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1. Field emission analysis of the European Spallation Source medium beta superconducting cavities

Author

M. Bertucci, A. Bosotti, A. D’Ambros, E. Del Core, A. T. Grimaldi, P. Michelato, L. Monaco, C. Pagani, R. Paparella, and D. Sertore

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

This paper presents a quantitative description of field emission in superconducting rf cavities. The goal is to fully reconstruct the physics involved in the phenomenon, from electron current generation at the emitter to the radiation pattern measured by the x-ray detector. The field emission process in the cavity was reconstructed using CST Particle Studio, and then the generation of x-ray radiation and its propagation toward the detectors were modeled analytically. The entire model was then applied to the specific case of the European Spallation Source medium beta superconducting cavities, and the theoretical predictions were cross-checked with experimental data collected during cavity vertical tests.

Published
2023
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2. Two-pass two-way acceleration in a superconducting continuous wave linac to drive low jitter x-ray free electron lasers

Author

A. Bacci, M. Rossetti Conti, A. Bosotti, S. Cialdi, S. Di Mitri, I. Drebot, L. Faillace, G. Ghiringhelli, P. Michelato, L. Monaco, M. Opromolla, R. Paparella, V. Petrillo, M. Placidi, E. Puppin, A. R. Rossi, G. Rossi, D. Sertore, and L. Serafini

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

We present a design study of an innovative scheme to generate high rep rate (MHz-class) GeV electron beams by adopting a two-pass two-way acceleration in a superconducting (SC) linac operated in continuous wave (CW) mode. The electron beam is accelerated twice by being reinjected in opposite direction of propagation into the linac after the first passage. Acceleration in opposite directions is accomplished thanks to standing waves supported in rf cavities. The task of recirculating the electron beam when it leaves the linac after first pass is performed by a bubble-shaped arc compressor composed by a sequence of double bend achromat. In this paper we address the main issues inherent to the two-pass acceleration process and the preservation of the electron beam quality parameters (emittance, energy spread, peak current) required to operate x-ray free electron lasers (FEL) with low jitters in the amplitude, spectral and temporal domain, as achieved by operating in seeding and/or oscillator mode a CW FEL up to 1 MHz rep rate. Detailed start-to-end simulations are shown to assess the capability of this new scheme to double the electron beam energy as well as to compress the electron bunch length from picoseconds down to tens of femtoseconds. The advantage of such a scheme is to halve the requested linac length for the same final electron beam energy, which is typically in the few GeV range, as needed to drive an x-ray FEL. The AC power to supply the cryogenic plant is also significantly reduced with respect to a conventional single-pass SC linac for the same final energy. We are reporting also x-ray FEL simulations for typical values of wavelengths of interest (in the 200 eV–8 keV photon energy range) to better illustrate the potentiality of this new scheme.

Published
2019
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3. Performance analysis of the European X-ray Free Electron Laser 3.9 GHz superconducting cavities

Author

M. Bertucci, A. Bignami, A. Bosotti, P. Michelato, L. Monaco, C. Pagani, R. Paparella, D. Sertore, C. Maiano, P. Pierini, and J. Chen

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

The limits of performance of the European XFEL 3.9 GHz superconducting cavities were investigated. Most cavities exhibited high field Q slope, reaching the breakdown field at approximately 22 MV/m. We hypothesize that this limit is a feature of high frequency cavities and can be explained by a thermal model incorporating field dependent surface resistance. The results obtained from simulations were in good agreement with experimental data obtained at 2 K.

Published
2019
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4. Validation of the superconducting 3.9 GHz cavity package for the European X-ray Free Electron Laser

Author

C. G. Maiano, J. Branlard, M. Hüning, K. Jensch, D. Kostin, A. Matheisen, W.-D. Möller, A. Sulimov, E. Vogel, A. Bosotti, J. F. Chen, M. Moretti, R. Paparella, P. Pierini, and D. Sertore

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

A full test of the cavity package concept under realistic operating condition was a necessary step before the assembly of the European XFEL (EXFEL) 3.9 GHz superconducting system and its installation in the accelerator. One cavity, equipped with magnetic shielding, power coupler and frequency tuner has been tested in a specially designed single cavity cryostat in one of the test benches of the DESY Accelerator Module Test Facility (AMTF). The cavity was operated at high pulsed power up to an accelerating field of 24 MV/m, above the quench accelerating field of 21 MV/m achieved during the continuous wave (CW) vertical qualification test and with a large margin with respect to the EXFEL maximum operating specification of 15 MV/m for the 3.9 GHz system. All subsystems under test—coupler, tuner, waveguide tuners, low level radio-frequency (LLRF) system—were qualified to their design performances.

Published
2017
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5. Fabrication and vertical test experience of the European X-ray Free Electron Laser 3.9 GHz superconducting cavities

Author

P. Pierini, M. Bertucci, A. Bosotti, J. F. Chen, C. G. Maiano, P. Michelato, L. Monaco, M. Moretti, C. Pagani, R. Paparella, D. Sertore, and E. Vogel

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

We report the experience of the production, processing and qualification testing of the superconducting radio frequency cavities at 3.9 GHz for the third harmonic system at the European XFEL (EXFEL) injector. The rf structure concept, originally developed for the FLASH FEL facility, was adapted to the new interfaces provided by the EXFEL design and the cavities were procured from a qualified vendor, delivered ready for the testing at the INFN infrastructure. A total of 23 cavities, three prototypes and two batches of 10, have been realized and tested up to specifications.

Published
2017
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6. Superconducting TESLA cavities

Author

B. Aune, R. Bandelmann, D. Bloess, B. Bonin, A. Bosotti, M. Champion, C. Crawford, G. Deppe, B. Dwersteg, D. A. Edwards, H. T. Edwards, M. Ferrario, M. Fouaidy, P.-D. Gall, A. Gamp, A. Gössel, J. Graber, D. Hubert, M. Hüning, M. Juillard, T. Junquera, H. Kaiser, G. Kreps, M. Kuchnir, R. Lange, M. Leenen, M. Liepe, L. Lilje, A. Matheisen, W.-D. Möller, A. Mosnier, H. Padamsee, C. Pagani, M. Pekeler, H.-B. Peters, O. Peters, D. Proch, K. Rehlich, D. Reschke, H. Safa, T. Schilcher, P. Schmüser, J. Sekutowicz, S. Simrock, W. Singer, M. Tigner, D. Trines, K. Twarowski, G. Weichert, J. Weisend, J. Wojtkiewicz, S. Wolff, and K. Zapfe

Subjects
Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

The conceptional design of the proposed linear electron-positron collider TESLA is based on 9-cell 1.3 GHz superconducting niobium cavities with an accelerating gradient of E_{acc}≥25 MV/m at a quality factor Q_{0}≥5×10^{9}. The design goal for the cavities of the TESLA Test Facility (TTF) linac was set to the more moderate value of E_{acc}≥15 MV/m. In a first series of 27 industrially produced TTF cavities the average gradient at Q_{0}=5×10^{9} was measured to be 20.1±6.2 MV/m, excluding a few cavities suffering from serious fabrication or material defects. In the second production of 24 TTF cavities, additional quality control measures were introduced, in particular, an eddy-current scan to eliminate niobium sheets with foreign material inclusions and stringent prescriptions for carrying out the electron-beam welds. The average gradient of these cavities at Q_{0}=5×10^{9} amounts to 25.0±3.2 MV/m with the exception of one cavity suffering from a weld defect. Hence only a moderate improvement in production and preparation techniques will be needed to meet the ambitious TESLA goal with an adequate safety margin. In this paper we present a detailed description of the design, fabrication, and preparation of the TESLA Test Facility cavities and their associated components and report on cavity performance in test cryostats and with electron beam in the TTF linac. The ongoing research and development towards higher gradients is briefly addressed.

