Author: "P. J. van den Berg" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"P. J. van den Berg"' showing total 241 results

Start Over Author "P. J. van den Berg"

241 results on '"P. J. van den Berg"'

51. Direct electronic measurement of Peltier cooling and heating in graphene

Author: I. J. Vera-Marun, J. J. van den Berg, F. K. Dejene, and B. J. van Wees
Subjects: Science
Abstract: The interaction of electric and thermal transport phenomena at the nanoscale leads to Seebeck and Peltier thermoelectric effects. Here, the authors directly detect the Peltier effect in graphene, and show that it can be reversed by controlling the type and density of the majority carriers using a back gate.
Published: 2016
Full Text: View/download PDF

52. The impact of primary care organization on avoidable hospital admissions for diabetes in 23 countries

Author: Tessa Van Loenen, Marjan J. Faber, Gert P. Westert, and Michael J. Van den Berg
Subjects: Avoidable hospitalization, diabetes, general practice, health services research, primary care, The Netherlands, Public aspects of medicine, RA1-1270
Abstract: Objective: Diabetes is a so-called ambulatory care sensitive condition. It is assumed that by appropriate and timely primary care, hospital admissions for complications of such conditions can be avoided. This study examines whether differences between countries in diabetes-related hospitalization rates can be attributed to differences in the organization of primary care in these countries. Design: Data on characteristics of primary care systems were obtained from the QUALICOPC study that includes surveys held among general practitioners and their patients in 34 countries. Data on avoidable hospitalizations were obtained from the OECD Health Care Quality Indicator project. Negative binomial regressions were carried out to investigate the association between characteristics of primary care and diabetes-related hospitalizations. Setting: A total of 23 countries. Subjects: General practitioners and patients. Main outcome measures: Diabetes-related avoidable hospitalizations. Results: Continuity of care was associated with lower rates of diabetes-related hospitalization. Broader task profiles for general practitioners and more medical equipment in general practice were associated with higher rates of admissions for uncontrolled diabetes. Countries where patients perceive better access to care had higher rates of hospital admissions for long-term diabetes complications. There was no association between disease management programmes and rates of diabetes-related hospitalization. Hospital bed supply was strongly associated with admission rates for uncontrolled diabetes and long-term complications. Conclusions: Countries with elements of strong primary care do not necessarily have lower rates of diabetes-related hospitalizations. Hospital bed supply appeared to be a very important factor in this relationship. Apparently, it takes more than strong primary care to avoid hospitalizations.Key points Countries with elements of strong primary care do not necessarily have lower rates of diabetes-related avoidable hospitalization. Hospital bed supply is strongly associated with admission rates for uncontrolled diabetes and long-term complications. Continuity of care was associated with lower rates of diabetes-related hospitalization. Better access to care, broader task profiles for general practitioners, and more medical equipment in general practice was associated with higher rates of admissions for diabetes.
Published: 2016
Full Text: View/download PDF

53. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author: Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A. Gordon Robertson, Toshinori Hinoue, Katherine A. Hoadley, Ewan A. Gibb, Jason Roszik, Kyle R. Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Julian M. Hess, J. Todd Auman, Suhn K. Rhie, Reanne Bowlby, Mitesh J. Borad, Rehan Akbani, Loretta K. Allotey, Adrian Ally, Domenico Alvaro, Jesper B. Andersen, Elizabeth L. Appelbaum, Arshi Arora, Miruna Balasundaram, Saianand Balu, Nabeel Bardeesy, Oliver F. Bathe, Stephen B. Baylin, Rameen Beroukhim, Mario Berrios, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Jay Bowen, Maria Consiglia Bragazzi, Denise Brooks, Vincenzo Cardinale, Rebecca Carlsen, Guido Carpino, Andre L. Carvalho, Roongruedee Chaiteerakij, Vishal C. Chandan, Andrew D. Cherniack, Lynda Chin, Juok Cho, Gina Choe, Eric Chuah, Sudha Chudamani, Carrie Cibulskis, Matthew G. Cordes, Daniel Crain, Erin Curley, Agostino Maria De Rose, Timothy Defreitas, John A. Demchok, Vikram Deshpande, Noreen Dhalla, Li Ding, Kimberley Evason, Ina Felau, Martin L. Ferguson, Wai Chin Foo, Antonio Franchitto, Scott Frazer, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Stacey B. Gabriel, Johanna Gardner, Julie M. Gastier-Foster, Eugenio Gaudio, Nils Gehlenborg, Giannicola Genovese, Mark Gerken, Gad Getz, Nasra H. Giama, Richard A. Gibbs, Felice Giuliante, Gian Luca Grazi, D. Neil Hayes, Apurva M. Hegde, David I. Heiman, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Mei Huang, Carolyn M. Hutter, Stuart R. Jefferys, Steven J.M. Jones, Corbin D. Jones, Katayoon Kasaian, Robin K. Kelley, Jaegil Kim, David E. Kleiner, Jean-Pierre A. Kocher, Lawrence N. Kwong, Phillip H. Lai, Peter W. Laird, Michael S. Lawrence, Kristen M. Leraas, Tara M. Lichtenberg, Pei Lin, Wenbin Liu, Jia Liu, Laxmi Lolla, Yiling Lu, Yussanne Ma, David Mallery, Elaine R. Mardis, Marco A. Marra, Marcus M. Matsushita, Michael Mayo, Michael D. McLellan, Autumn J. McRee, Sam Meier, Shaowu Meng, Matthew Meyerson, Piotr A. Mieczkowski, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Scott Morris, Lisle E. Mose, Catherine D. Moser, Taofic Mounajjed, Andrew J. Mungall, Karen Mungall, Bradley A. Murray, Rashi Naresh, Michael S. Noble, Daniel R. O’Brien, Joel S. Parker, Tushar C. Patel, Joseph Paulauskis, Robert Penny, Charles M. Perou, Amy H. Perou, Todd Pihl, Amie J. Radenbaugh, Nilsa C. Ramirez, W. Kimryn Rathmell, Jeffrey Roach, Lewis R. Roberts, Gordon Saksena, Chris Sander, Jacqueline E. Schein, Heather K. Schmidt, Steven E. Schumacher, Candace Shelton, Troy Shelton, Ronglai Shen, Margi Sheth, Yan Shi, Rachna Shroff, Janae V. Simons, Payal Sipahimalani, Tara Skelly, Heidi J. Sofia, Matthew G. Soloway, Hubert Stoppler, Josh Stuart, Qiang Sun, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, Leigh B. Thorne, Michael S. Torbenson, David J. Van Den Berg, Umadevi Veluvolu, Roel G.W. Verhaak, Doug Voet, Yunhu Wan, Zhining Wang, John N. Weinstein, Daniel J. Weisenberger, David A. Wheeler, Richard K. Wilson, Lisa Wise, Tina Wong, Ye Wu, Liu Xi, Liming Yang, Jean C. Zenklusen, Hailei Zhang, Jiashan (Julia) Zhang, and Erik Zmuda
Subjects: Biology (General), QH301-705.5
Published: 2017
Full Text: View/download PDF

54. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Author: Christopher J. Ricketts, Aguirre A. De Cubas, Huihui Fan, Christof C. Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A. Gibb, Rehan Akbani, Rameen Beroukhim, Donald P. Bottaro, Toni K. Choueiri, Richard A. Gibbs, Andrew K. Godwin, Scott Haake, A. Ari Hakimi, Elizabeth P. Henske, James J. Hsieh, Thai H. Ho, Rupa S. Kanchi, Bhavani Krishnan, David J. Kwaitkowski, Wembin Lui, Maria J. Merino, Gordon B. Mills, Jerome Myers, Michael L. Nickerson, Victor E. Reuter, Laura S. Schmidt, C. Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George Thomas, Benjamin G. Vincent, Cathy D. Vocke, David A. Wheeler, Lixing Yang, William T. Kim, A. Gordon Robertson, Paul T. Spellman, W. Kimryn Rathmell, W. Marston Linehan, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Toshinori Hinoue, Peter W. Laird, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival. : Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtype-specific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes. Keywords: clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma, CDKN2A, DNA hypermethylation, immune signature, chromatin remodeling, TCGA, PanCanAtlas
Published: 2018
Full Text: View/download PDF

55. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author: Qingsong Gao, Wen-Wei Liang, Steven M. Foltz, Gnanavel Mutharasu, Reyka G. Jayasinghe, Song Cao, Wen-Wei Liao, Sheila M. Reynolds, Matthew A. Wyczalkowski, Lijun Yao, Lihua Yu, Sam Q. Sun, Ken Chen, Alexander J. Lazar, Ryan C. Fields, Michael C. Wendl, Brian A. Van Tine, Ravi Vij, Feng Chen, Matti Nykter, Ilya Shmulevich, Li Ding, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy. : Gao et al. analyze a 9,624 sample TCGA cohort with 33 cancer types to detect gene fusion events. They provide a landscape of fusion events detected, relate fusions to gene expression, focus on kinase fusion structures, examine mutually exclusive mutation and fusion patterns, and highlight fusion druggability. Keywords: fusion, cancer, RNA, translocation, gene fusions
Published: 2018
Full Text: View/download PDF

56. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Author: Joel Saltz, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, Vu Nguyen, Dimitris Samaras, Kenneth R. Shroyer, Tianhao Zhao, Rebecca Batiste, John Van Arnam, Ilya Shmulevich, Arvind U.K. Rao, Alexander J. Lazar, Ashish Sharma, Vésteinn Thorsson, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: 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 tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment. : Tumor-infiltrating lymphocytes (TILs) were identified from standard pathology cancer images by a deep-learning-derived “computational stain” developed by Saltz et al. They processed 5,202 digital images from 13 cancer types. Resulting TIL maps were correlated with TCGA molecular data, relating TIL content to survival, tumor subtypes, and immune profiles. Keywords: digital pathology, immuno-oncology, machine learning, lymphocytes, tumor microenvironment, deep learning, tumor-infiltrating lymphocytes, artificial intelligence, bioinformatics, computer vision
Published: 2018
Full Text: View/download PDF

57. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

Author: Xinxin Peng, Zhongyuan Chen, Farshad Farshidfar, Xiaoyan Xu, Philip L. Lorenzi, Yumeng Wang, Feixiong Cheng, Lin Tan, Kamalika Mojumdar, Di Du, Zhongqi Ge, Jun Li, George V. Thomas, Kivanc Birsoy, Lingxiang Liu, Huiwen Zhang, Zhongming Zhao, Calena Marchand, John N. Weinstein, Oliver F. Bathe, Han Liang, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1—master regulators of carbohydrate metabolic subtypes—modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility. : Peng et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to characterize tumor subtypes based on the expression of seven metabolic pathways. They find metabolic expression subtypes are associated with patient survivals and suggest the therapeutic and predictive relevance of subtype-related master regulators. Keywords: The Cancer Genome Atlas, tumor subtypes, prognostic markers, somatic drivers, master regulator, therapeutic targets, drug sensitivity, carbohydrate metabolism
Published: 2018
Full Text: View/download PDF

58. Systematic Analysis of Splice-Site-Creating Mutations in Cancer

Author: Reyka G. Jayasinghe, Song Cao, Qingsong Gao, Michael C. Wendl, Nam Sy Vo, Sheila M. Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A. Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H. Payne, David Fenyö, Jeffrey H. Miner, Matthew J. Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, Li Ding, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases. : Jayasinghe et al. identify nearly 2,000 splice-site-creating mutations (SCMs) from over 8,000 tumor samples across 33 cancer types. They provide a more accurate interpretation of previously mis-annotated mutations, highlighting the importance of integrating data types to understand the functional and the clinical implications of splicing mutations in human disease. Keywords: splicing, RNA, mutations of clinical relevance
Published: 2018
Full Text: View/download PDF

59. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Author: Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, Andrew D. Cherniack, Huihui Fan, Hui Shen, Gregory P. Way, Casey S. Greene, Yuexin Liu, Rehan Akbani, Bin Feng, Lawrence A. Donehower, Chase Miller, Yang Shen, Mostafa Karimi, Haoran Chen, Pora Kim, Peilin Jia, Eve Shinbrot, Shaojun Zhang, Jianfang Liu, Hai Hu, Matthew H. Bailey, Christina Yau, Denise Wolf, Zhongming Zhao, John N. Weinstein, Lei Li, Li Ding, Gordon B. Mills, Peter W. Laird, David A. Wheeler, Ilya Shmulevich, Raymond J. Monnat, Jr., Yonghong Xiao, Chen Wang, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Toshinori Hinoue, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Min Wang, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy. : Knijnenburg et al. present The Cancer Genome Atlas (TCGA) Pan-Cancer analysis of DNA damage repair (DDR) deficiency in cancer. They use integrative genomic and molecular analyses to identify frequent DDR alterations across 33 cancer types, correlate gene- and pathway-level alterations with genome-wide measures of genome instability and impaired function, and demonstrate the prognostic utility of DDR deficiency scores. Keywords: The Cancer Genome Atlas PanCanAtlas project, DNA damage repair, somatic mutations, somatic copy-number alterations, epigenetic silencing, DNA damage footprints, mutational signatures, integrative statistical analysis, protein structure analysis
Published: 2018
Full Text: View/download PDF

60. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Author: Michael Seiler, Shouyong Peng, Anant A. Agrawal, James Palacino, Teng Teng, Ping Zhu, Peter G. Smith, Silvia Buonamici, Lihua Yu, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis. : Seiler et al. report that 119 splicing factor genes carry putative driver mutations over 33 tumor types in TCGA. The most common mutations appear to be mutually exclusive and are associated with lineage-independent altered splicing. Samples with these mutations show deregulation of cell-autonomous pathways and immune infiltration. Keywords: splicing, SF3B1, U2AF1, SRSF2, RBM10, FUBP1, cancer, mutation
Published: 2018
Full Text: View/download PDF

61. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

Author: Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, Augustin Luna, Chris Sander, Andrew D. Cherniack, Marco Mina, Giovanni Ciriello, Nikolaus Schultz, Yolanda Sanchez, Casey S. Greene, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Debyani Chakravarty, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Marc Ladanyi, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these “hidden responders” may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders. : Way et al. develop a machine-learning approach using PanCanAtlas data to detect Ras activation in cancer. Integrating mutation, copy number, and expression data, the authors show that their method detects Ras-activating variants in tumors and sensitivity to MEK inhibitors in cell lines. Keywords: Gene expression, machine learning, Ras, NF1, KRAS, NRAS, HRAS, pan-cancer, TCGA, drug sensitivity
Published: 2018
Full Text: View/download PDF

62. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Author: Hua-Sheng Chiu, Sonal Somvanshi, Ektaben Patel, Ting-Wen Chen, Vivek P. Singh, Barry Zorman, Sagar L. Patil, Yinghong Pan, Sujash S. Chatterjee, Anil K. Sood, Preethi H. Gunaratne, Pavel Sumazin, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts. : Chiu et al. present a pan-cancer analysis of lncRNA regulatory interactions. They suggest that the dysregulation of hundreds of lncRNAs target and alter the expression of cancer genes and pathways in each tumor context. This implies that hundreds of lncRNAs can alter tumor phenotypes in each tumor context. Keywords: lncRNA, regulation, modulation, cancer gene, pan-cancer, noncoding RNA, microRNA, RNA-binding proteins, interactome
Published: 2018
Full Text: View/download PDF

63. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Author: Zhongqi Ge, Jake S. Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang, Jianfang Liu, Craig D. Shriver, Hai Hu, Helen Piwnica-Worms, Li Ma, Han Liang, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies. : Ge et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to provide a comprehensive characterization of the ubiquitin pathway. They detect somatic driver candidates in the ubiquitin pathway and identify a cluster of patients with poor survival, highlighting the importance of this pathway in cancer development. Keywords: ubiquitin pathway, pan-cancer analysis, The Cancer Genome Atlas, tumor subtype, cancer prognosis, therapeutic targets, biomarker, FBXW7
Published: 2018
Full Text: View/download PDF

64. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

Author: Joshua D. Campbell, Christina Yau, Reanne Bowlby, Yuexin Liu, Kevin Brennan, Huihui Fan, Alison M. Taylor, Chen Wang, Vonn Walter, Rehan Akbani, Lauren Averett Byers, Chad J. Creighton, Cristian Coarfa, Juliann Shih, Andrew D. Cherniack, Olivier Gevaert, Marcos Prunello, Hui Shen, Pavana Anur, Jianhong Chen, Hui Cheng, D. Neil Hayes, Susan Bullman, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Sara Sadeghi, Karen L. Mungall, A. Gordon Robertson, Christopher Benz, Andre Schultz, Rupa S. Kanchi, Carl M. Gay, Apurva Hegde, Lixia Diao, Jing Wang, Wencai Ma, Pavel Sumazin, Hua-Sheng Chiu, Ting-Wen Chen, Preethi Gunaratne, Larry Donehower, Janet S. Rader, Rosemary Zuna, Hikmat Al-Ahmadie, Alexander J. Lazar, Elsa R. Flores, Kenneth Y. Tsai, Jane H. Zhou, Anil K. Rustgi, Esther Drill, Ronglei Shen, Christopher K. Wong, Joshua M. Stuart, Peter W. Laird, Katherine A. Hoadley, John N. Weinstein, Myron Peto, Curtis R. Pickering, Zhong Chen, Carter Van Waes, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Paul Spellman, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Toshinori Hinoue, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr., Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, and Armaz Mariamidze
Subjects: Biology (General), QH301-705.5
Abstract: Summary: This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches. : Campbell et al. reveal that squamous cell cancers from different tissue sites may be distinguished from other cancers and subclassified molecularly by recurrent alterations in chromosomes, DNA methylation, messenger and microRNA expression, or by mutations. These affect squamous cell pathways and programs that provide candidates for therapy. Keywords: genomics, transcriptomics, proteomics, head and neck squamous cell carcinoma, lung squamous cell carcinoma, esophageal squamous cell carcinoma, cervical squamous cell carcinoma, bladder carcinoma with squamous differentiation, human papillomavirus
Published: 2018
Full Text: View/download PDF

65. Preemptively and non-preemptively transplanted patients show a comparable hypercoagulable state prior to kidney transplantation compared to living kidney donors.

Author: Gertrude J Nieuwenhuijs-Moeke, Tamar A J van den Berg, Stephan J L Bakker, Marius C van den Heuvel, Michel M R F Struys, Ton Lisman, and Robert A Pol
Subjects: Medicine, Science
Abstract: To prevent renal graft thrombosis in kidney transplantation, centres use different perioperative anticoagulant strategies, based on various risk factors. In our centre, patients transplanted preemptively are considered at increased risk of renal graft thrombosis compared to patients who are dialysis-dependent at time of transplantation. Therefore these patients are given a single dose of 5000 IU unfractionated heparin intraoperatively before clamping of the vessels. We questioned whether there is a difference in haemostatic state between preemptively and non-preemptively transplanted patients and whether the distinction in intraoperative heparin administration used in our center is justified. For this analysis, citrate samples of patients participating in the VAPOR-1 trial were used and several haemostatic and fibrinolytic parameters were measured in 29 preemptively and 28 non-preemptively transplanted patients and compared to 37 living kidney donors. Sample points were: induction anaesthesia (T1), 5 minutes after reperfusion (T2) and 2 hours postoperative (T3). At T1, recipient groups showed comparable elevated levels of platelet factor 4 (PF4, indicating platelet activation), prothrombin fragment F1+2 and D-dimer (indicating coagulation activation) and Von Willebrand Factor (indicating endothelial activation) compared to the donors. The Clot Lysis Time (CLT, a measure of fibrinolytic potential) was prolonged in both recipient groups compared to the donors. At T3, F1+2, PF4 and CLT were higher in non-preemptively transplanted recipients compared to preemptively transplanted recipients. Compared to donors, non-preemptive recipients showed a prolonged CLT, but comparable levels of PF4 and D-dimer. In conclusion pre-transplantation, preemptively and non-preemptively transplanted patients show a comparable enhanced haemostatic state. A distinction in intraoperative heparin administration between preemptive and non-preemptive transplantation does not seem justified.
Published: 2018
Full Text: View/download PDF

66. Mid-term outcomes of the Absorb BVS versus second-generation DES: A systematic review and meta-analysis.

Author: Cordula M Felix, Victor J van den Berg, Sanne E Hoeks, Jiang Ming Fam, Mattie Lenzen, Eric Boersma, Peter C Smits, Patrick W Serruys, Yoshinobu Onuma, and Robert Jan M van Geuns
Subjects: Medicine, Science
Abstract: Bioresorbable Vascular Scaffolds (BVS) were introduced to overcome some of the limitations of drug-eluting stent (DES) for PCI. Data regarding the clinical outcomes of the BVS versus DES beyond 2 years are emerging.To study mid-term outcomes.We searched online databases (PubMed/Medline, Embase, CENTRAL), several websites, meeting presentations and scientific session abstracts until August 8th, 2017 for studies comparing Absorb BVS with second-generation DES. The primary outcome was target lesion failure (TLF). Secondary outcomes were all-cause mortality, myocardial infarction, target lesion revascularization (TLR) and definite/probable device thrombosis. Odds ratios (ORs) with 95% confidence intervals (CIs) were derived using a random effects model.Ten studies, seven randomized controlled trials and three propensity-matched observational studies, with a total of 7320 patients (BVS n = 4007; DES n = 3313) and a median follow-up duration of 30.5 months, were included. Risk of TLF was increased for BVS-treated patients (OR 1.34 [95% CI: 1.12-1.60], p = 0.001, I2 = 0%). This was also the case for all myocardial infarction (1.58 [95% CI: 1.27-1.96], p1 year) device thrombosis was 6.10 [95% CI: 1.40-26.65], p = 0.02).At mid-term follow-up, BVS was associated with an increased risk of TLF, MI, TLR and definite/probable device thrombosis, but this did not result in an increased risk of all-cause mortality.
Published: 2018
Full Text: View/download PDF

67. Shared decision making between patient and GP about referrals from primary care: Does gatekeeping make a difference?

Author: Alexandru M Rotar, Michael J Van Den Berg, Willemijn Schäfer, Dionne S Kringos, and Niek S Klazinga
Subjects: Medicine, Science
Abstract: Primary care faces challenging times in many countries, mainly caused by an ageing population. The GPs' role to match patients' demand with medical need becomes increasingly complex with the growing multiple conditions population. Shared decision-making (SDM) is recognized as ideal to the treatment decision making process. Understanding GPs' perception on SDM about patient referrals and whether patients' preferences are considered, becomes increasingly important for improving health outcomes and patient satisfaction. This study aims to 1) understand whether countries vary in how GPs perceive SDM, in patients' referral, 2) describe to what extent SDM in GPs' referrals differ between gatekeeping and non-gatekeeping systems, and 3) identify what factors GPs consider when referring to specialists and describing how this differs between gatekeeping and non-gatekeeping systems. Data were collected between October 2011 and December 2013 in 32 countries through the QUALICOPC study (Quality and Costs of Primary Care in Europe). The first question was answered by assessing GPs' perception on who takes the referral decision. For the second question, a multilevel logistic model was applied. For the third question we analysed the GPs' responses on what patient logistics and need arguments they consider in the referral process. We found: 1) variation in GPs reported SDM- 90% to 35%, 2) a negative correlation between gatekeeper systems and SDM-however, some countries strongly deviate and 3) GPs in gatekeeper systems more often consider patient interests, whereas in non-gatekeeping countries the GP's value more own experience with specialists and benchmarking information. Our findings imply that GPs in gatekeeper systems seem to be less inclined to SDM than GPs in a non-gatekeeping system. The relation between gatekeeping/non-gatekeeping and SDM is not straightforward. A more contextualized approach is needed to understand the relation between gatekeeping as a system design feature and its relation with and/or impact on SDM.
Published: 2018
Full Text: View/download PDF

68. Imperfect scaling in distributions of radar-derived rainfall fields

Author: M. J. van den Berg, L. Delobbe, and N. E. C. Verhoest
Subjects: Technology, Environmental technology. Sanitary engineering, TD1-1066, Geography. Anthropology. Recreation, Environmental sciences, GE1-350
Abstract: Fine-scale rainfall observations for modelling exercises are often not available, but rather coarser data derived from a variety of sources are used. Effectively using these data sources in models often requires the probability distribution of the data at the applicable scale. Although numerous models for scaling distributions exist, these are often based on theoretical developments, rather than on data. In this study, we develop a model based on the α-stable distribution of rainfall fields, and tested on 5 min radar data from a Belgian weather radar. We use these data to estimate functions that describe parameters of the distribution over various scales. Moreover, we study how the mean of the distribution and the intermittency change with scale, and validate and design functions to describe the shape parameter of the distribution. This information was combined into an effective model of the distribution.
Published: 2014
Full Text: View/download PDF

69. Anti-Oxidized LDL Antibodies and Coronary Artery Disease: A Systematic Review

Author: Victor J. van den Berg, Maxime M. Vroegindewey, Isabella Kardys, Eric Boersma, Dorian Haskard, Adam Hartley, and Ramzi Khamis
Subjects: myocardial infarction, inflammation, antibody, coronary angiography, coronary artery disease, Therapeutics. Pharmacology, RM1-950
Abstract: Antibodies to oxidized LDL (oxLDL) may be associated with improved outcomes in cardiovascular disease. However, analysis is restricted by heterogenous study design and endpoints. Our objective was to conduct a comprehensive systematic review assessing anti-oxLDL antibodies in relation to coronary artery disease (CAD). Through a systematic literature search, we identified all studies assessing the relationship of either, IgG or IgM ox-LDL/ copper-oxLDL/ malondialdehyde-LDL, with coronary atherosclerosis or cardiovascular events in populations with, and without, established CAD. Systematic review best practices were adhered to and study quality was assessed. An initial electronic database search identified 2059 records, which was subsequently followed by abstract and full-text review. Finally, we included 18 studies with over 1811 patients with CAD. The studies varied according to populations studied, conventional cardiovascular risk factors and interventional modalities used to assess CAD. IgM anti-oxLDL antibodies were found to indicate protection from more severe CAD and possibly cardiovascular events, whilst the relationship with IgG is more complex and difficult to elucidate, with studies reporting divergent results. In this systematic review, there is evidence that suggests a relationship between anti-oxLDL antibodies and CAD, especially for the IgM subclass. However, further studies, with well-characterized prospective cohorts, will be important to clarify these associations.
Published: 2019
Full Text: View/download PDF

70. Spatial analysis of positive and negative Q fever laboratory results for identifying high- and low-risk areas of infection in the Netherlands

Author: Elsa J. van den Berg, Cornelia C. H. Wielders, Peter M. Schneeberger, Marjolijn C. Wegdam-Blans, and Wim van der Hoek
Subjects: zoonosis, Coxiella burnetii, goats, the Netherlands, case–control, risk factors, epidemiology, Infectious and parasitic diseases, RC109-216
Abstract: Background: The Netherlands faced a large Q fever epidemic from 2007 to 2010, in which thousands of people were tested for the presence of antibodies against Coxiella burnetii as part of individual patient diagnosis. So far, only data of notified cases were used for the identification of high-risk areas, which can lead to misclassification of risk. Therefore, we identified high- and low-risk areas based on laboratory test results to make control measures more efficient. Methods: Data on diagnostic Q fever laboratory tests were obtained from two regional laboratories of medical microbiology in the high-incidence area in the south of the Netherlands. The proportion of patients testing positive was mapped per postal code area. Patients testing positive were compared to patients testing negative based on the distance between residential address and the nearest infected goat farm with adjustment for age and sex. Results and conclusion: Of 11,035 patients tested, 4,011 (36.4%) had a positive laboratory test result for Q fever. Maps showing the spatial pattern of tests performed and proportion of positive tests allowed for the identification of high- and low-risk Q fever areas. The proportion of patients testing positive was higher in areas close to infected goat farms compared to areas further away. Patients living 10 km away (OR 21.70, 95% CI 16.28–28.92). Laboratory test results have the potential to make control measures more efficient by identifying high-risk areas as well as low-risk areas.
Published: 2013
Full Text: View/download PDF

71. Multivariate return periods in hydrology: a critical and practical review focusing on synthetic design hydrograph estimation

Author: B. Gräler, M. J. van den Berg, S. Vandenberghe, A. Petroselli, S. Grimaldi, B. De Baets, and N. E. C. Verhoest
Subjects: Technology, Environmental technology. Sanitary engineering, TD1-1066, Geography. Anthropology. Recreation, Environmental sciences, GE1-350
Abstract: Most of the hydrological and hydraulic studies refer to the notion of a return period to quantify design variables. When dealing with multiple design variables, the well-known univariate statistical analysis is no longer satisfactory, and several issues challenge the practitioner. How should one incorporate the dependence between variables? How should a multivariate return period be defined and applied in order to yield a proper design event? In this study an overview of the state of the art for estimating multivariate design events is given and the different approaches are compared. The construction of multivariate distribution functions is done through the use of copulas, given their practicality in multivariate frequency analyses and their ability to model numerous types of dependence structures in a flexible way. A synthetic case study is used to generate a large data set of simulated discharges that is used for illustrating the effect of different modelling choices on the design events. Based on different uni- and multivariate approaches, the design hydrograph characteristics of a 3-D phenomenon composed of annual maximum peak discharge, its volume, and duration are derived. These approaches are based on regression analysis, bivariate conditional distributions, bivariate joint distributions and Kendall distribution functions, highlighting theoretical and practical issues of multivariate frequency analysis. Also an ensemble-based approach is presented. For a given design return period, the approach chosen clearly affects the calculated design event, and much attention should be given to the choice of the approach used as this depends on the real-world problem at hand.
Published: 2013
Full Text: View/download PDF

72. Copula-based downscaling of spatial rainfall: a proof of concept

Author: M. J. van den Berg, S. Vandenberghe, B. De Baets, and N. E. C. Verhoest
Subjects: Technology, Environmental technology. Sanitary engineering, TD1-1066, Geography. Anthropology. Recreation, Environmental sciences, GE1-350
Abstract: Fine-scale rainfall data is important for many hydrological applications. However, often the only data available is at a coarse scale. To bridge this gap in resolution, stochastic disaggregation methods can be used. Such methods generally assume that the distribution of the field is stationary, i.e. the distribution for the entire (fine-scale) field is the same as the distribution of a smaller region within the field. This assumption is generally incorrect and we provide a proof of concept of a method to estimate the distribution of a smaller region. In this method, a copula is used to construct a bivariate distribution describing the relation between the scales. This distribution is then used to estimate the distribution of the fine-scale rainfall within a single coarse-scale pixel, by conditioning on the coarse-scale rainfall depth.
Published: 2011
Full Text: View/download PDF

73. The Promise of Intravaginal Rings for Prevention: User Perceptions of Biomechanical Properties and Implications for Prevention Product Development.

