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1. May 2020: Is It Always COVID-19 No Matter What?

Author

Livrieri F, Ghidoni G, Piro R, Menzella F, Cavazza A, Lazzaretti C, Massari M, Montanari G, Fontana M, and Facciolongo NC

Subjects
covid-19, acute eosinophilic pneumonia, bronchoalveolar lavage, ground glass opacities, Medicine (General), R5-920
Abstract

Francesco Livrieri,1 Giulia Ghidoni,1 Roberto Piro,1 Francesco Menzella,1 Alberto Cavazza,2 Claudia Lazzaretti,3 Marco Massari,3 Gloria Montanari,1 Matteo Fontana,1 Nicola Cosimo Facciolongo1 1Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia- IRCCS, Reggio Emilia 42123, Italy; 2Pathology Unit, Azienda USL/IRCCS di Reggio Emilia, Reggio Emilia 42100, Italy; 3Infectious Diseases, Azienda Unità Sanitaria Locale, IRCCS di Reggio Emilia, Reggio Emilia, ItalyCorrespondence: Francesco LivrieriDepartment of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia- IRCCS, Reggio Emilia 42123, ItalyEmail francesco.livrieri@ausl.re.itAbstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a massive outbreak throughout the world. In this period, diseases other than coronavirus disease (COVID-19) have not disappeared; however, it is hard for doctors to diagnose diseases that can mimic the clinical, radiological, and laboratory features of COVID-19, especially rare lung diseases such as acute eosinophilic pneumonia (AEP). We report the clinical case of a young patient who presented to the Emergency Department with respiratory failure and clinical symptoms, radiological aspects, and blood tests compatible with COVID-19; two swabs and a serology test for SARS-CoV-2 were performed, both resulted negative, but the respiratory failure worsened. Peripheral eosinophilia guided us to consider the possibility of a rare disease such as AEP, even if radiology findings were not pathognomonic. Therefore, we decided to perform a flexible bronchoscopy with bronchoalveolar lavage (BAL) at the lingula, which showed the presence of eosinophilia greater than 40%. As a consequence, we treated the patient with high-dose corticosteroids that completely resolved the respiratory symptoms. This case report highlights the difficulty of making alternative diagnoses during the COVID-19 pandemic, especially for rare lung diseases such as AEP, which may have initial characteristics similar to COVID-19.Keywords: COVID-19, acute eosinophilic pneumonia, bronchoalveolar lavage, ground glass opacities

Published
2020

2. A Dangerous Consequence of the Recent Pandemic: Early Lung Fibrosis Following COVID-19 Pneumonia – Case Reports

Author

Scelfo C, Fontana M, Casalini E, Menzella F, Piro R, Zerbini A, Spaggiari L, Ghidorsi L, Ghidoni G, and Facciolongo NC

Subjects
covid-19, pulmonary fibrosis, critical care, viral disease, computed tomography, follow-up, Therapeutics. Pharmacology, RM1-950
Abstract

Chiara Scelfo,1 Matteo Fontana,1 Eleonora Casalini,1 Francesco Menzella,1 Roberto Piro,1 Alessandro Zerbini,2 Lucia Spaggiari,3 Luca Ghidorsi,1 Giulia Ghidoni,1 Nicola C Facciolongo1 1Department of Medical Specialties, Pneumology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy; 2Unit of Clinical Immunology, Allergy and Advanced Biotechnologies, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy; 3Department of Radiology, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, ItalyCorrespondence: Chiara Scelfo Email chiara.scelfo@ausl.re.itAbstract: The outbreak of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) started in China in December 2019. COVID-19 patients at presentation show a wide spectrum of clinical and pathological involvement. We report two cases of respiratory insufficiency due to COVID-19 pneumonia that occurred in adults without a history of respiratory diseases. Although these patients improved and were discharged from the acute ward, during the hospitalization they both progressed with a subsequent clinical and radiological worsening, pointing out one of the main concerns for these patients at discharge: the possibility of developing persistent lung abnormalities also in healthy people not having other risk factors. In conclusion, these cases represent two examples of early lung fibrosis in patients with COVID-19 pneumonia with different severity disease evolution and highlight the need for long-term follow-up strategies. The etiology of this fibrosis is under discussion: we suppose that it could be due to either a possible outcome of natural history of lung damage produced by ARDS, or to the lung injury related to high oxygen level or to the lung damage directly induced by viral infection or finally to the autoimmune response. At this moment, it is not possible to predict how many people will have consequences due to COVID-19 pneumonia, and therefore we believe that careful follow-up should be mandatory.Keywords: COVID-19, pulmonary fibrosis, critical care, viral disease, computed tomography, follow-up

Published
2020

7. The DataGrid Workload Management System: Challenges and Results

Author

Avellino, G., Beco, S., Cantalupo, B., Maraschini, A., Pacini, F., Sottilaro, M., Terracina, A., Colling, D., Giacomini, F., Ronchieri, E., Gianelle, A., Mazzucato, M., Peluso, R., Sgaravatto, M., Guarise, A., Piro, R., Werbrouck, A., Kouřil, D., Křenek, A., Matyska, L., Mulač, M., Pospíšil, J., Ruda, M., Salvet, Z., Sitera, J., Škrabal, J., Voců, M., Mezzadri, M., Prelz, F., Monforte, S., and Pappalardo, M.

