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612 results on '"FEDERICO, Alessandro"'

1. Structuring data analysis projects in the Open Science era with Kerblam!

Author

Visentin, Luca, Munaron, Luca, and Ruffinatti, Federico Alessandro

Subjects
Computer Science - Human-Computer Interaction, Quantitative Biology - Other Quantitative Biology
Abstract

Structuring data analysis projects, that is, defining the layout of files and folders needed to analyze data using existing tools and novel code, largely follows personal preferences. In this work, we look at the structure of several data analysis project templates and find little structural overlap. We highlight the parts that are similar between them, and propose guiding principles to keep in mind when one wishes to create a new data analysis project. Finally, we present Kerblam!, a project management tool that can expedite project data management, execution of workflow managers, and sharing of the resulting workflow and analysis outputs. We hope that, by following these principles and using Kerblam!, the landscape of data analysis projects can become more transparent, understandable, and ultimately useful to the wider community.

Published
2024

2. Structuring data analysis projects in the Open Science era with Kerblam! [version 1; peer review: awaiting peer review]

Author

Luca Visentin, Luca Munaron, and Federico Alessandro Ruffinatti

Subjects
Method Article, Articles, Project Management, reproducibility, open science, workflows, data management
Abstract

Background Structuring data analysis projects, that is, defining the layout of files and folders needed to analyze data using existing tools and novel code, largely follows personal preferences. Open Science calls for more accessible, transparent and understandable research. We believe that Open Science principles can be applied to the way data analysis projects are structured. Methods We examine the structure of several data analysis project templates by analyzing project template repositories present in GitHub. Through visualization of the resulting consensus structure, we draw observations regarding how the ecosystem of project structures is shaped, and what salient characteristics it has. Results Project templates show little overlap, but many distinct practices can be highlighted. We take them into account with the wider Open Science philosophy to draw a few fundamental Design Principles to guide researchers when designing a project space. We present Kerblam!, a project management tool that can work with such a project structure to expedite data handling, execute workflow managers, and share the resulting workflow and analysis outputs with others. Conclusions We hope that, by following these principles and using Kerblam!, the landscape of data analysis projects can become more transparent, understandable, and ultimately useful to the wider community.

Published
2025
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3. Development and validation of a new tool to estimate early mortality in patients with advanced cancer treated with immunotherapy

Author

De Giglio, Andrea, Leonetti, Alessandro, Comito, Francesca, Filippini, Daria Maria, Mollica, Veronica, Rihawi, Karim, Peroni, Marianna, Mazzaschi, Giulia, Ricciotti, Ilaria, Carosi, Francesca, Marchetti, Andrea, Rosellini, Matteo, Gagliano, Ambrogio, Favorito, Valentina, Nobili, Elisabetta, Gelsomino, Francesco, Melotti, Barbara, Marchese, Paola Valeria, Sperandi, Francesca, Di Federico, Alessandro, Buti, Sebastiano, Perrone, Fabiana, Massari, Francesco, Pantaleo, Maria Abbondanza, Tiseo, Marcello, and Ardizzoni, Andrea

Published
2024
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7. Tumor Immunophenotypic Correlates in Patients Aged 80 Years or Older With Non-Small Cell Lung Cancer and Outcomes to First-Line Pembrolizumab in PD-L1 High (≥50%) Patients

Author

Barrichello, Adriana P.C., Elkrief, Arielle, Ricciuti, Biagio, Ganta, Teja, Marron, Thomas U., Wang, Xinan, Lotter, William, Lindsay, James, Santo, Valentina, Cortellini, Alessio, Sharma, Bijaya, Felt, Kristen, Pfaff, Kathleen, Lamberti, Giuseppe, Pecci, Federica, Federico, Alessandro Di, Makarem, Maisam, Gandhi, Malini M., Nguyen, Tom, Haradon, Danielle, Vaz, Victor R., Johnson, Bruce E., Debnath, Neha, Wang, Yinghong, Kuang, Andrew G., Saeed, Anwaar, Radford, Maluki, Lovly, Christine M., Nebhan, Caroline A., Pinato, David J., Rodig, Scott J., Schoenfeld, Adam J., Awad, Mark M., Alessi, Joao V., and Naqash, Abdul Rafeh

Published
2025
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8. Gene Copy Deletion of STK11, KEAP1, and SMARCA4: Clinicopathologic Features and Association With the Outcomes of Immunotherapy With or Without Chemotherapy in Nonsquamous NSCLC

Author

Gandhi, Malini M., Elkrief, Arielle, Moore, Catherine Gutierrez, Ricciuti, Biagio, Alessi, Joao V., Richards, Allison L., Tischfield, Sam, Williams, Jessica, Lamberti, Giuseppe, Pecci, Federica, Di Federico, Alessandro, Makarem, Maisam, Johnson, Bruce E., Nishino, Mizuki, Sholl, Lynette M., Schoenfeld, Adam J., and Awad, Mark M.

Published
2025
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9. Real-world effectiveness and safety of bulevirtide monotherapy for up to 96 weeks in patients with HDV-related cirrhosis

Author

Degasperi, Elisabetta, Anolli, Maria Paola, Jachs, Mathias, Reiberger, Thomas, De Ledinghen, Victor, Metivier, Sophie, D’Offizi, Gianpiero, di Maria, Francesco, Schramm, Christoph, Schmidt, Hartmut, Zöllner, Caroline, Tacke, Frank, Dietz-Fricke, Christopher, Wedemeyer, Heiner, Papatheodoridi, Margarita, Papatheodoridis, George, Carey, Ivana, Agarwal, Kosh, Van Bömmel, Florian, Brunetto, Maurizia R., Cardoso, Mariana, Verucchi, Gabriella, Ciancio, Alessia, Zoulim, Fabien, Aleman, Soo, Semmo, Nasser, Mangia, Alessandra, Hilleret, Marie-Noelle, Merle, Uta, Santantonio, Teresa A., Coppola, Nicola, Pellicelli, Adriano, Roche, Bruno, Causse, Xavier, D’Alteroche, Louis, Dumortier, Jérome, Ganne, Nathalie, Heluwaert, Frederic, Ollivier, Isabelle, Roulot, Dominique, Viganò, Mauro, Loglio, Alessandro, Federico, Alessandro, Pileri, Francesca, Maracci, Monia, Tonnini, Matteo, Arpurt, Jean-Pierre, Barange, Karl, Billaud, Eric, Pol, Stanislas, Gervais, Anne, Minello, Anne, Rosa, Isabelle, Puoti, Massimo, and Lampertico, Pietro

