2,862 results on '"A. Petretto"'
Search Results
2. Inhibition of IL-11 signalling extends mammalian healthspan and lifespan
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Widjaja, Anissa A., Lim, Wei-Wen, Viswanathan, Sivakumar, Chothani, Sonia, Corden, Ben, Dasan, Cibi Mary, Goh, Joyce Wei Ting, Lim, Radiance, Singh, Brijesh K., Tan, Jessie, Pua, Chee Jian, Lim, Sze Yun, Adami, Eleonora, Schafer, Sebastian, George, Benjamin L., Sweeney, Mark, Xie, Chen, Tripathi, Madhulika, Sims, Natalie A., Hübner, Norbert, Petretto, Enrico, Withers, Dominic J., Ho, Lena, Gil, Jesus, Carling, David, and Cook, Stuart A.
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- 2024
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3. A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus
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Secci-Petretto, Giulia, Weiss, Steven, Gomes-dos-Santos, André, Persat, Henri, Machado, André M., Vasconcelos, Inês, Castro, L. Filipe C., and Froufe, Elsa
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- 2024
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4. Report on the occurrence of the hydromedusa Odessia maeotica (Ostroumoff, 1896) in the north-eastern Atlantic revealed by citizen science and integrative taxonomy
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Pires, Rita F. T., Froufe, Elsa, Secci-Petretto, Giulia, and dos Santos, Antonina
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- 2024
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5. Interleukin-11 causes alveolar type 2 cell dysfunction and prevents alveolar regeneration
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Benjamin Ng, Kevin Y. Huang, Chee Jian Pua, Sivakumar Viswanathan, Wei-Wen Lim, Fathima F. Kuthubudeen, Yu-Ning Liu, An An Hii, Benjamin L. George, Anissa A. Widjaja, Enrico Petretto, and Stuart A. Cook
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Science - Abstract
Abstract In lung disease, persistence of KRT8-expressing aberrant basaloid cells in the alveolar epithelium is associated with impaired tissue regeneration and pathological tissue remodeling. We analyzed single cell RNA sequencing datasets of human interstitial lung disease and found the profibrotic Interleukin-11 (IL11) cytokine to be highly and specifically expressed in aberrant KRT8+ basaloid cells. IL11 is similarly expressed by KRT8+ alveolar epithelial cells lining fibrotic lesions in a mouse model of interstitial lung disease. Stimulation of alveolar epithelial cells with IL11 causes epithelial-to-mesenchymal transition and promotes a KRT8-high state, which stalls the beneficial differentiation of alveolar type 2 (AT2)-to-AT1 cells. Inhibition of IL11-signaling in AT2 cells in vivo prevents the accumulation of KRT8+ cells, enhances AT1 cell differentiation and blocks fibrogenesis, which is replicated by anti-IL11 therapy. These data show that IL11 inhibits reparative AT2-to-AT1 differentiation in the damaged lung to limit endogenous alveolar regeneration, resulting in fibrotic lung disease.
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- 2024
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6. Human glioblastoma-derived cell membrane nanovesicles: a novel, cell-specific strategy for boron neutron capture therapy of brain tumors
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Alice Balboni, Giorgia Ailuno, Sara Baldassari, Giuliana Drava, Andrea Petretto, Nicole Grinovero, Ornella Cavalleri, Elena Angeli, Andrea Lagomarsino, Paolo Canepa, Alessandro Corsaro, Beatrice Tremonti, Federica Barbieri, Stefano Thellung, Paola Contini, Katia Cortese, Tullio Florio, and Gabriele Caviglioli
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Cell membrane ,Cancer treatment ,Bioinspired vesicles ,Cell internalization ,Proteomics ,Medicine ,Science - Abstract
Abstract Glioblastoma (GBM), one of the deadliest brain tumors, accounts for approximately 50% of all primary malignant CNS tumors, therefore novel, highly effective remedies are urgently needed. Boron neutron capture therapy, which has recently repositioned as a promising strategy to treat high-grade gliomas, requires a conspicuous accumulation of boron atoms in the cancer cells. With the aim of selectively deliver sodium borocaptate (BSH, a 12 B atoms-including molecule already employed in the clinics) to GBM cells, we developed novel cell membrane-derived vesicles (CMVs), overcoming the limits of natural extracellular vesicles as drug carriers, while maintaining their inherent homing abilities that make them preferable to fully synthetic nanocarriers. Purified cell membrane fragments, isolated from patient-derived GBM stem-like cell cultures, were used to prepare nanosized CMVs, which retained some membrane proteins specific of the GBM parent cells and were devoid of potentially detrimental genetic material. In vitro tests evidenced the targeting ability of this novel nanosystem and ruled out any cytotoxicity. The CMVs were successfully loaded with BSH, by following two different procedures, i.e. sonication and electroporation, demonstrating their potential applicability in GBM therapy.
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- 2024
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7. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows
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Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Blügel, Stefan, Bröder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, Garcia, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan P., Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kühne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K. H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Müller, Tiziano M. A., Petretto, Guido, Pickard, Chris J., Poncé, Samuel, Rignanese, Gian-Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E. P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, and Pizzi, Giovanni
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Condensed Matter - Materials Science ,Physics - Computational Physics - Abstract
In the past decades many density-functional theory methods and codes adopting periodic boundary conditions have been developed and are now extensively used in condensed matter physics and materials science research. Only in 2016, however, their precision (i.e., to which extent properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. We discuss here general recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z=1 to 96 and characterizing 10 prototypical cubic compounds for each element: 4 unaries and 6 oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Such effort is facilitated by deploying AiiDA common workflows that perform automatic input parameter selection, provide identical input/output interfaces across codes, and ensure full reproducibility. Finally, we discuss the extent to which the current results for total energies can be reused for different goals (e.g., obtaining formation energies)., Comment: Main text: 23 pages, 4 figures. Supplementary: 68 pages. Nature Review Physics 2023
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- 2023
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8. Multi-scalar data integration decoding risk genes for chronic kidney disease
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Ding, Shiqi, Guo, Jing, Chen, Huimei, and Petretto, Enrico
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- 2024
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9. Interleukin-11 causes alveolar type 2 cell dysfunction and prevents alveolar regeneration
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Ng, Benjamin, Huang, Kevin Y., Pua, Chee Jian, Viswanathan, Sivakumar, Lim, Wei-Wen, Kuthubudeen, Fathima F., Liu, Yu-Ning, Hii, An An, George, Benjamin L., Widjaja, Anissa A., Petretto, Enrico, and Cook, Stuart A.
