Pernice, Simone; Follia, Laura; Maglione, Alessandro; Pennisi, Marzio; Pappalardo, Francesco; Novelli, Francesco; Clerico, Marinella; Beccuti, Marco; Cordero, Francesca; Rolla, Simona
Background: Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS etiology remains partially unknown. Furthermore, the presence of various endogenous and exogenous factors can greatly influence the immune response of different individuals, making it difficult to study and understand the disease. This becomes more evident in a personalized-fashion […]
BMC Infectious Diseases
Pernice, Simone; Castagno, Paolo; Marcotulli, Linda; Maule, Milena Maria; Richiardi, Lorenzo; Moirano, Giovenale; Sereno, Matteo; Cordero, Francesca; Beccuti, Marco
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), the causative agent of the coronavirus disease 19 (COVID-19), is a highly transmittable virus. Since the first person-to-person transmission of SARS-CoV-2 was reported in Italy on February 21st, 2020, the number of people infected with SARS-COV-2 increased rapidly, mainly in northern Italian regions, including Piedmont. A strict lockdown was imposed on March 21st until May 4th when a gradual relaxation of the restrictions started. […]
Castagno, Paolo; Pernice, Simone; Ghetti, Gianni; Povero, Massimiliano; Pradelli, Lorenzo; Paolotti, Daniela; Balbo, Gianfranco; Sereno, Matteo; Beccuti, Marco
Background: Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemiologists can exploit to better understand the spreading characteristics of these diseases and to decide on vaccination policies, human interaction controls, and other social measures […]
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pernice, Simone; Beccuti, Marco; Romano, Greta; Pennisi, Marzio; Maglione, Alessandro; Cutrupi, Santina; Pappalardo, Francesco; Capra, Lorenzo; Franceschinis, Giuliana; De Pierro, Massimiliano; Balbo, Gianfranco; Cordero, Francesca; Calogero, Raffaele
Multiple Sclerosis (MS) is a chronic and potentially highly disabling disease that can cause permanent damage and deterioration of the central nervous system. In Europe it is the leading cause of non-traumatic disabilities in young adults, since more than 700,000 EU people suffer from MS. Although recent studies on MS pathophysiology have been performed, providing interesting results, MS remains a challenging disease. In this context, thanks to recent advances in software and hardware technologies, […]
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Totis, Niccolò; Tangherloni, Andrea; Beccuti, Marco; Cazzaniga, Paolo; Nobile, Marco S.; Besozzi, Daniela; Pennisi, Marzio; Pappalardo, Francesco
Mathematical modeling and computational analyses are essential tools to understand and gain novel insights on the functioning of complex biochemical systems. In the specific case of metabolic reaction networks, which are regulated by many other intracellular processes, various challenging problems hinder the definition of compact and fully calibrated mathematical models, as well as the execution of computationally efficient analyses of their emergent dynamics. These problems especially occur when […]
International Journal of Molecular Sciences
Ferrero, Giulio; Licheri, Nicola; Tarrero, Lucia Coscujuela; De Intinis, Carlo; Miano, Valentina; Calogero, Raffaele Adolfo; Cordero, Francesca; De Bortoli, Michele; Beccuti, Marco
Recent improvements in cost-effectiveness of high-throughput technologies has allowed RNA sequencing of total transcriptomes suitable for evaluating the expression and regulation of circRNAs, a relatively novel class of transcript isoforms with suggested roles in transcriptional and post-transcriptional gene expression regulation, as well as their possible use as biomarkers, due to their deregulation in various human diseases. A limited number of integrated workflows exists for prediction, characterization, […]
Wang, Shaorui; Romanak, Kevin A.; Tarallo, Sonia; Francavilla, Antonio; Viviani, Marco; Vineis, Paolo; Rothwell, Joseph A.; Mancini, Francesca Romana; Cordero, Francesca; Naccarati, Alessio; Severi, Gianluca; Venier, Marta
In this exploratory study, we measured for the first-time human exposure to about 90 semi-volatile organic chemicals (SVOCs) in France and Italy using silicone wristbands. Participants in France (n = 40) and in Italy (n = 31) wore a silicone wristband for five days during 2018 and 2019. Samples were analyzed for 39 polybrominated diphenyl ethers (PBDEs), 10 novel brominated flame retardants (nBFRs), 25 organophosphate esters (OPEs), and 18 polycyclic aromatic hydrocarbons (PAHs). In both groups, […]