Published
2004
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9. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Author

Mack, S. C., Witt, H., Piro, R. M., Gu, L., Zuyderduyn, S., Stütz, A. M., Wang, X., Gallo, M., Garzia, L., Zayne, K., Zhang, X., Ramaswamy, V., Jäger, N., Jones, D. T. W., Sill, M., Pugh, T. J., Ryzhova, M., Wani, K. M., Shih, D. J. H., Head, R., Remke, M., Bailey, S. D., Zichner, T., Faria, C. C., Barszczyk, M., Stark, S., Seker-Cin, H., Hutter, S., Johann, P., Bender, S., Hovestadt, V., Tzaridis, T., Dubuc, A. M., Northcott, P. A., Peacock, J., Bertrand, K. C., Agnihotri, S., Cavalli, F. M. G., Clarke, I., Nethery-Brokx, K., Creasy, C. L., Verma, S. K., Koster, J., Wu, X., Yao, Y., Milde, T., Sin-Chan, P., Zuccaro, J., Lau, L., Pereira, S., Castelo-Branco, P., Hirst, M., Marra, M. A., Roberts, S. S., Fults, D., Massimi, L., Cho, Y. J., Van Meter, T., Grajkowska, W., Lach, B., Kulozik, A. E., von Deimling, A., Witt, O., Scherer, S. W., Fan, X., Muraszko, K. M., Kool, M., Pomeroy, S. L., Gupta, N., Phillips, J., Huang, A., Tabori, U., Hawkins, C., Malkin, D., Kongkham, P. N., Weiss, W. A., Jabado, N., Rutka, J. T., Bouffet, E., Korbel, J. O., Lupien, M., Aldape, K. D., Bader, G. D., Eils, R., Lichter, P., Dirks, P. B., Pfister, S. M., Korshunov, A., and Taylor, M. D.

Published
2014
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12. Maintenance of datalog materialisations revisited

Author

Motik, B, Nenov, Y, Piro, R, and Horrocks, I

Abstract

Datalog is a rule-based formalism that can axiomatise recursive properties such as reachability and transitive closure. Datalog implementations often materialise (i.e., precompute and store) all facts entailed by a datalog program and a set of explicit facts. Queries can thus be answered directly in the materialised facts, which is beneficial to the performance of query answering, but the materialised facts must be updated whenever the explicit facts change. Rematerialising all facts ‘from scratch’ can be very inefficient, so numerous materialisation maintenance algorithms have been developed that aim to efficiently identify the facts that require updating and thus reduce the overall work. Most such approaches are variants of the counting or Delete/Rederive (DRed) algorithms. Algorithms in the former group maintain additional data structures and are usually applicable only if datalog rules are not recursive, which limits their applicability in practice. Algorithms in the latter group do not require additional data structures and can handle recursive rules, but they can be inefficient when facts have multiple derivations. Finally, to the best of our knowledge, these approaches have not been compared and their practical applicability has not been investigated. Datalog is becoming increasingly important in practice, so a more comprehensive understanding of the tradeoffs between different approaches to materialisation maintenance is needed. In this paper we present three such algorithms for datalog with stratified negation: a new counting algorithm that can handle recursive rules, an optimised variant of the DRed algorithm that does not repeat derivations, and a new Forward/Backward/Forward (FBF) algorithm that extends DRed to better handle facts with multiple derivations. Furthermore, we study the worst-case performance of these algorithms and compare the algorithms' behaviour on several examples. Finally, we present the results of an extensive, first-of-a-kind empirical evaluation in which we investigate the robustness and the scaling behaviour of our algorithms. We thus provide important theoretical and practical insights into all three algorithms that will provide invaluable guidance to future implementors of datalog systems.

Published
2019

13. Macrolide therapy is associated with lower mortality in community-acquired bacteraemic pneumonia

Author

Arnold, FW, Lopardo, G, Wiemken, TL, Kelley, R, Peyrani, P, Mattingly, WA, Feldman, C, Gnoni, M, Maurici, R, Ramirez, JA, Arnold, F, Ramirez, J, Ayesu, K, File, T, Burdette, S, Blatt, S, Restrepo, M, Bordon, J, Gross, P, Musher, D, Marrie, T, Weiss, K, Roig, J, Lode, H, Welte, T, Aliberti, S, Blasi, F, Cosentini, R, Legnani, D, Franzetti, F, Montano, N, Cervi, G, Rossi, P, Voza, A, Ostrowsky, B, Pesci, A, Nava, S, Vialea, P, Galavatti, V, Patricia, A, Dimas, C, Piro, R, Viscoli, C, Torres, A, Valenti, V, Ojales, DP, Bodi, M, Porras, J, Rello, J, Menendez, R, Stolz, D, Schuetz, P, Haubitz, S, Chalmers, J, Fardon, T, Benchetrit, G, Rodriguez, E, Corral, J, Gonzalez, J, de Vedia, L, Luna, C, Martinez, J, Marzoratti, L, Rodriguez, M, Videla, A, Saavedra, F, Lopez, H, Victorio, C, Riera, F, Jimenez, P, Fernandez, P, Parada, M, Fuenzalida, AD, Riquelme, R, Barros, M, Luna, JM, Toala, I, de Morvil, GAO, Fernandez, R, Aiello, G, Alvarez, P, Soca, A, Arteta, F, Delgado, J, Levy, G, Rivero, L, Rodriguez, B, Mirabal, MP, Mateo, M, Mendoza, M, and CAPO

Subjects
Community-acquired pneumonia, Antimicrobial treatment, Bacteremia, Mortality
Abstract

Background: Community-acquired pneumonia (CAP) has a potential complication of bacteremia. The objective of this study was to define the clinical outcomes of patients with CAP and bacteremia treated with and without a macrolide. Materials and methods: Secondary analysis of the Community-Acquired Pneumonia Organization database of hospitalized patients with CAP. Patients with a positive blood culture were categorized based on the presence or absence of a macrolide in their initial antimicrobial regimen, and severity of their CAP. Outcomes included inhospital all-cause mortality, 30-day mortality, length of stay, and time to clinical stability. Results: Among 549 patients with CAP and bacteremia, 247 (45%) were treated with a macrolide and 302 (55%) were not. The primary pathogen was Streptococcus pneumoniae (74%). Poisson regression with robust error variance models were used to compare the adjusted effects of each study group on the outcomes. The unadjusted 30-day mortality was 18.4% in the macrolide group, and 29.6% in the non-macrolide group (adjusted relative risk (aRR)0.81; 95% confidence interval (CI)0.50-1.33; P = 0.41). Unadjusted in-hospital all-cause mortality was 7.3% in the macrolide group, and 18.9% in the non-macrolide group (aRR 0.54, 95% CI 0.30-0.98; P = 0.043). Length of stay and time to clinical stability were not significantly different. Conclusions: In-hospital mortality, but not 30-day mortality, was significantly better in the macrolide group. Our data support the use of a macrolide in hospitalized patients with CAP and bacteraemia.

