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98 results on '"Amadio, G."'

1. Offloading electromagnetic shower transport to GPUs

Author

Amadio, G., Apostolakis, J., Buncic, P., Cosmo, G., Dosaru, D., Gheata, A., Hageboeck, S., Hahnfeld, J., Hodgkinson, M., Morgan, B., Novak, M., Petre, A. A., Pokorski, W., Ribon, A., Stewart, G. A., and Vila, P. M.

Subjects
High Energy Physics - Experiment, I.6.8
Abstract

Making general particle transport simulation for high-energy physics (HEP) single-instruction-multiple-thread (SIMT) friendly, to take advantage of accelerator hardware, is an important alternative for boosting the throughput of simulation applications. To date, this challenge is not yet resolved, due to difficulties in mapping the complexity of Geant4 components and workflow to the massive parallelism features exposed by graphics processing units (GPU). The AdePT project is one of the R\&D initiatives tackling this limitation and exploring GPUs as potential accelerators for offloading some part of the CPU simulation workload. Our main target is to implement a complete electromagnetic shower demonstrator working on the GPU. The project is the first to create a full prototype of a realistic electron, positron, and gamma electromagnetic shower simulation on GPU, implemented as either a standalone application or as an extension of the standard Geant4 CPU workflow. Our prototype currently provides a platform to explore many optimisations and different approaches. We present the most recent results and initial conclusions of our work, using both a standalone GPU performance analysis and a first implementation of a hybrid workflow based on Geant4 on the CPU and AdePT on the GPU., Comment: 8 pages, 4 figures, 20th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2021), to be published in Journal of Physics: Conference Series, editor Andrei Gheata

Published
2022
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2. GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP

Author

Amadio, G., Ananya, A., Apostolakis, J., Bandieramonte, M., Banerjee, S., Bhattacharyya, A., Bianchini, C., Bitzes, G., Canal, P., Carminati, F., Chaparro-Amaro, O., Cosmo, G., Licht, J. C. De Fine, Drogan, V., Duhem, L., Elvira, D., Fuentes, J., Gheata, A., Gheata, M., Gravey, M., Goulas, I., Hariri, F., Jun, S. Y., Konstantinov, D., Kumawat, H., Lima, J. G., Maldonado-Romo, A., Martínez-Castro, J., Mato, P., Nikitina, T., Novaes, S., Novak, M., Pedro, K., Pokorski, W., Ribon, A., Schmitz, R., Seghal, R., Shadura, O., Tcherniaev, E., Vallecorsa, S., Wenzel, S., and Zhang, Y.

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

Full detector simulation was among the largest CPU consumer in all CERN experiment software stacks for the first two runs of the Large Hadron Collider (LHC). In the early 2010's, the projections were that simulation demands would scale linearly with luminosity increase, compensated only partially by an increase of computing resources. The extension of fast simulation approaches to more use cases, covering a larger fraction of the simulation budget, is only part of the solution due to intrinsic precision limitations. The remainder corresponds to speeding-up the simulation software by several factors, which is out of reach using simple optimizations on the current code base. In this context, the GeantV R&D project was launched, aiming to redesign the legacy particle transport codes in order to make them benefit from fine-grained parallelism features such as vectorization, but also from increased code and data locality. This paper presents extensively the results and achievements of this R&D, as well as the conclusions and lessons learnt from the beta prototype., Comment: 34 pages, 26 figures, 24 tables

Published
2020

3. A Roadmap for HEP Software and Computing R&D for the 2020s

Author

Albrecht, J, Alves, AA, Amadio, G, Andronico, G, Anh-Ky, N, Aphecetche, L, Apostolakis, J, Asai, M, Atzori, L, Babik, M, Bagliesi, G, Bandieramonte, M, Banerjee, S, Barisits, M, Bauerdick, LAT, Belforte, S, Benjamin, D, Bernius, C, Bhimji, W, Bianchi, RM, Bird, I, Biscarat, C, Blomer, J, Bloom, K, Boccali, T, Bockelman, B, Bold, T, Bonacorsi, D, Boveia, A, Bozzi, C, Bracko, M, Britton, D, Buckley, A, Buncic, P, Calafiura, P, Campana, S, Canal, P, Canali, L, Carlino, G, Castro, N, Cattaneo, M, Cerminara, G, Cervantes Villanueva, J, Chang, P, Chapman, J, Chen, G, Childers, T, Clarke, P, Clemencic, M, Cogneras, E, Coles, J, Collier, I, Colling, D, Corti, G, Cosmo, G, Costanzo, D, Couturier, B, Cranmer, K, Cranshaw, J, Cristella, L, Crooks, D, Crépé-Renaudin, S, Currie, R, Dallmeier-Tiessen, S, De, K, De Cian, M, De Roeck, A, Delgado Peris, A, Derue, F, Di Girolamo, A, Di Guida, S, Dimitrov, G, Doglioni, C, Dotti, A, Duellmann, D, Duflot, L, Dykstra, D, Dziedziniewicz-Wojcik, K, Dziurda, A, Egede, U, Elmer, P, Elmsheuser, J, Elvira, VD, Eulisse, G, Farrell, S, Ferber, T, Filipcic, A, Fisk, I, Fitzpatrick, C, Flix, J, Formica, A, Forti, A, Franzoni, G, Frost, J, Fuess, S, Gaede, F, Ganis, G, Gardner, R, Garonne, V, and Gellrich, A

Subjects
physics.comp-ph, hep-ex, Networking and Information Technology R&D
Abstract

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to prepare for this software upgrade.

Published
2019

4. GeantV: Results from the Prototype of Concurrent Vector Particle Transport Simulation in HEP

Author

Amadio, G., Ananya, A., Apostolakis, J., Bandieramonte, M., Banerjee, S., Bhattacharyya, A., Bianchini, C., Bitzes, G., Canal, P., Carminati, F., Chaparro-Amaro, O., Cosmo, G., De Fine Licht, J. C., Drogan, V., Duhem, L., Elvira, D., Fuentes, J., Gheata, A., Gheata, M., Gravey, M., Goulas, I., Hariri, F., Jun, S. Y., Konstantinov, D., Kumawat, H., Lima, J. G., Maldonado-Romo, A., Martínez-Castro, J., Mato, P., Nikitina, T., Novaes, S., Novak, M., Pedro, K., Pokorski, W., Ribon, A., Schmitz, R., Seghal, R., Shadura, O., Tcherniaev, E., Vallecorsa, S., Wenzel, S., and Zhang, Y.

Published
2021
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5. Modeling of random bimodal structures of composites (application to solid propellants): I. Simulation of random packs

Author

Buryachenko, V. A., Jackson, T. L., and Amadio, G.

Subjects
Condensed Matter - Materials Science
Abstract

We consider a composite medium, which consists of a homogeneous matrix containing a statistically homogeneous set of multimodal spherical inclusions. This model is used to represent the morphology of heterogeneous solid propellants (HSP) that are widely used in the rocket industry. The Lubachevsky-Stillinger algorithm is used to generate morphological models of HSP with large polydisperse packs of spherical inclusions. We modify the algorithm by proposing a random shaking procedure that leads to the stabilization of a statistical distribution of the simulated structure that is homogeneous, highly mixed, and protocol independent (in sense that the statistical parameters estimated do not depend on the basic simulation algorithm). Increasing the number of shaking has a twofold effect. First, the system becomes more homogeneous and well-mixed. Second, the stochastic fluctuations of statistical parameters (such as e.g. radial distribution function, RDF), estimated by averaging of these structures, tend to diminish., Comment: 24 pages, 13 figures

Published
2012

6. Low-lying non-normal parity states in 8B measured by proton elastic scattering on 7Be

Author

Yamaguchi, H., Wakabayashi, Y., Amadio, G., Fujikawa, H., Teranishi, T., Saito, A., He, J. J., Nishimura, S., Togano, Y., Kwon, Y. K., Niikura, M., Iwasa, N., Inafuku, K., and Khiem, L. H.

Subjects
Nuclear Experiment
Abstract

A new measurement of proton resonance scattering on 7Be was performed up to the center-of-mass energy of 6.7 MeV using the low-energy RI beam facility CRIB (CNS Radioactive Ion Beam separator) at the Center for Nuclear Study of the University of Tokyo. The excitation function of 7Be+p elastic scattering above 3.5 MeV was measured successfully for the first time, providing important information about the resonance structure of the 8B nucleus. The resonances are related to the reaction rate of 7Be(p, gamma)8B, which is the key reaction in solar 8B neutrino production. Evidence for the presence of two negative parity states is presented. One of them is a 2- state observed as a broad s-wave resonance, the existence of which had been questionable. Its possible effects on the determination of the astrophysical S-factor of 7Be(p, gamma)8B at solar energy are discussed. The other state had not been observed in previous measurements, and its spin and parity were determined as 1-., Comment: 6 pages, 4 figures

Published
2008
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8. Challenges and opportunities integrating LLAMA into AdePT

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9359-2196) Hageböck, S., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., and (0000-0001-9359-2196) Hageböck, S.

Abstract

Particle transport simulations are a cornerstone of high-energy physics (HEP), constituting almost half of the entire computing workload performed in HEP. To boost the simulation throughput and energy efficiency, GPUs as accelerators have been explored in recent years, further driven by the increasing use of GPUs on HPCs. The Accelerated demonstrator of electromagnetic Particle Transport (AdePT) is an advanced prototype for offloading the simulation of electromagnetic showers in Geant4 to GPUs, and still undergoes continuous development and optimization. Improving memory layout and data access is vital to use modern, massively parallel GPU hardware efficiently, contributing to the challenge of migrating traditional CPU based data structures to GPUs in AdePT. The low-level abstraction of memory access (LLAMA) is a C++ library that provides a zero-runtime-overhead data structure abstraction layer, focusing on multidimensional arrays of nested, structured data. It provides a framework for defining and switching custom memory mappings at compile time to define data layouts and instrument data access, making LLAMA an ideal tool to tackle the memory-related optimization challenges in AdePT. Our contribution shares insights gained with LLAMA when instrumenting data access inside AdePT, complementing traditional GPU profiler outputs. We demonstrate traces of read/write counts to data structure elements as well as memory heatmaps. The acquired knowledge allowed for subsequent data layout optimizations.

Published
2023

9. LLAMA: The Low-Level Abstraction For Memory Access

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., (0000-0002-8258-3881) Bussmann, M., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., and (0000-0002-8258-3881) Bussmann, M.

Abstract

The performance gap between CPU and memory widens continuously. Choosing the best memory layout for each hardware architecture is increasingly important as more and more programs become memory bound. For portable codes that run across heterogeneous hardware architectures, the choice of the memory layout for data structures is ideally decoupled from the rest of a program. This can be accomplished via a zero-runtime-overhead abstraction layer, underneath which memory layouts can be freely exchanged. We present the Low-Level Abstraction of Memory Access (LLAMA), a C++ library that provides such a data structure abstraction layer with example implementations for multidimensional arrays of nested, structured data. LLAMA provides fully C++ compliant methods for defining and switching custom memory layouts for user-defined data types. The library is extensible with third-party allocators. Providing two close-to-life examples, we show that the LLAMA-generated AoS (Array of Structs) and SoA (Struct of Arrays) layouts produce identical code with the same performance characteristics as manually written data structures. Integrations into the SPEC CPU® lbm benchmark and the particle-in-cell simulation PIConGPU demonstrate LLAMA's abilities in real-world applications. LLAMA's layout-aware copy routines can significantly speed up transfer and reshuffling of data between layouts compared with naive element-wise copying. LLAMA provides a novel tool for the development of high-performance C++ applications in a heterogeneous environment.

Published
2023

10. Offloading electromagnetic shower transport to GPUs

Author

Amadio, G, primary, Apostolakis, J, additional, Buncic, P, additional, Cosmo, G, additional, Dosaru, D, additional, Gheata, A, additional, Hageboeck, S, additional, Hahnfeld, J, additional, Hodgkinson, M, additional, Morgan, B, additional, Novak, M, additional, Petre, A A, additional, Pokorski, W, additional, Ribon, A, additional, Stewart, G A, additional, and Vila, P M, additional

Published
2023
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11. Challenges and opportunities integrating LLAMA into AdePT

Author

Gruber, B. M., Amadio, G., and Hageböck, S.

