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101. A case of pseudovitamin D deficiency-like rickets in an infant treated with 1,25-dihydroxycholecalciferol. Preliminary note

Author: Vecchio, F., Carnevale, F., Paganetti, G., di Bitonto, G., and Marinelli, G.
Published: 1978
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102. Metal artifact reduction for radiation therapy: a simulation study

Author: Lo, Joseph Y., Gilat Schmidt, Taly, Chen, Guang-Hong, Jin, Yannan, Giantsoudi, Drosoula, Fu, Lin, Verburg, Joost, Gjesteby, Lars, Wang, Ge, Paganetti, Harald, and De Man, Bruno
Published: 2018
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103. Guidelines for the use and interpretation of assays for monitoring autophagy.

Author: Klionsky, Dj, Abdalla, Fc, Abeliovich, H, Abraham, Rt, Acevedo-Arozena, A, Adeli, K, Agholme, L, Agnello, M, Agostinis, P, Aguirre-Ghiso, Ja, Ahn, Hj, Ait-Mohamed, O, Ait-Si-Ali, S, Akematsu, T, Akira, S, Al-Younes, Hm, Al-Zeer, Ma, Albert, Ml, Albin, Rl, Alegre-Abarrategui, J, Aleo, Mf, Alirezaei, M, Almasan, A, Almonte-Becerril, M, Amano, A, Amaravadi, R, Amarnath, S, Amer, Ao, Andrieu-Abadie, N, Anantharam, V, Ann, Dk, Anoopkumar-Dukie, S, Aoki, H, Apostolova, N, Arancia, G, Aris, Jp, Asanuma, K, Asare, Ny, Ashida, H, Askanas, V, Askew, D, Auberger, P, Baba, M, Backues, Sk, Baehrecke, Eh, Bahr, Ba, Bai, Xy, Bailly, Y, Baiocchi, R, Baldini, G, Balduini, W, Ballabio, A, Bamber, Ba, Bampton, Et, Bánhegyi, G, Bartholomew, Cr, Bassham, Dc, Bast RC, Jr, Batoko, H, Bay, Bh, Beau, I, Béchet, Dm, Begley, Tj, Behl, C, Behrends, C, Bekri, S, Bellaire, B, Bendall, Lj, Benetti, L, Berliocchi, L, Bernardi, H, Bernassola, F, Besteiro, S, Bhatia-Kissova, I, Bi, X, Biard-Piechaczyk, M, Blum, J, Boise, Lh, Bonaldo, P, Boone, Dl, Bornhauser, Bc, Bortoluci, Kr, Bossis, I, Bost, F, Bourquin, Jp, Boya, P, Boyer-Guittaut, M, Bozhkov, Pv, Brady, Nr, Brancolini, C, Brech, A, Brenman, Je, Brennand, A, Bresnick, Eh, Brest, P, Bridges, D, Bristol, Ml, Brookes, P, Brown, Ej, Brumell, Jh, Brunetti-Pierri, N, Brunk, Ut, Bulman, De, Bultman, Sj, Bultynck, G, Burbulla, Lf, Bursch, W, Butchar, Jp, Buzgariu, W, Bydlowski, Sp, Cadwell, K, Cahová, M, Cai, D, Cai, J, Cai, Q, Calabretta, B, Calvo-Garrido, J, Camougrand, N, Campanella, M, Campos-Salinas, J, Candi, E, Cao, L, Caplan, Ab, Carding, Sr, Cardoso, Sm, Carew, J, Carlin, Cr, Carmignac, V, Carneiro, La, Carra, S, Caruso, Ra, Casari, G, Casas, C, Castino, R, Cebollero, E, Cecconi, F, Celli, J, Chaachouay, H, Chae, Hj, Chai, Cy, Chan, Dc, Chan, Ey, Chang, Rc, Che, Cm, Chen, Cc, Chen, Gc, Chen, Gq, Chen, M, Chen, Q, Chen, S, Chen, W, Chen, X, Chen, Yg, Chen, Y, Chen, Yj, Chen, Z, Cheng, A, Cheng, Ch, Cheng, Y, Cheong, H, Cheong, Jh, Cherry, S, Chess-Williams, R, Cheung, Zh, Chevet, E, Chiang, Hl, Chiarelli, R, Chiba, T, Chin, L, Chiou, Sh, Chisari, Fv, Cho, Ch, Cho, Dh, Choi, Am, Choi, D, Choi, K, Choi, Me, Chouaib, S, Choubey, D, Choubey, V, Chu, Ct, Chuang, Th, Chueh, Sh, Chun, T, Chwae, Yj, Chye, Ml, Ciarcia, R, Ciriolo, Mr, Clague, Mj, Clark, R, Clarke, Pg, Clarke, R, Codogno, P, Coller, Ha, Colombo, Mi, Comincini, S, Condello, M, Condorelli, F, Cookson, Mr, Coombs, Gh, Coppens, I, Corbalan, R, Cossart, P, Costelli, P, Costes, S, Coto-Montes, A, Couve, E, Coxon, Fp, Cregg, Jm, Crespo, Jl, Cronjé, Mj, Cuervo, Am, Cullen, Jj, Czaja, Mj, D'Amelio, M, Darfeuille-Michaud, A, Davids, Lm, Davies, Fe, De Felici, M, de Groot, Jf, de Haan, Ca, De Martino, L, De Milito, A, De Tata, V, Debnath, J, Degterev, A, Dehay, B, Delbridge, Lm, Demarchi, F, Deng, Yz, Dengjel, J, Dent, P, Denton, D, Deretic, V, Desai, Sd, Devenish, Rj, Di Gioacchino, M, Di Paolo, G, Di Pietro, C, Díaz-Araya, G, Díaz-Laviada, I, Diaz-Meco, Mt, Diaz-Nido, J, Dikic, I, Dinesh-Kumar, Sp, Ding, Wx, Distelhorst, Cw, Diwan, A, Djavaheri-Mergny, M, Dokudovskaya, S, Dong, Z, Dorsey, Fc, Dosenko, V, Dowling, Jj, Doxsey, S, Dreux, M, Drew, Me, Duan, Q, Duchosal, Ma, Duff, K, Dugail, I, Durbeej, M, Duszenko, M, Edelstein, Cl, Edinger, Al, Egea, G, Eichinger, L, Eissa, Nt, Ekmekcioglu, S, El-Deiry, W, Elazar, Z, Elgendy, M, Ellerby, Lm, Eng, Ke, Engelbrecht, Am, Engelender, S, Erenpreisa, J, Escalante, R, Esclatine, A, Eskelinen, El, Espert, L, Espina, V, Fan, H, Fan, J, Fan, Qw, Fan, Z, Fang, S, Fang, Y, Fanto, M, Fanzani, A, Farkas, T, Farré, Jc, Faure, M, Fechheimer, M, Feng, Cg, Feng, J, Feng, Q, Feng, Y, Fésüs, L, Feuer, R, Figueiredo-Pereira, Me, Fimia, Gm, Fingar, Dc, Finkbeiner, S, Finkel, T, Finley, Kd, Fiorito, F, Fisher, Ea, Fisher, Pb, Flajolet, M, Florez-McClure, Ml, Florio, S, Fon, Ea, Fornai, F, Fortunato, F, Fotedar, R, Fowler, Dh, Fox, H, Franco, R, Frankel, Lb, Fransen, M, Fuentes, Jm, Fueyo, J, Fujii, J, Fujisaki, K, Fujita, E, Fukuda, M, Furukawa, Rh, Gaestel, M, Gailly, P, Gajewska, M, Galliot, B, Galy, V, Ganesh, S, Ganetzky, B, Ganley, Ig, Gao, Fb, Gao, Gf, Gao, J, Garcia, L, Garcia-Manero, G, Garcia-Marcos, M, Garmyn, M, Gartel, Al, Gatti, E, Gautel, M, Gawriluk, Tr, Gegg, Me, Geng, J, Germain, M, Gestwicki, Je, Gewirtz, Da, Ghavami, S, Ghosh, P, Giammarioli, Am, Giatromanolaki, An, Gibson, Sb, Gilkerson, Rw, Ginger, Ml, Ginsberg, Hn, Golab, J, Goligorsky, M, Golstein, P, Gomez-Manzano, C, Goncu, E, Gongora, C, Gonzalez, Cd, Gonzalez, R, González-Estévez, C, González-Polo, Ra, Gonzalez-Rey, E, Gorbunov, Nv, Gorski, S, Goruppi, S, Gottlieb, Ra, Gozuacik, D, Granato, Ge, Grant, Gd, Green, Kn, Gregorc, A, Gros, F, Grose, C, Grunt, Tw, Gual, P, Guan, Jl, Guan, Kl, Guichard, Sm, Gukovskaya, A, Gukovsky, I, Gunst, J, Gustafsson, Ab, Halayko, Aj, Hale, An, Halonen, Sk, Hamasaki, M, Han, F, Han, T, Hancock, Mk, Hansen, M, Harada, H, Harada, M, Hardt, Se, Harper, Jw, Harris, Al, Harris, J, Harris, Sd, Hashimoto, M, Haspel, Ja, Hayashi, S, Hazelhurst, La, He, C, He, Yw, Hébert, Mj, Heidenreich, Ka, Helfrich, Mh, Helgason, Gv, Henske, Ep, Herman, B, Herman, Pk, Hetz, C, Hilfiker, S, Hill, Ja, Hocking, Lj, Hofman, P, Hofmann, Tg, Höhfeld, J, Holyoake, Tl, Hong, Mh, Hood, Da, Hotamisligil, G, Houwerzijl, Ej, Høyer-Hansen, M, Hu, B, Hu, Ca, Hu, Hm, Hua, Y, Huang, C, Huang, J, Huang, S, Huang, Wp, Huber, Tb, Huh, Wk, Hung, Th, Hupp, Tr, Hur, Gm, Hurley, Jb, Hussain, Sn, Hussey, Pj, Hwang, Jj, Hwang, S, Ichihara, A, Ilkhanizadeh, S, Inoki, K, Into, T, Iovane, V, Iovanna, Jl, Ip, Ny, Isaka, Y, Ishida, H, Isidoro, C, Isobe, K, Iwasaki, A, Izquierdo, M, Izumi, Y, Jaakkola, Pm, Jäättelä, M, Jackson, Gr, Jackson, Wt, Janji, B, Jendrach, M, Jeon, Jh, Jeung, Eb, Jiang, H, Jiang, Jx, Jiang, M, Jiang, Q, Jiang, X, Jiménez, A, Jin, M, Jin, S, Joe, Co, Johansen, T, Johnson, De, Johnson, Gv, Jones, Nl, Joseph, B, Joseph, Sk, Joubert, Am, Juhász, G, Juillerat-Jeanneret, L, Jung, Ch, Jung, Yk, Kaarniranta, K, Kaasik, A, Kabuta, T, Kadowaki, M, Kagedal, K, Kamada, Y, Kaminskyy, Vo, Kampinga, Hh, Kanamori, H, Kang, C, Kang, Kb, Kang, Ki, Kang, R, Kang, Ya, Kanki, T, Kanneganti, Td, Kanno, H, Kanthasamy, Ag, Kanthasamy, A, Karantza, V, Kaushal, Gp, Kaushik, S, Kawazoe, Y, Ke, Py, Kehrl, Jh, Kelekar, A, Kerkhoff, C, Kessel, Dh, Khalil, H, Kiel, Ja, Kiger, Aa, Kihara, A, Kim, Dr, Kim, Dh, Kim, Ek, Kim, Hr, Kim, J, Kim, Jh, Kim, Jc, Kim, Jk, Kim, Pk, Kim, Sw, Kim, Y, Kimchi, A, Kimmelman, Ac, King, J, Kinsella, Tj, Kirkin, V, Kirshenbaum, La, Kitamoto, K, Kitazato, K, Klein, L, Klimecki, Wt, Klucken, J, Knecht, E, Ko, Bc, Koch, Jc, Koga, H, Koh, Jy, Koh, Yh, Koike, M, Komatsu, M, Kominami, E, Kong, Hj, Kong, Wj, Korolchuk, Vi, Kotake, Y, Koukourakis, Mi, Kouri Flores, Jb, Kovács, Al, Kraft, C, Krainc, D, Krämer, H, Kretz-Remy, C, Krichevsky, Am, Kroemer, G, Krüger, R, Krut, O, Ktistakis, Nt, Kuan, Cy, Kucharczyk, R, Kumar, A, Kumar, R, Kumar, S, Kundu, M, Kung, Hj, Kurz, T, Kwon, Hj, La Spada, Ar, Lafont, F, Lamark, T, Landry, J, Lane, Jd, Lapaquette, P, Laporte, Jf, László, L, Lavandero, S, Lavoie, Jn, Layfield, R, Lazo, Pa, Le, W, Le Cam, L, Ledbetter, Dj, Lee, Aj, Lee, Bw, Lee, Gm, Lee, J, Lee, Jh, Lee, M, Lee, Sh, Leeuwenburgh, C, Legembre, P, Legouis, R, Lehmann, M, Lei, Hy, Lei, Qy, Leib, Da, Leiro, J, Lemasters, Jj, Lemoine, A, Lesniak, M, Lev, D, Levenson, Vv, Levine, B, Levy, E, Li, F, Li, Jl, Li, L, Li, S, Li, W, Li, Xj, Li, Yb, Li, Yp, Liang, C, Liang, Q, Liao, Yf, Liberski, Pp, Lieberman, A, Lim, Hj, Lim, Kl, Lim, K, Lin, Cf, Lin, Fc, Lin, J, Lin, Jd, Lin, K, Lin, Ww, Lin, Wc, Lin, Yl, Linden, R, Lingor, P, Lippincott-Schwartz, J, Lisanti, Mp, Liton, Pb, Liu, B, Liu, Cf, Liu, K, Liu, L, Liu, Qa, Liu, W, Liu, Yc, Liu, Y, Lockshin, Ra, Lok, Cn, Lonial, S, Loos, B, Lopez-Berestein, G, López-Otín, C, Lossi, L, Lotze, Mt, Lőw, P, Lu, B, Lu, Z, Luciano, F, Lukacs, Nw, Lund, Ah, Lynch-Day, Ma, Ma, Y, Macian, F, Mackeigan, Jp, Macleod, Kf, Madeo, F, Maiuri, L, Maiuri, Mc, Malagoli, D, Malicdan, Mc, Malorni, W, Man, N, Mandelkow, Em, Manon, S, Manov, I, Mao, K, Mao, X, Mao, Z, Marambaud, P, Marazziti, D, Marcel, Yl, Marchbank, K, Marchetti, P, Marciniak, Sj, Marcondes, M, Mardi, M, Marfe, G, Mariño, G, Markaki, M, Marten, Mr, Martin, Sj, Martinand-Mari, C, Martinet, W, Martinez-Vicente, M, Masini, M, Matarrese, P, Matsuo, S, Matteoni, R, Mayer, A, Mazure, Nm, Mcconkey, Dj, Mcconnell, Mj, Mcdermott, C, Mcdonald, C, Mcinerney, Gm, Mckenna, Sl, Mclaughlin, B, Mclean, Pj, Mcmaster, Cr, Mcquibban, Ga, Meijer, Aj, Meisler, Mh, Meléndez, A, Melia, Tj, Melino, G, Mena, Ma, Menendez, Ja, Menna-Barreto, Rf, Menon, Mb, Menzies, Fm, Mercer, Ca, Merighi, A, Merry, De, Meschini, S, Meyer, Cg, Meyer, Tf, Miao, Cy, Miao, Jy, Michels, Pa, Michiels, C, Mijaljica, D, Milojkovic, A, Minucci, S, Miracco, C, Miranti, Ck, Mitroulis, I, Miyazawa, K, Mizushima, N, Mograbi, B, Mohseni, S, Molero, X, Mollereau, B, Mollinedo, F, Momoi, T, Monastyrska, I, Monick, Mm, Monteiro, Mj, Moore, Mn, Mora, R, Moreau, K, Moreira, Pi, Moriyasu, Y, Moscat, J, Mostowy, S, Mottram, Jc, Motyl, T, Moussa, Ce, Müller, S, Muller, S, Münger, K, Münz, C, Murphy, Lo, Murphy, Me, Musarò, A, Mysorekar, I, Nagata, E, Nagata, K, Nahimana, A, Nair, U, Nakagawa, T, Nakahira, K, Nakano, H, Nakatogawa, H, Nanjundan, M, Naqvi, Ni, Narendra, Dp, Narita, M, Navarro, M, Nawrocki, St, Nazarko, Ty, Nemchenko, A, Netea, Mg, Neufeld, Tp, Ney, Pa, Nezis, Ip, Nguyen, Hp, Nie, D, Nishino, I, Nislow, C, Nixon, Ra, Noda, T, Noegel, Aa, Nogalska, A, Noguchi, S, Notterpek, L, Novak, I, Nozaki, T, Nukina, N, Nürnberger, T, Nyfeler, B, Obara, K, Oberley, Td, Oddo, S, Ogawa, M, Ohashi, T, Okamoto, K, Oleinick, Nl, Oliver, Fj, Olsen, Lj, Olsson, S, Opota, O, Osborne, Tf, Ostrander, Gk, Otsu, K, Ou, Jh, Ouimet, M, Overholtzer, M, Ozpolat, B, Paganetti, P, Pagnini, U, Pallet, N, Palmer, Ge, Palumbo, C, Pan, T, Panaretakis, T, Pandey, Ub, Papackova, Z, Papassideri, I, Paris, I, Park, J, Park, Ok, Parys, Jb, Parzych, Kr, Patschan, S, Patterson, C, Pattingre, S, Pawelek, Jm, Peng, J, Perlmutter, Dh, Perrotta, I, Perry, G, Pervaiz, S, Peter, M, Peters, Gj, Petersen, M, Petrovski, G, Phang, Jm, Piacentini, M, Pierre, P, Pierrefite-Carle, V, Pierron, G, Pinkas-Kramarski, R, Piras, A, Piri, N, Platanias, Lc, Pöggeler, S, Poirot, M, Poletti, A, Poüs, C, Pozuelo-Rubio, M, Prætorius-Ibba, M, Prasad, A, Prescott, M, Priault, M, Produit-Zengaffinen, N, Progulske-Fox, A, Proikas-Cezanne, T, Przedborski, S, Przyklenk, K, Puertollano, R, Puyal, J, Qian, Sb, Qin, L, Qin, Zh, Quaggin, Se, Raben, N, Rabinowich, H, Rabkin, Sw, Rahman, I, Rami, A, Ramm, G, Randall, G, Randow, F, Rao, Va, Rathmell, Jc, Ravikumar, B, Ray, Sk, Reed, Bh, Reed, Jc, Reggiori, F, Régnier-Vigouroux, A, Reichert, A, Reiners JJ, Jr, Reiter, Rj, Ren, J, Revuelta, Jl, Rhodes, Cj, Ritis, K, Rizzo, E, Robbins, J, Roberge, M, Roca, H, Roccheri, Mc, Rocchi, S, Rodemann, Hp, Rodríguez de Córdoba, S, Rohrer, B, Roninson, Ib, Rosen, K, Rost-Roszkowska, Mm, Rouis, M, Rouschop, Km, Rovetta, F, Rubin, Bp, Rubinsztein, Dc, Ruckdeschel, K, Rucker EB, 3rd, Rudich, A, Rudolf, E, Ruiz-Opazo, N, Russo, R, Rusten, Te, Ryan, Km, Ryter, Sw, Sabatini, Dm, Sadoshima, J, Saha, T, Saitoh, T, Sakagami, H, Sakai, Y, Salekdeh, Gh, Salomoni, P, Salvaterra, Pm, Salvesen, G, Salvioli, R, Sanchez, Am, Sánchez-Alcázar, Ja, Sánchez-Prieto, R, Sandri, M, Sankar, U, Sansanwal, P, Santambrogio, L, Saran, S, Sarkar, S, Sarwal, M, Sasakawa, C, Sasnauskiene, A, Sass, M, Sato, K, Sato, M, Schapira, Ah, Scharl, M, Schätzl, Hm, Scheper, W, Schiaffino, S, Schneider, C, Schneider, Me, Schneider-Stock, R, Schoenlein, Pv, Schorderet, Df, Schüller, C, Schwartz, Gk, Scorrano, L, Sealy, L, Seglen, Po, Segura-Aguilar, J, Seiliez, I, Seleverstov, O, Sell, C, Seo, Jb, Separovic, D, Setaluri, V, Setoguchi, T, Settembre, C, Shacka, Jj, Shanmugam, M, Shapiro, Im, Shaulian, E, Shaw, Rj, Shelhamer, Jh, Shen, Hm, Shen, Wc, Sheng, Zh, Shi, Y, Shibuya, K, Shidoji, Y, Shieh, Jj, Shih, Cm, Shimada, Y, Shimizu, S, Shintani, T, Shirihai, O, Shore, Gc, Sibirny, Aa, Sidhu, Sb, Sikorska, B, Silva-Zacarin, Ec, Simmons, A, Simon, Ak, Simon, Hu, Simone, C, Simonsen, A, Sinclair, Da, Singh, R, Sinha, D, Sinicrope, Fa, Sirko, A, Siu, Pm, Sivridis, E, Skop, V, Skulachev, Vp, Slack, R, Smaili, S, Smith, Dr, Soengas, M, Soldati, T, Song, X, Sood, Ak, Soong, Tw, Sotgia, F, Spector, Sa, Spies, Cd, Springer, W, Srinivasula, Sm, Stefanis, L, Steffan, J, Stendel, R, Stenmark, H, Stephanou, A, Stern, St, Sternberg, C, Stork, B, Strålfors, P, Subauste, C, Sui, X, Sulzer, D, Sun, J, Sun, Sy, Sun, Zj, Sung, Jj, Suzuki, K, Suzuki, T, Swanson, M, Swanton, C, Sweeney, St, Sy, Lk, Szabadkai, G, Tabas, I, Taegtmeyer, H, Tafani, M, Takács-Vellai, K, Takano, Y, Takegawa, K, Takemura, G, Takeshita, F, Talbot, Nj, Tan, K, Tanaka, K, Tang, D, Tanida, I, Tannous, Ba, Tavernarakis, N, Taylor, G, Taylor, Ga, Taylor, Jp, Terada, L, Terman, A, Tettamanti, G, Thevissen, K, Thompson, Cb, Thorburn, A, Thumm, M, Tian, F, Tian, Y, Tocchini-Valentini, G, Tolkovsky, Am, Tomino, Y, Tönges, L, Tooze, Sa, Tournier, C, Tower, J, Towns, R, Trajkovic, V, Travassos, Lh, Tsai, Tf, Tschan, Mp, Tsubata, T, Tsung, A, Turk, B, Turner, L, Tyagi, Sc, Uchiyama, Y, Ueno, T, Umekawa, M, Umemiya-Shirafuji, R, Unni, Vk, Vaccaro, Mi, Valente, Em, Van den Berghe, G, van der Klei, Ij, van Doorn, W, van Dyk, Lf, van Egmond, M, van Grunsven, La, Vandenabeele, P, Vandenberghe, Wp, Vanhorebeek, I, Vaquero, Ec, Velasco, G, Vellai, T, Vicencio, Jm, Vierstra, Rd, Vila, M, Vindis, C, Viola, G, Viscomi, Maria Teresa, Voitsekhovskaja, Ov, von Haefen, C, Votruba, M, Wada, K, Wade-Martins, R, Walker, Cl, Walsh, Cm, Walter, J, Wan, Xb, Wang, A, Wang, C, Wang, D, Wang, F, Wang, G, Wang, H, Wang, Hg, Wang, Hd, Wang, J, Wang, K, Wang, M, Wang, Rc, Wang, X, Wang, Yj, Wang, Y, Wang, Z, Wang, Zc, Wansink, Dg, Ward, Dm, Watada, H, Waters, Sl, Webster, P, Wei, L, Weihl, Cc, Weiss, Wa, Welford, Sm, Wen, Lp, Whitehouse, Ca, Whitton, Jl, Whitworth, Aj, Wileman, T, Wiley, Jw, Wilkinson, S, Willbold, D, Williams, Rl, Williamson, Pr, Wouters, Bg, Wu, C, Wu, Dc, Wu, Wk, Wyttenbach, A, Xavier, Rj, Xi, Z, Xia, P, Xiao, G, Xie, Z, Xu, Dz, Xu, J, Xu, L, Xu, X, Yamamoto, A, Yamashina, S, Yamashita, M, Yan, X, Yanagida, M, Yang, D, Yang, E, Yang, Jm, Yang, Sy, Yang, W, Yang, Wy, Yang, Z, Yao, Mc, Yao, Tp, Yeganeh, B, Yen, Wl, Yin, Jj, Yin, Xm, Yoo, Oj, Yoon, G, Yoon, Sy, Yorimitsu, T, Yoshikawa, Y, Yoshimori, T, Yoshimoto, K, You, Hj, Youle, Rj, Younes, A, Yu, L, Yu, Sw, Yu, Wh, Yuan, Zm, Yue, Z, Yun, Ch, Yuzaki, M, Zabirnyk, O, Silva-Zacarin, E, Zacks, D, Zacksenhaus, E, Zaffaroni, N, Zakeri, Z, Zeh HJ, 3rd, Zeitlin, So, Zhang, H, Zhang, Hl, Zhang, J, Zhang, Jp, Zhang, L, Zhang, My, Zhang, Xd, Zhao, M, Zhao, Yf, Zhao, Y, Zhao, Zj, Zheng, X, Zhivotovsky, B, Zhong, Q, Zhou, Cz, Zhu, C, Zhu, Wg, Zhu, Xf, Zhu, X, Zhu, Y, Zoladek, T, Zong, Wx, Zorzano, A, Zschocke, J, Zuckerbraun, B., Viscomi M. T. (ORCID:0000-0002-9096-4967), Klionsky, Dj, Abdalla, Fc, Abeliovich, H, Abraham, Rt, Acevedo-Arozena, A, Adeli, K, Agholme, L, Agnello, M, Agostinis, P, Aguirre-Ghiso, Ja, Ahn, Hj, Ait-Mohamed, O, Ait-Si-Ali, S, Akematsu, T, Akira, S, Al-Younes, Hm, Al-Zeer, Ma, Albert, Ml, Albin, Rl, Alegre-Abarrategui, J, Aleo, Mf, Alirezaei, M, Almasan, A, Almonte-Becerril, M, Amano, A, Amaravadi, R, Amarnath, S, Amer, Ao, Andrieu-Abadie, N, Anantharam, V, Ann, Dk, Anoopkumar-Dukie, S, Aoki, H, Apostolova, N, Arancia, G, Aris, Jp, Asanuma, K, Asare, Ny, Ashida, H, Askanas, V, Askew, D, Auberger, P, Baba, M, Backues, Sk, Baehrecke, Eh, Bahr, Ba, Bai, Xy, Bailly, Y, Baiocchi, R, Baldini, G, Balduini, W, Ballabio, A, Bamber, Ba, Bampton, Et, Bánhegyi, G, Bartholomew, Cr, Bassham, Dc, Bast RC, Jr, Batoko, H, Bay, Bh, Beau, I, Béchet, Dm, Begley, Tj, Behl, C, Behrends, C, Bekri, S, Bellaire, B, Bendall, Lj, Benetti, L, Berliocchi, L, Bernardi, H, Bernassola, F, Besteiro, S, Bhatia-Kissova, I, Bi, X, 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Y, Zoladek, T, Zong, Wx, Zorzano, A, Zschocke, J, Zuckerbraun, B., and Viscomi M. T. (ORCID:0000-0002-9096-4967)
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused o
Published: 2012

