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22 results on '"Peluso D"'

1. Poster Session Saturday 14 December - AM: 14/12/2013 08:30-12:30 * Location: Poster area

Author

Muraru, D., Addetia, K., Veronesi, F., Corsi, C., Mor-Avi, V., Yamat, M., Weinert, L., Lang, R., Badano, L., Faita, F., Di Lascio, N., Bruno, R., Bianchini, E., Ghiadoni, L., Sicari, R., Gemignani, V., Angelis, A., Ageli, K., Ioakimidis, N., Chrysohoou, C., Agelakas, A., Felekos, I., Vaina, S., Aznaourides, K., Vlachopoulos, C., Stefanadis, C., Nemes, A., Szolnoky, G., Gavaller, H., Gonczy, A., Kemeny, L., Forster, T., Ramalho, A., Placido, R., Marta, L., Menezes, M., Magalhaes, A., Cortez Dias, N., Martins, S., Almeida, A., Pinto, F., Nunes Diogo, A., Botezatu, C.-D., Enache, R., Popescu, B., Nastase, O., Coman, M., Ghiorghiu, I., Calin, A., Rosca, M., Beladan, C., Ginghina, C., Grapsa, J., Cabrita, I., Durighel, G., O'regan, D., Dawson, D., Nihoyannopoulos, P., Pellicori, P., Kallvikbacka-Bennett, A., Zhang, J., Lukaschuk, E., Joseph, A., Bourantas, C., Loh, H., Bragadeesh, T., Clark, A., Cleland, J., Lomax, S., Putzu, P., Diercx, R., Parsons, S., Dicken, B., Vered, Z., Adirevitz, L., Dragu, R., Blatt, A., Karev, E., Malca, Y., Roytvarf, A., Marek, D., Sovova, E., Berkova, M., Cihalik, C., Taborsky, M., Lindqvist, P., Tossavainen, E., Soderberg, S., Gonzales, M., Gustavsson, S., Henein, M., Sonne, C., Bott-Fluegel, L., Hauck, S., Lesevic, H., Hadamitzky, M., Wolf, P., Kolb, C., Bandera, F., Pellegrino, M., Generati, G., Donghi, V., Alfonzetti, E., Castelvecchio, S., Menicanti, L., Guazzi, M., Buchyte, S., Rinkuniene, D., Jurkevicius, R., Smarz, K., Zaborska, B., Jaxa-Chamiec, T., Maciejewski, P., Budaj, A., Santoro, A., Federico Alvino, F., Giovanni Antonelli, G., Roberta Molle, R., Matteo Bertini, M., Stefano Lunghetti, S., Sergio Mondillo, S., Henri, C., Magne, J., Dulgheru, R., Laaraibi, S., Voilliot, D., Kou, S., Pierard, L., Lancellotti, P., Szulik, M., Stabryla-Deska, J., Kalinowski, M., Sliwinska, A., Szymala, M., Lenarczyk, R., Kalarus, Z., Kukulski, T., Yiangou, K., Azina, C., Yiangou, A., Ioannides, M., Chimonides, S., Baysal, S., Pirat, B., Okyay, K., Bal, U., Muderrisoglu, H., Popovic, D., Ostojic, M., Petrovic, M., Vujisic-Tesic, B., Arandjelovic, A., Petrovic, I., Banovic, M., Popovic, B., Vukcevic, V., Damjanovic, S., Velasco Del Castillo, S., Onaindia Gandarias, J., Arana Achaga, X., Laraudogoitia Zaldumbide, E., Rodriguez Sanchez, I., Cacicedo De Bobadilla, A., Romero Pereiro, A., Aguirre Larracoechea, U., Salinas, T., Subinas, A., Elzbieciak, M., Wita, K., Grabka, M., Chmurawa, J., Doruchowska, A., Turski, M., Filipecki, A., Wybraniec, M., Mizia-Stec, K., Varho, V., Karjalainen, P., Lehtinen, T., Airaksinen, J., Ylitalo, A., Kiviniemi, T., Gargiulo, P., Galderisi, M., D' Amore, C., Lo Iudice, F., Savarese, G., Casaretti, L., Pellegrino, A., Fabiani, I., La Mura, L., Perrone Filardi, P., Kim, J. Y., Chung, W., Yu, J., Choi, Y., Park, C., Youn, H., Lee, M., Nagy, A., Manouras, A., Gunyeli, E., Gustafsson, U., Shahgaldi, K., Winter, R., Johnsson, J., Zagatina, A., Krylova, L., Zhuravskaya, N., Vareldzyan, Y., Tyurina, T., Clitsenko, O., Khalifa, E. A., Ashour, Z., Elnagar, W., Jung, I., Seo, H., Lee, S., Lim, D., Mizariene, V., Verseckaite, R., Janenaite, J., Jonkaitiene, R., Sanchez Espino, A., Bonaque Gonzalez, J., Merchan Ortega, G., Bolivar Herrera, N., Ikuta, I., Macancela Quinones, J., Gomez Recio, M., Silva Fazendas Adame, P. R., Caldeira, D., Stuart, B., Almeida, S., Cruz, I., Ferreira, A., Freire, G., Lopes, L., Cotrim, C., Pereira, H., Mediratta, A., Moss, J., Nayak, H., Al Amri, I., Debonnaire, P., Van Der Kley, F., Schalij, M., Bax, J., Ajmone Marsan, N., Delgado, V., Schmidt, F. P., Gniewosz, T., Jabs, A., Munzel, T., Jansen, T., Kaempfner, D., Hink, U., Von Bardeleben, R., Jose, J., George, O., Joseph, G., Adawi, S., Najjar, R., Ahronson, D., Shiran, A., Van Riel, A., Boerlage - Van Dijk, K., De Bruin - Bon, H., Araki, M., Meregalli, P., Koch, K., Vis, M., Mulder, B., Baan, J., Bouma, B., Marciniak, A., Elton, D., Glover, K., Campbell, I., Sharma, R., Batalha, S., Lourenco, C., Oliveira Da Silva, C., Caballero, L., Garcia-Lara, J., Gonzalez-Carrillo, J., Oliva, M., Saura, D., Garcia-Navarro, M., Espinosa, M., Pinar, E., Valdes, M., De La Morena, G., Barreiro Perez, M., Lopez Perez, M., Roy, D., Brecker, S., Venkateshvaran, A., Dash, P. K., Sola, S., Barooah, B., Govind, S. C., Brodin, L. A., Saura Espin, D., Caballero Jimenez, L., Gonzalez Carrillo, J., Oliva Sandoval, M., Lopez Ruiz, M., Garcia Navarro, M., Espinosa Garcia, M., Valdes Chavarri, M., De La Morena Valenzuela, G., Gatti, G., Dell'angela, L., Pinamonti, B., Benussi, B., Sinagra, G., Pappalardo, A., Hernandez, V., Saavedra, J., Gonzalez, A., Iglesias, P., Civantos, S., Guijarro, G., Monereo, S., Ikeda, M., Toh, N., Oe, H., Tanabe, Y., Watanabe, N., Ito, H., Ciampi, Q., Cortigiani, L., Pratali, L., Rigo, F., Villari, B., Picano, E., Yoon, J., Sohn, J., Kim, Y., Chang, H., Hong, G., Kim, T., Ha, J., Choi, B., Rim, S., Choi, E., Tibazarwa, K., Sliwa, K., Wonkam, A., Mayosi, B., Oryshchyn, N., Ivaniv, Y., Pavlyk, S., Lourenco, M. R., Azevedo, O., Moutinho, J., Nogueira, I., Fernandes, M., Pereira, V., Quelhas, I., Lourenco, A., Sunbul, M., Tigen, K., Karaahmet, T., Dundar, C., Ozben, B., Guler, A., Cincin, A., Bulut, M., Sari, I., Basaran, Y., Baydar, O., Kadriye