Subjects
particle transport simulation, High Energy Physics - Experiment (hep-ex), physics.comp-ph, hep-ex, GPU, Other Fields of Physics, FOS: Physical sciences, Computational Physics (physics.comp-ph), AdePT, LLAMA, Physics - Computational Physics, Particle Physics - Experiment, High Energy Physics - Experiment
Abstract

Particle transport simulations are a cornerstone of high-energy physics (HEP), constituting almost half of the entire computing workload performed in HEP. To boost the simulation throughput and energy efficiency, GPUs as accelerators have been explored in recent years, further driven by the increasing use of GPUs on HPCs. The Accelerated demonstrator of electromagnetic Particle Transport (AdePT) is an advanced prototype for offloading the simulation of electromagnetic showers in Geant4 to GPUs, and still undergoes continuous development and optimization. Improving memory layout and data access is vital to use modern, massively parallel GPU hardware efficiently, contributing to the challenge of migrating traditional CPU based data structures to GPUs in AdePT. The low-level abstraction of memory access (LLAMA) is a C++ library that provides a zero-runtime-overhead data structure abstraction layer, focusing on multidimensional arrays of nested, structured data. It provides a framework for defining and switching custom memory mappings at compile time to define data layouts and instrument data access, making LLAMA an ideal tool to tackle the memory-related optimization challenges in AdePT. Our contribution shares insights gained with LLAMA when instrumenting data access inside AdePT, complementing traditional GPU profiler outputs. We demonstrate traces of read/write counts to data structure elements as well as memory heatmaps. The acquired knowledge allowed for subsequent data layout optimizations.

Published
2023

12. LLAMA: The Low-Level Abstraction For Memory Access

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., (0000-0002-8258-3881) Bussmann, M., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., and (0000-0002-8258-3881) Bussmann, M.

Abstract

The performance gap between CPU and memory widens continuously. Choosing the best memory layout for each hardware architecture is increasingly important as more and more programs become memory bound. For portable codes that run across heterogeneous hardware architectures, the choice of the memory layout for data structures is ideally decoupled from the rest of a program. This can be accomplished via a zero-runtime-overhead abstraction layer, underneath which memory layouts can be freely exchanged. We present the Low-Level Abstraction of Memory Access (LLAMA), a C++ library that provides such a data structure abstraction layer with example implementations for multidimensional arrays of nested, structured data. LLAMA provides fully C++ compliant methods for defining and switching custom memory layouts for user-defined data types. The library is extensible with third-party allocators. Providing two close-to-life examples, we show that the LLAMA-generated AoS (Array of Structs) and SoA (Struct of Arrays) layouts produce identical code with the same performance characteristics as manually written data structures. Integrations into the SPEC CPU® lbm benchmark and the particle-in-cell simulation PIConGPU demonstrate LLAMA's abilities in real-world applications. LLAMA's layout-aware copy routines can significantly speed up transfer and reshuffling of data between layouts compared with naive element-wise copying. LLAMA provides a novel tool for the development of high-performance C++ applications in a heterogeneous environment.

Published
2022

13. Challenges and opportunities integrating LLAMA into AdePT

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9359-2196) Hageböck, S., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., and (0000-0001-9359-2196) Hageböck, S.

Abstract

Particle transport simulations are a cornerstone of high-energy physics (HEP), constituting almost half of the entire computing workload performed in HEP. To boost the simulation throughput and energy efficiency, GPUs as accelerators have been explored in recent years, further driven by the increasing use of GPUs on HPCs. The Accelerated demonstrator of electromagnetic Particle Transport (AdePT) is an advanced prototype for offloading the simulation of electromagnetic showers in Geant4 to GPUs, and still undergoes continuous development and optimization. Improving memory layout and data access is vital to use modern, massively parallel GPU hardware efficiently, contributing to the challenge of migrating traditional CPU based data structures to GPUs in AdePT. The low-level abstraction of memory access (LLAMA) is a C++ library that provides a zero-runtime-overhead data structure abstraction layer, focusing on multidimensional arrays of nested, structured data. It provides a framework for defining and switching custom memory mappings at compile time to define data layouts and instrument data access, making LLAMA an ideal tool to tackle the memory-related optimization challenges in AdePT. Our contribution shares insights gained with LLAMA when instrumenting data access inside AdePT, complementing traditional GPU profiler outputs. We demonstrate traces of read/write counts to data structure elements as well as memory heatmaps. The acquired knowledge allowed for subsequent data layout optimizations.

Published
2022

14. Data publication: LLAMA: The Low-Level Abstraction For Memory Access

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., (0000-0002-8258-3881) Bussmann, M., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., and (0000-0002-8258-3881) Bussmann, M.

Abstract

The performance gap between CPU and memory widens continuously. Choosing the best memory layout for each hardware architecture is increasingly important as more and more programs become memory bound. For portable codes that run across heterogeneous hardware architectures, the choice of the memory layout for data structures is ideally decoupled from the rest of a program. This can be accomplished via a zero-runtime-overhead abstraction layer, underneath which memory layouts can be freely exchanged. We present the Low-Level Abstraction of Memory Access (LLAMA), a C++ library that provides such a data structure abstraction layer with example implementations for multidimensional arrays of nested, structured data. LLAMA provides fully C++ compliant methods for defining and switching custom memory layouts for user-defined data types. The library is extensible with third-party allocators. Providing two close-to-life examples, we show that the LLAMA-generated AoS (Array of Structs) and SoA (Struct of Arrays) layouts produce identical code with the same performance characteristics as manually written data structures. Integrations into the SPEC CPU® lbm benchmark and the particle-in-cell simulation PIConGPU demonstrate LLAMA's abilities in real-world applications. LLAMA's layout-aware copy routines can significantly speed up transfer and reshuffling of data between layouts compared with naive element-wise copying. LLAMA provides a novel tool for the development of high-performance C++ applications in a heterogeneous environment.

Published
2022

15. LLAMA: The Low-Level Abstraction For Memory Access

Author

(0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., (0000-0002-8258-3881) Bussmann, M., (0000-0001-7848-1690) Gruber, B. M., (0000-0002-2102-7945) Amadio, G., (0000-0001-9750-6224) Blomer, J., (0000-0002-6702-2015) Matthes, A., (0000-0003-1642-0459) Widera, R., and (0000-0002-8258-3881) Bussmann, M.

Abstract

The performance gap between CPU and memory widens continuously. Choosing the best memory layout for each hardware architecture is increasingly important as more and more programs become memory bound. For portable codes that run across heterogeneous hardware architectures, the choice of the memory layout for data structures is ideally decoupled from the rest of a program. This can be accomplished via a zero-runtime-overhead abstraction layer, underneath which memory layouts can be freely exchanged. We present the Low-Level Abstraction of Memory Access (LLAMA), a C++ library that provides such a data structure abstraction layer with example implementations for multidimensional arrays of nested, structured data. LLAMA provides fully C++ compliant methods for defining and switching custom memory layouts for user-defined data types. The library is extensible with third-party allocators. Providing two close-to-life examples, we show that the LLAMA-generated AoS (Array of Structs) and SoA (Struct of Arrays) layouts produce identical code with the same performance characteristics as manually written data structures. Integrations into the SPEC CPU® lbm benchmark and the particle-in-cell simulation PIConGPU demonstrate LLAMA's abilities in real-world applications. LLAMA's layout-aware copy routines can significantly speed up transfer and reshuffling of data between layouts compared with naive element-wise copying. LLAMA provides a novel tool for the development of high-performance C++ applications in a heterogeneous environment.

Published
2021

16. GeantV

Author

Amadio, G., primary, Ananya, A., additional, Apostolakis, J., additional, Bandieramonte, M., additional, Banerjee, S., additional, Bhattacharyya, A., additional, Bianchini, C., additional, Bitzes, G., additional, Canal, P., additional, Carminati, F., additional, Chaparro-Amaro, O., additional, Cosmo, G., additional, De Fine Licht, J. C., additional, Drogan, V., additional, Duhem, L., additional, Elvira, D., additional, Fuentes, J., additional, Gheata, A., additional, Gheata, M., additional, Gravey, M., additional, Goulas, I., additional, Hariri, F., additional, Jun, S. Y., additional, Konstantinov, D., additional, Kumawat, H., additional, Lima, J. G., additional, Maldonado-Romo, A., additional, Martínez-Castro, J., additional, Mato, P., additional, Nikitina, T., additional, Novaes, S., additional, Novak, M., additional, Pedro, K., additional, Pokorski, W., additional, Ribon, A., additional, Schmitz, R., additional, Seghal, R., additional, Shadura, O., additional, Tcherniaev, E., additional, Vallecorsa, S., additional, Wenzel, S., additional, and Zhang, Y., additional

Published
2021
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17. Prevalence of acquired resistance mutations in a large cohort of perinatally infected HIV-1 patients

Author

Ungaro, R., Taramasso, L., Bruzzone, B., Vicenti, I., Galli, L., Borghi, V., Francisci, D., Pecorari, M., Zoncada, A., Callegaro, A. P., Paolini, E., Monno, L., Bonora, S., Di Biagio, A., ARCA Study Group, Giacometti, A., Butini, L., del Gobbo, R., Bagnarelli, P., Tacconi, D., Corbelli, G., Zanussi, S., Punzi, G., Maggiolo, F., Calza, L., Carla Re, M., Pristera, R., Turconi, P., Mandas, A., Tini, S., Amadio, G., Sighinolfi, L., Corsi, P., Di Pietro, M., Colao, G., Tosti, A., Setti, M., Cenderello, G., Trezzi, M., Orani, A., Arcidiacono, I., Degiuli, A., De Gennaro, M., Chiodera, A., Scalzini, A., Palvarini, L., Todaro, G., Rusconi, S., Gismondo, M. R., Micheli, V., Biondi, M. L., Capetti, A., Meraviglia, P., Boeri, E., Mussini, C., Soria, A., Vecchi, L., Santirocchi, M., Brustia, D., Ravanini, P., Dal Bello, F., Romano, N., Mancuso, S., Calzetti, C., Maserati, R., Filice, G., Baldanti, F., Parruti, G., Polilli, E., Sacchini, D., Martinelli, C., Consolini, R., Vatteroni, L., Vivarelli, A., Nerli, A., Lenzi, L., Magnani, G., Ortolani, P., Andreoni, M., Fimiani, C., Palmisano, L., Di Giambenedetto, S., Vullo, V., Turriziani, O., Montano, M., Antinori, A., Zaccarelli, M., Dentone, C., Gonnelli, A., De Luca, A., Palumbo, M., Ghisetti, V., Delle Foglie, P., Rossi, C., Mondino, V., Malena, M., Grossi, P., Seminari, E., Poletti, F., Ungaro R., Taramasso L., Bruzzone B., Vicenti I., Galli L., Borghi V., Francisci D., Pecorari M., Zoncada A., Callegaro A.P., Paolini E., Monno L., Bonora S., Di Biagio A., Giacometti A., Butini L., del Gobbo R., Bagnarelli P., Tacconi D., Corbelli G., Zanussi S., Punzi G., Maggiolo F., Calza L., Carla Re M., Pristera R., Turconi P., Mandas A., Tini S., Amadio G., Sighinolfi L., Corsi P., Di Pietro M., Colao G., Tosti A., Setti M., Cenderello G., Trezzi M., Orani A., Arcidiacono I., Degiuli A., De Gennaro M., Chiodera A., Scalzini A., Palvarini L., Todaro G., Rusconi S., Gismondo M.R., Micheli V., Biondi M.L., Capetti A., Meraviglia P., Boeri E., Mussini C., Soria A., Vecchi L., Santirocchi M., Brustia D., Ravanini P., Dal Bello F., Romano N., Mancuso S., Calzetti C., Maserati R., Filice G., Baldanti F., Parruti G., Polilli E., Sacchini D., Martinelli C., Consolini R., Vatteroni L., Vivarelli A., Nerli A., Lenzi L., Magnani G., Ortolani P., Andreoni M., Fimiani C., Palmisano L., Di Giambenedetto S., Vullo V., Turriziani O., Montano M., Antinori A., Zaccarelli M., Dentone C., Gonnelli A., De Luca A., Palumbo M., Ghisetti V., Delle Foglie P., Rossi C., Mondino V., Malena M., Grossi P., Seminari E., and Poletti F.

