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Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images [PDF]
, 2018 Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA Abdel-Rahman, Mohamed H., Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N., Agnew, Kathy, Ahn, Keunsoo, Ajani, Jaffer A., Akbani, Rehan, Akeredolu, Teniola, Al-Ahmadie, Hikmat, Albert, Monique, Alexopoulou, Iakovina, Ally, Adrian, Alvaro, Domenico, Anderson, Matthew L., Andry, Chris, Antenucci, Anna, Anur, Pavana, Appelbaum, Elizabeth L., Aredes, Natália D., Armenia, Joshua, Arnaout, Angel, Asa, Sylvia L., Auman, J. Todd, Aymerich, Marta, Aziz, Dina, Bailey, Matthew, Balasundaram, Miruna, Balu, Saianand, Barnett, Gene, Barnholtz-Sloan, Jill S., Barrett, Wendi, Bartlett, John, Bathe, Oliver, Batiste, Rebecca, Baudin, Eric, Baylin, Stephen, Becker, Karl-Friedrich, Beer, David, Behera, Madhusmita, Behrens, Carmen, Bell, Debra, Bell, Sue, Bellair, Michelle, Bennett, Joseph, Benz, Christopher, Berchuck, Andrew, Berger, Ashton C., Bergeron, Alain, Berkowitz, Ross, Bernard, Brady, Beroukhim, Rameen, Beuschlein, Felix, Bifulco, Carlo, Bigner, Darell, Birrer, Michael, Birsoy, Kivanc, Bocklage, Therese, Bodenheimer, Tom, Bondaruk, Jolanta, Bootwalla, Moiz S., Borad, Mitesh, Borgia, Jeffrey A., Bossler, Aaron, Botnariuc, Natalia, Boussioutas, Alex, Bowen, Jay, Bowlby, Reanne, Bowman, Rayleen, Bradford, Carol, Bragazzi, Maria Consiglia, Brat, Daniel J., Breggia, Anne, Brewer, Cathy, Brimo, Fadi, Broaddus, Russell, Brooks, Denise, Broom, Bradley M., Broudy, Thomas, Bryce, Alan H., Bubley, Glenn, Bueno, Raphael, Burnette, Andrew, Caesar-Johnson, Samantha J., Calatozzolo, Chiara, Campo, Elias, Campos, Benito, Caraman, Irina, Cardinale, Vincenzo, Carey, Francis, Carey, Thomas, Carlotti, Carlos Gilberto, Carlsen, Rebecca, Carney, Michael, Carpino, Guido, Carroll, Peter R., Carter, Candace, Carvalho, Andre L., Castle, Erik, Castro, Patricia D., Catto, James, Cebulla, Colleen M., Cernat, Mircea, Chabot, John, Chakravarty, Debyani, Chambwe, Nyasha, Chan, June M., Chan, Timothy A., Chandan, Vishal, Chang, Kyle, Chatila, Walid K., Chemencedji, Inga, Chen, Amy, Chen, Chu, Cheng, Feixiong, Cherniack, Andrew D., Chesla, David, Chevalier, Simone, Cheville, John, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Chung, Ki, Cibulskis, Carrie, Clipca, Adrian, Colman, Howard, Cope, Leslie, Copland, John A., Corcoran, Niall, Cordes, Matthew G., Costello, Tony, Cottingham, Sandra, Couce, Marta, Covington, Kyle, Crain, Daniel, Cramer, Daniel, Creaney, Jenette, Creighton, Chad J., Cuppini, Lucia, Curley, Erin, Cuzzubbo, Stefania, Czerniak, Bogdan, Danilova, Ludmila, Davis, Amy, de Bruijn, Ino, de Carvalho, Ana C., de Krijger, Ronald, De Rienzo, Assunta, De Rose, Agostino, Defreitas, Timothy, Delman, Keith, Demchok, John A., Desjardins, Laurence, Devine, Karen, Deyarmin, Brenda, Dhalla, Noreen, Dhanasekaran, Renumathy, Dhankani, Varsha, Dhir, Rajiv, Dimeco, Francesco, Ding, Li, Dinh, Huyen, Dinkin, Mikhail, Dipersio, John, Disaia, Philip, Doddapaneni, Harshavardhan, Donehower, Lawrence A., Doruc, Serghei, Dos