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- 2024
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10. Proteomics profiling and machine learning in nusinersen-treated patients with spinal muscular atrophy
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Panicucci, Chiara, Sahin, Eray, Bartolucci, Martina, Casalini, Sara, Brolatti, Noemi, Pedemonte, Marina, Baratto, Serena, Pintus, Sara, Principi, Elisa, D’Amico, Adele, Pane, Marika, Sframeli, Marina, Messina, Sonia, Albamonte, Emilio, Sansone, Valeria A., Mercuri, Eugenio, Bertini, Enrico, Sezerman, Ugur, Petretto, Andrea, and Bruno, Claudio
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- 2024
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11. Human glioblastoma-derived cell membrane nanovesicles: a novel, cell-specific strategy for boron neutron capture therapy of brain tumors
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Balboni, Alice, Ailuno, Giorgia, Baldassari, Sara, Drava, Giuliana, Petretto, Andrea, Grinovero, Nicole, Cavalleri, Ornella, Angeli, Elena, Lagomarsino, Andrea, Canepa, Paolo, Corsaro, Alessandro, Tremonti, Beatrice, Barbieri, Federica, Thellung, Stefano, Contini, Paola, Cortese, Katia, Florio, Tullio, and Caviglioli, Gabriele
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- 2024
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12. Second-harmonic generation tensors from high-throughput density-functional perturbation theory
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Trinquet, Victor, Naccarato, Francesco, Brunin, Guillaume, Petretto, Guido, Wirtz, Ludger, Hautier, Geoffroy, and Rignanese, Gian-Marco
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- 2024
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13. Transcriptomic imputation of genetic risk variants uncovers novel whole-blood biomarkers of Parkinson’s disease
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Chew, Gabriel, Mai, Aaron Shengting, Ouyang, John F., Qi, Yueyue, Chao, Yinxia, Wang, Qing, Petretto, Enrico, and Tan, Eng-King
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- 2024
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14. Zoledronic acid boosts γδ T-cell activity in children receiving αβ+ T and CD19+ cell-depleted grafts from an HLA-haplo-identical donor
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A. Bertaina, A. Zorzoli, A. Petretto, G. Barbarito, E. Inglese, P. Merli, C. Lavarello, L. P. Brescia, B. De Angelis, G. Tripodi, L. Moretta, F. Locatelli, and I. Airoldi
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γδ t cells ,haematopoietic stem cell transplantation ,leukemic patients ,proteomic ,zoledronic acid ,Immunologic diseases. Allergy ,RC581-607 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
We demonstrated that γδ T cells of patients given HLA-haploidentical HSCT after removal of αβ+ T cells and CD19+ B cells are endowed with the capacity of killing leukemia cells after ex vivo treatment with zoledronic acid (ZOL). Thus, we tested the hypothesis that infusion of ZOL in patients receiving this type of graft may enhance γδ T-cell cytotoxic activity against leukemia cells. ZOL was infused every 28 d in 43 patients; most were treated at least twice. γδ T cells before and after ZOL treatments were studied in 33 of these 43 patients, till at least 7 mo after HSCT by high-resolution mass spectrometry, flow-cytometry, and degranulation assay. An induction of Vδ2-cell differentiation, paralleled by increased cytotoxicity of both Vδ1 and Vδ2 cells against primary leukemia blasts was associated with ZOL treatment. Cytotoxic activity was further increased in Vδ2 cells, but not in Vδ1 lymphocytes in those patients given more than one treatment. Proteomic analysis of γδ T cells purified from patients showed upregulation of proteins involved in activation processes and immune response, paralleled by downregulation of proteins involved in proliferation. Moreover, a proteomic signature was identified for each ZOL treatment. Patients given three or more ZOL infusions had a better probability of survival in comparison to those given one or two treatments (86% vs. 54%, respectively, p = 0.008). Our data indicate that ZOL infusion in pediatric recipients of αβ T- and B-cell-depleted HLA-haploidentical HSCT promotes γδ T-cell differentiation and cytotoxicity and may influence the outcome of patients.
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- 2017
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15. Crystal Toolkit: A Web App Framework to Improve Usability and Accessibility of Materials Science Research Algorithms
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Horton, Matthew, Shen, Jimmy-Xuan, Burns, Jordan, Cohen, Orion, Chabbey, François, Ganose, Alex M., Guha, Rishabh, Huck, Patrick, Li, Hamming Howard, McDermott, Matthew, Montoya, Joseph, Moore, Guy, Munro, Jason, O'Donnell, Cody, Ophus, Colin, Petretto, Guido, Riebesell, Janosh, Wetizner, Steven, Wander, Brook, Winston, Donald, Yang, Ruoxi, Zeltmann, Steven, Jain, Anubhav, and Persson, Kristin A.
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Condensed Matter - Materials Science - Abstract
Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based apps to explore their own data or to help developers make their research algorithms accessible to a broader audience of scientists who might not have any training in computer programming and who would benefit from graphical interfaces. Crystal Toolkit comes with a library of ready-made components that can be assembled to make complex web apps: simulation of powder and single crystalline diffraction patterns, convex hull phase diagrams, Pourbaix diagrams, electronic band structures, analysis of local chemical environments and symmetry, and more. Crystal Toolkit is now powering the Materials Project website frontend, providing user-friendly access to its database of computed materials properties. In the future, it is hoped that new visualizations might be prototyped using Crystal Toolkit to help explore new forms of data being generated by the materials science community, and that this in turn can help new materials scientists develop intuition for how their data behaves and the insights that might be found within. Crystal Toolkit will remain a work-in-progress and is open to contributions from the community.
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- 2023
16. Investigating the footprint of post-domestication dispersal on the diversity of modern European, African and Asian goats
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Elena Petretto, Maria Luisa Dettori, María Gracia Luigi-Sierra, Antonia Noce, Michele Pazzola, Giuseppe Massimo Vacca, Antonio Molina, Amparo Martínez, Félix Goyache, Sean Carolan, The AdaptMap Consortium, and Marcel Amills
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Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Background Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of such genetic cline in European goat populations, but they were based on a limited number of microsatellite markers. Here, we have analyzed data generated by the AdaptMap project and other studies. More specifically, we have used the geographic coordinates and estimates of the observed (Ho) and expected (He) heterozygosities of 1077 European, 1187 African and 617 Asian goats belonging to 38, 43 and 22 different breeds, respectively, to find out whether genetic diversity and distance to Ganj Dareh, a Neolithic settlement in western Iran for which evidence of an early management of domestic goats has been obtained, are significantly correlated. Results Principal component and ADMIXTURE analyses revealed an incomplete regional differentiation of European breeds, but two genetic clusters representing Northern Europe and the British-Irish Isles were remarkably differentiated from the remaining European populations. In African breeds, we observed five main clusters: (1) North Africa, (2) West Africa, (3) East Africa, (4) South Africa, and (5) Madagascar. Regarding Asian breeds, three well differentiated West Asian, South Asian and East Asian groups were observed. For European and Asian goats, no strong evidence of significant correlations between Ho and He and distance to Ganj Dareh was found. In contrast, in African breeds we detected a significant gradient of diversity, which decreased with distance to Ganj Dareh. Conclusions The detection of a genetic cline associated with distance to the Ganj Dareh in African but not in European or Asian goat breeds might reflect differences in the post-domestication dispersal process and subsequent migratory movements associated with the management of caprine populations from these three continents.