Published
2018

14. Macrolide therapy is associated with lower mortality in community-acquired bacteraemic pneumonia

Author

Arnold, F, Lopardo, G, Wiemken, T, Kelley, R, Peyrani, P, Mattingly, W, Feldman, C, Gnoni, M, Maurici, R, Ramirez, J, Ayesu, K, File, T, Burdette, S, Blatt, S, Restrepo, M, Bordon, J, Gross, P, Musher, D, Marrie, T, Weiss, K, Roig, J, Lode, H, Welte, T, Aliberti, S, Blasi, F, Cosentini, R, Legnani, D, Franzetti, F, Montano, N, Cervi, G, Rossi, P, Voza, A, Ostrowsky, B, Pesci, A, Nava, S, Viale, P, Galavatti, V, Patricia, A, Dimas, C, Piro, R, Viscoli, C, Torres, A, Valenti, V, Ojales, D, Bodi, M, Porras, J, Rello, J, Menendez, R, Stolz, D, Schuetz, P, Haubitz, S, Chalmers, J, Fardon, T, Benchetrit, G, Rodriguez, E, Corral, J, Gonzalez, J, de Vedia, L, Luna, C, Martinez, J, Marzoratti, L, Rodriguez, M, Videla, A, Saavedra, F, Lopez, H, Victorio, C, Riera, F, Jimenez, P, Fernandez, P, Parada, M, Fuenzalida, A, Riquelme, R, Barros, M, Luna, J, Toala, I, Oze de Morvil, G, Fernandez, R, Aiello, G, Alvarez, P, Soca, A, Arteta, F, Delgado, J, Levy, G, Rivero, L, Rodriguez, B, Mirabal, M, Mateo, M, Mendoza, M, Arnold, Forest W., Lopardo, Gustavo, Wiemken, Timothy L., Kelley, Robert, Peyrani, Paula, Mattingly, William A., Feldman, Charles, Gnoni, Martin, Maurici, Rosemeri, Ramirez, Julio A., Arnold, Forest, Ramirez, Julio, Ayesu, Kwabena, File, Thomas, Burdette, Steven, Blatt, Stephen, Restrepo, Marcos, Bordon, Jose, Gross, Peter, Musher, Daniel, Marrie, Thomas, Weiss, Karl, Roig, Jorge, Lode, Harmut, Welte, Tobias, Aliberti, Stephano, Blasi, Francesco, Cosentini, Roberto, Legnani, Delfino, Franzetti, Fabio, Montano, Nicola, Cervi, Giulia, Rossi, Paolo, Voza, Antonio, Ostrowsky, Belinda, Pesci, Alberto, Nava, Stefano, Viale, Pierluigi, Galavatti, Vanni, Patricia, Aruj, Dimas, Carlos, Piro, Roberto, Viscoli, Claudio, Torres, Antoni, Valenti, Vincenzo, Ojales, Daniel Portela, Bodi, Maria, Porras, Jose, Rello, Jordi, Menendez, Rosario, Stolz, Daiana, Schuetz, Philipp, Haubitz, Sebastian, Chalmers, James, Fardon, Tom, Benchetrit, Guillermo, Rodriguez, Eduardo, Corral, Jorge, Gonzalez, Jose, de Vedia, Lautaro, Luna, Carlos, Martinez, Jorge, Marzoratti, Lucia, Rodriguez, Maria, Videla, Alejandro, Saavedra, Federico, Lopez, Horacio, Victorio, Carlos, Riera, Fernando, Jimenez, Patricio, Fernandez, Patricia, Parada, Maria, Fuenzalida, Alejandro Díaz, Riquelme, Raul, Barros, Manuel, Luna, Juan Manuel, Toala, Ivan, Oze de Morvil, Guillermo Arbo, Fernandez, Ricardo, Aiello, Gonzalo, Alvarez, Pablo, Soca, Ana, Arteta, Federico, Delgado, Jose, Levy, Gur, Rivero, Ludwig, Rodriguez, Benito, Mirabal, Mario Perez, Mateo, Marilyn, Mendoza, Myrna, Arnold, F, Lopardo, G, Wiemken, T, Kelley, R, Peyrani, P, Mattingly, W, Feldman, C, Gnoni, M, Maurici, R, Ramirez, J, Ayesu, K, File, T, Burdette, S, Blatt, S, Restrepo, M, Bordon, J, Gross, P, Musher, D, Marrie, T, Weiss, K, Roig, J, Lode, H, Welte, T, Aliberti, S, Blasi, F, Cosentini, R, Legnani, D, Franzetti, F, Montano, N, Cervi, G, Rossi, P, Voza, A, Ostrowsky, B, Pesci, A, Nava, S, Viale, P, Galavatti, V, Patricia, A, Dimas, C, Piro, R, Viscoli, C, Torres, A, Valenti, V, Ojales, D, Bodi, M, Porras, J, Rello, J, Menendez, R, Stolz, D, Schuetz, P, Haubitz, S, Chalmers, J, Fardon, T, Benchetrit, G, Rodriguez, E, Corral, J, Gonzalez, J, de Vedia, L, Luna, C, Martinez, J, Marzoratti, L, Rodriguez, M, Videla, A, Saavedra, F, Lopez, H, Victorio, C, Riera, F, Jimenez, P, Fernandez, P, Parada, M, Fuenzalida, A, Riquelme, R, Barros, M, Luna, J, Toala, I, Oze de Morvil, G, Fernandez, R, Aiello, G, Alvarez, P, Soca, A, Arteta, F, Delgado, J, Levy, G, Rivero, L, Rodriguez, B, Mirabal, M, Mateo, M, Mendoza, M, Arnold, Forest W., Lopardo, Gustavo, Wiemken, Timothy L., Kelley, Robert, Peyrani, Paula, Mattingly, William A., Feldman, Charles, Gnoni, Martin, Maurici, Rosemeri, Ramirez, Julio A., Arnold, Forest, Ramirez, Julio, Ayesu, Kwabena, File, Thomas, Burdette, Steven, Blatt, Stephen, Restrepo, Marcos, Bordon, Jose, Gross, Peter, Musher, Daniel, Marrie, Thomas, Weiss, Karl, Roig, Jorge, Lode, Harmut, Welte, Tobias, Aliberti, Stephano, Blasi, Francesco, Cosentini, Roberto, Legnani, Delfino, Franzetti, Fabio, Montano, Nicola, Cervi, Giulia, Rossi, Paolo, Voza, Antonio, Ostrowsky, Belinda, Pesci, Alberto, Nava, Stefano, Viale, Pierluigi, Galavatti, Vanni, Patricia, Aruj, Dimas, Carlos, Piro, Roberto, Viscoli, Claudio, Torres, Antoni, Valenti, Vincenzo, Ojales, Daniel Portela, Bodi, Maria, Porras, Jose, Rello, Jordi, Menendez, Rosario, Stolz, Daiana, Schuetz, Philipp, Haubitz, Sebastian, Chalmers, James, Fardon, Tom, Benchetrit, Guillermo, Rodriguez, Eduardo, Corral, Jorge, Gonzalez, Jose, de Vedia, Lautaro, Luna, Carlos, Martinez, Jorge, Marzoratti, Lucia, Rodriguez, Maria, Videla, Alejandro, Saavedra, Federico, Lopez, Horacio, Victorio, Carlos, Riera, Fernando, Jimenez, Patricio, Fernandez, Patricia, Parada, Maria, Fuenzalida, Alejandro Díaz, Riquelme, Raul, Barros, Manuel, Luna, Juan Manuel, Toala, Ivan, Oze de Morvil, Guillermo Arbo, Fernandez, Ricardo, Aiello, Gonzalo, Alvarez, Pablo, Soca, Ana, Arteta, Federico, Delgado, Jose, Levy, Gur, Rivero, Ludwig, Rodriguez, Benito, Mirabal, Mario Perez, Mateo, Marilyn, and Mendoza, Myrna