Kilickesmez, K., Ugur Coskun, U., Polat Canbolat, P., Veysel Oktay, V., Umit Yasar Sinan, U., Okay Abaci, O., Cuneyt Kocas, C., Sinan Uner, S., Serdar Kucukoglu, S., Zaroui, A., Mourali, M., Ben Said, R., Asmi, M., Aloui, H., Kaabachi, N., Mechmeche, R., Saberniak, J., Hasselberg, N., Borgquist, R., Platonov, P., Holst, A., Edvardsen, T., Haugaa, K., Eran, A., Yueksel, D., Er, F., Gassanov, N., Rosenkranz, S., Baldus, S., Guedelhoefer, H., Faust, M., Caglayan, E., Matveeva, N., Nartsissova, G., Chernjavskij, A., Ippolito, R., De Palma, D., Muscariello, R., Santoro, C., Raia, R., Schiano-Lomoriello, V., Gargiulo, F., Lipari, P., Bonapace, S., Zenari, L., Valbusa, F., Rossi, A., Lanzoni, L., Canali, G., Molon, G., Campopiano, E., Barbieri, E., Ikonomidis, I., Varoudi, M., Papadavid, E., Theodoropoulos, K., Papadakis, I., Pavlidis, G., Triantafyllidi, H., Anastasiou - Nana, M., Rigopoulos, D., Lekakis, J., Ozen, G., Durmus, E., Kivrak, T., Atas, H., Direskeneli, H., Stevanovic, A., Dekleva, M., Trajic, S., Paunovic, N., Simic, A., Khan, S., Mushemi-Blake, S., Jouhra, F., Dennes, W., Monaghan, M., Melikian, N., Shah, A., Maceira Gonzalez, A. M., Lopez-Lereu, M., Monmeneu, J., Igual, B., Estornell, J., Boraita, A., Kosmala, W., Rojek, A., Bialy, D., Mysiak, A., Przewlocka-Kosmala, M., Popescu, I., Mancas, S., Mornos, C., Serbescu, I., Ionescu, G., Ionac, A., Gaudron, P., Niemann, M., Herrmann, S., Hu, K., Liu, D., Wojciech, K., Frantz, S., Bijnens, B., Ertl, G., Weidemann, F., Cosin-Sales, J., Ruvira, J., Diago, J., Aguilar, J., Cruz, C., Pinho, T., Madureira, A., Lebreiro, A., Dias, C., Ramos, I., Silva Cardoso, J., Julia Maciel, M., De Meester, P., Van De Bruaene, A., Herijgers, P., Voigt, J.-U., Budts, W., Franzoso, F., Voser, E., Wohlmut, C., Kellenberger, C., Valsangiacomo Buechel, E., Carrero, C., Benger, J., Parcerisa, M., Falconi, M., Oberti, P., Granja, M., Cagide, A., Del Pasqua, A., Secinaro, A., Antonelli, G., Iacomino, M., Toscano, A., Chinali, M., Esposito, C., Carotti, A., Pongiglione, G., Rinelli, G., Youssef Moustafa, A., Al Murayeh, M., Al Masswary, A., Al Sheikh, K., Moselhy, M., Dardir, M., Deising, J., Butz, T., Suermeci, G., Liebeton, J., Wennemann, R., Tzikas, S., Van Bracht, M., Prull, M., Trappe, H.-J., Martin Hidalgo, M., Delgado Ortega, M., Ruiz Ortiz, M., Mesa Rubio, D., Carrasco Avalos, F., Seoane Garcia, T., Pan Alvarez-Ossorio, M., Lopez Aguilera, J., Puentes Chiachio, M., Suarez De Lezo Cruz Conde, J., Petrovic, M. T., Giga, V., Stepanovic, J., Tesic, M., Jovanovic, I., Djordjevic-Dikic, A., Piatkowski, R., Kochanowski, J., Scislo, P., Opolski, G., Vareldzhyan, Y., Bombardini, T., Gherardi, S., Leone, O., Michelotto, E., Ciccarone, A., Tarantino, N., Ostuni, V., Rubino, M., Genco, W., Santoro, G., Carretta, D., Romito, R., Colonna, P., Cameli, M., Lunghetti, S., Lisi, M., Curci, V., Cameli, P., Focardi, M., Favilli, R., Mondillo, S., Hoffmann, R., Barletta, G., Von Bardeleben, S., Kasprzak, J., Greis, C., Vanoverschelde, J., Becher, H., Machida, T., Izumo, M., Suzuki, K., Kaimijima, R., Mizukoshi, K., Manabe-Uematsu, M., Takai, M., Harada, T., Akashi, Y., Martin Garcia, A., Arribas-Jimenez, A., Cruz-Gonzalez, I., Nieto, F., Iscar, A., Merchan, S., Martin-Luengo, C., Brecht, A., Theres, L., Spethmann, S., Dreger, H., Baumann, G., Knebel, F., Jasaityte, R., Heyde, B., Rademakers, F., Claus, P., D'hooge, J., Lervik Nilsen, L. C., Lund, J., Brekke, B., Stoylen, A., Giraldeau, G., Duchateau, N., Gabrielli, L., Penela, D., Evertz, R., Mont, L., Brugada, J., Berruezo, A., Sitges, M., Kordybach, M., Kowalski, M., Hoffman, P., Pilichowska, E., Baran, J., Kulakowski, P., Wahi, S., Vollbon, W., Leano, R., Thomas, A., Bricknell, K., Holland, D., Napier, S., Stanton, T., Teferici, D., Qirko, S., Petrela, E., Dibra, A., Bajraktari, G., Bara, P., Sanchis Ruiz, L., Andrea, R., Falces, C., Perez-Villa, F., Sulemane, S., Panoulas, V., Bratsas, A., Tam, F., Abduch, M., Alencar, A., Coracin, F., Barban, A., Saboya, R., Dulley, F., Mathias, W., Vieira, M., Buccheri, S., Mangiafico, S., Arcidiacono, A., Bottari, V., Leggio, S., Tamburino, C., Monte, I. P., Spitzer, E., Beitzke, D., Kaneider, A., Pavo, N., Gottsauner-Wolf, M., Wolf, F., Loewe, C., Mushtaq, S., Andreini, D., Pontone, G., Bertella, E., Conte, E., Baggiano, A., Annoni, A., Cortinovis, S., Fiorentini, C., Pepi, M., Gustafsson, M., Alehagen, U., Dahlstrom, U., Johansson, P., Faden, G., Faggiano, P., Albertini, L., Reverberi, C., Gaibazzi, N., Taylor, R. J., Moody, W., Umar, F., Edwards, N., Townend, J., Steeds, R., Leyva, F., Mihaila, S., Piasentini, E., Peluso, D., Casablanca, S., Naso, P., Puma, L., Iliceto, S., Vinereanu, D., Ciciarello, F. L., Agati, L., Cimino, S., De Luca, L., Petronilli, V., Fedele, F., and Tsverava, M.

