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39 results on '"Bahceci I"'

1. Effects of infliximab against carbon tetrachloride-induced spleen toxicity in rats.

Author

BAHCECI, I., TUMKAYA, L., MERCANTEPE, T., YILMAZ, H., IBIK, Y. E., DURAN, O. F., and ARSLAN, N.

Abstract

OBJECTIVE: Carbon tetrachloride (CCl4) is a non-polar molecule used in industry in grain curing, insect-killing and especially in the production of chlorofluorocarbons. It is estimated that an average of 70,000 industry workers in Europe are exposed to this toxic compound. MATERIALS AND METHODS: Twenty-four male Sprague-Dawley rats were randomly allocated into four groups: control group (saline only, Group I), infliximab (INF) group (Group II), CCl4 group (Group III) and CCl4+INF group (Group IV). RESULTS: While there was an increase in the numerical density of CD3, CD68, and CD200R positive T lymphocytes and macrophages in the CCl4 administration group (p=0.000), this was not the case in the CCl4+INF administration group (p=0.000). CONCLUSIONS: TNF-a inhibitors have a protective effect against CCl4-induced spleen toxicity/inflammation as seen by the reduction in CD3, CD68, CD200R positive T lymphocytes and macrophages. [ABSTRACT FROM AUTHOR]

Published
2023

2. Oncogenic signaling pathways in the Cancer Genome Atlas

Author

Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., Chakravarty, D., Daian, F., Gao, Q., Bailey, M. H., Liang, W. -W., Foltz, S. M., Shmulevich, I., Ding, L., Heins, Z., Ochoa, A., Gross, B., Gao, J., Zhang, H., Kundra, R., Kandoth, C., Bahceci, I., Dervishi, L., Doğrusöz, Uğur, Zhou, W., Shen, H., Laird, P. W., Way, G. P., Greene, C. S., Liang, H., Xiao, Y., Wang, C., Iavarone, A., Berger, A. H., Bivona, T. G., Lazar, A. J., Hammer, G. D., Giordano, T., Kwong, L. N., McArthur, G., Huang, C., Tward, A. D., Frederick, M. J., McCormick, F., Meyerson, M., Caesar-Johnson, S. J., Demchok, J. A., Felau, I., Kasapi, M., Ferguson, M. L., Hutter, C. M., Sofia, H. J., Tarnuzzer, R., Wang, Z., Yang, L., Zenklusen, J. C., Zhang, J. J., Chudamani, S., Liu, J., Lolla, L., Naresh, R., Pihl, T., Sun, Q., Wan, Y., Wu, Y., Cho, J., DeFreitas, T., Frazer, S., Gehlenborg, N., Getz, G., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Meier, S., Noble, M. S., Saksena, G., Voet, D., Bernard, B., Chambwe, N., Dhankani, V., Knijnenburg, T., Kramer, R., Leinonen, K., Liu, Y., Miller, M., Reynolds, S., Thorsson, V., Zhang, W., Akbani, R., Broom, B. M., Hegde, A. M., Ju, Z., Kanchi, R. S., Korkut, A., Li, J., Ling, S., Liu W., Lu, Y., Mills, G. B., Ng, K. -S., Rao, A., Ryan, M., Wang, J., Weinstein, J. N., Zhang, J., Abeshouse, A., de, Bruijn, I., Gross, B. E., Heins, Z. J., La, K., Ladanyi, M., Nissan, M. G., Phillips, S. M., Reznik, E., Sander, C., Schultz, N., Sheridan, R., Sumer, S. O., Sun, Y., Taylor, B. S., Anur, P., Peto, M., Spellman, P., Benz, C., Stuart, J. M., Wong, C. K., Yau, C., Hayes, D. N., Parker, J. S., Wilkerson, M. D., Ally, A., Balasundaram, M., Bowlby, R., Brooks, D., Carlsen, R., Chuah, E., Dhalla, N., Holt, R., Jones, S. J. M., Kasaian, K., Lee, D., Ma, Y., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Mungall, K., Robertson, A. G., Sadeghi, S., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Tse, K., Wong, T., Berger, A. C., Beroukhim, R., Cherniack, A. D., Cibulskis, C., Gabriel, S. B., Gao, G. F., Ha, G., Schumacher, S. E., Shih, J., Kucherlapati, M. H., Kucherlapati, R. S., Baylin, S., Cope, L., Danilova, L., Bootwalla, M. S., Lai, P. H., Maglinte, D. T., Van, Den, Berg, D. J., Weisenberger, D. J., Auman, J. T., Balu, S., Bodenheimer, T., Fan, C., Hoadley, K. A., Hoyle, A. P., Jefferys, S. R., Jones, C. D., Meng, S., Mieczkowski, P. A., Mose, L. E., Perou, A. H., Perou, C. M., Roach, J., Shi, Y., Simons, J. V., Skelly, T., Soloway, M. G., Tan, D., Veluvolu, U., Fan, H., Hinoue, T., Bellair, M., Chang, K., Covington, K., Creighton, C. J., Dinh, H., Doddapaneni, H., Donehower, L. A., Drummond, J., Gibbs, R. A., Glenn, R., Hale, W., Han, Y., Hu, J., Korchina, V., Lee, S., Lewis, L., Li, W., Liu, X., Morgan, M., Morton, D., Muzny, D., Santibanez, J., Sheth, M., Shinbrot, E., Wang, L., Wang, M., Wheeler, D. A., Xi, L., Zhao, F., Hess, J., Appelbaum, E. L., Bailey, M., Cordes, M. G., Fronick, C. C., Fulton, L. A., Fulton, R. S., Mardis, E. R., McLellan, M. D., Miller, C. A., Schmidt, H. K., Wilson, R. K., Crain, D., Curley, E., Gardner, J., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, C., Shelton, T., Sherman, M., Thompson, E., Yena, P., Bowen, J., Gastier-Foster, J. M., Gerken, M., Leraas, K. M., Lichtenberg, T. M., Ramirez, N. C., Wise, L., Zmuda, E., Corcoran, N., Costello, T., Hovens, C., Carvalho, A. L., de, Carvalho, A. C., Fregnani, J. H., Longatto-Filho, A., Reis, R. M., Scapulatempo-Neto, C., Silveira, H. C. S., Vidal, D. O., Burnette, A., Eschbacher, J., Hermes, B., Noss, A., Singh, R., Anderson, M. L., Castro, P. D., Ittmann, M., Huntsman, D., Kohl, B., Le, X., Thorp, R., Andry, C., Duffy, E. R., Lyadov, V., Paklina, O., Setdikova, G., Shabunin, A., Tavobilov, M., McPherson, C., Warnick, R., Berkowitz, R., Cramer, D., Feltmate, C., Horowitz, N., Kibel, A., Muto, M., Raut, C. P., Malykh, A., Barnholtz-Sloan, J. S., Barrett, W., Devine, K., Fulop, J., Ostrom, Q. T., Shimmel, K., Wolinsky, Y., Sloan, A. E., De, Rose, A., Giuliante, F., Goodman, M., Karlan, B. Y., Hagedorn, C. H., Eckman, J., Harr, J., Myers, J., Tucker, K., Zach, L. A., Deyarmin, B., Hu, H., Kvecher, L., Larson, C., Mural, R. J., Somiari, S., Vicha, A., Zelinka, T., Bennett, J., Iacocca, M., Rabeno, B., Swanson, P., Latour, M., Lacombe, L., Têtu, B., Bergeron, A., McGraw, M., Staugaitis, S. M., Chabot, J., Hibshoosh, H., Sepulveda, A., Su, T., Wang, T., Potapova, O., Voronina, O., Desjardins, L., Mariani, O., Roman-Roman, S., Sastre, X., Stern, M. -H., Cheng, F., Signoretti, S., Berchuck, A., Bigner, D., Lipp, E., Marks, J., McCall, S., McLendon, R., Secord, A., Sharp, A., Behera, M., Brat, D. J., Chen, A., Delman, K., Force, S., Khuri, F., Magliocca, K., Maithel, S., Olson, J. J., Owonikoko, T., Pickens, A., Ramalingam, S., Shin, D. M., Sica, G., Van, Meir, E. G., Eijckenboom, W., Gillis, A., Korpershoek, E., Looijenga, L., Oosterhuis, W., Stoop, H., van, Kessel, K. E., Zwarthoff, E. C., Calatozzolo, C., Cuppini, L., Cuzzubbo, S., DiMeco, F., Finocchiaro, G., Mattei, L., Perin, A., Pollo, B., Chen, C., Houck, J., Lohavanichbutr, P., Hartmann, A., Stoehr, C., Stoehr, R., Taubert, H., Wach, S., Wullich, B., Kycler, W., Murawa, D., Wiznerowicz, M., Chung, K., Edenfield, W. J., Martin, J., Baudin, E., Bubley, G., Bueno, R., De, Rienzo, A., Richards, W. G., Kalkanis, S., Mikkelsen, T., Noushmehr, H., Scarpace, L., Girard, N., Aymerich, M., Campo, E., Giné, E., Guillermo, A. L., Van, Bang, N., Hanh, P. T., Phu, B. D., Tang, Y., Colman, H., Evason, K., Dottino, P. R., Martignetti, J. A., Gabra, H., Juhl, H., Akeredolu, T., Stepa, S., Hoon, D., Ahn, K., Kang, K. J., Beuschlein, F., Breggia, A., Birrer, M., Bell, D., Borad, M., Bryce, A. H., Castle, E., Chandan, V., Cheville, J., Copland, J. A., Farnell, M., Flotte, T., Giama, N., Ho, T., Kendrick, M., Kocher, J. -P., Kopp, K., Moser, C., Nagorney, D., O'Brien, D., O'Neill, B. P., Patel, T., Petersen, G., Que, F., Rivera, M., Roberts, L., Smallridge, R., Smyrk, T., Stanton, M., Thompson, R. H., Torbenson, M., Yang, J. D., Zhang, L., Brimo, F., Ajani, J. A., Gonzalez, A. M. A., Behrens, C., Bondaruk, J., Broaddus, R., Czerniak, B., Esmaeli, B., Fujimoto, J., Gershenwald, J., Guo, C., Logothetis, C., Meric-Bernstam, F