, Cluster Analysis, Connectome, Databases, Factual, Depressive Disorder, Major, Electroencephalography, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Psychotherapy, Stress Disorders, Post-Traumatic, Transcranial Magnetic Stimulation
Abstract

The understanding and treatment of psychiatric disorders, which are known to be neurobiologically and clinically heterogeneous, could benefit from the data-driven identification of disease subtypes. Here, we report the identification of two clinically relevant subtypes of post-traumatic stress disorder (PTSD) and major depressive disorder (MDD) on the basis of robust and distinct functional connectivity patterns, prominently within the frontoparietal control network and the default mode network. We identified the disease subtypes by analysing, via unsupervised and supervised machine learning, the power-envelope-based connectivity of signals reconstructed from high-density resting-state electroencephalography in four datasets of patients with PTSD and MDD, and show that the subtypes are transferable across independent datasets recorded under different conditions. The subtype whose functional connectivity differed most from those of healthy controls was less responsive to psychotherapy treatment for PTSD and failed to respond to an antidepressant medication for MDD. By contrast, both subtypes responded equally well to two different forms of repetitive transcranial magnetic stimulation therapy for MDD. Our data-driven approach may constitute a generalizable solution for connectome-based diagnosis.

Published
2021

17. Tumor budding to investigate local invasion, metastasis, and prognosis of head and neck carcinoma: A systematic review.

Author

Zanoletti, Elisabetta, Daloiso, Antonio, Nicolè, Lorenzo, Cazzador, Diego, Mondello, Tiziana, Franz, Leonardo, Astolfi, Laura, and Marioni, Gino

Subjects
TUMOR budding, SQUAMOUS cell carcinoma, HEAD & neck cancer, PROGNOSIS, CARCINOMA, NECK
Abstract

The aim of this systematic review is to shed light on the role of tumor budding (TB) in the biology, behavior, and prognosis of head and neck squamous cell carcinoma (HNSCC). A search was run in PubMed, Scopus, and Embase databases following PRISMA guidelines. After full‐text screening and application of inclusion/exclusion criteria, 36 articles were included. Several investigations support the prognostic role of TB, which might play a role in selecting rational treatment strategies. To achieve this goal, further research is needed for greater standardization in TB quantification. Although TB is not included as a negative prognostic factor in the current management guidelines, it might be reasonable to consider a closer follow‐up for HNSCC cases with high histopathological evidence of TB. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Cluster structure of functional networks estimated from high-resolution EEG data

Author

Sinatra, Roberta, Fallani, Fabrizio De Vico, Astolfi, Laura, Babiloni, Fabio, Cincotti, Febo, Latora, Vito, and Mattia, Donatella

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Neurons and Cognition
Abstract

We study the topological properties of functional connectivity patterns among cortical areas in the frequency domain. The cortical networks were estimated from high-resolution EEG recordings in a group of spinal cord injured patients and in a group of healthy subjects, during the preparation of a limb movement. We first evaluate global and local efficiency, as indicators of the structural connectivity respectively at a global and local scale. Then, we use the Markov Clustering method to analyse the division of the network into community structures. The results indicate large differences between the injured patients and the healthy subjects. In particular, the networks of spinal cord injured patient exhibited a higher density of efficient clusters. In the Alpha (7-12 Hz) frequency band, the two observed largest communities were mainly composed by the cingulate motor areas with the supplementary motor areas, and by the pre-motor areas with the right primary motor area of the foot. This functional separation strengthens the hypothesis of a compensative mechanism due to the partial alteration in the primary motor areas because of the effects of the spinal cord injury., Comment: 21 pages, 4 figures

Published
2008
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43. Dupilumab in the treatment of severe uncontrolled chronic rhinosinusitis with nasal polyps): a multicentric observational phase IV real‐life study (DUPIREAL)