Subjects
medicine.medical_specialty, Bundle branch block, business.industry, Left bundle branch block, Speckle tracking echocardiography, General Medicine, 030204 cardiovascular system & hematology, medicine.disease, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Radial function, Ventricle, Internal medicine, Cardiology, medicine, Radiology, Nuclear Medicine and imaging, In patient, Cardiology and Cardiovascular Medicine, business
Published
2013
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2. Reference values for aortic diameters obtained using both inner-­edge-­to-­inner-­edge and leading­-edge-­to-­leading-­edge methods in 190 healthy subjects

Author

Kocabay, G, Dal Bianco, L, Muraru, D, Peluso, D, Segafredo, B, Iliceto, S, Badano, L, Kocabay GK, Dal Bianco L, Muraru D, Peluso D, Segafredo B, Iliceto S, Badano L, Kocabay, G, Dal Bianco, L, Muraru, D, Peluso, D, Segafredo, B, Iliceto, S, Badano, L, Kocabay GK, Dal Bianco L, Muraru D, Peluso D, Segafredo B, Iliceto S, and Badano L

Abstract

ASE/EAE guidelines suggest to measure aortic diameters (AoD) using the leading edge-to-leading edge method (LEM), whereas ACC/AHA ones favor the inner edge-to-inner edge method (IEM) to increase reproducibility and consistency with MRI and CT. To obtain reference values of the AoD by transthoracic echocardiography using both LEM and IEM and to compare them, we prospectively studied 190 healthy volunteers (82 men, 44 + 14 years, range 18-80 years), using a Vivid E9 (GE Healthcare, Horten, Norway) with M5S probe and 2nd-harmonic imaging. On 2D images optimized for the aortic root and ascending aorta, a single observer performed offline measurements using LEM and IEM at the level of the aortic root (Ao-R), sino-tubular junction (STJ) and ascending aorta (AscAo, 1 cm from the STJ) at end-diastole (at R-wave on ECG). Reference AoD with both methods are reported in Table. As expected, at Bland-Altman’s analysis all AoD measured using LEM were significantly larger than those measured using IEM: Ao-R (bias= 3.1 mm; 95% LOA 0.9 – 5.3); STJ (bias=3.5 mm; 95% LOA 0.7 – 6.3), and AscAo (bias= 3.2 mm; 95% LOA 0.7 – 5.7). At multivariable regression analysis (including age, gender, body surface area (BSA), height, systolic blood pressure), age and BSA (adjusted R2= 0.42), were independent predictors of Ao-R diameters with both methods, while age, BSA and gender (adjusted R2 = 0.44) were independent predictors of AscAo diameter. Intra- and inter-observer variability was similar between LEM and IEM methods (2% vs 2%, p= 0.63, and 4% vs 5%, p=0.23 for AoR, respectively; and 3% vs 2%, p= 0.26, and 4% vs 6%, p= 0.15 for AscAo, respectively). This is the first report about reference values of the AoD obtained using both LEM and IEM, the difference in diameter measurement between the two methods, and the independent determinants of them in a largee population of healthy subjects.