Author: Kate Morrow Guthrie, Sara Vargas, Julia G Shaw, Rochelle K Rosen, Jacob J van den Berg, Patrick F Kiser, Karen Buckheit, Dana Bregman, Lara Thompson, Kathleen Jensen, Todd Johnson, and Robert W Buckheit
Subjects: Medicine, Science
Abstract: Intravaginal rings (IVRs) are currently under investigation as devices for the delivery of agents to protect against the sexual transmission of HIV and STIs, as well as pregnancy. To assist product developers in creating highly acceptable rings, we sought to identify characteristics that intravaginal ring users consider when making decisions about ring use or non-use. We conducted four semi-structured focus groups with 21 women (aged 18-45) who reported using an IVR in the past 12 months. Participants manipulated four prototype rings in their hands, discussed ring materials, dimensionality, and "behavior," and shared perceptions and appraisals. Five salient ring characteristics were identified: 1) appearance of the rings' surfaces, 2) tactile sensations of the cylinder material, 3) materials properties, 4) diameter of the cylinder, and 5) ring circumference. Pliability (or flexibility) was generally considered the most important mechanical property. Several ring properties (e.g., porousness, dimensionality) were associated with perceptions of efficacy. Women also revealed user behaviors that may impact the effectiveness of certain drugs, such as removing, rinsing and re-inserting the ring while bathing, and removing the ring during sexual encounters. As product developers explore IVRs as prevention delivery systems, it is critical to balance product materials and dimensions with use parameters to optimize drug delivery and the user experience. It is also critical to consider how user behaviors (e.g., removing the ring) might impact drug delivery.
Published: 2015
Full Text: View/download PDF

74. A discourse analytical view of two South African case studies on the effects on HIV/AIDS in marriage

Author: J A van den Berg, J van den Berg, R Nichol, and B de Klerk
Subjects: Practical Theology, BV1-5099
Abstract: South Africa is the country with the highest incidence of HIV / AIDS in the world. In order to understand the complex phenomenon experienced by people infected and affected by HIV/AIDS in South Africa, the diverse cultural landscape, amongst other factors, needs to be explored. In a qualitative study, the authors explore the impact of this phenomenon on marriage. Using psychiatric texts and by employing the method of Discourse� Analysis on two case studies, different ways of dealing with HIV/AIDS in marriage and the way it dramatically influences marriage are analysed. The impact of these previously untold stories of HIV/AIDS in marriage is seen especially in the lives of spouses who respond differently when managing this problem. In coping with the trauma of HIV/AIDS, spirituality plays a role. Using the biopsychosocial/spiritual-model within a post-modern view of therapy, the role of spirituality is described.� The research, viewed through a culture-sensitive lens, acknowledges the different ethical dilemmas involved. Certain limitations in the research methodology are discussed and the need for further research is highlighted.
Published: 2006
Full Text: View/download PDF

75. Clostridium difficile Ribotype 027, Toxinotype III, the Netherlands

Author: Ed J. Kuijper, Renate J. van den Berg, Sylvia Debast, Caroline E. Visser, Dick Veenendaal, Annet Troelstra, Tjallie van der Kooi, Susan van den Hof, and Daan W. Notermans
Subjects: Clostridium difficile, PCR ribotype 027, toxinotype IIII, epidemic, Harderwijk, dispatch, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: Outbreaks due to Clostridium difficile polymerase chain reaction (PCR) ribotype 027, toxinotype III, were detected in 7 hospitals in the Netherlands from April 2005 to February 2006. One hospital experienced at the same time a second outbreak due to a toxin A–negative C. difficile PCR ribotype 017 toxinotype VIII strain. The outbreaks are difficult to control.
Published: 2006
Full Text: View/download PDF

76. Primary care and avoidable hospitalisation for diabetes

Author: Tessa van Loenen, Michael J. van den Berg, and Gert P. Westert
Subjects: primary care, avoidable hospitalisation, diabetes, Medicine (General), R5-920
Published: 2013

77. The fluctuating natural course of CCSVI in MS patients and controls, a prospective follow-up.

Author: Petronella J Van den Berg and Leo H Visser
Subjects: Medicine, Science
Abstract: OBJECTIVES: A new treatable venous disorder, chronic cerebrospinal venous insufficiency (CCSVI), has been proposed in patients with multiple sclerosis. The natural course of CCSVI has not been examined yet. This is crucial given the fact that surgical procedures are increasingly offered to MS patients to treat venous stenosis. METHODS: To document the natural course of venous haemodynamics we performed extra- and transcranial echo colour Doppler (ECD) in 52 multiple sclerosis patients and 28 healthy controls (HC) and re-examined this group after a median period of 16 weeks. The reexamination was done being blinded to the initial findings and the patients did not undergo any intervention. RESULTS: The ECD examination at baseline showed CCSVI in 5 (9.6%) of the 52 multiple sclerosis patients and 0 HC (P = 0.26). At follow-up the diagnosis CCSVI could not be reconfirmed in 3 out of 5 patients at follow-up, while 2 new CCSVI-positive multiple sclerosis patients were detected. CONCLUSIONS: ECD examination shows a fluctuating natural course of the extracranial venous haemodynamics, which makes determination of CCSVI by ECD examination unreliable.
Published: 2013
Full Text: View/download PDF

78. Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome.

Author: Lukasz Krych, Camilla H F Hansen, Axel K Hansen, Frans W J van den Berg, and Dennis S Nielsen
Subjects: Medicine, Science
Abstract: BACKGROUND: A number of human diseases such as obesity and diabetes are associated with changes or imbalances in the gut microbiota (GM). Laboratory mice are commonly used as experimental models for such disorders. The introduction and dynamic development of next generation sequencing techniques have enabled detailed mapping of the GM of both humans and animal models. Nevertheless there is still a significant knowledge gap regarding the human and mouse common GM core and thus the applicability of the latter as an animal model. The aim of the present study was to identify inter- and intra-individual differences and similarities between the GM composition of particular mouse strains and humans. METHODOLOGY/PRINCIPAL FINDINGS: A total of 1509428 high quality tag-encoded partial 16S rRNA gene sequences determined using 454/FLX Titanium (Roche) pyro-sequencing reflecting the GM composition of 32 human samples from 16 individuals and 88 mouse samples from three laboratory mouse strains commonly used in diabetes research were analyzed using Principal Coordinate Analysis (PCoA), nonparametric multivariate analysis of similarity (ANOSIM) and alpha diversity measures. A reliable cutoff threshold for low abundant taxa estimated on the basis of the present study is recommended for similar trials. CONCLUSIONS/SIGNIFICANCE: Distinctive quantitative differences in the relative abundance of most taxonomic groups between the examined categories were found. All investigated mouse strains clustered separately, but with a range of shared features when compared to the human GM. However, both mouse fecal, caecal and human fecal samples shared to a large extent not only representatives of the same phyla, but also a substantial fraction of common genera, where the number of shared genera increased with sequencing depth. In conclusion, the GM of mice and humans is quantitatively different (in terms of abundance of specific phyla and species) but share a large qualitatively similar core.
Published: 2013
Full Text: View/download PDF

79. Economic conditions at the time of birth and cognitive abilities late in life: evidence from ten European countries.

Author: Gabriele Doblhammer, Gerard J van den Berg, and Thomas Fritze
Subjects: Medicine, Science
Abstract: With ageing populations, it becomes increasingly important to understand the determinants of cognitive ability among the elderly. We apply survey data of 17,070 respondents from ten countries to examine several domains of cognitive functioning at ages 60+, and we link them to the macro-economic deviations in the year of birth. We find that economic conditions at birth significantly influence cognitive functioning late in life in various domains. Recessions negatively influence numeracy, verbal fluency, recall abilities, as well as the score on the omnibus cognitive indicator. The results are robust; controlling for current characteristics does not change effect sizes and significance. We discuss possible causal social and biological pathways.
Published: 2013
Full Text: View/download PDF

80. A genome-wide scan for breast cancer risk haplotypes among African American women.

Author: Chi Song, Gary K Chen, Robert C Millikan, Christine B Ambrosone, Esther M John, Leslie Bernstein, Wei Zheng, Jennifer J Hu, Regina G Ziegler, Sarah Nyante, Elisa V Bandera, Sue A Ingles, Michael F Press, Sandra L Deming, Jorge L Rodriguez-Gil, Stephen J Chanock, Peggy Wan, Xin Sheng, Loreall C Pooler, David J Van Den Berg, Loic Le Marchand, Laurence N Kolonel, Brian E Henderson, Chris A Haiman, and Daniel O Stram
Subjects: Medicine, Science
Abstract: Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.
Published: 2013
Full Text: View/download PDF

81. Greater oxidative susceptibility of the surface monolayer in small dense LDL may contribute to differences in copper-induced oxidation among LDL density subfractions.

Author: D L Tribble, R M Krauss, M G Lansberg, P M Thiel, and J J van den Berg
Subjects: Biochemistry, QD415-436
Abstract: We monitored peroxidative stress in the surface monolayer as compared with the outer core of large, buoyant (d 1.025-1.032 g/ml) and small, dense (d 1.040-1.054 g/ml) low density lipoprotein (LDL) subfractions using the oxidation-labile fluorescent probes parinaric acid (PnA) and parinaric acid methyl ester (PnME), which partition preferentially into these respective regions of LDL. Oxidation was initiated either with CuSO4 (5 microM) or the iron (Fe3+)-containing lipophilic complex hemin (1.0 microM) plus cumene hydroperoxide to facilitate heme degradation. In the presence of Cu2+, PnA was depleted significantly more rapidly than PnME in dense (P = 0.039) but not in buoyant LDL, suggesting that surface vulnerability is enhanced in dense LDL particles. With hemin, PnA and PnME were similarly susceptible within both subfractions, although there was a trend toward slower loss of PnA in buoyant LDL (P = 0.10), consistent with the internal site of initiation and a greater surface resistance in buoyant particles. As indicated by conjugated diene lag times, dense LDL was more susceptible than buoyant LDL to oxidation by Cu2+ (P = 0.03) but not hemin (P = 0.68). These results suggest that the increased susceptibility of dense LDL to oxidation by external agents such as Cu2+ is at least partially mediated by an enhanced vulnerability of the surface compartment.
Published: 1995
Full Text: View/download PDF

82. Copper and gas-phase cigarette smoke inhibit plasma lecithin:cholesterol acyltransferase activity by different mechanisms.

Author: J K Bielicki, M R McCall, J J van den Berg, F A Kuypers, and T M Forte
Subjects: Biochemistry, QD415-436
Abstract: Cigarette smokers have reduced levels of plasma high density lipoprotein (HDL) compared to nonsmokers and are at risk of premature cardiovascular disease. Previous work from this laboratory has shown that exposure of human plasma to gas-phase cigarette smoke (CS) inhibited the activity of lecithin:cholesterol acyltransferase (LCAT), the enzyme that catalyzes the formation of cholesteryl ester in HDL and thereby promotes HDL maturation. As CS contains free radicals that could potentially oxidize plasma lipoproteins, we examined the involvement of lipid peroxidation in LCAT inhibition. Results obtained with CS were compared with those obtained by initiating lipid peroxidation with copper ions. Exposure of dialyzed human plasma to an equivalent of one-eighth of a cigarette at 15-min intervals resulted in a progressive loss of LCAT activity (50 and 90% reductions by 1 and 6 h, respectively). A similar pattern of LCAT inhibition was produced with copper (0.5 mM) where 50 and 97% reductions were observed at 1 and 6 h, respectively. To determine whether LCAT inhibition was related to lipid peroxidation, lipoprotein fractions corresponding to VLDL-IDL, LDL, and HDL were isolated from plasma exposed to CS or copper and analyzed for changes in TBARS, the polyunsaturated fatty acid arachidonate relative to palmitate (20:4/16:0 ratio), and vitamin E concentrations. Exposure of plasma for 6 h to CS had no effect on the levels of TBARS and 20:4/16:0 ratio; however, 6 h copper treatment (0.5 mM) caused a 3.0-, 4.0-, and 1.4-fold increase in TBARS and a 17, 25, and 13% reduction in the 20:4/16:0 ratio in VLDL-IDL, LDL, and HDL fractions, respectively. In addition, a complete depletion of lipoprotein vitamin E was observed with CS, whereas copper decreased vitamin E levels by approximately 50% in each fraction. Supplementation of plasma with either vitamin C (85 microM) or butylated hydroxytoluene (BHT, 0.45 mM) was unable to protect LCAT from CS. In contrast, BHT completely protected LCAT activity from inhibition by copper. We conclude that unlike copper, CS-induced inhibition of plasma LCAT activity was unrelated to free radical-induced lipid peroxidation. The inhibition of LCAT activity by cigarette smoke may contribute to the development of atherosclerosis by impairing HDL metabolism and the reverse cholesterol transport process.
Published: 1995
Full Text: View/download PDF

83. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults.

Author: Nadja Larsen, Finn K Vogensen, Frans W J van den Berg, Dennis Sandris Nielsen, Anne Sofie Andreasen, Bente K Pedersen, Waleed Abu Al-Soud, Søren J Sørensen, Lars H Hansen, and Mogens Jakobsen
Subjects: Medicine, Science
Abstract: BackgroundRecent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control.Methods and findingsThe study included 36 male adults with a broad range of age and body-mass indices (BMIs), among which 18 subjects were diagnosed with diabetes type 2. The fecal bacterial composition was investigated by real-time quantitative PCR (qPCR) and in a subgroup of subjects (N = 20) by tag-encoded amplicon pyrosequencing of the V4 region of the 16S rRNA gene. The proportions of phylum Firmicutes and class Clostridia were significantly reduced in the diabetic group compared to the control group (P = 0.03). Furthermore, the ratios of Bacteroidetes to Firmicutes as well as the ratios of Bacteroides-Prevotella group to C. coccoides-E. rectale group correlated positively and significantly with plasma glucose concentration (P = 0.04) but not with BMIs. Similarly, class Betaproteobacteria was highly enriched in diabetic compared to non-diabetic persons (P = 0.02) and positively correlated with plasma glucose (P = 0.04).ConclusionsThe results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies to control metabolic diseases by modifying the gut microbiota.
Published: 2010
Full Text: View/download PDF

84. Re-annotation is an essential step in systems biology modeling of functional genomics data.

Author: Bart H J van den Berg, Fiona M McCarthy, Susan J Lamont, and Shane C Burgess
Subjects: Medicine, Science
Abstract: One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data.
Published: 2010
Full Text: View/download PDF