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- 2024
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17. Second-harmonic generation tensors from high-throughput density-functional perturbation theory
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Victor Trinquet, Francesco Naccarato, Guillaume Brunin, Guido Petretto, Ludger Wirtz, Geoffroy Hautier, and Gian-Marco Rignanese
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Science - Abstract
Abstract Optical materials play a key role in enabling modern optoelectronic technologies in a wide variety of domains such as the medical or the energy sector. Among them, nonlinear optical crystals are of primary importance to achieve a broader range of electromagnetic waves in the devices. However, numerous and contradicting requirements significantly limit the discovery of new potential candidates, which, in turn, hinders the technological development. In the present work, the static nonlinear susceptibility and dielectric tensor are computed via density-functional perturbation theory for a set of 579 inorganic semiconductors. The computational methodology is discussed and the provided database is described with respect to both its data distribution and its format. Several comparisons with both experimental and ab initio results from literature allow to confirm the reliability of our data. The aim of this work is to provide a relevant dataset to foster the identification of promising nonlinear optical crystals in order to motivate their subsequent experimental investigation.
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- 2024
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18. Transcriptomic imputation of genetic risk variants uncovers novel whole-blood biomarkers of Parkinson’s disease
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Gabriel Chew, Aaron Shengting Mai, John F. Ouyang, Yueyue Qi, Yinxia Chao, Qing Wang, Enrico Petretto, and Eng-King Tan
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Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Blood-based gene expression signatures could potentially be used as biomarkers for PD. However, it is unclear whether genetically-regulated transcriptomic signatures can provide novel gene candidates for use as PD biomarkers. We leveraged on the Genotype-Tissue Expression (GTEx) database to impute whole-blood transcriptomic expression using summary statistics of three large-scale PD GWAS. A random forest classifier was used with the consensus whole-blood imputed gene signature (IGS) to discriminate between cases and controls. Outcome measures included Area under the Curve (AUC) of Receiver Operating Characteristic (ROC) Curve. We demonstrated that the IGS (n = 37 genes) is conserved across PD GWAS studies and brain tissues. IGS discriminated between cases and controls in an independent whole-blood RNA-sequencing study (1176 PD, 254 prodromal, and 860 healthy controls) with mean AUC and accuracy of 64.8% and 69.4% for PD cohort, and 78.8% and 74% for prodromal cohort. PATL2 was the top-performing imputed gene in both PD and prodromal PD cohorts, whose classifier performance varied with biological sex (higher performance for males and females in the PD and prodromal PD, respectively). Single-cell RNA-sequencing studies (scRNA-seq) of healthy humans and PD patients found PATL2 to be enriched in terminal effector CD8+ and cytotoxic CD4+ cells, whose proportions are both increased in PD patients. We demonstrated the utility of GWAS transcriptomic imputation in identifying novel whole-blood transcriptomic signatures which could be leveraged upon for PD biomarker derivation. We identified PATL2 as a potential biomarker in both clinical and prodromic PD.
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- 2024
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19. Extracellular vesicles from II trimester human amniotic fluid as paracrine conveyors counteracting oxidative stress
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Giorgia Senesi, Laura Guerricchio, Maddalena Ghelardoni, Nadia Bertola, Stefano Rebellato, Nicole Grinovero, Martina Bartolucci, Ambra Costa, Andrea Raimondi, Cristina Grange, Sara Bolis, Valentina Massa, Dario Paladini, Domenico Coviello, Assunta Pandolfi, Benedetta Bussolati, Andrea Petretto, Grazia Fazio, Silvia Ravera, Lucio Barile, Carolina Balbi, and Sveva Bollini
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Extracellular vesicles ,Amniotic fluid ,Paracrine effect ,Oxidative stress ,Cell viability ,Metabolic dysfunction ,Medicine (General) ,R5-920 ,Biology (General) ,QH301-705.5 - Abstract
Background: We previously demonstrated that the human amniotic fluid (hAF) from II trimester of gestation is a feasible source of stromal progenitors (human amniotic fluid stem cells, hAFSC), with significant paracrine potential for regenerative medicine. Extracellular vesicles (EVs) separated and concentrated from hAFSC secretome can deliver pro-survival, proliferative, anti-fibrotic and cardioprotective effects in preclinical models of skeletal and cardiac muscle injury. While hAFSC-EVs isolation can be significantly influenced by in vitro cell culture, here we profiled EVs directly concentrated from hAF as an alternative option and investigated their paracrine potential against oxidative stress. Methods: II trimester hAF samples were obtained as leftover material from prenatal diagnostic amniocentesis following written informed consent. EVs were separated by size exclusion chromatography and concentrated by ultracentrifugation. hAF-EVs were assessed by nanoparticle tracking analysis, transmission electron microscopy, Western Blot, and flow cytometry; their metabolic activity was evaluated by oximetric and luminometric analyses and their cargo profiled by proteomics and RNA sequencing. hAF-EV paracrine potential was tested in preclinical in vitro models of oxidative stress and dysfunction on murine C2C12 cells and on 3D human cardiac microtissue. Results: Our protocol resulted in a yield of 6.31 ± 0.98 × 109 EVs particles per hAF milliliter showing round cup-shaped morphology and 209.63 ± 6.10 nm average size, with relevant expression of CD81, CD63 and CD9 tetraspanin markers. hAF-EVs were enriched in CD133/1, CD326, CD24, CD29, and SSEA4 and able to produce ATP by oxygen consumption. While oxidative stress significantly reduced C2C12 survival, hAF-EV priming resulted in significant rescue of cell viability, with notable recovery of ATP synthesis and concomitant reduction of cell damage and lipid peroxidation activity. 3D human cardiac microtissues treated with hAF-EVs and experiencing H2O2 stress and TGFβ stimulation showed improved survival with a remarkable decrease in the onset of fibrosis. Conclusions: Our results suggest that leftover samples of II trimester human amniotic fluid can represent a feasible source of EVs to counteract oxidative damage on target cells, thus offering a novel candidate therapeutic option to counteract skeletal and cardiac muscle injury.
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- 2024
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20. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows
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Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Blügel, Stefan, Bröder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, Garcia, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan P., Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kühne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K. H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Müller, Tiziano M. A., Petretto, Guido, Pickard, Chris J., Poncé, Samuel, Rignanese, Gian-Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E. P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, and Pizzi, Giovanni
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- 2024
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21. Decoding frontotemporal and cell-type-specific vulnerabilities to neuropsychiatric disorders and psychoactive drugs
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Jiatong Ji, Honglu Chao, Huimei Chen, Jun Liao, Wenqian Shi, Yangfan Ye, Tian Wang, Yongping You, Ning Liu, Jing Ji, and Enrico Petretto
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frontal lobe ,temporal lobe ,psychiatric disorder ,single-cell RNA sequencing ,psychoactive drugs ,Biology (General) ,QH301-705.5 - Abstract
Frontotemporal lobe abnormalities are linked to neuropsychiatric disorders and cognition, but the role of cellular heterogeneity between temporal lobe (TL) and frontal lobe (FL) in the vulnerability to genetic risk factors remains to be elucidated. We integrated single-nucleus transcriptome analysis in ‘fresh’ human FL and TL with genetic susceptibility, gene dysregulation in neuropsychiatric disease and psychoactive drug response data. We show how intrinsic differences between TL and FL contribute to the vulnerability of specific cell types to both genetic risk factors and psychoactive drugs. Neuronal populations, specifically PVALB neurons, were most highly vulnerable to genetic risk factors for psychiatric disease. These psychiatric disease-associated genes were mostly upregulated in the TL, and dysregulated in the brain of patients with obsessive-compulsive disorder, bipolar disorder and schizophrenia. Among these genes, GRIN2A and SLC12A5, implicated in schizophrenia and bipolar disorder, were significantly upregulated in TL PVALB neurons and in psychiatric disease patients’ brain. PVALB neurons from the TL were twofold more vulnerable to psychoactive drugs than to genetic risk factors, showing the influence and specificity of frontotemporal lobe differences on cell vulnerabilities. These studies provide a cell type resolved map of the impact of brain regional differences on cell type vulnerabilities in neuropsychiatric disorders.