Published
2012

3. Quantitative analysis of mitral valve geometry by transthoracic three-dimensional echocardiography: reference values, feasibility and reproducibility

Author

Muraru, D, Cattarina, M, Dal Bianco, L, Peluso, D, Zoppellaro, G, Segafredo, B, Calore, C, Cucchini, U, Iliceto, S, Badano, L, Muraru D, Cattarina M, Dal Bianco L, Peluso D, Zoppellaro G, Segafredo B, Calore C, Cucchini U, Iliceto S, Badano L, Muraru, D, Cattarina, M, Dal Bianco, L, Peluso, D, Zoppellaro, G, Segafredo, B, Calore, C, Cucchini, U, Iliceto, S, Badano, L, Muraru D, Cattarina M, Dal Bianco L, Peluso D, Zoppellaro G, Segafredo B, Calore C, Cucchini U, Iliceto S, and Badano L

Abstract

Background: Quantitative analysis of mitral valve (MV) can discriminate among various mechanisms causing valve insufficiency. There are no established reference values for MV geometry, nor data on its feasibility and reproducibility with latest transthoracic 3D echocardiography (3DTTE). Methods: Eighty-one consecutive healthy volunteers (43+13 years, range 18-70; 33 men) with good apical window underwent a 3D full-volume acquisition of MV apparatus (32+2 vps) using Vivid E9 (BT 12, GE Healthcare, Horten, N). MV datasets were analyzed offline using a software recently developed for 3DTTE (TomTec MV assessment 2.0, Unterschleissheim, D). Intra- and inter-observer reproducibility were assessed in 15 subjects and expressed as intraclass correlation coefficients (ICC). Results: Five subjects were excluded due to low quality of 3D dataset with poor MV tracking (feasibility 94%). The average analysis time of one dataset (including manual editing) was 2’. Reference values of MV parameters and their reproducibility are reported in Table. Leaflet tenting and annulus measures were positively correlated with body surface area (BSA, r=0.34-0.53, p , 0.001), but not with age. After correcting for BSA, there were no gender differences in MV parameters. Conclusion: Quantitative analysis of MV by 3DTTE is highly feasible and reproducible, and reference values are reported. Our findings may support the implementation of MV quantitative analysis by 3DTTE in clinical settings.

Published
2012

4. Two-dimensional assessment of tricuspid annulus dynamics and diameters: study for new reference values

Author

Miglioranza, MH, Muraru, D, Peluso, D, Cucchini, U, Mihaila, S, Naso, P, Puma, L, Kocabay, G, Iliceto, S, Badano, L, Miglioranza, M, Muraru, D, Peluso, D, Cucchini, U, Mihaila, S, Naso, P, Puma, L, Kocabay, G, Iliceto, S, and Badano, L

Abstract

Background: Tricuspid annulus (TA) size and function plays an important role in decision-making process about the need of associated TA annuloplasty during left sided cardiac surgery. Recommendations about echo assessment of TA don't indicate the view and the timing where TA should be measured. Our aim was to study TA diameters and shortening in different 2D TTE views to assess the extent of their variability. Methods: Cross-sectional study of normal volunteers. TA was measured from 3 2DTTE views (apical 4-CH, LAX-RV inflow, SAX basal) at 5 time points during cardiac cycle. TA fractional shortening diameter was obtained as (TV opening early-filling – Mid-systole) / TV opening early-filling. Result: 100pts; 42%male; 44±13yrs. TA diameters are in the Table. Fractional shortening of TA was 22±7%, 18±8%, 31±16% in 4-CH, LAX-RV inflow and SAX basal views respectively. Conclusion: This study support new references values for TA evaluation using 2D TTE. Values vary according to 2D TTE view and cardiac cycle time, showing the dynamism and complex geometry of TA

Published
2013

5. Reference values for aortic diameters obtained using both inner-­edge-­to-­inner-­edge and leading­-edge-­to-­leading-­edge methods in 190 healthy subjects

Author

Kocabay GK, Dal Bianco L, Muraru D, Peluso D, Segafredo B, Iliceto S, Badano L, Kocabay, G, Dal Bianco, L, Muraru, D, Peluso, D, Segafredo, B, Iliceto, S, and Badano, L

Subjects
aorta, echocardiography, MED/11 - MALATTIE DELL'APPARATO CARDIOVASCOLARE, reference values
Abstract

ASE/EAE guidelines suggest to measure aortic diameters (AoD) using the leading edge-to-leading edge method (LEM), whereas ACC/AHA ones favor the inner edge-to-inner edge method (IEM) to increase reproducibility and consistency with MRI and CT. To obtain reference values of the AoD by transthoracic echocardiography using both LEM and IEM and to compare them, we prospectively studied 190 healthy volunteers (82 men, 44 + 14 years, range 18-80 years), using a Vivid E9 (GE Healthcare, Horten, Norway) with M5S probe and 2nd-harmonic imaging. On 2D images optimized for the aortic root and ascending aorta, a single observer performed offline measurements using LEM and IEM at the level of the aortic root (Ao-R), sino-tubular junction (STJ) and ascending aorta (AscAo, 1 cm from the STJ) at end-diastole (at R-wave on ECG). Reference AoD with both methods are reported in Table. As expected, at Bland-Altman’s analysis all AoD measured using LEM were significantly larger than those measured using IEM: Ao-R (bias= 3.1 mm; 95% LOA 0.9 – 5.3); STJ (bias=3.5 mm; 95% LOA 0.7 – 6.3), and AscAo (bias= 3.2 mm; 95% LOA 0.7 – 5.7). At multivariable regression analysis (including age, gender, body surface area (BSA), height, systolic blood pressure), age and BSA (adjusted R2= 0.42), were independent predictors of Ao-R diameters with both methods, while age, BSA and gender (adjusted R2 = 0.44) were independent predictors of AscAo diameter. Intra- and inter-observer variability was similar between LEM and IEM methods (2% vs 2%, p= 0.63, and 4% vs 5%, p=0.23 for AoR, respectively; and 3% vs 2%, p= 0.26, and 4% vs 6%, p= 0.15 for AscAo, respectively). This is the first report about reference values of the AoD obtained using both LEM and IEM, the difference in diameter measurement between the two methods, and the independent determinants of them in a largee population of healthy subjects.