85. The upgraded DO detector

Author: Vipin Bhatnagar, E. De La Cruz-Burelo, Laurent Chevalier, N. A. Kuchinsky, L. S. Vertogradov, Stephen Wimpenny, A. Bross, Y. Jacquier, Adam L. Lyon, Tiefu Zhao, N. Lahrichi, X. Zhang, T. Wlodek, B. Baumbaugh, Martin Grunewald, K. Genser, Ulrike Blumenschein, P. L.M. Podesta-Lerma, T. Marshall, Milos Lokajicek, Jean-Laurent Agram, Christian Autermann, A. Kostritski, Y. Arnoud, S. Lager, O. Dvornikov, M. Anastasoaie, U. Bassler, P. K. Mal, Darien Wood, Brad Abbott, Pierre Petroff, Sergey Denisov, D. Tompkins, P. Sheahan, S. E.K. Mattingly, M. Markus, V. Mikhailov, Chris Hays, K. J. Rani, A. Alton, V. V. Shary, L.V. Reddy, Vivek Jain, S. J. Hong, Paul Telford, Robert Hirosky, V. L. Malyshev, J. Rha, Alexander Khanov, F. Fleuret, Daniel R Claes, Yann Coadou, Nicholas John Hadley, C. P. Buszello, W. Kahl, S. Robinson, I. Churin, Regina Demina, R. Van Kooten, N. Jouravlev, Arnulf Quadt, Raimund Ströhmer, Michael A. Strauss, Michael Martens, R. Jayanti, B. Thooris, Marco Verzocchi, C. Magass, A. Besson, M. D. Corcoran, N. P. Kravchuk, V. A. Bezzubov, Elemer Nagy, G. Graham, Abdenour Lounis, A. Zieminski, Dugan O'Neil, E. G. Zverev, Joshua Thompson, R.J. Yarema, Arnaud Duperrin, H. S. Mao, V. Simak, Ted Zmuda, S. Blessing, Scott Snyder, V. S. Narasimhan, M. Abolins, J. P. Negret, D. Casey, E. Thomas, J. Huang, M. Vigneault, P. A. Rapidis, J. Lizarazo, A. M. Kalinin, V. M. Korablev, N. Spartana, Thomas Trefzger, E. J. Ramberg, S. N. Fatakia, Jaebeom Park, R. A. Sidwell, Suyong Choi, Rapson Gomez, A. Patwa, P. Padley, Denis Gelé, J. F. Bartlett, T. Moulik, R. P. Smith, Sophie Trincaz-Duvoid, M. Juarez, F. Borcherding, W. Pritchard, V. M. Podstavkov, Armen Vartapetian, R. J. Madaras, N. M. Cason, A. Goussiou, J. Steinberg, N. Gollub, R. F. Rodrigues, P. Lebrun, E. Machado, E. Hazen, R. Angstadt, D. Graham, S. N. Ahmed, B. Clement, Mitchell Wayne, D. Bonifas, Alberto Santoro, Yu. A. Gornushkin, David Colling, N. W. Reay, C. Rotolo, Christos Leonidopoulos, D. Beutel, J. Kasper, G. Sajot, J. Kozminski, Michael Shupe, Michael Hildreth, Dmitri Tsybychev, R. L. McCarthy, B. M. Sabirov, Y. Hu, C. Boswell, L. Lobo, Sascha Caron, H. Schellman, J. M. Kohli, R. DeMaat, G. Alkhazov, O. Boeriu, Marcia Begalli, J. G.R. Lima, Lorenzo Feligioni, Y. Kulik, L. Bagby, A. Yurkewicz, D. Kau, Kevin Black, Jovan Mitrevski, D. Toback, G. D. Alexeev, G. Martin-Chassard, A. Harel, Markus Klute, Sergio F Novaes, Norbert Wermes, K. Stevenson, Chris P. Barnes, B. Lavigne, Flera Rizatdinova, Ron Lipton, B. Olivier, S. Greder, Miguel Mostafa, Douglas Smith, Meenakshi Narain, Sherry Towers, Sarah Catherine Eno, Horst Severini, Ph Gris, A. Kryemadhi, Karel Smolek, J. P. Konrath, P. Schieferdecker, D. K. Cho, A. Stone, Wendy W. Davis, R. Zitoun, V. I. Rud, S. Söldner-Rembold, S. R. Hou, Alexandre Zabi, S. Uzunyan, Tobias Golling, Yonggang Huang, J. M. Hauptman, T. Scanlon, S. Kermiche, H. T. Diehl, T. A. Bolton, P. Verdier, Shuichi Kunori, Y. Pogorelov, J. Krane, P. Houben, R. Flores, K. M. Chan, Christian Zeitnitz, Cecilia Elena Gerber, Dhiman Chakraborty, V. Anosov, M. Roco, J. Womersley, Hyun-Chul Kim, John Parsons, Yurii Maravin, Junjie Zhu, F. Nang, Andrew White, R. Rechenmacher, Nikola Makovec, Mossadek Talby, B. Gómez, Yi Jiang, Suman Bala Beri, P. Laurens, M. Michaut, Gordon Watts, A. V. Kotwal, Harrison Prosper, Y. Xie, G. Ginther, D. Butler, J. Linnemann, Vivian O'Dell, H. Weerts, H. Dong, P. Ermolov, María Teresa Martín, M. Cooke, H. da Motta, D. Zieminska, M. Diesburg, D. Gillberg, A. A. Shishkin, A. Evdokimov, S. Desai, S. Grünendahl, J. Wittlin, Kristian Harder, V. Sirotenko, A. C. Le Bihan, Rupert Leitner, S. Fuess, M. Cristetiu, B. Davies, M. Wobisch, O. V. Eroshin, Y. Song, Md. Naimuddin, E. Chi, S.D. Kalmani, Shashikant Dugad, M. Merkin, Jianming Qian, J. Ellison, A. Juste, A. Melnitchouk, Steve Reucroft, Pm Tuts, P. Bonamy, Todd Adams, B. Gobbi, C. Tolian, M. Petteni, J. D. Degenhardt, S. W. Youn, E. Von Toerne, Wagner Carvalho, P. Demine, M.A. Baturitsky, J. M. Heinmiller, Hal Evans, Thomas Ferbel, A. K.A. Maciel, M. Ahsan, Sa. Jain, Dan Green, Emmanuel Busato, Alexander Leflat, V. M. Abazov, J. Raskowski, F. Touze, Nikos Varelas, L. Groer, A. M. Magnan, Thomas G Trippe, Karl Jakobs, A. Pompoš, T. Gadfort, A. S. Turcot, Phillip Gutierrez, Greg Landsberg, Sw. Banerjee, V. Hynek, Mark Raymond Adams, D. Karmanov, Q. Xu, T. Wijnen, M. Strovink, B. Connolly, L. Christofek, H. Zheng, D. Buchholz, Bing Zhou, Luis Mendoza, Lars Sonnenschein, G. Briskin, R. Hooper, D. Mendoza, T. Kurca, Pushpalatha C Bhat, S. Zviagintsev, A. Narayanan, M. B. Przybycien, Anurag Gupta, J. Lazoflores, A. Jonckheere, Marc Weber, S. Porokhovoy, P. Hanlet, Pedrame Bargassa, M. Utes, Pierre-Antoine Delsart, A. Jenkins, Helena Malbouisson, D. Chapin, Christophe Royon, Iain Alexander Bertram, V. V. Lipaev, K. Soustruznik, Kenneth Johns, M. Kopal, R. Chiche, Sudhir Malik, N. J. Buchanan, I. Ripp-Baudot, A. Meyer, P. Nagaraj, Jonas Strandberg, N. Parua, Ia Iashvili, J. Krider, R. K. Shivpuri, D. A. Stoyanova, K. Gounder, J. R. Kalk, Reiner Hauser, V. Buescher, Andrei Nomerotski, Michael Rijssenbeek, O. Atramentov, Sissel Hansen, A. Stefanik, W. D. Shephard, M. McKenna, Sharon Hagopian, K. Papageorgiou, V. Stolin, P. Skubic, Jean-Roch Vlimant, D. Skow, M. Vaz, Rodney Walker, Brajesh C Choudhary, M. Eads, M. Jaffré, M. A.C. Cummings, Raymond Brock, N. Wilcer, M. Larwill, V. Manakov, P. Tamburello, D. Coppage, G. Geurkov, J. N. Butler, R. Rucinski, Gavin Davies, Boaz Klima, P. van Gemmeren, S. Doulas, R. McCroskey, Andre Sznajder, J. Anderson, M. Doidge, L. Coney, T. Regan, Yuri Gershtein, F. Badaud, I. Katsanos, R. Beuselinck, P. D. Grannis, H. D. Wahl, T. Yasuda, V. White, S. N. Gurzhiev, A. Nurczyk, D. Wicke, Emmanuelle Perez, A. Baden, G. C. Blazey, Y. Yen, B. Zhang, Jean-Francois Grivaz, Y. A. Yatsunenko, S. H. Ahn, Arnaud Lucotte, B. Hoeneisen, Z. Ke, Alexander Kupco, J. Steele, N. A. Naumann, P.R. Vishwanath, H. J. Willutzki, J. Olsen, Y. Scheglov, Kaushik De, P. Russo, S. Baffioni, J. D. Hobbs, I. Hall, M. J. Ferreira, J. Warchol, A. Chandra, P. de Jong, Ricardo Piegaia, Florian Beaudette, M. Arov, R. Partridge, Gilvan Alves, J. Barreto, F. Yoffe, B. Satyanarayana, I.K. Prokhorov, K. Goldmann, B. Andrieu, P. Jonsson, E. Bockenthien, G. Bernardi, Freya Blekman, R. T. Neuenschwander, R. Hance, S. Tentindo-Repond, Carl Lindenmeyer, Heriberto Castilla-Valdez, D. Bauer, L. Canal, M. Bhattacharjee, F. Charles, G. Savage, I. Blackler, M. Bowden, Emanuela Barberis, Li Jingyuan, Kazunori Hanagaki, Dongliang Zhang, X. Meng, Marcel Vreeswijk, B. Spurlock, Thomas Hebbeker, M. Mulders, E.V. Komissarov, S. Chakrabarti, Peter Love, P. Johnson, P. Rubinov, T. Nunnemann, B. Baldin, A. Koubarovsky, C. Luo, Randy Ruchti, Manas Maity, M. A. Strang, J. Molina, C. Noeding, Reinhard Schwienhorst, M. H.G. Souza, Jan Stark, P. Polosov, Seo Won Lee, Henry Lubatti, Ashok Kumar, Charles Leggett, Juan Estrada, M. C. Cousinou, Julia S. Meyer, Zeno Dixon Greenwood, D. Käfer, A. Bellavance, M. Litmaath, A. A. Mayorov, K. W. Merritt, T. Vu Anh, M. Wegner, Mansoora Shamim, Carlos Avila, S. Sumowidagdo, S.A. Kahn, H. Greenlee, Sabine Crépé-Renaudin, J. Cammin, V. Oguri, C. Schwanenberger, W. M. Van Leeuwen, O. Peters, Marumi Kado, E. Galyaev, Liyuan Han, James C. Green, M. Zdrazil, Tulika Bose, S. Yacoob, C. Franklin, D. Huffman, W. M. Lee, N. Kirsch, P. Banerjee, M. Demarteau, A. Kharchilava, Z. M. Wang, David Miller, Carmen García, H. Haggerty, J. Dyer, A.A. Nozdrin, Gregory R Snow, G. Steinbrück, Andrew Brandt, S. Rapisarda, Andre Sopczak, M. Agelou, M. Binder, A. C.S. Assis Jesus, Guennadi Borissov, L. Sawyer, Philip Baringer, George Alverson, H. E. Fisk, Sergey Kuleshov, S. Protopopescu, Lev Dudko, C. Biscarat, E. Haggard, Aran Garcia-Bellido, P. Lewis, D. Hedin, M. Zanabria, Cristina Galea, Christophe Clement, D. Denisov, Elliott Cheu, S. Fu, W. C. Fisher, S. Moua, G. Gutierrez, Hwi Dong Yoo, S. Sengupta, A. S. Ito, Kirti Ranjan, H.E. Miettinen, Carsten Hensel, S. Kesisoglou, A. A. Vorobyov, A. V. Kozelov, D. Edmunds, M. Yan, S. Jabeen, Victor Daniel Elvira, S. Burke, W. E. Cooper, J. Hays, Xiuping Li, Q. Z. Li, V. V. Tokmenin, Neeti Parashar, S. Dean, Stephan Linn, A. Lobodenko, V. A. Bodyagin, Tae Jeong Kim, R. Bernhard, D. A. Wijngaarden, M. Gao, A. Cothenet, G. Hesketh, N. Oshima, M. P. Sanders, M. Zielinski, Daniel Bloch, J. Fast, Nikolay Terentyev, N. Wallace, M. Sosebee, Gustaaf Brooijmans, Sergey Burdin, A. Sanchez-Hernandez, Robert Kehoe, J. Lu, P. J. Van Den Berg, Jessica Levêque, K. Bos, Marc Besancon, J. Temple, T. Christiansen, Bobby Samir Acharya, H. A. Neal, Sung Keun Park, D. Meder, H. C. Shankar, V. Sorín, T. R. Wyatt, V. Zutshi, V. Vysotsky, B. G. Pope, M. A. Kubantsev, B. O. Oshinowo, W. Barg, Marvin Johnson, A. A. Schukin, M. R. Krishnaswamy, Sebastian Grinstein, O. Kouznetsov, E. Flattum, R. Yamada, M. Warsinsky, O. Bardon, T. Edwards, K. Yip, N. Xuan, L. Stutte, R. D. Schamberger, Timothy Andeen, R. E. Ray, L. Lueking, K. Krempetz, C. Miao, W. L. Prado Da Silva, S. Chopra, Andrew Askew, Zhengguo Zhao, Brigitte Vachon, D. Evans, Gregory J Pawloski, A.S. Dyshkant, M. Buehler, Jiri Kvita, V.V. Teterin, M. Lynker, J. Yu, X. F. Song, M. V. S. Rao, N. R. Stanton, J. Torborg, N. K. Mondal, Lev Uvarov, G. Le Meur, D. Shpakov, R. Jesik, S. Beauceron, Ariel Schwartzman, Melissa Ridel, Dorothee Schaile, G. Cisko, T. C. Bacon, Alexey Ferapontov, M. Wetstein, J. Bystricky, Zhenbin Wu, J. Foglesong, J. Fagan, Robert Harrington, A. Mendes, T. Fitzpatrick, Christian Schmitt, S. Nelson, R. Gelhaus, H. E. Montgomery, C. De La Taille, P. Mättig, K. Gray, E. Popkov, M. Hohlfeld, K. Del Signore, R. Illingworth, C. Han, D. Mihalcea, C. De Oliveira Martins, Victor Golovtsov, P. N. Ratoff, Emily Nurse, Elizabeth Gallas, T. McMahon, Maksym Titov, V. E. Kuznetsov, V. Gavrilov, D. Olis, Wendy Taylor, Allan G Clark, Roger Moore, R. Goodwin, Johannes Elmsheuser, J. T. Eltzroth, P. Neustroev, Laurent Duflot, David Cutts, R. Ramirez-Gomez, R. Kwarciany, Rupinder Kaur, Daniel Whiteson, Bradley Cox, S. J. De Jong, B. Kothari, J. Coss, D. Markley, A. A. Shchukin, L. Babukhadia, Frank Fiedler, E. Kajfasz, A. Magerkurth, A. Zatserklyaniy, N.A. Russakovich, M. Das, V. N. Evdokimov, Gervasio Gomez, Michael Begel, Eduardo De Moraes Gregores, G. A. Davis, Boris Tuchming, Luiz Mundim, J. F. Renardy, Limin Wang, Marc-Andre Pleier, M. Doets, N.V. Mokhov, B. Åsman, A. P. Heinson, T. H. Burnett, G. S. Muanza, R. E. Hall, D. Fein, M. Fortner, Don Lincoln, Erich Varnes, P. W. Balm, C. Hebert, Ulrich Heintz, M. Matulik, A. Bishoff, H. Jöstlein, S. Krzywdzinski, J. Green, A. Zylberstejn, Frank Filthaut, R. Kubinski, F. Lehner, D. M. Strom, B. C.K. Casey, Y. P. Merekov, E. Shabalina, J. Guglielmo, Kyoung-Ho Kim, Andy Haas, L. Phaf, G. W. Wilson, Frederic Deliot, Christopher George Tully, Y. M. Kharzheev, Patrick Slattery, G. J. Otero y Garzón, T. Toole, S. Uvarov, A. Boehnlein, H. L. Melanson, Ivor Fleck, J. Snow, B. Quinn, J. H. Christenson, Makoto Tomoto, David H. Adams, Alice Bean, F. Canelli, N. Oliveira, Maria Elena Pol, W. Gu, A. P. Kaan, J. Gardner, R. Choate, Walter Freeman, J. Kotcher, S. Anderson, Harald Fox, M. Vaupel, Y. D. Mutaf, I. A. Vasilyev, P. M. Perea, and F. Villeneuve-Seguier
Subjects: Nuclear and High Energy Physics, Physics::Instrumentation and Detectors, Tevatron, 01 natural sciences, Particle detector, law.invention, Nuclear physics, Data acquisition, law, 0103 physical sciences, Fermilab, 010306 general physics, Collider, Instrumentation, Physics, 010308 nuclear & particles physics, business.industry, Detector, Electrical engineering, Particle accelerator, D0 experiment, Experimental High Energy Physics, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Physics::Accelerator Physics, High Energy Physics::Experiment, business
Abstract: The DØ experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid-argon calorimeters and central muon detector, remaining from Run I, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DØ. © 2006 Elsevier B.V. All rights reserved.
Published: 2016