Journal for ImmunoTherapy of Cancer
Mandili, Giorgia; Curcio, Claudia; Bulfamante, Sara; Follia, Laura; Ferrero, Giulio; Mazza, Emanuela; Principe, Moitza; Cordero, Francesca; Satolli, Maria Antonietta; Spadi, Rosella; Evangelista, Andrea; Giordano, Daniele; Viet, Duy; Cappello, Paola; Novelli, Francesco
Background Pancreatic ductal adenocarcinoma (PDA) is an almost incurable tumor that is mostly resistant to chemotherapy (CT). Adaptive immune responses to tumor-associated antigens (TAA) have been reported, but immunotherapy (IT) clinical trials have not yet achieved any significant increase in survival, confirming the suppressive environment of PDA. As CT has immune-modulating properties, we investigated the effect of gemcitabine (GEM) in antitumor effector responses to TAA in patients with PDA. […]
International Journal of Molecular Sciences
Godel, Martina; Morena, Deborah; Ananthanarayanan, Preeta; Buondonno, Ilaria; Ferrero, Giulio; Hattinger, Claudia M.; Di Nicolantonio, Federica; Serra, Massimo; Taulli, Riccardo; Cordero, Francesca; Riganti, Chiara; Kopecka, Joanna
Doxorubicin (Dox) is one of the most important first-line drugs used in osteosarcoma therapy. Multiple and not fully clarified mechanisms, however, determine resistance to Dox. With the aim of identifying new markers associated with Dox-resistance, we found a global up-regulation of small nucleolar RNAs (snoRNAs) in human Dox-resistant osteosarcoma cells. We investigated if and how snoRNAs are linked to resistance. After RT-PCR validation of snoRNAs up-regulated in osteosarcoma cells with different […]
Mandili, Giorgia; Follia, Laura; Ferrero, Giulio; Katayama, Hiroyuki; Hong, Wang; Momin, Amin A.; Capello, Michela; Giordano, Daniele; Spadi, Rosella; Satolli, Maria Antonietta; Evangelista, Andrea; Hanash, Samir M.; Cordero, Francesca; Novelli, Francesco
Pancreatic Ductal Adenocarcinoma (PDA) is an aggressive malignancy with a very poor outcome. Although chemotherapy (CT) treatment has poor efficacy, it can enhance tumor immunogenicity. Tumor-Associated Antigens (TAA) are self-proteins that are overexpressed in tumors that may induce antibody production and can be PDA theranostic targets. However, the prognostic value of TAA-antibody association as Circulating Immune Complexes (CIC) has not yet been elucidated, mainly due to the lack of techniques […]
Tarallo, Sonia; Ferrero, Giulio; Gallo, Gaetano; Francavilla, Antonio; Clerico, Giuseppe; Luc, Alberto Realis; Manghi, Paolo; Thomas, Andrew Maltez; Vineis, Paolo; Segata, Nicola; Pardini, Barbara; Naccarati, Alessio; Cordero, Francesca
Page 2, third line from the bottom, the paragraph should read: “At the phylum level, the abundances of Proteobacteria and Verrucomicrobia in adenoma patients were significantly different from those seen in the healthy group. In particular, Verrucomicrobia showed the lowest abundance, whereas Proteobacteria showed intermediate abundance in the adenoma group (see Table S1A). Proteobacteria was the most significantly abundant phylum in the carcinoma group compared with both the healthy and adenoma groups, […]
Fortuna, Mariachiara; Vitalini, Francesca; Signorelli, Mirko; Furfaro, Emanuela; Marini, Federico; Janssenswillen, Gert; Porreca, Riccardo; Rossi, Riccardo L.; Guzzo, Andrea; Sirovich, Roberta; Melloncelli, Andrea; Salvi, Lorenzo; Signorelli, Serena; Chiarello, Filippo
The European R Users Meeting 2020 (e-Rum2020) was a conference that was held virtually in June 2020. Originally, e-Rum2020 had been planned as a physical event to be held in Milano. However, the spread of the COVID-19 pandemic and the declaration of a nationwide lockdown induced the Organizing Committee to fully rethink the event, and to turn it into a live virtual conference. In this article, we describe the challenges that we encountered during the organization of e-Rum2020, and how we reacted […]
Neppi-Mòdona, Marco; Sirovich, Roberta; Cicerale, Alessandro; Richard, Nathalie; Pradat-Diehl, Pascale; Sirigu, Angela; Duhamel, Jean René
Spatial attention is guided by the perceived salience and relevance of objects in the environment, a process considered to depend on a broad parieto-frontal cortical network. Signals arising from the limbic and nigrostriatal pathways conveying affective and motivational cues are also known to modulate visual selection, but the nature of this contribution and its relation to spatial attention remain unclear. We investigated the role of reward information in 15 patients with left hemispatial neglect […]
BMC Bioinformatics