Abstract

Background: Community-acquired pneumonia (CAP) has a potential complication of bacteremia. The objective of this study was to define the clinical outcomes of patients with CAP and bacteremia treated with and without a macrolide. Materials and methods: Secondary analysis of the Community-Acquired Pneumonia Organization database of hospitalized patients with CAP. Patients with a positive blood culture were categorized based on the presence or absence of a macrolide in their initial antimicrobial regimen, and severity of their CAP. Outcomes included in-hospital all-cause mortality, 30-day mortality, length of stay, and time to clinical stability. Results: Among 549 patients with CAP and bacteremia, 247 (45%) were treated with a macrolide and 302 (55%) were not. The primary pathogen was Streptococcus pneumoniae (74%). Poisson regression with robust error variance models were used to compare the adjusted effects of each study group on the outcomes. The unadjusted 30-day mortality was 18.4% in the macrolide group, and 29.6% in the non-macrolide group (adjusted relative risk (aRR)0.81; 95% confidence interval (CI)0.50–1.33; P = 0.41). Unadjusted in-hospital all-cause mortality was 7.3% in the macrolide group, and 18.9% in the non-macrolide group (aRR 0.54, 95% CI 0.30–0.98; P = 0.043). Length of stay and time to clinical stability were not significantly different. Conclusions: In-hospital mortality, but not 30-day mortality, was significantly better in the macrolide group. Our data support the use of a macrolide in hospitalized patients with CAP and bacteraemia

Published
2018

15. Dalla letteratura all'arte contemporanea: pensieri di un inesperto sui «Promessi sposi cancellati per venticinque lettori e dieci appestati» di Emilio Isgrò

Author

Giordano, A., Piro, R., Colombo, Michele, Michele Colombo (ORCID:0000-0002-4440-7334), Giordano, A., Piro, R., Colombo, Michele, and Michele Colombo (ORCID:0000-0002-4440-7334)

Abstract

The Promessi sposi cancellati per venticinque lettori e dieci appestati, made by conceptual artist Emilio Isgrò and first exposed in 2016, is both an artwork in itself and a means to understand Alessandro Manzoni’s novel in a new and unconventional way. Isgrò’s erasures of 35 copies of the 1840 edition of I promessi sposi prove to be a way of make words, and the absence of words, telling something unexpected.

Published
2018

18. Handling owl:sameAs via rewriting

Author

Motik, B., Nenov, Y., Piro, R., Ian Horrocks, Bonet, B, and Koenig, S

Subjects
FOS: Computer and information sciences, Databases, Artificial Intelligence (cs.AI), Computer Science - Databases, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Artificial Intelligence, Artificial Intelligence, Computing, Databases (cs.DB), Distributed, Parallel, and Cluster Computing (cs.DC), General Medicine, Knowledge Representation and Reasoning
Abstract

Rewriting is widely used to optimise owl:sameAs reasoning in materialisation based OWL 2 RL systems. We investigate issues related to both the correctness and efficiency of rewriting, and present an algorithm that guarantees correctness, improves efficiency, and can be effectively parallelised. Our evaluation shows that our approach can reduce reasoning times on practical data sets by orders of magnitude., This is the technical report supporting the AAAI 2015 Conference submission with the same title

Published
2016

19. Parallel OWL 2 RL materialisation in centralised, main-memory RDF systems

Author

Motik, B., Nenov, Y., Piro, R., Ian Horrocks, and Olteanu, D.