Subjects
Male, antiretroviral treatment, Infectious Disease Transmission, genotype, Human immunodeficiency virus (HIV), Drug Resistance, HIV Infections, Drug resistance, medicine.disease_cause, Retrospective Studie, Genotype, pol Gene Products, Human Immunodeficiency Viru, Prevalence, Medicine, Vertical, HIV Infection, Viral, pol Gene Products, Young adult, General Medicine, Infectious Diseases, Italy, Mutation (genetic algorithm), Female, Human Immunodeficiency Virus, Human, Microbiology (medical), Adult, Settore MED/17 - Malattie Infettive, Adolescent, Anti-HIV Agents, Young Adult, Acquired resistance, Drug Resistance, Viral, Humans, vertical HIV transmission, HIV-1, Mutation, Retrospective Studies, pol Gene Products, Human Immunodeficiency Virus, Infectious Disease Transmission, Vertical, HIV perinatally infection, business.industry, Anti-HIV Agent, Retrospective cohort study, Virology, Large cohort, business
Published
2019

18. Tolerability of bevacizumab in elderly ovarian cancer patients (Turbo study): A case-control study of a real-life experience

Author

Amadio, G., Marchetti, Claudia, Villani, Emanuele Rocco, Fusco, Domenico, Stollagli, F., Bottoni, C., Distefano, Maria Grazia, Colloca, Giuseppe Ferdinando, Scambia, Giovanni, Fagotti, Anna, Marchetti C. (ORCID:0000-0001-7098-8956), Villani E. R., Fusco D., Distefano M., Colloca G., Scambia G. (ORCID:0000-0003-2758-1063), Fagotti A. (ORCID:0000-0001-5579-335X), Amadio, G., Marchetti, Claudia, Villani, Emanuele Rocco, Fusco, Domenico, Stollagli, F., Bottoni, C., Distefano, Maria Grazia, Colloca, Giuseppe Ferdinando, Scambia, Giovanni, Fagotti, Anna, Marchetti C. (ORCID:0000-0001-7098-8956), Villani E. R., Fusco D., Distefano M., Colloca G., Scambia G. (ORCID:0000-0003-2758-1063), and Fagotti A. (ORCID:0000-0001-5579-335X)

Abstract

Objective: Bevacizumab maintenance following platinum-based chemotherapy is an effective treatment for epithelial ovarian cancer (EOC), both in primary and recurrent disease. Our aim was to identify criteria to select elderly patients who can safely benefit from bevacizumab addition. Methods: This is a case-control study on patients with primary or recurrent EOC who received platinum-based chemotherapy plus bevacizumab, between January 2015 and December 2016. Patient characteristics, treatment details and adverse events were reviewed and analyzed in 2 settings: younger (<65 years, group 1) and elderly (≥65 years, group 2). A binary logistic model was applied to correlate clinical variables and severe (grade ≥3) toxicity risk. Results: Overall, 283 patients with EOC were included, with 72 (25.4%) older patients compared with 211 (74.6%) younger women. Bevacizumab had been administered to 234 patients (82.7%) as first-line treatment and in 49 (17.3%) with recurrent disease. At diagnosis, elderly patients presented with at least one comorbidity and were taking at least 1 medication in 84.7% and 80.6% of the cases respectively, compared with correspondingly 47.4% and 37.4% in group 1 (p<0.001). Nonetheless, the occurrence of serious (grade ≥3) adverse events did not increase among the older group. Creatinine serum levels >1.1 g/dL, estimated glomerular filtration rate (eGFR) ≤60 mL/min, ≥3 comorbidities were independently associated with a higher severe toxicity. Conclusions: Elderly patients with EOC can safely be treated with bevacizumab; factors other than age, as higher creatinine serum levels, eGFR and number of comorbidities should be considered to better estimate bevacizumab-related toxicity risk.

Published
2020

19. Role of Retinoblastoma Protein Family (Rb/p105 and Rb2/p130) Expression in the Histopathological Classification of Borderline Ovarian Tumors

Author

Masciullo, Valeria, Valdivieso, P., Amadio, G., Santoro, Angela, Angelico, G., Sgambato, Alessandro, Boffo, S., Giordano, Alessandro, Scambia, Giovanni, Zannoni, Gian Franco, Masciullo V., Santoro A. (ORCID:0000-0002-6964-5152), Sgambato A. (ORCID:0000-0002-9487-4563), Giordano A. (ORCID:0000-0002-6978-0880), Scambia G. (ORCID:0000-0003-2758-1063), Zannoni G. F. (ORCID:0000-0003-1809-129X), Masciullo, Valeria, Valdivieso, P., Amadio, G., Santoro, Angela, Angelico, G., Sgambato, Alessandro, Boffo, S., Giordano, Alessandro, Scambia, Giovanni, Zannoni, Gian Franco, Masciullo V., Santoro A. (ORCID:0000-0002-6964-5152), Sgambato A. (ORCID:0000-0002-9487-4563), Giordano A. (ORCID:0000-0002-6978-0880), Scambia G. (ORCID:0000-0003-2758-1063), and Zannoni G. F. (ORCID:0000-0003-1809-129X)

Abstract

Borderline ovarian tumors (BOT) are uncommon but not rare epithelial ovarian neoplasms, intermediate between benign and malignant categories. Emerging knowledge supports the notion that subtypes of borderline ovarian tumors comprise distinct biologic, pathogenetic, and molecular entities, precluding a single unifying concept for BOT. The identification of valuable markers for the diagnosis and classification of these tumors is in need. Among the molecular candidates, the Retinoblastoma (Rb) family members Rb/p105 and Rb2/p130 seem to play a pivotal role in ovarian cancer. In particular, Rb/p105, when in the unphosphorylated form, acts as a growth suppressor controlling cell cycle and tumor progression; whereas, the phosphorylated form activates gene transcription and cellular proliferation. While Rb/p105 is ubiquitously confined to the nuclei of cycling and quiescent cells, Rb2/p130 activity is also regulated by intracellular localization. According to this, Rb family members could represent a novel marker in diagnosis and classification risk for patients with BOT. In this study, we evaluated the expression and subcellular localization of proteins of the retinoblastoma (Rb) gene family in 65 ovarian borderline tumors. Statistically significant differences were found in nuclear and cytoplasmic expressions of Rb/p105 and Rb2/p130 according to different examined histotypes. In detail, the nuclear expression of Rb/p105 and Rb2/p130 was more frequently detected in serous (84.6%) than sero-mucinous (42.1%) and mucinous (50%) types. Conversely, the cytoplasmic expression of Rb2/p130 was not detected in serous tumors and frequently observed in mucinous subtypes (80%). Our findings suggest that Rb proteins do not play a key role in the tumor progression of serous borderline tumors since any cases showed cytoplasmic localization. By contrast, the observed higher cytoplasmic expression of Rb2/p130 in intestinal mucinous BOTs is indicative of Rb protein family involvement in th

Published
2020

23. A Roadmap for HEP Software and Computing R&D for the 2020s

Author

Jr, AAA, Amadio, G, Anh-Ky, N, Aphecetche, L, Apostolakis, J, Asai, M, Atzori, L, Babik, M, Bagliesi, G, Bandieramonte, M, Barisits, M, Bauerdick, LAT, Belforte, S, Benjamin, D, Bernius, C, Bhimji, W, Bianchi, RM, Bird, I, Biscarat, C, Blomer, J, Bloom, K, Boccali, T, Bockelman, B, Bold, T, Bonacorsi, D, Boveia, A, Bozzi, C, Bracko, M, Britton, D, Buckley, A, Buncic, P, Calafiura, P, Campana, S, Canal, P, Canali, L, Carlino, G, Castro, N, Cattaneo, M, Cerminara, G, Chang, P, Chapman, J, Chen, G, Childers, T, Clarke, P, Clemencic, M, Cogneras, E, Collier, I, Corti, G, Cosmo, G, Costanzo, D, Couturier, B, Cranmer, K, Cranshaw, J, Cristella, L, Crooks, D, Crépé-Renaudin, S, Dallmeier-Tiessen, S, De, K, Cian, MD, Girolamo, AD, Dimitrov, G, Doglioni, C, Dotti, A, Duellmann, D, Duflot, L, Dykstra, D, Dziedziniewicz-Wojcik, K, Dziurda, A, Egede, U, Elmer, P, Elmsheuser, J, Elvira, VD, Eulisse, G, Ferber, T, Filipcic, A, Fisk, I, Fitzpatrick, C, Flix, J, Formica, A, Forti, A, Gaede, F, Ganis, G, Gardner, R, Garonne, V, Gellrich, A, Genser, K, George, S, Geurts, F, Gheata, A, Gheata, M, Giacomini, F, Giagu, S, Giffels, M, Gingrich, D, Girone, M, Gligorov, VV, Glushkov, I, Gohn, W, Lopez, JBG, Caballero, IG, Fernández, JRG, Govi, G, Grandi, C, Grasland, H, Gray, H, Grillo, L, Guan, W, Gutsche, O, Gyurjyan, V, Hanushevsky, A, Hariri, F, Hartmann, T, Harvey, J, Hauth, T, Hegner, B, Heinemann, B, Heinrich, L, Hernández, JM, Hildreth, M, Hodgkinson, M, Hoeche, S, Hristov, P, Huang, X, Ivanchenko, VN, Ivanov, T, Jashal, B, Jayatilaka, B, Jones, R, Jouvin, M, Jun, SY, Kagan, M, Kalderon, CW, Karavakis, E, Katz, DS, Kcira, D, Kersevan, BP, Kirby, M, Klimentov, A, Klute, M, Komarov, I, Koppenburg, P, Kowalkowski, J, Kreczko, L, Kuhr, T, Kutschke, R, Kuznetsov, V, Lampl, W, Lancon, E, Lange, D, Lassnig, M, Laycock, P, Leggett, C, Letts, J, Lewendel, B, Li, T, Lima, G, Linacre, J, Linden, T, Presti, GL, Lopienski, S, Love, P, Marshall, ZL, Martelli, E, Martin-Haugh, S, Mato, P, Mazumdar, K, McCauley, T, McFayden, J, McKee, S, McNab, A, Meinhard, H, Menasce, D, Lorenzo, PM, Mete, AS, Michelotto, M, Mitrevski, J, Moneta, L, Morgan, B, Mount, R, Moyse, E, Murray, S, Neubauer, MS, Novaes, S, Novak, M, Oyanguren, A, Ozturk, N, Pages, AP, Paganini, M, Pansanel, J, Pascuzzi, VR, Pearce, A, Pearson, B, Pedro, K, Perdue, G, Yzquierdo, AP-C, Perrozzi, L, Petersen, T, Petric, M, Piedra, J, Piilonen, L, Piparo, D, Pokorski, W, Polci, F, Potamianos, K, Psihas, F, Raven, G, Reuter, J, Ribon, A, Ritter, M, Robinson, J, Rodrigues, E, Roiser, S, Rousseau, D, Roy, G, Sailer, A, Sakuma, T, Santana, R, Sartirana, A, Schellman, H, Schovancová, J, Schramm, S, Schulz, M, Sciabà, A, Seidel, S, Sekmen, S, Serfon, C, Severini, H, Sexton-Kennedy, E, Seymour, M, Shapoval, I, Shiers, J, Shiu, J-G, Short, H, Siroli, GP, Skipsey, S, Smith, T, Snyder, S, Sokoloff, MD, Stadie, H, Stark, G, Stewart, G, Sánchez-Hernández, A, Templon, J, Tenaglia, G, Tsulaia, V, Tunnell, C, Vaandering, E, Valassi, A, Vallecorsa, S, Valsan, L, Gemmeren, PV, Vernet, R, Viren, B, Vlimant, J-R, Voss, C, Vuosalo, C, Sierra, CV, Wartel, R, Wenaus, T, Wenzel, S, Winklmeier, F, Wissing, C, Wuerthwein, F, Wynne, B, Xiaomei, Z, Yang, W, Yazgan, E, Jr, AAA, Amadio, G, Anh-Ky, N, Aphecetche, L, Apostolakis, J, Asai, M, Atzori, L, Babik, M, Bagliesi, G, Bandieramonte, M, Barisits, M, Bauerdick, LAT, Belforte, S, Benjamin, D, Bernius, C, Bhimji, W, Bianchi, RM, Bird, I, Biscarat, C, Blomer, J, Bloom, K, Boccali, T, Bockelman, B, Bold, T, Bonacorsi, D, Boveia, A, Bozzi, C, Bracko, M, Britton, D, Buckley, A, Buncic, P, Calafiura, P, Campana, S, Canal, P, Canali, L, Carlino, G, Castro, N, Cattaneo, M, Cerminara, G, Chang, P, Chapman, J, Chen, G, Childers, T, Clarke, P, Clemencic, M, Cogneras, E, Collier, I, Corti, G, Cosmo, G, Costanzo, D, Couturier, B, Cranmer, K, Cranshaw, J, Cristella, L, Crooks, D, Crépé-Renaudin, S, Dallmeier-Tiessen, S, De, K, Cian, MD, Girolamo, AD, Dimitrov, G, Doglioni, C, Dotti, A, Duellmann, D, Duflot, L, Dykstra, D, Dziedziniewicz-Wojcik, K, Dziurda, A, Egede, U, Elmer, P, Elmsheuser, J, Elvira, VD, Eulisse, G, Ferber, T, Filipcic, A, Fisk, I, Fitzpatrick, C, Flix, J, Formica, A, Forti, A, Gaede, F, Ganis, G, Gardner, R, Garonne, V, Gellrich, A, Genser, K, George, S, Geurts, F, Gheata, A, Gheata, M, Giacomini, F, Giagu, S, Giffels, M, Gingrich, D, Girone, M, Gligorov, VV, Glushkov, I, Gohn, W, Lopez, JBG, Caballero, IG, Fernández, JRG, Govi, G, Grandi, C, Grasland, H, Gray, H, Grillo, L, Guan, W, Gutsche, O, Gyurjyan, V, Hanushevsky, A, Hariri, F, Hartmann, T, Harvey, J, Hauth, T, Hegner, B, Heinemann, B, Heinrich, L, Hernández, JM, Hildreth, M, Hodgkinson, M, Hoeche, S, Hristov, P, Huang, X, Ivanchenko, VN, Ivanov, T, Jashal, B, Jayatilaka, B, Jones, R, Jouvin, M, Jun, SY, Kagan, M, Kalderon, CW, Karavakis, E, Katz, DS, Kcira, D, Kersevan, BP, Kirby, M, Klimentov, A, Klute, M, Komarov, I, Koppenburg, P, Kowalkowski, J, Kreczko, L, Kuhr, T, Kutschke, R, Kuznetsov, V, Lampl, W, Lancon, E, Lange, D, Lassnig, M, Laycock, P, Leggett, C, Letts, J, Lewendel, B, Li, T, Lima, G, Linacre, J, Linden, T, Presti, GL, Lopienski, S, Love, P, Marshall, ZL, Martelli, E, Martin-Haugh, S, Mato, P, Mazumdar, K, McCauley, T, McFayden, J, McKee, S, McNab, A, Meinhard, H, Menasce, D, Lorenzo, PM, Mete, AS, Michelotto, M, Mitrevski, J, Moneta, L, Morgan, B, Mount, R, Moyse, E, Murray, S, Neubauer, MS, Novaes, S, Novak, M, Oyanguren, A, Ozturk, N, Pages, AP, Paganini, M, Pansanel, J, Pascuzzi, VR, Pearce, A, Pearson, B, Pedro, K, Perdue, G, Yzquierdo, AP-C, Perrozzi, L, Petersen, T, Petric, M, Piedra, J, Piilonen, L, Piparo, D, Pokorski, W, Polci, F, Potamianos, K, Psihas, F, Raven, G, Reuter, J, Ribon, A, Ritter, M, Robinson, J, Rodrigues, E, Roiser, S, Rousseau, D, Roy, G, Sailer, A, Sakuma, T, Santana, R, Sartirana, A, Schellman, H, Schovancová, J, Schramm, S, Schulz, M, Sciabà, A, Seidel, S, Sekmen, S, Serfon, C, Severini, H, Sexton-Kennedy, E, Seymour, M, Shapoval, I, Shiers, J, Shiu, J-G, Short, H, Siroli, GP, Skipsey, S, Smith, T, Snyder, S, Sokoloff, MD, Stadie, H, Stark, G, Stewart, G, Sánchez-Hernández, A, Templon, J, Tenaglia, G, Tsulaia, V, Tunnell, C, Vaandering, E, Valassi, A, Vallecorsa, S, Valsan, L, Gemmeren, PV, Vernet, R, Viren, B, Vlimant, J-R, Voss, C, Vuosalo, C, Sierra, CV, Wartel, R, Wenaus, T, Wenzel, S, Winklmeier, F, Wissing, C, Wuerthwein, F, Wynne, B, Xiaomei, Z, Yang, W, and Yazgan, E

