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4. Explaining evolution via constrained persistent perfect phylogeny

Author

Bonizzoni, P, Carrieri, A, DELLA VEDOVA, G, Trucco, G, BONIZZONI, PAOLA, CARRIERI, ANNA PAOLA, DELLA VEDOVA, GIANLUCA, Trucco, G., Bonizzoni, P, Carrieri, A, DELLA VEDOVA, G, Trucco, G, BONIZZONI, PAOLA, CARRIERI, ANNA PAOLA, DELLA VEDOVA, GIANLUCA, and Trucco, G.

Abstract

Background: The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results: We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions: A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to expl

Published
2014

5. Species-driven persistent phylogeny

Author

Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, Trucco, G, Carrieri, AP, Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, Trucco, G, and Carrieri, AP

Abstract

The perfect phylogeny is a widely used model in phylogenetics, since it provides an effective representation of evolution of binary characters in several contexts, such as for example in haplotype inference. The model, which is conceptually the simplest among those actually used, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. Since a large number of biological phenomena cannot be modeled by the perfect phylogeny, it becomes important to find generalizations that retain the computational tractability of the original model, but are more flexible in modeling biological data when the infinite site assumption is violated, e.g. because of back mutations. In this paper, we introduce a new model-called species-driven persistent phylogeny-and we study the relations between three different formulations: perfect phylogeny, persistent phylogeny, galled trees, and species-driven persistent phylogeny. The species-driven persistent phylogeny model is intermediate between the perfect and the persistent phylogeny, since a perfect phylogeny allows no back mutations and a persistent phylogeny allows each character to back mutate only once. We describe an algorithm to compute a species-driven persistent phylogeny and we prove that every matrix admitting a galled-tree also admits a species-driven persistent phylogeny.

Published
2017

6. A colored graph approach to perfect phylogeny with persistent characters

Author

Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, Trucco, G, Carrieri, Anna Paola, Della Vedova, Gianluca, Rizzi, Raffaella, Trucco, Gabriella, Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, Trucco, G, Carrieri, Anna Paola, Della Vedova, Gianluca, Rizzi, Raffaella, and Trucco, Gabriella

Abstract

A main open question related to character-based tree reconstruction is designing generalizations of the Perfect Phylogeny approach that couple efficient algorithmic solutions to the capability of explaining the input binary data, by allowing back mutations of some characters. Following this goal, the Persistent Phylogeny model and the related tree reconstruction problem (the PPP problem) have been recently introduced: this model allows only one back mutation for each character. The investigation of the combinatorial properties and the complexity of the model is still open: the most important such question is whether the PPP problem is NP-hard. Here we propose a graph-based approach to the PPP problem by showing that instances can be represented by colored graphs, while the solutions are obtained by operations on such graphs. Indeed, we give a graph-based characterization of the solutions to the PPP problem by showing the relationship between certain sequences of graph operations on the instance graphs and traversals of a persistent phylogeny solving these instances. Based on this result and on some combinatorial properties of the instance graphs we are able to give a polynomial time algorithm for a restricted version of the PPP problem.

Published
2017

7. Cardiac surgery for patients with heart failure due to structural heart disease in Uganda: access to surgery and outcomes

Author

Grimaldi A, Ammirati E, Karam N, Vermi AC, De Concilio A, Trucco G, Aloi F, Arioli F, Figini F, Ferrarello S, Sacco FM, Grottola R, D'Arbela PG, Marijon E, Freers J, Mirabel M., ALFIERI , OTTAVIO, Grimaldi, A, Ammirati, E, Karam, N, Vermi, Ac, De Concilio, A, Trucco, G, Aloi, F, Arioli, F, Figini, F, Ferrarello, S, Sacco, Fm, Grottola, R, D'Arbela, Pg, Alfieri, Ottavio, Marijon, E, Freers, J, and Mirabel, M.

Abstract

Objective: Few data are available on heart failure (HF) in sub-Saharan Africa. We aimed to provide a current picture of HF aetiologies in urban Uganda, access to heart surgery, and outcomes. Methods: We prospectively collected clinical and echocardiographic data from 272 consecutive patients referred for suspected heart disease to a tertiary hospital in Kampala during seven non-governmental organisation (NGO) missions from 2009 to 2013. We focused the analysis on 140 patients who fulfilled standardised criteria of HF by echocardiography. Results: Rheumatic heart disease (RHD) was the leading cause of HF in 44 (31%) patients. Among the 50 children included (age

Published
2014

9. The binary perfect phylogeny with persistent characters

Author

Bonizzoni, P, Braghin, C, Dondi, R, Trucco, G, BONIZZONI, PAOLA, Trucco, G., Bonizzoni, P, Braghin, C, Dondi, R, Trucco, G, BONIZZONI, PAOLA, and Trucco, G.