., Moran, C., Ramondetta, L., Rice, D., Sood, A., Tamboli, P., Thompson, T., Troncoso, P., Tsao, A., Wistuba, I., Carter, C., Haydu, L., Hersey, P., Jakrot, V., Kakavand, H., Kefford, R., Lee, K., Long, G., Mann, G., Quinn, M., Saw, R., Scolyer, R., Shannon, K., Spillane, A., Stretch, J., Synott, M., Thompson, J., Wilmott, J., Al-Ahmadie, H., Chan, T. A., Ghossein, R., Gopalan, A., Levine, D. A., Reuter, V., Singer, S., Singh, B., Tien, N. V., Broudy, T., Mirsaidi, C., Nair, P., Drwiega, P., Miller, J., Smith, J., Zaren, H., Park, J. -W., Hung, N. P., Kebebew, E., Linehan, W. M., Metwalli, A. R., Pacak, K., Pinto, P. A., Schiffman, M., Schmidt, L. S., Vocke, C. D., Wentzensen, N., Worrell, R., Yang, H., Moncrieff, M., Goparaju, C., Melamed, J., Pass, H., Botnariuc, N., Caraman, I., Cernat, M., Chemencedji, I., Clipca, A., Doruc, S., Gorincioi, G., Mura, S., Pirtac, M., Stancul, I., Tcaciuc, D., Albert, M., Alexopoulou, I., Arnaout, A., Bartlett, J., Engel, J., Gilbert, S., Parfitt, J., Sekhon, H., Thomas, G., Rassl, D. M., Rintoul, R. C., Bifulco, C., Tamakawa, R., Urba, W., Hayward, N., Timmers, H., Antenucci, A., Facciolo, F., Grazi, G., Marino, M., Merola, R., de, Krijger, R., Gimenez-Roqueplo, A. -P., Piché, A., Chevalier, S., McKercher, G., Birsoy, K., Barnett, G., Brewer, C., Farver, C., Naska, T., Pennell, N. A., Raymond, D., Schilero, C., Smolenski, K., Williams, F., Morrison, C., Borgia, J. A., Liptay, M. J., Pool, M., Seder, C. W., Junker, K., Omberg, L., Dinkin, M., Manikhas, G., Alvaro, D., Bragazzi, M. C., Cardinale, V., Carpino, G., Gaudio, E., Chesla, D., Cottingham, S., Dubina, M., Moiseenko, F., Dhanasekaran, R., Becker, K. -F., Janssen, K. -P., Slotta-Huspenina, J., Abdel-Rahman, M. H., Aziz, D., Bell, S., Cebulla, C. M., Davis, A., Duell, R., Elder, J. B., Hilty, J., Kumar, B., Lang, J., Lehman, N. L., Mandt, R., Nguyen, P., Pilarski, R., Rai, K., Schoenfield, L., Senecal, K., Wakely, P., Hansen, P., Lechan, R., Powers, J., Tischler, A., Grizzle, W. E., Sexton, K. C., Kastl, A., Henderson, J., Porten, S., Waldmann, J., Fassnacht, M., Asa, S. L., Schadendorf, D., Couce, M., Graefen, M., Huland, H., Sauter, G., Schlomm, T., Simon, R., Tennstedt, P., Olabode, O., Nelson, M., Bathe, O., Carroll, P. R., Chan, J. M., Disaia, P., Glenn, P., Kelley, R. K., Landen, C. N., Phillips, J., Prados, M., Simko, J., Smith-McCune, K., VandenBerg, S., Roggin, K., Fehrenbach, A., Kendler, A., Sifri, S., Steele, R., Jimeno, A., Carey, F., Forgie, I., Mannelli, M., Carney, M., Hernandez, B., Campos, B., Herold-Mende, C., Jungk, C., Unterberg, A., von, Deimling, A., Bossler, A., Galbraith, J., Jacobus, L., Knudson, M., Knutson, T., Ma, D., Milhem, M., Sigmund, R., Godwin, A. K., Madan, R., Rosenthal, H. G., Adebamowo, C., Adebamowo, S. N., Boussioutas, A., Beer, D., Mes-Masson, A. -M., Saad, F., Bocklage, T., Landrum, L., Mannel, R., Moore, K., Moxley, K., Postier, R., Walker, J., Zuna, R., Feldman, M., Valdivieso, F., Dhir, R., Luketich, J., Pinero, E. M. M., Quintero-Aguilo, M., Carlotti, C. G., Jr., Dos, Santos, J. S., Kemp, R., Sankarankuty, A., Tirapelli, D., Catto, J., Agnew, K., Swisher, E., Creaney, J., Robinson, B., Shelley, C. S., Godwin, E. M., Kendall, S., Shipman, C., Bradford, C., Carey, T., Haddad, A., Moyer, J., Peterson, L., Prince, M., Rozek, L., Wolf, G., Bowman, R., Fong, K. M., Yang, I., Korst, R., Rathmell, W. K., Fantacone-Campbell, J. L., Hooke, J. A., Kovatich, A. J., Shriver, C. D., DiPersio, J., Drake, B., Govindan, R., Heath, S., Ley, T., Van, Tine, B., Westervelt, P., Rubin, M. A., Lee, J. I., Aredes, N. D., Mariamidze, A., Van, Allen, E. M., Ciriello, G., The, Cancer, Genome, Atlas, Research, Network.tif, Doğrusöz, Uğur, Cancer Genome Atlas Research Network, Caesar-Johnson, S.J., Demchok, J.A., Felau, I., Kasapi, M., Ferguson, M.L., Hutter, C.M., Sofia, H.J., Tarnuzzer, R., Wang, Z., Yang, L., Zenklusen, J.C., Zhang, J.J., Chudamani, S., Liu, J., Lolla, L., Naresh, R., Pihl, T., Sun, Q., Wan, Y., Wu, Y., Cho, J., DeFreitas, T., Frazer, S., Gehlenborg, N., Getz, G., Heiman, D.I., Kim, J., Lawrence, M.S., Lin, P., Meier, S., Noble, M.S., Saksena, G., Voet, D., Zhang, H., Bernard, B., Chambwe, N., Dhankani, V., Knijnenburg, T., Kramer, R., Leinonen, K., Liu, Y., Miller, M., Reynolds, S., Shmulevich, I., Thorsson, V., Zhang, W., Akbani, R., Broom, B.M., Hegde, A.M., Ju, Z., Kanchi, R.S., Korkut, A., Li, J., Liang, H., Ling, S., Liu, W., Lu, Y., Mills, G.B., Ng, K.S., Rao, A., Ryan, M., Wang, J., Weinstein, J.N., Zhang, J., Abeshouse, A., Armenia, J., Chakravarty, D., Chatila, W.K., de Bruijn, I., Gao, J., Gross, B.E., Heins, Z.J., Kundra, R., La, K., Ladanyi, M., Luna, A., Nissan, M.G., Ochoa, A., Phillips, S.M., Reznik, E., Sanchez-Vega, F., Sander, C., Schultz, N., Sheridan, R., Sumer, S.O., Sun, Y., Taylor, B.S., Anur, P., Peto, M., Spellman, P., Benz, C., Stuart, J.M., Wong, C.K., Yau, C., Hayes, D.N., Parker, J.S., Wilkerson, M.D., Ally, A., Balasundaram, M., Bowlby, R., Brooks, D., Carlsen, R., Chuah, E., Dhalla, N., Holt, R., Jones, SJM, Kasaian, K., Lee, D., Ma, Y., Marra, M.A., Mayo, M., Moore, R.A., Mungall, A.J., Mungall, K., Robertson, A.G., Sadeghi, S., Schein, J.E., Sipahimalani, P., Tam, A., Thiessen, N., Tse, K., Wong, T., Berger, A.C., Beroukhim, R., Cherniack, A.D., Cibulskis, C., Gabriel, S.B., Gao, G.F., Ha, G., Meyerson, M., Schumacher, S.E., Shih, J., Kucherlapati, M.H., Kucherlapati, R.S., Baylin, S., Cope, L., Danilova, L., Bootwalla, M.S., Lai, P.H., Maglinte, D.T., Van Den Berg, D.J., Weisenberger, D.J., Auman, J.T., Balu, S., Bodenheimer, T., Fan, C., Hoadley, K.A., Hoyle, A.P., Jefferys, S.R., Jones, C.D., Meng, S., Mieczkowski, P.A., Mose, L.E., Perou, A.H., Perou, C.M., Roach, J., Shi, Y., Simons, J.V., Skelly, T., Soloway, M.G., Tan, D., Veluvolu, U., Fan, H., Hinoue, T., Laird, P.W., Shen, H., Zhou, W., Bellair, M., Chang, K., Covington, K., Creighton, C.J., Dinh, H., Doddapaneni, H., Donehower, L.A., Drummond, J., Gibbs, R.A., Glenn, R., Hale, W., Han, Y., Hu, J., Korchina, V., Lee, S., Lewis, L., Li, W., Liu, X., Morgan, M., Morton, D., Muzny, D., Santibanez, J., Sheth, M., Shinbrot, E., Wang, L., Wang, M., Wheeler, D.A., Xi, L., Zhao, F., Hess, J., Appelbaum, E.L., Bailey, M., Cordes, M.G., Ding, L., Fronick, C.C., Fulton, L.A., Fulton, R.S., Kandoth, C., Mardis, E.R., McLellan, M.D., Miller, C.A., Schmidt, H.K., Wilson, R.K., Crain, D., Curley, E., Gardner, J., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, C., Shelton, T., Sherman, M., Thompson, E., Yena, P., Bowen, J., Gastier-Foster, J.M., Gerken, M., Leraas, K.M., Lichtenberg, T.M., Ramirez, N.C., Wise, L., Zmuda, E., Corcoran, N., Costello, T., Hovens, C., Carvalho, A.L., de Carvalho, A.C., Fregnani, J.H., Longatto-Filho, A., Reis, R.M., Scapulatempo-Neto, C., Silveira, HCS, Vidal, D.O., Burnette, A., Eschbacher, J., Hermes, B., Noss, A., Singh, R., Anderson, M.L., Castro, P.D., Ittmann, M., Huntsman, D., Kohl, B., Le, X., Thorp, R., Andry, C., Duffy, E.R., Lyadov, V., Paklina, O., Setdikova, G., Shabunin, A., Tavobilov, M., McPherson, C., Warnick, R., Berkowitz, R., Cramer, D., Feltmate, C., Horowitz, N., Kibel, A., Muto, M., Raut, C.P., Malykh, A., Barnholtz-Sloan, J.S., Barrett, W., Devine, K., Fulop, J., Ostrom, Q.T., Shimmel, K., Wolinsky, Y., Sloan, A.E., De