Published
2000
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9. A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

Author

G. Gambardella, G. Viscido, B. Tumaini, A. Isacchi, R. Bosotti, and D. di Bernardo

Subjects
Science
Abstract

The impact of tumour heterogeneity on drug response in breast cancer is not fully understood. Here, the authors characterise cell lines from all main breast cancer subtypes using single-cell RNA-seq and train a deconvolution algorithm to predict drug responses in heterogeneous tumour cell populations.

Published
2022
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11. Evidence for a pathogenic role of extrafollicular, IL-10–producing CCR6⁺B helper T cells in systemic lupus erythematosus

Author

Facciotti, F., Larghi, P., Bosotti, R., Vasco, C., Gagliani, N., Cordiglierif, C., Mazzarag, S., Ranzani, V., Rottoli, E., Curti, S., Penatti, A., Karnani, B., Kobayashi, Y., Crosti, M., Bombaci, M., van Hamburg, J. P., Rossetti, G., Gualtierotti, R., Gerosa, M., Gatti, S., Torretta, S., Pignataro, L., Tas, S. W., Abrignani, S., Pagani, M., Grassi, F., Meroni, P. L., Flavell, R. A., and Geginat, J.

Published
2020

12. RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

Author

Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, and Alfredo Pulvirenti

Subjects
RNA-seq, Stand-alone software, Cloud deployment, Pipeline, Docker, ncRNAs, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Results Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. Conclusions RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.

Published
2021
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13. Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors are associated with disease progression

Author

Bonnal, Raoul J. P., Rossetti, Grazisa, Lugli, Enrico, De Simone, Marco, Gruarin, Paola, Brummelman, Jolanda, Drufuca, Lorenzo, Passaro, Marco, Bason, Ramona, Gervasoni, Federica, Della Chiara, Giulia, D’Oria, Claudia, Martinovic, Martina, Curti, Serena, Ranzani, Valeria, Cordiglieri, Chiara, Alvisi, Giorgia, Mazza, Emilia Maria Cristina, Oliveto, Stefania, Silvestri, Ylenia, Carelli, Elena, Mazzara, Saveria, Bosotti, Roberto, Sarnicola, Maria Lucia, Godano, Chiara, Bevilacqua, Valeria, Lorenzo, Mariangela, Siena, Salvatore, Bonoldi, Emanuela, Sartore-Bianchi, Andrea, Amatu, Alessio, Veronesi, Giulia, Novellis, Pierluigi, Alloisio, Marco, Giani, Alessandro, Zucchini, Nicola, Opocher, Enrico, Ceretti, Andrea Pisani, Mariani, Nicolò, Biffo, Stefano, Prati, Daniele, Bardelli, Alberto, Geginat, Jens, Lanzavecchia, Antonio, Abrignani, Sergio, and Pagani, Massimiliano

Published
2021
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14. Fotobiomodulazione e xerostomia

Author

Porrini, Massimo, primary, Barenghi, Livia, additional, Pulicari, Federica, additional, Ghizzoni, Martina, additional, Modugno, Francesco Paolo, additional, Bosotti, Moreno, additional, Pellegrini, Matteo, additional, and Spadari, Francesco, additional

Published
2024
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15. Photobiomodulation and Miescher’s cheilitis granulomatosa: case report

Author

Massimo Porrini, Umberto Garagiola, Margherita Rossi, Moreno Bosotti, Sonia Marino, Aldo Bruno Giannì, Letterio Runza, and Francesco Spadari

Subjects
Diode laser, Photobiomodulation, Miescher granulomatous cheilitis, Orofacial granulomatosis, Dentistry, RK1-715, Surgery, RD1-811
Abstract

Abstract Background Miescher’s cheilitis granulomatosa (MCG) is a rare chronic inflammatory disease and is known as the monosymptomatic clinical form of Melkersson-Rosenthal syndrome (MRS). It is characterised by swelling of one or both lips and more frequently affects the upper lip. Histopathological findings show the presence of numerous inflammatory infiltrates and granuloma formations. Pharmacological treatments and surgery have provided results that are positive yet insufficiently stable in the long term. The clinical case described is of a 68-year-old female patient with a diagnosis of MCG of the upper lip. Case presentation The patient was diagnosed and treated at the Oral Medicine and Oral Pathology outpatient clinic of Maxillofacial and Odontostomatology Unit, Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico. The patient was recommended localised treatments of photobiomodulation (PBM) using a diode laser with a 635 nm and 980 nm dual-wavelength (λ) approach, a 600-micron fibre, and a handpiece with a 1-cm-diameter lens at 300 mW. Three treatments a week were administered for four weeks for a total of 12 treatment sessions (T 1–T 12). After that, the patient had a long follow-up period of about 2 years. The therapeutic results were clear from the initial stages of treatment. There was an immediate, gradual, and consistent reduction in labial swelling. A reduction in the size of the lip by about 35% at T 10–T 12 was observed, returning the size and volume of the upper lip within the normal clinical range. The painful symptoms subsided after the seventh treatment (T 7). The histopathological check at 3 months and the follow-up in particular confirmed the disease was in remission with satisfactorily stable treatment results. Moreover, the patient did not use any other treatments on the area from the early laser treatments through to the end of the follow-up period. Conclusions Our experience describes a clinical case of MCG treated with PBM and effectively resolved with a reduction of the lip swelling. The real success of the treatment emerged over time, showing that the tissue healing was stable. In absence of any collateral phenomena, this confirms the effective and documented therapeutic potential of PBM for chronic inflammatory infiltrates.

Published
2020
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17. A MHz-repetition-rate hard X-ray free-electron laser driven by a superconducting linear accelerator