Abstract

The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper, we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem of reconstructing a near perfect phylogeny over a binary set of characters where characters are persistent: characters can be gained and lost at most once. Based on this notion, we define the problem of the Persistent Perfect Phylogeny (referred as P-PP). We restate the P-PP problem as a special case of the Incomplete Directed Perfect Phylogeny, called Incomplete Perfect Phylogeny with Persistent Completion, (refereed as IP-PP), where the instance is an incomplete binary matrix MM having some missing entries, denoted by symbol ??, that must be determined (or completed) as 00 or 11 so that MM admits a binary perfect phylogeny. We show that the IP-PP problem can be reduced to a problem over an edge colored graph since the completion of each column of the input matrix can be represented by a graph operation. Based on this graph formulation, we develop an exact algorithm for solving the P-PP problem that is exponential in the number of characters and polynomial in the number of species

Published
2012

11. Monitoring the quality of laboratories and the prevalence of resistance to antituberculosis drugs: Italy, 1998–2000

Author

Migliori, G. B., Fattorini, L., Vaccarino, R., Besozzi, G., Saltini, C., Orefici, G., Iona, E., Matteelli, A., Fiorentini, F., Codecasa, L. R., Casali, Lucio, Cassone, A., De Santis, A., Giorgio, V., Vinciguerra, P., Angarano, G., Petrozzi, L., Costa, D., Gozzellino, F., Perboni, A., Marchetti, D., Pascali, A., Falcone, F., Mariano, V., Rizza, F., Pretto, P., Turano, A., Carosi, G. P., Farris, A. G., Ligia, G. P., Orani, G., Farris, B., Foschi, C., Trucco, G., Aiolfi, S., Ceruti, T., Parpanesi, M., Calabro, S., Felisatti, G., Tortoli, E., Nutini, S., Montini, G., D'Ambrosio, V., Ceraminiello, A., Bernorio, S., Buono, L., Montesano, P., Vinci, E., Sabato, E., Gamba, S., Crepaldi, P., Magliano, E., Penati, V., Vaccarino, P., Astolfi, A., Bertoli, G., Rupianesi, F., Losi, M., Richeldi, L., Ferrara, Giovanni, Minuccio, E., Napolitano, G., Molinari, G. L., Saini, L., Garzone, A., Vertuccio, C., Marcias, S., Menozzi, M., Marone, P., Peona, V., Nascimbene, C., Pasi, A., Cascina, A., Monaco, A., Penza, O., Pasticci, Maria Bruna, Bistoni, F., Sposini, T., Colorizio, V., Confalonieri, M., Bottrighi, P., Macor, G., Moretti, G., Fatigante, R., Barbaro, A., Agati, G., Zaccara, F., Viola, S., Le Donne, R., Farinelli, G., Mancini, D., Ermeti, M., Longi, R., Tronci, M., Bisetti, A., Altieri, A., and Fadda, G.

Subjects
Pulmonary and Respiratory Medicine, medicine.medical_specialty, Tuberculosis, Prevalence of resistance, Drug Resistance, Antitubercular Agents, Drug resistance, Proficiency testing, Drug, Immigrant, Susceptibility testing, Emigration and Immigration, Humans, Italy, Laboratories, Prevalence, Drug Resistance, Multiple, Bacterial, Tuberculosis, Multidrug-Resistant, Internal medicine, medicine, Ethambutol, business.industry, Public health, Isoniazid, Bacterial, Multidrug-Resistant, medicine.disease, Surgery, Streptomycin, business, Multiple, Rifampicin, medicine.drug
Abstract

In 1998 a network of 20 regional tuberculosis (TB) laboratories (the Italian Multicentre Study on Resistance to Antituberculosis drugs (SMIRA) network) was established in Italy to implement proficiency testing and to monitor the prevalence of drug resistance nationwide. The network managed 30% of all TB cases reported in Italy each year. The aim of the present report is to describe: 1) the accuracy of drug-susceptibility testing in the network; 2) the prevalence of drug resistance for the period 1998-2000. Data were collected from the network laboratories. Sensitivity to streptomycin and ethambutol increased from the first survey (1998-1999) to the second survey (2000) from 87.7 to 91.9%. Specificity, predictive values for resistance and susceptibility, efficiency and reproducibility were consistent in both surveys. In previously untreated cases, the prevalence of multidrug-resistance was the same in both surveys (1.2%), while a slight decrease from the first to the second survey was observed for monoresistance to rifampicin (from 0.8 to 0.4%) and isoniazid (from 2.9 to 2%). The significant association found between isoniazid resistance and immigration is a useful indicator for both clinicians managing individual tuberculosis cases and public health services planning control strategies.

Published
2003

12. Weighted don't cares

Author

Bernasconi, Anna, Ciriani, V., Fiser, P., and Trucco, G.