Santos, Jose Sebastião, Dottino, Peter R., Drake, Bettina, Drummond, Jennifer, Drwiega, Paul, Dubina, Michael, Duell, Rebecca, Duffy, Elizabeth R., Eckman, John, Edenfield, W. Jeffrey, Eijckenboom, Wil, Elder, J. Bradley, Engel, Jay, Eschbacher, Jennifer, Esmaeli, Bita, Evason, Kimberley, Facciolo, Francesco, Fan, Cheng, Fan, Huihui, Fantacone-Campbell, J. Leigh, Farnell, Michael, Farver, Carol, Fassnacht, Martin, Fehrenbach, Ashley, Felau, Ina, Feldman, Michael, Feltmate, Colleen, Ferguson, Martin L., Finocchiaro, Gaetano, Flotte, Thomas, Fong, Kwun M., Force, Seth, Forgie, Ian, Frazer, Scott, Fregnani, José H., Fronick, Catrina C., Fujimoto, Junya, Fulop, Jordonna, Fulton, Lucinda A., Fulton, Robert S., Gabra, Hani, Gabriel, Stacey B., Galbraith, Joseph, Gao, Galen F., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Gerken, Mark, Gershenwald, Jeffrey, Getz, Gad, Ghossein, Ronald, Giama, Nasra, Gibbs, Richard A., Gilbert, Sebastien, Gillis, Ad, Gimenez-Roqueplo, Anne-Paule, Giné, Eva, Giordano, Thomas, Girard, Nicolas, Giuliante, Felice, Glenn, Pat, Glenn, Robert, Godwin, Andrew K., Godwin, Eryn M., Gonzalez, Ana Maria Angulo, Goodman, Marc, Gopalan, Anuradha, Goparaju, Chandra, Gorincioi, Ghenadie, Govindan, Ramaswamy, Graefen, Markus, Grazi, Gianluca, Grizzle, William E., Gross, Benjamin E., Guillermo, Armando López, Guo, Charles, Gupta, Rajarsi, Ha, Gavin, Haddad, Andrea, Hagedorn, Curt H., Hale, Walker, Han, Yi, Hanh, Phan Thi, Hansen, Paul, Harr, Jodi, Hartmann, Arndt, Haydu, Lauren, Hayes, D. Neil, Hayward, Nicholas, Heath, Sharon, Hegde, Apurva M., Heiman, David I., Heins, Zachary J., Henderson, Joel, Hermes, Beth, Hernandez, Brenda, Herold-Mende, Christel, Hersey, Peter, Hess, Julian, Hibshoosh, Hanina, Hilty, Joe, Hinoue, Toshinori, Ho, Thai, Hoadley, Katherine A., Holt, Robert, Hooke, Jeffrey A., Hoon, Dave, Horowitz, Neil, Hou, Le, Houck, John, Hovens, Christopher, Hoyle, Alan P., Hu, Hai, Hu, Jianhong, Huland, Hartwig, Hung, Nguyen Phi, Huntsman, David, Hutter, Carolyn M., Iacocca, Mary, Ittmann, Michael, Jacobus, Laura, Jakrot, Valerie, Janssen, Klaus-Peter, Jefferys, Stuart R., Jimeno, Antonio, Jones, Corbin D., Jones, Steven J. M., Ju, Zhenlin, Juhl, Hartmut, Jungk, Christin, Junker, Kerstin, Kakavand, Hojabr, Kalkanis, Steven, Kanchi, Rupa S., Kandoth, Cyriac, Kang, Koo Jeong, Karlan, Beth Y., Kasaian, Katayoon, Kasapi, Melpomeni, Kastl, Alison, Kebebew, Electron, Kefford, Richard, Kelley, Robin K., Kemp, Rafael, Kendall, Sara, Kendler, Ady, Kendrick, Michael, Khuri, Fadlo, Kibel, Adam, Kim, Jaegil, Knijnenburg, Theo, Knudson, Michael, Knutson, Tina, Kocher, Jean-Pierre, Kohl, Bernard, Kopp, Karla, Korchina, Viktoriya, Korkut, Anil, Korpershoek, Esther, Korst, Robert, Kovatich, Albert J., Kramer, Roger, Kucherlapati, Melanie H., Kucherlapati, Raju S., Kumar, Bahavna, Kundra, Ritika, Kurc, Tahsin, Kvecher, Leonid, Kycler, Witold, La, Konnor, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Landen, Charles N., Landrum, Lisa, Lang, James, Larson, Caroline, Latour, Mathieu, Lau, Kevin, Lawrence, Michael S., Lazar, Alexander