86. Search for Charged Higgs Bosons Decaying into Top and Bottom Quarks in pp Collisions

Author: J. Steele, G. Ginther, K. M. Chan, N. Parua, T. Kuhl, N. Parashar, E. Shabalina, T. Trefzger, M. Jaffré, H. Yin, Jun Guo, Q. Z. Li, C. De Oliveira Martins, V. V. Shary, M. Rijssenbeek, Alexander Kupco, E. Nagy, Maksym Titov, S. Protopopescu, H. da Motta, D. Gillberg, G. Kertzscher, A. S. Ito, Avto Kharchilava, M. Shamim, V. Hynek, V. V. Lipaev, J. Lellouch, Pedro G Mercadante, D. Boline, Randy Ruchti, J. Rieger, S. J. Park, G. D. Alexeev, O. Atramentov, Alexander Khanov, X. B. Bu, J. Sekaric, I. A. Vasilyev, P. Houben, H. E. Fisk, Sergio F Novaes, M. Zielinski, M. Pangilinan, N. Oshima, Shabnam Jabeen, M. Merkin, H. J. Lubatti, R. F. Rodrigues, A. Zieminski, C. Magass, Theodoros Christoudias, Dugan O'Neil, T. H. Burnett, A. Sopczak, A. F. Barfuss, J. Stark, M. Arov, Mitchell Wayne, H. Schellman, J. M. Kohli, Y. Scheglov, Y. W. Liu, J. Mitrevski, C. Belanger-Champagne, F. Villeneuve-Seguier, T. Toole, P. Verdier, J. Zhu, M. Fortner, P. N. Ratoff, M. D. Corcoran, Aran Garcia-Bellido, G. Grenier, D. Bauer, V. Simak, B. Penning, G. Gutierrez, Gilvan Alves, Vladimir Gavrilov, N. A. Naumann, R. McCarthy, G. Sajot, L. Han, Alexander Grohsjean, W. Geist, Denis Gelé, A. Patwa, Tim Scanlon, S. Söldner-Rembold, B. Hoeneisen, Stefan Grünendahl, A. L. Lyon, G. W. Wilson, J. T. Linnemann, N. K. Mondal, Lev Uvarov, V. A. Kuzmin, H. D. Yoo, B. Åsman, C. Biscarat, J. A. Benitez, K. Yip, Z. Liu, J. Clutter, M. Begalli, B. Gómez, P. Tamburello, P. M. Tuts, M. Cooke, Raymond Brock, Boaz Klima, R. Schwienhorst, W. L. Prado Da Silva, V. Sirotenko, Karl Jakobs, I. Katsanos, R. Beuselinck, I. Ripp-Baudot, M. Vaupel, W. M. Lee, Y. Pogorelov, L. Christofek, Ph Gris, H. B. Prosper, Ulrich Heintz, A. Meyer, Phillip Gutierrez, E. W. Varnes, M. Mulhearn, Shashikant Dugad, M. H. Kirby, T. Schliephake, E. E. Boos, Dmitry Smirnov, L. S. Vertogradov, V. Kaushik, U. Bassler, P. J. van den Berg, G. Weber, Frank Filthaut, Gustaaf Brooijmans, A. Evdokimov, A. V. Popov, M. Diesburg, S. Uvarov, S. Robinson, Meenakshi Narain, J. M. Kalk, J. Haley, Sara Strandberg, V. V. Tokmenin, Andrew Askew, M. Voutilainen, Y. Maravin, Heriberto Castilla-Valdez, Wendy Taylor, A.S. Dyshkant, Pushpalatha C Bhat, Emanuela Barberis, S. Cihangir, A. Alton, V. Cuplov, O. Mundal, D. A. Stoyanova, Regina Demina, P.F. Ermolov, Jiri Kvita, G. J. Otero Y Garzón, T. Millet, Brigitte Vachon, P. L.M. Podesta-Lerma, Reiner Hauser, M. Naimuddin, Michael John Owen, C. Hensel, Fabrice Couderc, A. C.S. Assis Jesus, H. Hoeth, Guennadi Borissov, C. Zeitnitz, W. M. Van Leeuwen, I. Torchiani, M. A. Strang, R. Luna, B. C.K. Casey, Helio Nogima, Maxim Perfilov, Samuel Calvet, Y. Enari, A. Tanasijczuk, J. D. Degenhardt, Deidre Brown, Zeno Dixon Greenwood, A. Melnitchouk, V. Siccardi, Ashok Kumar, Y. Hu, R. Unalan, M. Arthaud, Liang Li, B. Zhou, Elizabeth Gallas, J. G.R. Lima, D. Schaile, Jean-Arcady Meyer, V. M. Podstavkov, E. Strauss, J. F. Bartlett, Tae Jeong Kim, D. MacKin, V. Bunichev, D. Wicke, M. S. Rangel, P. Slattery, W. C. Fisher, L. Bagby, M. Lokajicek, Cristina Galea, P. Banerjee, Lev Dudko, Robert Kehoe, L. Bellantoni, Helena Malbouisson, N. Wermes, A. Das, H. Greenlee, Y. A. Yatsunenko, J. Warchol, Y. Arnoud, A. Sanchez-Hernandez, J. N. Butler, P. D. Grannis, P. Haefner, Michael Begel, Zdenek Hubacek, Philip Baringer, F. Rizatdinova, J. Kraus, A. Rakitine, R. Hirosky, M. Abolins, H. Severini, Eduardo De Moraes Gregores, Marvin Johnson, R. Van Kooten, Tulika Bose, M. Buehler, L. Stutte, R. Bernhard, S. Banerjee, G. Pawloski, W. E. Cooper, M. S. Anzelc, S. Sumowidagdo, Sarah Catherine Eno, V. Zutshi, L. Sonnenschein, M. Verzocchi, H. A. Neal, A. Chandra, A. V. Kozelov, Roger Moore, P. Vokac, V. O'Dell, P. K. Mal, H. D. Wahl, J. Hays, R. Jesik, M. Wetstein, L. Sawyer, Freya Blekman, M. Petteni, K. A. Johns, C. Potter, Luiz Mundim, A. Bross, Suyong Choi, P. Skubic, Ernest Aguilo, K. Herner, F. Charles, Sharon Hagopian, S. Desai, D. Zieminska, Mark Raymond Adams, A. Bean, B. Baldin, H. T. Diehl, Arnaud Duperrin, A. Wenger, A. K.A. Maciel, S. Hossain, S. J. De Jong, T. A. Bolton, A. Boehnlein, D. Lam, Alexander Leflat, D. Karmanov, G. Safronov, M. Demarteau, T. Moulik, J. Parsons, Jiaming Yu, Christian Schwanenberger, V. L. Malyshev, M. A. Pleier, N. Gollub, Brad Abbott, Sergey Burdin, M. Kirsch, M. Eads, M. Anastasoaie, V. Buescher, Richard B. Lipton, L. Wang, Sudhir Malik, E. G. Zverev, Ia Iashvili, Arnulf Quadt, M. Besançon, S. Lammers, Brajesh C Choudhary, P. Padley, R. Piegaia, J. Ellison, M. Ahsan, Sa. Jain, S. Fuess, S. P. Denisov, Andrew Brandt, B. Spurlock, L. Mendoza, D. Tsybychev, M. Aoki, Andy Haas, L. S. Ancu, John Hobbs, B. Martin, G. C. Blazey, B. Andrieu, Elliott Cheu, C. Garcia, S. J. Wimpenny, T. Kurca, Frank Fiedler, Marc Weber, B. Tuchming, E. Kajfasz, P. Svoisky, S. Uzunyan, A. White, R. J. Madaras, Gregorio Bernardi, Frederic Deliot, D. Denisov, J. Barreto, Victor Daniel Elvira, R. K. Mommsen, A. V. Ferapontov, T. Nunnemann, Jeroen Hegeman, N. Osman, Jean-Francois Grivaz, Hal Evans, D. Chakraborty, P. Love, B. Quinn, Y. M. Kharzheev, J. Piper, S. Yacoob, D. Duggan, K. W. Merritt, G. Obrant, A. A. Shchukin, E. von Toerne, R. Ströhmer, P. Jonsson, Y. Xie, B. Sanghi, G. Alkhazov, D. V. Bandurin, Thomas Hebbeker, Don Lincoln, D. Khatidze, D. Onoprienko, P. Mättig, A. Magerkurth, R. Otec, R. Illingworth, C. Ochando, P. Polozov, J. P. Negret, T. Ferbel, Kristian Harder, H. S. Mao, J. Snow, R. D. Schamberger, Calvin A. Johnson, P. Rubinov, D. Cutts, Wagner Carvalho, Greg Landsberg, Timothy Andeen, Carlos Avila, R. Yamada, J. P. Konrath, Sabine Crépé-Renaudin, M. Ćwiok, H. Dong, Pedrame Bargassa, K. Soustruznik, J. Strandberg, P. A. Kasper, A. Bellavance, J. Qian, D. Buchholz, N. J. Buchanan, C. Royon, S. K. Park, B. G. Pope, A. Jonckheere, M. P. Sanders, Jing Li, Florent Lacroix, T. Zhao, T. Yasuda, Anna Goussiou, L. Duflot, L. Welty-Rieger, Y. Peters, A. P. Heinson, Krisztian Peters, J. Dyer, Gregory R Snow, F. Tissandier, G. S. Muanza, K. Ranjan, I. Hall, M. Rominsky, R. E. Hall, B. S. Acharya, P. Vint, H. Nilsen, Daniel Bloch, Aaron Dominguez, T. R. Wyatt, C. Jarvis, S. W. Youn, G. Watts, M. Sosebee, M. Hohlfeld, F. Badaud, Maria Elena Pol, S. Anderson, Harald Fox, P. Pétroff, Vipin Bhatnagar, E. De La Cruz-Burelo, M. H.L.S. Wang, Kenneth Bloom, R. Wagner, Christopher George T. Tully, P. Rich, L. Zivkovic, M. Wobisch, D. Strom, R. Partridge, V. M. Abazov, S. Reucroft, Iain Alexander Bertram, V. N. Evdokimov, V. A. Bezzubov, Martin Grunewald, Michael Hildreth, D. Kau, F. Guo, Darien Wood, A. Lobodenko, Amnon Harel, Nicholas John Hadley, C. P. Buszello, S. Chakrabarti, A. Schwartzman, N. Khalatyan, S. Blessing, George Alverson, S. Beale, D. Hedin, B. Tiller, Nikos Varelas, R. K. Shivpuri, P. Renkel, D. R. Claes, Gavin Davies, Philippe Calfayan, G. Savage, S. M. Lietti, Kaushik De, S. Snyder, J. Cammin, M. C. Cousinou, S. Fu, V. Stolin, G. Hesketh, Martin J. Strauss, P. Lebrun, D. K. Cho, S. Kermiche, Suman Bala Beri, F. Chevallier, A. Juste, Todd Adams, P. Neustroev, J. Osta, D. Edmunds, T. Gadfort, Andre Sznajder, Yuri Gershtein, J. M. Hauptman, Cecilia Elena Gerber, Universidad de Buenos Aires, Centro Brasileiro de Pesquisas Físicas, Universidade do Estado do Rio de Janeiro (UERJ), Universidade Federal do ABC (UFABC), Universidade Estadual Paulista (UNESP), University of Alberta, Simon Fraser University, Burnaby, York University, McGill University, University of Science and Technology of China, Universidad de Los Andes, Charles University, Czech Technical University, Academy of Sciences of the Czech Republic, Universidad San Francisco de Quito, CNRS/IN2P3, Institut National Polytechnique de Grenoble, Univ Paris-Sud, IN2P3/CNRS, CEA, Université de Lyon, RWTH Aachen University, Universität Bonn, Universität Freiburg, Universität Mainz, Ludwig-Maximilians-Universität München, University of Wuppertal, Panjab University, Delhi University, Tata Institute of Fundamental Research, University College Dublin, Korea University, SungKyunKwan University, CINVESTAV, FOM-Institute NIKHEF and University of Amsterdam/NIKHEF, Radboud University Nijmegen/NIKHEF, Joint Institute for Nuclear Research, Institute for Theoretical and Experimental Physics, Moscow State University, Institute for High Energy Physics, Petersburg Nuclear Physics Institute, Lund University, Stockholm University, Uppsala University, Lancaster University, Imperial College, University of Manchester, University of Arizona, University of California, California State University, Florida State University, Fermi National Accelerator Laboratory, University of Illinois at Chicago, Northern Illinois University, Northwestern University, Indiana University, University of Notre Dame, Purdue University Calumet, Iowa State University, University of Kansas, Kansas State University, Louisiana Tech University, University of Maryland, Boston University, Northeastern University, University of Michigan, Michigan State University, University of Mississippi, University of Nebraska, Princeton University, State University of New York, Columbia University, University of Rochester, Brookhaven National Laboratory, Langston University, University of Oklahoma, Oklahoma State University, Brown University, University of Texas, Southern Methodist University, Rice University, University of Virginia, University of Washington, Augustana College, University of Liverpool, ICN-UNAM, Georg-August-University, Helsinki Institute of Physics, and Universitt Zrich
Subjects: Quark, Physics, Particle physics, 010308 nuclear & particles physics, High Energy Physics::Phenomenology, Tevatron, General Physics and Astronomy, Type (model theory), 01 natural sciences, law.invention, law, 0103 physical sciences, Higgs boson, Production (computer science), High Energy Physics::Experiment, Fermilab, 010306 general physics, Collider, Boson
Abstract: Made available in DSpace on 2022-04-28T20:54:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-05-14 We describe a search for production of a charged Higgs boson, qq̄′→H+, reconstructed in the tb̄ final state in the mass range 180≤MH+≤300GeV. The search was undertaken at the Fermilab Tevatron collider with a center-of-mass energy s=1.96TeV and uses 0.9fb-1 of data collected with the D0 detector. We find no evidence for charged Higgs boson production and set upper limits on the production cross section in the types I, II, and III two-Higgs-doublet models (2HDMs). An excluded region in the (MH+, tanβ) plane for type I 2HDM is presented. © 2009 The American Physical Society. Universidad de Buenos Aires, Buenos Aires LAFEX Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro Universidade Federal Do ABC, Santo André Instituto de Física Teórica Universidade Estadual Paulista, São Paulo University of Alberta, Edmonton, AB Simon Fraser University, Burnaby, British Columbia York University, Toronto, ON McGill University, Montreal, QC University of Science and Technology of China, Hefei Universidad de Los Andes, Bogotá, Colombia Center for Particle Physics Charles University, Prague Czech Technical University, Prague Center for Particle Physics Institute of Physics Academy of Sciences of the Czech Republic, Prague Universidad San Francisco de Quito, Quito Ecuador LPC Univ Blaise Pascal CNRS/IN2P3, Clermont LPSC Université Joseph Fourier Grenoble 1 Institut National Polytechnique de Grenoble CPPM Aix-Marseille Université CNRS/IN2P3, Marseille LAL Univ Paris-Sud, IN2P3/CNRS, Orsay LPNHE IN2P3/CNRS, Universités Paris VI and VII, Paris DAPNIA/Service de Physique des Particules CEA, Saclay IPHC Université Louis Pasteur et Université de Haute Alsace CNRS/IN2P3, Strasbourg IPNL Université Lyon 1 CNRS/IN2P3, Villeurbanne Université de Lyon, Lyon III. Physikalisches Institut A RWTH Aachen University, Aachen Physikalisches Institut Universität Bonn, Bonn Physikalisches Institut Universität Freiburg, Freiburg Institut für Physik Universität Mainz, Mainz Ludwig-Maximilians-Universität München, München Fachbereich Physik University of Wuppertal, Wuppertal Panjab University, Chandigarh Delhi University, Delhi Tata Institute of Fundamental Research, Mumbai University College Dublin, Dublin Korea Detector Laboratory Korea University, Seoul SungKyunKwan University, Suwon CINVESTAV, Mexico City FOM-Institute NIKHEF and University of Amsterdam/NIKHEF, Amsterdam Radboud University Nijmegen/NIKHEF, Nijmegen Joint Institute for Nuclear Research, Dubna 98195 Institute for Theoretical and Experimental Physics, Moscow Moscow State University, Moscow Institute for High Energy Physics, Protvino Petersburg Nuclear Physics Institute, St. Petersburg Lund University, Lund Royal Institute of Technology Stockholm University, Stockholm Uppsala University, Uppsala Lancaster University, Lancaster Imperial College, London University of Manchester, Manchester University of Arizona, Tucson, AZ 85721 Lawrence Berkeley National Laboratory University of California, Berkeley, CA 94720 California State University, Fresno, CA 93740 University of California, Riverside, CA 92521 Florida State University, Tallahassee, FL 32306 Fermi National Accelerator Laboratory, Batavia, IL 60510 University of Illinois at Chicago, Chicago, IL 60607 Northern Illinois University, DeKalb, IL 60115 Northwestern University, Evanston, IL 60208 Indiana University, Bloomington, IN 47405 University of Notre Dame, Notre Dame, IN 46556 Purdue University Calumet, Hammond, IN 46323 Iowa State University, Ames, IA 50011 University of Kansas, Lawrence, KS 66045 Kansas State University, Manhattan, KS 66506 Louisiana Tech University, Ruston, LA 71272 University of Maryland, College Park, MD 20742 Boston University, Boston, MA 02215 Northeastern University, Boston, MA 02115 University of Michigan, Ann Arbor, MI 48109 Michigan State University, East Lansing, MI 48824 University of Mississippi, University, MS 38677 University of Nebraska, Lincoln, NE 68588 Princeton University, Princeton, NJ 08544 State University of New York, Buffalo, NY 14260 Columbia University, New York, NY 10027 University of Rochester, Rochester, NY 14627 State University of New York, Stony Brook, NY 11794 Brookhaven National Laboratory, Upton, NY 11973 Langston University, Langston, OK 73050 University of Oklahoma, Norman, OK 73019 Oklahoma State University, Stillwater, OK 74078 Brown University, Providence, RI 02912 University of Texas, Arlington, TX 76019 Southern Methodist University, Dallas, TX 75275 Rice University, Houston, TX 77005 University of Virginia, Charlottesville, VA 22901 University of Washington, Seattle, WA 98195 Augustana College, Sioux Falls, SD University of Liverpool, Liverpool ICN-UNAM, Mexico City Physikalisches Institut Georg-August-University, Gttingen Helsinki Institute of Physics, Helsinki Universitt Zrich, Zrich Instituto de Física Teórica Universidade Estadual Paulista, São Paulo
Published: 2016