Published
2012

13. Surveillance of anti-tuberculosis drug resistance: Results of the 1998/1999 proficiency testing in Italy

Author

Migliori GB, Ambrosetti M, Fattorini L, Penati V, Vaccarino P, Besozzi G, Ortona L, Saltini C, Orefici G, Moro ML, Iona E, Cassone A, De Santis A, Giorgio V, Vinciguerra P, Angarano G, Petrozzi L, Costa D, Gozzellino F, Perboni A, Marchetti D, Pascali A, Falcone F, Mariano V, Rizza F, Pretto P, Turano A, Matteelli A, Carosi GP, Tedoldi S, Pinsi G, Farris AG, Ligia GP, Orani G, Farris B, Foschi C, Trucco G, Aiolfi S, Ceruti T, Parpanesi M, Calabro S, Felisatti G, Tortoli E, Nutini S, Montini G, Fiorentini F, D'Ambrosio V, Ceraminiello A, Bernorio S, Buono L, Montesano P, Vinci E, Sabato E, Gamba S, Crepaldi P, Bertoli G, Rupianesi F, Losi M, Richeldi L, Ferrara G, Muccio E, Napolitano G, Molinari GL, Saini L, Garzone A, Vertuccio C, Marcias, Menozzi, Marone P, Peona, Nascimbene, Pasi, Cascina, Casali, Monaco, Penza, Pasticci, M.B., Bistoni, Sposini, Colorizio, Confalonieri M, Bottrighi P, Orsi, Schiavi, Macor, Moretti, Fatigante, Barbaro, Agati, Zacarra, Viola, Le Donne, Farinelli, Mancini, Ermeti, Migliori, Gb, Ambrosetti, M, Fattorini, L, Penati, V, Vaccarino, P, Besozzi, G, Ortona, L, Saltini, C, Orefici, G, Moro, Ml, Iona, E, Cassone, A, De Santis, A, Giorgio, V, Vinciguerra, P, Angarano, G, Petrozzi, L, Costa, D, Gozzellino, F, Perboni, A, Marchetti, D, Pascali, A, Falcone, F, Mariano, V, Rizza, F, Pretto, P, Turano, A, Matteelli, A, Carosi, Gp, Tedoldi, S, Pinsi, G, Farris, Ag, Ligia, Gp, Orani, G, Farris, B, Foschi, C, Trucco, G, Aiolfi, S, Ceruti, T, Parpanesi, M, Calabro, S, Felisatti, G, Tortoli, E, Nutini, S, Montini, G, Fiorentini, F, D'Ambrosio, V, Ceraminiello, A, Bernorio, S, Buono, L, Montesano, P, Vinci, E, Sabato, E, Gamba, S, Crepaldi, P, Bertoli, G, Rupianesi, F, Losi, M, Richeldi, L, Ferrara, G, Muccio, E, Napolitano, G, Molinari, Gl, Saini, L, Garzone, A, Vertuccio, C, Marcias, Menozzi, Marone, P, Peona, Nascimbene, Pasi, Cascina, Casali, Monaco, Penza, Pasticci, M., B., Bistoni, Sposini, Colorizio, Confalonieri, M, Bottrighi, P, Orsi, Schiavi, Macor, Moretti, Fatigante, Barbaro, Agati, Zacarra, Viola, Le, Donne, Farinelli, Mancini, and Ermeti

Subjects
Tuberculosi, Drug susceptibility testing, Proficiency testing
Published
2000

15. Surveillance of anti-tuberculosis drug resistance: Results of the 1998/1999 proficiency testing in Italy

Author

Migliori, Gb, Ambrosetti, M, Fattorini, L, Penati, V, Vaccarino, P, Besozzi, G, Ortona, L, Saltini, C, Orefici, G, Moro, Ml, Iona, E, Cassone, A, De Santis, A, Giorgio, V, Vinciguerra, P, Angarano, G, Petrozzi, L, Costa, D, Gozzellino, F, Perboni, A, Marchetti, D, Pascali, A, Falcone, F, Mariano, V, Rizza, F, Pretto, P, Turano, A, Matteelli, A, Carosi, Gp, Tedoldi, S, Pinsi, G, Farris, Ag, Ligia, Gp, Orani, G, Farris, B, Foschi, C, Trucco, G, Aiolfi, S, Ceruti, T, Parpanesi, M, Calabro, S, Felisatti, G, Tortoli, E, Nutini, S, Montini, G, Fiorentini, F, D'Ambrosio, V, Ceraminiello, A, Bernorio, S, Buono, L, Montesano, P, Vinci, E, Sabato, E, Gamba, S, Crepaldi, P, Bertoli, G, Rupianesi, F, Losi, M, Richeldi, L, Ferrara, G, Muccio, E, Napolitano, G, Molinari, Gl, Saini, L, Garzone, A, Vertuccio, C, Marcias, Menozzi, Marone, P, Peona, Nascimbene, Pasi, Cascina, Casali, Monaco, Penza, Pasticci, M. B., Bistoni, Sposini, Colorizio, Confalonieri, M, Bottrighi, P, Orsi, Schiavi, Macor, Moretti, Fatigante, Barbaro, Agati, Zacarra, Viola, Donne, Le, Farinelli, Mancini, and Ermeti