Subjects
Computer Science, Description Logics
Abstract

We present a novel approach to parallel materialisation (i.e., fixpoint computation) of OWL RL Knowledge Bases in centralised, main-memory, multi-core RDF systems. Our approach comprises a datalog reasoning algorithm that evenly distributes the workload to cores, and an RDF indexing data structure that supports efficient, ‘mostly’ lock-free parallel updates. Our empirical evaluation shows that our approach parallelises computation very well so, with 16 physical cores, materialisation can be up to 13.9 times faster than with just one core.

Published
2016

20. Nerve ablation after bronchial thermoplasty and sustained improvement in severe asthma

Author

Facciolongo, N., primary, Di Stefano, A., additional, Pietrini, V., additional, Galeone, C., additional, Bellanova, F., additional, Menzella, F., additional, Scichilone, N., additional, Piro, R., additional, Bajocchi, G. L., additional, Balbi, B., additional, Agostini, L., additional, Salsi, P. P., additional, Formisano, D., additional, and Lusuardi, M., additional

Published
2018
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23. RDFox: a highly-scalable RDF store

Author

Nenov, Y, Piro, R, Motik, B, Horrocks, I, Wu, Z, Banerjee, J, Arenas, M, Corcho, Ó, Simperl, E, Strohmaier, M, d'Aquin, M, Srinivas, K, Groth, PT, Dumontier, M, Heflin, J, Thirunarayan, K, Staab, S, Arenas, M, Corcho, Ó, Simperl, E, Strohmaier, M, d'Aquin, M, Srinivas, K, Groth, P, Dumontier, M, Heflin, J, Thirunarayan, K, and Staab, S

Subjects
Theoretical computer science, Computer science, Search engine indexing, Scalability, Systems architecture, SPARQL, Byte, computer.file_format, RDF, Data structure, computer, Datalog, computer.programming_language
Abstract

We present RDFox—a main-memory, scalable, centralised RDF store that supports materialisation-based parallel datalog reasoning and SPARQL query answering. RDFox uses novel and highlyefficient parallel reasoning algorithms for the computation and incremental update of datalog materialisations with efficient handling of owl: sameAs. In this system description paper, we present an overview of the system architecture and highlight the main ideas behind our indexing data structures and our novel reasoning algorithms. In addition, we evaluate RDFox on a high-end SPARC T5-8 server with 128 physical cores and 4TB of RAM. Our results show that RDFox can effectively exploit such a machine, achieving speedups of up to 87 times, storage of up to 9.2 billion triples, memory usage as low as 36.9 bytes per triple, importation rates of up to 1 million triples per second, and reasoning rates of up to 6.1 million triples per second.

Published
2015

24. Determination of the palm oil addition in food.

Author

Rovellini, P., Berneri, R., Cotti Piccinelli, E., Piro, R., Miano, B., and Sangiorgi, E.

Subjects
PALM oil, VEGETABLE oils, LIPID analysis, SATURATED fatty acids, TOCOTRIENOL, TRIGLYCERIDES
Abstract

Palm oil (PO) is the most widely consumed vegetable oil on the planet. PO has a high percent of saturated fatty acids that are not favourable to the health. From December 2014, all food items sold in Europe must list palm oil in their ingredients if it is in the product. However, many food items are declared as PO free, and in the actual regulation there are no official methods to verify this statement. Therefore, there is a strong need to develop analytical methods for this purpose. In this work, screening methods with fast DART-MS analysis and confirmatory methods for the determination of PO in food were defined. DART-MS analysis with ion trap or high resolution mass spectrometry can be used as screening method, meanwhile the determination of both tocotrienols and triacylglycerols with HPLC can be used as confirmation method. PO addition was detectable up to 1%. [ABSTRACT FROM AUTHOR]

Published
2019

25. Individualizing duration of antibiotic therapy in community-acquired pneumonia

Author

Aliberti, S, Ramirez, J, Giuliani, F, Wiemken, T, Sotgiu, G, Tedeschi, S, Carugati, M, Valenti, V, Marchioni, M, Camera, M, Piro, R, Del Forno, M, Milani, G, Faverio, P, Richeldi, L, Deotto, M, Villani, M, Voza, A, Tobaldini, E, Bernardi, M, Bellone, A, Bassetti, M, Blasi, F, Aliberti, Stefano, Ramirez, Julio, Giuliani, Fabio, Wiemken, Timothy, Sotgiu, Giovanni, Tedeschi, Sara, Carugati, Manuela, Valenti, Vincenzo, Marchioni, Marco, Camera, Marco, Piro, Roberto, Del Forno, Manuela, Milani, Giuseppe, Faverio, Paola, Richeldi, Luca, Deotto, Martina, Villani, Massimiliano, Voza, Antonio, Tobaldini, Eleonora, Bernardi, Mauro, Bellone, Andrea, Bassetti, Matteo, Blasi, Francesco, Aliberti, S, Ramirez, J, Giuliani, F, Wiemken, T, Sotgiu, G, Tedeschi, S, Carugati, M, Valenti, V, Marchioni, M, Camera, M, Piro, R, Del Forno, M, Milani, G, Faverio, P, Richeldi, L, Deotto, M, Villani, M, Voza, A, Tobaldini, E, Bernardi, M, Bellone, A, Bassetti, M, Blasi, F, Aliberti, Stefano, Ramirez, Julio, Giuliani, Fabio, Wiemken, Timothy, Sotgiu, Giovanni, Tedeschi, Sara, Carugati, Manuela, Valenti, Vincenzo, Marchioni, Marco, Camera, Marco, Piro, Roberto, Del Forno, Manuela, Milani, Giuseppe, Faverio, Paola, Richeldi, Luca, Deotto, Martina, Villani, Massimiliano, Voza, Antonio, Tobaldini, Eleonora, Bernardi, Mauro, Bellone, Andrea, Bassetti, Matteo, and Blasi, Francesco