Published
2025
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10. STK11 mutations correlate with poor prognosis for advanced NSCLC treated with first-line immunotherapy or chemo-immunotherapy according to KRAS, TP53, KEAP1, and SMARCA4 status

Author

De Giglio, Andrea, De Biase, Dario, Favorito, Valentina, Maloberti, Thais, Di Federico, Alessandro, Zacchini, Federico, Venturi, Giulia, Parisi, Claudia, Gustavo Dall’Olio, Filippo, Ricciotti, Ilaria, Gagliano, Ambrogio, Melotti, Barbara, Sperandi, Francesca, Altimari, Annalisa, Gruppioni, Elisa, Tallini, Giovanni, Gelsomino, Francesco, Montanaro, Lorenzo, and Ardizzoni, Andrea

Published
2025
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11. Early monitoring of plasma KRAS G12C with digital PCR predicts antitumor response to immunotherapy or sotorasib in advanced NSCLC: A brief report

Author

De Giglio, Andrea, Zacchini, Federico, Venturi, Giulia, Di Federico, Alessandro, Parisi, Claudia, Dall’Olio, Filippo Gustavo, Ricciotti, Ilaria, Favorito, Valentina, Gagliano, Ambrogio, De Biase, Dario, Maloberti, Thais, Altimari, Annalisa, Gruppioni, Elisa, Tallini, Giovanni, Melotti, Barbara, Sperandi, Francesca, Gelsomino, Francesco, Montanaro, Lorenzo, and Ardizzoni, Andrea

Published
2024
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13. Myosteatosis is closely associated with sarcopenia and significantly worse outcomes in patients with cirrhosis

Author

Iannone, Giulia, Serri, Paola, Bertino, Gaetano, Balsano, Clara, Iapadre, Nerio, Maida, Marcello, Sacerdoti, David, Natola, Leonardo Antonio, Ciacci, Carolina, Santonicola, Antonella, Cozzolongo, Raffaele, Surace, Lorenzo Antonio, Fracanzani, Anna Ludovica, Cespiati, Annalisa, Federico, Alessandro, Romeo, Mario, Grieco, Antonio, Marrone, Giuseppe, Vizioli, Luca, Di Cola, Simone, D’Amico, Gennaro, Caraceni, Paolo, Schepis, Filippo, Loredana, Simone, Lampertico, Pietro, Toniutto, Pierluigi, Martini, Silvia, Maimone, Sergio, Colecchia, Antonio, Svegliati Barone, Gianluca, Alessandria, Carlo, Aghemo, Alessio, Crocè, Saveria Lory, Adinolfi, Luigi Elio, Rendina, Maria, Lapenna, Lucia, Pompili, Enrico, Zaccherini, Giacomo, Saltini, Dario, Iavarone, Massimo, Tosetti, Giulia, Martelletti, Carolina, Nassisi, Veronica, Ferrarese, Alberto, Giovo, Ilaria, Masetti, Chiara, Pugliese, Nicola, Campigotto, Michele, Nevola, Riccardo, and Merli, Manuela

Published
2024
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14. Three-Year Overall Survival Outcomes and Correlative Analyses in Patients With NSCLC and High (50%–89%) Versus Very High (≥90%) Programmed Death-Ligand 1 Expression Treated With First-Line Pembrolizumab or Cemiplimab

Author

Ricciuti, Biagio, Elkrief, Arielle, Lin, Jessica, Zhang, Jianjun, Alessi, Joao V., Lamberti, Giuseppe, Gandhi, Malini, Di Federico, Alessandro, Pecci, Federica, Wang, Xinan, Makarem, Maisam, Hidalgo Filho, Cassio Murilo, Gorria, Teresa, Saini, Arushi, Pabon, Cindy, Lindsay, James, Pfaff, Kathleen L., Welsh, Emma L., Nishino, Mizuki, Sholl, Lynette M., Rodig, Scott, Kilickap, Saadettin, Rietschel, Petra, McIntyre, Debra AG., Pouliot, Jean-Francois, Altan, Mehmet, Gainor, Justin F., Heymach, John V., Schoenfeld, Adam J., and Awad, Mark M.

Published
2024
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15. A holistic evaluation of patients with chronic Hepatitis D virus (HDV) infection enrolled in the Italian PITER-B and delta cohort