Author

Decking, W., Abeghyan, S., Abramian, P., Abramsky, A., Aguirre, A., Albrecht, C., Alou, P., Altarelli, M., Altmann, P., Amyan, K., Anashin, V., Apostolov, E., Appel, K., Auguste, D., Ayvazyan, V., Baark, S., Babies, F., Baboi, N., Bak, P., Balandin, V., Baldinger, R., Baranasic, B., Barbanotti, S., Belikov, O., Belokurov, V., Belova, L., Belyakov, V., Berry, S., Bertucci, M., Beutner, B., Block, A., Blöcher, M., Böckmann, T., Bohm, C., Böhnert, M., Bondar, V., Bondarchuk, E., Bonezzi, M., Borowiec, P., Bösch, C., Bösenberg, U., Bosotti, A., Böspflug, R., Bousonville, M., Boyd, E., Bozhko, Y., Brand, A., Branlard, J., Briechle, S., Brinker, F., Brinker, S., Brinkmann, R., Brockhauser, S., Brovko, O., Brück, H., Brüdgam, A., Butkowski, L., Büttner, T., Calero, J., Castro-Carballo, E., Cattalanotto, G., Charrier, J., Chen, J., Cherepenko, A., Cheskidov, V., Chiodini, M., Chong, A., Choroba, S., Chorowski, M., Churanov, D., Cichalewski, W., Clausen, M., Clement, W., Cloué, C., Cobos, J. A., Coppola, N., Cunis, S., Czuba, K., Czwalinna, M., D’Almagne, B., Dammann, J., Danared, H., de Zubiaurre Wagner, A., Delfs, A., Delfs, T., Dietrich, F., Dietrich, T., Dohlus, M., Dommach, M., Donat, A., Dong, X., Doynikov, N., Dressel, M., Duda, M., Duda, P., Eckoldt, H., Ehsan, W., Eidam, J., Eints, F., Engling, C., Englisch, U., Ermakov, A., Escherich, K., Eschke, J., Saldin, E., Faesing, M., Fallou, A., Felber, M., Fenner, M., Fernandes, B., Fernández, J. M., Feuker, S., Filippakopoulos, K., Floettmann, K., Fogel, V., Fontaine, M., Francés, A., Martin, I. Freijo, Freund, W., Freyermuth, T., Friedland, M., Fröhlich, L., Fusetti, M., Fydrych, J., Gallas, A., García, O., Garcia-Tabares, L., Geloni, G., Gerasimova, N., Gerth, C., Geßler, P., Gharibyan, V., Gloor, M., Głowinkowski, J., Goessel, A., Gołębiewski, Z., Golubeva, N., Grabowski, W., Graeff, W., Grebentsov, A., Grecki, M., Grevsmuehl, T., Gross, M., Grosse-Wortmann, U., Grünert, J., Grunewald, S., Grzegory, P., Feng, G., Guler, H., Gusev, G., Gutierrez, J. L., Hagge, L., Hamberg, M., Hanneken, R., Harms, E., Hartl, I., Hauberg, A., Hauf, S., Hauschildt, J., Hauser, J., Havlicek, J., Hedqvist, A., Heidbrook, N., Hellberg, F., Henning, D., Hensler, O., Hermann, T., Hidvégi, A., Hierholzer, M., Hintz, H., Hoffmann, F., Hoffmann, Markus, Hoffmann, Matthias, Holler, Y., Hüning, M., Ignatenko, A., Ilchen, M., Iluk, A., Iversen, J., Iversen, J., Izquierdo, M., Jachmann, L., Jardon, N., Jastrow, U., Jensch, K., Jensen, J., Jeżabek, M., Jidda, M., Jin, H., Johansson, N., Jonas, R., Kaabi, W., Kaefer, D., Kammering, R., Kapitza, H., Karabekyan, S., Karstensen, S., Kasprzak, K., Katalev, V., Keese, D., Keil, B., Kholopov, M., Killenberger, M., Kitaev, B., Klimchenko, Y., Klos, R., Knebel, L., Koch, A., Koepke, M., Köhler, S., Köhler, W., Kohlstrunk, N., Konopkova, Z., Konstantinov, A., Kook, W., Koprek, W., Körfer, M., Korth, O., Kosarev, A., Kosiński, K., Kostin, D., Kot, Y., Kotarba, A., Kozak, T., Kozak, V., Kramert, R., Krasilnikov, M., Krasnov, A., Krause, B., Kravchuk, L., Krebs, O., Kretschmer, R., Kreutzkamp, J., Kröplin, O., Krzysik, K., Kube, G., Kuehn, H., Kujala, N., Kulikov, V., Kuzminych, V., La Civita, D., Lacroix, M., Lamb, T., Lancetov, A., Larsson, M., Le Pinvidic, D., Lederer, S., Lensch, T., Lenz, D., Leuschner, A., Levenhagen, F., Li, Y., Liebing, J., Lilje, L., Limberg, T., Lipka, D., List, B., Liu, J., Liu, S., Lorbeer, B., Lorkiewicz, J., Lu, H. H., Ludwig, F., Machau, K., Maciocha, W., Madec, C., Magueur, C., Maiano, C., Maksimova, I., Malcher, K., Maltezopoulos, T., Mamoshkina, E., Manschwetus, B., Marcellini, F., Marinkovic, G., Martinez, T., Martirosyan, H., Maschmann, W., Maslov, M., Matheisen, A., Mavric, U., Meißner, J., Meissner, K., Messerschmidt, M., Meyners, N., Michalski, G., Michelato, P., Mildner, N., Moe, M., Moglia, F., Mohr, C., Mohr, S., Möller, W., Mommerz, M., Monaco, L., Montiel, C., Moretti, M., Morozov, I., Morozov, P., Mross, D., Mueller, J., Müller, C., Müller, J., Müller, K., Munilla, J., Münnich, A., Muratov, V., Napoly, O., Näser, B., Nefedov, N., Neumann, Reinhard, Neumann, Rudolf, Ngada, N., Noelle, D., Obier, F., Okunev, I., Oliver, J. A., Omet, M., Oppelt, A., Ottmar, A., Oublaid, M., Pagani, C., Paparella, R., Paramonov, V., Peitzmann, C., Penning, J., Perus, A., Peters, F., Petersen, B., Petrov, A., Petrov, I., Pfeiffer, S., Pflüger, J., Philipp, S., Pienaud, Y., Pierini, P., Pivovarov, S., Planas, M., Pławski, E., Pohl, M., Polinski, J., Popov, V., Prat, S., Prenting, J., Priebe, G., Pryschelski, H., Przygoda, K., Pyata, E., Racky, B., Rathjen, A., Ratuschni, W., Regnaud-Campderros, S., Rehlich, K., Reschke, D., Robson, C., Roever, J., Roggli, M., Rothenburg, J., Rusiński, E., Rybaniec, R., Sahling, H., Salmani, M., Samoylova, L., Sanzone, D., Saretzki, F., Sawlanski, O., Schaffran, J., Schlarb, H., Schlösser, M., Schlott, V., Schmidt, C., Schmidt-Foehre, F., Schmitz, M., Schmökel, M., Schnautz, T., Schneidmiller, E., Scholz, M., Schöneburg, B., Schultze, J., Schulz, C., Schwarz, A., Sekutowicz, J., Sellmann, D., Semenov, E., Serkez, S., Sertore, D., Shehzad, N., Shemarykin, P., Shi, L., Sienkiewicz, M., Sikora, D., Sikorski, M., Silenzi, A., Simon, C., Singer, W., Singer, X., Sinn, H., Sinram, K., Skvorodnev, N., Smirnow, P., Sommer, T., Sorokin, A., Stadler, M., Steckel, M., Steffen, B., Steinhau-Kühl, N., Stephan, F., Stodulski, M., Stolper, M., Sulimov, A., Susen, R., Świerblewski, J., Sydlo, C., Syresin, E., Sytchev, V., Szuba, J., Tesch, N., Thie, J., Thiebault, A., Tiedtke, K., Tischhauser, D., Tolkiehn, J., Tomin, S., Tonisch, F., Toral, F., Torbin, I., Trapp, A., Treyer, D., Trowitzsch, G., Trublet, T., Tschentscher, T., Ullrich, F., Vannoni, M., Varela, P., Varghese, G., Vashchenko, G., Vasic, M., Vazquez-Velez, C., Verguet, A., Vilcins-Czvitkovits, S., Villanueva, R., Visentin, B., Viti, M., Vogel, E., Volobuev, E., Wagner, R., Walker, N., Wamsat, T., Weddig, H., Weichert, G., Weise, H., Wenndorf, R., Werner, M., Wichmann, R., Wiebers, C., Wiencek, M., Wilksen, T., Will, I., Winkelmann, L., Winkowski, M., Wittenburg, K., Witzig, A., Wlk, P., Wohlenberg, T., Wojciechowski, M., Wolff-Fabris, F., Wrochna, G., Wrona, K., Yakopov, M., Yang, B., Yang, F., Yurkov, M., Zagorodnov, I., Zalden, P., Zavadtsev, A., Zavadtsev, D., Zhirnov, A., Zhukov, A., Ziemann, V., Zolotov, A., Zolotukhina, N., Zummack, F., and Zybin, D.