Abstract

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R\&D activities required to prepare for this software upgrade.

Published
2018

24. Declining Prevalence of HIV-1 Drug Resistance in Antiretroviral Treatment-exposed Individuals in Western Europe

Author

De Luca, A, Dunn, D, Zazzi, M, Camacho, R, Torti, C, Fanti, I, Kaiser, R, Sönnerborg, A, Codoñer, Fm, Van Laethem, K, Vandamme, Am, Bansi, L, Ghisetti, V, van de Vijver DA, Asboe, D, Prosperi, Mc, Di Giambenedetto, S, Collaborators: Giacometti A, SEHERE collaboration in C. h. a. i. n., Butini, L, del Gobbo, R, Menzo, S, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Maggiolo, F, Callegaro, A, Calza, L, Pristerà, R, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Colao, G, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Monforte, Ad, Cicconi, P, Rusconi, S, Gismondo, Mr, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Pecorari, M, Soria, A, Vecchi, L, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, Rita, De Luca, A, Dunn, D, Zazzi, M, Camacho, R, Torti, C, Fanti, I, Kaiser, R, Sönnerborg, A, Codoñer, F, Van Laethem, K, Vandamme, A, Bansi, L, Ghisetti, V, Van De Vijver, D, Asboe, D, Prosperi, M, Di Giambenedetto, S, Mancuso, S, and Virology

Subjects
Male, Multivariate analysis, Databases, Factual, Drug Resistance, HIV Infections, Drug resistance, 0302 clinical medicine, Retrospective Studie, Risk Factors, Epidemiology, Genotype, pol Gene Products, Human Immunodeficiency Viru, Odds Ratio, Prevalence, Immunology and Allergy, HIV Infection, 030212 general & internal medicine, pol Gene Products, Viral, Multivariate Analysi, media_common, 0303 health sciences, Drug Resistance Prevalence HIV-1, Middle Aged, Resistance mutation, 3. Good health, Reverse Transcriptase Inhibitor, Europe, Infectious Diseases, Reverse Transcriptase Inhibitors, epidemiology, Female, Multiple, Human Immunodeficiency Virus, Human, Drug, Adult, medicine.medical_specialty, Evolution, media_common.quotation_subject, Sexual Behavior, antiretroviral therapy, Infectious Disease, Biology, Settore MED/17 - MALATTIE INFETTIVE, Evolution, Molecular, 03 medical and health sciences, Databases, SDG 3 - Good Health and Well-being, Drug Resistance, Multiple, Viral, medicine, Humans, HIV Protease Inhibitor, Factual, Retrospective Studies, 030306 microbiology, Risk Factor, Molecular, Retrospective cohort study, Odds ratio, HIV Protease Inhibitors, CD4 Lymphocyte Count, drug resistance, genotyping, HIV-1, Multivariate Analysis, Mutation, pol Gene Products, Human Immunodeficiency Virus, Immunology, Demography
Abstract

HIV-1 drug resistance represents a major obstacle to infection and disease control. This retrospective study analyzes trends and determinants of resistance in antiretroviral treatment (ART)-exposed individuals across 7 countries in Europe. Of 20 323 cases, 80% carried at least one resistance mutation: these declined from 81% in 1997 to 71% in 2008. Predicted extensive 3-class resistance was rare (3.2% considering the cumulative genotype) and peaked at 4.5% in 2005, decreasing thereafter. The proportion of cases exhausting available drug options dropped from 32% in 2000 to 1% in 2008. Reduced risk of resistance over calendar years was confirmed by multivariable analysis. © 2013 The Author.

Published
2013
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25. Verification of Electromagnetic Physics Models for Parallel Computing Architectures in the GeantV Project

Author

Amadio, G, primary, Apostolakis, J, additional, Bandieramonte, M, additional, Behera, S P, additional, Brun, R, additional, Canal, P, additional, Carminati, F, additional, Cosmo, G, additional, Duhem, L, additional, Elvira, D, additional, Folger, G, additional, Gheata, A, additional, Gheata, M, additional, Goulas, I, additional, Hariri, F, additional, Jun, S Y, additional, Konstantinov, D, additional, Kumawat, H, additional, Ivantchenko, V, additional, Lima, G, additional, Nikitina, T, additional, Novak, M, additional, Pokorski, W, additional, Ribon, A, additional, Seghal, R, additional, Shadura, O, additional, Vallecorsa, S, additional, and Wenzel, S, additional

Published
2017
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26. Stochastic optimization of GeantV code by use of genetic algorithms

Author

Amadio, G., primary, Apostolakis, J., additional, Bandieramonte, M., additional, Behera, S.P., additional, Brun, R., additional, Canal, P., additional, Carminati, F., additional, Cosmo, G., additional, Duhem, L., additional, Elvira, D., additional, Folger, G., additional, Gheata, A., additional, Gheata, M., additional, Goulas, I., additional, Hariri, F., additional, Jun, S.Y., additional, Konstantinov, D., additional, Kumawat, H., additional, Ivantchenko, V., additional, Lima, G., additional, Nikitina, T., additional, Novak, M., additional, Pokorski, W., additional, Ribon, A., additional, Seghal, R., additional, Shadura, O., additional, Vallecorsa, S., additional, and Wenzel, S., additional

Published
2017
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27. Performance of GeantV EM Physics Models

Author

Amadio, G, primary, Ananya, A, additional, Apostolakis, J, additional, Aurora, A, additional, Bandieramonte, M, additional, Bhattacharyya, A, additional, Bianchini, C, additional, Brun, R, additional, Canal, P, additional, Carminati, F, additional, Cosmo, G, additional, Duhem, L, additional, Elvira, D, additional, Folger, G, additional, Gheata, A, additional, Gheata, M, additional, Goulas, I, additional, Iope, R, additional, Jun, S Y, additional, Lima, G, additional, Mohanty, A, additional, Nikitina, T, additional, Novak, M, additional, Pokorski, W, additional, Ribon, A, additional, Seghal, R, additional, Shadura, O, additional, Vallecorsa, S, additional, Wenzel, S, additional, and Zhang, Y, additional

Published
2017
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28. Genotypic resistance profiles associated with virological failure to darunavir-containing regimens: a cross-sectional analysis

Author

Sterrantino, G, Zaccarelli, M, Colao, G, Baldanti, F, Di Giambenedetto, S, Carli, T, Maggiolo, F, Zazzi, M, Giacometti, A, Butini, L, Del Gobbo, R, Bagnarelli, P, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Callegaro, A, Calza, L, Re, MC, Pristera, R, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, di Biagio, A, Penco, G, Trezzi, M, Orani, A, Pardelli, R, Arcidiacono, I, Degiuli, A, de Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Cicconi, P, Rusconi, S, Gismondo, MR, Micheli, V, Biondi ML, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Pecorari, M, Soria, A, Vecchi, L, Gerardo, AO, Santirocchi, M, Brustia, D, Maggiore, AO, Ravanini, P, Bello, FD, Romano, N, MANCUSO, Salvatrice, Calzetti, C, Maserati, R, Filice, G, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, di Giambenedetto, S, Colafigli, M, Vullo, V, Turriziani, O, Montano, M, Antinori, A, Dentone, C, Gonnelli, A, de Luca, A, Palumbo, M, Ghisetti, V, Bonora, S, Foglie, PD, Rossi, C, Mondino, V, Malena, M, Grossi, P, Seminari, E, Poletti, F., Sterrantino, G, Zaccarelli, M, Colao, G, Baldanti, F, Di Giambenedetto, S, Carli, T, Maggiolo, F, Zazzi, M, Giacometti, A, Butini, L, Del Gobbo, R, Bagnarelli, P, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Callegaro, A, Calza, L, Re, MC, Pristera, R, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, di Biagio, A, Penco, G, Trezzi, M, Orani, A, Pardelli, R, Arcidiacono, I, Degiuli, A, de Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Cicconi, P, Rusconi, S, Gismondo, MR, Micheli, V, Biondi ML, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Pecorari, M, Soria, A, Vecchi, L, Gerardo, AO, Santirocchi, M, Brustia, D, Maggiore, AO, Ravanini, P, Bello, FD, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, di Giambenedetto, S, Colafigli, M, Vullo, V, Turriziani, O, Montano, M, Antinori, A, Dentone, C, Gonnelli, A, de Luca, A, Palumbo, M, Ghisetti, V, Bonora, S, Foglie, PD, Rossi, C, Mondino, V, Malena, M, Grossi, P, Seminari, E, and Poletti, F