Author

Aghemo, Alessio, Baiguera, Chiara, Battezzati, Pier Maria, Battistella, Sara, Bavetta, Maria Grazia, Bertoni, Costanza, Boni, Carolina, Brambilla, Paola, Bray, Antonella, Briano, Federica, Carmenini, Enrico, Castelli, Francesco, Cavalletto, Luisa, Cerini, Federica, Chidichimo, Luciana, Colella, Elisa, Cologni, Giuliana, Como, Silvia, Corsini, Romina, Costa, Chiara, Cotugno, Rosa, Cretella, Silvia, De Angelis, Fernando, De Leo, Pasqualina, Perri, Giovanni Di, Falbo, Elisabetta, Ferrigno, Luigina, Fornasiere, Ezio, Francisci, Daniela, Gatti, Pietro, Lampertico, Pietro, Lenci, Ilaria, Licata, Anna, Maida, Ivana, Marzano, Alfredo, Mastroianni, Antonio, Mazzaro, Cesare, Monti, Monica, Nardone, Gerardo, Nicolini, Laura Ambra, Passigato, Nicola, Pasticci, Maria Bruna, Pierotti, Piera, Pinchera, Biagio, Pollicino, Teresa, Porcu, Carmen, Quartini, Giulia, Rancatore, Gabriele, Romeo, Mario, Rumi, Maria Grazia, Saracino, Annalisa, Schioppa, Ornella, Serio, Ilaria, Soffredini, Roberta, Tata, Xhimi, Tizzani, Marco, Tonnini, Matteo, Torti, Carlo, Valenti, Daniela, Zaltron, Serena, Zoncada, Alessia, Kondili, Loreta A., Brancaccio, Giuseppina, Tosti, Maria Elena, Coco, Barbara, Quaranta, Maria Giovanna, Messina, Vincenzo, Ciancio, Alessia, Morisco, Filomena, Cossiga, Valentina, Claar, Ernesto, Rosato, Valerio, Ciarallo, Marianna, Cacciola, Irene, Ponziani, Francesca Romana, Cerrito, Lucia, Coppola, Roberta, Longobardi, Francesco, Biliotti, Elisa, Rianda, Alessia, Barbaro, Francesco, Coppola, Nicola, Stanzione, Maria, Barchiesi, Francesco, Fagiuoli, Stefano, Viganò, Mauro, Massari, Marco, Russo, Francesco Paolo, Ferrarese, Alberto, Laccabue, Diletta, Di Marco, Vito, Blanc, Pierluigi, Marrone, Aldo, Morsica, Giulia, Federico, Alessandro, Ieluzzi, Donatella, Rocco, Alba, Foschi, Francesco Giuseppe, Soria, Alessandro, Chessa, Luchino, Milella, Michele, Rosselli Del Turco, Elena, Madonia, Salvatore, Chemello, Liliana, Gentile, Ivan, Toniutto, Pierluigi, Bassetti, Matteo, Surace, Lorenzo, Baiocchi, Leonardo, Pellicelli, Adriano, De Santis, Adriano, Puoti, Massimo, Degasperi, Elisabetta, Niro, Grazia Anna, Zignego, Anna Linda, Craxi, Antonio, Raimondo, Giovanni, Santantonio, Teresa Antonia, Brunetto, Maurizia Rossana, and Gaeta, Giovanni Battista

Published
2024
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17. Osteoblast Response to Widely Ranged Texturing Conditions Obtained through High Power Laser Beams on Ti Surfaces

Author

Federico Alessandro Ruffinatti, Tullio Genova, Ilaria Roato, Martina Perin, Giorgia Chinigò, Riccardo Pedraza, Olivio Della Bella, Francesca Motta, Elisa Aimo Boot, Domenico D’Angelo, Giorgio Gatti, Giorgia Scarpellino, Luca Munaron, and Federico Mussano

Subjects
titanium implants, surface roughness, cell adhesion, protein adsorption, surface free energy, Biotechnology, TP248.13-248.65, Medicine (General), R5-920
Abstract

Titanium and titanium alloys are the prevailing dental implant materials owing to their favorable mechanical properties and biocompatibility, but how roughness dictates the biological response is still a matter of debate. In this study, laser texturing was used to generate eight paradigmatic roughened surfaces, with the aim of studying the early biological response elicited on MC3T3-E1 pre-osteoblasts. Prior to cell tests, the samples underwent SEM analysis, optical profilometry, protein adsorption assay, and optical contact angle measurement with water and diiodomethane to determine surface free energy. While all the specimens proved to be biocompatible, supporting similar cell viability at 1, 2, and 3 days, surface roughness could impact significantly on cell adhesion. Factorial analysis and linear regression showed, in a robust and unprecedented way, that an isotropic distribution of deep and closely spaced valleys provides the best condition for cell adhesion, to which both protein adsorption and surface free energy were highly correlated. Overall, here the authors provide, for the first time, a thorough investigation of the relationship between roughness parameters and osteoblast adhesion that may be applied to design and produce new tailored interfaces for implant materials.

Published
2024
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19. Noninvasive Assessment of portal Hypertension in Patients With Primary Biliary Cholangitis is Affected by Severity of Cholestasis

Author

Calvaruso, Vincenza, Celsa, Ciro, Cristoferi, Laura, Scaravaglio, Miki, Smith, Rachel, Kaur, Senamjit, Di Maria, Gabriele, Capodicasa, Luigi, Pennisi, Grazia, Gerussi, Alessio, Nofit, Eugenia, Malinverno, Federica, Lampertico, Pietro, Cazzagon, Nora, Marzioni, Marco, Vespasiani-Gentilucci, Umberto, Colapietro, Francesca, Andreone, Pietro, De Nalda, Ana Lleo, Rigamonti, Cristina, Viganò, Mauro, Giannini, Edoardo Giovanni, Russello, Maurizio, Vanni, Ester, Cerini, Federica, Orlandini, Alessia, Brunetto, Maurizia, Niro, Grazia Anna, Vettori, Giovanni, Castellaneta, Antonino, Cardinale, Vincenzo, Alvaro, Domenico, Mega, Andrea, Palitti, Valeria Pace, Cossiga, Valentina, Morisco, Filomena, Bellanti, Federico, Baiocchi, Leonardo, Fabris, Luca, Persico, Marcello, Degasperi, Elisabetta, Labanca, Sara, Bonaiuto, Emanuela, Pezzato, Francesco, Federico, Alessandro, Petta, Salvatore, Di Marco, Vito, Mells, George F., Culver, Emma, Invernizzi, Pietro, Cammà, Calogero, and Carbone, Marco

Published
2024
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20. Improved Event-Free Survival After Complete or Major Pathologic Response in Patients With Resectable NSCLC Treated With Neoadjuvant Chemoimmunotherapy Regardless of Adjuvant Treatment: A Systematic Review and Individual Patient Data Meta-Analysis