Rose, A., Giuliante, F., Goodman, M., Karlan, B.Y., Hagedorn, C.H., Eckman, J., Harr, J., Myers, J., Tucker, K., Zach, L.A., Deyarmin, B., Hu, H., Kvecher, L., Larson, C., Mural, R.J., Somiari, S., Vicha, A., Zelinka, T., Bennett, J., Iacocca, M., Rabeno, B., Swanson, P., Latour, M., Lacombe, L., Têtu, B., Bergeron, A., McGraw, M., Staugaitis, S.M., Chabot, J., Hibshoosh, H., Sepulveda, A., Su, T., Wang, T., Potapova, O., Voronina, O., Desjardins, L., Mariani, O., Roman-Roman, S., Sastre, X., Stern, M.H., Cheng, F., Signoretti, S., Berchuck, A., Bigner, D., Lipp, E., Marks, J., McCall, S., McLendon, R., Secord, A., Sharp, A., Behera, M., Brat, D.J., Chen, A., Delman, K., Force, S., Khuri, F., Magliocca, K., Maithel, S., Olson, J.J., Owonikoko, T., Pickens, A., Ramalingam, S., Shin, D.M., Sica, G., Van Meir, E.G., Eijckenboom, W., Gillis, A., Korpershoek, E., Looijenga, L., Oosterhuis, W., Stoop, H., van Kessel, K.E., Zwarthoff, E.C., Calatozzolo, C., Cuppini, L., Cuzzubbo, S., DiMeco, F., Finocchiaro, G., Mattei, L., Perin, A., Pollo, B., Chen, C., Houck, J., Lohavanichbutr, P., Hartmann, A., Stoehr, C., Stoehr, R., Taubert, H., Wach, S., Wullich, B., Kycler, W., Murawa, D., Wiznerowicz, M., Chung, K., Edenfield, W.J., Martin, J., Baudin, E., Bubley, G., Bueno, R., De Rienzo, A., Richards, W.G., Kalkanis, S., Mikkelsen, T., Noushmehr, H., Scarpace, L., Girard, N., Aymerich, M., Campo, E., Giné, E., Guillermo, A.L., Van Bang, N., Hanh, P.T., Phu, B.D., Tang, Y., Colman, H., Evason, K., Dottino, P.R., Martignetti, J.A., Gabra, H., Juhl, H., Akeredolu, T., Stepa, S., Hoon, D., Ahn, K., Kang, K.J., Beuschlein, F., Breggia, A., Birrer, M., Bell, D., Borad, M., Bryce, A.H., Castle, E., Chandan, V., Cheville, J., Copland, J.A., Farnell, M., Flotte, T., Giama, N., Ho, T., Kendrick, M., Kocher, J.P., Kopp, K., Moser, C., Nagorney, D., O'Brien, D., O'Neill, B.P., Patel, T., Petersen, G., Que, F., Rivera, M., Roberts, L., Smallridge, R., Smyrk, T., Stanton, M., Thompson, R.H., Torbenson, M., Yang, J.D., Zhang, L., Brimo, F., Ajani, J.A., Gonzalez, AMA, Behrens, C., Bondaruk, J., Broaddus, R., Czerniak, B., Esmaeli, B., Fujimoto, J., Gershenwald, J., Guo, C., Lazar, A.J., Logothetis, C., Meric-Bernstam, F., Moran, C., Ramondetta, L., Rice, D., Sood, A., Tamboli, P., Thompson, T., Troncoso, P., Tsao, A., Wistuba, I., Carter, C., Haydu, L., Hersey, P., Jakrot, V., Kakavand, H., Kefford, R., Lee, K., Long, G., Mann, G., Quinn, M., Saw, R., Scolyer, R., Shannon, K., Spillane, A., Stretch, J., Synott, M., Thompson, J., Wilmott, J., Al-Ahmadie, H., Chan, T.A., Ghossein, R., Gopalan, A., Levine, D.A., Reuter, V., Singer, S., Singh, B., Tien, N.V., Broudy, T., Mirsaidi, C., Nair, P., Drwiega, P., Miller, J., Smith, J., Zaren, H., Park, J.W., Hung, N.P., Kebebew, E., Linehan, W.M., Metwalli, A.R., Pacak, K., Pinto, P.A., Schiffman, M., Schmidt, L.S., Vocke, C.D., Wentzensen, N., Worrell, R., Yang, H., Moncrieff, M., Goparaju, C., Melamed, J., Pass, H., Botnariuc, N., Caraman, I., Cernat, M., Chemencedji, I., Clipca, A., Doruc, S., Gorincioi, G., Mura, S., Pirtac, M., Stancul, I., Tcaciuc, D., Albert, M., Alexopoulou, I., Arnaout, A., Bartlett, J., Engel, J., Gilbert, S., Parfitt, J., Sekhon, H., Thomas, G., Rassl, D.M., Rintoul, R.C., Bifulco, 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S., Shin D.M., Sica G., Van Meir E.G., Eijckenboom W., Gillis A., Korpershoek E., Looijenga L., Oosterhuis W., Stoop H., van Kessel K.E., Zwarthoff E.C., Calatozzolo C., Cuppini L., Cuzzubbo S., DiMeco F., Finocchiaro G., Mattei L., Perin A., Pollo B., Chen C., Houck J., Lohavanichbutr P., Hartmann A., Stoehr C., Stoehr R., Taubert H., Wach S., Wullich B., Kycler W., Murawa D., Wiznerowicz M., Chung K., Edenfield W.J., Martin J., Baudin E., Bubley G., Bueno R., De Rienzo A., Richards W.G., Kalkanis S., Mikkelsen T., Noushmehr H., Scarpace L., Girard N., Aymerich M., Campo E., Gine E., Guillermo A.L., Van Bang N., Hanh P.T., Phu B.D., Tang Y., Colman H., Evason K., Dottino P.R., Martignetti J.A., Gabra H., Juhl H., Akeredolu T., Stepa S., Hoon D., Ahn K., Kang K.J., Beuschlein F., Breggia A., Birrer M., Bell D., Borad M., Bryce A.H., Castle E., Chandan V., Cheville J., Copland J.A., Farnell M., Flotte T., Giama N., Ho T., Kendrick M., Kocher J.-P., Kopp K., Moser C., Nagorney D., O'Brien D., O'Neill B.P., Patel T., Petersen G., Que F., Rivera M., Roberts L., Smallridge R., Smyrk T., Stanton M., Thompson R.H., Torbenson M., Yang J.D., Zhang L., Brimo F., Ajani J.A., Gonzalez A.M.A., Behrens C., Bondaruk J., Broaddus R., Czerniak B., Esmaeli B., Fujimoto J., Gershenwald J., Guo C., Logothetis C., Meric-Bernstam F., Moran C., Ramondetta L., Rice D., Sood A., Tamboli P., Thompson T., Troncoso P., Tsao A., Wistuba I., Carter C., Haydu L., Hersey P., Jakrot V., Kakavand H., Kefford R., Lee K., Long G., Mann G., Quinn M., Saw R., Scolyer R., Shannon K., Spillane A., Stretch J., Synott M., Thompson J., Wilmott J., Al-Ahmadie H., Chan T.A., Ghossein R., Gopalan A., Levine D.A., Reuter V., Singer S., Singh B., Tien N.V., Broudy T., Mirsaidi C., Nair P., Drwiega P., Miller J., Smith J., Zaren H., Park J.-W., Hung N.P., Kebebew E., Linehan W.M., Metwalli A.R., Pacak K., Pinto P.A., Schiffman M., Schmidt L.S., Vocke C.D., Wentzensen N., Worrell R., Yang H., Moncrieff M., Goparaju C., Melamed J., Pass H., Botnariuc N., Caraman I., Cernat M., Chemencedji I., Clipca A., Doruc S., Gorincioi G., Mura S., Pirtac M., Stancul I., Tcaciuc D., Albert M., Alexopoulou I., Arnaout A., Bartlett J., Engel J., Gilbert S., Parfitt J., Sekhon H., Thomas G., Rassl D.M., Rintoul R.C., Bifulco C., Tamakawa R., Urba W., Hayward N., Timmers H., Antenucci A., Facciolo F., Grazi G., Marino M., Merola R., de Krijger R., Gimenez-Roqueplo A.-P., Piche A., Chevalier S., McKercher G., Birsoy K., Barnett G., Brewer C., Farver C., Naska T., Pennell N.A., Raymond D., Schilero C., Smolenski K., Williams F., Morrison C., Borgia J.A., Liptay M.J., Pool M., Seder C.W., Junker K., Omberg L., Dinkin M., Manikhas G., Alvaro D., Bragazzi M.C., Cardinale V., Carpino G., Gaudio E., Chesla D., Cottingham S., Dubina M., Moiseenko F., Dhanasekaran R., Becker K.-F., Janssen K.-P., Slotta-Huspenina J., Abdel-Rahman M.H., Aziz D., Bell S., Cebulla C.M., Davis A., Duell R., Elder J.B., Hilty J., Kumar B., Lang J., Lehman N.L., Mandt R., Nguyen P., Pilarski R., Rai K., Schoenfield L., Senecal K., Wakely P., Hansen P., Lechan R., Powers J., Tischler A., Grizzle W.E., Sexton K.C., Kastl A., Henderson J., Porten S., Waldmann J., Fassnacht M., Asa S.L., Schadendorf D., Couce M., Graefen M., Huland H., Sauter G., Schlomm T., Simon R., Tennstedt P., Olabode O., Nelson M., Bathe O., Carroll P.R., Chan J.M., Disaia P., Glenn P., Kelley R.K., Landen C.N., Phillips J., Prados M., Simko J., Smith-McCune K., VandenBerg S., Roggin K., Fehrenbach A., Kendler A., Sifri S., Steele R., Jimeno A., Carey F., Forgie I., Mannelli M., Carney M., Hernandez B., Campos B., Herold-Mende C., Jungk C., Unterberg A., von Deimling A., Bossler A., Galbraith J., Jacobus L., Knudson M., Knutson T., Ma D., Milhem M., Sigmund R., Godwin A.K., Madan R., Rosenthal H.G., Adebamowo C., Adebamowo S.N., Boussioutas A., Beer D., Mes-Masson A.-M., Saad F., Bocklage T., Landrum L., Mannel R., Moore K., Moxley K., Postier R., Walker J., Zuna R., Feldman M., Valdivieso F., Dhir R., Luketich J., Pinero E.M.M., Quintero-Aguilo M., Carlotti C.G., Dos Santos J.S., Kemp R., Sankarankuty A., Tirapelli D., Catto J., Agnew K., Swisher E., Creaney J., Robinson B., Shelley C.S., Godwin E.M., Kendall S., Shipman C., Bradford C., Carey T., Haddad A., Moyer J., Peterson L., Prince M., Rozek L., Wolf G., Bowman R., Fong K.M., Yang I., Korst R., Rathmell W.K., Fantacone-Campbell J.L., Hooke J.A., Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Van Allen E.M., and Ciriello G.