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- 2024
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22. Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy
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Antonella Riva, Eray Sahin, Greta Volpedo, Andrea Petretto, Chiara Lavarello, Rossella Di Sapia, Davide Barbarossa, Nasibeh Riahi Zaniani, Ilaria Craparotta, Maria Chiara Barbera, Uğur Sezerman, Annamaria Vezzani, Pasquale Striano, and Teresa Ravizza
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Seizures ,Status epilepticus ,Intestine ,Metagenomics ,Inflammation ,Metabolomics ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
A dysfunctional gut microbiota-brain axis is emerging as a potential pathogenic mechanism in epilepsy, particularly in pediatric forms of epilepsy. To add new insights into gut-related changes in acquired epilepsy that develops early in life, we used a multi-omics approach in a rat model with a 56% incidence of epilepsy.The presence of spontaneous seizures was assessed in adult rats (n = 46) 5 months after status epilepticus induced by intra-amygdala kainate at postnatal day 13, by 2 weeks (24/7) ECoG monitoring. Twenty-six rats developed epilepsy (Epi) while the remaining 20 rats (No-Epi) did not show spontaneous seizures. At the end of ECoG monitoring, all rats and their sham controls (n = 20) were sacrificed for quantitative histopathological and immunohistochemical analyses of the gut structure, glia and macrophages, as well as RTqPCR analysis of inflammation/oxidative stress markers.By comparing Epi, No-Epi rats, and sham controls, we found structural, cellular, and molecular alterations reflecting a dysfunctional gut, which were specifically associated with epilepsy. In particular, the villus height-to-crypt depth ratio and number of Goblet cells were reduced in the duodenum of Epi rats vs both No-Epi rats and sham controls (p
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- 2024
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23. Multi-tissue profiling of oxylipins reveal a conserved up-regulation of epoxide:diol ratio that associates with white adipose tissue inflammation and liver steatosis in obesityResearch in context
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Charlotte Hateley, Antoni Olona, Laura Halliday, Matthew L. Edin, Jeong-Hun Ko, Roberta Forlano, Ximena Terra, Fred B. Lih, Raúl Beltrán-Debón, Penelopi Manousou, Sanjay Purkayastha, Krishna Moorthy, Mark R. Thursz, Guodong Zhang, Robert D. Goldin, Darryl C. Zeldin, Enrico Petretto, and Jacques Behmoaras
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Obesity ,Metabolic syndrome ,Oxylipins ,Epoxides ,Diols ,12,13-EpOME:DiHOME ,Medicine ,Medicine (General) ,R5-920 - Abstract
Summary: Background: Obesity drives maladaptive changes in the white adipose tissue (WAT) which can progressively cause insulin resistance, type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated liver disease (MASLD). Obesity-mediated loss of WAT homeostasis can trigger liver steatosis through dysregulated lipid pathways such as those related to polyunsaturated fatty acid (PUFA)-derived oxylipins. However, the exact relationship between oxylipins and metabolic syndrome remains elusive and cross-tissue dynamics of oxylipins are ill-defined. Methods: We quantified PUFA-related oxylipin species in the omental WAT, liver biopsies and plasma of 88 patients undergoing bariatric surgery (female N = 79) and 9 patients (female N = 4) undergoing upper gastrointestinal surgery, using UPLC-MS/MS. We integrated oxylipin abundance with WAT phenotypes (adipogenesis, adipocyte hypertrophy, macrophage infiltration, type I and VI collagen remodelling) and the severity of MASLD (steatosis, inflammation, fibrosis) quantified in each biopsy. The integrative analysis was subjected to (i) adjustment for known risk factors and, (ii) control for potential drug-effects through UPLC-MS/MS analysis of metformin-treated fat explants ex vivo. Findings: We reveal a generalized down-regulation of cytochrome P450 (CYP)-derived diols during obesity conserved between the WAT and plasma. Notably, epoxide:diol ratio, indicative of soluble epoxide hydrolyse (sEH) activity, increases with WAT inflammation/fibrosis, hepatic steatosis and T2DM. Increased 12,13-EpOME:DiHOME in WAT and liver is a marker of worsening metabolic syndrome in patients with obesity. Interpretation: These findings suggest a dampened sEH activity and a possible role of fatty acid diols during metabolic syndrome in major metabolic organs such as WAT and liver. They also have implications in view of the clinical trials based on sEH inhibition for metabolic syndrome. Funding: Wellcome Trust (PS3431_WMIH); Duke-NUS (Intramural Goh Cardiovascular Research Award (Duke-NUS-GCR/2022/0020); National Medical Research Council (OFLCG22may-0011); National Institute of Environmental Health Sciences (Z01 ES025034); NIHR Imperial Biomedical Research Centre.