Published
2020
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18. LASA Superconducting RF Cavities for Particle Accelerators

Author

Pagani, Carlo, Bellandi, Andrea, Bertucci, Michele, Bignami, Andrea, Bosotti, Angelo, Chen, Jin Fang, Michelato, Paolo, Monaco, Laura, Paparella, Rocco, Sertore, Daniele, Maiano, Cecilia, Pierini, Paolo, Pirani, Saeid, Bortignon, Pier Francesco, editor, Lodato, Giuseppe, editor, Meroni, Emanuela, editor, Paris, Matteo G.A., editor, Perini, Laura, editor, and Vicini, Alessandro, editor

Published
2018
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19. Epigenetic Control of Mitochondrial Fission Enables Self-Renewal of Stem-like Tumor Cells in Human Prostate Cancer

Author

Civenni, Gianluca, Bosotti, Roberto, Timpanaro, Andrea, Vàzquez, Ramiro, Merulla, Jessica, Pandit, Shusil, Rossi, Simona, Albino, Domenico, Allegrini, Sara, Mitra, Abhishek, Mapelli, Sarah N., Vierling, Luca, Giurdanella, Martina, Marchetti, Martina, Paganoni, Alyssa, Rinaldi, Andrea, Losa, Marco, Mira-Catò, Enrica, D'Antuono, Rocco, Morone, Diego, Rezai, Keyvan, D'Ambrosio, Gioacchino, Ouafik, L’Houcine, Mackenzie, Sarah, Riveiro, Maria E., Cvitkovic, Esteban, Carbone, Giuseppina M., and Catapano, Carlo V.

Published
2019
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25. An intestinal Th17 subset is associated with inflammation in Crohn’s Disease and activated by adherent-invasive Escherichia coli (AIEC)

Author

Paroni, Moira, primary, Leccese, Gabriella, additional, Ranzani, Valeria, additional, Moschetti, Giorgia, additional, Chiara, Matteo, additional, Perillo, Federica, additional, Ferri, Sara, additional, Clemente, Francesca, additional, Noviello, Daniele, additional, Conforti, Francesco Simone, additional, Ferrero, Stefano, additional, Karnani, Bhavna, additional, Bosotti, Roberto, additional, Vasco, Chiara, additional, Curti, Serena, additional, Crosti, Maria Cristina, additional, Gruarin, Paola, additional, Rossetti, Grazisa, additional, Conte, Maria Pia, additional, Vecchi, Maurizio, additional, Pagani, Massimiliano, additional, Landini, Paolo, additional, Facciotti, Federica, additional, Abrignani, Sergio, additional, Caprioli, Flavio, additional, and Geginat, Jens, additional

Published
2023
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28. Establishment and genomic characterization of the new chordoma cell line Chor-IN-1

Author

Roberta Bosotti, Paola Magnaghi, Sebastiano Di Bella, Liviana Cozzi, Carlo Cusi, Fabio Bozzi, Nicola Beltrami, Giovanni Carapezza, Dario Ballinari, Nadia Amboldi, Rosita Lupi, Alessio Somaschini, Laura Raddrizzani, Barbara Salom, Arturo Galvani, Silvia Stacchiotti, Elena Tamborini, and Antonella Isacchi

Subjects
Medicine, Science
Abstract

Abstract Chordomas are rare, slowly growing tumors with high medical need, arising in the axial skeleton from notochord remnants. The transcription factor “brachyury” represents a distinctive molecular marker and a key oncogenic driver of chordomas. Tyrosine kinase receptors are also expressed, but so far kinase inhibitors have not shown clear clinical efficacy in chordoma patients. The need for effective therapies is extremely high, but the paucity of established chordoma cell lines has limited preclinical research. Here we describe the isolation of the new Chor-IN-1 cell line from a recurrent sacral chordoma and its characterization as compared to other chordoma cell lines. Chor-IN-1 displays genomic identity to the tumor of origin and has morphological features, growth characteristics and chromosomal abnormalities typical of chordoma, with expression of brachyury and other relevant biomarkers. Chor-IN-1 gene variants, copy number alterations and kinome gene expression were analyzed in comparison to other four chordoma cell lines, generating large scale DNA and mRNA genomic data that can be exploited for the identification of novel pharmacological targets and candidate predictive biomarkers of drug sensitivity in chordoma. The establishment of this new, well characterized chordoma cell line provides a useful tool for the identification of drugs active in chordoma.

Published
2017
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29. Supplementary Figures 1-6 and Tables 1-2 from Entrectinib, a Pan–TRK, ROS1, and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications

Author

Ardini, Elena, primary, Menichincheri, Maria, primary, Banfi, Patrizia, primary, Bosotti, Roberta, primary, De Ponti, Cristina, primary, Pulci, Romana, primary, Ballinari, Dario, primary, Ciomei, Marina, primary, Texido, Gemma, primary, Degrassi, Anna, primary, Avanzi, Nilla, primary, Amboldi, Nadia, primary, Saccardo, Maria Beatrice, primary, Casero, Daniele, primary, Orsini, Paolo, primary, Bandiera, Tiziano, primary, Mologni, Luca, primary, Anderson, David, primary, Wei, Ge, primary, Harris, Jason, primary, Vernier, Jean-Michel, primary, Li, Gang, primary, Felder, Eduard, primary, Donati, Daniele, primary, Isacchi, Antonella, primary, Pesenti, Enrico, primary, Magnaghi, Paola, primary, and Galvani, Arturo, primary

Published
2023
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30. Data from Afatinib Is a New Therapeutic Approach in Chordoma with a Unique Ability to Target EGFR and Brachyury

Author

Magnaghi, Paola, primary, Salom, Barbara, primary, Cozzi, Liviana, primary, Amboldi, Nadia, primary, Ballinari, Dario, primary, Tamborini, Elena, primary, Gasparri, Fabio, primary, Montagnoli, Alessia, primary, Raddrizzani, Laura, primary, Somaschini, Alessio, primary, Bosotti, Roberta, primary, Orrenius, Christian, primary, Bozzi, Fabio, primary, Pilotti, Silvana, primary, Galvani, Arturo, primary, Sommer, Josh, primary, Stacchiotti, Silvia, primary, and Isacchi, Antonella, primary

Published
2023
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31. Data from Entrectinib, a Pan–TRK, ROS1, and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications

Author

Ardini, Elena, primary, Menichincheri, Maria, primary, Banfi, Patrizia, primary, Bosotti, Roberta, primary, De Ponti, Cristina, primary, Pulci, Romana, primary, Ballinari, Dario, primary, Ciomei, Marina, primary, Texido, Gemma, primary, Degrassi, Anna, primary, Avanzi, Nilla, primary, Amboldi, Nadia, primary, Saccardo, Maria Beatrice, primary, Casero, Daniele, primary, Orsini, Paolo, primary, Bandiera, Tiziano, primary, Mologni, Luca, primary, Anderson, David, primary, Wei, Ge, primary, Harris, Jason, primary, Vernier, Jean-Michel, primary, Li, Gang, primary, Felder, Eduard, primary, Donati, Daniele, primary, Isacchi, Antonella, primary, Pesenti, Enrico, primary, Magnaghi, Paola, primary, and Galvani, Arturo, primary

Published
2023
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32. Supplementary Materials and Methods, Tables S1-S2, and Figures S1-S6 from Afatinib Is a New Therapeutic Approach in Chordoma with a Unique Ability to Target EGFR and Brachyury