104. The mTOR kinase inhibitor Everolimus decreases S6 kinase phosphorylation but fails to reduce mutant huntingtin levels in brain and is not neuroprotective in the R6/2 mouse model of Huntington's disease

Author: Fox, JH, Connor, T, Chopra, V, Dorsey, K, Kama, JA, Bleckmann, D, Betschart, C, Hoyer, D, Frentzel, S, DiFiglia, M, Paganetti, P, Hersch, SM, Fox, JH, Connor, T, Chopra, V, Dorsey, K, Kama, JA, Bleckmann, D, Betschart, C, Hoyer, D, Frentzel, S, DiFiglia, M, Paganetti, P, and Hersch, SM
Abstract: BACKGROUND: Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion within the huntingtin gene. Mutant huntingtin protein misfolds and accumulates within neurons where it mediates its toxic effects. Promoting mutant huntingtin clearance by activating macroautophagy is one approach for treating Huntington's disease (HD). In this study, we evaluated the mTOR kinase inhibitor and macroautophagy promoting drug everolimus in the R6/2 mouse model of HD. RESULTS: Everolimus decreased phosphorylation of the mTOR target protein S6 kinase indicating brain penetration. However, everolimus did not activate brain macroautophagy as measured by LC3B Western blot analysis. Everolimus protected against early declines in motor performance; however, we found no evidence for neuroprotection as determined by brain pathology. In muscle but not brain, everolimus significantly decreased soluble mutant huntingtin levels. CONCLUSIONS: Our data suggests that beneficial behavioral effects of everolimus in R6/2 mice result primarily from effects on muscle. Even though everolimus significantly modulated its target brain S6 kinase, this did not decrease mutant huntingtin levels or provide neuroprotection.
Published: 2010

105. Full-length huntingtin levels modulate body weight by influencing insulin-like growth factor 1 expression

Author: Pouladi, M. A., primary, Xie, Y., additional, Skotte, N. H., additional, Ehrnhoefer, D. E., additional, Graham, R. K., additional, Kim, J. E., additional, Bissada, N., additional, Yang, X. W., additional, Paganetti, P., additional, Friedlander, R. M., additional, Leavitt, B. R., additional, and Hayden, M. R., additional
Published: 2010
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106. B12-unresponsive methylmalonic aciduria in a female infant

Author: Vecchio, F., Carnevale, F., Paganetti, G., di Bitonto, G., Penza, R., and Francioso, G.
Published: 1980
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107. LBH589, A Hydroxamic Acid-Derived HDAC Inhibitor, is Neuroprotective in Mouse Models of Huntington’s Disease

Author: Chopra, Vanita, Quinti, Luisa, Khanna, Prarthana, Paganetti, Paolo, Kuhn, Rainer, Young, Anne B., Kazantsev, Aleksey G., and Hersch, Steven
Abstract: Background:Modulation of gene transcription by HDAC inhibitors has been shown repeatedly to be neuroprotective in cellular, invertebrate, and rodent models of Huntington’s disease (HD). It has been difficult to translate these treatments to the clinic, however, because existing compounds have limited potency or brain bioavailability. Objective:In the present study, we assessed the therapeutic potential of LBH589, an orally bioavailable hydroxamic acid-derived nonselective HDAC inhibitor in mouse models of HD. Method:The efficacy of LBH589 is tested in two HD mouse models using various biochemical, behavioral and neuropathological outcome measures. Results:We show that LBH589 crosses the blood brain barrier; induces histone hyperacetylation and prevents striatal neuronal shrinkage in R6/2 HD mice. In full-length knock-in HD mice LBH589-treatment improves motor performance and reduces neuronal atrophy. Conclusions:Our efficacious results of LBH589 in fragment and full-length mouse models of HD suggest that LBH589 is a promising candidate for clinical assessment in HD patients and provides confirmation that non-selective HDAC inhibitors can be viable clinical candidates.
Published: 2016
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108. Automated Monte Carlo Simulation of Proton Therapy Treatment Plans

Author: Verburg, Joost Mathijs, Grassberger, Clemens, Dowdell, Stephen, Schuemann, Jan, Seco, Joao, and Paganetti, Harald
Abstract: Simulations of clinical proton radiotherapy treatment plans using general purpose Monte Carlo codes have been proven to be a valuable tool for basic research and clinical studies. They have been used to benchmark dose calculation methods, to study radiobiological effects, and to develop new technologies such as in vivorange verification methods. Advancements in the availability of computational power have made it feasible to perform such simulations on large sets of patient data, resulting in a need for automated and consistent simulations. A framework called MCAUTO was developed for this purpose. Both passive scattering and pencil beam scanning delivery are supported. The code handles the data exchange between the treatment planning system and the Monte Carlo system, which requires not only transfer of plan and imaging information but also translation of institutional procedures, such as output factor definitions. Simulations are performed on a high-performance computing infrastructure. The simulation methods were designed to use the full capabilities of Monte Carlo physics models, while also ensuring consistency in the approximations that are common to both pencil beam and Monte Carlo dose calculations. Although some methods need to be tailored to institutional planning systems and procedures, the described procedures show a general road map that can be easily translated to other systems.
Published: 2016
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109. Fractionated Lung IMPT Treatments: Sensitivity to Setup Uncertainties and Motion Effects Based on Single-Field Homogeneity