Published
2012

6. Quantitative analysis of mitral valve geometry by transthoracic three-dimensional echocardiography: reference values, feasibility and reproducibility

Author

Muraru D, Cattarina M, Dal Bianco L, Peluso D, Zoppellaro G, Segafredo B, Calore C, Cucchini U, Iliceto S, Badano L, Muraru, D, Cattarina, M, Dal Bianco, L, Peluso, D, Zoppellaro, G, Segafredo, B, Calore, C, Cucchini, U, Iliceto, S, and Badano, L

Subjects
mitral valve, healthy volunteers
Abstract

Background: Quantitative analysis of mitral valve (MV) can discriminate among various mechanisms causing valve insufficiency. There are no established reference values for MV geometry, nor data on its feasibility and reproducibility with latest transthoracic 3D echocardiography (3DTTE). Methods: Eighty-one consecutive healthy volunteers (43+13 years, range 18-70; 33 men) with good apical window underwent a 3D full-volume acquisition of MV apparatus (32+2 vps) using Vivid E9 (BT 12, GE Healthcare, Horten, N). MV datasets were analyzed offline using a software recently developed for 3DTTE (TomTec MV assessment 2.0, Unterschleissheim, D). Intra- and inter-observer reproducibility were assessed in 15 subjects and expressed as intraclass correlation coefficients (ICC). Results: Five subjects were excluded due to low quality of 3D dataset with poor MV tracking (feasibility 94%). The average analysis time of one dataset (including manual editing) was 2’. Reference values of MV parameters and their reproducibility are reported in Table. Leaflet tenting and annulus measures were positively correlated with body surface area (BSA, r=0.34-0.53, p , 0.001), but not with age. After correcting for BSA, there were no gender differences in MV parameters. Conclusion: Quantitative analysis of MV by 3DTTE is highly feasible and reproducible, and reference values are reported. Our findings may support the implementation of MV quantitative analysis by 3DTTE in clinical settings.

Published
2012

7. Ascending aorta diameters measured by echocardiography using both leading edge-to-leading edge and inner edge-to-inner edge conventions in healthy volunteers

Author

Muraru, D, Maffessanti, F, Kocabay, G, Peluso, D, Bianco Lucia, D, Piasentini, E, Jose Seena, P, Iliceto, S, Badano, L, Muraru Denisa, Maffessanti Francesco, Kocabay Gonenc, Peluso Diletta, Bianco Lucia Dal, Piasentini Eleonora, Jose Seena Padayattil, Iliceto Sabino, Badano Luigi, Muraru, D, Maffessanti, F, Kocabay, G, Peluso, D, Bianco Lucia, D, Piasentini, E, Jose Seena, P, Iliceto, S, Badano, L, Muraru Denisa, Maffessanti Francesco, Kocabay Gonenc, Peluso Diletta, Bianco Lucia Dal, Piasentini Eleonora, Jose Seena Padayattil, Iliceto Sabino, and Badano Luigi

Abstract

AIMS: Reference ranges of ascending aorta diameters (AAoD) for two-dimensional echocardiography (2DE) using inner edge (IE) convention are lacking, preventing the comparison of AAoD measurements by 2DE with those obtained by other imaging modalities. METHODS AND RESULTS: We used harmonic imaging 2DE to prospectively study 218 healthy volunteers (56% women, 42 ± 15 years, 18-80 years). Measurements were performed at the level of aortic root (AoR), sinotubular junction (STJ), and proximal tubular portion (TAo, 1 cm from the STJ) using both leading edge (LE) and IE conventions at end-diastole and end-systole. Feasibility of AAoD measurements between end-diastole and end-systole was similar at AoR and STJ levels, but it was significantly different at TAo level (82 vs. 96%, respectively, P < 0.0001). Ascending aorta diameters indexed to height were larger in men than in women (P < 0.0001). After adjusting for the effect of gender, only age and body surface area (BSA) were independent predictors of AAoD at multivariable analysis. Average end-diastolic AoR, STJ, and TAo diameters measured using IE convention were similar between genders (17 ± 2, 15 ± 2, and 15 ± 2 mm/m(2), respectively). Corresponding AAoD measured using the LE convention were 18 ± 2, 16 ± 2, and 17 ± 4 mm/m(2), respectively. On average, the end-systolic AAoD measured using LE were 2 mm larger than those performed using IE or at end-diastole. Mean aortic wall thickness was 2.4 ± 0.8 mm. CONCLUSION: End-diastolic AAoD measured using IE were significantly smaller than those obtained either using LE convention or at end-systole. Gender-specific reference values for AAoD indexed for BSA should be used to identify ascending aorta pathology.