Author

Magnaghi, Paola, primary, Salom, Barbara, primary, Cozzi, Liviana, primary, Amboldi, Nadia, primary, Ballinari, Dario, primary, Tamborini, Elena, primary, Gasparri, Fabio, primary, Montagnoli, Alessia, primary, Raddrizzani, Laura, primary, Somaschini, Alessio, primary, Bosotti, Roberta, primary, Orrenius, Christian, primary, Bozzi, Fabio, primary, Pilotti, Silvana, primary, Galvani, Arturo, primary, Sommer, Josh, primary, Stacchiotti, Silvia, primary, and Isacchi, Antonella, primary

Published
2023
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33. Supplementary Materials and Methods from Entrectinib, a Pan–TRK, ROS1, and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications

Author

Ardini, Elena, primary, Menichincheri, Maria, primary, Banfi, Patrizia, primary, Bosotti, Roberta, primary, De Ponti, Cristina, primary, Pulci, Romana, primary, Ballinari, Dario, primary, Ciomei, Marina, primary, Texido, Gemma, primary, Degrassi, Anna, primary, Avanzi, Nilla, primary, Amboldi, Nadia, primary, Saccardo, Maria Beatrice, primary, Casero, Daniele, primary, Orsini, Paolo, primary, Bandiera, Tiziano, primary, Mologni, Luca, primary, Anderson, David, primary, Wei, Ge, primary, Harris, Jason, primary, Vernier, Jean-Michel, primary, Li, Gang, primary, Felder, Eduard, primary, Donati, Daniele, primary, Isacchi, Antonella, primary, Pesenti, Enrico, primary, Magnaghi, Paola, primary, and Galvani, Arturo, primary

Published
2023
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35. Supplementary Data from Transcriptional Analysis of an E2F Gene Signature as a Biomarker of Activity of the Cyclin-Dependent Kinase Inhibitor PHA-793887 in Tumor and Skin Biopsies from a Phase I Clinical Study

Author

Locatelli, Giuseppe, primary, Bosotti, Roberta, primary, Ciomei, Marina, primary, Brasca, Maria G., primary, Calogero, Raffaele, primary, Mercurio, Ciro, primary, Fiorentini, Francesco, primary, Bertolotti, Matteo, primary, Scacheri, Emanuela, primary, Scaburri, Angela, primary, Galvani, Arturo, primary, Pesenti, Enrico, primary, De Baere, Thierry, primary, Soria, Jean-Charles, primary, Lazar, Vladimir, primary, and Isacchi, Antonella, primary

Published
2023
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36. Data from Afatinib Is a New Therapeutic Approach in Chordoma with a Unique Ability to Target EGFR and Brachyury

Author

Antonella Isacchi, Silvia Stacchiotti, Josh Sommer, Arturo Galvani, Silvana Pilotti, Fabio Bozzi, Christian Orrenius, Roberta Bosotti, Alessio Somaschini, Laura Raddrizzani, Alessia Montagnoli, Fabio Gasparri, Elena Tamborini, Dario Ballinari, Nadia Amboldi, Liviana Cozzi, Barbara Salom, and Paola Magnaghi

Abstract

Chordomas are rare bone tumors with no approved therapy. These tumors express several activated tyrosine kinase receptors, which prompted attempts to treat patients with tyrosine kinase inhibitors. Although clinical benefit was observed in phase II clinical trials with imatinib and sorafenib, and sporadically also with EGFR inhibitors, therapies evaluated to date have shown modest activity. With the goal of identifying new drugs with immediate therapeutic potential for chordoma patients, we collected clinically approved drugs and other advanced inhibitors of MET, PDGFRβ, and EGFR tyrosine kinases, and assessed their antiproliferative activity against a panel of chordoma cell lines. Chordoma cell lines were not responsive to MET and PDGFRβ inhibitors. U-CH1 and UM-Chor1 were sensitive to all EGFR inhibitors, whereas the remaining cell lines were generally insensitive to these drugs. Afatinib was the only EGFR inhibitor with activity across the chordoma panel. We then investigated the molecular mechanisms behind the responses observed and found that the antiproliferative IC50s correlate with the unique ability of afatinib to promote degradation of EGFR and brachyury, an embryonic transcription factor considered a key driver of chordoma. Afatinib displayed potent antitumor efficacy in U-CH1, SF8894, CF322, and CF365 chordoma tumor models in vivo. In the panel analyzed, high EGFR phosphorylation and low AXL and STK33 expression correlated with higher sensitivity to afatinib and deserve further investigation as potential biomarkers of response. These data support the use of afatinib in clinical trials and provide the rationale for the upcoming European phase II study on afatinib in advanced chordoma. Mol Cancer Ther; 17(3); 603–13. ©2017 AACR.

Published
2023
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37. Supplementary Figures 1-6 and Tables 1-2 from Entrectinib, a Pan–TRK, ROS1, and ALK Inhibitor with Activity in Multiple Molecularly Defined Cancer Indications

Author

Arturo Galvani, Paola Magnaghi, Enrico Pesenti, Antonella Isacchi, Daniele Donati, Eduard Felder, Gang Li, Jean-Michel Vernier, Jason Harris, Ge Wei, David Anderson, Luca Mologni, Tiziano Bandiera, Paolo Orsini, Daniele Casero, Maria Beatrice Saccardo, Nadia Amboldi, Nilla Avanzi, Anna Degrassi, Gemma Texido, Marina Ciomei, Dario Ballinari, Romana Pulci, Cristina De Ponti, Roberta Bosotti, Patrizia Banfi, Maria Menichincheri, and Elena Ardini

Abstract

Supplementary Figure 1. Efficacy of entrectinib on KM12 xenograft model using the scheduling 4 days on/ 3 days off. Supplementary Figure 2. Mechanism of action of entrectinib compared to crizotinib in ALK-dependent Ba/F3 cells. Supplementary Figure 3. Cell cycle distrivbution of Karpas-299 and SR-786 cells treated with entrectinib for different periods of time Supplementary Figure 4. Mechanism of action studies of entrectinib in additional ALK-dependent ALCL models Supplementary Figure 5. In vivo efficacy of entrectinib on NCI-H2228 xenograft model using the scheduling 4 days on/ 3 days off Supplementary Figure 6. Representative magnetic resonance images of mice bearing intracranial tumors treated with vehicle, entrectinib or crizotinib Supplementary Table 1. List of human tumor cell lines treated with entrectinib Supplementary Table 2. Pharmacokinetic paramenters of entrectinib evaluated after repeated administration of compound in CD1 mice.

Published
2023
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38. Supplementary Materials and Methods, Tables S1-S2, and Figures S1-S6 from Afatinib Is a New Therapeutic Approach in Chordoma with a Unique Ability to Target EGFR and Brachyury

Author

Antonella Isacchi, Silvia Stacchiotti, Josh Sommer, Arturo Galvani, Silvana Pilotti, Fabio Bozzi, Christian Orrenius, Roberta Bosotti, Alessio Somaschini, Laura Raddrizzani, Alessia Montagnoli, Fabio Gasparri, Elena Tamborini, Dario Ballinari, Nadia Amboldi, Liviana Cozzi, Barbara Salom, and Paola Magnaghi

Abstract

Supplementary Table S1: Short Tandem Repeat (STR) fingerprinting; Supplementary Table S2: Anti-proliferative activity of MET and PDGFR inhibitors in chordoma cell lines; Supplementary Figure S1: Live-cell kinetic analysis of afatinib activity in U-CH1 cell line; Supplementary Figure S2: Effect of dacomitinib on EGFR and brachyury proteins; Supplementary Figure S3: Effect of EGFR and brachyury siRNA on U-CH1 cell viability and target proteins levels; Supplementary Figure S4: Analysis of the mechanism of afatinib-induced EGFR and brachyury down-modulation in U-CH1 chordoma cell line; Supplementary Figure S5: EGFR localization and phosphorylation in the different chordoma cell lines; Supplementary Figure S6: Short term pharmaco-dynamic response to afatinib.