Abstract

International experts suggest tailoring antibiotic duration in community-acquired pneumonia (CAP) according to patients' characteristics. We aimed to assess the effectiveness of an individualized approach to antibiotic duration based on time in which CAP patients reach clinical stability during hospitalization. In a multicenter, non-inferiority, randomized, controlled trial hospitalized adult patients with CAP reaching clinical stability within 5 days after hospitalization were randomized to a standard vs. individualized antibiotic duration. In the Individualized group, antibiotics were discontinued 48 h after the patient reached clinical stability, with at least five days of total antibiotic treatment. Early failure within 30 days was the primary composite outcome. 135 patients were randomized to the Standard group and 125 to the Individualized group. The trial was interrupted by the safety committee because of an apparent inferiority of the Individualized group over the Standard treatment: 14 (11.2%) patients in the Individualized group experienced early failure vs. 10 (7.4%) patients in the Standard group, p = 0.200, at the intention-to-treat analysis. 30-day mortality rate was four-time higher in the Individualized group than the Standard group. Shortening antibiotic duration according to patients' characteristics still remains an open question.

Published
2017

26. Prior tuberculin skin test does not induce a false positive result of T-cell interferon-gamma release assays

Author

Losi, M, Ferrara, G, Luppi, F, Piro, R, Cerri, S, Tallarico, S, Andreani, A, D’Amico, R, Roversi, P, Meacci, M, Meccugni, B, Marchetti Dori, I, Caracciolo, R, Fabbri, L, Richeldi, L, Losi M, Ferrara G, Luppi F, Piro R, Cerri S, Tallarico S, Andreani A, D’Amico R, Roversi P, Meacci M, Meccugni B, Marchetti Dori I, Caracciolo R, Fabbri LM, Richeldi L, Losi, M, Ferrara, G, Luppi, F, Piro, R, Cerri, S, Tallarico, S, Andreani, A, D’Amico, R, Roversi, P, Meacci, M, Meccugni, B, Marchetti Dori, I, Caracciolo, R, Fabbri, L, Richeldi, L, Losi M, Ferrara G, Luppi F, Piro R, Cerri S, Tallarico S, Andreani A, D’Amico R, Roversi P, Meacci M, Meccugni B, Marchetti Dori I, Caracciolo R, Fabbri LM, and Richeldi L

Published
2008

27. Indagini su un episodio di elevata mortalità in Tortora dal collare orientale (Streptopelia decaocto)

Author

Frasnelli M., Taddei R., Raffini E., Corazzari V, Fiorentini L., Tosi G., Fedrizzi G., Piro R., Lavazza A., Gelmetti D., Bonfante F., Gelmini L., Terregino C., COTTI, CLAUDIA, DE MARCO, MARIA ALESSANDRA, DELOGU, MAURO, MONINI M., BABSA S., RUGGERI F.M., LAVAZZA A., CORDIOLI P., E. BROCCHI (EDS.), Frasnelli M., Taddei R., Raffini E., Corazzari V, Fiorentini L., Tosi G., Fedrizzi G., Piro R., Lavazza A., Gelmetti D., Bonfante F., Cotti C., Gelmini L., Terregino C., De Marco M.A., and Delogu M.

Subjects
TORTORA DAL COLLARE ORIENTALE (STREPTOPELIA DECAOCTO), ELEVATA MORTALITÀ
Abstract

Nelle prime due settimane di gennaio 2011, circa 3.000 carcasse di tortore dal collare (Streptopelia decaocto) a vita libera sono state rinvenute nei pressi di un sito industriale, in provincia di Ravenna, dedito alla lavorazione di partite di semi o loro residui. L’esame autoptico di 322 soggetti evidenziava prevalentemente un grave danno renale, epatomegalia e ipoplasia splenica. Gli esami istologici a livello del rene mostravano nefrosi associata a necrosi tubulari e una nefrite interstiziale linfoplasmacellulare. Inoltre, si osservavano deplezione linfocitaria nella milza unitamente ad emosiderosi splenica ed epatica. La stima dell’età su 46 soggetti identificava il 78% di adulti e il 22% di giovani (entro il primo anno di vita). Le analisi chimiche sulle ingesta e su pool di fegati non evidenziavano tossicità da pesticidi clorurati e fosforati, carbammati, triazine, piretroidi, stricnina, neonicotinoidi, Pb, Cd, Cr, Hg, Zn, Cu, micotossine, perossidi. Indagini molecolari (RT-PCR Real-Time) escludevano la presenza di virus influenzali, mentre veniva evidenziato RNA di Paramyxovirus aviario tipo 1 (APMV-1) tramite RTPCR in 176 su 193 animali analizzati. L’isolamento di 27 ceppi di APMV-1 è stato ottenuto inoculando pool di organi su uova embrionate di pollo SPF. Tali ceppi risultavano patogeni in base alla sequenza aminoacidica del sito di clivaggio della proteina di fusione. Il sequenziamento parziale del gene F ha permesso di identificare 2 differenti genotipi cocircolanti: il lineaggio 4b (APMV-1 ceppo piccione) e un distinto cluster genetico del lineaggio 4.

Published
2011

28. Incremental Update of Datalog Materialisation: the Backward/Forward Algorithm

Author

Motik, B., Nenov, Y., Piro, R., Ian Horrocks, Bonet, B, and Koenig, S

Subjects
Databases, Artificial Intelligence, Computer Science, General Medicine, Knowledge Representation and Reasoning
Abstract

Datalog-based systems often materialise all consequences of a datalog program and the data, allowing users' queries to be evaluated directly in the materialisation. This process, however, can be computationally intensive, so most systems update the materialisation incrementally when input data changes. We argue that existing solutions, such as the well-known Delete/Rederive (DRed) algorithm, can be inefficient in cases when facts have many alternate derivations. As a possible remedy, we propose a novel Backward/Forward (B/F) algorithm that tries to reduce the amount of work by a combination of backward and forward chaining. In our evaluation, the B/F algorithm was several orders of magnitude more efficient than the DRed algorithm on some inputs, and it was never significantly less efficient.