Author

Marinelli, Daniele, Nuccio, Antonio, Di Federico, Alessandro, Ambrosi, Francesca, Bertoglio, Pietro, Faccioli, Eleonora, Ferrara, Roberto, Ferro, Alessandra, Giusti, Raffaele, Guerrera, Francesco, Mammana, Marco, Pittaro, Alessandra, Sepulcri, Matteo, Viscardi, Giuseppe, and Gallina, Filippo Tommaso

Published
2024
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25. Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC

Author

Alessi, Joao V., Wang, Xinan, Elkrief, Arielle, Ricciuti, Biagio, Li, Yvonne Y., Gupta, Hersh, Spurr, Liam F., Rizvi, Hira, Luo, Jia, Pecci, Federica, Lamberti, Giuseppe, Recondo, Gonzalo, Venkatraman, Deepti, Di Federico, Alessandro, Gandhi, Malini M., Vaz, Victor R., Nishino, Mizuki, Sholl, Lynette M., Cherniack, Andrew D., Ladanyi, Marc, Price, Adam, Richards, Allison L., Donoghue, Mark, Lindsay, James, Sharma, Bijaya, Turner, Madison M., Pfaff, Kathleen L., Felt, Kristen D., Rodig, Scott J., Lin, Xihong, Meyerson, Matthew L., Johnson, Bruce E., Christiani, David C., Schoenfeld, Adam J., and Awad, Mark M.

Published
2023
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28. Profiling the risk of hepatocellular carcinoma after long-term HCV eradication in patients with liver cirrhosis in the PITER cohort

Author

Panetta, Valentina, Gaeta, Giovanni Battista, Filomia, Roberto, Coco, Barbara, Monti, Monica, Amoruso, Daniela Caterina, Madonia, Salvatore, Ieluzzi, Donatella, Taliani, Gloria, Badia, Lorenzo, Migliorino, Guglielmo Marco, Giorgini, Alessia, Masarone, Mario, Blanc, Pierluigi, Cossiga, Valentina, De Siena, Martina, Tata, Xhimi, Rumi, Maria Grazia, Chessa, Luchino, Lampertico, Pietro, Ferrari, Carlo, Gentile, Ivan, Parruti, Giustino, Baiocchi, Leonardo, Ciancio, Alessia, Invernizzi, Pietro, Federico, Alessandro, Torti, Carlo, Morsica, Giulia, Andreone, Pietro, Aghemo, Alessio, Popoli, Patrizia, Vella, Stefano, Kondili, Loreta A., Quaranta, Maria Giovanna, Cavalletto, Luisa, Calvaruso, Vincenza, Ferrigno, Luigina, D'Ambrosio, Roberta, Simonelli, Ilaria, Brancaccio, Giuseppina, Raimondo, Giovanni, Brunetto, Maurizia R., Zignego, Anna Linda, Coppola, Carmine, Iannone, Andrea, Biliotti, Elisa, Verucchi, Gabriella, Massari, Marco, Licata, Anna, Barbaro, Francesco, Persico, Marcello, Russo, Francesco Paolo, Morisco, Filomena, Pompili, Maurizio, Viganò, Mauro, Puoti, Massimo, Santantonio, Teresa, Villa, Erica, Craxì, Antonio, and Chemello, Liliana

Published
2023
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30. Clinicopathologic and Genomic Factors Impacting Efficacy of First-Line Chemoimmunotherapy in Advanced NSCLC

Author

Alessi, Joao V., Elkrief, Arielle, Ricciuti, Biagio, Wang, Xinan, Cortellini, Alessio, Vaz, Victor R., Lamberti, Giuseppe, Frias, Rosa L., Venkatraman, Deepti, Fulgenzi, Claudia A.M., Pecci, Federica, Recondo, Gonzalo, Di Federico, Alessandro, Barrichello, Adriana, Park, Hyesun, Nishino, Mizuki, Hambelton, Grace M., Egger, Jacklynn V., Ladanyi, Marc, Digumarthy, Subba, Johnson, Bruce E., Christiani, David C., Lin, Xihong, Gainor, Justin F., Lin, Jessica J., Pinato, David J., Schoenfeld, Adam J., and Awad, Mark M.

Published
2023
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31. Trends in chronic hepatitis B virus infection in Italy over a 10-year period: Clues from the nationwide PITER and MASTER cohorts toward elimination

Author

Pasulo, Luisa, Coppola, Carmine, Pisano, Federica, Romano, Mariarosaria, Porcu, Carmen, Bottalico, Irene Francesca, Cossiga, Valentina, Tata, Xhimi, Sagnelli, Caterina, Pierotti, Piera, Degasperi, Elisabetta, Rosato, Valerio, Badia, Lorenzo, Ieluzzi, Dontella, Monti, Monica, Bavetta, Maria Grazia, Cavalletto, Luisa, Toniutto, Pierluigi, Fornasiere, Ezio, Colecchia, Antonio, Ferrarese, Alberto, Nardone, Gerardo, Rocco, Alba, Viganò, Mauro, Foschi, Francesco Giuseppe, Conti, Fabio, Morsica, Giulia, Salpietro, Stefania, Torti, Carlo, Costa, Chiara, Federico, Alessandro, Dallio, Marcello, Giorgini, Alessia, Anselmo, Marco, De Leo, Pasqualina, Zaltron, Serena, Cambianica, Anna, Piscaglia, Fabio, Serio, Ilaria, Schivazappa, Simona, Mastroianni, Antonio, Chidichimo, Luciana, Massari, Marco, Mazzaro, Cesare, Marrone, Aldo, D'Amore, Francesca Maria, D'Offizi, Gianpiero, Licata, Anna, Niro, Grazia Anna, Pollicino, Teresa, Aghemo, Alessio, Brancaccio, Giuseppina, Coco, Barbara, Nardi, Alessandra, Quaranta, Maria Giovanna, Tosti, Maria Elena, Ferrigno, Luigina, Cacciola, Irene, Messina, Vincenzo, Chessa, Luchino, Morisco, Filomena, Milella, Michele, Barbaro, Francesco, Ciancio, Alessia, Russo, Francesco Paolo, Coppola, Nicola, Blanc, Pierluigi, Claar, Ernesto, Verucchi, Gabriella, Puoti, Massimo, Zignego, Anna Linda, Chemello, Liliana, Madonia, Salvatore, Fagiuoli, Stefano, Marzano, Alfredo, Ferrari, Carlo, Lampertico, Pietro, Di Marco, Vito, Craxì, Antonio, Santantonio, Teresa Antonia, Raimondo, Giovanni, Brunetto, Maurizia R., Gaeta, Giovanni Battista, and Kondili, Loreta A.