Published
2023
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39. Data from Transcriptional Analysis of an E2F Gene Signature as a Biomarker of Activity of the Cyclin-Dependent Kinase Inhibitor PHA-793887 in Tumor and Skin Biopsies from a Phase I Clinical Study

Author

Antonella Isacchi, Vladimir Lazar, Jean-Charles Soria, Thierry De Baere, Enrico Pesenti, Arturo Galvani, Angela Scaburri, Emanuela Scacheri, Matteo Bertolotti, Francesco Fiorentini, Ciro Mercurio, Raffaele Calogero, Maria G. Brasca, Marina Ciomei, Roberta Bosotti, and Giuseppe Locatelli

Abstract

A transcriptional signature of the pan–cyclin-dependent kinase (Cdk) inhibitor PHA-793887 was evaluated as a potential pharmacodynamic and/or response biomarker in tumor and skin biopsies from patients treated in a phase I clinical study. We first analyzed the expression of a number of known E2F-dependent genes that were predicted to be modulated after Cdk2 and Cdk4 inhibition in xenograft tumor and skin samples of mice treated with the compound. This panel of 58 selected genes was then analyzed in biopsies from seven patients treated with PHA-793887 in a phase I dose escalation clinical trial in solid tumors. Quantitative real-time PCR or microarray analyses were done in paired skin and tumor biopsies obtained at baseline and at cycle 1. Analysis by quantitative real-time PCR of the signature in skin biopsies of patients treated at three different doses showed significant transcriptional downregulation with a dose-response correlation. These data show that PHA-793887 modulates genes involved in cell cycle regulation and proliferation in a clinical setting. The observed changes are consistent with its mechanism of action and correlate with target modulation in skin and with clinical benefit in tumors. Mol Cancer Ther; 9(5); 1265–73. ©2010 AACR.

Published
2023
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41. Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs

Author

Crippa, Stefania, primary, Conti, Anastasia, additional, Vavassori, Valentina, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Rivis, Silvia, additional, Bosotti, Roberto, additional, Scala, Serena, additional, Pirroni, Stefania, additional, Jofra-Hernandez, Raisa, additional, Santi, Ludovica, additional, Basso-Ricci, Luca, additional, Merelli, Ivan, additional, Genovese, Pietro, additional, Aiuti, Alessandro, additional, Naldini, Luigi, additional, Di Micco, Raffaella, additional, and Bernardo, Maria Ester, additional

Published
2023
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43. Photobiomodulation as a Therapeutic Strategy in Burning Mouth Syndrome: A Scoping Review

Author

Porrini, Massimo, Pulicari, Federica, Spadari, Francesco, Pellegrini, Matteo, Ghizzoni, Martina, and Bosotti, Moreno

Subjects
Oral Biology and Oral Pathology, Dentistry, FOS: Clinical medicine, Medicine and Health Sciences, Diseases
Abstract

Burning Mouth Syndrome (BMS) is considered an atypical oral clinical-symptomatological condition because etiopathogenesis is not yet fully clarified. It is mainly characterized by the symptom of burning, which occurs chronically and with various intensities. They are essential for making a diagnosis of BMS, clinical negativities, and instrumental investigations. It mainly affects the female sex, in the pre-post-climactic phases. A peripheral neuropathic matrix of the pain symptom has been repeatedly demonstrated. However, this subjectivity is associated with personalities with anxiety-depressive traits, affective-behavioral difficulties, and disorders of the psycho-algogenic sphere. Numerous treatments are reported in the literature, which has rarely met lasting healing parameters. In this clinical landscape, Photobiomodulation Therapy (PBMT) can be considered a possible therapeutic alternative. Our study aims to present a scoping review of how photobiomodulation is used in BMS therapy and to analyze the outcome of the therapy.

Published
2023
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45. Author Correction: A MHz-repetition-rate hard X-ray free-electron laser driven by a superconducting linear accelerator