Subjects
0301 basic medicine, cancer genome atlas, cancer genomics, combination therapy, pan-cancer, PanCanAtlas, precision oncology, signaling pathways, TCGA, therapeutics, whole exome sequencing, Signaling pathways, Somatic cell, Wnt Protein, Cancer Genome Atlas Research Network, Biochemistry, Medical and Health Sciences, Phosphatidylinositol 3-Kinases, Transforming Growth Factor beta, Neoplasms, Databases, Genetic, LS2_1, Cancer genomics, LS4_6, 610 Medicine & health, 11 Medical and Health Sciences, Cancer, biology, Wnt signaling pathway, cancer genomic, Precision oncology, Biological Sciences, Cell cycle, DNA methylation, Signal transduction, CICLO CELULAR, Life Sciences & Biomedicine, Genes, Neoplasm, Humans, Neoplasms/genetics, Neoplasms/pathology, Phosphatidylinositol 3-Kinases/genetics, Phosphatidylinositol 3-Kinases/metabolism, Signal Transduction/genetics, Transforming Growth Factor beta/genetics, Transforming Growth Factor beta/metabolism, Tumor Suppressor Protein p53/genetics, Tumor Suppressor Protein p53/metabolism, Wnt Proteins/genetics, Wnt Proteins/metabolism, Biotechnology, Human, Signal Transduction, signaling pathway, EXPRESSION, Biochemistry & Molecular Biology, GENES, Pan-cancer, Therapeutics, General Biochemistry, Genetics and Molecular Biology, NO, Databases, 03 medical and health sciences, Genetic, Genetics, Combination therapy, Protein kinase B, Gene, SIGNATURES, Cancer genome atlas, Science & Technology, LANDSCAPE, MUTATIONS, Biochemistry, Genetics and Molecular Biology(all), Human Genome, Whole exome sequencing, Cell Biology, Transforming growth factor beta, cancer genome atla, 06 Biological Sciences, COMPREHENSIVE MOLECULAR CHARACTERIZATION, Wnt Proteins, therapeutic, Good Health and Well Being, 030104 developmental biology, Genes, PanCanAtla, biology.protein, Cancer research, Neoplasm, Phosphatidylinositol 3-Kinase, Tumor Suppressor Protein p53, Digestive Diseases, Genetics and Molecular Biology(all), Developmental Biology
Abstract