Author: Dowdell, Stephen, Grassberger, Clemens, Sharp, Greg, and Paganetti, Harald
Abstract: Treatment uncertainties in radiotherapy are either systematic or random. This study evaluates the sensitivity of fractionated intensity-modulated proton therapy (IMPT) lung treatments to systematic and random setup uncertainties. Treatments in which single-field homogeneity was restricted to within ±20% (IMPT20%) were compared to full IMPT (IMPTfull) for 10 patients with lung cancer. Four-dimensional Monte Carlo calculations were performed using patient computed tomography geometries with ±5 mm systematic or random setup uncertainties applied over a 35 × 2.5Gy(RBE) treatment course. Fifty fractionated courses were simulated for each patient using both IMPT delivery methods with random setup uncertainties applied each fraction and for 3 energy-dependent spot sizes (big spots, s˜18-9 mm; intermediate spots, s˜11-5 mm; and small spots, s˜4-2 mm). These results were compared to Monte Carlo recalculations of the original treatment plan assuming zero setup uncertainty. Results are presented as the difference in equivalent uniform dose (?EUD), V95(?V95), and target dose homogeneity (?D1-D99). Over the whole patient cohort, the ?EUD was 2.0 ± 0.5 (big spots), 1.9 ± 0.7 (intermediate spots), and 1.3 ± 0.4 (small spots) times more sensitive to ±5 mm systematic setup uncertainties in IMPTfullcompared to IMPT20%. IMPTfullis 1.9 ± 0.9 (big spots), 2.1 ± 1.1 (intermediate spots), and 1.5 ± 0.6 (small spots) times more sensitive to random setup uncertainties than IMPT20%over a fractionated treatment course. The ?V95is at least 1.4 times more sensitive to systematic and random setup uncertainties for IMPTfullfor all spot sizes considered. The ?D1-D99values coincided within uncertainty limits for both IMPT delivery methods for the 3 spot sizes considered, with higher mean values always observed for IMPTfull. The paired t-test indicated that variations observed between IMPTfulland IMPT20%were significantly different for the majority of scenarios. Significantly larger variations were observed in ?EUD and ?V95in IMPTfulllung treatments in addition to higher mean ?D1-D99. The steep intra-target dose gradients in IMPTfullmake it more susceptible to systematic and random setup uncertainties.
Published: 2016
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110. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Author: Klionsky, Daniel J, Abdelmohsen, Kotb, Abe, Akihisa, Abedin, Md Joynal, Abeliovich, Hagai, Acevedo Arozena, Abraham, Adachi, Hiroaki, Adams, Christopher M, Adams, Peter D, Adeli, Khosrow, Adhihetty, Peter J, Adler, Sharon G, Agam, Galila, Agarwal, Rajesh, Aghi, Manish K, Agnello, Maria, Agostinis, Patrizia, Aguilar, Patricia V, Aguirre-Ghiso, Julio, Airoldi, Edoardo M, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akporiaye, Emmanuel T, Al-Rubeai, Mohamed, Albaiceta, Guillermo M, Albanese, Chris, Albani, Diego, Albert, Matthew L, Aldudo, Jesus, Algül, Hana, Alirezaei, Mehrdad, Alloza, Iraide, Almasan, Alexandru, Almonte-Beceril, Maylin, Alnemri, Emad S, Alonso, Covadonga, Altan-Bonnet, Nihal, Altieri, Dario C, Alvarez, Silvia, Alvarez-Erviti, Lydia, Alves, Sandro, Amadoro, Giuseppina, Amano, Atsuo, Amantini, Consuelo, Ambrosio, Santiago, Amelio, Ivano, Amer, Amal O, Amessou, Mohamed, Amon, Angelika, An, Zhenyi, Anania, Frank A, Andersen, Stig U, Andley, Usha P, Andreadi, Catherine K, Andrieu-Abadie, Nathalie, Anel, Alberto, Ann, David K, Anoopkumar-Dukie, Shailendra, Antonioli, Manuela, Aoki, Hiroshi, Apostolova, Nadezda, Aquila, Saveria, Aquilano, Katia, Araki, Koichi, Arama, Eli, Aranda, Agustin, Araya, Jun, Arcaro, Alexandre, Arias, Esperanza, Arimoto, Hirokazu, Ariosa, Aileen R, Armstrong, Jane L, Arnould, Thierry, Arsov, Ivica, Asanuma, Katsuhiko, Askanas, Valerie, Asselin, Eric, Atarashi, Ryuichiro, Atherton, Sally S, Atkin, Julie D, Attardi, Laura D, Auberger, Patrick, Auburger, Georg, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Avantaggiati, Maria Laura, Avrahami, Limor, Awale, Suresh, Azad, Neelam, Bachetti, Tiziana, Backer, Jonathan M, Bae, Dong-Hun, Bae, Jae-sung, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric H, Baek, Seung-Hoon, Baghdiguian, Stephen, Bagniewska-Zadworna, Agnieszka, Bai, Hua, Bai, Jie, Bai, Xue-Yuan, Bailly, Yannick, Balaji, Kithiganahalli Narayanaswamy, Balduini, Walter, Ballabio, Andrea, Balzan, Rena, Banerjee, Rajkumar, Bánhegyi, Gábor, Bao, Haijun, Barbeau, Benoit, Barrachina, Maria D, Barreiro, Esther, Bartel, Bonnie, Bartolomé, Alberto, Bassham, Diane C, Bassi, Maria Teresa, Bast, Robert C, Basu, Alakananda, Batista, Maria Teresa, Batoko, Henri, Battino, Maurizio, Bauckman, Kyle, Baumgarner, Bradley L, Bayer, K Ulrich, Beale, Rupert, Beaulieu, Jean-François, Beck, George R., Becker, Christoph, Beckham, J David, Bédard, Pierre-André, Bednarski, Patrick J, Begley, Thomas J, Behl, Christian, Behrends, Christian, Behrens, Georg MN, Behrns, Kevin E, Bejarano, Eloy, Belaid, Amine, Belleudi, Francesca, Bénard, Giovanni, Berchem, Guy, Bergamaschi, Daniele, Bergami, Matteo, Berkhout, Ben, Berliocchi, Laura, Bernard, Amélie, Bernard, Monique, Bernassola, Francesca, Bertolotti, Anne, Bess, Amanda S, Besteiro, Sébastien, Bettuzzi, Saverio, Bhalla, Savita, Bhattacharyya, Shalmoli, Bhutia, Sujit K, Biagosch, Caroline, Bianchi, Michele Wolfe, Biard-Piechaczyk, Martine, Billes, Viktor, Bincoletto, Claudia, Bingol, 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Scott J, Bultynck, Geert, Bumbasirevic, Vladimir, Burelle, Yan, Burke, Robert E, Burmeister, Margit, Bütikofer, Peter, Caberlotto, Laura, Cadwell, Ken, Cahova, Monika, Cai, Dongsheng, Cai, Jingjing, Cai, Qian, Calatayud, Sara, Camougrand, Nadine, Campanella, Michelangelo, Campbell, Grant R, Campbell, Matthew, Campello, Silvia, Candau, Robin, Caniggia, Isabella, Cantoni, Lavinia, Cao, Lizhi, Caplan, Allan B, Caraglia, Michele, Cardinali, Claudio, Cardoso, Sandra Morais, Carew, Jennifer S, Carleton, Laura A, Carlin, Cathleen R, Carloni, Silvia, Carlsson, Sven R, Carmona-Gutierrez, Didac, Carneiro, Leticia AM, Carnevali, Oliana, Carra, Serena, Carrier, Alice, Carroll, Bernadette, Casas, Caty, Casas, Josefina, Cassinelli, Giuliana, Castets, Perrine, Castro-Obregon, Susana, Cavallini, Gabriella, Ceccherini, Isabella, Cecconi, Francesco, Cederbaum, Arthur I, Ceña, Valentín, Cenci, Simone, Cerella, Claudia, Cervia, Davide, Cetrullo, Silvia, Chaachouay, Hassan, Chae, Han-Jung, Chagin, Andrei S, Chai, Chee-Yin, Chakrabarti, Gopal, Chamilos, Georgios, Chan, Edmond YW, Chan, Matthew TV, Chandra, Dhyan, Chandra, Pallavi, Chang, Chih-Peng, Chang, Raymond Chuen-Chung, Chang, Ta Yuan, Chatham, John C, Chatterjee, Saurabh, Chauhan, Santosh, Che, Yongsheng, Cheetham, Michael E, Cheluvappa, Rajkumar, Chen, Chun-Jung, Chen, Gang, Chen, Guang-Chao, Chen, Guoqiang, Chen, Hongzhuan, Chen, Jeff W, Chen, Jian-Kang, Chen, Min, Chen, Mingzhou, Chen, Peiwen, Chen, Qi, Chen, Quan, Chen, Shang-Der, Chen, Si, Chen, Steve S-L, Chen, Wei, Chen, Wei-Jung, Chen, Wen Qiang, Chen, Wenli, Chen, Xiangmei, Chen, Yau-Hung, Chen, Ye-Guang, Chen, Yin, Chen, Yingyu, Chen, Yongshun, Chen, Yu-Jen, Chen, Yue-Qin, Chen, Yujie, Chen, Zhen, Chen, Zhong, Cheng, Alan, Cheng, Christopher HK, Cheng, Hua, Cheong, Heesun, Cherry, Sara, Chesney, Jason, Cheung, Chun Hei Antonio, Chevet, Eric, Chi, Hsiang Cheng, Chi, Sung-Gil, Chiacchiera, Fulvio, Chiang, Hui-Ling, Chiarelli, Roberto, Chiariello, Mario, Chieppa, Marcello, Chin, Lih-Shen, Chiong, Mario, Chiu, Gigi NC, Cho, Dong-Hyung, Cho, Ssang-Goo, Cho, William C, Cho, Yong-Yeon, Cho, Young-Seok, Choi, Augustine MK, Choi, Eui-Ju, Choi, Eun-Kyoung, Choi, Jayoung, Choi, Mary E, Choi, Seung-Il, Chou, Tsui-Fen, Chouaib, Salem, Choubey, Divaker, Choubey, Vinay, Chow, Kuan-Chih, Chowdhury, Kamal, Chu, Charleen T, Chuang, Tsung-Hsien, Chun, Taehoon, Chung, Hyewon, Chung, Taijoon, Chung, Yuen-Li, Chwae, Yong-Joon, Cianfanelli, Valentina, Ciarcia, Roberto, Ciechomska, Iwona A, Ciriolo, Maria Rosa, Cirone, Mara, Claerhout, Sofie, Clague, Michael J, Clària, Joan, Clarke, Peter GH, Clarke, Robert, Clementi, Emilio, Cleyrat, Cédric, Cnop, Miriam, Coccia, Eliana M, Cocco, Tiziana, Codogno, Patrice, Coers, Jörn, Cohen, Ezra EW, Colecchia, David, Coletto, Luisa, Coll, Núria S, Colucci-Guyon, Emma, Comincini, Sergio, Condello, Maria, Cook, Katherine L, Coombs, Graham H, Cooper, Cynthia D, Cooper, J Mark, Coppens, Isabelle, Corasaniti, Maria Tiziana, Corazzari, Marco, Corbalan, Ramon, Corcelle-Termeau, Elisabeth, Cordero, Mario D, Corral-Ramos, Cristina, Corti, Olga, Cossarizza, Andrea, Costelli, Paola, Costes, Safia, Cotman, Susan L, Coto-Montes, Ana, Cottet, Sandra, Couve, Eduardo, Covey, Lori R, Cowart, L Ashley, Cox, Jeffery S, Coxon, Fraser P, Coyne, Carolyn B, Cragg, Mark S, Craven, Rolf J, Crepaldi, Tiziana, Crespo, Jose L, Criollo, Alfredo, Crippa, Valeria, Cruz, Maria Teresa, Cuervo, Ana Maria, Cuezva, Jose M, Cui, Taixing, Cutillas, Pedro R, Czaja, Mark J, Czyzyk-Krzeska, Maria F, Dagda, Ruben K, Dahmen, Uta, Dai, Chunsun, Dai, Wenjie, Dai, Yun, Dalby, Kevin N, Dalla Valle, Luisa, Dalmasso, Guillaume, D'Amelio, Marcello, Damme, Markus, Darfeuille-Michaud, Arlette, Dargemont, Catherine, Darley-Usmar, Victor M, Dasarathy, Srinivasan, Dasgupta, Biplab, Dash, Srikanta, Dass, Crispin R, Davey, Hazel Marie, Davids, Lester M, Dávila, David, Davis, Roger J, Dawson, Ted M, Dawson, Valina L, Daza, Paula, de Belleroche, Jackie, de Figueiredo, Paul, de Figueiredo, Regina Celia Bressan Queiroz, de la Fuente, José, De Martino, Luisa, De Matteis, Antonella, De Meyer, Guido RY, De Milito, Angelo, De Santi, Mauro, de Souza, Wanderley, De Tata, Vincenzo, De Zio, Daniela, Debnath, Jayanta, Dechant, Reinhard, Decuypere, Jean-Paul, Deegan, Shane, Dehay, Benjamin, Del Bello, Barbara, Del Re, Dominic P, Delage-Mourroux, Régis, Delbridge, Lea MD, Deldicque, Louise, Delorme-Axford, Elizabeth, Deng, Yizhen, Dengjel, Joern, Denizot, Melanie, Dent, Paul, Der, Channing J, Deretic, Vojo, Derrien, Benoît, Deutsch, Eric, Devarenne, Timothy P, Devenish, Rodney J, Di Bartolomeo, Sabrina, Di Daniele, Nicola, Di Domenico, Fabio, Di Nardo, Alessia, Di Paola, Simone, Di Pietro, Antonio, Di Renzo, Livia, DiAntonio, Aaron, Díaz-Araya, Guillermo, Díaz-Laviada, Ines, Diaz-Meco, Maria T, Diaz-Nido, Javier, Dickey, Chad A, Dickson, Robert C, Diederich, Marc, Digard, Paul, Dikic, Ivan, Dinesh-Kumar, Savithrama P, Ding, Chan, Ding, Wen-Xing, Ding, Zufeng, Dini, Luciana, Distler, Jörg HW, Diwan, Abhinav, Djavaheri-Mergny, Mojgan, Dmytruk, Kostyantyn, Dobson, Renwick CJ, Doetsch, Volker, Dokladny, Karol, Dokudovskaya, Svetlana, Donadelli, Massimo, Dong, X Charlie, Dong, Xiaonan, Dong, Zheng, Donohue, Terrence M, Doran, Kelly S, D'Orazi, Gabriella, Dorn, Gerald W, Dosenko, Victor, Dridi, Sami, Drucker, Liat, Du, Jie, Du, Li-Lin, Du, Lihuan, du Toit, André, Dua, Priyamvada, Duan, Lei, Duann, Pu, Dubey, Vikash Kumar, Duchen, Michael R, Duchosal, Michel A, Duez, Helene, Dugail, Isabelle, Dumit, Verónica I, Duncan, Mara C, Dunlop, Elaine A, Dunn, William A, Dupont, Nicolas, Dupuis, Luc, Durán, Raúl V, Durcan, Thomas M, Duvezin-Caubet, Stéphane, Duvvuri, Umamaheswar, Eapen, Vinay, Ebrahimi-Fakhari, Darius, Echard, Arnaud, Eckhart, Leopold, Edelstein, Charles L, Edinger, Aimee L, Eichinger, Ludwig, Eisenberg, Tobias, Eisenberg-Lerner, Avital, Eissa, N Tony, El-Deiry, Wafik S, El-Khoury, Victoria, Elazar, Zvulun, Eldar-Finkelman, Hagit, Elliott, Chris JH, Emanuele, Enzo, Emmenegger, Urban, Engedal, Nikolai, Engelbrecht, Anna-Mart, Engelender, Simone, Enserink, Jorrit M, Erdmann, Ralf, Erenpreisa, Jekaterina, Eri, Rajaraman, Eriksen, Jason L, Erman, Andreja, Escalante, Ricardo, Eskelinen, Eeva-Liisa, Espert, Lucile, Esteban-Martínez, Lorena, Evans, Thomas J, Fabri, Mario, Fabrias, Gemma, Fabrizi, Cinzia, Facchiano, Antonio, Færgeman, Nils J, Faggioni, Alberto, Fairlie, W Douglas, Fan, Chunhai, Fan, Daping, Fan, Jie, Fang, Shengyun, Fanto, Manolis, Fanzani, Alessandro, Farkas, Thomas, Faure, Mathias, Favier, Francois B, Fearnhead, Howard, Federici, Massimo, Fei, Erkang, Felizardo, Tania C, Feng, Hua, Feng, Yibin, Feng, Yuchen, Ferguson, Thomas A, Fernández, Álvaro F, Fernandez-Barrena, Maite G, Fernandez-Checa, Jose C, Fernández-López, Arsenio, Fernandez-Zapico, Martin E, Feron, Olivier, Ferraro, Elisabetta, Ferreira-Halder, Carmen Veríssima, Fesus, Laszlo, Feuer, Ralph, Fiesel, Fabienne C, Filippi-Chiela, Eduardo C, Filomeni, Giuseppe, Fimia, Gian Maria, Fingert, John H, Finkbeiner, Steven, Finkel, Toren, Fiorito, Filomena, Fisher, Paul B, Flajolet, Marc, Flamigni, Flavio, Florey, Oliver, Florio, Salvatore, Floto, R Andres, Folini, Marco, Follo, Carlo, Fon, Edward A, Fornai, Francesco, Fortunato, Franco, Fraldi, Alessandro, Franco, Rodrigo, Francois, Arnaud, François, Aurélie, Frankel, Lisa B, Fraser, Iain DC, Frey, Norbert, Freyssenet, Damien G, Frezza, Christian, Friedman, Scott L, Frigo, Daniel E, Fu, Dongxu, Fuentes, José M, Fueyo, Juan, Fujitani, Yoshio, Fujiwara, Yuuki, Fujiya, Mikihiro, Fukuda, Mitsunori, Fulda, Simone, Fusco, Carmela, Gabryel, Bozena, Gaestel, Matthias, Gailly, Philippe, Gajewska, Malgorzata, Galadari, Sehamuddin, Galili, Gad, Galindo, Inmaculada, Galindo, Maria F, Galliciotti, Giovanna, Galluzzi, Lorenzo, Galluzzi, Luca, Galy, Vincent, Gammoh, Noor, Gandy, Sam, Ganesan, Anand K, Ganesan, Swamynathan, Ganley, Ian G, Gannagé, Monique, Gao, Fen-Biao, Gao, Feng, Gao, Jian-Xin, García Nannig, Lorena, García Véscovi, Eleonora, Garcia-Macía, Marina, Garcia-Ruiz, Carmen, Garg, Abhishek D, Garg, Pramod Kumar, Gargini, Ricardo, Gassen, Nils Christian, Gatica, Damián, Gatti, Evelina, Gavard, Julie, Gavathiotis, Evripidis, Ge, Liang, Ge, Pengfei, Ge, Shengfang, Gean, Po-Wu, Gelmetti, Vania, Genazzani, Armando A, Geng, Jiefei, Genschik, Pascal, Gerner, Lisa, Gestwicki, Jason E, Gewirtz, David A, Ghavami, Saeid, Ghigo, Eric, Ghosh, Debabrata, Giammarioli, Anna Maria, Giampieri, Francesca, Giampietri, Claudia, Giatromanolaki, Alexandra, Gibbings, Derrick J, Gibellini, Lara, Gibson, Spencer B, Ginet, Vanessa, Giordano, Antonio, Giorgini, Flaviano, Giovannetti, Elisa, Girardin, Stephen E, Gispert, Suzana, Giuliano, Sandy, Gladson, Candece L, Glavic, Alvaro, Gleave, Martin, Godefroy, Nelly, Gogal, Robert M, Gokulan, Kuppan, Goldman, Gustavo H, Goletti, Delia, Goligorsky, Michael S, Gomes, Aldrin V, Gomes, Ligia C, Gomez, Hernando, Gomez-Manzano, Candelaria, Gómez-Sánchez, Rubén, Gonçalves, Dawit AP, Goncu, Ebru, Gong, Qingqiu, Gongora, Céline, Gonzalez, Carlos B, Gonzalez-Alegre, Pedro, Gonzalez-Cabo, Pilar, González-Polo, Rosa Ana, Goping, Ing Swie, Gorbea, Carlos, Gorbunov, Nikolai V, Goring, Daphne R, Gorman, Adrienne M, Gorski, Sharon M, Goruppi, Sandro, Goto-Yamada, Shino, Gotor, Cecilia, Gottlieb, Roberta A, Gozes, Illana, Gozuacik, Devrim, Graba, Yacine, Graef, Martin, Granato, Giovanna E, Grant, Gary Dean, Grant, Steven, Gravina, Giovanni Luca, Green, Douglas R, Greenhough, Alexander, Greenwood, Michael T, Grimaldi, Benedetto, Gros, Frédéric, Grose, Charles, Groulx, Jean-Francois, Gruber, Florian, Grumati, Paolo, Grune, Tilman, Guan, Jun-Lin, Guan, Kun-Liang, Guerra, Barbara, Guillen, Carlos, Gulshan, Kailash, Gunst, Jan, Guo, Chuanyong, Guo, Lei, Guo, Ming, Guo, Wenjie, Guo, Xu-Guang, Gust, Andrea A, Gustafsson, Åsa B, Gutierrez, Elaine, Gutierrez, Maximiliano G, Gwak, Ho-Shin, Haas, Albert, Haber, James E, Hadano, Shinji, Hagedorn, Monica, Hahn, 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Wen, Xin, Wen, Yunfei, Westermann, Benedikt, Weyand, Cornelia M, White, Anthony R, White, Eileen, Whitton, J Lindsay, Whitworth, Alexander J, Wiels, Joëlle, Wild, Franziska, Wildenberg, Manon E, Wileman, Tom, Wilkinson, Deepti Srinivas, Wilkinson, Simon, Willbold, Dieter, Williams, Chris, Williams, Katherine, Williamson, Peter R, Winklhofer, Konstanze F, Witkin, Steven S, Wohlgemuth, Stephanie E, Wollert, Thomas, Wolvetang, Ernst J, Wong, Esther, Wong, G William, Wong, Richard W, Wong, Vincent Kam Wai, Woodcock, Elizabeth A, Wright, Karen L, Wu, Chunlai, Wu, Defeng, Wu, Gen Sheng, Wu, Jian, Wu, Junfang, Wu, Mian, Wu, Min, Wu, Shengzhou, Wu, William KK, Wu, Yaohua, Wu, Zhenlong, Xavier, Cristina PR, Xavier, Ramnik J, Xia, Gui-Xian, Xia, Tian, Xia, Weiliang, Xia, Yong, Xiao, Hengyi, Xiao, Jian, Xiao, Shi, Xiao, Wuhan, Xie, Chuan-Ming, Xie, Zhiping, Xie, Zhonglin, Xilouri, Maria, Xiong, Yuyan, Xu, Chuanshan, Xu, Congfeng, Xu, Feng, Xu, Haoxing, Xu, Hongwei, Xu, Jian, Xu, Jianzhen, Xu, Jinxian, Xu, Liang, Xu, Xiaolei, Xu, Yangqing, Xu, Ye, Xu, Zhi-Xiang, Xu, Ziheng, Xue, Yu, Yamada, Takahiro, Yamamoto, Ai, Yamanaka, Koji, Yamashina, Shunhei, Yamashiro, Shigeko, Yan, Bing, Yan, Bo, Yan, Xianghua, Yan, Zhen, Yanagi, Yasuo, Yang, Dun-Sheng, Yang, Jin-Ming, Yang, Liu, Yang, Minghua, Yang, Pei-Ming, Yang, Peixin, Yang, Qian, Yang, Wannian, Yang, Wei Yuan, Yang, Xuesong, Yang, Yi, Yang, Ying, Yang, Zhifen, Yang, Zhihong, Yao, Meng-Chao, Yao, Pamela J, Yao, Xiaofeng, Yao, Zhenyu, Yao, Zhiyuan, Yasui, Linda S, Ye, Mingxiang, Yedvobnick, Barry, Yeganeh, Behzad, Yeh, Elizabeth S, Yeyati, Patricia L, Yi, Fan, Yi, Long, Yin, Xiao-Ming, Yip, Calvin K, Yoo, Yeong-Min, Yoo, Young Hyun, Yoon, Seung-Yong, Yoshida, Ken-Ichi, Yoshimori, Tamotsu, Young, Ken H, Yu, Huixin, Yu, Jane J, Yu, Jin-Tai, Yu, Jun, Yu, Li, Yu, W Haung, Yu, Xiao-Fang, Yu, Zhengping, Yuan, Junying, Yuan, Zhi-Min, Yue, Beatrice YJT, Yue, Jianbo, Yue, Zhenyu, Zacks, David N, Zacksenhaus, Eldad, Zaffaroni, Nadia, Zaglia, Tania, Zakeri, Zahra, Zecchini, Vincent, Zeng, Jinsheng, Zeng, Min, Zeng, Qi, Zervos, Antonis S, Zhang, Donna D, Zhang, Fan, Zhang, Guo, Zhang, Guo-Chang, Zhang, Hao, Zhang, Hong, Zhang, Hong, Zhang, Hongbing, Zhang, Jian, Zhang, Jian, Zhang, Jiangwei, Zhang, Jianhua, Zhang, Jing-pu, Zhang, Li, Zhang, Lin, Zhang, Lin, Zhang, Long, Zhang, Ming-Yong, Zhang, Xiangnan, Zhang, Xu Dong, Zhang, Yan, Zhang, Yang, Zhang, Yanjin, Zhang, Yingmei, Zhang, Yunjiao, Zhao, Mei, Zhao, Wei-Li, Zhao, Xiaonan, Zhao, Yan G, Zhao, Ying, Zhao, Yongchao, Zhao, Yu-xia, Zhao, Zhendong, Zhao, Zhizhuang J, Zheng, Dexian, Zheng, Xi-Long, Zheng, Xiaoxiang, Zhivotovsky, Boris, Zhong, Qing, Zhou, Guang-Zhou, Zhou, Guofei, Zhou, Huiping, Zhou, Shu-Feng, Zhou, Xu-jie, Zhu, Hongxin, Zhu, Hua, Zhu, Wei-Guo, Zhu, Wenhua, Zhu, Xiao-Feng, Zhu, Yuhua, Zhuang, Shi-Mei, Zhuang, Xiaohong, Ziparo, Elio, Zois, Christos E, Zoladek, Teresa, Zong, Wei-Xing, Zorzano, Antonio, and Zughaier, Susu M
Published: 2016
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111. Using γ-Secretase Inhibitors to Distinguish the Generation of the Aβ Peptides Terminating at Val-40 and Ala-42.