Published
2014

8. Two-dimensional assessment of tricuspid annulus dynamics and diameters: study for new reference values

Author

Miglioranza, M, Muraru, D, Peluso, D, Cucchini, U, Mihaila, S, Naso, P, Puma, L, Kocabay, G, Iliceto, S, Badano, L, Miglioranza, MH, Miglioranza, M, Muraru, D, Peluso, D, Cucchini, U, Mihaila, S, Naso, P, Puma, L, Kocabay, G, Iliceto, S, Badano, L, and Miglioranza, MH

Abstract

Background: Tricuspid annulus (TA) size and function plays an important role in decision-making process about the need of associated TA annuloplasty during left sided cardiac surgery. Recommendations about echo assessment of TA don't indicate the view and the timing where TA should be measured. Our aim was to study TA diameters and shortening in different 2D TTE views to assess the extent of their variability. Methods: Cross-sectional study of normal volunteers. TA was measured from 3 2DTTE views (apical 4-CH, LAX-RV inflow, SAX basal) at 5 time points during cardiac cycle. TA fractional shortening diameter was obtained as (TV opening early-filling – Mid-systole) / TV opening early-filling. Result: 100pts; 42%male; 44±13yrs. TA diameters are in the Table. Fractional shortening of TA was 22±7%, 18±8%, 31±16% in 4-CH, LAX-RV inflow and SAX basal views respectively. Conclusion: This study support new references values for TA evaluation using 2D TTE. Values vary according to 2D TTE view and cardiac cycle time, showing the dynamism and complex geometry of TA

Published
2013

9. Right atrial size and function assessed with three-dimensional and speckle-tracking echocardiography in 200 healthy volunteers

Author

Peluso, D, Badano, L, Muraru, D, DAL BIANCO, L, Cucchini, U, Kocabay, G, Kovàcs, A, Casablanca, S, Iliceto, S, PELUSO, DILETTA MARIA, BADANO, LUIGI, MURARU, DENISA, DAL BIANCO, LUCIA, CUCCHINI, UMBERTO, Kocabay, Gonenc, Kovàcs, Attila, Casablanca, Simona, ILICETO, SABINO, Peluso, D, Badano, L, Muraru, D, DAL BIANCO, L, Cucchini, U, Kocabay, G, Kovàcs, A, Casablanca, S, Iliceto, S, PELUSO, DILETTA MARIA, BADANO, LUIGI, MURARU, DENISA, DAL BIANCO, LUCIA, CUCCHINI, UMBERTO, Kocabay, Gonenc, Kovàcs, Attila, Casablanca, Simona, and ILICETO, SABINO

Abstract

AIMS: Right atrial (RA) size predicts the outcome in some pathological conditions but reference values for RA volumes and myocardial function remain to be defined. Thus, we used two-dimensional speckle-tracking echocardiography (2D-STE) and three-dimensional echocardiography (3DE) to define normative reference values of RA volumes and function. METHODS AND RESULTS: Two hundreds healthy volunteers (43 ± 15 years, range 18-75; 44% men) underwent two-dimensional echocardiography (2DE) to obtain RA volumes and longitudinal strain (LS) of RA wall using 2D-STE, and 3DE to measure maximal (Vmax), minimal, and preA volumes to calculate total, passive, and active emptying volumes (TotEV, PassEV, and ActEV) and emptying fractions (TotEF, PassEF, and ActEF). Three-dimensional echocardiography volumes (Vmax, 52 ± 15 mL vs. 41 ± 14 mL), EVs (TotEV, 33 ± 10 mL vs. 24 ± 9 mL), and EFs (TotEF, 63 ± 9 vs. 58 ± 9%) were larger than 2DE ones (all P < 0.0001). Indexed 3D volumes were significantly larger in men than in women. RA TotEF correlated with total LS (r = 0.24, P = 0.025) and PassEF with positive LS (LSpos; r = 0.34, P < 0.0001). Ageing was associated with a decrease in passive (LSpos, r = -041; PassEV, r = -0.26; PassEF, r = -0.38; all P < 0.0001) and an increase in active RA function (negative LS, r = 0.34; ActEV, r = 0.25; all P < 0.0001; and ActEF, r = 0.15; P = 0.035) in order to maintain TotEV (r = -0.14, P = 0.05). CONCLUSION:Our study provides normative values for RA volumes and function measured by 3DE and 2D-STE in a relatively large cohort of healthy subjects with a wide age range. These data will help clinicians to identify RA remodelling and dysfunction.

Published
2013

10. SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.

Author

Licata L, Lo Surdo P, Iannuccelli M, Palma A, Micarelli E, Perfetto L, Peluso D, Calderone A, Castagnoli L, and Cesareni G

Subjects
Animals, Humans, Protein Interaction Maps, Databases, Factual, Signal Transduction, Software
Abstract

The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2020
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11. DISNOR: a disease network open resource.

Author

Lo Surdo P, Calderone A, Iannuccelli M, Licata L, Peluso D, Castagnoli L, Cesareni G, and Perfetto L

Subjects
Data Curation, Gene Regulatory Networks, Genetic Association Studies, Humans, Internet, Mutation, Polymorphism, Single Nucleotide, Search Engine, Signal Transduction genetics, Software, User-Computer Interface, Databases, Genetic, Disease genetics
Abstract

DISNOR is a new resource that aims at exploiting the explosion of data on the identification of disease-associated genes to assemble inferred disease pathways. This may help dissecting the signaling events whose disruption causes the pathological phenotypes and may contribute to build a platform for precision medicine. To this end we combine the gene-disease association (GDA) data annotated in the DisGeNET resource with a new curation effort aimed at populating the SIGNOR database with causal interactions related to disease genes with the highest possible coverage. DISNOR can be freely accessed at http://DISNOR.uniroma2.it/ where >3700 disease-networks, linking ∼2600 disease genes, can be explored. For each disease curated in DisGeNET, DISNOR links disease genes by manually annotated causal relationships and offers an intuitive visualization of the inferred 'patho-pathways' at different complexity levels. User-defined gene lists are also accepted in the query pipeline. In addition, for each list of query genes-either annotated in DisGeNET or user-defined-DISNOR performs a gene set enrichment analysis on KEGG-defined pathways or on the lists of proteins associated with the inferred disease pathways. This function offers additional information on disease-associated cellular pathways and disease similarity., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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12. SIGNOR: a database of causal relationships between biological entities.