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy. An integrated analysis of genetic alterations in 10 signaling pathways in >9,000 tumors profiled by TCGA highlights significant representation of individual and co-occurring actionable alterations in these pathways, suggesting opportunities for targeted and combination therapies. Michael Seiler, Peter G. Smith, Ping Zhu, Silvia Buonamici, and Lihua Yu are employees of H3 Biomedicine, Inc. Parts of this work are the subject of a patent application: WO2017040526 titled “Splice variants associated with neomorphic sf3b1 mutants.” Shouyoung Peng, Anant A. Agrawal, James Palacino, and Teng Teng are employees of H3 Biomedicine, Inc. Andrew D. Cherniack, Ashton C. Berger, and Galen F. Gao receive research support from Bayer Pharmaceuticals. Gordon B. Mills serves on the External Scientific Review Board of Astrazeneca. Anil Sood is on the Scientific Advisory Board for Kiyatec and is a shareholder in BioPath. Jonathan S. Serody receives funding from Merck, Inc. Kyle R. Covington is an employee of Castle Biosciences, Inc. Preethi H. Gunaratne is founder, CSO, and shareholder of NextmiRNA Therapeutics. Christina Yau is a part-time employee/consultant at NantOmics. Franz X. Schaub is an employee and shareholder of SEngine Precision Medicine, Inc. Carla Grandori is an employee, founder, and shareholder of SEngine Precision Medicine, Inc. Robert N. Eisenman is a member of the Scientific Advisory Boards and shareholder of Shenogen Pharma and Kronos Bio. Daniel J. Weisenberger is a consultant for Zymo Research Corporation. Joshua M. Stuart is the founder of Five3 Genomics and shareholder of NantOmics. Marc T. Goodman receives research support from Merck, Inc. Andrew J. Gentles is a consultant for Cibermed. Charles M. Perou is an equity stock holder, consultant, and Board of Directors member of BioClassifier and GeneCentric Diagnostics and is also listed as an inventor on patent applications on the Breast PAM50 and Lung Cancer Subtyping assays. Matthew Meyerson receives research support from Bayer Pharmaceuticals; is an equity holder in, consultant for, and Scientific Advisory Board chair for OrigiMed; and is an inventor of a patent for EGFR mutation diagnosis in lung cancer, licensed to LabCorp. Eduard Porta-Pardo is an inventor of a patent for domainXplorer. Han Liang is a shareholder and scientific advisor of Precision Scientific and Eagle Nebula. Da Yang is an inventor on a pending patent application describing the use of antisense oligonucleotides against specific lncRNA sequence as diagnostic and therapeutic tools. Yonghong Xiao was an employee and shareholder of TESARO, Inc. Bin Feng is an employee and shareholder of TESARO, Inc. Carter Van Waes received research funding for the study of IAP inhibitor ASTX660 through a Cooperative Agreement between NIDCD, NIH, and Astex Pharmaceuticals. Raunaq Malhotra is an employee and shareholder of Seven Bridges, Inc. Peter W. Laird serves on the Scientific Advisory Board for AnchorDx. Joel Tepper is a consultant at EMD Serono. Kenneth Wang serves on the Advisory Board for Boston Scientific, Microtech, and Olympus. Andrea Califano is a founder, shareholder, and advisory board member of DarwinHealth, Inc. and a shareholder and advisory board member of Tempus, Inc. Toni K. Choueiri serves as needed on advisory boards for Bristol-Myers Squibb, Merck, and Roche. Lawrence Kwong receives research support from Array BioPharma. Sharon E. Plon is a member of the Scientific Advisory Board for Baylor Genetics Laboratory. Beth Y. Karlan serves on the Advisory Board of Invitae.

Published
2018
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3. Prolidase activity and oxidative stress in patients with major depressive disorder

Author

Mh, Kokacya, Bahceci B, Bahceci I, Ar, Dilek, Recep Dokuyucu, RTEÜ, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, Bahçeci, Bülent, Bahçeci, İlkay, and Dilek, Aziz Ramazan

Subjects
Adult, Male, MDD, Depressive Disorder, Major, Dipeptidases, Proline, Major depressive disorder, behavioral disciplines and activities, Oxidative Stress, Prolidase activity, Oxidative stress, mental disorders, Humans, Female, prolidase activity - oxidative stress - major depressive disorder - MDD - proline
Abstract

Dokuyucu, Recep/0000-0001-7881-8871 WOS: 000346149600003 PubMed: 25377365 Background: the aim of the current study was to determine whether the serum prolidase levels are associated with the etiopathogenesis of depression. Subjects and methods: This study included 29 patients with major depressive disorder (MDD), who were consecutively recruited from the psychiatric outpatient clinic, and 30 healthy individuals recruited from the general community. Each patient underwent a detailed diagnostic evaluation by two psychiatrists using the Structured Clinical Interview for DSM-IV (SCID-I). Serum prolidase activity and oxidative parameters were measured in the patient and control groups. the severity of depressive symptoms was assessed using the Hamilton Depression Rating Scale. Results: Serum prolidase level was significantly higher in patients with MDD compared to healthy subjects (p