Subjects
Male, Time Factors, Cross-sectional study, Human immunodeficiency virus (HIV), Drug Resistance, HIV Infections, Drug resistance, medicine.disease_cause, Cohort Studies, Antiretroviral Therapy, Highly Active, Ritonavir-boosted darunavir, Genotype, HIV Infection, Treatment Failure, Viral, Genotypic resistance, Darunavir, Sulfonamides, General Medicine, Middle Aged, Virological failure, Infectious Diseases, Female, Human, medicine.drug, Adult, Microbiology (medical), Logistic Model, Time Factor, Antiretroviral Therapy, Settore MED/17 - MALATTIE INFETTIVE, Sulfonamide, Drug Resistance, Viral, medicine, Humans, Highly Active, Protease inhibitors, Cross-Sectional Studies, HIV Protease Inhibitors, HIV-1, Logistic Models, Mutation, HIV Protease Inhibitor, Cross-Sectional Studie, business.industry, Antiretroviral therapy, Virology, Protease inhibitor, Cohort Studie, business
Abstract

Introduction: This study aimed at defining protease (PR) resistance mutations associated with darunavir (DRV) failure and PR resistance evolution at DRV failure in a large database of treatment-experienced human immunodeficiency virus (HIV) patients. Results: Overall, 1,104 patients were included: 118 (10.7%) failed at a median observation time of 16 months. The mean number of PR mutations at baseline was 2.7, but it was higher in patients who subsequently failed DRV. In addition, the number of PR mutations increased at failure. The increase in the mean number of mutations was completely related to mutations considered to be associated with DRV resistance following the indications of the main DRV clinical trials. Discussion The higher statistical difference at baseline between failing versus non-failing patients was observed for the V32I and I84V mutations. At DRV failure, the major increase was still observed for V32I; I54L, V11I, T74P and I50V also increased. Despite the increment in the mean number of mutations per patient between baseline and failure, in 21 patients (17.8%) at baseline and 36 (30.5%) at failure, no PR mutation was detected. Conclusion: The HIV-DB interpretation algorithm identified few patients with full DRV resistance at baseline and few patients developed full resistance at DRV failure, indicating that complete resistance to DRV is uncommon. © Springer-Verlag 2011.

Published
2012

29. No pol mutation is associated independently with the lack of immune recovery in patients infected with HIV and failing antiretroviral therapy

Author

Gianotti, N1, Galli, L, Zazzi, M, Ghisetti, V, Bonora, S, Micheli, V, Meraviglia, P, Corsi, P, Bruzzone, B, Menzo, S, Di Giambenedetto, S, De Luca, A, Filice, G, Penco, G, Castagna, A, Collaborators Giacometti A, ARCA database i. n. i. t. i. a. t. i. v. e., Butini, L, del Gobbo, R, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Maggiolo, F, Callegaro, A, Calza, L, Re, Mc, Pristerà, R, Turconi, P, Mandas, A, Tini, S, Carnevale, G, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Di Pietro, M, Bartalesi, F, Colao, G, Tosti, A, Di Biagio, A, Setti, M, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Gianotti, N, Cicconi, P, Rusconi, S, Gismondo, Mr, Biondi, Ml, Capetti, A, Boeri, E, Pecorari, M, Mussini, C, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, Antinori, A, Vullo, Vincenzo, Turriziani, O, Perno, Cf, Montano, M, Cenderello, G, Gonnelli, A, Romano, L, Palumbo, M, Delle Foglie, P, Rossi, C, Poletti, F, Mondino, V, Malena, M, Lattuada, E., Gianotti, N, Galli, L, Zazzi, M, Ghisetti, V, Bonora, S, Micheli, V, Meraviglia, P, Corsi, P, Bruzzone, B, Menzo, S, Di Giambenedetto, S, De Luca, A, Filice, G, Penco, G, Castagna, A, Mancuso, S, Gianotti N, Galli L, Zazzi M, Ghisetti V, Bonora S, Micheli V, Meraviglia P, Corsi P, Bruzzone B, Menzo S, Di Giambenedetto S, De Luca A, Filice G, Penco G, Castagna A, Giacometti A, Butini L, del Gobbo R, Tacconi D, Corbelli G, Zanussi S, Monno L, Punzi G, Maggiolo F, Callegaro A, Calza L, Re MC, Pristerà R, Turconi P, Mandas A, Tini S, Carnevale G, Paolini E, Amadio G, Sighinolfi L, Zuccati G, Morfini M, Manetti R, Di Pietro M, Bartalesi F, Colao G, Tosti A, Di Biagio A, Setti M, Trezzi M, Orani A, Pardelli R, De Gennaro M, Chiodera A, Scalzini A, Palvarini L, Almi P, Todaro G, Cicconi P, Rusconi S, Gismondo MR, Biondi ML, Capetti A, Boeri E, Pecorari M, Mussini C, Santirocchi M, Brustia D, Ravanini P, Dal Bello F, Romano N, Mancuso S, Calzetti C, Maserati R, Baldanti F, Francisci D, Parruti G, Polilli E, Sacchini D, Martinelli C, Consolini R, Vatteroni L, Vivarelli A, Nerli A, Lenzi L, Magnani G, Ortolani P, Andreoni M, Palamara G, Fimiani C, Palmisano L, Antinori A, Vullo V, Turriziani O, Perno CF, Montano M, Cenderello G, Gonnelli A, Romano L, Palumbo M, Delle Foglie P, Rossi C, Poletti F, Mondino V, Malena M, Lattuada E., Gianotti, Nicola, Galli, Laura, Zazzi, Maurizio, Ghisetti, Valeria, Bonora, Stefano, Micheli, Valeria, Meraviglia, Paola, Corsi, Paola, Bruzzone, Bianca, Menzo, Stefano, Di Giambenedetto, Simona, De Luca, Andrea, Filice, Gaetano, Penco, Giovanni, and Castagna, Antonella

Subjects
Male, HIV Infections, Drug resistance, Logistic regression, Resistance to nucleoside reverse transcriptase inhibitor, CD4+ T-lymphocyte, Retrospective Studie, Immunopathology, Antiretroviral Therapy, Highly Active, Resistance to non-nucleoside reverse transcriptase inhibitor, genetics, Resistance to protease inhibitor, HIV Infection, resistance to nucleoside reverse transcriptase inhibitors, Viral, Sida, resistance to protease inhibitors, biology, Reverse-transcriptase inhibitor, Viral Load, Genes, pol, drug therapy/immunology/virology, Reverse Transcriptase Inhibitor, Infectious Diseases, Treatment Outcome, resistance to non-nucleoside reverse transcriptase inhibitors, Reverse Transcriptase Inhibitors, Female, Viral load, medicine.drug, Human, pol, Anti-HIV Agents, Antiretroviral Therapy, Viremia, Infectious Disease, Settore MED/17 - MALATTIE INFETTIVE, pharmacology/therapeutic use, Acquired immunodeficiency syndrome (AIDS), Virology, Drug Resistance, Viral, medicine, Humans, Highly Active, Retrospective Studies, pharmacology/therapeutic use, Antiretroviral Therapy, Highly Active, CD4 Lymphocyte Count, Drug Resistance, genetics, Female, Genes, pol, HIV Infections, drug therapy/immunology/virology, HIV-1, drug effects/enzymology/genetics, Humans, Male, Mutation, Retrospective Studies, Reverse Transcriptase Inhibitors, therapeutic use, Treatment Outcome, Viral Load, drug resistance, Anti-HIV Agent, biology.organism_classification, medicine.disease, CD4 Lymphocyte Count, Genes, drug effects/enzymology/genetics, therapeutic use, Mutation, CD4+ T-lymphocytes, HIV-1
Abstract

An investigation was undertaken to determine whether specific pol mutations hinder long-term immune recovery regardless of virological response. In total, 826 patients with >50 HIV RNA copies/ml, who underwent genotypic resistance testing between 1 January 2000 and 31 December 2003 after >3 years of antiretroviral treatment, and were followed up for >3 years after genotypic resistance testing, were analyzed retrospectively. The outcome of the study was the lack of immune recovery after >3 years of follow-up, defined as a slope by linear regression 50 copies/ml divided by the number of HIV RNA measurements during follow-up. Logistic regression was used for univariable and multivariable analysis. Median (Q1, Q3) values at baseline were the following: age 40 (37, 45) years, years on antiretroviral therapy 4.45 (3.65, 5.47), HIV RNA 3.91 (3.39, 4.53) log 10 copies/ml, CD4+ T-cell 358 (211, 524)/μl. After 3.13 years of follow-up, 375 patients (45.4%) showed a lack of immune recovery. The risk of lack of immune recovery increased independently with increasing baseline CD4+ counts (OR=1.104 per 50-cell increase, 95% CI=1.069-1.142, P

Published
2011

30. Low Rate of Virological Failure and Maintenance of Susceptibility to HIV-1 Protease Inhibitors with First-Line Lopinavir/Ritonavir-Based Antiretroviral Treatment in Clinical Practice

Author

Prosperi, Mc, Zazzi, M, Punzi, G, Monno, L, Colao, G, Corsi, P, Di Giambenedetto, S, Meini, G, Ghisetti, V, Bonora, S, Pecorari, M, Gismondo, Mr, Bagnarelli, P, Carli, T, De Luca, A, ARCA Collaborative Group, Giacometti, A, Butini, L, del Gobbo, R, Menzo, S, Tacconi, D, Corbelli, G, Zanussi, S, Maggiolo, F, Callegaro, A, Calza, L, Re, Mc, Raffaele, P, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Galli, L, Di Pietro, M, Bartalesi, F, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Monforte, A, Cicconi, P, Rusconi, S, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Soria, A, Vecchi, L, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, Rita, Clinic of Infectious Diseases, Università cattolica del Sacro Cuore [Roma] (Unicatt), Molecular Biology, Microbiology and Virology, Bari University Hospital, Clinical Infectious Diseases, Careggi University Hospital, Unit of Infectious Diseases, Catholic Universisty of Sacred Heart, A. Savoia Hospital, infectiuos diseases, Università degli studi di Torino (UNITO), Modena University Hospital, L. Sacco University Hospital, Ancona University Hospital, Grosseto General Hospital, Institute of Infectious Diseases, Sacro Cuore Catholic University, Infectious Diseases Unit, University Hospital of Siena, Prosperi, M, Zazzi, M, Punzi, G, Monno, L, Colao, G, Corsi, P, Di Giambenedetto, S, Meini, G, Ghisetti, V, Bonora, S, Pecorari, M, Gismondo, M, Bagnarelli, P, Carli, T, De Luca, A, Mancuso, S, Prosperi MC, Zazzi M, Punzi G, Monno L, Colao G, Corsi P, Di Giambenedetto S, Meini G, Ghisetti V, Bonora S, Pecorari M, Gismondo MR, Bagnarelli P, Carli T, De Luca A, ARCA Collaborative Group [.., Giacometti A, Butini L, del Gobbo R, Menzo S, Tacconi D, Corbelli G, Zanussi S, Maggiolo F, Callegaro A, Calza L, Re MC, Raffaele P, Turconi P, Mandas A, Tini S, Zoncada A, Paolini E, Amadio G, Sighinolfi L, and ]