Author

Perfetto L, Briganti L, Calderone A, Cerquone Perpetuini A, Iannuccelli M, Langone F, Licata L, Marinkovic M, Mattioni A, Pavlidou T, Peluso D, Petrilli LL, Pirrò S, Posca D, Santonico E, Silvestri A, Spada F, Castagnoli L, and Cesareni G

Subjects
Humans, Internet, Intracellular Signaling Peptides and Proteins chemistry, Phosphoprotein Phosphatases chemistry, Phosphoprotein Phosphatases metabolism, Protein Kinases chemistry, Protein Kinases metabolism, Databases, Protein, Signal Transduction
Abstract

Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy by providing a scaffold of prior experimental evidence of causal relationships between biological entities. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are complexes, chemicals, phenotypes and stimuli. The information captured in SIGNOR can be represented as a signed directed graph illustrating the activation/inactivation relationships between signalling entities. Each entry is associated to the post-translational modifications that cause the activation/inactivation of the target proteins. More than 4900 modified residues causing a change in protein concentration or activity have been curated and linked to the modifying enzymes (about 351 human kinases and 94 phosphatases). Additional modifications such as ubiquitinations, sumoylations, acetylations and their effect on the modified target proteins are also annotated. This wealth of structured information can support experimental approaches based on multi-parametric analysis of cell systems after physiological or pathological perturbations and to assemble large logic models., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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13. Ascending aorta diameters measured by echocardiography using both leading edge-to-leading edge and inner edge-to-inner edge conventions in healthy volunteers.

Author

Muraru D, Maffessanti F, Kocabay G, Peluso D, Dal Bianco L, Piasentini E, Jose SP, Iliceto S, and Badano LP

Subjects
Adolescent, Adult, Aged, Aged, 80 and over, Cardiovascular Diseases diagnostic imaging, Diastole, Female, Humans, Male, Middle Aged, Prospective Studies, Reference Values, Reproducibility of Results, Risk Assessment, Risk Factors, Systole, Aorta diagnostic imaging, Echocardiography, Healthy Volunteers
Abstract

Aims: Reference ranges of ascending aorta diameters (AAoD) for two-dimensional echocardiography (2DE) using inner edge (IE) convention are lacking, preventing the comparison of AAoD measurements by 2DE with those obtained by other imaging modalities., Methods and Results: We used harmonic imaging 2DE to prospectively study 218 healthy volunteers (56% women, 42 ± 15 years, 18-80 years). Measurements were performed at the level of aortic root (AoR), sinotubular junction (STJ), and proximal tubular portion (TAo, 1 cm from the STJ) using both leading edge (LE) and IE conventions at end-diastole and end-systole. Feasibility of AAoD measurements between end-diastole and end-systole was similar at AoR and STJ levels, but it was significantly different at TAo level (82 vs. 96%, respectively, P < 0.0001). Ascending aorta diameters indexed to height were larger in men than in women (P < 0.0001). After adjusting for the effect of gender, only age and body surface area (BSA) were independent predictors of AAoD at multivariable analysis. Average end-diastolic AoR, STJ, and TAo diameters measured using IE convention were similar between genders (17 ± 2, 15 ± 2, and 15 ± 2 mm/m(2), respectively). Corresponding AAoD measured using the LE convention were 18 ± 2, 16 ± 2, and 17 ± 4 mm/m(2), respectively. On average, the end-systolic AAoD measured using LE were 2 mm larger than those performed using IE or at end-diastole. Mean aortic wall thickness was 2.4 ± 0.8 mm., Conclusion: End-diastolic AAoD measured using IE were significantly smaller than those obtained either using LE convention or at end-systole. Gender-specific reference values for AAoD indexed for BSA should be used to identify ascending aorta pathology.

Published
2014
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14. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Author

Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, and Hermjakob H

Subjects
Internet, Software, Databases, Protein, Protein Interaction Mapping
Abstract

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

Published
2014
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15. Right atrial size and function assessed with three-dimensional and speckle-tracking echocardiography in 200 healthy volunteers.

Author

Peluso D, Badano LP, Muraru D, Dal Bianco L, Cucchini U, Kocabay G, Kovàcs A, Casablanca S, and Iliceto S

Subjects
Adult, Age Factors, Aged, Cohort Studies, Echocardiography methods, Female, Healthy Volunteers, Humans, Male, Middle Aged, Observer Variation, Organ Size, Reference Values, Reproducibility of Results, Sensitivity and Specificity, Sex Factors, Atrial Function physiology, Echocardiography, Three-Dimensional methods, Heart Atria anatomy & histology, Heart Atria diagnostic imaging, Image Interpretation, Computer-Assisted
Abstract