Author

De Corso Eugenio, Pasquini, Ernesto, Trimarchi, Matteo, La Mantia Ignazio, Pagella, Fabio, Ottaviano, Giancarlo, Garzaro, Massimiliano, Pipolo, Carlotta, Torretta, Sara, Seccia, Veronica, Cantone, Elena, Ciofalo, Andrea, Lucidi, Daniela, Fadda Gian Luca, Pafundi Pia Clara, Settimi, Stefano, Montuori, Claudio, Anastasi, Francesca, Pagliuca, Giulio, Ghidini, Angelo, Cavaliere, Carlo, Maffei, Marianna, Bussu, Francesco, Gallo, Stefania, Canevari Frank Rikki Mauritz, Paludetti, Gaetano, Galli, Jacopo, Spanu, Camilla, Porru Davide Paolo, Lo Verde Simone, Corbò, Marco, Cantiani, Alessandro, Furno, Daniela, D’Agostino, Giuseppe, D’Auria Leandro Maria, De Maio Gabriele, Di Bella Giuseppe Alberto, Penazzi, Daniele, Mele Dario Antonio, Di Cesare Tiziana, Andrea, Rampi, Umberto, Tanzini, Saccardo, Tommaso, Roccuzzo, Giuseppe, Cipolla, Federica, Ragusa, Martina, Grigaliute, Egle, Alicandri Ciufelli Matteo, Roncadi, Leonardo, Rizzo, Davide, De Vita Carla, Farneti, Paolo, Todero, Gabriella, Cristofani‐mencacci, Lodovica, Statuti, Erica, Cavallo, Giovanni, Urbanelli, Anastasia, Ferrella, Francesco, Arnone, Flavio, Di Nola Claudio, Pignataro, Lorenzo, Nava, Nicolò, Russo, Paolo, Savastano, Vincenzo, Masieri, Simonetta, Dell’Era, Valeria, Aluffi Valletti Paolo, Sovardi, Fabio, Siragusa, Vera, Clemenzi, Veronica, Stolfa, Andrea, Simoni, Edi, and Astolfi, Laura

Subjects
dupilumab, smell, biologics, dupireal, crswnp, asthma, biologics, chronic rhinosinusitis with nasal polyps, dupilumab, smell, asthma, chronic rhinosinusitis with nasal polyps
Published
2023

44. Characterization of a decellularized rat larynx: comparison between microscopy techniques

Author

Gentilin, Erica, Simoni, Edi, Albertin, Giovanna, Candito, Mariarita, Sandrin, Deborah, Romanato, Filippo, Martini, Alessandro, Nicolai, Piero, and Astolfi, Laura

Subjects
Microscopy, Confocal, Tissue Scaffolds, Tissue Engineering, Hyaline cartilage, General Medicine, Extracellular matrix, Rats, Elastin, Elastic cartilage, Collagen, Glycosaminoglycans, Two-photon microscopy, Larynx, Anatomy, Developmental Biology
Abstract

No effective method has yet been developed to efficiently reconstruct the larynx and restore its function. Decellularization has recently been tested for this purpose with very promising results. The goal of decellularization is to remove cells leaving an intact scaffold made of an extracellular matrix (ECM). Although the use of hematoxylin/eosin and Masson trichrome stains is widely accepted to highlight tissue structure, the methods based on evaluation of collagen and elastin are considered highly variable. The aim of this study was to develop a whole organ decellularization protocol and compare the qualitative and quantitative efficiency of some microscopy techniques for collagen and elastin detection in paraffin-embedded tissues.HE, Masson Trichrome and DAPI staining as well as DNA quantification were used to evaluate decellularization efficiency. Van Gieson stain, Picrosirius Red stain (PRS) and multiphoton laser scanning microscopy (MPM) were carried out for collagen detection and quantitative assessment. Polarized PRS was used to investigate collagen network, and Weigert stain and MPM were used to detect and estimate elastin content.The decellularization process removed the cellular components without affecting glycosaminoglycan, collagen and elastin content. Concerning collagen quantification, Van Gieson stain underestimated collagen content, while PRS, apparently less fading, did not reach reliable results when used as quantitative method. MPM effectively quantified collagen content. Collagen fibers were visualized much better under polarized light microscopy, allowing to underline that decellularization process affects the homogeneity of 3D collagen network. Concerning elastin detection, Weigert stain and MPM produced overlapping results.An efficient protocol to decellularize the whole larynx was developed, allowing the removal of cells without affecting ECM integrity. The results supported the use of non-polarized PRS to highlight collagen, even the thin fibers, second harmonic generation for major fibrillar collagens and polarized PRS for 3D collagen network. Concerning elastin, Weigert stain and MPM showed similar results, thus the use of MPM, rather than that of the Weigert stain, may be suitable to avoid the additional time and costs of a histological staining.

Published
2023

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