87. Occurrence of <scp>CCSVI</scp> in patients with <scp>MS</scp> and its relationship with iron metabolism and varicose veins

Author: G. B. Van den Berg, P. J. Van den Berg, L. W. Westerhuis, and Leo H. Visser
Subjects: Male, medicine.medical_specialty, Multiple Sclerosis, Ultrasonography, Doppler, Transcranial, Iron, Venous stasis, Varicose Veins, Internal medicine, Varicose veins, medicine, Humans, Telangiectasia, Expanded Disability Status Scale, business.industry, Multiple sclerosis, Odds ratio, Middle Aged, medicine.disease, Surgery, Peripheral, Chronic cerebrospinal venous insufficiency, Spinal Cord, Venous Insufficiency, Neurology, Cardiology, Female, Neurology (clinical), medicine.symptom, business
Abstract: Background and purpose A new treatable venous disorder, chronic cerebrospinal venous insufficiency (CCSVI), has been proposed in patients with multiple sclerosis (MS). Its relationship with iron metabolism is suggested, but has not been examined prospectively. Methods We performed extra- and transcranial echo colour Doppler (ECD) in 90 patients with MS and 41 healthy controls (HC). Indices of iron metabolism and the presence of peripheral signs of impaired venous flow were also examined. Results The ECD examination showed CCSVI in 8 (9%) of the 90 patients with MS and 0 HC (P = 0.11). The 8 CCSVI-positive MS patients were older (P = 0.02), had less often relapsing–remitting-MS (P = 0.02) and had more neurological disability assessed by expanded disability status scale (EDSS, P = 0.001) and longer duration of disease (P = 0.02) in comparison with the 82 CCSVI-negative MS patients. Multivariate analysis revealed that EDSS remained an independent factor associated with CCSVI (odds ratio 1.89, 95%CI 1.17–3.05, P-value = 0.009). CCSVI MS patients more often had bilateral telangiectasia at the legs (P = 0.008), reticular veins (P = 0.006) and venous stasis dermatitis (P = 0.004). No relationship was found between CCSVI and impaired iron metabolism in patients with MS. Conclusions CCSVI is uncommon and is a secondary epiphenomenon in MS and related to more neurological disability and the presence of varicose veins at the legs.
Published: 2012

88. Extra- and Transcranial Echo Colour Doppler in the Diagnosis of Chronic Cerebrospinal Venous Insufficiency

Author: Leo H. Visser and P J Van den Berg
Subjects: medicine.medical_specialty, Multiple Sclerosis, Supine position, Ultrasonography, Doppler, Transcranial, business.industry, Multiple sclerosis, Venous drainage, General Medicine, medicine.disease, Cerebral Veins, Cerebrovascular Disorders, Chronic cerebrospinal venous insufficiency, Stenosis, Venous Insufficiency, Deep cerebral vein, Azygos Vein, medicine, Colour doppler, Humans, In patient, Radiology, Jugular Veins, Cardiology and Cardiovascular Medicine, business
Abstract: A new venous disorder, chronic cerebrospinal venous insufficiency (CCSVI), has been proposed in patients with multiple sclerosis (MS). It is a vascular condition characterized by an impaired cerebrospinal venous drainage due to obstructions in the main extracranial cerebrovenous outflow routes (i.e. internal jugular veins [IJV] and/or azygos veins). In this review, the studies which assessed the prevalence of CCSVI in MS by echo colour Doppler (ECD) will be discussed. The technical aspects of determination of the five CCSVI criteria: (1) reflux in the IJV and/or vertebral veins in supine and upright position, (2) reflux in the deep cerebral veins, (3) high-resolution B-mode proximal IJV stenosis, (4) flow not Doppler detectable in IJVs and/or vertebral veins (VVs) and (5) reverted postural control of the main cerebrovenous outflow pathway are described in detail. We conclude that so far there are many studies with contradictory results, and as yet a strong scientific base to support the evidence for a causative relationship of CCSVI and MS is lacking. Recent studies call into question the validity of using ECD as a proper and reliable test for the diagnosis of CCSVI. One explanation for the variety in interpretation of the individual CCSVI criteria, with the wide-ranging percentages CCSVI, could be the different methods by using ECD to determine various criteria.
Published: 2012

89. Dependence of the tt¯ production cross section on the transverse momentum of the top quark

Author: Y. W. Liu, D. Bauer, U. Bassler, G. Gutierrez, Gilvan Alves, S. Robinson, Regina Demina, M. Arov, W. C. Yang, Samuel Calvet, M. Padilla, M. Kirsch, Alexander Grohsjean, T. Moulik, G. Sajot, Y. Hu, D. Smirnov, M. S. Rangel, Maxim Perfilov, Lev Uvarov, D. Jamin, Grigory Safronov, S. Chakrabarti, P. Renkel, Sergey Burdin, M. Eads, S. P. Denisov, I. Ripp-Baudot, A. Meyer, J. Snow, K. Peters, P. Rubinov, M. Abolins, Sarah Catherine Eno, F. Badaud, N. K. Mondal, H. T. Diehl, T. A. Bolton, A. Boehnlein, J. Ellison, P. Neustroev, Sa. Jain, R. Jesik, S. Fuess, P. Verdier, Wade Cameron Fisher, T. Kurca, Horst Severini, Marc Weber, M. Pangilinan, T. H. Burnett, Emanuela Barberis, Hakjae Lee, R. Magaña-Villalba, S. W. Cho, G. Obrant, Junjie Zhu, K. A. Johns, L. Bellantoni, S. Schlobohm, X. B. Bu, B. Sanghi, Sung Keun Park, V. A. Kuzmin, H. Greenlee, Michael Mulhearn, Richard B. Lipton, D. M. Strom, Dmitri Tsybychev, R. L. McCarthy, Andrew White, Shabnam Jabeen, M. Merkin, A. Bross, J. M. Hauptman, Cecilia Elena Gerber, P. D. Grannis, Raimund Ströhmer, V. Simak, Ashok Kumar, A. F. Barfuss, V. A. Bezzubov, B. Spurlock, G. Ginther, Sabine Lammers, Zeno Dixon Greenwood, J. A. Benitez, J. P. Negret, D. Buchholz, P. Padley, G. C. Blazey, D. N. Brown, Raymond Brock, Serban Protopopescu, A. Das, M. Sosebee, Jianming Qian, Cristina Galea, Jeroen Hegeman, Suyong Choi, R. Beuselinck, K. Devaughan, Christophe Royon, Tulika Bose, R. Luna-Garcia, M. Aoki, Andy Haas, P. Vint, R. Yamada, Michael Hildreth, D. Menezes, Jean-Francois Grivaz, Mitchell Wayne, H. Schellman, J. M. Kohli, Anna Goussiou, S. Söldner-Rembold, P. Skubic, A. V. Popov, Ulrich Heintz, Darren Price, P. K. Mal, S. Chevalier-Théry, R. Otec, John Hobbs, P. Jonsson, Pedro G Mercadante, G. Golovanov, L. Duflot, J. K. Lim, Stefan Grünendahl, J. Orduna, Gustaaf Brooijmans, Maria Elena Pol, J. Barreto, G. S. Muanza, W. M. Van Leeuwen, Frank Filthaut, M. Diesburg, D. Karmanov, A. Jonckheere, Sergio F Novaes, S. Hossain, H. D. Wahl, P. N. Ratoff, Suneel Dutt, Thomas Hebbeker, S. Uzunyan, Mary Beth Adams, B. Gómez, B. Tuchming, Amnon Harel, O. Atramentov, L. S. Vertogradov, Y. Peters, P. M. Tuts, Maksym Titov, Hua-Lei Yin, A. Sanchez-Hernandez, V. Zutshi, J. Martínez-Ortega, Bjoern Penning, C. Belanger-Champagne, J. F. Bartlett, I. Hall, A. Lobodenko, J. Warchol, S. J. De Jong, Meng Wang, Helio Nogima, P. Rich, C. Zeitnitz, A. Tanasijczuk, E. E. Boos, D. A. Stoyanova, Heriberto Castilla-Valdez, C. L. McGivern, Gregory R Snow, S. Beale, B. C.K. Casey, D. Khatidze, P. Polozov, Andrew Askew, Y. Arnoud, R. Bernhard, Sudhir Malik, Ia Iashvili, Brajesh C Choudhary, B. Åsman, G. Grenier, A. P. Heinson, V. M. Podstavkov, M. A. Pleier, M. Fortner, Zhanqiang Liu, M. A. Carrasco-Lizarraga, Arnulf Quadt, Elemer Nagy, Kristian Harder, D. Cutts, P. Haefner, Tiefu Zhao, S. W. Youn, M. P. Sanders, Yurii Maravin, Vladimir Gavrilov, Gordon Watts, L. S. Ancu, Peter Love, W. Geng, E. De La Cruz-Burelo, Andrew Brandt, L. Zivkovic, A. A. Shchukin, Y. N. Kharzheev, Yuji Enari, W. E. Cooper, P. Svoisky, D. Wicke, J. K. Kraus, Gregorio Bernardi, D. Denisov, M. Cooke, V. Kaushik, Michael Begel, R. Nayyar, Robert Kehoe, Dennis Stephen Mackin, Jean-Arcady Meyer, L. Bagby, Greg Landsberg, V. Sirotenko, Frank Fiedler, J. Clutter, Hal Evans, Alexey Ferapontov, Sw. Banerjee, K. Herner, G. Weber, Md. Naimuddin, Thomas Ferbel, Daria Zieminska, Ph Gris, M. Prewitt, R. D. Schamberger, Eduardo De Moraes Gregores, E. Kajfasz, P. Houben, M. H. Kirby, M. M. Meijer, Kirti Ranjan, Carsten Hensel, H. E. Fisk, E. Strauss, P. Mättig, Arnaud Duperrin, Lars Sonnenschein, N. Khalatyan, S. Yacoob, Marvin Johnson, A. L. Lyon, D. Chakraborty, T. R. Wyatt, K. M. Chan, Phillip Gutierrez, M. Wetstein, Aran Garcia-Bellido, P. L.M. Podesta-Lerma, T. Yasuda, Jun Guo, Q. Z. Li, Jong-Sung Yu, T. Dorland, R. Illingworth, A. Leflat, A. V. Kozelov, Luiz Mundim, Don Lincoln, Erich Varnes, Marco Verzocchi, Theodoros Christoudias, E. G. Zverev, K. Soustruznik, W. M. Lee, T. Nunnemann, Aaron Dominguez, B. Baldin, G. Alkhazov, M. Buehler, D. V. Bandurin, George Alverson, Mark Richard James Williams, A. Evdokimov, Daniel Duggan, Ernest Aguilo, S. Cihangir, Fabrice Couderc, A. Patwa, S. Desai, Mark Owen, J. A. Parsons, J. Osta, Petr Vokac, D. Onoprienko, D. Hedin, Brad Abbott, M. Vesterinen, Philip Baringer, Sharon Hagopian, A. K.A. Maciel, J. Piper, Frederic Deliot, Marcia Begalli, Liang Li, P. Lebrun, V. M. Abazov, V. V. Tokmenin, Pierre Petroff, Christopher George Tully, Harald Fox, G. Facini, H. A. Neal, G. Otero y Garzon, B. Calpas, M. Ćwiok, Lev Dudko, Calvin A. Johnson, J. T. Linnemann, Guennadi Borissov, Meenakshi Narain, O. Mundal, K. Yip, N. Osman, I. Heredia-De La Cruz, R. Van Kooten, G. D. Alexeev, Flera Rizatdinova, Elizaveta Shabalina, H. Nilsen, P. A. Kasper, Hwi Dong Yoo, Zdenek Hubacek, Patrick Slattery, M. D. Corcoran, A. Chandra, R. Unalan, L. Stutte, R. Piegaia, Andre Sopczak, Jonas Strandberg, N. Huske, A.S. Dyshkant, G. Savage, Jiri Kvita, L. Han, S. Greder, Iain Alexander Bertram, M. Jaffré, Joseph Haley, Pushpalatha C Bhat, D. Gerbaudo, Maiko Takahashi, B. Tiller, Elliott Cheu, T. Schliephake, W. Geist, Michael Rijssenbeek, Dorothee Schaile, A. Alton, B. Hoeneisen, Lee Sawyer, Alexander Kupco, S. Zelitch, Victor Daniel Elvira, I. Katsanos, E. Carrera, M. A. Strang, N. Parua, D. Vilanova, Randy Ruchti, D. Lam, I. A. Vasilyev, M. Demarteau, M. Hohlfeld, Wendy Taylor, V. Parihar, V. Bunichev, V. V. Shary, Avto Kharchilava, Neeti Parashar, T. Hoang, Alexander Khanov, V. N. Evdokimov, Markus Wobisch, A. Dubey, I. Razumov, B. S. Acharya, S. Uvarov, M. Rominsky, M. Zielinski, J. Hays, B. Quinn, C. Schwanenberger, Alice Bean, Volker Buescher, T. Gadfort, Vipin Bhatnagar, Y. A. Yatsunenko, Viatcheslav Stolin, R. Partridge, Kenneth Bloom, V. L. Malyshev, Carlos Avila, Graham Wilson, D. Gillberg, A. S. Ito, A. Melnitchouk, S. J. Park, V. V. Lipaev, J. Lellouch, D. Boline, Nikos Varelas, Bing Zhou, Luis Mendoza, Stephen Wimpenny, J. Backusmayes, Martin Grunewald, Milos Lokajicek, F. Guo, Darien Wood, C. P. Buszello, Yuehong Xie, S. Blessing, Scott Snyder, R. K. Shivpuri, D. R. Claes, Gavin Davies, Philippe Calfayan, S. M. Lietti, Y. Scheglov, Kaushik De, Jan Stark, Henry Lubatti, J. Cammin, J. Sekaric, Michael A. Strauss, Chong-Yu Xu, D. K. Cho, T. Scanlon, S. Kermiche, Suman Bala Beri, V. Hynek, A. Juste, Todd Adams, D. Edmunds, Zhenyu Ye, Yuri Gershtein, E. Camacho-Pérez, Reinhard Schwienhorst, M. C. Cousinou, David T. Johnston, G. Hesketh, P. J. Van Den Berg, Marc Besancon, and Robert Hirosky
Subjects: Quantum chromodynamics, Physics, Nuclear and High Energy Physics, Top quark, Particle physics, Luminosity (scattering theory), 010308 nuclear & particles physics, Bar (music), High Energy Physics::Phenomenology, Perturbative QCD, Jet (particle physics), 01 natural sciences, Nuclear physics, 0103 physical sciences, High Energy Physics::Experiment, Production (computer science), 010306 general physics, Lepton
Abstract: We present a measurement of the differential cross section for $t\bar{t}$ events produced in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV as a function of the transverse momentum ($p_T$) of the top quark. The selected events contain a high-$p_T$ lepton ($\ell$), four or more jets, and a large imbalance in $p_T$, and correspond to 1 fb${}^{-1}$ of integrated luminosity recorded with the D0 detector. Each event must have at least one candidate for a $b$ jet. Objects in the event are associated through a constrained kinematic fit to the $t\bar{t}\to WbW\bar{b} \to \ell\nu b q\bar{q}'\bar{b}$ process. Results from next-to-leading-order perturbative QCD calculations agree with the measured differential cross section. Comparisons are also provided to predictions from Monte Carlo event generators using QCD calculations at different levels of precision.
Published: 2010