Author: Walker, John M., Hooper, Nigel M., Paganetti, Paolo A., and Staufenbiel, Matthias
Abstract: A large body of evidence suggests a causative role of β-amyloid (Aβ) in the pathogenesis of Alzheimer's disease (reviewed in refs. 1 and 2). Aβ is neurotoxic and toxicity requires the formation of amyloid fibrils similar to those found in senile plaques (3). Autosomal dominant mutations linked to Alzheimer's disease were identified in three different genes (4 ,5). All mutations apparently alter amyloid precursor protein (APP) metabolism to increase the generation of Aβ peptides terminating at amino acid Ala-42. Due to the tendency of the longer Aβ peptides to more readily form fibrils (7), these may accelerate Aβ deposition, which ultimately leads to more aggressive, early onset forms of Alzheimer's disease (8). With the transgenic expression of APP in mice this was explored further (9). Whereas a twofold overexpression of APP did not lead to Aβ deposition, the same quantitative expression of APP with a mutation at codon 717 known to increase the formation of Aβ42 led to the appearance of Aβ deposits at the age of 18 mo. These data suggest that the Aβ load in the brain as well as the amyloidogenic properties of the Aβ isoforms directly regulate deposition and senile plaque formation. [ABSTRACT FROM AUTHOR]
Published: 2000
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112. Electrophoretic Separation and Immunoblotting of Aβ1-40and Aβ1-42.

Author: Walker, John M., Hooper, Nigel M., Staufenbiel, Matthias, and Paganetti, Paolo A.
Abstract: The main protein component of the plaques found in the brains of Alzheimer's disease patients is Aβ, a peptide of 39 to 43 amino acids (reviewed in refs. 1 and 2). Two major Aβ isoforms have been identified in the brains of affected individuals ending at amino acids 40 and 42, respectively (3). The longer form, Aβ42, aggregates more rapidly in vitro (4) and is preferentially deposited in vivo (3 ,5,6). Normally, Aβ is secreted as an apparently soluble molecule (7 -9). It is generated by all cultured cells expressing its precursor protein, APP, and can be detected in vivo in the cerebrospinal fluid (10) and in plasma (11). Mutations linked to familial forms of Alzheimer's disease have been found in the APP gene as well as two other genes encoding presenilin 1 and presenilin 2. They were shown to alter APP metabolism and, in particular, to either increase total Aβ or the relative abundance of the longer Aβ42 isoform (12-17). These observations have led to the hypothesis that Aβ42 may play a critical role in amyloid plaque formation and the development of Alzheimer's disease. Obviously methods discriminating between the two major Aβ species are important in order to study this notion. [ABSTRACT FROM AUTHOR]
Published: 2000
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113. 72 Characterization of S182 (presenilin 1) and its effect on ßA4

Author: Staufenbiel, M., primary, Baumann, K.-H., additional, Sturchler-Pierrat, C., additional, Wiederhold, K.-H., additional, Probst, A., additional, Paganetti, P., additional, Frey, P., additional, Yankner, B., additional, and Sommer, B., additional
Published: 1996
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114. A Recommendation on How to Analyze In-Room PET for In Vivo Proton Range Verification Using a Distal PET Surface Method

Author: Min, Chul Hee, Zhu, Xuping, Grogg, Kira, El Fakhri, Georges, Winey, Brian, and Paganetti, Harald
Abstract: We describe the rationale and implementation of a method for analyzing in-room positron emission tomography (PET) data to verify the proton beam range. The method is based on analyzing distal PET surfaces after passive scattering proton beam delivery. Typically in vivo range verification is done by comparing measured and predicted PET distribution for a single activity level at a selected activity line along the beam passage. In the method presented here, we suggest using a middle point method based on dual PET activity levels to minimize the uncertainty due to local variations in the PET activity. Furthermore, we introduce 2-dimensional (2D) PET activity level surfaces based on 3-dimensional maps of the PET activities along the beam passage. This allows determining not only average range differences but also range difference distributions as well as root mean square deviations (RMSDs) for a more comprehensive range analysis. The method is demonstrated using data from 8 patients who were scanned with an in-room PET scanner. For each of the 8 patients, the average range difference was less than 5 mm and the RMSD was 4 to 11 mm between the measured and simulated PET activity level surfaces for single-field treatments. An ongoing protocol at our institution allows the use of a single field for patients being imaged for the PET range verification study at 1 fraction during their treatment course. Visualizing the range difference distributions using the PET surfaces offers a convenient visual verification of range uncertainties in 2D. Using the distal activity level surfaces of simulated and measured PET distributions at the middle of 25% and 50% activity level is a robust method for in vivo range verification.
Published: 2015
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115. Biological Considerations When Comparing Proton Therapy With Photon Therapy.

Author: Paganetti, Harald and van Luijk, Peter
Abstract: Owing to the limited availability of data on the outcome of proton therapy, treatments are generally optimized based on broadly available data on photon-based treatments. However, the microscopic pattern of energy deposition of protons differs from that of photons, leading to a different biological effect. Consequently, proton therapy needs a correction factor (relative biological effectiveness) to relate proton doses to photon doses, and currently, a generic value is used. Moreover, the macroscopic distribution of dose in proton therapy differs compared with photon treatments. Although this may offer new opportunities to reduce dose to normal tissues, it raises the question whether data obtained from photon-based treatments offer sufficient information on dose–volume effects to optimally use unique features of protons. In addition, there are potential differences in late effects due to low doses of secondary radiation outside the volume irradiated by the primary beam. This article discusses the controversies associated with these 3 issues when comparing proton and photon therapy. [Copyright &y& Elsevier]
Published: 2013
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116. PRELIMINARY STUDY OF PROTON RADIOGRAPHY IMAGING QUALITIES USING GEANT4 MONTE CARLO SIMULATIONS.

Author: DEPAUW, NICOLAS, DANTO, SYLVAIN, BEDNARZ, BRYAN, PAGANETTI, HARALD, FINK, YOEL, and SECO, JOAO
Subjects: RADIOGRAPHY, MONTE Carlo method, SIMULATION methods & models, PROTON-proton interactions, CANCER treatment
Abstract: Proton radiography imaging qualities have been studied using Monte Carlo simulations. A specific phantom, made of different common tissues, was implemented for simulations using the Massachusetts General Hospital treatment proton beam, pure 230- and 490-MeV proton beams, and a pure 100-keVX-ray beam. Along with spatial resolution, the signal-to-noise ratio and the contrast-to-noise ratio were specified and compared for each tissue type and geometry, using filtered radiographs taking into account only primary proton interactions, both primary and secondary proton interactions, and both contributions while performing angular and energetic cuts. This work particularly highlights the faculty for proton radiography to image both low- and high-density tissues. This could play an important role in diagnosing specific tumor types, such as lung cancer, for which conventional radiography operates poorly. [ABSTRACT FROM AUTHOR]
Published: 2011
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117. COMPARISON OF PARTICLE-TRACKING FEATURES IN GEANT4 AND MCNPX CODES FOR APPLICATIONS IN MAPPING OF PROTON RANGE UNCERTAINTY.

Author: BEDNARZ, BRYAN, CHEN, GTY, PAGANETTI, HARALD, HAN, BIN, DING, AIPING, and XU, X. GEORGE
Subjects: RADIOTHERAPY, TUMORS, MONTE Carlo method, PROTONS, ALGORITHMS
Abstract: The accuracy of proton therapy is partially limited by uncertainties that result from changing pathological conditions in the patient such as tumor motion and shrinkage. These uncertainties can be minimized with the help of a time-resolved range telescope. Monte Carlo methods can help improve the performance of range telescopes by tracking proton interactions on a particle-by-particle basis thus broadening our understanding on the behavior of protons within the patient and the detector. This paper compared the proton multiple coulomb scattering algorithms in the Monte Carlo codes MCNPX and Geant4 to well-established scattering theories. We focus only on beam energies associated with proton imaging. Despite slight discrepancies between scattering algorithms, both codes appear to be capable of providing useful particle-tracking information for applications such as the proton range telescope. [ABSTRACT FROM AUTHOR]
Published: 2011
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118. The disulphide bonds in the catalytic domain of BACE are critical but not essential for amyloid precursor protein processing activity.

Author: Fischer, F., Molinari, M., Bodendorf, U., and Paganetti, P.
Subjects: AMYLOID beta-protein precursor, PROTEIN folding
Abstract: β-Site APP-cleaving enzyme (BACE) initiates the processing of the amyloid precursor protein (APP) leading to the generation of β-amyloid, the main component of Alzheimer's disease senile plaques. BACE (Asp2, memapsin 2) is a type I transmembrane aspartic protease responsible for the β-secretase cleavage of APP producing a soluble form of the ectodomain (sAPPβ) and the membrane-bound, carboxy-terminal intermediates C99 and C89. BACE maturation involves cysteine bridge formation, N-glycosylation and propeptide removal. We investigated variants of BACE in which the disulphide bonds of the catalytic domain spanning between Cys216/Cys420, Cys278/Cys443 and Cys330/Cys380 were removed by mutagenesis. When transfected in cultured cells, these mutants showed impaired maturation. Nevertheless, a fraction of mutated protein retained both the competence to mature as well as the activity to process APP. For the generation of a functional enzyme the conserved Cys330/Cys380 bond was the most critical, whereas the two bonds between Cys216/Cys420 and Cys278/Cys443, which are typical for the membrane-bound BACE, appeared to be less important. [ABSTRACT FROM AUTHOR]
Published: 2002
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119. Expression of human β-secretase in the mouse brain increases the steady-state level of β-amyloid.