Subjects
Drug susceptibility testing, Tuberculosis, Proficiency testing
Published
2000

28. Restoration of atrioventricular conduction after surgical removal of a hydatid cyst of the interventricular septum

Author

Trucco G, Viara A, De Paulis R, Ottino Gm, and Villani M

Subjects
Adult, Male, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Heart block, Hydatid cyst, Echinococcosis, Heart Conduction System, Surgical removal, parasitic diseases, Heart Septum, medicine, Humans, Echinococcal cyst, Cyst, cardiovascular diseases, Interventricular septum, business.industry, Atrioventricular conduction, Anatomy, medicine.disease, humanities, Surgery, Heart Block, medicine.anatomical_structure, Atrioventricular Node, cardiovascular system, Cardiomyopathies, Cardiology and Cardiovascular Medicine, business, Atrioventricular block, circulatory and respiratory physiology
Abstract

A young man with syncope and complete heart block was found to have an echinococcal cyst in the interventricular septum. The block disappeared after surgical removal of the cyst.

Published
1987

31. Surveillance of anti-tuberculosis drug resistance: Results of the 1998/1999 proficiency testing in Italy

Author

Migliori, G. B., Ambrosetti, M., Fattorini, L., Penati, V., Vaccarino, P., Besozzi, G., Ortona, L., Saltini, C., Orefici, G., Moro, M. L., Iona, E., Cassone, A., Santis, A., Giorgio, V., Vinciguerra, P., Angarano, G., Petrozzi, L., Costa, D., Gozzellino, F., Perboni, A., Marchetti, D., Pascali, A., Falcone, F., Mariano, V., Rizza, F., Pretto, P., Turano, A., Alberto Matteelli, Carosi, G. P., Tedoldi, S., Pinsi, G., Farris, A. G., Ligia, G. P., Orani, G., Farris, B., Foschi, C., Trucco, G., Aiolfi, S., Ceruti, T., Parpanesi, M., Calabro, S., Felisatti, G., Tortoli, E., Nutini, S., Montini, G., Fiorentini, F., D Ambrosio, V., Ceraminiello, A., Bernorio, S., Buono, L., Montesano, P., Vinci, E., Sabato, E., Gamba, S., Crepaldi, P., Bertoli, G., Rupianesi, F., Losi, M., Richeldi, L., Ferrara, G., Minuccio, E., Napolitano, G., Molinari, G. L., Saini, L., Garzone, A., Vertuccio, C., Marcias, S., Menozzi, M., Marone, P., Peona, V., Nascimbene, C., Pasi, A., Cascina, A., Casali, L., Monaco, A., Penza, O., Pasticci, M. B., Bistoni, F., Sposini, T., Colorizio, V., Confalonieri, M., Bottrighi, P., Orsi, A., Schiavi, L., Macor, G., Moretti, G., Fatigante, R., Barbaro, A., Agati, G., Zacarra, F., Viola, S., Le Donne, R., Farinelli, G., Mancini, D., and Ermeti, M.

33. Prevalence of resistance to anti-tuberculosis drugs: Results of the 1998/99 national survey in Italy

Author

Giovanni Battista Migliori, Fattorini, L., Vaccarino, R., Besozzi, G., Saltini, C., Orefici, G., Iona, E., Matteelli, A., Fiorentini, F., Codecasa, L. R., Casali, L., Cassone, A., Santis, A., Giorgio, V., Vinciguerra, P., Angarano, G., Petrozzi, L., Costa, D., Gozzellino, F., Perboni, A., Marchetti, D., Pascali, A., Falcone, F., Mariano, V., Rizza, F., Pretto, P., Turano, A., Carosi, G. P., Farris, A. G., Ligia, G. P., Orani, G., Farris, B., Foschi, C., Trucco, G., Aiolfi, S., Ceruti, T., Parpanesi, M., Calabro, S., Felisatti, G., Tortoli, E., Nutini, S., Montini, G., D Ambrosio, V., Ceraminiello, A., Bernorio, S., Buono, L., Montesano, P., Vinci, E., Sabato, E., Gamba, S., Crepaldi, P., Magliano, E., Penati, V., Vaccarino, P., Astolfi, A., Bertoli, G., Rupianesi, F., Losi, M., Richeldi, L., Ferrara, G., Minuccio, E., Napolitano, G., Molinari, G. L., Saini, L., Garzone, A., Vertuccio, C., Marcias, S., Menozzi, M., Marone, P., Peona, V., Nascimbene, C., Pasi, A., Cascina, A., Monaco, A., Penza, O., Pasticci, M. B., Bistoni, F., Sposini, T., Colorizio, V., Confalonieri, M., Bottrighi, P., Macor, G., Moretti, G., Fatigante, R., Barbaro, A., Agati, G., Zaccara, F., Viola, S., Le Donne, R., Farinelli, G., Mancini, D., Ermeti, M., Longi, R., Tronci, M., Bisetti, A., Altieri, A., and Fadda, G.