Subjects
Male, Lopinavir/ritonavir, HIV Infections, boosted protease inhibitor, Lopinavir, Cohort Studies, 0302 clinical medicine, Antiretroviral Therapy, Highly Active, virologic failure, HIV Infection, Treatment Failure, 030212 general & internal medicine, Pyrimidinone, 0303 health sciences, education.field_of_study, lopinavir/ritonavir, Viral Load, Resistance mutation, first-line antiretroviral therapy, Reverse Transcriptase Inhibitor, 3. Good health, Treatment Outcome, Infectious Diseases, RNA, Viral, Reverse Transcriptase Inhibitors, Medicine, Drug Therapy, Combination, Female, Survival Analysi, Viral load, Human, medicine.drug, Anti-HIV Agents, Population, Pyrimidinones, Settore MED/17 - MALATTIE INFETTIVE, Emtricitabine, human immunodeficiency virus type 1, 03 medical and health sciences, Virology, Drug Resistance, Viral, antiretroviral drug resistance, medicine, Humans, Protease inhibitor (pharmacology), education, HIV Protease Inhibitor, Ritonavir, 030306 microbiology, business.industry, Anti-HIV Agent, HIV Protease Inhibitors, Survival Analysis, HIV-1, Cohort Studie, business
Abstract

Protease inhibitor (PI)-resistant HIV-1 has hardly ever been detected at failed boosted PI-based first-line antiretroviral regimens in clinical trials. However, this phenomenon has not been investigated in clinical practice. To address this gap, data from patients starting a first-line lopinavir/ritonavir (LPV/rtv)-based therapy with available baseline HIV-1 RNA load, a viral genotype and follow-up viral load after 3 and 6 months of treatment were extracted from the Italian Antiretroviral Resistance Cohort Analysis (ARCA) observational database. Based on survival analysis, 39 (7.1%) and 43 (7.8%) of the 548 examined patient cases had an HIV-1 RNA >500 and >50 copies/ml, respectively, after 6 months of treatment. Cox proportional hazard models detected baseline HIV-1 RNA (RH 1.79, 95%CI 1.10-2.92 per 1 - log10 increase, P = 0.02) and resistance to the nucleoside backbone (RH 1.04, 95%CI 1.02-1.06 per 10-point increase using the Stanford HIVdb algorithm, P < 0.001) as independent predictors of HIV-1 RNA at >500 copies/ml, but not at the >50 copies/ml cutoff criteria. Higher baseline viral load, older patient age, heterosexual route of infection and use of tenofovir/emtricitabine were predictors of failure at month 3 using the 50-copy and/or 500-copy threshold. Resistance to LPV/rtv did not occur or increase in any of the available 36 follow-up HIV-1 genotypes. Resistance to the nucleoside backbone (M184V) developed in four cases. Despite the likely differences in patient population and adherence, both the low rate of virological failure and the lack of development of LPV/rtv resistance documented in clinical trials are thus confirmed in clinical practice. J. Med. Virol. 82:1996-2003, 2010. © 2010 Wiley-Liss, Inc.

Published
2010
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32. Electromagnetic Physics Models for Parallel Computing Architectures

Author

Amadio, G, primary, Ananya, A, additional, Apostolakis, J, additional, Aurora, A, additional, Bandieramonte, M, additional, Bhattacharyya, A, additional, Bianchini, C, additional, Brun, R, additional, Canal, P, additional, Carminati, F, additional, Duhem, L, additional, Elvira, D, additional, Gheata, A, additional, Gheata, M, additional, Goulas, I, additional, Iope, R, additional, Jun, S Y, additional, Lima, G, additional, Mohanty, A, additional, Nikitina, T, additional, Novak, M, additional, Pokorski, W, additional, Ribon, A, additional, Seghal, R, additional, Shadura, O, additional, Vallecorsa, S, additional, Wenzel, S, additional, and Zhang, Y, additional

Published
2016
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33. GeantV: from CPU to accelerators

Author

Amadio, G, primary, Ananya, A, additional, Apostolakis, J, additional, Arora, A, additional, Bandieramonte, M, additional, Bhattacharyya, A, additional, Bianchini, C, additional, Brun, R, additional, Canal, P, additional, Carminati, F, additional, Duhem, L, additional, Elvira, D, additional, Gheata, A, additional, Gheata, M, additional, Goulas, I, additional, Iope, R, additional, Jun, S, additional, Lima, G, additional, Mohanty, A, additional, Nikitina, T, additional, Novak, M, additional, Pokorski, W, additional, Ribon, A, additional, Sehgal, R, additional, Shadura, O, additional, Vallecorsa, S, additional, Wenzel, S, additional, and Zhang, Y, additional

Published
2016
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34. Wein

Author

Benvegnin, L., Jermstad, A., Östby, O., Monti, E., de Astis, Holzbach, F., Amadio, G., Paronetta, L., Perazzo, A. A., Arbrecchi, A. C., Marcille, R., Jaulmes, P., Ferré, L., Archinard, P., Espil, L., Capt, E., Sumuleanu, C., Ghimicescu, G., Ionescu, M. V., Konek, F., Wettstein, E., Béis, C., Peynaud, E., Schindler, J., Kozák, K., Berg, P., Schulze, G., Heiduschka, A., Sommer, H., Mohler, H., and Internationales Landwirtschaftsinstitut

Published
1938
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36. A novel methodology for large-scale phylogeny partition

Author

Prosperi, Mattia C. F., Ciccozzi, Massimo, Fanti, Iuri, Saladini, Francesco, Pecorari, Monica, Borghi, Vanni, Di Giambenedetto, Simona, Bruzzone, Bianca, Capetti, Amedeo, Vivarelli, Angela, Rusconi, Stefano, Maria Carla, Re, Gismondo, Maria Rita, Sighinolfi, Laura, Gray, Rebecca R., Salemi, Marco, Zazzi, Maurizio, De Luca, Andrea, Giacometti, A, Butini, L, Menzo, S, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Maggiolo, F, Callegaro, A, Calza, L, Re, Mc, Pristerà, R, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Colao, G, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Cicconi, P, Rusconi, S, Gismondo, Mr, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Pecorari, M, Soria, A, Vecchi, L, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Dionisio, D, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, De Luca, A, Fadda, G, Vullo, Vincenzo, Turriziani, Ombretta, Montano, M, Cenderello, G, Gonnelli, A, Palumbo, M, Ghisetti, V, Bonora, S, Delle Foglie, P, Rossi, C, Grossi, P, Seminari, E, Poletti, F, Mondino, V, Malena, M, Lattuada, E., Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, Borghi V, Di Giambenedetto S, Bruzzone B, Capetti A, Vivarelli A, Rusconi S, Re MC, Gismondo MR, Sighinolfi L, Gray RR, Salemi M, Zazzi M, De Luca A, ARCA collaborative group., Prosperi, M, Ciccozzi, M, Fanti, I, Saladini, F, Pecorari, M, Borghi, V, Di Giambenedetto, S, Bruzzone, B, Capetti, A, Vivarelli, A, Rusconi, S, Re, M, Gismondo, M, Sighinolfi, L, Gray, R, Salemi, M, Zazzi, M, De Luca, A, and Mancuso, S

Subjects
Genetics and Molecular Biology (all), Male, pol, Theoretical computer science, Inference, Gene Products, pol, General Physics and Astronomy, HIV Infections, Biology, Network topology, Settore MED/17 - MALATTIE INFETTIVE, Biochemistry, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Physics and Astronomy (all), 0302 clinical medicine, Search algorithm, phylogenetic analysis, virus transmission, Gene Products, Humans, HIV Infection, 030212 general & internal medicine, Phylogeny, 030304 developmental biology, Algorithms, Classification, Female, HIV-1, Biochemistry, Genetics and Molecular Biology (all), Chemistry (all), Genetics, 0303 health sciences, Multidisciplinary, Phylogenetic tree, Node (networking), HIV, General Chemistry, Partition (database), Algorithm, Identification (information), Transmission (telecommunications), METHODOLOGY, Human
Abstract

Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics. © 2011 Macmillan Publishers Limited. All rights reserved.

Published
2011
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37. Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study

Author

Prosperi, Mc1, Mackie, N, Di Giambenedetto, S, Zazzi, M, Camacho, R, Fanti, I, Torti, C, Sönnerborg, A, Kaiser, R, Codoñer, Fm, Van Laethem, K, Bansi, L, van de Vijver DA, Geretti, Am, De Luca, A, Giacometti A, SEHERE c. o. n. s. o. r. t. i. u. m., Butini, L, del Gobbo, R, Menzo, S, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Maggiolo, F, Callegaro, A, Calza, L, Carla Re, M, Pristerà, R, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Colao, G, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, d'Arminio Monforte, A, Cicconi, P, Rusconi, S, Gismondo, Mr, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Pecorari, M, Soria, A, Vecchi, L, Santirocchi, M, Brustia, D, Ravanini, P, Bello, Fd, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Dionisio, D, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, Fadda, G, Vullo, Vincenzo, Turriziani, O, Montano, M, Cenderello, G, Gonnelli, A, Palumbo, M, Ghisetti, V, Bonora, S, Foglie, Pd, Rossi, C, Grossi, P, Seminari, E, Poletti, F, Mondino, V, Malena, M, Lattuada, E, Lengauer, T, Däumer, M, Hoffmann, D, Schülter, E, Müller, C, Oette, M, Reuter, S, Esser, S, Fätkenheuer, G, Rockstroh, J, Incardona, F, Rosen Zvi, M, Clotet, B, Thalme, A, Svedhem, V, Bratt, G, Gargiulo, F, Lapadula, G, Manca, N, Paraninfo, G, Quiros Roldan, E, Carosi, G, Castelnuovo, F, Vandamme, Am, Van Wijngaerden, E, Ainsworth, J, Anderson, J, Babiker, A, Dunn, D, Easterbrook, P, Fisher, M, Gazzard, B, Garrett, N, Gilson, R, Gompels, M, Hill, T, Johnson, M, Leen, C, Orkin, C, Phillips, A, Pillay, D, Porter, K, Post, F, Sabin, C, Sadiq, T, Schwenk, A, Walsh, J, Delpech, V, Palfreeman, A, Glabay, A, Lynch, J, Hand, J, de Souza, C, Perry, N, Tilbury, S, Churchill, D, Nelson, M, Waxman, M, Mandalia, S, Kall, M, Korat, H, Taylor, C, Ibrahim, F, Campbell, L, James, L, Brima, N, Williams, I, Youle, M, Lampe, F, Smith, C, Grabowska, H, Chaloner, C, Puradiredja, Di, Weber, J, Ramzan, F, Carder, M, Wilson, A, Dooley, D, Asboe, D, Pozniak, A, Cameron, S, Cane, P, Chadwick, D, Clark, D, Collins, S, Lazarus, L, Dolling, D, Fearnhill, E, Castro, H, Coughlin, K, Zuckerman, M, Booth, C, Goldberg, D, Hale, A, Kaye, S, Kellam, P, Leigh Brown, A, Smit, E, Templeton, K, Tilston, P, Tong, W, Zhang, H, Ushiro Lumb, I, Oliver, T, Bibby, D, Mitchell, S, Mbisa, T, Wildfire, A, Tandy, R, Shepherd, J, Maclean, A, Bennett, D, Hopkins, M, Garcia Diaz, A, Kirk, S, Sloot, P. M., Virology, Prosperi, M, Mackie, N, di Giambenedetto, S, Zazzi, M, Camacho, R, Fanti, I, Torti, C, Sönnerborg, A, Kaiser, R, Codoñer, F, van laethem, K, Bansi, L, van de Vijver, D, Geretti, A, de luca, A, and Mancuso, S

Subjects
Male, Drug Resistance, HIV Infections, Drug resistance, Cohort Studies, 0302 clinical medicine, Genotype, HIV Infection, Pharmacology (medical), 030212 general & internal medicine, Viral, 0303 health sciences, Proteolytic enzymes, Genotypic testing, HIV, Viral load, Adult, Anti-HIV Agents, CD4 Lymphocyte Count, Europe, Female, HIV-1, Humans, RNA, Viral, Viral Proteins, Drug Resistance, Viral, Mutation, Missense, Viral Load, Pharmacology, Infectious Diseases, 3. Good health, Cohort, Cohort study, Human, Microbiology (medical), Biology, Settore MED/17 - MALATTIE INFETTIVE, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Viral Protein, 030306 microbiology, Anti-HIV Agent, Virology, Reverse transcriptase, Regimen, genotypic testing, viral load, Immunology, Mutation, RNA, Missense, Cohort Studie
Abstract