Author: Bodendorf, U., Danner, S., Fischer, F., Stefani, M., Sturchler-Pierrat, C., Wiederhold, K-H., Staufenbiel, M., and Paganetti, P.
Subjects: AMYLOID beta-protein precursor, TRANSGENIC mice, PROTEOLYTIC enzymes
Abstract: β-Site APP-cleaving enzyme (BACE) initiates the processing of the amyloid precursor protein (APP) leading to the generation of β-amyloid, the main component of Alzheimer's disease senile plaques. BACE (Asp2, memapsin 2) is a type I transmembrane aspartyl protease and is responsible for the β-secretase cleavage of APP producing different endoproteolytic fragments referred to as the carboxy-terminal C99, C89 and the soluble ectodomain sAPPβ. Here we describe two transgenic mouse lines expressing human BACE in the brain. Overexpression of BACE augments the amyloidogenic processing of APP as demonstrated by decreased levels of full-length APP and increased levels of C99 and C89 in vivo. In mice expressing huBACE in addition to human APP wild-type or carrying the Swedish mutation, the induction of APP processing characterized by elevated C99, C89 and sAPPβ, results in increased brain levels of β-amyloid peptides Aβ40 and Aβ42 at steady-state. [ABSTRACT FROM AUTHOR]
Published: 2002
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120. Evaluation of permanent alopecia in pediatric medulloblastoma patients treated with proton radiation

Author: Min, Chul Hee, Paganetti, Harald, Winey, Brian A, Adams, Judith, MacDonald, Shannon M, Tarbell, Nancy J, and Yock, Torunn I
Subjects: Permanent alopecia, Proton therapy, Pediatric medulloblastoma, Monte Carlo simulation
Abstract: Background: To precisely calculate skin dose and thus to evaluate the relationship between the skin dose and permanent alopecia for pediatric medulloblastoma patients treated with proton beams. Methods: The dosimetry and alopecia outcomes of 12 children with medulloblastoma (ages 4-15 years) comprise the study cohort. Permanent alopecia was assessed and graded after completion of the entire therapy. Skin threshold doses of permanent alopecia were calculated based on the skin dose from the craniospinal irradiation (CSI) plan using the concept of generalized equivalent uniform dose (gEUD) and accounting for chemotherapy intensity. Monte Carlo simulations were employed to accurately assess uncertainties due to beam range prediction and secondary particles. Results: Increasing the dose of the CSI field or the dose given by the boost field to the posterior fossa increased total skin dose delivered in that region. It was found that permanent alopecia could be correlated with CSI dose with a threshold of about 21 Gy (relative biological effectiveness, RBE) with high dose chemotherapy and 30 Gy (RBE) with conventional chemotherapy. Conclusions: Our results based on 12 patients provide a relationship between the skin dose and permanent alopecia for pediatric medulloblastoma patients treated with protons. The alopecia risk as assessed with gEUD could be predicted based on the treatment plan information.
Published: 2014
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121. Lifetime Increased Cancer Risk in Mice Following Exposure to Clinical Proton Beam–Generated Neutrons

Author: Gerweck, Leo Edward, Huang, Peigen, Lu, Hsiao-ming, Paganetti, Harald, and Zhou, Yenong
Abstract: Purpose To evaluate the lifespan and risk of cancer following whole-body exposure of mice to neutrons generated by a passively scattered clinical SOBP proton beam. Methods and Materials Three hundred young adult female FVB/N mice, 152 test and 148 control, were entered into the experiment. Mice were placed in an annular cassette around a cylindrical phantom, which was positioned lateral to the mid SOBP of a 165 MeV, clinical proton beam. The average distance from the edge of the mid SOBP to the conscious active mice was 21.5 cm. The phantom was irradiated with once daily fractions of 25 Gy, 4 days per week, for 6 weeks. The age at death and cause of death, i.e., cancer and type vs. non-cancer causes, were assessed over the lifespan of the mice. Results Exposure of mice to a dose of 600 Gy of proton beam generated neutrons, reduced the median lifespan of the mice by 4.2% (Kaplan-Meier cumulative survival, P = 0.053). The relative risk of death from cancer in neutron exposed vs. control mice was 1.40 for cancer of all types (P = 0.0006) and 1.22 for solid cancers (P = 0.09). For a typical 60 Gy dose of clinical protons, the observed 22% increased risk of solid cancer would be expected to decrease by a factor of 10. Conclusions Exposure of mice to neutrons generated by a proton dose which exceeds a typical course of radiotherapy by a factor of 10, resulted in a statistically significant increase in the background incidence of leukemia and a marginally significant increase in solid cancer. The results indicate that the risk of out-of-field 2nd solid cancers from SOBP proton generated neutrons and typical treatment schedules, is 6 - 10 times less than is suggested by current neutron risk estimates.
Published: 2014
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122. Guidelines for the use and interpretation of assays for monitoring autophagy