Published
2015
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29. Prior tuberculin skin test does not induce a false positive result of T-cell interferon-gamma release assays

Author

Losi M, Ferrara G, Luppi F, Piro R, Cerri S, Tallarico S, Andreani A, D’Amico R, Roversi P, Meacci M, Meccugni B, Marchetti Dori I, Caracciolo R, Fabbri LM, Richeldi L, Losi, M, Ferrara, G, Luppi, F, Piro, R, Cerri, S, Tallarico, S, Andreani, A, D’Amico, R, Roversi, P, Meacci, M, Meccugni, B, Marchetti Dori, I, Caracciolo, R, Fabbri, L, and Richeldi, L

Subjects
Tuberculin skin test, T-cell interferon-gamma release assays
Published
2008

31. Noi, persona politica

Author

Librandi, Rita, Piro, Rosa, Librandi, R ( Rita ), Piro, R ( Rosa ), La Fauci, Nunzio, Librandi, Rita, Piro, Rosa, Librandi, R ( Rita ), Piro, R ( Rosa ), and La Fauci, Nunzio

Published
2016

32. Endobronchial Hamartoma Subtotally Occluding the Right Main Bronchus and Mimicking Bronchial Carcinoid Tumor

Author

Lococo, Filippo, Galeone, C., Lasagni, L., Carbonelli, C., Tagliavini, E., Piro, R., Zucchi, L., Sgarbi, G., Lococo F. (ORCID:0000-0002-9383-5554), Lococo, Filippo, Galeone, C., Lasagni, L., Carbonelli, C., Tagliavini, E., Piro, R., Zucchi, L., Sgarbi, G., and Lococo F. (ORCID:0000-0002-9383-5554)

Abstract

Hamartomas are very rarely identified as an endobronchial lesion. Herein, we describe a peculiar case of a 55-year-old woman with persistent cough and increasing dyspnea and radiological detection of a solid lesion subtotally occluding the main right bronchus. Despite the radiological and radiometabolic (18-fluoro-2-deoxy-d-glucose positron emission tomography/computer tomography scan) features were highly suspected for bronchial carcinoid, the definitive diagnosis after endoscopic removal was indicative of an endobronchial hamartoma. When considering differential diagnosis of an endobronchial lesion, the physicians should take firmly in mind such rare entity and, accordingly, bronchoscopy and bronchoscopic biopsy should be done as first step in management of all cases presenting with endobronchial lesions.

Published
2016

38. Flexible Job Submission Using Web Services: The gLite WMProxy Experience

Author

Avellino, G., Beco, S., Cavallini, A., Maraschini, A., Pacini, F., Parrini, A., Scarcella, C., Sottilaro, M., Terracina, A., Dvorak, F., Kouril, D., Krenek, A., Matyska, L., Mulac, M., Pospisil, J., Ruda, M., Salvet, Z., Sitera, J., Skrabal, J., Vocu, M., Monforte, S., Pappalardo, M., Andreozzi, S., Cecchi, M., Ciaschini, V., Ferrari, T., Giacomini, F., Lops, R., Ronchieri, E., Venturi, V., Fiorentino, G., Martellli, V., Mezzadri, M., Molinari, E., Prelz, F., Rebatto, D., Andreetto, P., Borgia, A. S., Dorigo, A., Giannelle, A., Marzolla, M., Mordacchini, M., Sgaravatto, M., Zangrando, L., Guarise, A., Patania, G., Piro, R., and Werbrouck, A.

Subjects
gLite, WMProxy, Web Services, gLite, Grid Computing, Job Submission, Grid Computing, Web Services, Job Submission, WMProxy
Published
2006

41. Supporting the Development Process of the DataGrid Workload Management System Software with GNU autotools, CVS and RPM

Author

Gianelle, A., Peluso, R., Sgaravatto, M., Giacomini, F., Ronchieri, E., Avellino, G., Cantalupo, B., Beco, S., Maraschini, A., Pacini, F., Guarise, A., Piro, R., Werbrouck, A., Kouril, D., Krenek, A., Kabela, Z., Matyska, L., Mulac, M., Pospisil, J., Ruda, M., Salvet, Z., Sitera, J., Vocu, M., Mezzadri, M., Prelz, F., Monforte, S., Pappalardo, M., and Colling, D.

Subjects
Concurrent Version System CVS, datagrid, Workload Management System, Concurrent Version System CVS, GNU autotools, datagrid, Workload Management System, GNU autotools, Computing and Computers
Abstract

DataGrid is project funded by the European Commission to develop and deploy distributed computing components for reference applications in the domains of Particle Physics, Earth Observation and Bioinformatics. The software development is shared among nine contractual partners, in seven different countries, and is organized in work-packages covering different areas. In this paper, we discuss how combination of Concurrent Version System, GNU autotools and other tools and practices was organised to allow the development, build, test and distribution of the DataGrid Workload Management Sys-tem. This is the product of one speci_c work-package that is not only characterised by rather high internal geographic and administrative dispersion (four institutions with de-velopers at nine different locations in three countries), but by the fact we had to integrate and interface to dozen of third-party code packages coming from different sources, and to the software products coming from other three development work-packages internal to the project. high level of central co-ordination needed to be maintained for project-wide steering, and this had also to be re_ected in the software development infrastructure, while maintaining ease-of-use for distributed developers and automated procedures wherever possible.