35. Evaluation of tuberculosis treatment results in Italy, report 1998

Author

Centis, R., Ianni, A., Migliori, G. B., Casali, L., Agati, G., Aiolfi, S., Altieri, A., Ambrosetti, M., Angarano, G., Arossa, W., Bagnasco, G., Bazzerla, G., Berra, A., Besozzi, G., Bottrighi, P., Bugiani, M., Calabro, S., Castiglioni, G., Cavallero, M., Cicchitto, G., luigi codecasa, Colorizio, V., Confalonieri, M., D Ambrosio, L., D Ambrosio, V., Dellatommasa, S., Di Pisa, G., Ermeti, M., Faccini, E., Falcone, F., Farinelli, G., Fatigante, R., Farris, B., Fatur Volante, T., Felisatti, G., Ferranti, P., Fiorentini, F., Foschi, C., Garzone, A., Giorgio, V., Gozzellino, F., Jacopino, L., Lauriello, G., Le Donne, R., Longi, R., Macor, G., Mancini, D., Marchesani, M. F., Marcias, S., Mariano, V., Mennea, G., Monaco, A., Montesano, G., Moretti, G., Napolitano, G., Nardini, S., Nutini, S., Orani, G., Orsi, A., Parpanesi, M., Pasi, A., Penza, O., Perboni, A., Petrozzi, L., Pretto, P., Rossi, S., Sabato, E., Saini, L., Schiavi, L., Tazza, R., Trucco, G., Vertuccio, C., Viviani, U., Volante, M., Vinciguerra, P., Viola, S., Zaccara, F., Barelle, L., Bertoli, G., Bisetti, A., Bistoni, F., Buono, L., Carbonara, S., Carosi, G. P., Cascina, A., Cassone, A., Costa, D., Crepaldi, P., Santis, A., Diamare, F., Fabbro, L., Fadda, G., Farris, A. G., Fattorini, L., Ferrara, G., Gamba, S., Iona, E., and Losi, M.

43. A colored graph approach to perfect phylogeny with persistent characters

Author

Gabriella Trucco, Raffaella Rizzi, Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, and Trucco, G

Subjects
0301 basic medicine, General Computer Science, 0102 computer and information sciences, 01 natural sciences, Theoretical Computer Science, law.invention, Combinatorics, 03 medical and health sciences, Pathwidth, Chordal graph, law, Trivially perfect graph, Perfect graph, Line graph, Cograph, Mathematics, Character-based evolution, Computer Science (all), INF/01 - INFORMATICA, Graph theory, 030104 developmental biology, 010201 computation theory & mathematics, Persistent phylogeny, Perfect phylogeny, Graph operations, Graph product, MathematicsofComputing_DISCRETEMATHEMATICS
Abstract

A main open question related to character-based tree reconstruction is designing generalizations of the Perfect Phylogeny approach that couple efficient algorithmic solutions to the capability of explaining the input binary data, by allowing back mutations of some characters. Following this goal, the Persistent Phylogeny model and the related tree reconstruction problem (the PPP problem) have been recently introduced: this model allows only one back mutation for each character. The investigation of the combinatorial properties and the complexity of the model is still open: the most important such question is whether the PPP problem is NP-hard. Here we propose a graph-based approach to the PPP problem by showing that instances can be represented by colored graphs, while the solutions are obtained by operations on such graphs. Indeed, we give a graph-based characterization of the solutions to the PPP problem by showing the relationship between certain sequences of graph operations on the instance graphs and traversals of a persistent phylogeny solving these instances. Based on this result and on some combinatorial properties of the instance graphs we are able to give a polynomial time algorithm for a restricted version of the PPP problem.

