Browsing by Author "Tang, Y."

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Open Access
Autopipelining for data stream processing
(Institute of Electrical and Electronics Engineers, 2013) Tang, Y.; Gedik, B.
Stream processing applications use online analytics to ingest high-rate data sources, process them on-the-fly, and generate live results in a timely manner. The data flow graph representation of these applications facilitates the specification of stream computing tasks with ease, and also lends itself to possible runtime exploitation of parallelization on multicore processors. While the data flow graphs naturally contain a rich set of parallelization opportunities, exploiting them is challenging due to the combinatorial number of possible configurations. Furthermore, the best configuration is dynamic in nature; it can differ across multiple runs of the application, and even during different phases of the same run. In this paper, we propose an autopipelining solution that can take advantage of multicore processors to improve throughput of streaming applications, in an effective and transparent way. The solution is effective in the sense that it provides good utilization of resources by dynamically finding and exploiting sources of pipeline parallelism in streaming applications. It is transparent in the sense that it does not require any hints from the application developers. As a part of our solution, we describe a light-weight runtime profiling scheme to learn resource usage of operators comprising the application, an optimization algorithm to locate best places in the data flow graph to explore additional parallelism, and an adaptive control scheme to find the right level of parallelism. We have implemented our solution in an industrial-strength stream processing system. Our experimental evaluation based on microbenchmarks, synthetic workloads, as well as real-world applications confirms that our design is effective in optimizing the throughput of stream processing applications without requiring any changes to the application code. © 1990-2012 IEEE.
Open Access
Facile synthesis of luminescent AgInS2–ZnS solid solution nanorods
(Wiley-VCH Verlag, 2013-04-16) Yang, X.; Tang, Y.; Tan S.T.; Bosman, M.; Dong, Z.; Leck K.S.; Ji Y.; Demir, Hilmi Volkan; Sun, X. W.
Highly luminescent semiconducting AgInS2–ZnS solid solution nanorods are successfully prepared by a facile one-pot solvothermal method. The resulting solid solution nanorods with length of 32 ± 5 nm are formed by fast growth of the AgInS2-rich solid solution head, followed by slow growth of the ZnS-rich solid solution tail. Photoluminescence studies on the solid solution nanorods reveal strong photoluminescence with peak emission wavelengths tunable from 650 to 700 nm.
Open Access
Light extraction efficiency enhancement of colloidal quantum dot light-emitting diodes using large-scale nanopillar arrays
(Wiley-VCH Verlag, 2014) Yang, X.; Dev, K.; Wang, J.; Mutlugun, E.; Dang, C.; Zhao Y.; Liu, S.; Tang, Y.; Tan S.T.; Sun, X. W.; Demir, Hilmi Volkan
A colloidal quantum dot light-emitting diode (QLED) is reported with substantially enhanced light extraction efficiency by applying a layer of large-scale, low-cost, periodic nanopillar arrays. Zinc oxide nanopillars are grown on the glass surface of the substrate using a simple, efficient method of non-wetting templates. With the layer of ZnO nanopillar array as an optical outcoupling medium, a record high current efficiency (CE) of 26.6 cd/A is achieved for QLEDs. Consequently, the corresponding external quantum efficiency (EQE) of 9.34% reaches the highest EQE value for green-emitting QLEDs. Also, the underlying physical mechanisms enabling the enhanced light-extraction are investigated, which leads to an excellent agreement of the numerical results based on the mode theory with the experimental measurements. This study is the first account for QLEDs offering detailed insight into the light extraction efficiency enhancement of QLED devices. The method demonstrated here is intended to be useful not only for opening up a ubiquitous strategy for designing high-performance QLEDs but also with respect to fundamental research on the light extraction in QLEDs.
Open Access
Oncogenic signaling pathways in the Cancer Genome Atlas
(Cell Press, 2018) 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.; 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.; Wang, J.; Zhang, H.; 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.; 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, 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.; Zhang, H.; 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.; 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, 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.; Giordano, T.; 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.; Cherniack, A. D.; Ciriello, G.; Sander, C.; Schultz, N.; The, Cancer, Genome, Atlas, Research, Network.tif
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.