Published
2014

15. Prolidase activity and oxidative stress in patients with schizophrenia: A preliminary study

Author

Bahceci, B., Bagcioglu, E., Kokacya, M. H., Dilek, A. R., Bahceci, I., Salih Selek, RTEÜ, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, Bahçeci, Bülent, Dilek, Aziz Ramazan, and Bahçeci, İlkay

Subjects
Glutamat, Prolidase activity, Proline, Schizophrenia
Abstract

Selek, Salih/0000-0001-5197-5682 WOS: 000349195700005 PubMed: 25842545 Objective: To determine whether serum prolidase levels are associated with the etiopathogenesis of schizophrenia. Methods: the study was conducted at the psychiatry outpatient clinics of the University Hospitals of Recep Tayyip Erdogan and Afyonkocatepe in spring 2013. It comprised patients with schizophrenia who were consecutively recruited from the Psychiatry outpatient clinics of the hospital. An equal number of healthy individuals were recruited from the community. Each patient underwent a detailed diagnostic evaluation by psychiatry residents by using the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders-IV. Serum prolidase activity and oxidative parameters were measured in patient and control groups. the severity of psychotic symptoms was assessed using the positive and negative syndrome scale. SPSS 16 was used for statitistical analysis. Results: There were 30 subjects in each group, with 18(60%)females among the patients and 21(70%) among the controls. Serum prolidase level was significantly higher in schizophrenia patients compared to the controls (p

26. The Relationship Between Laboratory Findings and Mortality in COVID-19 Patients Requiring Intensive Care.

Author

Bahceci I, Mercantepe F, Duran OF, Yildiz S, and Sahin K

Abstract

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shows a wide clinical manifestation from asymptomatic infection to life-threatening respiratory failure. This study aimed to determine the relationship between the survival and demographic data, comorbidity status, and laboratory parameters of coronavirus disease 2019 (COVID-19) patients requiring intensive care., Material and Methods: We retrospectively analyzed 236 patients requiring intensive care whose diagnosis was confirmed by the SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) test. The patients were divided into two groups in terms of survival. Demographic data; procalcitonin and C-reactive protein (CRP) levels; leukocyte, lymphocyte, and neutrophil counts in hemogram and neutrophil-to-lymphocyte ratio (NLR) levels; and lower respiratory and blood cultures were examined, and the relationships between these parameters and survival were evaluated with hypothesis testing., Results:  In the study, 156 (66.1%) males and 80 (33.9%) females, a total of 236 patients, were included. Sixty-seven (28.3%) surviving patients were determined as Group 1, and 169 (71.7%) deceased patients were determined as Group 2. A statistically significant difference was found between the groups in terms of mean age (p<0.001) and gender distribution (p=0.011). In laboratory parameters, a significant difference was observed between the groups in lymphocyte count (p=0.001), NLR (p<0.001), and procalcitonin levels (p<0.001). Although leukocyte (p=0.075), neutrophil (p=0.031), and CRP (p=0.112) levels were higher in Group 2, there was no statistical difference. Mortality was found to be higher in patients with comorbidity (p=0.012) or co-infection (p=0.002)., Conclusion: High levels of neutrophil count, NLR, and procalcitonin; low lymphocyte count; the presence of comorbidity; and secondary bacterial infection were found to be associated with mortality in COVID-19 patients in the intensive care unit., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Bahceci et al.)

Published
2023
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27. Inhibition of methotrexate induced toxicity in the adult rat spleen by adalimumab.

Author

Bahceci İ, Tumkaya L, Mercantepe T, Aslan N, Duran ÖF, Soztanaci US, and Yazıcı ZA

Subjects
Rats, Animals, Rats, Sprague-Dawley, Adalimumab toxicity, Macrophages, Methotrexate toxicity, Spleen
Abstract

Methotrexate (MTX) has been in use for the treatment of rheumatoid arthritis (RA), psoriasis, and cancer since 1948. Its toxic side effects on tissues and organs have been well documented but splenotoxicity has not been addressed. This study set out to investigate this issue by examining the effectiveness of anti-TNFα agents against MTX-induced toxicity in T lymphocytes and macrophages via the regulation of CD3, CD68, and CD200R. Twenty-four Sprague Dawley rats were allocated to three groups: control (received saline solution only), MTX (20   mg/kg of single-dose of MTX), and Ada + MTX (single dose of 10   mg/kg Adalimumab before MTX administration). The spleens were removed 5   days after MTX administration. The number of CD3+/mm3cells for the control, MTX and Ada + MTX groups were, respectively, 2.69   ±   0.86, 20.51   ±   2.7, ( p   =   0.000) and 11.07   ±   2.01 ( p   =   0.000). The number of CD68+ macrophages/mm3 in the control, MTX and Ada + MTX groups were, respectively, 8.62   ±   1.08, 38.19   ±   1.37 ( p   =   0.000), and 16.87   ±   12.57 ( p   =   0.000). The number of macrophages that were CD200R+/mm3 in the control, MTX, and Ada + MTX groups were 3.33   ±   1.66, 25.77   ±   2.37 ( p   =   0.000), and 8.68   ±   2.66 ( p   =   0.000), respectively. We also observed that Ada reduced the numerical densities of these cells following MTX administration ( p   <   0.05). Ada may, therefore, be a promising candidate for the prevention of the deleterious effects on T lymphocytes and macrophages of MTX-induced toxicity.

Published
2023
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28. Secondary Bacterial Infection Rates Among Patients With COVID-19.

Author

Bahceci I, Yildiz IE, Duran OF, Soztanaci US, Kirdi Harbawi Z, Senol FF, and Demiral G

Abstract

Objective The aim of this study was to determine the factors and rates of secondary bacterial infections developed in patients after the diagnosis of COVID-19 and antimicrobial susceptibility to guide the empirical treatment and contribute to epidemiological data. Materials and Methods In our study, 1,055 patients diagnosed with COVID-19, hospitalized at Recep Tayyip Erdoğan University Training and Research Hospital, Rize, between the dates March 24, 2020 and December 31, 2020, were recruited. The diagnoses of all patients were confirmed by positive SARS-CoV-2 polymerase chain reaction (PCR) tests. In addition, the blood and respiratory tract cultures of the patients recruited in the study were analyzed retrospectively. Results Ninety-two (8.7%) patients were found to have microbiologically proven respiratory or circulatory tract infections via microbial culture results. Respiratory tract infections were detected as monomicrobial in 44 patients and as polymicrobial in 17 patients, among a total of 61 patients. In addition, 59 (64.1%) patients were male patients, and 33 (35.9%) were female patients. Among the microorganisms grown in blood cultures,  coagulase - negative staphylococci  with a percentage of 31% and  Acinetobacter baumannii  with a percentage of 27.5% were prominent. In respiratory tract cultures, A. baumannii constitutes the majority with a percentage of 33.3%, followed by  Staphylococcus aureus  and  Klebsiella pneumoniae  with a percentage of 9.5% each. The most resistant bacteria were  A. baumannii , resistant to all antibiotics other than colistin. Conclusion Secondary bacterial infection rates in patients with COVID-19 are lower than influenza pandemic. However, the frequency of empirical antibiotics use seems relatively high., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2022, Bahceci et al.)

Published
2022
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29. Dynamic thiol/disulphide balance in patients undergoing hypotensive anesthesia in elective septoplasties.