Published
2017

44. Articoli 131, 132 e 133

Author

Patroni Griffi Andrea, Commenti di A. Morrone, D. Tega, M. D’Amico, M. Cavino, G. Rivosecchi, F. Palermo, A. Pin, F. Alicino, G. Repetto, P. Bonetti, A. Guazzarotti, T. Groppi. - Parte prima. Diritti e doveri dei cittadini. - Titolo I. Rapporti civili. Commenti di C. Martinelli, M. Cecchetti, M. Orofino, L. Castelli, F. Rosa, F. Clementi, I. Ruggiu, P. Tanzarella, G.E. Vigevani, F.G. Pizzetti, D. Morana, F. Dal Canto, N. Pignatelli, G. Martinico, R. Calvano, A. Cardone. - Titolo II. Rapporti etico-sociali. Commenti di F. Biondi, G. Matucci, A. Sperti, G. Scaccia, A. Iannuzzi, M. Benvenuti. - Titolo III. Rapporti economici. Commenti di E. Ferioli, M. Della Morte, C. Tripodina, G. Arconzo, A. Celotto, L. Lorello, L. Cassetti, Q. Camerlengo, F. Furlan, E. Mostacci, F. Pizzolato e F. Mattassoglio, G. Pistorio, R. Manfrellotti. - Titolo IV. Rapporti politici. Commenti di M. Rubechi, S. Curreri, L. Trucco, G. Tarli Barbieri, T.F. Giupponi, S. Sileoni, A. Morelli. - Parte seconda. Ordinamento della Repubblica. - Titolo I. Il Parlamento. Commenti di N. Lupo, E. Cavasino, E. Gianfrancesco, S. Leone, L. Scaffardi, S. Sileoni, E. Mostacci, G. Romeo, A. Mastromarino, F. Biondi, I. Ciolli, M. Cosulich, C. Martinelli, M. Cuniberti, P.L. Petrillo, G. Piccirilli, M. Plutino, P. Passaglia, F. Dal Canto, I. Pellizzone, F. Rosa, F. Ghera, G. Tarli Barbieri, A. Vedaschi, E. Longo, O. Pollicino, T.F. Giupponi, G.G. Carboni. - Titolo II. Il Presidente della Repubblica. Commenti di F. Clementi, F. Furlan, G. Grasso, M. Cavino, M. Olivetti, F. Pastore, M. Oliviero e M.C. Locchi. - Titolo III. Il Governo. Commenti di C. Bassu, J.O. Frosini, C. Bologna, P. Milazzo, P. Veronesi, A. Valastro e N. Pettinari, M. Di Folco, P. Bonetti. - Titolo IV. La Magistratura. Commenti di E. Bindi, F.G. Pizzetti, G. Arconzo, G. Ferri, A. Deffenu, P. Martino, A. Apostoli, A. Pin, S. Catalano, A. Baraggia, G. Sorrenti, S. Pajno. - Titolo V. Le Regioni, le Province, i Comuni. Commenti di F. Fabrizzi, A. Morelli, S. Ninatti e G. Tiberi, L. Cuocolo, D. Morana, M. Massa, M. Caielli, E.C. Raffiotta, G. Rivosecchi, M. Cecchetti, G. Fontana, D. Coduti, M. Belletti, G. D’Alessandro, S. Pajno, A. Sterpa, S. Calzolaio, A. Patroni Griffi. - Titolo VI. Garanzie costituzionali. Commenti di G. D’Amico, D. Tega, E. Lamarque, V. Marcenò, Q. Camerlengo, A. Buratti. - Disposizioni transitorie e finali. Commento di P. Scarlatti., Clementi, Cuocolo, Rosa, Vigevani, and PATRONI GRIFFI, Andrea

Subjects
Regioni italiane, modifiche territoriali, articolo 131 Costituzione, articolo 132 Costituzione, articolo 133 Costituzione
Published
2018

45. Species-driven persistent phylogeny

Author

Raffaella Rizzi, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco, Paola Bonizzoni, Bonizzoni, P, Carrieri, A, Della Vedova, G, Rizzi, R, and Trucco, G

Subjects
0301 basic medicine, Algebra and Number Theory, Perfect phylogeny, Computer science, INF/01 - INFORMATICA, Information System, Theoretical Computer Science, 03 medical and health sciences, 030104 developmental biology, persistent perfect phylogeny, Computational Theory and Mathematics, Phylogenetics, Evolutionary biology, perfect phylogeny, Information Systems, galled-tree
Abstract

The perfect phylogeny is a widely used model in phylogenetics, since it provides an effective representation of evolution of binary characters in several contexts, such as for example in haplotype inference. The model, which is conceptually the simplest among those actually used, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. Since a large number of biological phenomena cannot be modeled by the perfect phylogeny, it becomes important to find generalizations that retain the computational tractability of the original model, but are more flexible in modeling biological data when the infinite site assumption is violated, e.g. because of back mutations. In this paper, we introduce a new model-called species-driven persistent phylogeny-and we study the relations between three different formulations: perfect phylogeny, persistent phylogeny, galled trees, and species-driven persistent phylogeny. The species-driven persistent phylogeny model is intermediate between the perfect and the persistent phylogeny, since a perfect phylogeny allows no back mutations and a persistent phylogeny allows each character to back mutate only once. We describe an algorithm to compute a species-driven persistent phylogeny and we prove that every matrix admitting a galled-tree also admits a species-driven persistent phylogeny.