Author: Klionsky, Daniel J., Abdalla, Fabio C., Abeliovich, Hagai, Abraham, Robert T., Acevedo-Arozena, Abraham, Adeli, Khosrow, Agholme, Lotta, Agnello, Maria, Agostinis, Patrizia, Aguirre-Ghiso, Julio A., Ahn, Hyung Jun, Ait-Mohamed, Ouardia, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akira, Shizuo, Al-Younes, Hesham M., Al-Zeer, Munir A., Albert, Matthew L., Albin, Roger L., Alegre-Abarrategui, Javier, Aleo, Maria Francesca, Alirezaei, Mehrdad, Almasan, Alexandru, Almonte-Becerril, Maylin, Amano, Atsuo, Amaravadi, Ravi K., Amarnath, Shoba, Amer, Amal O., Andrieu-Abadie, Nathalie, Anantharam, Vellareddy, Ann, David K., Anoopkumar-Dukie, Shailendra, Aoki, Hiroshi, Apostolova, Nadezda, Arancia, Giuseppe, Aris, John P., Asanuma, Katsuhiko, Asare, Nana Y.O., Ashida, Hisashi, Askanas, Valerie, Askew, David S., Auberger, Patrick, Baba, Misuzu, Backues, Steven K., Baehrecke, Eric H., Bahr, Ben A., Bai, Xue-Yuan, Bailly, Yannick, Baiocchi, Robert, Baldini, Giulia, Balduini, Walter, Ballabio, Andrea, Bamber, Bruce A., Bampton, Edward T.W., Juhász, Gábor, Bartholomew, Clinton R., Bassham, Diane C., Bast, Robert C., Batoko, Henri, Bay, Boon-Huat, Beau, Isabelle, Béchet, Daniel M., Begley, Thomas J., Behl, Christian, Behrends, Christian, Bekri, Soumeya, Bellaire, Bryan, Bendall, Linda J., Benetti, Luca, Berliocchi, Laura, Bernardi, Henri, Bernassola, Francesca, Besteiro, Sébastien, Bhatia-Kissova, Ingrid, Bi, Xiaoning, Biard-Piechaczyk, Martine, Blum, Janice S., Boise, Lawrence H., Bonaldo, Paolo, Boone, David L., Bornhauser, Beat C., Bortoluci, Karina R., Bossis, Ioannis, Bost, Frédéric, Bourquin, Jean-Pierre, Boya, Patricia, Boyer-Guittaut, Michaël, Bozhkov, Peter V., Brady, Nathan R, Brancolini, Claudio, Brech, Andreas, Brenman, Jay E., Brennand, Ana, Bresnick, Emery H., Brest, Patrick, Bridges, Dave, Bristol, Molly L., Brookes, Paul S., Brown, Eric J., Brumell, John H., Brunetti-Pierri, Nicola, Brunk, Ulf T., Bulman, Dennis E., Bultman, Scott J., Bultynck, Geert, Burbulla, Lena F., Bursch, Wilfried, Butchar, Jonathan P., Buzgariu, Wanda, Bydlowski, Sergio P., Cadwell, Ken, Cahová, Monika, Cai, Dongsheng, Cai, Jiyang, Cai, Qian, Calabretta, Bruno, Calvo-Garrido, Javier, Camougrand, Nadine, Campanella, Michelangelo, Campos-Salinas, Jenny, Candi, Eleonora, Cao, Lizhi, Caplan, Allan B., Carding, Simon R., Cardoso, Sandra M., Carew, Jennifer S., Carlin, Cathleen R., Carmignac, Virginie, Carneiro, Leticia A.M., Carra, Serena, Caruso, Rosario A., Casari, Giorgio, Casas, Caty, Castino, Roberta, Cebollero, Eduardo, Cecconi, Francesco, Celli, Jean, Chaachouay, Hassan, Chae, Han-Jung, Chai, Chee-Yin, Chan, David C., Chan, Edmond Y., Chang, Raymond Chuen-Chung, Che, Chi-Ming, Chen, Ching-Chow, Chen, Guang-Chao, Chen, Guo-Qiang, Chen, Min, Chen, Quan, Chen, Steve S.-L., Chen, WenLi, Chen, Xi, Chen, Xiangmei, Chen, Xiequn, Chen, Ye-Guang, Chen, Yingyu, Chen, Yongqiang, Chen, Yu-Jen, Chen, Zhixiang, Cheng, Alan, Cheng, Christopher H.K., Cheng, Yan, Cheong, Heesun, Cheong, Jae-Ho, Cherry, Sara, Chess-Williams, Russ, Cheung, Zelda H., Chevet, Eric, Chiang, Hui-Ling, Chiarelli, Roberto, Chiba, Tomoki, Chin, Lih-Shen, Chiou, Shih-Hwa, Chisari, Francis V., Cho, Chi Hin, Cho, Dong-Hyung, Choi, Augustine M.K., Choi, DooSeok, Choi, Kyeong Sook, Choi, Mary E., Chouaib, Salem, Choubey, Divaker, Choubey, Vinay, Chu, Charleen T., Chuang, Tsung-Hsien, Chueh, Sheau-Huei, Chun, Taehoon, Chwae, Yong-Joon, Chye, Mee-Len, Ciarcia, Roberto, Ciriolo, Maria R., Clague, Michael J., Clark, Robert S.B., Clarke, Peter G.H., Clarke, Robert, Codogno, Patrice, Coller, Hilary A., Colombo, María I., Comincini, Sergio, Condello, Maria, Condorelli, Fabrizio, Cookson, Mark R., Coombs, Graham H., Coppens, Isabelle, Corbalan, Ramon, Cossart, Pascale, Costelli, Paola, Costes, Safia, Coto-Montes, Ana, Couve, Eduardo, Coxon, Fraser P., Cregg, James M., Crespo, José L., Cronjé, Marianne J., Cuervo, Ana Maria, Cullen, Joseph J., Czaja, Mark J., D'Amelio, Marcello, Darfeuille-Michaud, Arlette, Davids, Lester M., Davies, Faith E., De Felici, Massimo, de Groot, John F., de Haan, Cornelis A.M., De Martino, Luisa, De Milito, Angelo, De Tata, Vincenzo, Debnath, Jayanta, Degterev, Alexei, Dehay, Benjamin, Delbridge, Lea M.D., Demarchi, Francesca, Deng, Yi Zhen, Dengjel, Jörn, Dent, Paul, Denton, Donna, Deretic, Vojo, Desai, Shyamal D., Devenish, Rodney J., Di Gioacchino, Mario, Di Paolo, Gilbert, Di Pietro, Chiara, Díaz-Araya, Guillermo, Díaz-Laviada, Inés, Diaz-Meco, Maria T., Diaz-Nido, Javier, Dikic, Ivan, Dinesh-Kumar, Savithramma P., Ding, Wen-Xing, Distelhorst, Clark W., Diwan, Abhinav, Djavaheri-Mergny, Mojgan, Dokudovskaya, Svetlana, Dong, Zheng, Dorsey, Frank C., Dosenko, Victor, Dowling, James J., Doxsey, Stephen, Dreux, Marlène, Drew, Mark E., Duan, Qiuhong, Duchosal, Michel A., Duff, Karen E., Dugail, Isabelle, Durbeej, Madeleine, Duszenko, Michael, Edelstein, Charles L., Edinger, Aimee L., Egea, Gustavo, Eichinger, Ludwig, Eissa, N. Tony, Ekmekcioglu, Suhendan, El-Deiry, Wafik S., Elazar, Zvulun, Elgendy, Mohamed, Ellerby, Lisa M., Eng, Kai Er, Engelbrecht, Anna-Mart, Engelender, Simone, Erenpreisa, Jekaterina, Escalante, Ricardo, Esclatine, Audrey, Eskelinen, Eeva-Liisa, Espert, Lucile, Espina, Virginia, Fan, Huizhou, Fan, Jia, Fan, Qi-Wen, Fan, Zhen, Fang, Shengyun, Fang, Yongqi, Fanto, Manolis, Fanzani, Alessandro, Farkas, Thomas, Farre, Jean-Claude, Faure, Mathias, Fechheimer, Marcus, Feng, Carl G., Feng, Jian, Feng, Qili, Feng, Youji, Fésüs, László, Feuer, Ralph, Figueiredo-Pereira, Maria E., Fimia, Gian Maria, Fingar, Diane C., Finkbeiner, Steven, Finkel, Toren, Finley, Kim D., Fiorito, Filomena, Fisher, Edward A., Fisher, Paul B., Flajolet, Marc, Florez-McClure, Maria L., Florio, Salvatore, Fon, Edward A., Fornai, Francesco, Fortunato, Franco, Fotedar, Rati, Fowler, Daniel H., Fox, Howard S., Franco, Rodrigo, Frankel, Lisa B., Fransen, Marc, Fuentes, José M., Fueyo, Juan, Fujii, Jun, Fujisaki, Kozo, Fujita, Eriko, Fukuda, Mitsunori, Furukawa, Ruth H., Gaestel, Matthias, Gailly, Philippe, Gajewska, Malgorzata, Galliot, Brigitte, Galy, Vincent, Ganesh, Subramaniam, Ganetzky, Barry, Ganley, Ian G., Gao, Fen-Biao, Gao, George F., Gao, Jinming, Garcia, Lorena, Garcia-Manero, Guillermo, Garcia-Marcos, Mikel, Garmyn, Marjan, Gartel, Andrei L., Gatti, Evelina, Gautel, Mathias, Gawriluk, Thomas R., Gegg, Matthew E., Geng, Jiefei, Germain, Marc, Gestwicki, Jason E., Gewirtz, David A., Ghavami, Saeid, Ghosh, Pradipta, Giammarioli, Anna M., Giatromanolaki, Alexandra N., Gibson, Spencer B., Gilkerson, Robert W., Ginger, Michael L., Ginsberg, Henry N., Golab, Jakub, Goligorsky, Michael S., Golstein, Pierre, Gomez-Manzano, Candelaria, Goncu, Ebru, Gongora, Céline, Gonzalez, Claudio D., Gonzalez, Ramon, González-Estévez, Cristina, González-Polo, Rosa Ana, Gonzalez-Rey, Elena, Gorbunov, Nikolai V., Gorski, Sharon, Goruppi, Sandro, Gottlieb, Roberta A., Gozuacik, Devrim, Granato, Giovanna Elvira, Grant, Gary D., Green, Kim N., Gregorc, Ales, Gros, Frédéric, Grose, Charles, Grunt, Thomas W., Gual, Philippe, Guan, Jun-Lin, Guan, Kun-Liang, Guichard, Sylvie M., Gukovskaya, Anna S., Gukovsky, Ilya, Gunst, Jan, Gustafsson, Åsa B., Halayko, Andrew J., Hale, Amber N., Halonen, Sandra K., Hamasaki, Maho, Han, Feng, Han, Ting, Hancock, Michael K., Hansen, Malene, Harada, Hisashi, Harada, Masaru, Hardt, Stefan E., Harper, J. Wade, Harris, Adrian L., Harris, James, Harris, Steven D., Hashimoto, Makoto, Haspel, Jeffrey A., Hayashi, Shin-ichiro, Hazelhurst, Lori A., He, Congcong, He, You-Wen, Hébert, Marie-Josée, Heidenreich, Kim A., Helfrich, Miep H., Helgason, Gudmundur V., Henske, Elizabeth P., Herman, Brian, Herman, Paul K., Hetz, Claudio, Hilfiker, Sabine, Hill, Joseph A., Hocking, Lynne J., Hofman, Paul, Hofmann, Thomas G., Höhfeld, Jörg, Holyoake, Tessa L., Hong, Ming-Huang, Hood, David A., Hotamisligil, Gökhan S., Houwerzijl, Ewout J., Høyer-Hansen, Maria, Hu, Bingren, Hu, Chien-an A., Hu, Hong-Ming, Hua, Ya, Huang, Canhua, Huang, Ju, Huang, Shengbing, Huang, Wei-Pang, Huber, Tobias B., Huh, Won-Ki, Hung, Tai-Ho, Hupp, Ted R., Hur, Gang Min, Hurley, James B., Hussain, Sabah N.A., Hussey, Patrick J., Hwang, Jung Jin, Hwang, Seungmin, Ichihara, Atsuhiro, Ilkhanizadeh, Shirin, Inoki, Ken, Into, Takeshi, Iovane, Valentina, Iovanna, Juan L., Ip, Nancy Y., Isaka, Yoshitaka, Ishida, Hiroyuki, Isidoro, Ciro, Isobe, Ken-ichi, Iwasaki, Akiko, Izquierdo, Marta, Izumi, Yotaro, Jaakkola, Panu M., Jäättelä, Marja, Jackson, George R., Jackson, William T., Janji, Bassam, Jendrach, Marina, Jeon, Ju-Hong, Jeung, Eui-Bae, Jiang, Hong, Jiang, Hongchi, Jiang, Jean X., Jiang, Ming, Jiang, Qing, Jiang, Xuejun, Jiang, Xuejun, Jiménez, Alberto, Jin, Meiyan, Jin, Shengkan V., Joe, Cheol O., Johansen, Terje, Johnson, Daniel E., Johnson, Gail V.W., Jones, Nicola L., Joseph, Bertrand, Joseph, Suresh K., Joubert, Annie M., Juhász, Gábor, Juillerat-Jeanneret, Lucienne, Jung, Chang Hwa, Jung, Yong-Keun, Kaarniranta, Kai, Kaasik, Allen, Kabuta, Tomohiro, Kadowaki, Motoni, Kågedal, Katarina, Kamada, Yoshiaki, Kaminskyy, Vitaliy O., Kampinga, Harm H., Kanamori, Hiromitsu, Kang, Chanhee, Kang, Khong Bee, Kang, Kwang Il, Kang, Rui, Kang, Yoon-A, Kanki, Tomotake, Kanneganti, Thirumala-Devi, Kanno, Haruo, Kanthasamy, Anumantha G., Kanthasamy, Arthi, Karantza, Vassiliki, Kaushal, Gur P., Kaushik, Susmita, Kawazoe, Yoshinori, Ke, Po-Yuan, Kehrl, John H., Kelekar, Ameeta, Kerkhoff, Claus, Kessel, David H., Khalil, Hany, Kiel, Jan A.K.W., Kiger, Amy A., Kihara, Akio, Kim, Deok Ryong, Kim, Do-Hyung, Kim, Dong-Hou, Kim, Eun-Kyoung, Kim, Hyung-Ryong, Kim, Jae-Sung, Kim, Jeong Hun, Kim, Jin Cheon, Kim, John K., Kim, Peter K., Kim, Seong Who, Kim, Yong-Sun, Kim, Yonghyun, Kimchi, Adi, Kimmelman, Alec C., King, Jason S., Kinsella, Timothy J., Kirkin, Vladimir, Kirshenbaum, Lorrie A., Kitamoto, Katsuhiko, Kitazato, Kaio, Klein, Ludger, Klimecki, Walter T., Klucken, Jochen, Knecht, Erwin, Ko, Ben C.B., Koch, Jan C., Koga, Hiroshi, Koh, Jae-Young, Koh, Young Ho, Koike, Masato, Komatsu, Masaaki, Kominami, Eiki, Kong, Hee Jeong, Kong, Wei-Jia, Korolchuk, Viktor I., Kotake, Yaichiro, Koukourakis, Michael I., Flores, Juan B. Kouri, Kovács, Attila L., Kraft, Claudine, Krainc, Dimitri, Krämer, Helmut, Kretz-Remy, Carole, Krichevsky, Anna M., Kroemer, Guido, Krüger, Rejko, Krut, Oleg, Ktistakis, Nicholas T., Kuan, Chia-Yi, Kucharczyk, Roza, Kumar, Ashok, Kumar, Raj, Kumar, Sharad, Kundu, Mondira, Kung, Hsing-Jien, Kurz, Tino, Kwon, Ho Jeong, La Spada, Albert R., Lafont, Frank, Lamark, Trond, Landry, Jacques, Lane, Jon D., Lapaquette, Pierre, Laporte, Jocelyn F., László, Lajos, Lavandero, Sergio, Lavoie, Josée N., Layfield, Robert, Lazo, Pedro A., Le, Weidong, Le Cam, Laurent, Ledbetter, Daniel J., Lee, Alvin J.X., Lee, Byung-Wan, Lee, Gyun Min, Lee, Jongdae, lee, Ju-hyun, Lee, Michael, Lee, Myung-Shik, Lee, Sug Hyung, Leeuwenburgh, Christiaan, Legembre, Patrick, Legouis, Renaud, Lehmann, Michael, Lei, Huan-Yao, Lei, Qun-Ying, Leib, David A., Leiro, José, Lemasters, John J., Lemoine, Antoinette, Lesniak, Maciej S., Lev, Dina, Levenson, Victor V., Levine, Beth, Levy, Efrat, Li, Faqiang, Li, Jun-Lin, Li, Lian, Li, Sheng, Li, Weijie, Li, Xue-Jun, Li, Yan-Bo, Li, Yi-Ping, Liang, Chengyu, Liang, Qiangrong, Liao, Yung-Feng, Liberski, Pawel P., Lieberman, Andrew, Lim, Hyunjung J., Lim, Kah-Leong, Lim, Kyu, Lin, Chiou-Feng, Lin, Fu-Cheng, Lin, Jian, Lin, Jiandie D., Lin, Kui, Lin, Wan-Wan, Lin, Weei-Chin, Lin, Yi-Ling, Linden, Rafael, Lingor, Paul, Lippincott-Schwartz, Jennifer, Lisanti, Michael P., Liton, Paloma B., Liu, Bo, Liu, Chun-Feng, Liu, Kaiyu, Liu, Leyuan, Liu, Qiong A., Liu, Wei, Liu, Young-Chau, Liu, Yule, Lockshin, Richard A., Lok, Chun-Nam, Lonial, Sagar, Loos, Benjamin, Lopez-Berestein, Gabriel, López-Otín, Carlos, Lossi, Laura, Lotze, Michael T., Low, Peter, Lu, Binfeng, Lu, Bingwei, Lu, Bo, Lu, Zhen, Luciano, Fréderic, Lukacs, Nicholas W., Lund, Anders H., Lynch-Day, Melinda A., Ma, Yong, Macian, Fernando, MacKeigan, Jeff P., Macleod, Kay F., Madeo, Frank, Maiuri, Luigi, Maiuri, Maria Chiara, Malagoli, Davide, Malicdan, May Christine V., Malorni, Walter, Man, Na, Mandelkow, Eva-Maria, Manon, Stephen, Manov, Irena, Mao, Kai, Mao, Xiang, Mao, Zixu, Marambaud, Philippe, Marazziti, Daniela, Marcel, Yves L., Marchbank, Katie, Marchetti, Piero, Marciniak, Stefan J., Marcondes, Mateus, Mardi, Mohsen, Marfe, Gabriella, Mariño, Guillermo, Markaki, Maria, Marten, Mark R., Martin, Seamus J., Martinand-Mari, Camille, Martinet, Wim, Martinez-Vicente, Marta, Masini, Matilde, Matarrese, Paola, Matsuo, Saburo, Matteoni, Raffaele, Mayer, Andreas, Mazure, Nathalie M., McConkey, David J., McConnell, Melanie J., McDermott, Catherine, McDonald, Christine, McInerney, Gerald M., McKenna, Sharon L., McLaughlin, BethAnn, McLean, Pamela J., McMaster, Christopher R., McQuibban, G. Angus, Meijer, Alfred J., Meisler, Miriam H., Meléndez, Alicia, Melia, Thomas J., Melino, Gerry, Mena, Maria A., Menendez, Javier A., Menna-Barreto, Rubem F. S., Menon, Manoj B., Menzies, Fiona M., Mercer, Carol A., Merighi, Adalberto, Merry, Diane E., Meschini, Stefania, Meyer, Christian G., Meyer, Thomas F., Miao, Chao-Yu, Miao, Jun-Ying, Michels, Paul A.M., Michiels, Carine, Mijaljica, Dalibor, Milojkovic, Ana, Minucci, Saverio, Miracco, Clelia, Miranti, Cindy K., Mitroulis, Ioannis, Miyazawa, Keisuke, Mizushima, Noboru, Mograbi, Baharia, Mohseni, Simin, Molero, Xavier, Mollereau, Bertrand, Mollinedo, Faustino, Momoi, Takashi, Monastyrska, Iryna, Monick, Martha M., Monteiro, Mervyn J., Moore, Michael N., Mora, Rodrigo, Moreau, Kevin, Moreira, Paula I., Moriyasu, Yuji, Moscat, Jorge, Mostowy, Serge, Mottram, Jeremy C., Motyl, Tomasz, Moussa, Charbel E.-H., Müller, Sylke, Muller, Sylviane, Münger, Karl, Münz, Christian, Murphy, Leon O., Murphy, Maureen E., Musarò, Antonio, Mysorekar, Indira, Nagata, Eiichiro, Nagata, Kazuhiro, Nahimana, Aimable, Nair, Usha, Nakagawa, Toshiyuki, Nakahira, Kiichi, Nakano, Hiroyasu, Nakatogawa, Hitoshi, Nanjundan, Meera, Naqvi, Naweed I., Narendra, Derek P., Narita, Masashi, Navarro, Miguel, Nawrocki, Steffan T., Nazarko, Taras Y., Nemchenko, Andriy, Netea, Mihai G., Neufeld, Thomas P., Ney, Paul A., Nezis, Ioannis P., Nguyen, Huu Phuc, Nie, Daotai, Nishino, Ichizo, Nislow, Corey, Nixon, Ralph A., Noda, Takeshi, Noegel, Angelika A., Nogalska, Anna, Noguchi, Satoru, Notterpek, Lucia, Novak, Ivana, Nozaki, Tomoyoshi, Nukina, Nobuyuki, Nürnberger, Thorsten, Nyfeler, Beat, Obara, Keisuke, Oberley, Terry D., Oddo, Salvatore, Ogawa, Michinaga, Ohashi, Toya, Okamoto, Koji, Oleinick, Nancy L., Oliver, F. Javier, Olsen, Laura J., Olsson, Stefan, Opota, Onya, Osborne, Timothy F., Ostrander, Gary K., Otsu, Kinya, Ou, Jing-hsiung James, Ouimet, Mireille, Overholtzer, Michael, Ozpolat, Bulent, Paganetti, Paolo, Pagnini, Ugo, Pallet, Nicolas, Palmer, Glen E., Palumbo, Camilla, Pan, Tianhong, Panaretakis, Theocharis, Pandey, Udai Bhan, Papackova, Zuzana, Papassideri, Issidora, Paris, Irmgard, Park, Junsoo, Park, Ohkmae K., Parys, Jan B., Parzych, Katherine R., Patschan, Susann, Patterson, Cam, Pattingre, Sophie, Pawelek, John M., Peng, Jianxin, Perlmutter, David H., Perrotta, Ida, Perry, George, Pervaiz, Shazib, Peter, Matthias, Peters, Godefridus J., Petersen, Morten, Petrovski, Goran, Phang, James M., Piacentini, Mauro, Pierre, Philippe, Pierrefite-Carle, Valérie, Pierron, Gérard, Pinkas-Kramarski, Ronit, Piras, Antonio, Piri, Natik, Platanias, Leonidas C., Pöggeler, Stefanie, Poirot, Marc, Poletti, Angelo, Poüs, Christian, Pozuelo-Rubio, Mercedes, Prætorius-Ibba, Mette, Prasad, Anil, Prescott, Mark, Priault, Muriel, Produit-Zengaffinen, Nathalie, Progulske-Fox, Ann, Proikas-Cezanne, Tassula, Przedborski, Serge, Przyklenk, Karin, Puertollano, Rosa, Puyal, Julien, Qian, Shu-Bing, Qin, Liang, Qin, Zheng-Hong, Quaggin, Susan E., Raben, Nina, Rabinowich, Hannah, Rabkin, Simon W., Rahman, Irfan, Rami, Abdelhaq, Ramm, Georg, Randall, Glenn, Randow, Felix, Rao, V. Ashutosh, Rathmell, Jeffrey C., Ravikumar, Brinda, Ray, Swapan K., Reed, Bruce H., Reed, John C., Reggiori, Fulvio, Régnier-Vigouroux, Anne, Reichert, Andreas S., Reiners, John J., Reiter, Russel J., Ren, Jun, Revuelta, José L., Rhodes, Christopher J., Ritis, Konstantinos, Rizzo, Elizete, Robbins, Jeffrey, Roberge, Michel, Roca, Hernan, Roccheri, Maria C., Rocchi, Stephane, Rodemann, H. Peter, Rodríguez de Córdoba, Santiago, Rohrer, Bärbel, Roninson, Igor B., Rosen, Kirill, Rost-Roszkowska, Magdalena M., Rouis, Mustapha, Rouschop, Kasper M.A., Rovetta, Francesca, Rubin, Brian P., Rubinsztein, David C., Ruckdeschel, Klaus, Rucker, Edmund B., Rudich, Assaf, Rudolf, Emil, Ruiz-Opazo, Nelson, Russo, Rossella, Rusten, Tor Erik, Ryan, Kevin M., Ryter, Stefan W., Sabatini, David M., Sadoshima, Junichi, Saha, Tapas, Saitoh, Tatsuya, Sakagami, Hiroshi, Sakai, Yasuyoshi, Salekdeh, Ghasem Hoseini, Salomoni, Paolo, Salvaterra, Paul M., Salvesen, Guy, Salvioli, Rosa, Sanchez, Anthony M.J., Sánchez-Alcázar, José A., Sánchez-Prieto, Ricardo, Sandri, Marco, Sankar, Uma, Sansanwal, Poonam, Santambrogio, Laura, Saran, Shweta, Sarkar, Sovan, Sarwal, Minnie, Sasakawa, Chihiro, Sasnauskiene, Ausra, Sass, Miklós, Sato, Ken, Sato, Miyuki, Schapira, Anthony H.V., Scharl, Michael, Schätzl, Hermann M., Scheper, Wiep, Schiaffino, Stefano, Schneider, Claudio, Schneider, Marion E., Schneider-Stock, Regine, Schoenlein, Patricia V., Schorderet, Daniel F., Schüller, Christoph, Schwartz, Gary K., Scorrano, Luca, Sealy, Linda, Seglen, Per O., Segura-Aguilar, Juan, Seiliez, Iban, Seleverstov, Oleksandr, Sell, Christian, Seo, Jong Bok, Separovic, Duska, Setaluri, Vijayasaradhi, Setoguchi, Takao, Settembre, Carmine, Shacka, John J., Shanmugam, Mala, Shapiro, Irving M., Shaulian, Eitan, Shaw, Reuben J., Shelhamer, James H., Shen, Han-Ming, Shen, Wei-Chiang, Sheng, Zu-Hang, Shi, Yang, Shibuya, Kenichi, Shidoji, Yoshihiro, Shieh, Jeng-Jer, Shih, Chwen-Ming, Shimada, Yohta, Shimizu, Shigeomi, Shintani, Takahiro, Shirihai, Orian S., Shore, Gordon C., Sibirny, Andriy A., Sidhu, Stan B., Sikorska, Beata, Silva-Zacarin, Elaine C.M., Simmons, Alison, Simon, Anna Katharina, Simon, Hans-Uwe, Simone, Cristiano, Simonsen, Anne, Sinclair, David A., Singh, Rajat, Sinha, Debasish, Sinicrope, Frank A., Sirko, Agnieszka, Siu, Parco M., Sivridis, Efthimios, Skop, Vojtech, Skulachev, Vladimir P., Slack, Ruth S., Smaili, Soraya S., Smith, Duncan R., Soengas, Maria S., Soldati, Thierry, Song, Xueqin, Sood, Anil K., Soong, Tuck Wah, Sotgia, Federica, Spector, Stephen A., Spies, Claudia D., Springer, Wolfdieter, Srinivasula, Srinivasa M., Stefanis, Leonidas, Steffan, Joan S., Stendel, Ruediger, Stenmark, Harald, Stephanou, Anastasis, Stern, Stephan T., Sternberg, Cinthya, Stork, Björn, Strålfors, Peter, Subauste, Carlos S., Sui, Xinbing, Sulzer, David, Sun, Jiaren, Sun, Shi-Yong, Sun, Zhi-Jun, Sung, Joseph J.Y., Suzuki, Kuninori, Suzuki, Toshihiko, Swanson, Michele S., Swanton, Charles, Sweeney, Sean T., Sy, Lai-King, Szabadkai, György, Tabas, Ira, Taegtmeyer, Heinrich, Tafani, Marco, Takács-Vellai, Krisztina, Takano, Yoshitaka, Takegawa, Kaoru, Takemura, Genzou, Takeshita, Fumihiko, Talbot, Nicholas J., Tan, Kevin S.W., Tanaka, Keiji, Tanaka, Kozo, Tang, Daolin, Tang, Dingzhong, Tanida, Isei, Tannous, Bakhos A., Tavernarakis, Nektarios, Taylor, Graham S., Taylor, Gregory A., Taylor, J. Paul, Terada, Lance S., Terman, Alexei, Tettamanti, Gianluca, Thevissen, Karin, Thompson, Craig B., Thorburn, Andrew, Thumm, Michael, Tian, FengFeng, Tian, Yuan, Tocchini-Valentini, Glauco, Tolkovsky, Aviva M., Tomino, Yasuhiko, Tönges, Lars, Tooze, Sharon A., Tournier, Cathy, Tower, John, Towns, Roberto, Trajkovic, Vladimir, Travassos, Leonardo H., Tsai, Ting-Fen, Tschan, Mario P., Tsubata, Takeshi, Tsung, Allan, Turk, Boris, Turner, Lorianne S., Tyagi, Suresh C., Uchiyama, Yasuo, Ueno, Takashi, Umekawa, Midori, Umemiya-Shirafuji, Rika, Unni, Vivek K., Vaccaro, Maria I., Valente, Enza Maria, Van den Berghe, Greet, van der Klei, Ida J., van Doorn, Wouter G., van Dyk, Linda F., van Egmond, Marjolein, van Grunsven, Leo A., Vandenabeele, Peter, Vandenberghe, Wim P., Vanhorebeek, Ilse, Vaquero, Eva C., Velasco, Guillermo, Vellai, Tibor, Vicencio, José Miguel, Vierstra, Richard D., Vila, Miquel, Vindis, Cécile, Viola, Giampietro, Viscomi, Maria Teresa, Voitsekhovskaja, Olga V., von Haefen, Clarissa, Votruba, Marcela, Wada, Keiji, Wade-Martins, Richard, Walker, Cheryl L., Walsh, Craig M., Walter, Jochen, Wan, Xiang-Bo, Wang, Aimin, Wang, Chenguang, Wang, Dawei, Wang, Fan, Wang, Fen, Wang, Guanghui, Wang, Haichao, Wang, Hong-Gang, Wang, Horng-Dar, Wang, Jin, Wang, Ke, Wang, Mei, Wang, Richard C., Wang, Xinglong, Wang, Xiujie J., Wang, Ying-Jan, Wang, Yipeng, Wang, Zhen-Bo, Wang, Zhigang Charles, Wang, Zhinong, Wansink, Derick G., Ward, Diane M., Watada, Hirotaka, Waters, Sarah L., Webster, Paul, Wei, Lixin, Weihl, Conrad C., Weiss, William A., Welford, Scott M., Wen, Long-Ping, Whitehouse, Caroline A., Whitton, J. Lindsay, Whitworth, Alexander J., Wileman, Tom, Wiley, John W., Wilkinson, Simon, Willbold, Dieter, Williams, Roger L., Williamson, Peter R., Wouters, Bradly G., Wu, Chenghan, Wu, Dao-Cheng, Wu, William K.K., Wyttenbach, Andreas, Xavier, Ramnik J., Xi, Zhijun, Xia, Pu, Xiao, Gengfu, Xie, Zhiping, Xie, Zhonglin, Xu, Da-zhi, Xu, Jianzhen, Xu, Liang, Xu, Xiaolei, Yamamoto, Ai, Yamamoto, Akitsugu, Yamashina, Shunhei, Yamashita, Michiaki, Yan, Xianghua, Yanagida, Mitsuhiro, Yang, Dun-Sheng, Yang, Elizabeth, Yang, Jin-Ming, Yang, Shi Yu, Yang, Wannian, Yang, Wei Yuan, Yang, Zhifen, Yao, Meng-Chao, Yao, Tso-Pang, Yeganeh, Behzad, Yen, Wei-Lien, Yin, Jia-Jing, Yin, Xiao-Ming, Yoo, Ook-Joon, Yoon, Gyesoon, Yoon, Seung-Yong, Yorimitsu, Tomohiro, Yoshikawa, Yuko, Yoshimori, Tamotsu, Yoshimoto, Kohki, You, Ho Jin, Youle, Richard J., Younes, Anas, Yu, Li, Yu, Long, Yu, Seong-Woon, Yu, Wai Haung, Yuan, Zhi-Min, Yue, Zhenyu, Yun, Cheol-Heui, Yuzaki, Michisuke, Zabirnyk, Olga, Silva-Zacarin, Elaine, Zacks, David, Zacksenhaus, Eldad, Zaffaroni, Nadia, Zakeri, Zahra, Zeh, Herbert J., Zeitlin, Scott O., Zhang, Hong, Zhang, Hui-Ling, Zhang, Jianhua, Zhang, Jing-Pu, Zhang, Lin, Zhang, Long, Zhang, Ming-Yong, Zhang, Xu Dong, Zhao, Mantong, Zhao, Yi-Fang, Zhao, Ying, Zhao, Zhizhuang J., Zheng, Xiaoxiang, Zhivotovsky, Boris, Zhong, Qing, Zhou, Cong-Zhao, Zhu, Changlian, Zhu, Wei-Guo, Zhu, Xiao-Feng, Zhu, Xiongwei, Zhu, Yuangang, Zoladek, Teresa, Zong, Wei-Xing, Zorzano, Antonio, Zschocke, Jürgen, and Zuckerbraun, Brian
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Published: 2012
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123. Design and Testing of a Simulation Framework for Dosimetric Motion Studies Integrating an Anthropomorphic Computational Phantom into Four-dimensional Monte Carlo