90. Search for single top quarks in the tau + jets channel using 4.8 fb−1 of pp¯ collision data

Author: Guennadi Borissov, I. Heredia-De La Cruz, Marco Verzocchi, Theodoros Christoudias, W. C. Fisher, Dugan O'Neil, A. Patwa, Mark Owen, Neeti Parashar, Marcia Begalli, I. Razumov, M. Zielinski, J. Hays, M. Buehler, Mark Richard James Williams, Meenakshi Narain, A. Sanchez-Hernandez, V. Zutshi, Raimund Ströhmer, V. Simak, Andrew Askew, Sharon Hagopian, A. K.A. Maciel, Sabine Lammers, P. Padley, D. Edmunds, T. Gadfort, D. A. Stoyanova, T. Nunnemann, B. Baldin, G. S. Muanza, R. Piegaia, Zhenyu Ye, Mansoora Shamim, M. A. Carrasco-Lizarraga, Mitchell Wayne, E. Aguilo, H. Schellman, J. M. Kohli, Yuri Gershtein, P. Rich, C. L. McGivern, Andre Sopczak, C. Zeitnitz, Arnulf Quadt, K. Devaughan, Elemer Nagy, Stefan Grünendahl, D. Karmanov, Sudhir Malik, E. G. Zverev, Ia Iashvili, Brajesh C Choudhary, D. Menezes, Elliott Cheu, T. Schliephake, Victor Daniel Elvira, W. M. Van Leeuwen, B. Gómez, G. C. Blazey, D. Wicke, V. V. Tokmenin, B. Tuchming, Michael Begel, G. Facini, B. C.K. Casey, I. Torchiani, R. Yamada, E. Camacho-Pérez, Suneel Dutt, A. Alton, Meng Wang, Nikos Varelas, Bing Zhou, Luis Mendoza, H. A. Neal, J. T. Linnemann, O. Mundal, K. Yip, Eduardo De Moraes Gregores, Dennis Stephen Mackin, D. Duggan, R. Unalan, G. Alkhazov, Jean-Francois Grivaz, Sergio F Novaes, P. Polozov, Aaron Dominguez, R. Van Kooten, Reinhard Schwienhorst, V. M. Abazov, L. Stutte, A.S. Dyshkant, Jiri Kvita, D. Gerbaudo, Luiz Mundim, P. Jonsson, Helio Nogima, Stephen Wimpenny, D. V. Bandurin, M. D. Corcoran, P. Verdier, P. Renkel, M. P. Sanders, Yurii Maravin, Vladimir Gavrilov, Gordon Watts, W. C. Yang, Maxim Perfilov, L. Han, J. Sekaric, Michael A. Strauss, Thomas Hebbeker, B. Sanghi, J. Backusmayes, Martin Grunewald, Y. A. Yatsunenko, Chong-Yu Xu, Y. N. Kharzheev, Milos Lokajicek, Mary Beth Adams, Marvin Johnson, T. H. Burnett, Jean-Arcady Meyer, L. Bagby, V. Shary, V. Sirotenko, V. A. Kuzmin, U. Bassler, A. Das, M. Sosebee, L. Bellantoni, J. Clutter, Md. Naimuddin, S. Robinson, Viatcheslav Stolin, A. L. Lyon, F. Guo, Phillip Gutierrez, P. Lebrun, A. V. Kozelov, J. A. Benitez, Z. Liu, Darien Wood, M. Ćwiok, K. M. Chan, Dorothee Schaile, Regina Demina, C. P. Buszello, Ulrich Heintz, P. D. Grannis, Carlos Avila, S. Sumowidagdo, S. Greder, Iain Alexander Bertram, M. A. Strang, P. A. Kasper, S. Hossain, P. Neustroev, P. K. Mal, D. K. Cho, M. Hohlfeld, Wendy Taylor, S. Blessing, Jun Guo, Q. Z. Li, Frank Filthaut, Samuel Calvet, T. Scanlon, S. Kermiche, M. Pangilinan, S. Cihangir, V. Bunichev, Roger Moore, M. Diesburg, Scott Snyder, S. Desai, Petr Vokac, D. N. Brown, G. Sajot, Y. Hu, Suyong Choi, Suman Bala Beri, V. Hynek, Michael Rijssenbeek, M. S. Rangel, S. Zelitch, E. De La Cruz-Burelo, Fabrice Couderc, G. Golovanov, A. Tanasijczuk, R. K. Shivpuri, T. Moulik, M. Padilla, J. A. Parsons, J. Osta, A. Juste, Yuji Enari, P. Skubic, S. Schlobohm, Andrew Brandt, L. Zivkovic, H. Greenlee, Todd Adams, D. Jamin, Grigory Safronov, S. Chakrabarti, B. Calpas, J. F. Bartlett, R. Nayyar, Robert Kehoe, Liang Li, Kirti Ranjan, Carsten Hensel, D. R. Claes, Gavin Davies, Philippe Calfayan, Maria Elena Pol, A. Leflat, V. N. Evdokimov, D. M. Strom, Lev Dudko, B. S. Acharya, Sarah Catherine Eno, Horst Severini, M. C. Cousinou, S. M. Lietti, Frederic Deliot, Alexey Ferapontov, Dmitri Tsybychev, R. L. McCarthy, Hakjae Lee, Junjie Zhu, Gregorio Bernardi, M. Wetstein, Christopher George Tully, P. Rubinov, H. Nilsen, D. Denisov, David T. Johnston, A. Bross, Peter Love, Christophe Royon, W. Geng, N. Huske, Richard B. Lipton, Kristian Harder, H. D. Wahl, Y. Scheglov, Kaushik De, Jan Stark, Hal Evans, Thomas Ferbel, M. Prewitt, Lars Sonnenschein, N. Osman, Patrick Slattery, A. Chandra, F. Badaud, H. E. Fisk, G. Savage, Hwi Dong Yoo, Zdenek Hubacek, Jonas Strandberg, E. Strauss, M. Jaffré, D. Cutts, Henry Lubatti, N. Khalatyan, S. Yacoob, Serban Protopopescu, Robert Hirosky, X. B. Bu, E. E. Boos, Heriberto Castilla-Valdez, Wagner Carvalho, Sergey Burdin, Greg Landsberg, M. Eads, K. Herner, A. Evdokimov, Avto Kharchilava, T. Hoang, Alexander Khanov, D. Buchholz, Joseph Haley, G. Hesketh, J. Cammin, P. J. Van Den Berg, M. Aoki, Andy Haas, S. P. Denisov, S. Söldner-Rembold, M. M. Meijer, George Alverson, P. Haefner, Marc Besancon, K. Soustruznik, T. Yasuda, Aran Garcia-Bellido, Anna Goussiou, Harald Fox, Alexander Kupco, I. Katsanos, R. Jesik, K. A. Johns, D. Hedin, Graham Wilson, Y. W. Liu, D. Gillberg, D. Bauer, G. Weber, Tiefu Zhao, D. Chakraborty, S. W. Youn, J. K. Kraus, A. F. Barfuss, V. A. Bezzubov, Michael Mulhearn, J. P. Negret, N. Parua, D. Vilanova, Randy Ruchti, Gregory R Snow, A. S. Ito, A. Melnitchouk, S. J. Park, Jeroen Hegeman, Maiko Takahashi, R. Luna-Garcia, S. J. De Jong, Don Lincoln, I. A. Vasilyev, Vipin Bhatnagar, Erich Varnes, Michael Hildreth, P. L.M. Podesta-Lerma, R. Partridge, V. V. Lipaev, J. Lellouch, D. Boline, S. Uzunyan, J. M. Hauptman, Cecilia Elena Gerber, Benjamin M. Martin, G. Ginther, Y. Xie, Amnon Harel, S. Chevalier-Théry, Brad Abbott, Pierre Petroff, Kenneth Bloom, V. L. Malyshev, Jianming Qian, G. Gutierrez, Gilvan Alves, A. A. Shchukin, Frank Fiedler, E. Kajfasz, M. Vesterinen, J. Martínez-Ortega, Bjoern Penning, C. Belanger-Champagne, Florent Lacroix, D. Khatidze, M. Cooke, L. Duflot, Karl Jakobs, V. Kaushik, J. K. Lim, P. Vint, M. Kirsch, A. V. Popov, B. Åsman, Philip Baringer, D. Smirnov, J. Piper, A. P. Heinson, T. Dorland, Gustaaf Brooijmans, S. Uvarov, S. Banerjee, Andrew White, M. A. Pleier, B. Quinn, R. E. Hall, C. Schwanenberger, Alice Bean, J. Snow, Volker Buescher, K. Peters, John Hobbs, J. Barreto, Sung Keun Park, A. Jonckheere, L. S. Ancu, I. Hall, A. Lobodenko, Daria Zieminska, R. Otec, P. N. Ratoff, Y. Peters, R. D. Schamberger, P. M. Tuts, Maksym Titov, Hua-Lei Yin, T. R. Wyatt, Pushpalatha C Bhat, P. Mättig, W. Geist, B. Hoeneisen, Lee Sawyer, R. Illingworth, E. Carrera, Calvin A. Johnson, J. Warchol, D. Lam, M. Demarteau, Elizaveta Shabalina, G. D. Alexeev, Flera Rizatdinova, R. Magaña-Villalba, S. W. Cho, G. Obrant, Shabnam Jabeen, Raymond Brock, R. Beuselinck, L. S. Vertogradov, R. G. Wagner, Y. Arnoud, P. G. Mercadante, R. Bernhard, W. E. Cooper, Arnaud Duperrin, Jong-Sung Yu, B. Tiller, Emanuela Barberis, M. Abolins, Markus Wobisch, S. Beale, Ashok Kumar, A. Dubey, G. Grenier, N. K. Mondal, H. T. Diehl, T. A. Bolton, Y. Pogorelov, A. Boehnlein, J. Ellison, M. Ahsan, Sa. Jain, S. Fuess, T. Kurca, Marc Weber, P. Svoisky, I. Ripp-Baudot, A. Meyer, Tulika Bose, V. Parihar, J. Orduna, B. Spurlock, Zeno Dixon Greenwood, D. Onoprienko, G. Otero y Garzon, O. Atramentov, Cristina Galea, M. Merkin, V. M. Podstavkov, M. Arov, M. Fortner, Alexander Grohsjean, Lev Uvarov, Ph Gris, P. Houben, M. H. Kirby, A. Wenger, M. Rominsky, and W. M. Lee
Subjects: Quark, Physics, Nuclear and High Energy Physics, Top quark, Particle physics, Muon, 010308 nuclear & particles physics, Tevatron, 01 natural sciences, law.invention, Nuclear physics, law, 0103 physical sciences, High Energy Physics::Experiment, Production (computer science), Fermilab, 010306 general physics, Collider, Lepton
Abstract: We present the first direct search for single top quark production using tau leptons. The search is based on 4.8 fb$^{-1}$ of integrated luminosity collected in $p\bar{p}$ collisions at $\sqrt{s}$=1.96 TeV with the D0 detector at the Fermilab Tevatron Collider. We select events with a final state including an isolated tau lepton, missing transverse energy, two or three jets, one or two of them $b$ tagged. We use a multivariate technique to discriminate signal from background. The number of events observed in data in this final state is consistent with the signal plus background expectation. We set in the tau+jets channel an upper limit on the single top quark cross section of \TauLimObs pb at the 95% C.L. This measurement allows a gain of 4% in expected sensitivity for the observation of single top production when combining it with electron+jets and muon+jets channels already published by the D0 collaboration with 2.3 fb$^{-1}$ of data. We measure a combined cross section of $\SuperCombineXSall$ pb, which is the most precise measurement to date.
Published: 2010