Published
2017

46. Explaining evolution via constrained persistent perfect phylogeny

Author

Gabriella Trucco, Anna Paola Carrieri, Gianluca Della Vedova, Paola Bonizzoni, Bonizzoni, P, Carrieri, A, DELLA VEDOVA, G, and Trucco, G

Subjects
Genetics, fixed-parameter complexity, Theoretical computer science, Models, Genetic, Perfect phylogeny, Computer science, Research, Open problem, INF/01 - INFORMATICA, Tree (graph theory), Evolution, Molecular, persistent perfect phylogeny, Character (mathematics), perfect phylogeny, Quantitative Biology::Populations and Evolution, Graph (abstract data type), Computational problem, Special case, Time complexity, Algorithms, Phylogeny, Biotechnology
Abstract

Background: The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results: We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions: A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model.

Published
2014

47. The Binary Perfect Phylogeny with Persistent characters

Author

Gabriella Trucco, Paola Bonizzoni, Riccardo Dondi, Chiara Braghin, Bonizzoni, P, Braghin, C, Dondi, R, and Trucco, G

Subjects
Discrete mathematics, FOS: Computer and information sciences, algorithm, General Computer Science, Settore INF/01 - Informatica, Perfect phylogeny, Generalization, phylogenetic reconstruction, parsimony models, Unordered pair, Binary number, Theoretical Computer Science, Combinatorics, Computational Engineering, Finance, and Science (cs.CE), Exact algorithm, Computer Science - Data Structures and Algorithms, Graph (abstract data type), Logical matrix, Data Structures and Algorithms (cs.DS), Special case, Computer Science - Computational Engineering, Finance, and Science, Computer Science(all), Mathematics
Abstract

The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem of reconstructing a near perfect phylogeny over a binary set of characters where characters are persistent: characters can be gained and lost at most once. Based on this notion, we define the problem of the Persistent Perfect Phylogeny (referred as P-PP). We restate the P-PP problem as a special case of the Incomplete Directed Perfect Phylogeny, called Incomplete Perfect Phylogeny with Persistent Completion, (refereed as IP-PP), where the instance is an incomplete binary matrix M having some missing entries, denoted by symbol ?, that must be determined (or completed) as 0 or 1 so that M admits a binary perfect phylogeny. We show that the IP-PP problem can be reduced to a problem over an edge colored graph since the completion of each column of the input matrix can be represented by a graph operation. Based on this graph formulation, we develop an exact algorithm for solving the P-PP problem that is exponential in the number of characters and polynomial in the number of species., Comment: 13 pages, 3 figures

Published
2011
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48. Analysis of TCR Vbeta repertoire and cytokine gene expression in patients with idiopathic dilated cardiomyopathy

Author

William A. Rudert, Francis X. McGowan, Gerard J. Boyle, Massimo Trucco, Patrizia Luppi, Catherine Haluszczak, Giuliana Trucco, David N. Finegold, Anna Licata, Luppi,P, Licata, A, Haluszczak, C, Rudert, WA, Trucco, G, McGowan, FX Jr, Finegold, D, Boyle, GJ, and Trucco, M.

Subjects
Cardiomyopathy, Dilated, Interleukin 2, Myocarditis, CD8 Antigens, Receptors, Antigen, T-Cell, alpha-beta, T cell, Immunology, Cardiomyopathy, Gene Expression, chemical and pharmacologic phenomena, Picornaviridae, Biology, HLA-DQ alpha-Chains, Immunoenzyme Techniques, Interferon-gamma, Immune system, Antigen, HLA-DQ Antigens, Idiopathic dilated cardiomyopathy, medicine, HLA-DQ beta-Chains, Humans, Immunology and Allergy, RNA, Messenger, Antigens, Viral, Interleukin-6, Reverse Transcriptase Polymerase Chain Reaction, Histocompatibility Testing, Myocardium, IDC, cytokines, immune mechanisms, medicine.disease, Enterovirus B, Human, medicine.anatomical_structure, CD4 Antigens, Leukocytes, Mononuclear, Cytokines, Interleukin-2, Interleukin-4, CD8, Interleukin-1, medicine.drug
Abstract

Although the etiopathogenesis of idiopathic dilated cardiomyopathy (IDC) is still unclear, it is widely accepted that a complex interplay between viral infections and immune mechanisms is the basis of disease genesis. Previously, we showed that heart-infiltrating T cells of patients suffering from acute, fulminant Coxsackie virus B3+-IDC shared a preferential usage of three variable gene segments of the T cell receptor beta chain-(TCR-Vbeta) encoding families Vbeta3, 7 and 13.1. This indicated the possible presence of a superantigen-driven immune response. Here, we further investigated the IDC immunological scenario by analysing different phenotypes of heart-infiltrating cells: TCR repertoires, cytokine expression and presence of enterovirus-specific antigens. IDC patients who underwent heart transplantation at different times after the onset of heart failure were studied. A cardiac infiltrate of CD4+ and CD8+ T cells was present together with activated macrophages. Furthermore, the same Vbeta gene families, previously found to be skewed in hearts from fulminant cases of CVB3+-IDC, together with two additional Vbeta gene families, Vbeta1 and 5B, were increased. IL-1beta, IL-2, IL-6 and IFN-gamma were expressed in the myocardium while others, like IL-4 were not. In conclusion, an orchestrated complex of immune mechanisms seems to be the basis of IDC etiopathogenesis.