Background and objectives: Guidelines indicate a plasma HIV-1 RNA load of 500-1000 copies/mL as the minimal threshold for antiretroviral drug resistance testing. Resistance testing at lower viral load levels may be useful to guide timely treatment switches, although data on the clinical utility of this remain limited. We report here the influence of viral load levels on the probability of detecting drug resistance mutations (DRMs) and other mutations by routine genotypic testing in a large multicentre European cohort, with a focus on tests performed at a viral load

Published
2011

38. Neoadjuvant Chemotherapy Followed by Maintenance Therapy With or Without Bevacizumab in Unresectable High-Grade Serous Ovarian Cancer: A Case-Control Study

Author

Petrillo, M, Paris, I, Vizzielli, G, Amadio, G, Cosentino, F, Salutari, V, Scambia, Giovanni, Fagotti, Anna, Scambia, Giovanni (ORCID:0000-0003-2758-1063), Petrillo, M, Paris, I, Vizzielli, G, Amadio, G, Cosentino, F, Salutari, V, Scambia, Giovanni, Fagotti, Anna, and Scambia, Giovanni (ORCID:0000-0003-2758-1063)

Abstract

OBJECTIVE: The aim of this study was to compare the toxicity, perioperative outcomes of interval debulking surgery (IDS), and duration of progression-free survival (PFS) in women with unresectable high-grade serous advanced ovarian cancer (AOC) receiving neoadjuvant chemotherapy (NACT) with or without bevacizumab. METHODS: Twenty-five patients with high-grade serous AOC treated with bevacizumab-based NACT (cases) were matched according to initial disease extension assessed by laparoscopy, and age, in a 1:2 ratio, with 50 high-grade serous AOC patients treated with standard NACT without bevacizumab (controls). RESULTS: Both groups received a median of four NACT cycles before IDS (p = 0.867), and the median time interval between NACT and IDS was 27 days in both groups (p = 0.547). Twenty-two cases (88.0 %) showed complete/partial radiologic response compared with 36 controls (72.3 %; p = 0.054). A higher percentage of cases showed complete serological response (48 vs. 35.1 %; p = 0.041). At IDS, complete cytoreduction was achieved in 20 cases (80.0 %) and 36 controls (72.3 %) [p = 0.260]. No differences were observed between groups in terms of surgical complexity score, perioperative outcomes, surgical complications, and chemotherapy-related adverse events. One death due to gastrointestinal perforation was observed among cases. Cases showed a longer median PFS compared with controls (18 months vs. 10 months; p = 0.001), and the administration of bevacizumab (hazard ratio 3.786; p = 0.001) retained a prognostic role for longer PFS at multivariate analysis. CONCLUSIONS: The incorporation of bevacizumab in NACT prolongs PFS without affecting the safety of IDS. The risk of gastrointestinal perforation should be considered prior to attempting bevacizumab-based NACT in women with diffuse bowel involvement at initial laparoscopic evaluation.

Published
2015

39. First experience of vectorizing electromagnetic physics models for detector simulation

Author

Amadio, G, primary, Apostolakis, J, additional, Bandieramonte, M, additional, Bianchini, C, additional, Bitzes, G, additional, Brun, R, additional, Canal, P, additional, Carminati, F, additional, Licht, J de Fine, additional, Duhem, L, additional, Elvira, D, additional, Gheata, A, additional, Jun, S Y, additional, Lima, G, additional, Novak, M, additional, Presbyterian, M, additional, Shadura, O, additional, Seghal, R, additional, and Wenzel, S, additional

Published
2015
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40. The GeantV project: preparing the future of simulation

Author

Amadio, G, primary, Apostolakis, J, additional, Bandieramonte, M, additional, Bhattacharyya, A, additional, Bianchini, C, additional, Brun, R, additional, Canal, Ph, additional, Carminati, F, additional, Duhem, L, additional, Elvira, D, additional, de Fine Licht, J, additional, Gheata, A, additional, Iope, R L, additional, Lima, G, additional, Mohanty, A, additional, Nikitina, T, additional, Novak, M, additional, Pokorski, W, additional, Seghal, R, additional, Shadura, O, additional, Vallecorsa, S, additional, and Wenzel, S, additional

Published
2015
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41. Low rate of virological failure and maintenance of susceptibility to HIV-1 protease inhibitors with first-line lopinavir/ritonavir-based antiretroviral treatment in clinical practice

Author

Prosperi, Mc1, Zazzi, M, Punzi, G, Monno, L, Colao, G, Corsi, P, Di Giambenedetto, S, Meini, G, Ghisetti, V, Bonora, S, Pecorari, M, Gismondo, Mr, Bagnarelli, P, Carli, T, De Luca, A, Collaborators Giacometti A, ARCA Collaborative G. r. o. u. p., Butini, L, del Gobbo, R, Menzo, S, Tacconi, D, Corbelli, G, Zanussi, S, Maggiolo, F, Callegaro, A, Calza, L, Re, Mc, Raffaele, P, Turconi, P, Mandas, A, Tini, S, Zoncada, A, Paolini, E, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Galli, L, Di Pietro, M, Bartalesi, F, Tosti, A, Di Biagio, A, Setti, M, Bruzzone, B, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Monforte, Ad, Cicconi, P, Rusconi, S, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Boeri, E, Mussini, C, Soria, A, Vecchi, L, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Baldanti, F, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, R, Vatteroni, L, Vivarelli, A, Dionisio, D, Nerli, A, Lenzi, L, Magnani, G, Ortolani, P, Andreoni, M, Palamara, G, Fimiani, C, Palmisano, L, Vullo, Vincenzo, Turriziani, O, Montano, M, Cenderello, G, Gonnelli, A, Palumbo, M, Delle Foglie, P, Rossi, C, Poletti, F, Mondino, V, Malena, M, and Lattuada, E.

Published
2010

42. Controversies in the Management of Endometrial Cancer

Author

Masciullo, V., Amadio, G., Lo Russo, D., Raimondo, I., Giordano, A., and Scambia, G.

Subjects
Article Subject
Abstract

Endometrial cancer (EC) remains the most common malignancy of the female genital tract. The median age at diagnosis is the sixth decade, with abnormal uterine bleeding at the presentation in 90% of the patients. Surgical treatment, including complete hysterectomy, removal of remaining adnexal structures, and an appropriate surgical staging, represents the milestone of curative therapy for patients with EC. Adjuvant therapy is necessary in patients at high risk of recurrence. Conservative treatment approaches should be used in selected cases for women with a desire of fertility preservation. This review summarizes the management of EC and discusses current controversies regarding the role of lymphadenectomy and radiotherapy in patients with intermediate-risk tumors confined to the uterus.

Published
2010
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43. Rules-based HIV-1 genotypic resistance interpretation systems predict 8 week and 24 week virological antiretroviral treatment outcome and benefit from drug potency weighting

Author

Zazzi, M, Prosperi, M, Vicenti, I, Di Giambenedetto, S, Callegaro, A, Bruzzone, B, Baldanti, F, Gonnelli, A, Boeri, E, Paolini, E, Rusconi, S, Giacometti, A, Maggiolo, F, Menzo, S, De Luca, A, ARCA Collaborative Group, Butini, L, del Gobbo, R, Tacconi, D, Corbelli, G, Zanussi, S, Monno, L, Punzi, G, Calza, L, Re, Mc, Pristerà, R, Turconi, P, Mandas, A, Tini, S, Carnevale, G, Amadio, G, Sighinolfi, L, Zuccati, G, Morfini, M, Manetti, R, Corsi, P, Galli, L, Di Pietro, M, Bartalesi, F, Colao, G, Tosti, A, Di Biagio, A, Setti, M, Penco, G, Trezzi, M, Orani, A, Pardelli, R, De Gennaro, M, Chiodera, A, Scalzini, A, Palvarini, L, Almi, P, Todaro, G, Cicconi, P, Gismondo, Mr, Micheli, V, Biondi, Ml, Gianotti, N, Capetti, A, Meraviglia, P, Mussini, C, Pecorari, M, Santirocchi, M, Brustia, D, Ravanini, P, Dal Bello, F, Romano, N, Mancuso, S, Calzetti, C, Maserati, R, Filice, G, Francisci, D, Parruti, G, Polilli, E, Sacchini, D, Martinelli, C, Consolini, Rita, Zazzi, M, Prosperi, M, Vicenti, I, Di Giambenedetto, S, Callegaro, A, Bruzzone, B, Baldanti, F, Gonnelli, A, Boeri, E, Paolini, E, Rusconi, S, Giacometti, A, Maggiolo, F, Menzo, S, De Luca, A, Mancuso, S, Zazzi M, Prosperi M, Vicenti I, Di Giambenedetto S, Callegaro A, Bruzzone B, Baldanti F, Gonnelli A, Boeri E, Paolini E, Rusconi S, Giacometti A, Maggiolo F, Menzo S, De Luca A, ARCA Collaborative Group: [.., Butini L, del Gobbo R, Tacconi D, Corbelli G, Zanussi S, Monno L, Punzi G, Calza L, Re M C, Pristerà R, Turconi P, Mandas A, Tini S, and ]

Subjects
Male, interpretation system, HIV Infections, Drug resistance, Logistic regression, Retrospective Studie, HIV Infection, Pharmacology (medical), Microbial Sensitivity Test, Middle Aged, Prognosis, genotype, drug resistance, algorithm, Algorithm, Treatment Outcome, Infectious Diseases, Italy, RNA, Viral, Female, Cohort study, Human, Microbiology (medical), Adult, medicine.medical_specialty, Genotype, Logistic Model, Anti-HIV Agents, Prognosi, antiretroviral, Microbial Sensitivity Tests, Internal medicine, medicine, Potency, Animals, Humans, Retrospective Studies, Pharmacology, Receiver operating characteristic, business.industry, Animal, Anti-HIV Agent, Retrospective cohort study, Odds ratio, genotype, drug potency weighting, Weighting, Logistic Models, ROC Curve, Immunology, HIV-1, business
Abstract

Objectives: To test retrospectively the ability of four freely available rules-based expert systems to predict short- and medium-term virological outcome following an antiretroviral treatment switch in pre-treated HIV-1 patients. Methods: The HIV-1 genotype interpretation systems (GISs) HIVdb, ANRS, Rega and AntiRetroScan were tested for their accuracy in predicting response to highly active antiretroviral therapy using 8 week (n = 765) and 24 week (n = 634) follow-up standardized treatment change episodes extracted from the Italian Antiretroviral Resistance Cohort Analysis (ARCA) database. A genotypic sensitivity score (GSS) was derived for each genotype-treatment pair for the different GISs and tested as a predictor of virological treatment outcome by univariable and multivariable logistic regression as well as by receiver operating characteristic curve analysis. The two systems implementing drug potency weights (AntiRetroScan and Rega) were evaluated with and without this correction factor. Results: All four GSSs were strong predictors of virological treatment outcome at both 8 and 24 weeks after adjusting for baseline viro-immunological parameters and previous drug exposure (odds ratios ranging from 2.04 to 2.43 per 1 unit GSS increase; P < 0.001 for all the systems). The accuracy of AntiRetroScan and Rega was significantly increased by drug potency weighting with respect to the unweighted versions (P ≤ 0.001). HIVdb and ANRS also increased their performance with the same drug potency weighting adopted by AntiRetroScan and Rega, respectively (P < 0.001 for both analyses). Conclusions: Currently available GISs are valuable tools for assisting antiretroviral treatment choices. Drug potency weighting can increase the accuracy of all systems. © The Author 2009. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.

Published
2009

44. Do stars shine brigther with radioactive ion (Beams)?

Author

Cherubini, Silvio, Spitaleri, C., Amadio, G., Coc, A., Crucilla, V., Gulino, M., Hayakawa, S., Iwasa, N., Kuto, S., Kubono, S., LA COGNATA, M., Lamia, Livio, Motobayashi, T., Nishimura, S., Pizzone, R. G., Puglia, Sebastiana, Rapisarda, G. G., Romano, Stefano, DE SEREVILLE, N., Sergi, M. L., Teranishi, T., Tudisco, S., Tumino, A., Wakabayashi, Y., and Yamaguchi, H.