Published
2023
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32. Tumor Microenvironment Modulates Invadopodia Activity of Non-Selected and Acid-Selected Pancreatic Cancer Cells and Its Sensitivity to Gemcitabine and C18-Gemcitabine

Author

Tiago M. A. Carvalho, Madelaine Magalì Audero, Maria Raffaella Greco, Marilena Ardone, Teresa Maggi, Rosanna Mallamaci, Barbara Rolando, Silvia Arpicco, Federico Alessandro Ruffinatti, Alessandra Fiorio Pla, Natalia Prevarskaya, Tomas Koltai, Stephan J. Reshkin, and Rosa Angela Cardone

Subjects
hypoxia, cell invasion, extracellular acidosis, invadopodia, chemoresistance, Cytology, QH573-671
Abstract

Background: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease with high mortality due to early metastatic dissemination and high chemoresistance. All these factors are favored by its extracellular matrix (ECM)-rich microenvironment, which is also highly hypoxic and acidic. Gemcitabine (GEM) is still the first-line therapy in PDAC. However, it is quickly deaminated to its inactive metabolite. Several GEM prodrugs have emerged to improve its cytotoxicity. Here, we analyzed how the acidic/hypoxic tumor microenvironment (TME) affects the response of PDAC cell death and invadopodia-mediated ECM proteolysis to both GEM and its C18 prodrug. Methods: For this, two PDAC cell lines, PANC-1 and Mia PaCa-2 were adapted to pHe 6.6 or not for 1 month, grown as 3D organotypic cultures and exposed to either GEM or C18 in the presence and absence of acidosis and the hypoxia inducer, deferoxamine. Results: We found that C18 has higher cytotoxic and anti-invadopodia activity than GEM in all culture conditions and especially in acid and hypoxic environments. Conclusions: We propose C18 as a more effective approach to conventional GEM in developing new therapeutic strategies overcoming PDAC chemoresistance.

Published
2024
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34. Amplification of Wild-Type RET Represents a Novel Molecular Subtype of Several Cancer Types With Clinical Response to Selpercatinib

Author

Gandhi, Malini M., Ricciuti, Biagio, Harada, Guilherme, Repetto, Matteo, Gildenberg, Melissa S., Singh, Ankit, Li, Yvonne Y., Gagné, Andréanne, Wang, Xinan, Aizer, Ayal, Fitzgerald, Kelly, Nishino, Mizuki, Alessi, Joao, Pecci, Federica, Di Federico, Alessandro, Fisch, Adam, Drilon, Alexander, Nardi, Valentina, Sholl, Lynette, Awad, Mark M., and Rotow, Julia

Published
2023
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36. Patterns of renal toxicity from the combination of pemetrexed and pembrolizumab for advanced nonsquamous non-small-cell lung cancer (NSCLC): A single-center experience

Author

De Giglio, Andrea, Grandinetti, Valeria, Aprile, Marta, Borelli, Greta, Campus, Anita, Croci Chiocchini, Anna Laura, Busutti, Marco, Vischini, Gisella, Di Federico, Alessandro, Sperandi, Francesca, Melotti, Barbara, Ardizzoni, Andrea, La Manna, Gaetano, and Gelsomino, Francesco

Published
2022
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38. Rare ATG7 genetic variants predispose patients to severe fatty liver disease

Author

Borroni, Vittorio, Liguori, Antonio, Ronzoni, Luisa, Cherubini, Alessandro, Santoro, Luigi, Tomasi, Melissa, Lombardi, Angela, Ostadreza, Mahnoosh, Casirati, Elia, Marini, Ilaria, Maier, Silvia, Rosso, Chiara, Baroni, Gianluca Svegliati, Santaniello, Carlo, Dallio, Marcello, Baselli, Guido A., Jamialahmadi, Oveis, Pelusi, Serena, Ciociola, Ester, Malvestiti, Francesco, Saracino, Marco, Dongiovanni, Paola, Maggioni, Marco, Bianco, Cristiana, Tavaglione, Federica, Cespiati, Annalisa, Mancina, Rosellina M., D’Ambrosio, Roberta, Vaira, Valentina, Petta, Salvatore, Miele, Luca, Vespasiani-Gentilucci, Umberto, Federico, Alessandro, Pihlajamaki, Jussi, Bugianesi, Elisabetta, Fracanzani, Anna L., Reeves, Helen L., Soardo, Giorgio, Prati, Daniele, Romeo, Stefano, and Valenti, Luca VC.

Published
2022
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39. CIC-39Na reverses the thrombocytopenia that characterizes tubular aggregate myopathy

Author

Cordero-Sanchez, Celia, Pessolano, Emanuela, Riva, Beatrice, Vismara, Mauro, Trivigno, Silvia Maria Grazia, Clemente, Nausicaa, Aprile, Silvio, Ruffinatti, Federico Alessandro, Portararo, Paola, Filigheddu, Nicoletta, Zaggia, Ivan, Bhela, Irene P., Serafini, Marta, Pirali, Tracey, Colombo, Mario P., Torti, Mauro, Sangaletti, Sabina, Bertoni, Alessandra, and Genazzani, Armando A.

Published
2022
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40. Deep Learning Model for Predicting Immunotherapy Response in Advanced Non−Small Cell Lung Cancer.