Author

Decking, W., Abeghyan, S., Abramian, P., Abramsky, A., Aguirre, A., Albrecht, C., Alou, P., Altarelli, M., Altmann, P., Amyan, K., Anashin, V., Apostolov, E., Appel, K., Auguste, D., Ayvazyan, V., Baark, S., Babies, F., Baboi, N., Bak, P., Balandin, V., Baldinger, R., Baranasic, B., Barbanotti, S., Belikov, O., Belokurov, V., Belova, L., Belyakov, V., Berry, S., Bertucci, M., Beutner, B., Block, A., Blöcher, M., Böckmann, T., Bohm, C., Böhnert, M., Bondar, V., Bondarchuk, E., Bonezzi, M., Borowiec, P., Bösch, C., Bösenberg, U., Bosotti, A., Böspflug, R., Bousonville, M., Boyd, E., Bozhko, Y., Brand, A., Branlard, J., Briechle, S., Brinker, F., Brinker, S., Brinkmann, R., Brockhauser, S., Brovko, O., Brück, H., Brüdgam, A., Butkowski, L., Büttner, T., Calero, J., Castro-Carballo, E., Cattalanotto, G., Charrier, J., Chen, J., Cherepenko, A., Cheskidov, V., Chiodini, M., Chong, A., Choroba, S., Chorowski, M., Churanov, D., Cichalewski, W., Clausen, M., Clement, W., Cloué, C., Cobos, J. A., Coppola, N., Cunis, S., Czuba, K., Czwalinna, M., D’Almagne, B., Dammann, J., Danared, H., de Zubiaurre Wagner, A., Delfs, A., Delfs, T., Dietrich, F., Dietrich, T., Dohlus, M., Dommach, M., Donat, A., Dong, X., Doynikov, N., Dressel, M., Duda, M., Duda, P., Eckoldt, H., Ehsan, W., Eidam, J., Eints, F., Engling, C., Englisch, U., Ermakov, A., Escherich, K., Eschke, J., Saldin, E., Faesing, M., Fallou, A., Felber, M., Fenner, M., Fernandes, B., Fernández, J. M., Feuker, S., Filippakopoulos, K., Floettmann, K., Fogel, V., Fontaine, M., Francés, A., Martin, I. Freijo, Freund, W., Freyermuth, T., Friedland, M., Fröhlich, L., Fusetti, M., Fydrych, J., Gallas, A., García, O., Garcia-Tabares, L., Geloni, G., Gerasimova, N., Gerth, C., Geßler, P., Gharibyan, V., Gloor, M., Głowinkowski, J., Goessel, A., Gołębiewski, Z., Golubeva, N., Grabowski, W., Graeff, W., Grebentsov, A., Grecki, M., Grevsmuehl, T., Gross, M., Grosse-Wortmann, U., Grünert, J., Grunewald, S., Grzegory, P., Feng, G., Guler, H., Gusev, G., Gutierrez, J. L., Hagge, L., Hamberg, M., Hanneken, R., Harms, E., Hartl, I., Hauberg, A., Hauf, S., Hauschildt, J., Hauser, J., Havlicek, J., Hedqvist, A., Heidbrook, N., Hellberg, F., Henning, D., Hensler, O., Hermann, T., Hidvégi, A., Hierholzer, M., Hintz, H., Hoffmann, F., Hoffmann, Markus, Hoffmann, Matthias, Holler, Y., Hüning, M., Ignatenko, A., Ilchen, M., Iluk, A., Iversen, J., Iversen, J., Izquierdo, M., Jachmann, L., Jardon, N., Jastrow, U., Jensch, K., Jensen, J., Jeżabek, M., Jidda, M., Jin, H., Johansson, N., Jonas, R., Kaabi, W., Kaefer, D., Kammering, R., Kapitza, H., Karabekyan, S., Karstensen, S., Kasprzak, K., Katalev, V., Keese, D., Keil, B., Kholopov, M., Killenberger, M., Kitaev, B., Klimchenko, Y., Klos, R., Knebel, L., Koch, A., Koepke, M., Köhler, S., Köhler, W., Kohlstrunk, N., Konopkova, Z., Konstantinov, A., Kook, W., Koprek, W., Körfer, M., Korth, O., Kosarev, A., Kosiński, K., Kostin, D., Kot, Y., Kotarba, A., Kozak, T., Kozak, V., Kramert, R., Krasilnikov, M., Krasnov, A., Krause, B., Kravchuk, L., Krebs, O., Kretschmer, R., Kreutzkamp, J., Kröplin, O., Krzysik, K., Kube, G., Kuehn, H., Kujala, N., Kulikov, V., Kuzminych, V., La Civita, D., Lacroix, M., Lamb, T., Lancetov, A., Larsson, M., Le Pinvidic, D., Lederer, S., Lensch, T., Lenz, D., Leuschner, A., Levenhagen, F., Li, Y., Liebing, J., Lilje, L., Limberg, T., Lipka, D., List, B., Liu, J., Liu, S., Lorbeer, B., Lorkiewicz, J., Lu, H. H., Ludwig, F., Machau, K., Maciocha, W., Madec, C., Magueur, C., Maiano, C., Maksimova, I., Malcher, K., Maltezopoulos, T., Mamoshkina, E., Manschwetus, B., Marcellini, F., Marinkovic, G., Martinez, T., Martirosyan, H., Maschmann, W., Maslov, M., Matheisen, A., Mavric, U., Meißner, J., Meissner, K., Messerschmidt, M., Meyners, N., Michalski, G., Michelato, P., Mildner, N., Moe, M., Moglia, F., Mohr, C., Mohr, S., Möller, W., Mommerz, M., Monaco, L., Montiel, C., Moretti, M., Morozov, I., Morozov, P., Mross, D., Mueller, J., Müller, C., Müller, J., Müller, K., Munilla, J., Münnich, A., Muratov, V., Napoly, O., Näser, B., Nefedov, N., Neumann, Reinhard, Neumann, Rudolf, Ngada, N., Noelle, D., Obier, F., Okunev, I., Oliver, J. A., Omet, M., Oppelt, A., Ottmar, A., Oublaid, M., Pagani, C., Paparella, R., Paramonov, V., Peitzmann, C., Penning, J., Perus, A., Peters, F., Petersen, B., Petrov, A., Petrov, I., Pfeiffer, S., Pflüger, J., Philipp, S., Pienaud, Y., Pierini, P., Pivovarov, S., Planas, M., Pławski, E., Pohl, M., Polinski, J., Popov, V., Prat, S., Prenting, J., Priebe, G., Pryschelski, H., Przygoda, K., Pyata, E., Racky, B., Rathjen, A., Ratuschni, W., Regnaud-Campderros, S., Rehlich, K., Reschke, D., Robson, C., Roever, J., Roggli, M., Rothenburg, J., Rusiński, E., Rybaniec, R., Sahling, H., Salmani, M., Samoylova, L., Sanzone, D., Saretzki, F., Sawlanski, O., Schaffran, J., Schlarb, H., Schlösser, M., Schlott, V., Schmidt, C., Schmidt-Foehre, F., Schmitz, M., Schmökel, M., Schnautz, T., Schneidmiller, E., Scholz, M., Schöneburg, B., Schultze, J., Schulz, C., Schwarz, A., Sekutowicz, J., Sellmann, D., Semenov, E., Serkez, S., Sertore, D., Shehzad, N., Shemarykin, P., Shi, L., Sienkiewicz, M., Sikora, D., Sikorski, M., Silenzi, A., Simon, C., Singer, W., Singer, X., Sinn, H., Sinram, K., Skvorodnev, N., Smirnow, P., Sommer, T., Sorokin, A., Stadler, M., Steckel, M., Steffen, B., Steinhau-Kühl, N., Stephan, F., Stodulski, M., Stolper, M., Sulimov, A., Susen, R., Świerblewski, J., Sydlo, C., Syresin, E., Sytchev, V., Szuba, J., Tesch, N., Thie, J., Thiebault, A., Tiedtke, K., Tischhauser, D., Tolkiehn, J., Tomin, S., Tonisch, F., Toral, F., Torbin, I., Trapp, A., Treyer, D., Trowitzsch, G., Trublet, T., Tschentscher, T., Ullrich, F., Vannoni, M., Varela, P., Varghese, G., Vashchenko, G., Vasic, M., Vazquez-Velez, C., Verguet, A., Vilcins-Czvitkovits, S., Villanueva, R., Visentin, B., Viti, M., Vogel, E., Volobuev, E., Wagner, R., Walker, N., Wamsat, T., Weddig, H., Weichert, G., Weise, H., Wenndorf, R., Werner, M., Wichmann, R., Wiebers, C., Wiencek, M., Wilksen, T., Will, I., Winkelmann, L., Winkowski, M., Wittenburg, K., Witzig, A., Wlk, P., Wohlenberg, T., Wojciechowski, M., Wolff-Fabris, F., Wrochna, G., Wrona, K., Yakopov, M., Yang, B., Yang, F., Yurkov, M., Zagorodnov, I., Zalden, P., Zavadtsev, A., Zavadtsev, D., Zhirnov, A., Zhukov, A., Ziemann, V., Zolotov, A., Zolotukhina, N., Zummack, F., and Zybin, D.

Published
2020
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46. Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs

Author

Crippa, Stefania, primary, Conti, Anastasia, additional, Vavassori, Valentina, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Rivis, Silvia, additional, Bosotti, Roberto, additional, Scala, Serena, additional, Pirroni, Stefania, additional, Jofra-Hernandez, Raisa, additional, Santi, Ludovica, additional, Basso-Ricci, Luca, additional, Merelli, Ivan, additional, Genovese, Pietro, additional, Aiuti, Alessandro, additional, Naldini, Luigi, additional, Di Micco, Raffaella, additional, and Bernardo, Maria Ester, additional

Published
2022
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47. Non-parametric MANOVA Methods for Detecting Differentially Expressed Genes in Real-Time RT-PCR Experiments

Author

Bassani, Niccoló, Ambrogi, Federico, Bosotti, Roberta, Bertolotti, Matteo, Isacchi, Antonella, Biganzoli, Elia, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Masulli, Francesco, editor, Peterson, Leif E., editor, and Tagliaferri, Roberto, editor

Published
2010
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48. Comprehensive kinome NGS targeted expression profiling by KING-REX

Author

Ettore Rizzo, Vincenzo Nigro, Alessio Somaschini, Sebastiano Di Bella, Antonella Leone, Margherita Mutarelli, Giovanni Carapezza, Diego di Bernardo, Laura Raddrizzani, Roberta Bosotti, Rosita Lupi, Antonella Isacchi, Carlo Cusi, Paolo Magni, Carapezza, G, Cusi, C, Rizzo, E, Raddrizzani, L, Di Bella, S, Somaschini, A, Leone, A, Lupi, R, Mutarelli, M, Nigro, V, di Bernardo, D, Magni, P, Isacchi, A, Bosotti, R, Carapezza, G., Cusi, C., Rizzo, E., Raddrizzani, L., Di Bella, S., Somaschini, A., Leone, A., Lupi, R., Mutarelli, M., Nigro, V., Di Bernardo, D., Magni, P., Isacchi, A., and Bosotti, R.