J., Lazar, Alexander J., Le, Xuan, Lechan, Ronald, Lee, Darlene, Lee, Jung Il, Lee, Kenneth, Lee, Sandra, Lehman, Norman L., Leinonen, Kalle, Leraas, Kristen M., Levine, Douglas A., Lewis, Lora, Ley, Timothy, Li, Jun, Li, Wei, Liang, Han, Lichtenberg, Tara M., Lin, Pei, Linehan, W. Marston, Ling, Shiyun, Lipp, Eric, Liptay, Michael J., Liu, Jia, Liu, Wenbin, Liu, Xiuping, Liu, Yuexin, Logothetis, Christopher, Lohavanichbutr, Pawadee, Lolla, Laxmi, Long, Georgina, Longatto-Filho, Adhemar, Looijenga, Leendert, Lu, Yiling, Luketich, James, Luna, Augustin, Lyadov, Vladimir, Ma, Deqin, Ma, Yussanne, Madan, Rashna, Maglinte, Dennis T., Magliocca, Kelly, Maithel, Shishir, Mallery, David, Malykh, Andrei, Mandt, Randy, Manikhas, George, Mann, Graham, Mannel, Robert, Mannelli, Massimo, Mardis, Elaine R., Mariamidze, Armaz, Mariani, Odette, Marino, Mirella, Marks, Jeffrey, Marra, Marco A., Martignetti, John A., Martin, Julie, Mattei, Luca, Mayo, Michael, Mccall, Shannon, Mcgraw, Mary, Mckercher, Ginette, Mclellan, Michael D., Mclendon, Roger, Mcpherson, Christopher, Meier, Sam, Melamed, Jonathan, Meng, Shaowu, Meric-Bernstam, Funda, Merola, Roberta, Mes-Masson, Anne-Marie, Metwalli, Adam R., Meyerson, Matthew, Mieczkowski, Piotr A., Mikkelsen, Tom, Milhem, Mohammed, Miller, Christopher A., Miller, Judy, Miller, Michael, Mills, Gordon B., Mirsaidi, Cyrus, Moiseenko, Fedor, Moncrieff, Marc, Moore, Kathleen, Moore, Richard A., Moran, Cesar, Morgan, Margaret, Morris, Scott, Morrison, Carl, Morton, Donna, Mose, Lisle E., Moser, Catherine, Moxley, Katherine, Moyer, Jeffey, Mungall, Andrew J., Mungall, Karen, Mura, Sergiu, Mural, Richard J., Murawa, Dawid, Muto, Michael, Muzny, Donna, Myers, Jerome, Nagorney, David, Nair, Praveen, Naresh, Rashi, Naska, Theresa, Nelson, Mark, Ng, Kwok-Shing, Nguyen, Phuong, Nguyen, Vu, Nissan, Moriah G., Noble, Michael S., Noss, Ardene, Noushmehr, Houtan, O'Brien, Daniel, O'Neill, Brian Patrick, Ochoa, Angelica, Olabode, Oluwole, Olson, Jeffrey J., Omberg, Larsson, Oosterhuis, Wolter, Ostrom, Quinn T., Owonikoko, Taofeek, Pacak, Karel, Paklina, Oxana, Parfitt, Jeremy, Park, Joong-Won, Parker, Joel S., Pass, Harvey, Patel, Tushar, Paulauskis, Joseph, Pennell, Nathan A., Penny, Robert, Perin, Alessandro, Perou, Amy H., Perou, Charles M., Petersen, Gloria, Peterson, Lisa, Peto, Myron, Phillips, Joanna, Phillips, Sarah M., Phu, Bui Duc, Piché, Alain, Pickens, Alan, Pihl, Todd, Pilarski, Robert, Pinero, Edna M. Mora, Pinto, Peter A., Pirtac, Maria, Pollo, Bianca, Pool, Mark, Porten, Sima, Postier, Russel, Potapova, Olga, Powers, James, Prados, Michael, Prince, Mark, Que, Florencia, Quinn, Michael, Quintero-Aguilo, Mario, Rabeno, Brenda, Rai, Karan, Ramalingam, Suresh, Ramirez, Nilsa C., Ramondetta, Lois, Rao, Arvind, Rao, Arvind U. K., Rassl, Doris M., Rathmell, W. Kimryn, Raut, Chandrajit P., Raymond, Daniel, Reis, Rui M., Reuter, Victor, Reynolds, Sheila, Reznik, Ed, Rice, David, Richards, William G., Rintoul, Robert C., Rivera, Michael, Roach, Jeffrey, Roberts, Lewis, Robertson, A. Gordon, Robinson, Bruce, Roggin, Kevin, Roman-Roman, Sergio, Rosenthal, Howard