Author

Rakaee, Mehrdad, Tafavvoghi, Masoud, Ricciuti, Biagio, Alessi, Joao V., Cortellini, Alessio, Citarella, Fabrizio, Nibid, Lorenzo, Perrone, Giuseppe, Adib, Elio, Fulgenzi, Claudia A. M., Hidalgo Filho, Cassio Murilo, Di Federico, Alessandro, Jabar, Falah, Hashemi, Sayed, Houda, Ilias, Richardsen, Elin, Rasmussen Busund, Lill-Tove, Donnem, Tom, Bahce, Idris, and Pinato, David J.

Published
2025
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41. Clinical Applications of Artificial Intelligence (AI) in Human Cancer: Is It Time to Update the Diagnostic and Predictive Models in Managing Hepatocellular Carcinoma (HCC)?

Author

Romeo, Mario, Dallio, Marcello, Napolitano, Carmine, Basile, Claudio, Di Nardo, Fiammetta, Vaia, Paolo, Iodice, Patrizia, and Federico, Alessandro

Subjects
CHRONIC hepatitis B, ARTIFICIAL intelligence, LIVER cancer, MACHINE learning, HEPATOCELLULAR carcinoma
Abstract

In recent years, novel findings have progressively and promisingly supported the potential role of Artificial intelligence (AI) in transforming the management of various neoplasms, including hepatocellular carcinoma (HCC). HCC represents the most common primary liver cancer. Alarmingly, the HCC incidence is dramatically increasing worldwide due to the simultaneous "pandemic" spreading of metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD currently constitutes the leading cause of chronic hepatic damage (steatosis and steatohepatitis), fibrosis, and liver cirrhosis, configuring a scenario where an HCC onset has been reported even in the early disease stage. On the other hand, HCC represents a serious plague, significantly burdening the outcomes of chronic hepatitis B (HBV) and hepatitis C (HCV) virus-infected patients. Despite the recent progress in the management of this cancer, the overall prognosis for advanced-stage HCC patients continues to be poor, suggesting the absolute need to develop personalized healthcare strategies further. In this "cold war", machine learning techniques and neural networks are emerging as weapons, able to identify the patterns and biomarkers that would have normally escaped human observation. Using advanced algorithms, AI can analyze large volumes of clinical data and medical images (including routinely obtained ultrasound data) with an elevated accuracy, facilitating early diagnosis, improving the performance of predictive models, and supporting the multidisciplinary (oncologist, gastroenterologist, surgeon, radiologist) team in opting for the best "tailored" individual treatment. Additionally, AI can significantly contribute to enhancing the effectiveness of metabolomics–radiomics-based models, promoting the identification of specific HCC-pathogenetic molecules as new targets for realizing novel therapeutic regimens. In the era of precision medicine, integrating AI into routine clinical practice appears as a promising frontier, opening new avenues for liver cancer research and treatment. [ABSTRACT FROM AUTHOR]

Published
2025
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42. Dysgeusia in MASLD-related advanced chronic liver disease (ACLD): a silent driver towards the "Bermuda" triangle of malnutrition-sarcopenia-frailty severely affecting prognosis.

Author

Dallio, Marcello, Romeo, Mario, Di Nardo, Fiammetta, Napolitano, Carmine, Vaia, Paolo, Iadanza, Giorgia, Olivieri, Simone, Coppola, Annachiara, Niosi, Marco, and Federico, Alessandro

Subjects
BODY composition, MEDICAL sciences, DIETARY patterns, NUTRITION, LOGISTIC regression analysis, SARCOPENIA
Abstract

Background: Dysgeusia is a distortion of the sense of taste whose prevalence and relationship with nutritional status in Metabolic dysfunction-associated Steatotic Liver Disease (MASLD)-related advanced chronic liver disease (ACLD) have never been systematically explored. Methods: 200 MASLD patients [60 ≤ F3 fibrosis, 70 compensated ACLD (cACLD), and 70 decompensated (dACLD)] were enrolled. At baseline, the Child–Pugh (CP) score was determined. Dietary habits, body composition, and frailty were evaluated. The European Working Group (EWGSOP2) criteria defined sarcopenia. Dysgeusia was assessed by the Dysgeusia-Total-Score (DTS). A visual analog scale identified appetite impairment (VASAI). During a 6-month follow-up, liver-related decompensation events (LRDEs) were recorded. Results: The prevalence of dysgeusia increased with the liver disease progression, appearing significantly higher in ACLD compared with ≤ F3 (65.7% vs 5%, p:0.003), as well as in dACLD compared to cACLD patients (58.5 vs 7.1% p < 0.0001). On 41 dACLD patients presenting dysgeusia, 37 (90.2%) showed a significant impairment of appetite levels. In dACLD, the CP score was positively correlated with both DTS (R:0.742) and VASAI (R:0.704), as well as DTS was directly correlated with VASAI (R:0.765) (all p < 0.0001). Compared with dACLD patients without dysgeusia, dysgeusia-affected dACLD patients presented a lower daily protein intake (g/kg/die) (1.55 ± 0.192 vs 1.34 ± 0.15, p < 0.0001). Sarcopenia (70.7 vs 41.3%) and frailty (69.29 vs 37.9%) were significantly more prevalent in dysgeusia-affected dACLD individuals (both p < 0.0001). These patients showed a higher risk of LRDEs occurrence during the follow-up [HR:2.205; C.I. 95%:1.186–4.099; p:0.01]. Logistic regression analysis revealed dysgeusia (aOR: 3.32), appetite impairment (aOR:1.32), sarcopenia (aOR: 3.75), and frailty (aOR:3.03) significantly associated with this outcome (all p < 0.0001). Conclusions: Dysgeusia appears predominant in MASLD-dACLD and, via appetite impairment, in a close relationship with malnutrition, sarcopenia, and frailty, negatively influencing patients' outcomes. [ABSTRACT FROM AUTHOR]

Published
2025
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43. FLAME: Training and Validating a Newly Conceived Model Incorporating Alpha-Glutathione-S-Transferase Serum Levels for Predicting Advanced Hepatic Fibrosis and Acute Cardiovascular Events in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD).