Pernice, Simone; Follia, Laura; Maglione, Alessandro; Pennisi, Marzio; Pappalardo, Francesco; Novelli, Francesco; Clerico, Marinella; Beccuti, Marco; Cordero, Francesca; Rolla, Simona
Background: Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS etiology remains partially unknown. Furthermore, the presence of various endogenous and exogenous factors can greatly influence the immune response of different individuals, making it difficult to study and understand the disease. This becomes more evident in a personalized-fashion […]
BMC Infectious Diseases
Pernice, Simone; Castagno, Paolo; Marcotulli, Linda; Maule, Milena Maria; Richiardi, Lorenzo; Moirano, Giovenale; Sereno, Matteo; Cordero, Francesca; Beccuti, Marco
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), the causative agent of the coronavirus disease 19 (COVID-19), is a highly transmittable virus. Since the first person-to-person transmission of SARS-CoV-2 was reported in Italy on February 21st, 2020, the number of people infected with SARS-COV-2 increased rapidly, mainly in northern Italian regions, including Piedmont. A strict lockdown was imposed on March 21st until May 4th when a gradual relaxation of the restrictions started. […]
BMC Bioinformatics
Castagno, Paolo; Pernice, Simone; Ghetti, Gianni; Povero, Massimiliano; Pradelli, Lorenzo; Paolotti, Daniela; Balbo, Gianfranco; Sereno, Matteo; Beccuti, Marco
Background: Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemiologists can exploit to better understand the spreading characteristics of these diseases and to decide on vaccination policies, human interaction controls, and other social measures […]
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pernice, Simone; Beccuti, Marco; Romano, Greta; Pennisi, Marzio; Maglione, Alessandro; Cutrupi, Santina; Pappalardo, Francesco; Capra, Lorenzo; Franceschinis, Giuliana; De Pierro, Massimiliano; Balbo, Gianfranco; Cordero, Francesca; Calogero, Raffaele
Multiple Sclerosis (MS) is a chronic and potentially highly disabling disease that can cause permanent damage and deterioration of the central nervous system. In Europe it is the leading cause of non-traumatic disabilities in young adults, since more than 700,000 EU people suffer from MS. Although recent studies on MS pathophysiology have been performed, providing interesting results, MS remains a challenging disease. In this context, thanks to recent advances in software and hardware technologies, […]
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Totis, Niccolò; Tangherloni, Andrea; Beccuti, Marco; Cazzaniga, Paolo; Nobile, Marco S.; Besozzi, Daniela; Pennisi, Marzio; Pappalardo, Francesco
Mathematical modeling and computational analyses are essential tools to understand and gain novel insights on the functioning of complex biochemical systems. In the specific case of metabolic reaction networks, which are regulated by many other intracellular processes, various challenging problems hinder the definition of compact and fully calibrated mathematical models, as well as the execution of computationally efficient analyses of their emergent dynamics. These problems especially occur when […]
International Journal of Molecular Sciences
Ferrero, Giulio; Licheri, Nicola; Tarrero, Lucia Coscujuela; De Intinis, Carlo; Miano, Valentina; Calogero, Raffaele Adolfo; Cordero, Francesca; De Bortoli, Michele; Beccuti, Marco
Recent improvements in cost-effectiveness of high-throughput technologies has allowed RNA sequencing of total transcriptomes suitable for evaluating the expression and regulation of circRNAs, a relatively novel class of transcript isoforms with suggested roles in transcriptional and post-transcriptional gene expression regulation, as well as their possible use as biomarkers, due to their deregulation in various human diseases. A limited number of integrated workflows exists for prediction, characterization, […]
Environmental Pollution
Wang, Shaorui; Romanak, Kevin A.; Tarallo, Sonia; Francavilla, Antonio; Viviani, Marco; Vineis, Paolo; Rothwell, Joseph A.; Mancini, Francesca Romana; Cordero, Francesca; Naccarati, Alessio; Severi, Gianluca; Venier, Marta
In this exploratory study, we measured for the first-time human exposure to about 90 semi-volatile organic chemicals (SVOCs) in France and Italy using silicone wristbands. Participants in France (n = 40) and in Italy (n = 31) wore a silicone wristband for five days during 2018 and 2019. Samples were analyzed for 39 polybrominated diphenyl ethers (PBDEs), 10 novel brominated flame retardants (nBFRs), 25 organophosphate esters (OPEs), and 18 polycyclic aromatic hydrocarbons (PAHs). In both groups, […]