G., Rozek, Laura, Rubin, Mark A., Ryan, Michael, Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saltz, Joel, Samaras, Dimitris, Sanchez-Vega, Francisco, Sander, Chris, Sankarankuty, Ajith, Santibanez, Jireh, Sastre, Xavier, Sauter, Guido, Saw, Robyn, Scapulatempo-Neto, Cristovam, Scarpace, Lisa, Schadendorf, Dirk, Schein, Jacqueline E., Schiffman, Mark, Schilero, Cathy, Schlomm, Thorsten, Schmidt, Heather K., Schmidt, Laura S., Schoenfield, Lynn, Schultz, Nikolaus, Schumacher, Steven E., Scolyer, Richard, Secord, Angeles, Seder, Christopher W., Sekhon, Harman, Senecal, Kelly, Sepulveda, Antonia, Setdikova, Galiya, Sexton, Katherine C., Shabunin, Alexey, Shannon, Kerwin, Sharma, Ashish, Sharp, Alexis, Shelley, Carl Simon, Shelton, Candace, Shelton, Troy, Shen, Hui, Sheridan, Robert, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shimmel, Kristen, Shin, Dong M., Shinbrot, Eve, Shipman, Cassaundra, Shmulevich, Ilya, Shmulevich, Ilya, Shriver, Craig D., Shroyer, Kenneth R., Sica, Gabriel, Sifri, Suzanne, Sigmund, Rita, Signoretti, Sabina, Silveira, Henrique C. S., Simko, Jeffry, Simon, Ronald, Simons, Janae V., Singer, Samuel, Singh, Bhuvanesh, Singh, Pankaj, Singh, Rosy, Sipahimalani, Payal, Skelly, Tara, Sloan, Andrew E., Slotta-Huspenina, Julia, Smallridge, Robert, Smith, Jennifer, Smith-McCune, Karen, Smolenski, Kathy, Smyrk, Thomas, Sofia, Heidi J., Soloway, Matthew G., Somiari, Stella, Sood, Anil, Spellman, Paul, Spillane, Andrew, Stancul, Irina, Stanton, Melissa, Staugaitis, Susan M., Steele, Ruth, Stepa, Serghei, Stern, Marc-Henri, Stoehr, Christine, Stoehr, Robert, Stoop, Hans, Stretch, Onathan, Stuart, Joshua M., Su, Tao, Sumer, S. Onur, Sun, Qiang, Sun, Yichao, Swanson, Patricia, Swisher, Elizabeth, Synott, Maria, Tam, Angela, Tamakawa, Raina, Tamboli, Pheroze, Tan, Donghui, Tang, Yufang, Tarnuzzer, Roy, Taubert, Helge, Tavobilov, Mikhail, Taylor, Barry S., Tcaciuc, Diana, Tennstedt, Pierre, Thiessen, Nina, Thomas, George, Thompson, Eric, Thompson, John, Thompson, R. Houston, Thompson, Timothy, Thorp, Richard, Thorsson, Vesteinn, Thorsson, Vésteinn, Tien, Nguyen Viet, Timmers, Henri, Tirapelli, Daniela, Tischler, Arthur, Torbenson, Michael, Troncoso, Patricia, Tsao, Anne, Tse, Kane, Tucker, Kelinda, Têtu, Bernard, Unterberg, Andreas, Urba, Walter, Valdivieso, Federico, Van Arnam, John, Van Bang, Nguyen, Van Den Berg, David J., van Kessel, Kim E., Van Meir, Erwin G., Van Tine, Brian, Vandenberg, Scott, Veluvolu, Umadevi, Vicha, Ales, Vidal, Daniel O., Vocke, Cathy D., Voet, Doug, von Deimling, Andreas, Voronina, Olga, Wach, Sven, Wakely, Paul, Waldmann, Jens, Walker, Joan, Wan, Yunhu, Wang, Jing, Wang, Jioajiao, Wang, Linghua, Wang, Min, Wang, Timothy, Wang, Zhining, Warnick, Ronald, Weinstein, John N., Weisenberger, Daniel J., Wentzensen, Nicolas, Westervelt, Peter, Wheeler, David A., Wilkerson, Matthew D., Williams, Felicia, Wilmott, James, Wilson, Richard K., Wise, Lisa, Wistuba, Ignacio, Wiznerowicz, Maciej, Wolf, Gregory, Wolinsky, Yingli, Wong, Christopher K., Wong, Tina, Worrell, Robert, Wu, Ye, Wullich, Bernd, Xi, Liu, Yang, Hannah, Yang, Ian, Yang, Ju