Author

Dallio, Marcello, Romeo, Mario, Di Nardo, Fiammetta, Vaia, Paolo, Napolitano, Carmine, Ventriglia, Lorenzo, Coppola, Annachiara, Silvestrin, Alessia, Olivieri, Simone, and Federico, Alessandro

Subjects
HEPATIC fibrosis, FATTY liver, CHRONIC active hepatitis, PRINCIPAL components analysis, VIRAL hepatitis
Abstract

Alpha-Glutathione-S-transferase (alphaGST) is a liver enzyme whose serum levels increase with the worsening of fibrosis in alcoholic and viral chronic hepatitis. Its usefulness in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) remains unexplored. From January 2016 to December 2017, 200 patients with MASLD and 30 controls were enrolled. AlphaGST serum levels were measured. Variables related to advanced fibrosis (AF) were selected via Principal Component Analysis (PCA), and the best cut-off (BCO) was estimated using ROC analysis. Liver stiffness measurement (LSM), NAFLD fibrosis (NFS), Fibrosis-4 (FIB-4), and BMI-AST/ALT Ratio-Diabetes (BARD) scores were determined. The first acute cardiovascular events (ACE) in ACE-naïve subjects were recorded over five years. A validation cohort of 60 MASLD patients was enrolled from January 2018 to May 2019 and followed for five years. AlphaGST levels increased with fibrosis stage (p < 0.0001) in both cohorts, showing high accuracy in predicting AF (TrC: AUC 0.89, VlC: AUC 0.89). PCA-selected variables were HbA1c, HDL, and alphaGST, forming the "FLAME" model. FLAME showed superior predictive performance for AF and ACEs compared to other models and scores. FLAME represents a novel tool that accurately predicts AF and ACEs in MASLD. [ABSTRACT FROM AUTHOR]

Published
2025
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44. Transcriptomic data of bevacizumab-adapted colorectal adenocarcinoma cells HCT-116

Author

Sala Cesare, Lottini Tiziano, Lastraioli Elena, Ruffinatti Federico Alessandro, Visentin Luca, and Arcangeli Annarosa

Subjects
Gene expression, HCT116, Bevacizumab, Bioinformatic analysis, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390
Abstract

A bioinformatic approach was applied to evaluate the effect of treatment with Bevacizumab on the gene expression profile of colorectal adenocarcinoma cells. The transcriptomic profile of Bevacizumab-adapted HCT-116 (Bev/A) colorectal adenocarcinoma cells was determined and compared with that of the corresponding control cell line by Agilent microarray analysis. Raw data were preprocessed, normalized, filtered, and subjected to a differential expression analysis using standard R/Bioconductor packages (i.e., limma, RankProd). As consequence of Bevacizumab adaptation, 166 differentially expressed genes (DEGs) emerged, most of them (123) resulted downregulated and 43 overexpressed. The list of statistically significant dysregulated genes was used as an input for functional overrepresentation analysis using ToppFun web tool. Such analysis pointed at cell adhesion, cell migration, extracellular matrix organization and angiogenesis as the main dysregulated biological process involved in Bevacizumab-adaptation of HCT116 cells. In addition, gene set enrichment analysis was performed using GSEA, searching for enriched terms within the Hallmarks (H), Canonical Pathways (CP), and Gene Ontology (GO) gene sets. GO terms that showed significant enrichment included: transportome, vascularization, cell adhesion and cytoskeleton, extra cellular matrix (ECM), differentiation and epithelial–mesenchymal transition (EMT), inflammation and immune response. Raw and normalized microarray data were deposited in the Gene Expression Omnibus (GEO) public repository with accession number GSE221948.

Published
2023
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47. Cutaneous Kaposi's Sarcoma Following Long-Term Infliximab Treatment in a Patient with HIV-Negative Antibiotic-Dependent Chronic Pouchitis: Considerations on an Exceptional Finding.

Author

Pellegrino, Raffaele, Palladino, Giovanna, Pagliuca, Francesca, Lucà, Stefano, Federico, Alessandro, and Gravina, Antonietta Gerarda

Subjects
PHYSICAL diagnosis, ANTI-inflammatory agents, KAPOSI'S sarcoma, ULTRASONIC imaging, CHRONIC diseases, MONOCLONAL antibodies, ILEITIS, INFLIXIMAB, MEDICAL screening
Abstract

In managing ulcerative colitis (UC), anti-tumour necrosis factor (TNF) agents are among the primary choices. Evidence suggests anti-TNF does not significantly increase malignancy risk (apart from lymphoma and melanoma), though uncertainties persist due to inconsistent long-term data. Kaposi's sarcoma (KS), induced by human herpesvirus type-8 (HHV-8), is a multifocal neoplasm linked to immunosuppressive therapies, primarily affecting the skin and gastrointestinal tract. KS cases during anti-TNF therapy for UC are anecdotal. We report a rare occurrence of KS in the setting of the long-term use of the standard maintenance dose of infliximab (initiated in 2010) in a 56-year-old male patient with UC diagnosed in 2001. The patient underwent restorative proctocolectomy with ileal J-pouch-anal anastomosis in 2002 and subsequently developed chronic antibiotic-dependent pouchitis. Given the secondary loss of response to infliximab, a switch to vedolizumab was performed. In April 2024, the patient reported the presence of a skin lesion on the right leg. Following surgery, a rhomboid-shaped skin area was removed, encompassing the irregular, greyish KS lesion. The histopathological analysis confirmed the diagnosis of patch-like KS. We continued vedolizumab due to its gut-selective profile. The patient is in clinical remission and under dermatological follow-up with no lesion recurrence. [ABSTRACT FROM AUTHOR]

Published
2024
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48. Too Many Couch Potatoes Among Middle-Aged Inflammatory Bowel Disease Patients: Findings from the "BE-FIT-IBD-2" Study.