Journal for ImmunoTherapy of Cancer
Mandili, Giorgia; Curcio, Claudia; Bulfamante, Sara; Follia, Laura; Ferrero, Giulio; Mazza, Emanuela; Principe, Moitza; Cordero, Francesca; Satolli, Maria Antonietta; Spadi, Rosella; Evangelista, Andrea; Giordano, Daniele; Viet, Duy; Cappello, Paola; Novelli, Francesco
Background Pancreatic ductal adenocarcinoma (PDA) is an almost incurable tumor that is mostly resistant to chemotherapy (CT). Adaptive immune responses to tumor-associated antigens (TAA) have been reported, but immunotherapy (IT) clinical trials have not yet achieved any significant increase in survival, confirming the suppressive environment of PDA. As CT has immune-modulating properties, we investigated the effect of gemcitabine (GEM) in antitumor effector responses to TAA in patients with PDA. […]
International Journal of Molecular Sciences
Godel, Martina; Morena, Deborah; Ananthanarayanan, Preeta; Buondonno, Ilaria; Ferrero, Giulio; Hattinger, Claudia M.; Di Nicolantonio, Federica; Serra, Massimo; Taulli, Riccardo; Cordero, Francesca; Riganti, Chiara; Kopecka, Joanna
Doxorubicin (Dox) is one of the most important first-line drugs used in osteosarcoma therapy. Multiple and not fully clarified mechanisms, however, determine resistance to Dox. With the aim of identifying new markers associated with Dox-resistance, we found a global up-regulation of small nucleolar RNAs (snoRNAs) in human Dox-resistant osteosarcoma cells. We investigated if and how snoRNAs are linked to resistance. After RT-PCR validation of snoRNAs up-regulated in osteosarcoma cells with different […]
Cancers
Mandili, Giorgia; Follia, Laura; Ferrero, Giulio; Katayama, Hiroyuki; Hong, Wang; Momin, Amin A.; Capello, Michela; Giordano, Daniele; Spadi, Rosella; Satolli, Maria Antonietta; Evangelista, Andrea; Hanash, Samir M.; Cordero, Francesca; Novelli, Francesco
Pancreatic Ductal Adenocarcinoma (PDA) is an aggressive malignancy with a very poor outcome. Although chemotherapy (CT) treatment has poor efficacy, it can enhance tumor immunogenicity. Tumor-Associated Antigens (TAA) are self-proteins that are overexpressed in tumors that may induce antibody production and can be PDA theranostic targets. However, the prognostic value of TAA-antibody association as Circulating Immune Complexes (CIC) has not yet been elucidated, mainly due to the lack of techniques […]
mSystems
Tarallo, Sonia; Ferrero, Giulio; Gallo, Gaetano; Francavilla, Antonio; Clerico, Giuseppe; Luc, Alberto Realis; Manghi, Paolo; Thomas, Andrew Maltez; Vineis, Paolo; Segata, Nicola; Pardini, Barbara; Naccarati, Alessio; Cordero, Francesca
Page 2, third line from the bottom, the paragraph should read: “At the phylum level, the abundances of Proteobacteria and Verrucomicrobia in adenoma patients were significantly different from those seen in the healthy group. In particular, Verrucomicrobia showed the lowest abundance, whereas Proteobacteria showed intermediate abundance in the adenoma group (see Table S1A). Proteobacteria was the most significantly abundant phylum in the carcinoma group compared with both the healthy and adenoma groups, […]
R Journal
Fortuna, Mariachiara; Vitalini, Francesca; Signorelli, Mirko; Furfaro, Emanuela; Marini, Federico; Janssenswillen, Gert; Porreca, Riccardo; Rossi, Riccardo L.; Guzzo, Andrea; Sirovich, Roberta; Melloncelli, Andrea; Salvi, Lorenzo; Signorelli, Serena; Chiarello, Filippo
The European R Users Meeting 2020 (e-Rum2020) was a conference that was held virtually in June 2020. Originally, e-Rum2020 had been planned as a physical event to be held in Milano. However, the spread of the COVID-19 pandemic and the declaration of a nationwide lockdown induced the Organizing Committee to fully rethink the event, and to turn it into a live virtual conference. In this article, we describe the challenges that we encountered during the organization of e-Rum2020, and how we reacted […]
Cortex
Neppi-Mòdona, Marco; Sirovich, Roberta; Cicerale, Alessandro; Richard, Nathalie; Pradat-Diehl, Pascale; Sirigu, Angela; Duhamel, Jean René
Spatial attention is guided by the perceived salience and relevance of objects in the environment, a process considered to depend on a broad parieto-frontal cortical network. Signals arising from the limbic and nigrostriatal pathways conveying affective and motivational cues are also known to modulate visual selection, but the nature of this contribution and its relation to spatial attention remain unclear. We investigated the role of reward information in 15 patients with left hemispatial neglect […]