Dong, Yang, Liming, Yau, Christina, Yena, Peggy, Zach, Leigh Anne, Zaren, Howard, Zelinka, Tomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Hongxin, Zhang, Hongzheng, Zhang, Jiashan (Julia), Zhang, Jiexin, Zhang, Lizhi, Zhang, Wei, Zhao, Fengmei, Zhao, Tianhao, Zhou, Wanding, Zmuda, Erik, Zuna, Rosemary, Zwarthoff, Ellen C. +740 morecore +3 more sourcesPredictors of response and rational combinations for the novel MCL‐1 inhibitor MIK665 in acute myeloid leukemia
Molecular Oncology, EarlyView.This study characterizes the responses of primary acute myeloid leukemia (AML) patient samples to the MCL‐1 inhibitor MIK665. The results revealed that monocytic differentiation is associated with MIK665 sensitivity. Conversely, elevated ABCB1 expression is a potential biomarker of resistance to the treatment, which can be overcome by the combination ...Joseph Saad, Rhiannon Newman, Elmira Khabusheva, Sofia Aakko, Eric Durand, Mahesh Tambe, Heikki Kuusanmäki, Alun Parsons, Juho J. Miettinen, Komal Kumar Javarappa, Ezgi June Olgac, Nemo Ikonen, Mika Kontro, Kimmo Porkka, Heiko Maacke, Janghee Woo, Ensar Halilovic, Caroline A. Heckman +17 morewiley +1 more sourceResponse to highly active antiretroviral therapy among severely immuno-compromised HIV-infected patients in Cambodia. [PDF]
, 2007 BACKGROUND: HAART efficacy was evaluated in a real-life setting in Phnom Penh (Médecins Sans Frontières programme) among severely immuno-compromised patients.Akileswaran, Babiker, Badri, Braitstein, Calmy, Carr, Coetzee, Cozzi-Lepri, Dragsted, Egger, Ferradini, French, Furber, Hirsch, Ivers, Kaufmann, Keiser, Laurent, Lawn, Le Moing, Mahajan, Matthews, Mocroft, Pean, Ratnam, Severe, Shetty, Smit, Smith, Sungkanuparph, van Leth +30 morecore +3 more sourcesThe IFNγ‐CIITA‐MHC II axis modulates melanoma cell susceptibility to NK‐cell‐mediated cytotoxicity
Molecular Oncology, EarlyView.Natural killer (NK) cells play a central role in anti‐melanoma immunity. However, melanoma cells adapt during co‐culture by upregulating CIITA and MHC II in response to interferon gamma (IFNγ), thereby evading NK‐cell lysis. Blocking IFNγ signaling or treatment with dimethyl fumarate/simvastatin counteracts this immune escape and maintains NK‐cell ...Lena C. M. Krause, Rixa‐Mareike Köhn, Christian Ickes, Julia Lenger, Jonas Fischer, Sabrina Cappello, Ivan Bogeski +6 morewiley +1 more sourceInactivation of cytidine triphosphate synthase 1 prevents fatal auto-immunity in mice
Nature CommunicationsDe novo synthesis of the pyrimidine, cytidine triphosphate (CTP), is crucial for DNA/RNA metabolism and depends on the CTP synthetases, CTPS1 and −2. Partial CTPS1 deficiency in humans has previously been shown to lead to immunodeficiency, with impaired ...Claire Soudais, Romane Schaus, Camille Bachelet, Norbert Minet, Sara Mouasni, Cécile Garcin, Caique Lopes Souza, Pierre David, Clara Cousu, Hélène Asnagli, Andrew Parker, Paul Palmquist-Gomes, Fernando E. Sepulveda, Sébastien Storck, Sigolène M. Meilhac, Alain Fischer, Emmanuel Martin, Sylvain Latour +17 moredoaj +1 more source