Author

Gravina, Antonietta Gerarda, Pellegrino, Raffaele, Palladino, Giovanna, Zanini, Annalisa, Federico, Alessandro, and Zingone, Fabiana

Subjects
INFLAMMATORY bowel diseases, OLDER patients, AGE groups, OLDER people, REGRESSION analysis
Abstract

Background: Regular physical activity (PA) is desirable, regardless of age, even in patients with chronic conditions such as inflammatory bowel disease (IBD). Aims: This study aims to assess PA levels and related barriers/facilitators in IBD patients, stratifying them into age groups (with a threshold of 50 years). Methods: The International PA Questionnaire (IPAQ) assessed PA levels regarding resting metabolic rate (Met) in minutes per week (min/wk). Patient-reported outcomes 2 (PRO-2) evaluated disease activity. Results: Among the 237 enrolled patients, PA rates were found to differ significantly in terms of patients being sufficiently active (55% vs. 39.8%), inactive (39.6% vs. 59.1%), and engaging in health-enhancing PA (5.4% vs. 1.1%) between patients under and at least 50 years old, respectively (p < 0.001). Overall, PA levels followed this trend, being higher in younger patients [892 (446.5–1439) vs. 545.25 (257–1210.47) Met min/wk, p = 0.007]. Individuals aged at least 50 years tend to have lower PA at regression analysis (OR: 3.302, p = 0.018). Patients aged at least 50 years perceived IBD as more of a barrier to PA (p = 0.04). Bowel urgency is a significant barrier, especially in older patients (p = 0.022). Conclusions: Age is an unmodifiable factor impacting and influencing PA levels. Strategies to recover exercise levels in older IBD patients should be encouraged. [ABSTRACT FROM AUTHOR]

Published
2024
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49. Systemic Oxidative Stress Correlates with Sarcopenia and Pruritus Severity in Primary Biliary Cholangitis (PBC): Two Independent Relationships Simultaneously Impacting the Quality of Life—Is the Low Absorption of Cholestasis-Promoted Vitamin D a Puzzle Piece?

Author

Dallio, Marcello, Romeo, Mario, Di Nardo, Fiammetta, Napolitano, Carmine, Vaia, Paolo, Ventriglia, Lorenzo, Coppola, Annachiara, Olivieri, Simone, Niosi, Marco, and Federico, Alessandro

Subjects
VITAMIN D metabolism, CIRRHOSIS of the liver, QUESTIONNAIRES, SCIENTIFIC observation, OXIDATIVE stress, SEVERITY of illness index, ITCHING, MUSCLE strength, QUALITY of life, SARCOPENIA, VITAMIN D, CHOLESTASIS
Abstract

Background: Unlike other chronic liver disorders, in primary biliary cholangitis (PBC), systemic oxidative stress (SOS) worsens along with liver disease progression status (DPS), influencing muscle metabolism, muscle quantity (MQ), and itch pathways. Synergistically, cholestasis contributes to reduced vitamin D absorption, with a negative impact on MM and SOS. Despite this evidence, the prevalence of sarcopenia in PBC, and the SOS-MQ relationship comparing PBC with other CLDs, has never been investigated. Moreover, the relationship between vitamin D and MQ-SOS, and the correlation between SOS and pruritus severity, remains unexplored in PBC. Methods: A total of 40 MASLD, 52 chronic HBV infections, 50 chronic HCV infections, and 41 ursodeoxycholic acid/antioxidant-naïve PBC patients were enrolled. Biochemical, nutritional, and liver stiffness (LSM) data were collected, and sarcopenia was assessed after a normalizing 3-month dietetic–physical exercise regimen. The d-ROMs/BAP tests evaluated SOS. The validated "PBC-40 questionnaire" estimated pruritus and quality of life (QoL). Results: Unlike other CLDs, in PBC patients, sarcopenia was more prevalent in initial mild fibrosis (PBC: 57.10% vs. MASLD: 30.76%, HBV: 22.60%, HCV: 20.70%, all p < 0.0001), and SOS significantly correlated with MQ (dROMs-ASM/h2, p: 0.0002; BAP-ASM/h2: p: 0.0092). PBC patients presented lower vitamin D levels and a significant correlation of these with SOS and MQ (all p < 0.0001). SOS also correlated with pruritus severity (dROMs, R: 0.835; BAP, R: −0.775, p < 0.0001). QoL impairment was significantly more represented in PBC individuals with sarcopenia, SOS imbalance, and relevant pruritus (p: 0.0228). Conclusions: In PBC, SOS correlates with MQ impairment and pruritus severity, configuring two independent relationships simultaneously impacting QoL. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Conversational LLM Chatbot ChatGPT-4 for Colonoscopy Boston Bowel Preparation Scoring: An Artificial Intelligence-to-Head Concordance Analysis.

Author

Pellegrino, Raffaele, Federico, Alessandro, and Gravina, Antonietta Gerarda

Subjects
*CHATGPT, *LANGUAGE models, *CHATBOTS, *ARTIFICIAL intelligence, *COLONOSCOPY
Abstract

Background/objectives:To date, no studies have evaluated Chat Generative Pre-Trained Transformer (ChatGPT) as a large language model chatbot in optical applications for digestive endoscopy images. This study aimed to weigh the performance of ChatGPT-4 in assessing bowel preparation (BP) quality for colonoscopy. Methods: ChatGPT-4 analysed 663 anonymised endoscopic images, scoring each according to the Boston BP scale (BBPS). Expert physicians scored the same images subsequently. Results: ChatGPT-4 deemed 369 frames (62.9%) to be adequately prepared (i.e., BBPS > 1) compared to 524 frames (89.3%) assessed by human assessors. The agreement was slight (κ: 0.099, p = 0.0001). The raw human BBPS score was higher at 3 (2–3) than that of ChatGPT-4 at 2 (1–3), demonstrating moderate concordance (W: 0.554, p = 0.036). Conclusions: ChatGPT-4 demonstrates some potential in assessing BP on colonoscopy images, but further refinement is still needed. [ABSTRACT FROM AUTHOR]

Published
2024
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