Author

Kazancioglu L, Batcik S, Arpa M, Erdivanli B, Ozergin Coskun Z, Celebi Erdivanli O, Bahceci I, Kazdal H, Erel O, and Neselioglu S

Subjects
Adolescent, Adult, Female, Homeostasis, Humans, Middle Aged, Oxidative Stress, Pilot Projects, Sulfhydryl Compounds, Young Adult, Anesthesia, Disulfides
Abstract

Objective: We aimed to investigate the effects of hypotensive anaesthesia on oxidative stress with serum thiol/disulphide balance in patients undergoing elective septoplasty procedures under general anaesthesia., Methods: Seventy-two patients between the ages of 18-60, with a physical condition I -II, according to the American Society of Anesthesiologists, were included in this prospective observational study. Septoplasty was chosen for standard surgical stress. According to the maintenance of anaesthesia, patients were divided into the groups as Hypotensive Anaesthesia (n = 40) and Normotensive Anaesthesia (n = 32). Serum thiol/disulphide levels were measured by the method developed by Erel & Neşelioğlu., Results: The native thiol and total thiol values of both groups measured at the 60th min intraoperatively were significantly lower than the preoperative values (both P < .01). Intraoperatively, at the 60th min, there was no significant difference in terms of post-native thiol and post-total thiol levels between hypotensive and normotensive anaesthesia groups (P = .68 and .81, respectively). Age >40 years and female gender were found to have a significant effect on dynamic oxidative stress (P = .002 and .001, respectively)., Conclusion: This pilot study has found that hypotensive anaesthesia had no adverse effect on dynamic thiol/disulphide balance in elective surgeries., (© 2021 John Wiley & Sons Ltd.)

Published
2021
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30. Relationship between disease and disease severity and semaphorin 5A and hemogram level in obsessive-compulsive disorder.

Author

Karatas KS, Bahceci I, Telatar TG, Bahceci B, and Hocaoglu C

Subjects
Humans, Lymphocytes, Neutrophils, Severity of Illness Index, Obsessive-Compulsive Disorder diagnosis, Semaphorins blood
Abstract

Objective: Semaphorin 5A (SEMA 5A) is a neuroprotein that regulates the formation of excitatory synapses between neurons, important in autoimmunity, inflammatory processes and behaviors. This study aimed to investigate the SEMA 5A levels in patients with obsessive-compulsive disorder (OCD) diagnosed for the first time and evaluate the relationship of disease and disease severity with the blood SEMA 5A level and hemogram., Methods: More than 41,465 patients who applied to the psychiatry clinic from January 2018 to December 2020 were evaluated according to the DSM-5 criteria; 57 patients diagnosed with OCD for the first time, who met the inclusion criteria, were included in the study. Disease severity was investigated administering the Yale Brown Obsessive Compulsion Scale. The peripheral blood SEMA 5A level and hemogram were measured and evaluated in relation to platelet (PLT) activity, neutrophil-lymphocyte ratio (NLR), PLT-lymphocyte ratio (PLR), monocyte-lymphocyte ratio (MLR), C-reactive protein (CRP), and compared with control group of 26 people., Results: The comparison of the groups revealed a significant difference in SEMA 5A and CRP level, neutrophil count and percentage, lymphocyte count, PLT activity. A significant correlation was found between disease and SEMA 5A level, NLR, PLR, and PLT parameters in diagnosis of OCD. As the severity of OCD increased, the SEMA 5A level and PLT count decreased, while the PDW and MLR values increased., Conclusion: In patients with OCD, a relationship was found between plasma SEMA 5A, PLT activity, NLR, PLR, and MLR activity levels with disease and the disease severity.

Published
2021
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31. The protective role of fosfomycin in lung injury due to oxidative stress and inflammation caused by sepsis.

Author

Yildiz IE, Topcu A, Bahceci I, Arpa M, Tumkaya L, Mercantepe T, Batcik S, and Yildiz Y

Subjects
Acute Lung Injury etiology, Acute Lung Injury pathology, Animals, Anti-Bacterial Agents pharmacology, Antioxidants pharmacology, Male, Rats, Rats, Sprague-Dawley, Acute Lung Injury drug therapy, Anti-Inflammatory Agents pharmacology, Fosfomycin pharmacology, Inflammation complications, Oxidative Stress, Protective Agents pharmacology, Sepsis physiopathology
Abstract

Aim: Early and prompt treatment of sepsis by effective antibiotics against susceptible organisms may be lifesaving. However, increased antibiotic resistance and side effects of chemotherapeutic agents limiting their tolerability result in a restricted use of medications. This has led to an increased search for solution oriented novel treatments and therapeutic targets, as well as investigations on the pathogenesis and physiology of sepsis. In this study, we aimed to examine the antioxidant and anti-inflammatory effects of fosfomycin in sepsis resulting from other causes., Main Methods: Sprague Dawley rats were assigned into three groups. Randomly selected control rats received intraperitoneal saline solution only. Only caecal puncture and ligation were carried out in the caecal ligation and puncture (CLP) group, while in the CLP + fosfomycin group (CLP + FOS), together with sepsis due to caecal puncture and ligation, 500 mg/kg of FOS was administered intraperitoneally (i.p.)., Key Findings: As compared to the control group, elevated TBARS and TNF-α levels as well as increased expression of NF-kB/p65 and TLR-4 and reduced -SH levels were found in the lung tissue of CLP rats. On the other hand, TBARS and TNF-α levels were reduced and NF-kB/p65 and TLR-4 expressions were decreased together with increase in total -SH levels among CLP + FOS (500 mg/kg i.p.) rats., Significance: FOS treatment may represent a promising agent in terms of reducing the sepsis-related lung injury due to its antimicrobial effects as well as its antioxidant and anti-inflammatory properties., (Copyright © 2021. Published by Elsevier Inc.)

Published
2021
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32. COVID-19 infection produces subarachnoid hemorrhage; acting now to understand its cause: A short communication.

Author

Batcik OE, Kanat A, Cankay TU, Ozturk G, Kazancıoglu L, Kazdal H, Gundogdu H, Ozdemir B, Bahceci I, Kostakoglu U, Batcik S, Gundogdu O, and Sevilgen G

Subjects
Adult, Fatal Outcome, Female, Humans, Male, Middle Aged, COVID-19 complications, COVID-19 diagnostic imaging, Comprehension, Subarachnoid Hemorrhage diagnostic imaging, Subarachnoid Hemorrhage etiology
Abstract

In the medical literature, some case reports on the association of the COVID-19 infection and occurrence of spontaneous subarachnoid hemorrhage (SAH)have been reported Aim of the present paper is to search the causes of this association The diagnosis of COVID-19 was based on the real-time reverse-transcription polymerase chain reaction (PCR) test and computed tomography (CT) of the chest. There were four patients, whose median ages were 46,758, ranged 36-54 years). In conclusion, Spontaneous SAH can occur in the early and late course of COVID-19 infection. Its early recognition of the patient with spontaneous SAH is imperative., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Published
2021
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33. Correlation of Suicidal Thoughts and Toxoplasmosis in Patients With Depression.

Author

Bahceci I, Bahceci B, Senturk S, Yildiz IE, and Yazici ZA

Abstract

Objective We investigated the correlation between serum anti- Toxplasma gondii IgG and suicidal thoughts in depressive patients. Methods Depressive patients with (n = 100) and without (n = 100) suicidal thoughts along with 100 healthy control subjects were recruited for this study. In all three groups, a semi-structured clinical interview form called Structured Clinical Interview for DSM-IV (Diagnostic and Statistical Manual of Mental Disorders) Axis-I Disorder (SCID-I), Hamilton Depression Rating Scale (HAMD), suicidal behavior scale, and a sociodemographic data form were completed. Sera from all participants were taken, and anti-toxoplasma IgG was measured by Enzyme Linked Immunosorbent Assay (ELISA)-Chemiluminescent Microparticle Immunoassay. Statistical analysis of the data was performed. Results The serum anti-toxoplasma IgG levels of patients with suicidal thoughts were significantly higher than those without suicidal thoughts and the controls, which were 80.04 ± 40.66, 78 ± 14.82, and 19.98 ± 14.65, respectively, p < 0.001. There was no correlation between toxoplasma IgG and HAMD score in patients lacking suicidal thoughts (r = -0.112, p = 0.463). Conclusion This study shows a correlation between seropositivity for anti- Toxoplasma gondii IgG and depression with suicidal thoughts., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2021, Bahceci et al.)