Author: Riboldi, M., Chen, G. T. Y., Baroni, G., Paganetti, H., and Seco, J.
Abstract: We have designed a simulation framework for motion studies in radiation therapy by integrating the anthropomorphic NCAT phantom into a 4D Monte Carlo dose calculation engine based on DPM. Representing an artifact-free environment, the system can be used to identify class solutions as a function of geometric and dosimetric parameters. A pilot dynamic conformal study for three lesions (~ 2.0 cm) in the right lung was performed (70 Gy prescription dose). Tumor motion changed as a function of tumor location, according to the anthropomorphic deformable motion model. Conformal plans were simulated with 0 to 2 cm margin for the aperture, with additional 0.5 cm for beam penumbra. The dosimetric effects of intensity modulated radiotherapy (IMRT) vs. conformal treatments were compared in a static case. Results show that the Monte Carlo simulation framework can model tumor tracking in deformable anatomy with high accuracy, providing absolute doses for IMRT and conformal radiation therapy. A target underdosage of up to 3.67 Gy (lower lung) was highlighted in the composite dose distribution mapped at exhale. Such effects depend on tumor location and treatment margin and are affected by lung deformation and ribcage motion. In summary, the complexity in the irradiation of moving targets has been reduced to a controlled simulation environment, where several treatment options can be accurately modeled and quantified The implemented tools will be utilized for extensive motion study in lung/liver irradiation.
Published: 2008
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124. Consequences of Individual N-glycan Deletions and of Proteasomal Inhibition on Secretion of Active BACE

Author: Vanoni, Omar, Paganetti, Paolo, and Molinari, Maurizio
Abstract: BACE is an aspartic protease involved in the production of a toxic peptide accumulating in the brain of Alzheimer's disease patients. After attainment of the native structure in the endoplasmic reticulum (ER), BACE is released into the secretory pathway. To better understand the mechanisms regulating protein biogenesis in the mammalian ER, we determined the fate of five variants of soluble BACE with 4, 3, 2, 1, or 0 N-linked glycans. The number of N-glycans displayed on BACE correlated directly with folding and secretion rates and with the yield of active BACE harvested from the cell culture media. Addition of a single N-glycan was sufficient to recruit the calnexin chaperone system and/or for oligosaccharide de-glucosylation by the ER-resident α-glucosidase II. Addition of 1–4 N-glycans progressively enhanced the dissociation rate from BiP and reduced the propensity of newly synthesized BACE to enter aberrant soluble and insoluble aggregates. Finally, inhibition of the proteasome increased the yield of active BACE. This shows that active protein normally targeted for destruction can be diverted for secretion, as if for BACE the quality control system would be acting too stringently in the ER lumen, thus causing loss of functional polypeptides.
Published: 2008
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125. Monte Carlo calculations for absolute dosimetry to determine machine outputs for proton therapy fields

Author: Paganetti, Harald
Abstract: The prescribed dose in radiation therapy has to be converted into machine monitor units for patient treatment. This is done routinely for each spread-out Bragg peak (SOBP) field either by calibration measurements, by using analytical algorithms or by relying on empirical data. At the Northeast Proton Therapy Center, a monitor unit corresponds to a fixed amount of charge collected in a segmented transmission ionization chamber inside the treatment head. The goal of this work was to use a detailed Monte Carlo model of the treatment head to calculate the dose delivered to the patient as a function of ionization chamber reading, i.e. to yield absolute dose in patients in terms of machine monitor units. The results show excellent agreement with measurements. For 50 SOBP fields considered in this study, the mean absolute difference between the experimental and the calculated value is 1.5%, where [?]50% of the fields agree within 1%. This is within the uncertainties of the data. The Monte Carlo method has advantages over analytical algorithms because it takes into account scattered and secondary radiation, does not rely on empirical parameters, and provides a tool to study the influence of parts of the treatment head on the ionization chamber reading. Compared to experimental methods the Monte Carlo method has the advantage of being able to verify the dose in the patient geometry.
Published: 2006

126. The prediction of output factors for spread-out proton Bragg peak fields in clinical practice

Author: Kooy, Hanne HMK, Rosenthal, Stanley SJR, Engelsman, Martijn ME, Mazal, Alejandro AM, Slopsema, Roelf RLS, Paganetti, Harald HP, and Flanz, Jacob JBF
Abstract: The reliable prediction of output factors for spread-out proton Bragg peak (SOBP) fields in clinical practice remained unrealized due to a lack of a consistent theoretical framework and the great number of variables introduced by the mechanical devices necessary for the production of such fields. These limitations necessitated an almost exclusive reliance on manual calibration for individual fields and empirical, ad hoc, models. We recently reported on a theoretical framework for the prediction of output factors for such fields. In this work, we describe the implementation of this framework in our clinical practice. In our practice, we use a treatment delivery nozzle that uses a limited, and constant, set of mechanical devices to produce SOBP fields over the full extent of clinical penetration depths, or ranges, and modulation widths. This use of a limited set of mechanical devices allows us to unfold the physical effects that affect the output factor. We describe these effects and their incorporation into the theoretical framework. We describe the calibration and protocol for SOBP fields, the effects of apertures and range-compensators and the use of output factors in the treatment planning process.
Published: 2005

127. Simulation of organ-specific patient effective dose due to secondary neutrons in proton radiation treatment

Author: Jiang, Hongyu HJ, Wang, Brian BW, Xu, X XGX, Suit, Herman HDS, and Paganetti, Harald HP
Abstract: Cancer patients undergoing radiation treatment are exposed to high doses to the target (tumour), intermediate doses to adjacent tissues and low doses from scattered radiation to all parts of the body. In the case of proton therapy, secondary neutrons generated in the accelerator head and inside the patient reach many areas in the patient body. Due to the improved efficacy of management of cancer patients, the number of long term survivors post-radiation treatment is increasing substantially. This results in concern about the risk of radiation-induced cancer appearing at late post-treatment times. This paper presents a case study to determine the effective dose from secondary neutrons in patients undergoing proton treatment. A whole-body patient model, VIP-Man, was employed as the patient model. The geometry dataset generated from studies made on VIP-Man was implemented into the GEANT4 Monte Carlo code. Two proton treatment plans for tumours in the lung and paranasal sinus were simulated. The organ doses and ICRP-60 radiation and tissue weighting factors were used to calculate the effective dose. Results show whole body effective doses for the two proton plans of 0.162 Sv and 0.0266 Sv, respectively, to which the major contributor is due to neutrons from the proton treatment nozzle. There is a substantial difference among organs depending on the treatment site.
Published: 2005

128. Structure-Based Design, Synthesis, and Memapsin 2 (BACE) Inhibitory Activity of Carbocyclic and Heterocyclic Peptidomimetics

Author: Hanessian, S., Yun, H., Hou, Y., Yang, G., Bayrakdarian, M., Therrien, E., Moitessier, N., Roggo, S., Veenstra, S., Tintelnot-Blomley, M., Rondeau, J.-M., Ostermeier, C., Strauss, A., Ramage, P., Paganetti, P., Neumann, U., and Betschart, C.
Abstract: Molecular modeling based on the X-ray crystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM99-2) of BACE led to the design and synthesis of a series of constrained P1 analogues. A cyclopentane ring was incorporated in 1 spanning the P1 Ala methyl group and the adjacent methylene carbon atom of the chain. Progressive truncation at the P2−P4 sites led to a potent truncated analogue 5 with good selectivity over Cathepsin D. Using the same backbone replacement concept, a series of cyclopentane, cyclopentanone, tetrahydrofuran, pyrrolidine, and pyrrolidinone analogues were synthesized with considerable variation at the P and P sites. The cyclopentanone and 2-pyrrolidinone analogues 45 and 57 showed low nM BACE inhibition. X-ray cocrystal structures of two analogues 5 and 45 revealed excellent convergence with the original inhibitor 1 structure while providing new insights into other interactions which could be exploited for future modifications.
Published: 2005

129. 4D Monte Carlo simulation of proton beam scanning: modelling of variations in time and space to study the interplay between scanning pattern and time-dependent patient geometry

Author: Paganetti, H HP, Jiang, H HJ, and Trofimov, A AT
Abstract: When dosimetric effects in time-dependent geometries are studied, usually either the results of individual three-dimensional (3D) calculations are combined or probability-based approaches are applied. These methods may become cumbersome and time-consuming if high time resolution is required or if the geometry is complex. Furthermore, it is difficult to study double-dynamic systems, e.g., to investigate the influence of time-dependent beam delivery (i.e., magnetically moving beam spots in proton beam scanning) on the dose deposition in a moving target. We recently introduced the technique of 4D Monte Carlo dose calculation to model continuously changing geometries. In intensity modulated proton therapy, dose is delivered by individual pristine Bragg curves. Dose spots are positioned in the patient by varying magnetic field and beam energy. If the movement of these dose spots occurs during significant respiratory motion, interplay effects can take place. Because of the inhomogeneity of individual subfields, the consequences of motion can be more severe than in conventional proton therapy. We demonstrate how the technique of 4D Monte Carlo can be used to study interplay effects in proton beam scanning. Time-dependent beam delivery to a changing patient geometry is simulated in a single 4D dose calculation. Interplay effects between respiratory motion and beam scanning speed are demonstrated.
Published: 2005

130. Significance and Implementation of RBE Variations in Proton Beam Therapy

Author: Paganetti, H.
Abstract: Key to radiation therapy is to apply a high tumor-destroying dose while protecting healthy tissue, especially near organs at risk. To optimize treatment for ion therapy not the dose but the dose multiplied by the relative biological effectiveness (RBE) is decisive. Proton therapy has been based on the use of a generic RBE, which is applied to all treatments independent of dose/fraction, position in the spread-out Bragg peak (SOBP), initial beam energy or the particular tissue. Dependencies of the RBE on various physical and biological properties are disregarded. The variability of RBE in clinical situations is believed to be within 10–20%. This is in the same range of effects that receive high attention these days, i.e., patient set-up uncertainties, organ motion effects, and dose calculation accuracy all affecting proton as well as conventional radiation therapy. Elevated RBE values can be expected near the edges of the target, thus probably near critical structures. This is because the edges show lower doses and, depending on the treatment plan, may be identical with the beam's distal edge, where dose is deposited in part by high-LET protons. We assess the rationale for the continued use of a generic RBE and whether the magnitude of RBE variation with treatment parameters is small relative to our abilities to determine RBE's. Two aspects have to be considered. Firstly, the available information from experimental studies and secondly, our ability to calculate RBE values for a given treatment plan based on parameters extracted from such experiments.We analyzed published RBE values for in vitro and in vivo endpoints. The values for cell survival in vitro indicate a substantial spread between the diverse cell lines. The average value at mid SOBP over all dose levels is ≈ 1.2 in vitro and ≈ 1.1 in vivo. Both in vitro and in vivo data indicate a statistically significant increase in RBE for lower doses per fraction, which is much smaller for in vivo systems. The experimental in vivo data indicate that continued employment of a generic RBE value of 1.1 is reasonable. At present, there seems to be too much uncertainty in the RBE value for any human tissue to propose RBE values specific for tissue, dose/fraction, etc. There is a clear need for prospective assessments of normal tissue reactions in proton irradiated patients and determinations of RBE values for several late responding tissues in animal systems, especially as a function of dose in the range of 1–4 Gy. However, there is a measurable increase in RBE over the terminal few mm of the SOBP, which results in an extension of the bio-effective range of the beam of a few mm. This needs to be considered in treatment planning, particularly for single field plans or for an end of range in or close to a critical structure.To assess our ability to calculate RBE values we studied two approaches, which are both based on the track structure theory of radiation action. RBE calculations are difficult since both the physical input parameters, i.e., LET distributions, and, even more so, the biological input parameters, i.e., local cellular response, have to be known with high accuracy. Track structure theory provides a basis for predicting dose-response curves for particle irradiation. However, designed for heavy ion applications the models show weaknesses in the prediction of proton radiation effects. We conclude that, at present, RBE modeling in treatment planning involves significant uncertainties. To incorporate RBE variations in treatment planning there has to be a reliable biological model to calculate RBE values based on the physical characteristics of the radiation field and based on well-known biological input parameters. In order to do detailed model calculations more experimental data, in particular for in vivo endpoints, are needed.
Published: 2003
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131. A Splice Variant of β-Secretase Deficient in the Amyloidogenic Processing of the Amyloid Precursor Protein*