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- 2024
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24. Extracellular vesicles from II trimester human amniotic fluid as paracrine conveyors counteracting oxidative stress
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Senesi, Giorgia, Guerricchio, Laura, Ghelardoni, Maddalena, Bertola, Nadia, Rebellato, Stefano, Grinovero, Nicole, Bartolucci, Martina, Costa, Ambra, Raimondi, Andrea, Grange, Cristina, Bolis, Sara, Massa, Valentina, Paladini, Dario, Coviello, Domenico, Pandolfi, Assunta, Bussolati, Benedetta, Petretto, Andrea, Fazio, Grazia, Ravera, Silvia, Barile, Lucio, Balbi, Carolina, and Bollini, Sveva
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- 2024
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25. Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains
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Rastogi, Mohit, Bartolucci, Martina, Nanni, Marina, Aloisio, Michelangelo, Vozzi, Diego, Petretto, Andrea, Contestabile, Andrea, and Cancedda, Laura
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- 2024
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26. WWP2 Regulates Renal Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts
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Chen, Huimei, You, Ran, Guo, Jing, Zhou, Wei, Chew, Gabriel, Devapragash, Nithya, Loh, Jui Zhi, Gesualdo, Loreto, Li, Yanwei, Jiang, Yuteng, Tan, Elisabeth Li Sa, Chen, Shuang, Pontrelli, Paola, Pesce, Francesco, Behmoaras, Jacques, Zhang, Aihua, and Petretto, Enrico
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- 2024
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27. Long-Term Outcomes of Transcatheter vs Surgical Aortic Valve Replacement: Meta-analysis of Randomized Trials
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Talanas, Giuseppe, Laconi, Angelo, Kereiakes, Dean J., Merella, Pierluigi, Reardon, Michael J., Spano, Andrea, Petretto, Gerardo, Lauriola, Francesco, Casula, Marta, Micheluzzi, Valentina, Isgender, Mehriban, Chatzizisis, Yiannis, Farkouh, Michael E., Lansky, Alexandra J., Piazza, Nicolo, Portoghese, Michele, Casu, Gavino, and Navarese, Eliano Pio
- Published
- 2024
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28. Multi-tissue profiling of oxylipins reveal a conserved up-regulation of epoxide:diol ratio that associates with white adipose tissue inflammation and liver steatosis in obesity
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Hateley, Charlotte, Olona, Antoni, Halliday, Laura, Edin, Matthew L., Ko, Jeong-Hun, Forlano, Roberta, Terra, Ximena, Lih, Fred B., Beltrán-Debón, Raúl, Manousou, Penelopi, Purkayastha, Sanjay, Moorthy, Krishna, Thursz, Mark R., Zhang, Guodong, Goldin, Robert D., Zeldin, Darryl C., Petretto, Enrico, and Behmoaras, Jacques
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- 2024
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- View/download PDF
29. A critical view on autoantibodies in lupus nephritis: Concrete knowledge based on evidence
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Bruschi, Maurizio, Angeletti, Andrea, Prunotto, Marco, Meroni, Pier Luigi, Ghiggeri, Gian Marco, Moroni, Gabriella, Sinico, Renato Alberto, Franceschini, Franco, Fredi, Micaela, Vaglio, Augusto, Cavalli, Andrea, Scapozza, Leonardo, Patel, Jigar J., Tan, John C., Lo, Ken C., Cavagna, Lorenzo, Petretto, Andrea, Pratesi, Federico, Migliorini, Paola, Locatelli, Francesco, Pazzola, Giulia, Pesce, Giampaola, Giannese, Domenico, Manfredi, Angelo, Ramirez, Giuseppe A., Esposito, Pasquale, Murdaca, Giuseppe, Negrini, Simone, Bui, Federica, Trezzi, Barbara, Emmi, Giacomo, Cavazzana, Ilaria, Binda, Valentina, Fenaroli, Paride, Pisan, Isabella, Montecucco, Carlomaurizio, Santoro, Domenico, Scolari, Francesco, Mescia, Federica, Volpi, Stefano, Mosca, Marta, Tincani, Angela, Ravelli, Angelo, Murtas, Corrado, Candiano, Giovanni, Caridi, Gianluca, La Porta, Edoardo, and Verrina, Enrico
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- 2024
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- View/download PDF
30. Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy
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Riva, Antonella, Sahin, Eray, Volpedo, Greta, Petretto, Andrea, Lavarello, Chiara, Di Sapia, Rossella, Barbarossa, Davide, Zaniani, Nasibeh Riahi, Craparotta, Ilaria, Barbera, Maria Chiara, Sezerman, Uğur, Vezzani, Annamaria, Striano, Pasquale, and Ravizza, Teresa
- Published
- 2024
- Full Text
- View/download PDF
31. Pluripotent stem cell-derived committed cardiac progenitors remuscularize damaged ischemic hearts and improve their function in pigs
- Author
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Yap, Lynn, Chong, Li Yen, Tan, Clarissa, Adusumalli, Swarnaseetha, Seow, Millie, Guo, Jing, Cai, Zuhua, Loo, Sze Jie, Lim, Eric, Tan, Ru San, Grishina, Elina, Soong, Poh Loong, Lath, Narayan, Ye, Lei, Petretto, Enrico, and Tryggvason, Karl
- Published
- 2023
- Full Text
- View/download PDF
32. Proteomics reveals specific biological changes induced by the normothermic machine perfusion of donor kidneys with a significant up-regulation of Latexin
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Zaza, Gianluigi, Neri, Flavia, Bruschi, Maurizio, Granata, Simona, Petretto, Andrea, Bartolucci, Martina, di Bella, Caterina, Candiano, Giovanni, Stallone, Giovanni, Gesualdo, Loreto, and Furian, Lucrezia
- Published
- 2023
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- View/download PDF
33. Combination of ab initio descriptors and machine learning approach for the prediction of the plasticity mechanisms in β-metastable Ti alloys
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M. Coffigniez, P.-P. De Breuck, L. Choisez, M. Marteleur, M.J. van Setten, G. Petretto, G.-M. Rignanese, and P.J. Jacques
- Subjects
β-metastable titanium alloys ,Plasticity mechanisms ,Machine learning ,Ab initio ,TRIP ,Twip ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
This study proposes a machine-learning (ML) model combining ab initio calculations and an experimental dataset of 201 alloys (in addition to pure Ti) to predict the activated plasticity mechanisms in β-Ti alloys. This methodology is shown to be more efficient than the so-called Bo¯-Md¯ approach, achieving 82% prediction accuracy while the Bo-Md approach leads to 52% correct predictions on the same dataset. In addition, four new alloy compositions were produced to verify the model validity. Specific cases where the present model disagreed with the Bo-Md predictions were chosen to increase the benefits of the produced results. The plasticity mechanisms of the four alloys experimentally confirmed the validity of the ML model. This approach particularly helps the design of specific Ti alloys exhibiting a high work hardening rate owing to the simultaneous activations of the Transformation-Induced Plasticity (TRIP) and mechanical twinning (TWIP) effects. Indeed, the class corresponding to the combination of TRIP and TWIP effects reach a prediction accuracy of 88%.
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- 2024
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- View/download PDF
34. Polydopamine nanoparticles as a non-pharmaceutical tool in the treatment of fatty liver disease
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Alessio Carmignani, Matteo Battaglini, Martina Bartolucci, Andrea Petretto, Mirko Prato, and Gianni Ciofani
- Subjects
Polydopamine nanoparticles ,Non-alcoholic fatty liver disease ,Antioxidants ,Hepatic steatosis ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
Non-alcoholic fatty liver disease (NAFLD), or hepatic steatosis, has become one of the most common pathologies among liver-related disorders. The rapid accumulation of fat in this organ, and the consequent increment in oxidative stress levels, have been recognized as one of the main factors involved in the pathological mechanism underlying hepatic steatosis, and progressive non-alcoholic steatohepatitis. Experimental and epidemiological data have shown how antioxidant compounds rich in phenolic groups, such as resveratrol and quercetin, are particular efficient in contrasting the onset of this pathology. In this work, an in vitro model of NAFLD was established based on oleic acid-treated HepG2 cells. Steatotic cells were treated with polydopamine nanoparticles (PDNPs), biocompatible polymeric nanostructures rich in phenolic groups with high antioxidant power. PDNP treatment has shown to be effective in counteracting the hallmarks characterizing hepatic steatosis, and a reduction in the accumulation of lipids has been observed. Further analyses showed a significant reduction in triglyceride and cholesterol levels, jointly to reduced levels of oxidative stress. All these data, corroborated by proteomics and gene ontology analysis, suggest PDNPs to be a promising pharmaceutical candidate for the prevention and treatment of hepatic steatosis.