Published
2005

43. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

Author

Mack, S, Mack, S, Witt, H, Piro, R, Gu, L, Zuyderduyn, S, Stütz, A, Wang, X, Gallo, M, Garzia, L, Zayne, K, Zhang, X, Ramaswamy, V, Jäger, N, Jones, D, Sill, M, Pugh, T, Ryzhova, M, Wani, K, Shih, D, Head, R, Remke, M, Bailey, S, Zichner, T, Faria, C, Barszczyk, M, Stark, S, Seker-Cin, H, Hutter, S, Johann, P, Bender, S, Hovestadt, V, Tzaridis, T, Dubuc, A, Northcott, P, Peacock, J, Bertrand, K, Agnihotri, S, Cavalli, F, Clarke, I, Nethery-Brokx, K, Creasy, C, Verma, S, Koster, J, Wu, X, Yao, Y, Milde, T, Sin-Chan, P, Zuccaro, J, Lau, L, Pereira, S, Castelo-Branco, P, Hirst, M, Marra, M, Roberts, S, Fults, D, Massimi, L, Cho, Y, Van Meter, T, Grajkowska, W, Lach, B, Kulozik, A, von Deimling, A, Witt, O, Scherer, S, Fan, X, Muraszko, K, Kool, M, Pomeroy, S, Jabado, N, Rutka, J, Bouffet, E, Korbel, J, Lupien, M, Aldape, K, Bader, G, Eils, R, Lichter, P, Dirks, P, Pfister, S, Korshunov, A, Taylor, M, Huang, A, Tabori, U, Hawkins, C, Malkin, D, Kongkham, P, Gupta, Nalin, Phillips, Joanna, Weiss, William, Mack, S, Mack, S, Witt, H, Piro, R, Gu, L, Zuyderduyn, S, Stütz, A, Wang, X, Gallo, M, Garzia, L, Zayne, K, Zhang, X, Ramaswamy, V, Jäger, N, Jones, D, Sill, M, Pugh, T, Ryzhova, M, Wani, K, Shih, D, Head, R, Remke, M, Bailey, S, Zichner, T, Faria, C, Barszczyk, M, Stark, S, Seker-Cin, H, Hutter, S, Johann, P, Bender, S, Hovestadt, V, Tzaridis, T, Dubuc, A, Northcott, P, Peacock, J, Bertrand, K, Agnihotri, S, Cavalli, F, Clarke, I, Nethery-Brokx, K, Creasy, C, Verma, S, Koster, J, Wu, X, Yao, Y, Milde, T, Sin-Chan, P, Zuccaro, J, Lau, L, Pereira, S, Castelo-Branco, P, Hirst, M, Marra, M, Roberts, S, Fults, D, Massimi, L, Cho, Y, Van Meter, T, Grajkowska, W, Lach, B, Kulozik, A, von Deimling, A, Witt, O, Scherer, S, Fan, X, Muraszko, K, Kool, M, Pomeroy, S, Jabado, N, Rutka, J, Bouffet, E, Korbel, J, Lupien, M, Aldape, K, Bader, G, Eils, R, Lichter, P, Dirks, P, Pfister, S, Korshunov, A, Taylor, M, Huang, A, Tabori, U, Hawkins, C, Malkin, D, Kongkham, P, Gupta, Nalin, Phillips, Joanna, and Weiss, William

Abstract

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

Published
2014

45. Determination of trans-Galactooligosaccharides in Selected Food Products by Ion-Exchange Chromatography: collaborative study

Author

De, Slegte, Bakx, E., Bastiaans, H.J.A.P., Benet, S., Brunt, K., Grenier-Loustalot, Marie-Florence, Heutink, M.A.T., Hischenhuber, C., Karppinen, S., Mengerink, G.W., Müller-Warner, B., Nieminen, A., Nijboer, F.N., Piro, R., Prandin, L., Rohrer, J.S., Saarinen, K., Sanders, P., Sangiorgi, E., Schols, H.A., Schoterman, H.C., Siponen, S., Stahl, B., Stöber, P., Thomas, D.H., Viscogliosi, Henri, Friesland Coberco Dairy Foods, Corporate Research, Friesland Coberco Dairy Foods, Service Central d'Analyse (SCA), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and Bussy, Agnès

Subjects
[CHIM.ANAL] Chemical Sciences/Analytical chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry
Abstract

International audience; Eleven collaborating laboratories assayed 7 blind duplicate pairs of food and feed products for trans-galactooligosaccharides. The 7 laboratory sample pairs ranged from low (2%) to high levels (15%). Following the proposed method, the test samples were treated with β-galactosidase and the released galactose was determined by ion-exchange chromatography. Repeatability standard deviation ranged from 2.9 to 11.6%; reproducibility standard deviation ranged from 4.6 to 11.6%.

Published
2002

48. Socio-environmental impacts of new housing development at infill and greenfield sites - methodical design for a multicriteria assessment

Author

Ganser, R., Piro, R., Schetke, Sophie, Kötter, T., Haase, Dagmar, Ganser, R., Piro, R., Schetke, Sophie, Kötter, T., and Haase, Dagmar

Abstract

Despite decreasing population in an increasing number of German urban agglomerations, urban expansion and land development pressure is still the main driver behind massive land consumption. This negatively affects natural resources and fosters the loss of ecosystem services in the surrounding suburban areas. Since the high annual land consumption rates have not yet abated, the German Federal government established a quantitative benchmark which aims to reduce land consumption from 113 hectares (280 acres) per day in 2008 to 30 hectares (75 acres) per day in 2020 (http://www.nachhaltigkeitsrat.de). In order to realize this significant step, stakeholders need to focus on more compact settlement development and to use infill strategies. Options include both brownfield development and densification strategies. Despite obvious positive effects of reduced land consumption and protection of natural resources in suburban areas, the specific socio-environmental impacts of infill development remain unclear, especially with regard to residents´ quality of life (QoL) and the provision of urban ecosystem services (UES) including the provision of local climate regulation, recreation or aesthetic features. This study introduces an innovative methodical design for a multicriteria assessment (MCA) of the socio-environmental impacts of new infill development compared to suburban – especially greenfield – development. The multicriteria assessment focuses on the provisioning benefits of urban green space for urban residents. So doing, it bridges the gap between the two concepts of quality of life and urban ecosystems services. The study presents an integrative multicriteria assessment scheme which can be applied by both urban planners and scientists. We show that infill development does not equal a decrease in the environmental conditions in cities.

Published
2012

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