Author: Bodendorf, Ursula, Fischer, Frauke, Bodian, Dale, Multhaup, Gerd, and Paganetti, Paolo
Abstract: β-Secretase (BACE) initiates the amyloidogenic processing of the amyloid precursor protein leading to the generation of the β-amyloid, the main component of Alzheimer's disease senile plaques. BACE is a type I transmembrane aspartyl protease of 501 amino acids. Here we describe a novel BACE mRNA lacking 132 base pairs that is expressed in the pancreas but not in the brain. Sequence alignment indicates that the deleted fragment matches the terminal two-thirds of exon 3. The new BACE variant is short of a 44-amino acid region located between the two catalytic aspartyl residues. Accordingly, a 50-kDa form of BACE (BACE457) is detected in the human pancreas. When expressed in cells, BACE457 colocalizes with the marker for the endoplasmic reticulum BiP. Moreover, BACE457 remains in a proenzymatic and endoglycosidase H-sensitive state, suggesting that its transport along the secretory pathway is blocked at the level of the endoplasmic reticulum. Notably, this novel form of BACE does not contribute to the processing of the amyloid precursor protein. Our findings suggest that tissue-specific splicing of the BACE mRNA may explain the observation that in the human pancreas robust transcription of the BACE gene does not translate into recovered enzymatic activity.
Published: 2001
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132. HERMAN D. SUIT, MD, DPhil1929–2022A Giant of Modern Radiation Oncology

Author: Kirsch, David G., Willett, Christopher, Paganetti, Harald, Schuemann, Jan, Held, Kathryn D., and Jain, Rakesh
Published: 2022
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133. Uncertainties and correction methods when modeling passive scattering proton therapy treatment heads with Monte Carlo

Author: Bednarz, Bryan, Lu, Hsiao-ming, Engelsman, Martijn, and Paganetti, Harald
Abstract: Monte Carlo models of proton therapy treatment heads are being used to improve beam delivery systems and to calculate the radiation field for patient dose calculations. The achievable accuracy of the model depends on the exact knowledge of the treatment head geometry and time structure, the material characteristics, and the underlying physics. This work aimed at studying the uncertainties in treatment head simulations for passive scattering proton therapy. The sensitivities of spread-out Bragg peak (SOBP) dose distributions on material densities, mean ionization potentials, initial proton beam energy spread and spot size were investigated. An improved understanding of the nature of these parameters may help to improve agreement between calculated and measured SOBP dose distributions and to ensure that the range, modulation width, and uniformity are within clinical tolerance levels. Furthermore, we present a method to make small corrections to the uniformity of spread-out Bragg peaks by utilizing the time structure of the beam delivery. In addition, we re-commissioned the models of the two proton treatment heads located at our facility using the aforementioned correction methods presented in this paper.
Published: 2011
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134. The mTOR Kinase Inhibitor Everolimus Decreases S6 Kinase Phosphorylation But Fails to Reduce Mutant Huntingtin Levels in Brain and is not Neuroprotective in the R6/2 Mouse Model of Huntington's Disease

Author: Fox, Jonathan H, Connor, Teal, Dorsey, Kate, Kama, Jibrin A, Bleckmann, Dorothee, Betschart, Claudia, Hoyer, Daniel, Frentzel, Stefan, Paganetti, Paolo, Chopra, Vanita, DiFiglia, Marian, and Hersch, Steven M.
Abstract: Background: Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion within the huntingtin gene. Mutant huntingtin protein misfolds and accumulates within neurons where it mediates its toxic effects. Promoting mutant huntingtin clearance by activating macroautophagy is one approach for treating Huntington's disease (HD). In this study, we evaluated the mTOR kinase inhibitor and macroautophagy promoting drug everolimus in the R6/2 mouse model of HD. Results: Everolimus decreased phosphorylation of the mTOR target protein S6 kinase indicating brain penetration. However, everolimus did not activate brain macroautophagy as measured by LC3B Western blot analysis. Everolimus protected against early declines in motor performance; however, we found no evidence for neuroprotection as determined by brain pathology. In muscle but not brain, everolimus significantly decreased soluble mutant huntingtin levels. Conclusions: Our data suggests that beneficial behavioral effects of everolimus in R6/2 mice result primarily from effects on muscle. Even though everolimus significantly modulated its target brain S6 kinase, this did not decrease mutant huntingtin levels or provide neuroprotection.
Published: 2010
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135. Distinct processing of endogenous and overexpressed recombinant presenilin 1

Author: Baumann, K., Paganetti, P. A., Sturchler-Pierrat, C., Wong, C., Hartmann, H., Cescato, R., Frey, P., Yankner, B. A., Sommer, B., and Staufenbiel, M.
Published: 1997
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136. Calculation of Relative Biological Effectiveness for Proton Beams Using Biological Weighting Functions

Author: Paganetti, H., Olko, P., Kobus, H., Becker, R., Schmitz, T., Walgorski, M. P. R., Filges, D., and Mueller-Gaertner, H.-W.
Published: 1997
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137. Lack of -amyloid production in M19 cells deficient in site 2 processing of the sterol regulatory element binding proteins

Author: Manni, M. E., Cescato, R., and Paganetti, P. A.
Published: 1998
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138. Calpain inhibitor I decreases A4 secretion from human embryonal kidney cells expressing -amyloid precursor protein carrying the APP670/671 double mutation

Author: Klafki, H.-W., Paganetti, P. A., Sommer, B., and Staufenbiel, M.
Published: 1995
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139. The Carboxyl Termini of β-Amyloid Peptides 1-40 and 1-42 Are Generated by Distinct γ-Secretase Activities*

Author: Klafki, H.-W., Abramowski, D., Swoboda, R., Paganetti, P.A., and Staufenbiel, M.
Abstract: We have studied the effects of peptide aldehyde protease inhibitors on the secretion of β-amyloid peptide 1-40 (Aβ(1-40)) and Aβ(1-42) by HEK 293 and COS-1 cells expressing β-amyloid precursor protein with the Swedish double mutation. A multiphasic SDS-polyacrylamide gel electrophoresis system was used for the discrimination of Aβ(1-40) and Aβ(1-42). Calpain inhibitor I, carbobenzoxyl-Leu-Leu-leucinal, and calpeptin were found to reduce the amount of Aβ(1-40) released into the medium in a dose-dependent manner. The reduction of Aβ(1-40) after treatment with 50 μMcalpain inhibitor I or 5 μMcarbobenzoxyl-Leu-Leu-leucinal was accompanied by a slight increase of Aβ(1-42) released into the medium. These observations suggest that the cleavages at residues 40 and 42 are accomplished by different enzyme activities.
Published: 1996
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140. Glioblastoma infiltration into central nervous system tissue in vitro: involvement of a metalloprotease.

Author: Paganetti, P A, Caroni, P, and Schwab, M E
Abstract: Differentiated oligodendrocytes and central nervous system (CNS) myelin are nonpermissive substrates for neurite growth and for cell attachment and spreading. This property is due to the presence of membrane-bound inhibitory proteins of 35 and 250 kD and is specifically neutralized by monoclonal antibody IN-1 (Caroni, P., and M. E. Schwab. 1988. Neuron. 1:85-96). Using rat optic nerve explants, CNS frozen sections, cultured oligodendrocytes or CNS myelin, we show here that highly invasive CNS tumor line (C6 glioblastoma) was not inhibited by these myelin-associated inhibitory components. Lack of inhibition was due to a specific mechanism as the metalloenzyme blocker 1,10-phenanthroline and two synthetic dipeptides containing metalloprotease-blocking sequences (gly-phe, tyr-tyr) specifically impaired C6 cell spreading on CNS myelin. In the presence of these inhibitors, C6 cells were affected by the IN-1-sensitive inhibitors in the same manner as control cells, e.g., 3T3 fibroblasts or B16 melanomas. Specific blockers of the serine, cysteine, and aspartyl protease classes had no effect. C6 cell spreading on inhibitor-free substrates such as CNS gray matter, peripheral nervous system myelin, glass, or poly-D-lysine was not sensitive to 1,10-phenanthroline. The nonpermissive substrate properties of CNS myelin were strongly reduced by incubation with a plasma membrane fraction prepared from C6 cells. This reduction was sensitive to the same inhibitors of metalloproteases. In our in vitro model for CNS white matter invasion, cell infiltration of optic nerve explants, which occurred with C6 cells but not with 3T3 fibroblasts or B16 melanomas, was impaired by the presence of the metalloprotease blockers. These results suggest that C6 cell infiltrative behavior in CNS white matter in vitro occurs by means of a metalloproteolytic activity, which probably acts on the myelin-associated inhibitory substrates.
Published: 1988
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141. Lack of β‐amyloid production in M19 cells deficient in site 2 processing of the sterol regulatory element binding proteins

Author: Manni, Mara E, Cescato, Renzo, and Paganetti, Paolo A
Abstract: The processing of the amyloid precursor protein (APP) and the sterol regulatory element binding protein show remarkable analogies. Following a first lumenal cleavage, both proteins undergo a cleavage within the transmembrane domain by enzymatic activities named γ‐secretase and S2P, respectively. We analyzed the processing of APP in the mutant Chinese hamster ovary (CHO) cell line M19 which lacks the S2P gene encoding for a putative metalloprotease. In these cells, we were not able to detect any β‐amyloid production from endogenous or transiently overexpressed APP, although the transport of APP along the secretory pathway, its processing by α‐ and β‐secretase, as well as its secretion were normal. This strongly suggests that the γ‐secretase cleavage in M19 cells is severely impaired.
Published: 1998
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142. The probability of prompt and delayed fission of muonic237Np

Author: Schrieder, W., David, P., Hänscheid, H., Konijn, J., de Laat, C. T. A. M., Paganetti, H., Petitjean, C., Reist, H. W., Risse, F., Rösel, Ch., Schaller, L. A., Schellenberg, L., Sinha, A. K., Taal, A., and Trautmann, N.
Abstract: Fission fragments from the reaction237Np(µ-,?,f) have been measured in coincidence with muonic X-rays. The efficiency of the fission fragment detector is determined from (µ-,?,f)-data of the same experiment. The total fission probability perµ-stopPt has been measured as well as the fission probabilities Pf of the non-radiative muonic (3d?1s)- and (2p?1s)-transitions; the latter has been divided into two parts leading to different mean excitation energiesE:Pt=(54±17)%,Pf(3d?1s)=(41±21)%,Pf(2p?1s,E=6.218 MeV)=(61±19)%, andPf(2p?1s,E=6.525 MeV)=(57±18)%. The influence of the muon on the fission barrier is discussed. The fission probability after muon capture is compared with a calculated value using a distribution of nuclear excitation energies following muon capture and the fission probability as measured in a238U(3He,af)-reaction.
Published: 1991
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143. Effect of alkalizing agents on the processing of the -amyloid precursor protein

Author: Schrader-Fischer, G. and Paganetti, P. A.
Published: 1996
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144. Delayed muon induced fission of209Bi and the role of meson-exchange currents

Author: Paganetti, H., David, P., Hänscheid, H., Konijn, J., de Laat, C. T. A. M., Lourens, W., Risse, F., Rösel, Ch., Schaller, L. A., and Taal, A.
Abstract: The probability for delayed muon induced fission of209Bi has been determined from a (µ-,f1f2) measurement. The measured fission probability Pf=(4.2±0.7)×10-5 is compared with theoretical predictions. The high fission threshold reaction seems well suited for studying the influence of two-body meson-exchange currents in nuclear muon capture.
Published: 1992
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145. The carboxyl termini of beta-amyloid peptides 1-40 and 1-42 are generated by distinct gamma-secretase activities.

Author: Klafki, H, Abramowski, D, Swoboda, R, Paganetti, P A, and Staufenbiel, M
Abstract: We have studied the effects of peptide aldehyde protease inhibitors on the secretion of beta-amyloid peptide 1-40 (Abeta(1-40)) and Abeta(1-42) by HEK 293 and COS-1 cells expressing beta-amyloid precursor protein with the Swedish double mutation. A multiphasic SDS-polyacrylamide gel electrophoresis system was used for the discrimination of Abeta(1-40) and Abeta(1-42). Calpain inhibitor I, carbobenzoxyl-Leu-Leu-leucinal, and calpeptin were found to reduce the amount of Abeta(1-40) released into the medium in a dose-dependent manner. The reduction of Abeta(1-40) after treatment with 50 microM calpain inhibitor I or 5 microM carbobenzoxyl-Leu-Leu-leucinal was accompanied by a slight increase of Abeta(1-42) released into the medium. These observations suggest that the cleavages at residues 40 and 42 are accomplished by different enzyme activities.
Published: 1996

146. Intracellular accumulation of beta-amyloid in cells expressing the Swedish mutant amyloid precursor protein.

Author: Martin, B L, Schrader-Fischer, G, Busciglio, J, Duke, M, Paganetti, P, and Yankner, B A
Abstract: beta-Amyloid (beta A) is a normal metabolic product of the amyloid precursor protein (APP) that accumulates in senile plaques in Alzheimer's disease. Cells that express the Swedish mutant APP (Sw-APP) associated with early onset Alzheimer's disease overproduce beta A. In this report, we show that expression of Sw-APP gives rise to cell-associated beta A, which is not detected in cells that express wild-type APP. Cell-associated beta A is rapidly generated, is trypsin-resistant, and is not derived from beta A uptake, indicating that it is generated from intracellular processing of Sw-APP. Intracellular and secreted beta A are produced with different kinetics. The generation of intracellular beta A is partially resistant to monensin and a 20 degrees C temperature block but is completely inhibited by brefeldin A, suggesting that it occurs in the Golgi complex. Monensin, brefeldin A, and a 20 degrees C temperature block almost completely inhibit beta A secretion without causing increased cellular retention of beta A, suggesting that secreted beta A is generated in a post-Golgi compartment. These results suggest that the metabolism of Sw-APP gives rise to intracellular and secreted forms of beta A through distinct processing pathways. Pathological conditions may therefore alter both the level and sites of accumulation of beta A. It remains to be determined whether the intracellular form of beta A plays a role in the formation of amyloid plaques.
Published: 1995

147. Hadamard transform imager and imaging spectrometer

Author: Swift, Roderick D., Wattson, Richard B., Decker, John A., Paganetti, Ralph, and Harwit, Martin
Abstract: An imager and a spectrometric imager, which achieve multiplexing by the use of binary optical encoding masks, have been built and tested. The masks are based on orthogonal, pseudorandom digital codes derived from Hadamard matrices. The spatial (and/or spectral) data are therefore obtained in the form of a Hadamard transform of the spatial (and/or spectral) scene; computer algorithms are used to decode the data and reconstruct images of the original scene. The hardware, algorithms processing and display facility are described. A number of spatial and spatial/spectral images, obtained in the laboratory, are presented. We present an analysis of the situations for which the multiplex advantage may be gained and of the limitations of the technique. Potential applications of the spectrometric imager are discussed. The spectrometric imager is covered by U.S. Patent 3,720,469 assigned to Spectral Imaging Inc., Concord, Mass.
Published: 1976

148. Intracellular Accumulation of β-Amyloid in Cells Expressing the Swedish Mutant Amyloid Precursor Protein (*)

Author: Martin, Bronwyn L., Schrader-Fischer, Gesine, Busciglio, Jorge, Duke, Maraid, Paganetti, Paolo, and Yankner, Bruce A.
Abstract: β-Amyloid (βA) is a normal metabolic product of the amyloid precursor protein (APP) that accumulates in senile plaques in Alzheimer's disease. Cells that express the Swedish mutant APP (Sw-APP) associated with early onset Alzheimer's disease overproduce βA. In this report, we show that expression of Sw-APP gives rise to cell-associated βA, which is not detected in cells that express wild-type APP. Cell-associated βA is rapidly generated, is trypsin-resistant, and is not derived from βA uptake, indicating that it is generated from intracellular processing of Sw-APP. Intracellular and secreted βA are produced with different kinetics. The generation of intracellular βA is partially resistant to monensin and a 20°C temperature block but is completely inhibited by brefeldin A, suggesting that it occurs in the Golgi complex. Monensin, brefeldin A, and a 20°C temperature block almost completely inhibit βA secretion without causing increased cellular retention of βA, suggesting that secreted βA is generated in a post-Golgi compartment. These results suggest that the metabolism of Sw-APP gives rise to intracellular and secreted forms of βA through distinct processing pathways. Pathological conditions may therefore alter both the level and sites of accumulation of βA. It remains to be determined whether the intracellular form of βA plays a role in the formation of amyloid plaques.
Published: 1995
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149. Predicting In Vitro Cancer Cell Survival Based on Measurable Cell Characteristics

Author: Oesten, Hakan, Neubeck, Cläre von, Jakob, Aline, Enghardt, Wolfgang, Krause, Mechthild, McMahon, Stephen J., Grassberger, Clemens, Paganetti, Harald, and Lühr, Armin
Published: 2019
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150. Why Is Proton Beam Therapy So Controversial?

Author: Paganetti, Harald and Zietman, Anthony
Published: 2015
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