Subjects
0106 biological sciences, lcsh:QH426-470, RNA Stability, lcsh:Biotechnology, Kinome gene expression, Druggability, Computational biology, Biology, Proteomics, 01 natural sciences, NGS RNA targeted panel, Transcriptome, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene expression, Genetics, Kinome, Gene, 030304 developmental biology, 0303 health sciences, Methodology Article, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Gene expression profiling, lcsh:Genetics, DNA microarray, Gene Fusion, Protein Kinases, 010606 plant biology & botany, Biotechnology
Abstract

Background Protein kinases are enzymes controlling different cellular functions. Genetic alterations often result in kinase dysregulation, making kinases a very attractive class of druggable targets in several human diseases. Existing approved drugs still target a very limited portion of the human ‘kinome’, demanding a broader functional knowledge of individual and co-expressed kinase patterns in physiologic and pathologic settings. The development of novel rapid and cost-effective methods for kinome screening is therefore highly desirable, potentially leading to the identification of novel kinase drug targets. Results In this work, we describe the development of KING-REX (KINase Gene RNA EXpression), a comprehensive kinome RNA targeted custom assay-based panel designed for Next Generation Sequencing analysis, coupled with a dedicated data analysis pipeline. We have conceived KING-REX for the gene expression analysis of 512 human kinases; for 319 kinases, paired assays and custom analysis pipeline features allow the evaluation of 3′- and 5′-end transcript imbalances as readout for the prediction of gene rearrangements. Validation tests on cell line models harboring known gene fusions demonstrated a comparable accuracy of KING-REX gene expression assessment as in whole transcriptome analyses, together with a robust detection of transcript portion imbalances in rearranged kinases, even in complex RNA mixtures or in degraded RNA. Conclusions These results support the use of KING-REX as a rapid and cost effective kinome investigation tool in the field of kinase target identification for applications in cancer biology and other human diseases. Electronic supplementary material The online version of this article (10.1186/s12864-019-5676-3) contains supplementary material, which is available to authorized users.

Published
2019
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50. Brixsino High-Flux Dual X-Ray and THz Radiation Source Based on Energy Recovery Linacs

Author

Drebot, Illya, Abbracchio, Maria Pia, Altilia, S., Andreone, Antonello, Bacci, Alberto, Bertucci, Michele, Bosotti, Angelo, Broggi, Francesco, Calandrino, Riccardo, Canella, Francesco, Capra, Stefano, Cardarelli, Paolo, Cialdi, Simone, Cipriani, Daniele, Citterio, Mauro, Delvecchio, Antonella, Esposito, Adolfo, Ferragut, Rafael, Galzerano, Gianluca, Giammarchi, Marco, Giannotti, Dario, Giove, Dario, Koral, Can, Latorre, Stefano, Lenardi, Cristina, Masullo, Maria Rosaria, Mazaheri, Z., Meroni, Chiara, Mettivier, Giovanni, Michelato, Paolo, Monaco, Laura, Opromolla, Michele, Pagani, Carlo, Paparella, Rocco, Papari, G.P., Paparo, Domenico, Paroli, Bruno, Passarelli, Andrea, Paternò, Gianfranco, Petrillo, Vittoria, Piccirillo, B., Prelz, Francesco, Puppin, Ezio, Rossetti Conti, Marcello, Rossi, Andrea, Rossi, Lucio, Rubano, A., Ruijter, Marcel, Russo, Paolo, Samsam, Sanae, Serafini, Luca, Sertore, Daniele, Sorbi, Massimo, Statera, Marco, Suerra, Edoardo, Taibi, Angelo, Torresin, Alberto, Torri, Verardo, Vanzulli, A., Frank Zimmermann (CERN, Meyrin, Switzerland), Hitoshi Tanaka (RIKEN, Hyogo, Japan), Porntip Sudmuang (SRLI, Nakhon, Thailand), Prapong Klysubun (SRLI, Nakhon, Thailand), Prapaiwan Sunwong (SRLI, Nakhon, Thailand), Thakonwat Chanwattana (SRLI, Nakhon, Thailand), Christine Petit-Jean-Genaz (CERN, Meyrin, Switzerland), Volker R.W. Schaa (GSI, Darmstadt, Germany), Drebot, Illya, Pia Abbracchio, Maria, Altilia, S., Andreone, Antonello, Bacci, Alberto, Bertucci, Michele, Bosotti, Angelo, Broggi, Francesco, Calandrino, Riccardo, Canella, Francesco, Capra, Stefano, Cardarelli, Paolo, Cialdi, Simone, Cipriani, Daniele, Citterio, Mauro, Delvecchio, Antonella, Esposito, Adolfo, Ferragut, Rafael, Galzerano, Gianluca, Giammarchi, Marco, Giannotti, Dario, Giove, Dario, Koral, Can, Latorre, Stefano, Lenardi, Cristina, Masullo, Maria Rosaria, Mazaheri, Z., Meroni, Chiara, Mettivier, Giovanni, Michelato, Paolo, Monaco, Laura, Opromolla, Michele, Pagani, Carlo, Paparella, Rocco, Papari, G. P., Paparo, Domenico, Paroli, Bruno, Passarelli, Andrea, Paternò, Gianfranco, Petrillo, Vittoria, Piccirillo, B., Prelz, Francesco, Puppin, Ezio, Rossetti Conti, Marcello, SALVO ROSSI, Andrea, Rossi, Lucio, Rubano, A., Ruijter, Marcel, Russo, Paolo, Samsam, Sanae, Serafini, Luca, Sertore, Daniele, Sorbi, Massimo, Statera, Marco, Suerra, Edoardo, Taibi, Angelo, Torresin, Alberto, Torri, Verardo, and Vanzulli, A.

Subjects
electron, Energy Recovery Linac, laser, electron, radiation, photon, cavity, CW-SC, photon, Physics::Optics, MC2: Photon Sources and Electron Accelerators, cavity, ICS, CW-SC, Energy Recovery Linac, Accelerator Physics, NO, laser, radiation, ICS, Physics::Accelerator Physics
Abstract

We present the conceptual design of a compact light source named BriXSinO. BriXSinO was born as demonstrator of the Marix project, but it is also a dual high flux radiation source Inverse Compton Source (ICS) of X-ray and Free-Electron Laser of THz spectral range radiation conceived for medical applications and general applied research. The accelerator is a push-pull CW-SC Energy Recovery Linac (ERL) based on superconducting cavities technology and allows to sustain MW-class beam power with almost just one hundred kW active power dissipation/consumption. ICS line produces 33 keV monochromatic X-Rays via Compton scattering of the electron beam with a laser system in Fabry-Pérot cavity at a repetition rate of 100 MHz. The THz FEL oscillator is based on an undulator imbedded in optical cavity and generates THz wavelengths from 15 to 50 micron., Proceedings of the 13th International Particle Accelerator Conference, IPAC2022, Bangkok, Thailand

Published
2022

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