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- 2024
- Full Text
- View/download PDF
35. Hybrid epithelial-mesenchymal status of lung cancer dictates metastatic success through differential interaction with NK cells
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Ugo Pastorino, Massimo Milione, Paola Orecchia, Massimo Moro, Gabriella Sozzi, Monica Parodi, Giovanni Centonze, Fabio Murianni, Francesca Andriani, Ilaria Roato, Cecilia Gardelli, Melissa Balsamo, Giulia Taiè, Andrea Petretto, Chiara Lavarello , Luca Roz, Massimo Vitale, and Giulia Bertolini
- Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Background Epithelial to mesenchymal transition (EMT) endows cancer cells with pro-metastatic properties, which appear most effective when cells enter an intermediate hybrid (H) state, characterized by integrated mesenchymal (M) and epithelial (E) traits. The reasons for this advantage are poorly known and, especially, it is totally unexplored whether the interplay between H-cells and NK cells could have a role. Here we characterize the pro-metastatic mechanics of non-small cell lung cancer (NSCLC) H-cells and their subset of cancer-initiating cells (CICs), dissecting crucial interactions with NK cells.Methods Human lung cancer cell lines and sublines representative of E, M, or H states, assessed by proteomics, were analyzed in vivo for their tumor-forming and disseminating capabilities. Interactions with NK cells were investigated in vitro using migration assays, cytotoxic degranulation assays, and evaluation of CD133+ CICs modulation after coculture, and validated in vivo through NK cell neutralization assays. Correlation between EMT status, NK cell infiltration, and survival data, was evaluated in a cohort of surgically resected NSCLC cases (n=79).Results We demonstrated that H-cells, have limited dissemination capability but show the highest potential to initiate metastases in vivo. This property was related to their ability to escape NK cell surveillance. Mechanistically, H-cells expressed low levels of NK-attracting chemokines (CXCL1 and CXCL8), generating poorly infiltrated metastases. Accordingly, proteomics and GO enrichment analysis of E, H, M cell lines showed that the related secretory processes could change during EMT.Furthermore, H-CICs uniquely expressed high levels of the inhibitory ligand B7-H3, which protected H-CIC from NK cell-mediated clearance. In vivo neutralization assays confirmed that, indeed, the pro-metastatic properties of H-cells are poorly controlled by NK cells.Finally, the analysis of patients revealed that detection of hybrid phenotypes associated with low NK infiltration in NSCLC clinical specimens could identify a subset of patients with poor prognosis.Conclusions Our study demonstrates that H-cells play a central role in the metastatic spread in NSCLC. Such pro-metastatic advantage of H-cells is supported by their altered interaction with NK cells and by the critical role of B7-H3 in preserving their H-CIC component, indicating B7-H3 as a potential target in combined NK-based therapies.
- Published
- 2024
- Full Text
- View/download PDF
36. Common workflows for computing material properties using different quantum engines
- Author
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Huber, Sebastiaan P., Bosoni, Emanuele, Bercx, Marnik, Bröder, Jens, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Garcia, Alberto, Genovese, Luigi, Gresch, Dominik, Johnston, Conrad, Petretto, Guido, Poncé, Samuel, Rignanese, Gian-Marco, Sewell, Christopher J., Smit, Berend, Tseplyaev, Vasily, Uhrin, Martin, Wortmann, Daniel, Yakutovich, Aliaksandr V., Zadoks, Austin, Zarabadi-Poor, Pezhman, Zhu, Bonan, Marzari, Nicola, and Pizzi, Giovanni
- Subjects
Condensed Matter - Materials Science - Abstract
The prediction of material properties through electronic-structure simulations based on density-functional theory has become routinely common, thanks, in part, to the steady increase in the number and robustness of available simulation packages. This plurality of codes and methods aiming to solve similar problems is both a boon and a burden. While providing great opportunities for cross-verification, these packages adopt different methods, algorithms, and paradigms, making it challenging to choose, master, and efficiently use any one for a given task. Leveraging recent advances in managing reproducible scientific workflows, we demonstrate how developing common interfaces for workflows that automatically compute material properties can tackle the challenge mentioned above, greatly simplifying interoperability and cross-verification. We introduce design rules for reproducible and reusable code-agnostic workflow interfaces to compute well-defined material properties, which we implement for eleven different quantum engines and use to compute three different material properties. Each implementation encodes carefully selected simulation parameters and workflow logic, making the implementer's expertise of the quantum engine directly available to non-experts. Full provenance and reproducibility of the workflows is guaranteed through the use of the AiiDA infrastructure. All workflows are made available as open-source and come pre-installed with the Quantum Mobile virtual machine, making their use straightforward.
- Published
- 2021
- Full Text
- View/download PDF
37. The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/[beta]-catenin to RTK/MAPK signaling
- Author
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Madan, Babita, Wadia, Shawn R., Patnaik, Siddhi, Harmston, Nathan, Tan, Emile, Tan, Iain Bee Huat, Nes, W. David, Petretto, Enrico, and Virshup, David M.
- Subjects
Cholesterol -- Physiological aspects -- Genetic aspects -- Analysis ,Colorectal cancer -- Genetic aspects ,Amino acids -- Analysis -- Physiological aspects -- Genetic aspects ,Fatty acids -- Physiological aspects -- Analysis -- Genetic aspects ,Oxidases -- Genetic aspects -- Physiological aspects -- Analysis ,Cell differentiation -- Physiological aspects -- Analysis -- Genetic aspects ,Health care industry - Abstract
Wnts, cholesterol, and MAPK signaling are essential for development and adult homeostasis. Here, we report that fatty acid hydroxylase domain containing 2 (FAXDC2), a previously uncharacterized enzyme, functions as a methyl sterol oxidase catalyzing C4 demethylation in the Kandutsch-Russell branch of the cholesterol biosynthesis pathway. FAXDC2, a paralog of MSMO1, regulated the abundance of the specific C4-methyl sterols lophenol and dihydro-T-MAS. Highlighting its clinical relevance, FAXDC2 was repressed in Wnt/[beta]-catenin-high cancer xenografts, in a mouse genetic model of Wnt activation, and in human colorectal cancers. Moreover, in primary human colorectal cancers, the sterol lophenol, regulated by FAXDC2, accumulated in the cancerous tissues and not in adjacent normal tissues. FAXDC2 linked Wnts to RTK/MAPK signaling. Wnt inhibition drove increased recycling of RTKs and activation of the MAPK pathway, and this required FAXDC2. Blocking Wnt signaling in Wnt-high cancers caused both differentiation and senescence; and this was prevented by knockout of FAXDC2. Our data show the integration of 3 ancient pathways, Wnts, cholesterol synthesis, and RTK/MAPK signaling, in cellular proliferation and differentiation., Introduction During animal development and in adult stem cell niches, the balance between stemness, proliferation, and differentiation is regulated by Wnt/[beta]-catenin signaling (1, 2). Wnts are secreted palmitoleated glycoproteins that [...]