Published
2021
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34. PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Author

Bahceci I, Dogrusoz U, La KC, Babur Ö, Gao J, and Schultz N

Subjects
Humans, Genomics methods, Metabolic Networks and Pathways, Neoplasms metabolism, Signal Transduction, Software
Abstract

Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene., Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution., Availability and Implementation: The PathwayMapper tool is accessible at http://pathwaymapper.org and the code is available on Github ( https://github.com/iVis-at-Bilkent/pathway-mapper )., Contact: ivis@cs.bilkent.edu.tr., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Published
2017
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35. Oxidative status and prolidase activities in generalized anxiety disorder.

Author

Ercan AC, Bahceci B, Polat S, Cenker OC, Bahceci I, Koroglu A, Sahin K, and Hocaoglu C

Subjects
Adult, Biomarkers blood, Case-Control Studies, Female, Humans, Male, Young Adult, Anxiety Disorders enzymology, Dipeptidases blood, Oxidative Stress physiology
Abstract

Objective: Prolidase (Pro), an intracellular enzyme necessary for collagen turnover, matrix remodelling and cell growth has been shown to be related to Oxidative Stress (OS). To our knowledge, serum Pro activity in generalized anxiety disorder (GAD) has not been documented yet. In this study, we aimed to evaluate OS and its relation with Pro activity in patients diagnosed with GAD., Method: Thirty untreated GAD patients and 30 healthy controls were included in the study. Blood samples were collected from all subjects to quantify total oxidant status (TOS), total antioxidant status (TAS) and Pro activity. Oxidative stress index (OSI), the ratio of TOS to TAS, is calculated to evaluate the balance between antioxidants and oxidants. Hamilton Anxiety Rating Scale (HARS) was used to determine the anxiety levels of all subjects., Results: GAD group demonstrated statistically significantly higher TOS, OSI and Pro levels, when compared with the control group (t=2.947, p=0.005; t=2.874, p=0.006; and t=9.396, p<0.001 respectively). HARS scores were found to be positively correlated with TOS, OSI and Pro levels (p=0.008, r=0.338; p=0.008, r=0.339; and p<0.001, r=0.751 respectively)., Conclusion: The degree of severity of OS is correlated with the levels of Pro. Thus, Pro might be the target enzyme, promising to be a marker for the follow-up of GAD patients. To the best of our knowledge, this study is the first to report a significant relation between Pro activity and GAD., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Published
2017
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36. SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Author

Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, and Demir E

Subjects
Access to Information, Computer Graphics, Internet, Software, Systems Biology methods, Web Browser, Signal Transduction physiology, Statistics as Topic methods, Technology methods
Abstract

Background: Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases., Results: Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis., Conclusion: SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms.

Published
2015
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37. Prolidase activity and oxidative stress in patients with schizophrenia: a preliminary study.

Author

Bahceci B, Bagcioglu E, Kokacya MH, Dilek AR, Bahceci I, and Selek S

Subjects
Adult, Case-Control Studies, Female, Humans, Male, Schizophrenia metabolism, Young Adult, Dipeptidases metabolism, Glutamic Acid metabolism, Oxidative Stress, Schizophrenia enzymology, Synaptic Transmission physiology
Abstract

Objective: To determine whether serum prolidase levels are associated with the etiopathogenesis of schizophrenia., Methods: The study was conducted at the psychiatry outpatient clinics of the University Hospitals of Recep Tayyip Erdogan and Afyonkocatepe in spring 2013. It comprised patients with schizophrenia who were consecutively recruited from the Psychiatry outpatient clinics of the hospital. An equal number of healthy individuals were recruited from the community. Each patient underwent a detailed diagnostic evaluation by psychiatry residents by using the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders-IV. Serum prolidase activity and oxidative parameters were measured in patient and control groups.The severity of psychotic symptoms was assessed using the positive and negative syndrome scale. SPSS 16 was used for statitistical analysis., Results: There were 30 subjects in each group, with 18 (60%) females among the patients and 21 (70%) among the controls. Serum prolidase level was significantly higher in schizophrenia patients compared to the controls (p < 0.001). Total Oxidative Stress and Oxidative Stress Index parameters were found to be significantly different between the patients and the controls (p = 0.024 and p < 0.001). Serum prolidase level did not show any correlation with markers of oxidative stress in the patients., Conclusion: Prolidase activity, glutamate transmission and oxidative stress may be inter-related in the etiopathogenesis of schizophrenia.

Published
2015

38. Elevated nucleosome level and oxidative stress in schizophrenia patients.

Author

Bahceci B, Kokacya MH, Copoglu US, Bahceci I, Sahin K, Bagcioglu E, and Dokuyucu R

Subjects
Adult, Female, Humans, Male, Psychiatric Status Rating Scales, Schizophrenia blood, Schizophrenia diagnosis, Nucleosomes metabolism, Oxidative Stress physiology, Schizophrenia genetics
Abstract

Aim: The aim of this study was to investigate the effect of oxidative stress on nucleosome levels and its relation with the clinical features in schizophrenia patients., Material and Method: Thirty schizophrenia patients and 30 healthy controls were enrolled in this study. Patients were diagnosed with schizophrenia according to the 4th edition of the Diagnostic and Statistical Manual for Mental Disorders (DSM-IV). The control group consisted of 30 healthy subjects matched to the patients with regard to age and gender and who had no history of any psychiatric disorder. The severity of schizophrenia symptoms in the patients was evaluated using the Positive and Negative Syndrome Scale (PANSS) and the Clinical Global Impression Severity Scale (CGI-S). Physical and neurological examinations were performed in each of the patients and controls., Results: Nucleosome, total oxidant levels and OSI values were higher in schizophrenia patients than in controls (p<0.05). There was no significant difference in the total antioxidant levels. There was a positive correlation between the nucleosome level and PANSS positive subscale (p=0.028, r=0.402). There was a positive correlation between TAS and age (p=0.025, r=0.289), PANSS total (p<0.001, r=0.604). There was a negative correlation between OSI and PANSS total (p=0.019, r=-0.427), PANSS positive subscale (p=0.043, r=-0.372). There was a negative correlation between TOS and PANS total (p=0.028, r=-0.402)., Conclusion: In this study we found a correlation between nucleosome level and PANSS positive subscale. To our knowledge, this is the first study that evaluates oxidative stress and nucleosomes released from apoptotic cells together (Tab. 2, Ref. 50).

Published
2015
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39. Prolidase activity and oxidative stress in patients with major depressive disorder.

Author

Kokacya MH, Bahceci B, Bahceci I, Dilek AR, and Dokuyucu R

Subjects
Adult, Female, Humans, Male, Depressive Disorder, Major blood, Dipeptidases blood, Oxidative Stress physiology
Abstract

Background: The aim of the current study was to determine whether the serum prolidase levels are associated with the etiopathogenesis of depression., Subjects and Methods: This study included 29 patients with major depressive disorder (MDD), who were consecutively recruited from the psychiatric outpatient clinic, and 30 healthy individuals recruited from the general community. Each patient underwent a detailed diagnostic evaluation by two psychiatrists using the Structured Clinical Interview for DSM-IV (SCID-I). Serum prolidase activity and oxidative parameters were measured in the patient and control groups. The severity of depressive symptoms was assessed using the Hamilton Depression Rating Scale., Results: Serum prolidase level was significantly higher in patients with MDD compared to healthy subjects (p<0.001). Total Oxidant Status (TOS) levels and Oxidative Stress Index (OSI) were also significantly higher in patients with MDD (p<0.001), whereas no significant difference was observed between the groups in the TAS levels (p=0.297). Serum prolidase level did not show any correlation with markers of oxidative stress in patients with MDD., Conclusion: Increased serum prolidase levels in patients with MDD may be interpreted as the interaction of prolidase activity, glutamate transmission and oxidative stress. It is suggested that prolidase activity is involved in the etiopathogenesis of depressive disorder.

Published
2014

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