Published
2008

45. Measurement of the 18F(p,alpha)15O reaction in nova conditions

Author

Cherubini, Silvio, Spitaleri, C., Crucilla', V., Gulino, M., LA COGNATA, M., Lamia, Livio, Pizzone, R. G., Puglia, Sebastiana, Rapisarda, G. G., Romano, Stefano, Sergi, M. L., Tumino, A., Kubono, S., Yamaguchi, H., Wakabayashi, Y., Hayakawa, S., Amadio, G., Iwasa, N., Kato, S., Komatsubara, Y., Nishimura, S., Teranishi, T., Coc, A., and DE SEREVILLE, N.

Published
2008

46. Direct and indirect measurement of the 18F(p,a)15O reaction in novae

Author

Cherubini, Silvio, Spitaleri, C., Crucilla, V., Gulino, M., LA COGNATA, M., Lamia, Livio, Pizzone, R. G., Puglia, S. M. R., Rapisarda, G. G., Romano, Stefano, Sergi, M. L., Tudisco, S., Tumino, A., Kubonu, S., Yamaguchi, H., Wakabayashi, Y., Amadio, G., Hayakawa, S., Iwasa, N., Kato, S., Nishimura, S., and Teranishi, T.

Published
2007

47. Emerging drugs for endometrial cancer

Author

Amadio, G, Masciullo, V, Ferrandina, Maria Gabriella, Scambia, Giovanni, Ferrandina, Maria Gabriella (ORCID:0000-0003-4672-4197), Scambia, Giovanni (ORCID:0000-0003-2758-1063), Amadio, G, Masciullo, V, Ferrandina, Maria Gabriella, Scambia, Giovanni, Ferrandina, Maria Gabriella (ORCID:0000-0003-4672-4197), and Scambia, Giovanni (ORCID:0000-0003-2758-1063)

Abstract

INTRODUCTION: From the dualistic classification that divides endometrial cancer (EC) into two types with distinct underlying molecular profiling, histopathology and clinical behavior, arises a deeper understanding of the carcinogenesis pathways. EC treatment comprises different and multimodal therapeutic approaches, such as chemotherapy, radiation therapy or combinations of novel drugs; however, few of these regimens have truly improved progression-free or survival rates in advanced and metastatic settings. AREAS COVERED: We reviewed the main molecular pathways involved in EC carcinogenesis through a wide literature search of novel compounds that alone or in combination with traditional drugs have been investigated or are currently under investigation in randomized clinical trials. EXPERT OPINION: The molecular therapies mainly discussed in this review are potential therapeutic candidates for more effective and specific treatments. In the genomic era, a deeper knowledge about molecular characteristics of cancer provides the hope for the development of better therapeutic approaches. Targeting both genetic and epigenetic alterations, attacking tumor cells using cell-surface markers overexpressed in tumor tissue, reactivating antitumor immune responses and identifying predictive biomarkers represent the emerging strategies and the major challenges.

Published
2014

48. Clinical utility of trabectedin for the treatment of ovarian cancer: Current evidence

Author

Mascilini, F, Amadio, G, Di Stefano, M, Ludovisi, M, Di Legge, A, Conte, C, De Vincenzo, Rosa Pasqualina, Ricci, C, Masciullo, V, Salutari, V, Scambia, Giovanni, Ferrandina, Maria Gabriella, De Vincenzo, R (ORCID:0000-0001-7408-0435), Scambia, Giovanni (ORCID:0000-0003-2758-1063), Ferrandina, Maria Gabriella (ORCID:0000-0003-4672-4197), Mascilini, F, Amadio, G, Di Stefano, M, Ludovisi, M, Di Legge, A, Conte, C, De Vincenzo, Rosa Pasqualina, Ricci, C, Masciullo, V, Salutari, V, Scambia, Giovanni, Ferrandina, Maria Gabriella, De Vincenzo, R (ORCID:0000-0001-7408-0435), Scambia, Giovanni (ORCID:0000-0003-2758-1063), and Ferrandina, Maria Gabriella (ORCID:0000-0003-4672-4197)

Abstract

Among the pharmaceutical options available for treatment of ovarian cancer, attention has been increasingly focused on trabectedin (ET-743), a drug which displays a unique mechanism of action and has been shown to be active in several human malignancies. Currently, single agent trabectedin is approved for treatment of patients with advanced soft tissue sarcoma after failure of anthracyclines and ifosfamide, and in association with pegylated liposomal doxorubicin for treatment of patients with relapsed partially platinum-sensitive ovarian cancer. This review aims at summarizing the available evidence about the clinical role of trabectedin in the management of patients with epithelial ovarian cancer. Novel perspectives coming from a better understanding of trabectedin mechanisms of action and definition of patients subgroups likely susceptible to benefit of trabectedin treatment are also presented.

Published
2014

49. A Prognostic Model for Estimating the Time to Virologic Failure in HIV-1 Infected Patients Undergoing a New Combination Antiretroviral Therapy Regimen

Author

PProsperi MC, Di Giambenedetto S, Fanti I, Meini G, Bruzzone B, Callegaro A, Penco G, Bagnarelli P, Micheli V, Paolini E, Di Biagio A, Ghisetti V, Di Pietro M, Zazzi M, De Luca A, Giacometti A, Butini L, del Gobbo R, Menzo S, Tacconi D, Corbelli G, Zanussi S, Monno L, Punzi G, Maggiolo F, CALZA, LEONARDO, RE, MARIA CARLA, Pristerà R, Turconi P, Mandas A, Tini S, Carnevale G, Amadio G, Sighinolfi L, Zuccati G, Morfini M, Manetti R, Galli L, Bartalesi F, Colao G, Tosti A, Setti M, Trezzi M, Orani A, Pardelli R, De Gennaro M, Chiodera A, Scalzini A, Palvarini L, Almi P, Todaro G, Gianotti N, Cicconi P, Rusconi S, Gismondo MR, Biondi ML, Capetti A, Meraviglia P, Boeri E, Pecorari M, Mussini C, Santirocchi M, Brustia D, Ravanini P, Dal Bello F, Romano N, Mancuso S, Calzetti C, Maserati R, Baldanti F, Francisci D, Parruti G, Polilli E, Sacchini D, Martinelli C, Consolini R, Vatteroni L, Vivarelli A, Nerli A, Lenzi L, Magnani G, Ortolani P, Andreoni M, Palamara G, Fimiani C, Palmisano L, Antinori A, Vullo V, Turriziani O, Perno CF, Montano M, Cenderello G, Gonnelli A, Romano L, Palumbo M, Bonora S, Delle Foglie P, Rossi C, Poletti F, Mondino V, Malena M, Lattuada E., PProsperi MC, Di Giambenedetto S, Fanti I, Meini G, Bruzzone B, Callegaro A, Penco G, Bagnarelli P, Micheli V, Paolini E, Di Biagio A, Ghisetti V, Di Pietro M, Zazzi M, De Luca A, Giacometti A, Butini L, del Gobbo R, Menzo S, Tacconi D, Corbelli G, Zanussi S, Monno L, Punzi G, Maggiolo F, Calza L, Re MC, Pristerà R, Turconi P, Mandas A, Tini S, Carnevale G, Amadio G, Sighinolfi L, Zuccati G, Morfini M, Manetti R, Galli L, Bartalesi F, Colao G, Tosti A, Setti M, Trezzi M, Orani A, Pardelli R, De Gennaro M, Chiodera A, Scalzini A, Palvarini L, Almi P, Todaro G, Gianotti N, Cicconi P, Rusconi S, Gismondo MR, Biondi ML, Capetti A, Meraviglia P, Boeri E, Pecorari M, Mussini C, Santirocchi M, Brustia D, Ravanini P, Dal Bello F, Romano N, Mancuso S, Calzetti C, Maserati R, Baldanti F, Francisci D, Parruti G, Polilli E, Sacchini D, Martinelli C, Consolini R, Vatteroni L, Vivarelli A, Nerli A, Lenzi L, Magnani G, Ortolani P, Andreoni M, Palamara G, Fimiani C, Palmisano L, Antinori A, Vullo V, Turriziani O, Perno CF, Montano M, Cenderello G, Gonnelli A, Romano L, Palumbo M, Bonora S, Delle Foglie P, Rossi C, Poletti F, Mondino V, Malena M, Lattuada E., Prosperi, M, Di Giambenedetto, S, Fanti, I, Meini, G, Bruzzone, B, Callegaro, A, Penco, G, Bagnarelli, P, Micheli, V, Paolini, E, Di Biagio, A, Ghisetti, V, Di Pietro, M, Zazzi, M, De Luca, A, and Mancuso, S

Subjects
Oncology, Male, Adult, Anti-HIV Agents, Cohort Studies, Drug Therapy, Combination, Female, HIV Infections, HIV-1, Humans, Middle Aged, Proportional Hazards Models, Treatment Failure, Viral Load, 0302 clinical medicine, ANTIRETROVIRAL THERAPY, Medicine, HIV Infection, 030212 general & internal medicine, 0303 health sciences, Health Policy, 3. Good health, Computer Science Applications, Censoring (clinical trials), Cohort, Combination, lcsh:R858-859.7, Viral load, Human, Research Article, Cart, medicine.medical_specialty, antiretroviral therapy, Health Informatics, Settore MED/17 - MALATTIE INFETTIVE, lcsh:Computer applications to medicine. Medical informatics, 03 medical and health sciences, Drug Therapy, Internal medicine, Survival analysis, 030306 microbiology, business.industry, Proportional hazards model, ANTIRETROVIRAL DRUGS, Anti-HIV Agent, HIV, GENOTYPES, Discontinuation, Regimen, Immunology, Proportional Hazards Model, Cohort Studie, business
Abstract

Background HIV-1 genotypic susceptibility scores (GSSs) were proven to be significant prognostic factors of fixed time-point virologic outcomes after combination antiretroviral therapy (cART) switch/initiation. However, their relative-hazard for the time to virologic failure has not been thoroughly investigated, and an expert system that is able to predict how long a new cART regimen will remain effective has never been designed. Methods We analyzed patients of the Italian ARCA cohort starting a new cART from 1999 onwards either after virologic failure or as treatment-naïve. The time to virologic failure was the endpoint, from the 90th day after treatment start, defined as the first HIV-1 RNA > 400 copies/ml, censoring at last available HIV-1 RNA before treatment discontinuation. We assessed the relative hazard/importance of GSSs according to distinct interpretation systems (Rega, ANRS and HIVdb) and other covariates by means of Cox regression and random survival forests (RSF). Prediction models were validated via the bootstrap and c-index measure. Results The dataset included 2337 regimens from 2182 patients, of which 733 were previously treatment-naïve. We observed 1067 virologic failures over 2820 persons-years. Multivariable analysis revealed that low GSSs of cART were independently associated with the hazard of a virologic failure, along with several other covariates. Evaluation of predictive performance yielded a modest ability of the Cox regression to predict the virologic endpoint (c-index≈0.70), while RSF showed a better performance (c-index≈0.73, p < 0.0001 vs. Cox regression). Variable importance according to RSF was concordant with the Cox hazards. Conclusions GSSs of cART and several other covariates were investigated using linear and non-linear survival analysis. RSF models are a promising approach for the development of a reliable system that predicts time to virologic failure better than Cox regression. Such models might represent a significant improvement over the current methods for monitoring and optimization of cART.

Published
2011
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50. Trabectedin in Patients with Brca Mutated and Brcaness Phenotype Advanced Ovarian Cancer (Aoc): Phase Ii Prospective Mito-15 Study

Author

Lorusso, D., primary, Ferrandina, G., additional, Pignata, S., additional, Sorio, R., additional, Amadio, G., additional, Mosconi, A.M., additional, Pisano, C., additional, Mangili, G., additional, Masini, C., additional, Artioli, G., additional, Narducci, F., additional, Di Napoli, M., additional, Rigamonti, C., additional, Raspagliesi, F., additional, and Scambia, G., additional

Published
2014
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