- Published
- 2024
- Full Text
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38. Evaluation of volatile and chemical profile of sherry-like white wine Vernaccia di Oristano from Sardinia by comprehensive targeted and untargeted approach
- Author
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Petretto, Giacomo, Urgeghe, Pietro Paolo, Cabizza, Roberto, and Del Caro, Alessandra
- Published
- 2023
- Full Text
- View/download PDF
39. Polydopamine nanoparticles as a non-pharmaceutical tool in the treatment of fatty liver disease
- Author
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Carmignani, Alessio, Battaglini, Matteo, Bartolucci, Martina, Petretto, Andrea, Prato, Mirko, and Ciofani, Gianni
- Published
- 2024
- Full Text
- View/download PDF
40. Combination of ab initio descriptors and machine learning approach for the prediction of the plasticity mechanisms in β-metastable Ti alloys
- Author
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Coffigniez, M., De Breuck, P.-P., Choisez, L., Marteleur, M., van Setten, M.J., Petretto, G., Rignanese, G.-M., and Jacques, P.J.
- Published
- 2024
- Full Text
- View/download PDF
41. OPTIMADE, an API for exchanging materials data
- Author
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Andersen, Casper W., Armiento, Rickard, Blokhin, Evgeny, Conduit, Gareth J., Dwaraknath, Shyam, Evans, Matthew L., Fekete, Ádám, Gopakumar, Abhijith, Gražulis, Saulius, Merkys, Andrius, Mohamed, Fawzi, Oses, Corey, Pizzi, Giovanni, Rignanese, Gian-Marco, Scheidgen, Markus, Talirz, Leopold, Toher, Cormac, Winston, Donald, Aversa, Rossella, Choudhary, Kamal, Colinet, Pauline, Curtarolo, Stefano, Di Stefano, Davide, Draxl, Claudia, Er, Suleyman, Esters, Marco, Fornari, Marco, Giantomassi, Matteo, Govoni, Marco, Hautier, Geoffroy, Hegde, Vinay, Horton, Matthew K., Huck, Patrick, Huhs, Georg, Hummelshøj, Jens, Kariryaa, Ankit, Kozinsky, Boris, Kumbhar, Snehal, Liu, Mohan, Marzari, Nicola, Morris, Andrew J., Mostofi, Arash, Persson, Kristin A., Petretto, Guido, Purcell, Thomas, Ricci, Francesco, Rose, Frisco, Scheffler, Matthias, Speckhard, Daniel, Uhrin, Martin, Vaitkus, Antanas, Villars, Pierre, Waroquiers, David, Wolverton, Chris, Wu, Michael, and Yang, Xiaoyu
- Subjects
Condensed Matter - Materials Science - Abstract
The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification., Comment: 11 pages, 1 table
- Published
- 2021
- Full Text
- View/download PDF
42. Statistical Analysis Applied to the Production of Mirto Liqueur
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Roberta Addis, Alberto Mannu, Giorgio Pintore, and Giacomo Luigi Petretto
- Subjects
anthocyanin ,design of experiments ,Myrtus communis ,antioxidant activity ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Preparation of myrtle liqueur through ethanol-based extraction is a widely employed methodology. Nevertheless, optimization of existing processes is possible, especially through a modern statistical multivariate approach. In this context, a Design of Experiments (DoE) approach was used to quantitatively assess for the first time the effect of the time, ethanol concentration, temperature, and the ratio between the Myrtus communis berries’ weight and the extractant volume (v/w) on the amounts of anthocyanins, volatile compounds and dry residues in the liqueur. The kinetic profile relative to the volatile fraction variation during the process was described by gas chromatography (GC), while spectrophotometric analysis allowed quantification of the total anthocyanins and total polyphenols. Multiple response analysis showed that the maximum efficiencies in terms of the considered parameters (desirability function) were reached by setting the temperature to 25 °C and the ethanol percentage to 96% after 20 days of processing. Some hints as to the chemical instability and not negligible sensitivity of anthocyanins in relation to the experimental conditions for longer extraction times were also observed. The statistical model represents a novel tool for industrial production of myrtle liqueur.
- Published
- 2024
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43. Proteomic Changes Induced by the Immunosuppressant Everolimus in Human Podocytes
- Author
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Maurizio Bruschi, Simona Granata, Giovanni Candiano, Andrea Petretto, Martina Bartolucci, Xhuliana Kajana, Sonia Spinelli, Alberto Verlato, Michele Provenzano, and Gianluigi Zaza
- Subjects
mTOR-inhibitors ,everolimus ,podocytes ,kidney transplantation ,proteomics ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
mTOR inhibitors (mTOR-Is) may induce proteinuria in kidney transplant recipients through podocyte damage. However, the mechanism has only been partially defined. Total cell lysates and supernatants of immortalized human podocytes treated with different doses of everolimus (EVE) (10, 100, 200, and 500 nM) for 24 h were subjected to mass spectrometry-based proteomics. Support vector machine and partial least squares discriminant analysis were used for data analysis. The results were validated in urine samples from 28 kidney transplant recipients receiving EVE as part of their immunosuppressive therapy. We identified more than 7000 differentially expressed proteins involved in several pathways, including kinases, cell cycle regulation, epithelial–mesenchymal transition, and protein synthesis, according to gene ontology. Among these, after statistical analysis, 65 showed an expression level significantly and directly correlated with EVE dosage. Polo-Like Kinase 1 (PLK1) content was increased, whereas osteopontin (SPP1) content was reduced in podocytes and supernatants in a dose-dependent manner and significantly correlated with EVE dose (p < 0.0001, FDR < 5%). Similar results were obtained in the urine of kidney transplant patients. This study analyzed the impact of different doses of mTOR-Is on podocytes, helping to understand not only the biological basis of their therapeutic effects but also the possible mechanisms underlying proteinuria.
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- 2024
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44. Spatiotemporal Mechanisms of the Coexistence of Reintroduced Scimitar-Horned Oryx and Native Dorcas Gazelle in Sidi Toui National Park, Tunisia
- Author
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Marouane Louhichi, Touhami Khorchani, Marie Petretto, Douglas Eifler, Maria Eifler, Kamel Dadi, Ali Zaidi, Yamna Karssene, and Mohsen Chammem
- Subjects
activity patterns ,antelopes ,arid ecosystem ,camera-trap ,management and conservation ,modelling habitat suitability ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Examining the distribution patterns and spatiotemporal niche overlap of sympatric species is crucial for understanding core concepts in community ecology and for the effective management of multi-species habitats within shared landscapes. Using data from 26 camera-traps, recorded over two years (December 2020–November 2022), in Sidi Toui National Park (STNP), Tunisia, we investigate habitat use and activity patterns of the scimitar-horned oryx (n = 1865 captures) and dorcas gazelle (n = 1208 captures). Using information theory and multi-model inference methods, along with the Pianka index, we evaluated the habitat characteristics influencing species distribution and their spatial niche overlap. To delineate daily activity patterns, we applied kernel density estimation. Our findings indicate minimal spatial overlap and distinct environmental factors determining suitable habitats for each species. Furthermore, we found significant temporal niche overlaps, indicative of synchrony in daily activity patterns, with both species showing peak activity at dawn and dusk. Our results indicated that oryx and gazelle differ in at least one dimension of their ecological niche at the current density levels, which contributes to their long-term and stable coexistence in STNP.