Aims: Right atrial (RA) size predicts the outcome in some pathological conditions but reference values for RA volumes and myocardial function remain to be defined. Thus, we used two-dimensional speckle-tracking echocardiography (2D-STE) and three-dimensional echocardiography (3DE) to define normative reference values of RA volumes and function., Methods and Results: Two hundreds healthy volunteers (43 ± 15 years, range 18-75; 44% men) underwent two-dimensional echocardiography (2DE) to obtain RA volumes and longitudinal strain (LS) of RA wall using 2D-STE, and 3DE to measure maximal (Vmax), minimal, and preA volumes to calculate total, passive, and active emptying volumes (TotEV, PassEV, and ActEV) and emptying fractions (TotEF, PassEF, and ActEF). Three-dimensional echocardiography volumes (Vmax, 52 ± 15 mL vs. 41 ± 14 mL), EVs (TotEV, 33 ± 10 mL vs. 24 ± 9 mL), and EFs (TotEF, 63 ± 9 vs. 58 ± 9%) were larger than 2DE ones (all P < 0.0001). Indexed 3D volumes were significantly larger in men than in women. RA TotEF correlated with total LS (r = 0.24, P = 0.025) and PassEF with positive LS (LSpos; r = 0.34, P < 0.0001). Ageing was associated with a decrease in passive (LSpos, r = -041; PassEV, r = -0.26; PassEF, r = -0.38; all P < 0.0001) and an increase in active RA function (negative LS, r = 0.34; ActEV, r = 0.25; all P < 0.0001; and ActEF, r = 0.15; P = 0.035) in order to maintain TotEV (r = -0.14, P = 0.05)., Conclusion: Our study provides normative values for RA volumes and function measured by 3DE and 2D-STE in a relatively large cohort of healthy subjects with a wide age range. These data will help clinicians to identify RA remodelling and dysfunction.

Published
2013
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16. MINT, the molecular interaction database: 2012 update.

Author

Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, and Cesareni G

Subjects
Algorithms, Animals, Humans, Mice, Proteins chemistry, Proteins genetics, Rats, Databases, Protein, Protein Interaction Mapping
Abstract

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.

Published
2012
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17. MINT, the molecular interaction database: 2009 update.

Author

Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, and Cesareni G

Subjects
Animals, Computational Biology trends, Databases, Protein, ErbB Receptors metabolism, Genome, Viral, Humans, Information Storage and Retrieval methods, Internet, Programming Languages, Protein Binding, Protein Structure, Tertiary, Software, Computational Biology methods, Databases, Genetic, Databases, Nucleic Acid, Protein Interaction Mapping
Abstract

MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.

Published
2010
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18. Predictors and time-related impact of distal embolization during primary angioplasty.

Author

Napodano M, Ramondo A, Tarantini G, Peluso D, Compagno S, Fraccaro C, Frigo AC, Razzolini R, and Iliceto S

Subjects
Aged, Coronary Angiography, Electrocardiography, Female, Humans, Male, Middle Aged, Myocardial Infarction pathology, Myocardial Reperfusion, Myocardium pathology, Necrosis, Prospective Studies, Thromboembolism diagnostic imaging, Time Factors, Treatment Outcome, Angioplasty, Balloon, Coronary adverse effects, Myocardial Infarction therapy, Thromboembolism etiology
Abstract

Aims: We sought to identify predictors of distal embolization (DE) occurring during primary percutaneous coronary intervention (p-PCI) as well as to assess its impact on both myocardial reperfusion and necrosis, according to time-to-treatment., Methods and Results: Clinical and angiographic characteristics were prospectively assessed in 400 consecutive patients who underwent p-PCI, in order to identify predictors of DE. The impact of DE on Thrombolysis in Myocardial Infarction (TIMI) flow, myocardial blush, and troponin I (TnI) was assessed according to symptom onset-to-balloon time. DE occurred in 64 (16%) patients and did not change with time-to-treatment (P = 0.87). The occlusion pattern of infarct-related artery (IRA), treatment of right coronary artery, higher TIMI thrombus score, longer lesion, and large IRA diameter were predictors of DE. The rate of TIMI 0/1 and myocardial blush 0/1 was higher in patients exhibiting DE when time-to-treatment was < or =6 h (P < 0.0001), while TnI was higher in patients with DE when time-to-treatment was <3 h., Conclusion: DE during p-PCI occurs more often in the presence of high thrombus burden lesion. It reduces the effectiveness of myocardial reperfusion within 6 h and enhances myocardial damage within 3 h after symptom onset. Afterwards, it does not affect myocardial reperfusion or the extent of myocardial damage.

Published
2009
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19. VirusMINT: a viral protein interaction database.

Author

Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, Sacco F, Tinti M, Smolyar A, Castagnoli L, Vidal M, Cusick ME, and Cesareni G

Subjects
Computer Graphics, Databases, Protein, Protein Interaction Mapping, Viral Proteins metabolism
Abstract

Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database (http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40.

Published
2009
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20. 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Author

Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, and Helmer-Citterich M

Subjects
Algorithms, Amino Acid Sequence, Conserved Sequence, Databases, Protein, Internet, Models, Molecular, Programming Languages, Sequence Alignment, Structural Homology, Protein, Computational Biology methods, Computer Graphics, Protein Conformation, Software
Abstract

3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/

Published
2007
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21. SH3-Hunter: discovery of SH3 domain interaction sites in proteins.

Author

Ferraro E, Peluso D, Via A, Ausiello G, and Helmer-Citterich M

Subjects
Amino Acid Motifs, Amino Acid Sequence, Binding Sites, Humans, Models, Molecular, Peptide Library, Protein Binding, Protein Structure, Tertiary, Sensitivity and Specificity, src Homology Domains, Computational Biology methods, Neural Networks, Computer, Peptides chemistry
Abstract

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide-domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence. SH3-Hunter evaluates which peptide-domain pair represents a possible interaction pair and produces as output a list of significant interaction sites for each query protein. Each proposed interaction site is associated to a propensity score and sensitivity and precision levels for the prediction. The server prediction capability is based on a neural network model integrating high-throughput pep-spot data with structural information extracted from known SH3-peptide complexes.

Published
2007
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22. pdbFun: mass selection and fast comparison of annotated PDB residues.

Author

Ausiello G, Zanzoni A, Peluso D, Via A, and Helmer-Citterich M

Subjects
Algorithms, Internet, Proteins chemistry, Systems Integration, Time Factors, Amino Acids chemistry, Databases, Protein, Protein Conformation, Software
Abstract

pdbFun (http://pdbfun.uniroma2.it) is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format.

Published
2005
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