Published
2001

49. Combined transarterial chemoembolization and thermal ablation in candidates to liver transplantation with hepatocellular carcinoma: pathological findings and post-transplant outcome.

Author

Fronda M, Susanna E, Doriguzzi Breatta A, Gazzera C, Patrono D, Piccione F, Bertero L, Ciferri F, Carucci P, Gaia S, Rolle E, Vocino Trucco G, Bergamasco L, Tandoi F, Cassoni P, Romagnoli R, Fonio P, and Calandri M

Subjects
Humans, Male, Female, Retrospective Studies, Middle Aged, Treatment Outcome, Aged, Combined Modality Therapy, Adult, Neoplasm Staging, Survival Rate, Microwaves therapeutic use, Catheter Ablation methods, Carcinoma, Hepatocellular therapy, Carcinoma, Hepatocellular pathology, Carcinoma, Hepatocellular surgery, Liver Neoplasms therapy, Liver Neoplasms pathology, Liver Neoplasms surgery, Chemoembolization, Therapeutic methods, Liver Transplantation
Abstract

Objectives: Evaluating the pathological response and the survival outcomes of combined thermal ablation (TA) and transarterial chemoembolization (TACE) as a bridge or downstaging for liver transplantation (LT) in patients with hepatocellular carcinoma (HCC) > 3 cm., Materials and Methods: A retrospective review encompassed 36 consecutive patients who underwent combined TA-TACE as bridging or downstaging before LT. Primary objectives included necrosis of the target lesion at explant pathology, post-LT overall survival (OS) and post-LT recurrence-free survival (RFS). For OS and RFS, a comparison with 170 patients subjected to TA alone for nodules <3 cm in size was also made., Results: Out of the 36 patients, 63.9% underwent TA-TACE as bridging, while 36.1% required downstaging. The average node size was 4.25 cm. All cases were discussed in a multidisciplinary tumor board to assess the best treatment for each patient. Half received radiofrequency (RF), and the other half underwent microwave (MW). All nodes underwent drug-eluting beads (DEB) TACE with epirubicin. The mean necrosis percentage was 65.9% in the RF+TACE group and 83.3% in the MW+TACE group (p-value = 0.099). OS was 100% at 1 year, 100% at 3 years and 94.7% at 5 years. RFS was 97.2% at 1 year, 94.4% at 3 years and 90% at 5 years. Despite the different sizes of the lesions, OS and RFS did not show significant differences with the cohort of patients subjected to TA alone., Conclusions: The study highlights the effectiveness of combined TA-TACE for HCC>3 cm, particularly for bridging and downstaging to LT, achieving OS and RFS rates significantly exceeding 80% at 1, 3 and 5 years., (© 2024. The Author(s).)

Published
2024
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50. Changes in categorization or nomenclature within neuroendocrine tumors.

Author

Vocino Trucco G and Volante M

Subjects
Humans, Female, Neuroendocrine Tumors classification, Neuroendocrine Tumors pathology, Terminology as Topic, World Health Organization
Abstract

Abstract: The 5th edition of the World Health Organization (WHO) classification of neuroendocrine neoplasms (NENs) is built to achieve a uniform terminology and to define a similar diagnostic scheme across different anatomic locations. Since the 4th edition, a chapter discussing NENs in nonneuroendocrine organs has been introduced, which proposes a binary system for classification segregating well-differentiated neoplasms, termed neuroendocrine tumors (NETs), and poorly differentiated neoplasms, termed neuroendocrine carcinomas (NECs). A grading system for NETs is based on mitotic index and/or Ki-67 index and/or necrosis, depending on the different locations. Although this approach has been already well established in the digestive system, it modifies and homogenizes the classification of NENs in the urinary tract, in female genital organs, and in the male genital system. In the lung and thymus, the double terminology of carcinoid/NET, already introduced in the 5th edition of the WHO classification of thoracic tumors, is endorsed. This approach undoubtedly helps the multidisciplinary approach for the diagnosis and clinical management of patients affected by these neoplasms, without losing site-specific characteristics that influence the clinical and biological behavior of tumors in different anatomical sites. Other major advances of the new WHO scheme are the homogenization of epidemiological data and the correct integration of data from prospective future studies aimed at the definition of molecular profiles and at the identification of tumor type-specific and patient-specific therapeutic approaches.

Published
2024
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