- Published
- 2024
- Full Text
- View/download PDF
45. Ferroelectricity and multiferroicity in anti-Ruddlesden-Popper structures
- Author
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Markov, Maxime, Alaerts, Louis, Miranda, Henrique P. C., Petretto, Guido, Chen, Wei, George, Janine, Bousquet, Eric, Ghosez, Philippe, Rignanese, Gian-Marco, and Hautier, Geoffroy
- Subjects
Condensed Matter - Materials Science ,Physics - Computational Physics - Abstract
Combining ferroelectricity with other properties such as visible light absorption or long-range magnetic order requires the discovery of new families of ferroelectric materials. Here, through the analysis of a high-throughput database of phonon band structures, we identify a new structural family of anti-Ruddlesden-Popper phases A$_4$X$_2$O (A=Ca, Sr, Ba, Eu, X=Sb, P, As, Bi) showing ferroelectric and anti-ferroelectric behaviors. The discovered ferroelectrics belong to the new class of hyperferroelectrics which polarize even under open-circuit boundary conditions. The polar distortion involves the movement of O anions against apical A cations and is driven by geometric effects resulting from internal chemical strains. Within this new structural family, we show that Eu$_4$Sb$_2$O combines coupled ferromagnetic and ferroelectric order at the same atomic site, a very rare occurrence in materials physics., Comment: 21 pages, 4 figures with supplemental information attached
- Published
- 2020
- Full Text
- View/download PDF
46. OPTIMADE, an API for exchanging materials data.
- Author
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Andersen, Casper W, Armiento, Rickard, Blokhin, Evgeny, Conduit, Gareth J, Dwaraknath, Shyam, Evans, Matthew L, Fekete, Ádám, Gopakumar, Abhijith, Gražulis, Saulius, Merkys, Andrius, Mohamed, Fawzi, Oses, Corey, Pizzi, Giovanni, Rignanese, Gian-Marco, Scheidgen, Markus, Talirz, Leopold, Toher, Cormac, Winston, Donald, Aversa, Rossella, Choudhary, Kamal, Colinet, Pauline, Curtarolo, Stefano, Di Stefano, Davide, Draxl, Claudia, Er, Suleyman, Esters, Marco, Fornari, Marco, Giantomassi, Matteo, Govoni, Marco, Hautier, Geoffroy, Hegde, Vinay, Horton, Matthew K, Huck, Patrick, Huhs, Georg, Hummelshøj, Jens, Kariryaa, Ankit, Kozinsky, Boris, Kumbhar, Snehal, Liu, Mohan, Marzari, Nicola, Morris, Andrew J, Mostofi, Arash A, Persson, Kristin A, Petretto, Guido, Purcell, Thomas, Ricci, Francesco, Rose, Frisco, Scheffler, Matthias, Speckhard, Daniel, Uhrin, Martin, Vaitkus, Antanas, Villars, Pierre, Waroquiers, David, Wolverton, Chris, Wu, Michael, and Yang, Xiaoyu
- Abstract
The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
- Published
- 2021
47. First Confirmed Record of the Smalltooth Sand Tiger, Odontapis Ferox, in Galicia (NW Spain)
- Author
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Mucientes, Gonzalo, Vilas-Arrondo, Nair, Secci-Petretto, Giulia, Vázquez, Uxía, Pin, Xabier, López, Alfredo, Castro, L. Filipe C., and Froufe, Elsa
- Published
- 2023
- Full Text
- View/download PDF
48. Chemical characterization, antioxidant and cytotoxic activity of hydroalcoholic extract from the albedo and flavedo of Citrus limon var. pompia Camarda
- Author
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Rosa, Antonella, Petretto, Giacomo Luigi, Maldini, Mariateresa, Tirillini, Bruno, Chessa, Mario, Pintore, Giorgio, and Sarais, Giorgia
- Published
- 2023
- Full Text
- View/download PDF
49. Pluripotent stem cell-derived committed cardiac progenitors remuscularize damaged ischemic hearts and improve their function in pigs
- Author
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Lynn Yap, Li Yen Chong, Clarissa Tan, Swarnaseetha Adusumalli, Millie Seow, Jing Guo, Zuhua Cai, Sze Jie Loo, Eric Lim, Ru San Tan, Elina Grishina, Poh Loong Soong, Narayan Lath, Lei Ye, Enrico Petretto, and Karl Tryggvason
- Subjects
Medicine - Abstract
Abstract Ischemic heart disease, which is often associated with irreversibly damaged heart muscle, is a major global health burden. Here, we report the potential of stem cell-derived committed cardiac progenitors (CCPs) have in regenerative cardiology. Human pluripotent embryonic stem cells were differentiated to CCPs on a laminin 521 + 221 matrix, characterized with bulk and single-cell RNA sequencing, and transplanted into infarcted pig hearts. CCPs differentiated for eleven days expressed a set of genes showing higher expression than cells differentiated for seven days. Functional heart studies revealed significant improvement in left ventricular ejection fraction at four and twelve weeks following transplantation. We also observed significant improvements in ventricular wall thickness and a reduction in infarction size after CCP transplantation (p-value
- Published
- 2023
- Full Text
- View/download PDF
50. Common workflows for computing material properties using different quantum engines
- Author
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Huber, Sebastiaan P, Bosoni, Emanuele, Bercx, Marnik, Bröder, Jens, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Garcia, Alberto, Genovese, Luigi, Gresch, Dominik, Johnston, Conrad, Petretto, Guido, Poncé, Samuel, Rignanese, Gian-Marco, Sewell, Christopher J, Smit, Berend, Tseplyaev, Vasily, Uhrin, Martin, Wortmann, Daniel, Yakutovich, Aliaksandr V, Zadoks, Austin, Zarabadi-Poor, Pezhman, Zhu, Bonan, Marzari, Nicola, and Pizzi, Giovanni
- Subjects
cond-mat.mtrl-sci - Abstract
The prediction of material properties through electronic-structuresimulations based on density-functional theory has become routinely common,thanks, in part, to the steady increase in the number and robustness ofavailable simulation packages. This plurality of codes and methods aiming tosolve similar problems is both a boon and a burden. While providing greatopportunities for cross-verification, these packages adopt different methods,algorithms, and paradigms, making it challenging to choose, master, andefficiently use any one for a given task. Leveraging recent advances inmanaging reproducible scientific workflows, we demonstrate how developingcommon interfaces for workflows that automatically compute material propertiescan tackle the challenge mentioned above, greatly simplifying interoperabilityand cross-verification. We introduce design rules for reproducible and reusablecode-agnostic workflow interfaces to compute well-defined material properties,which we implement for eleven different quantum engines and use to computethree different material properties. Each implementation encodes carefullyselected simulation parameters and workflow logic, making the implementer'sexpertise of the quantum engine directly available to non-experts. Fullprovenance and reproducibility of the workflows is guaranteed through the useof the AiiDA infrastructure. All workflows are made available as open-sourceand come pre-installed with the Quantum Mobile virtual machine, making theiruse straightforward.
- Published
- 2021
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