91. Measurement of the t-channel single top quark production cross section

Author: D. Menezes, Michiel Sanders, M. C. Cousinou, Suneel Dutt, P. Svoisky, M. Arthaud, A. Alton, Meng Wang, David T. Johnston, Andrew White, S. Fu, Helio Nogima, John Hobbs, J. Barreto, S. J. De Jong, V. V. Shary, R. Magaña-Villalba, S. W. Cho, G. Hesketh, G. Obrant, C. Belanger-Champagne, D. Khatidze, P. J. Van Den Berg, M. Cooke, V. Kaushik, Thomas Nunnemann, Marc Besancon, T. Dorland, Y. N. Kharzheev, Shabnam Jabeen, G. Alkhazov, Z. Hubacek, Avto Kharchilava, M. Merkin, D. V. Bandurin, T. Hoang, Jean-Arcady Meyer, L. Bagby, B. Sanghi, Calvin A. Johnson, W. M. Van Leeuwen, H. Nilsen, B. C.K. Casey, Marco Verzocchi, D. Onoprienko, Theodoros Christoudias, Dugan O'Neil, A. Patwa, Robert Hirosky, A. A. Shchukin, Frank Fiedler, E. Kajfasz, T. Kuhl, Christophe Royon, P. Polozov, H. Evans, U. Bassler, Michael A. Strauss, Chong-Yu Xu, K. M. Chan, Dhiman Chakraborty, M. Abolins, Pushpalatha C Bhat, P. Lebrun, P. Skubic, Marcia Begalli, J. P. Konrath, H. J. Lubatti, D. Duggan, S. Robinson, P. Verdier, Y. W. Liu, Meenakshi Narain, Sergio F Novaes, Z. D. Greenwood, H. D. Wahl, D. Buchholz, Regina Demina, D. Bauer, Raymond Brock, Boaz Klima, B. Penning, J. Haley, Samuel Calvet, P. Haefner, D. K. Cho, Kristian Harder, T. Scanlon, S. Kermiche, W. Geist, Elizaveta Shabalina, M. Ćwiok, M. Naimuddin, B. Tiller, Pedro G Mercadante, Kenneth Johns, Suman Bala Beri, V. Hynek, A. Sanchez-Hernandez, Y. Enari, G. Gutierrez, Yurii Maravin, M. Ahsan, Vladimir Gavrilov, R. Beuselinck, S. W. Youn, M. M. Meijer, V. A. Kuzmin, Marvin Johnson, J. K. Kraus, T. Moulik, A. Juste, Gordon Watts, Todd Adams, B. Hoeneisen, Anna Goussiou, Lee Sawyer, P. A. Kasper, A. Bellavance, S. Uvarov, P. L.M. Podesta-Lerma, A. L. Lyon, M. Padilla, W. Geng, A. V. Kozelov, M. Buehler, Mark Richard James Williams, Y. A. Yatsunenko, D. Jamin, Grigory Safronov, S. Chakrabarti, E. E. Boos, T. Yasuda, Z. Liu, Aaron Dominguez, M. Kirsch, D. Smirnov, P. Rubinov, Viatcheslav Stolin, James Linnemann, H. T. Diehl, T. A. Bolton, Y. Pogorelov, Heriberto Castilla-Valdez, N. Khalatyan, S. Yacoob, Gregory R Snow, D. Edmunds, T. Gadfort, P. Calfayan, Zhenyu Ye, Brad Abbott, Yuri Gershtein, M. Owen, Pierre Petroff, Sergey Denisov, A. Das, B. Quinn, V. Sirotenko, J. Clutter, Phillip Gutierrez, George Alverson, V. Zutshi, C. Schwanenberger, J. Snow, K. Peters, Sung Keun Park, A. V. Ferapontov, H. E. Fisk, E. Strauss, Sharon Hagopian, S. Hossain, E. De La Cruz-Burelo, D. Hedin, R. Van Kooten, Carlos Avila, S. Sumowidagdo, A. K.A. Maciel, R. Jesik, Laurent Duflot, P. Neustroev, Andrew Brandt, Alice Bean, L. Zivkovic, K. W. Merritt, A. Boehnlein, J. F. Bartlett, S. Beale, W. M. Lee, M. D. Corcoran, Robert Kehoe, E. Carrera, D. Lam, M. Demarteau, R. Ströhmer, Reinhard Schwienhorst, Vipin Bhatnagar, X. B. Bu, Kirti Ranjan, A. F. Barfuss, V. A. Bezzubov, Wagner Carvalho, Greg Landsberg, V. Simak, K. Herner, J. P. Negret, S. Cihangir, Carsten Hensel, Fabrice Couderc, R. Luna-Garcia, Pedrame Bargassa, R. Partridge, Aran Garcia-Bellido, Guennadi Borissov, I. Heredia-De La Cruz, Michael Hildreth, P. Vint, K. Jakobs, J. Ellison, S. Fuess, T. Kurca, L. S. Ancu, D. N. Brown, Marc Weber, Markus Wobisch, A. V. Popov, M. Hohlfeld, K. Soustruznik, L. Welty-Rieger, R. Otec, Nikos Varelas, Luis Mendoza, R. K. Shivpuri, W. C. Fisher, S. Uzunyan, A. Dubey, G. Grenier, Wendy Taylor, V. Bunichev, Gavin Davies, Liang Li, Roger Moore, L. S. Vertogradov, M. A. Strang, M. Wetstein, R. G. Wagner, Harrison Prosper, P. N. Ratoff, P. M. Tuts, Y. Xie, Gustaaf Brooijmans, Kenneth Bloom, Neeti Parashar, H. Lee, Ricardo Piegaia, G. C. Blazey, I. Ripp-Baudot, Y. Peters, A. Meyer, Amnon Harel, V. L. Malyshev, Maksym Titov, J. Warchol, David Cutts, Lev Dudko, I. Torchiani, V. M. Abazov, V. Siccardi, Sergey Burdin, M. Eads, R. Yamada, J. M. Hauptman, Hua-Lei Yin, Ernest Aguilo, Cecilia Elena Gerber, S. Desai, M. Zielinski, J. Hays, Jean-Francois Grivaz, Y. Arnoud, S. M. Lietti, Suyong Choi, Y. Scheglov, G. Ginther, F. Badaud, Alexander Leflat, Hwi Dong Yoo, S. Greder, Iain Alexander Bertram, M. A. Pleier, Daniel Wicke, P. Jonsson, Kaushik De, Michael Rijssenbeek, R. D. Schamberger, S. Zelitch, Jianming Qian, Thomas Hebbeker, B. Calpas, Florian Lacroix, R. Bernhard, G. D. Alexeev, A. Khanov, Michael Mulhearn, V. N. Evdokimov, P. A. Love, G. S. Muanza, Marc Escalier, M. Jaffré, Maria Elena Pol, F. Rizatdinova, Gilvan Alves, Jeroen Hegeman, Daniel R Claes, Yann Coadou, Gregorio Bernardi, D. Denisov, N. Huske, G. Sajot, Y. Hu, M. S. Rangel, Thomas Ferbel, M. Prewitt, Lars Sonnenschein, Arnaud Duperrin, M. S. Anzelc, Sarah Catherine Eno, I. Katsanos, N. Parua, D. Vilanova, Randy Ruchti, L. Han, G. J. Otero Y Garzón, C. Zeitnitz, Junjie Zhu, A. Kupco, Harald Fox, P. Rich, Arnulf Quadt, M. Arov, Alexander Grohsjean, Jan Stark, J. Strandberg, A. Jonckheere, N. K. Mondal, Lev Uvarov, Elemer Nagy, Maiko Takahashi, I. A. Vasilyev, I. Hall, P. Mättig, A. Lobodenko, N. Oshima, Daria Zieminska, R. Illingworth, J. Cammin, T. R. Wyatt, A. Evdokimov, Dennis Stephen Mackin, Stephen Wimpenny, Philip Baringer, J. Piper, W. E. Cooper, S. Banerjee, J. Backusmayes, Martin Grunewald, Milos Lokajicek, F. Guo, Darien Wood, T. H. Burnett, C. P. Buszello, J. A. Benitez, S. Blessing, Scott Snyder, Ulrich Heintz, P. K. Mal, Frank Filthaut, B. Zhou, M. Diesburg, A. Tanasijczuk, Christophe Ochando, Christopher George Tully, N. Osman, Patrick Slattery, Andrew Askew, D. A. Stoyanova, A. Chandra, C. L. McGivern, B. Baldin, P. Vokac, Michael Begel, Eduardo De Moraes Gregores, Mansoora Shamim, Luiz Mundim, P. Renkel, M. A. Carrasco-Lizarraga, Andre Sopczak, Elliott Cheu, T. Schliephake, Victor Daniel Elvira, S. Schlobohm, W. C. Yang, H. Greenlee, D. M. Strom, Maxim Perfilov, A. Rakitine, A. Bross, L. Bellantoni, Serban Protopopescu, P. D. Grannis, M. Aoki, Andy Haas, J. K. Lim, B. Åsman, A. P. Heinson, Mark Sosebee, R. E. Hall, B. Spurlock, G. Weber, Don Lincoln, Erich Varnes, M. Vesterinen, D. Schaile, Ron Lipton, K. Devaughan, Mark Raymond Adams, D. Karmanov, Sudhir Malik, E. G. Zverev, Ia Iashvili, Brajesh C Choudhary, V. V. Tokmenin, G. Facini, Bobby Samir Acharya, H. A. Neal, O. Mundal, K. Yip, R. Unalan, L. Stutte, Jinhong Yu, A.S. Dyshkant, Jiri Kvita, Sabine Lammers, P. Padley, Mitchell Wayne, H. Schellman, J. M. Kohli, Stefan Grünendahl, B. Gómez, B. Tuchming, T. Zhao, J. Sekaric, Shilpi Jain, H. Severini, Jun Guo, Q. Z. Li, John Parsons, J. Osta, Graham Wilson, D. Gillberg, Brian Thomas Martin, A. S. Ito, A. Melnitchouk, S. J. Park, V. V. Lipaev, J. Lellouch, D. Tsybychev, Frederic Deliot, G. Savage, D. Boline, M. Pangilinan, A. Wenger, R. L. McCarthy, V. Buescher, C. Galea, S. Söldner-Rembold, M. Rominsky, O. Atramentov, V. M. Podstavkov, M. Fortner, Ph Gris, P. Houben, M. H. Kirby, Emanuela Barberis, Ashok Kumar, Tulika Bose, J. Orduna, Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de l'Accélérateur Linéaire (LAL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Sud - Paris 11 (UP11), Département Recherches Subatomiques (DRS-IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de Physique Nucléaire de Lyon (IPNL), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), D0, D0 (Tevatron, IHEF, IOP, FNWI), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Aix Marseille Université (AMU)
Subjects: Physics, Quark, Nuclear and High Energy Physics, Particle physics, Top quark, 010308 nuclear & particles physics, Hadron, Electroweak interaction, Tevatron, FOS: Physical sciences, 01 natural sciences, law.invention, Standard Model, High Energy Physics - Experiment, Nuclear physics, High Energy Physics - Experiment (hep-ex), law, 0103 physical sciences, Experimental High Energy Physics, [PHYS.HEXP]Physics [physics]/High Energy Physics - Experiment [hep-ex], ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, High Energy Physics::Experiment, Fermilab, 010306 general physics, Collider
Abstract: The D0 collaboration reports direct evidence for electroweak production of single top quarks through the t-channel exchange of a virtual W boson. This is the first analysis to isolate an individual single top quark production channel. We select events containing an isolated electron or muon, missing transverse energy, and two, three or four jets from 2.3 fb^-1 of ppbar collisions at the Fermilab Tevatron Collider. One or two of the jets are identified as containing a b hadron. We combine three multivariate techniques optimized for the t-channel process to measure the t- and s-channel cross sections simultaneously. We measure cross sections of 3.14 +0.94 -0.80 pb for the t-channel and 1.05 +-0.81 pb for the s-channel. The measured t-channel result is found to have a significance of 4.8 standard deviations and is consistent with the standard model prediction., 7 pages, 6 figures
Published: 2010

92. Measurement of Z/γ∗+jet+X angular distributions in pp¯ collisions at s=1.96 TeV

Author: Avto Kharchilava, B. Tiller, I. Ripp-Baudot, A. Meyer, T. Hoang, Alexander Khanov, B. Sanghi, L. Duflot, Ernest Aguilo, J. K. Lim, S. Desai, D. A. Stoyanova, F. Badaud, Petr Vokac, C. L. McGivern, P. Haefner, R. Magaña-Villalba, S. W. Cho, G. Obrant, Tiefu Zhao, S. W. Youn, Shabnam Jabeen, J. K. Kraus, B. Åsman, Pedro G Mercadante, Markus Wobisch, Michael A. Strauss, P. L.M. Podesta-Lerma, Graham Wilson, R. Van Kooten, M. D. Corcoran, A. P. Heinson, L. Han, Brad Abbott, B. Spurlock, Zeno Dixon Greenwood, M. A. Strang, B. Calpas, Pierre Petroff, M. Buehler, Michael Begel, Mark Richard James Williams, A. V. Ferapontov, D. Gillberg, Eduardo De Moraes Gregores, Christophe Ochando, A. Dubey, J. M. Hauptman, G. Grenier, A. Sanchez-Hernandez, Brian Thomas Martin, V. Zutshi, Chong-Yu Xu, Cecilia Elena Gerber, A. S. Ito, A. Melnitchouk, S. Cihangir, K. Devaughan, S. Uvarov, Luiz Mundim, P. Lebrun, R. E. Hall, Sharon Hagopian, Terry Richard Wyatt, Wendy Taylor, A. K.A. Maciel, Cristina Galea, M. Merkin, V. Bunichev, Raymond Brock, Boaz Klima, R. Beuselinck, Robert Hirosky, Fabrice Couderc, B. Quinn, E. E. Boos, S. J. Park, Marc-Andre Pleier, D. K. Cho, V. M. Abazov, C. Schwanenberger, Alice Bean, Roger Moore, T. Scanlon, S. Kermiche, N. Huske, Andrew Askew, V. Shary, G. Ginther, Y. W. Liu, Heriberto Castilla-Valdez, D. Bauer, W. M. Lee, P. Renkel, D. Karmanov, L. S. Ancu, V. V. Lipaev, J. Lellouch, V. Siccardi, Jianming Qian, Suman Bala Beri, V. Hynek, R. Piegaia, A. Juste, Todd Adams, Raimund Ströhmer, P. Svoisky, Frederic Deliot, Christopher George Tully, M. Arthaud, G. Gutierrez, Gilvan Alves, V. Simak, Sabine Lammers, S. Greder, Iain Alexander Bertram, X. B. Bu, Michael Rijssenbeek, D. Boline, S. Zelitch, A. Chandra, L. S. Vertogradov, Sudhir Malik, E. G. Zverev, S. Schlobohm, Ia Iashvili, Brajesh C Choudhary, M. Pangilinan, M. A. Carrasco-Lizarraga, H. Greenlee, Guennadi Borissov, M. Arov, R. G. Wagner, M. C. Cousinou, D. M. Strom, Vipin Bhatnagar, B. S. Acharya, P. Mättig, G. S. Muanza, N. Osman, David T. Johnston, Patrick Slattery, R. Partridge, I. Heredia-De La Cruz, Karl Jakobs, D. Menezes, Y. Arnoud, Jean-Francois Grivaz, Liang Li, M. Kirsch, D. Smirnov, T. Nunnemann, B. Baldin, Mansoora Shamim, A. Bross, Alexander Grohsjean, P. Vint, T. H. Burnett, R. Bernhard, W. E. Cooper, Lev Uvarov, S. Fu, R. Illingworth, M. Abolins, Serban Protopopescu, P. Padley, Kenneth Bloom, Christophe Royon, W. C. Fisher, V. N. Evdokimov, G. Hesketh, V. L. Malyshev, Marco Verzocchi, J. A. Benitez, Theodoros Christoudias, Z. Liu, Lev Dudko, J. T. Linnemann, Suneel Dutt, D. Onoprienko, G. Otero y Garzon, Dmitri Tsybychev, R. L. McCarthy, J. Snow, A. F. Barfuss, Calvin A. Johnson, V. A. Bezzubov, M. Aoki, Andy Haas, G. Weber, Arnaud Duperrin, Neeti Parashar, P. J. Van Den Berg, Marc Besancon, N. K. Mondal, A. Alton, A. V. Popov, Meng Wang, Elizaveta Shabalina, A. Patwa, Mark Owen, Helio Nogima, Ulrich Heintz, H. Nilsen, P. K. Mal, Frank Filthaut, J. P. Negret, Hwi Dong Yoo, Maria Elena Pol, R. Luna-Garcia, Jong-Sung Yu, H. D. Wahl, D. Chakraborty, Marcia Begalli, Andre Sopczak, Michael Hildreth, S. Söldner-Rembold, Mitchell Wayne, H. Schellman, J. M. Kohli, H. T. Diehl, T. A. Bolton, M. Diesburg, Don Lincoln, Erich Varnes, Y. Pogorelov, A. Boehnlein, D. Edmunds, T. Gadfort, W. M. Van Leeuwen, Zhenyu Ye, B. C.K. Casey, Zdenek Hubacek, Y. N. Kharzheev, Jean-Arcady Meyer, L. Bagby, Elliott Cheu, T. Schliephake, K. Peters, Victor Daniel Elvira, Yuri Gershtein, P. Rich, C. Zeitnitz, Arnulf Quadt, A. Tanasijczuk, M. Zielinski, L. Welty-Rieger, J. Hays, H. E. Fisk, E. Strauss, Sung Keun Park, K. A. Johns, Meenakshi Narain, J. Haley, Gustaaf Brooijmans, W. C. Yang, J. Ellison, M. Ahsan, Jonas Strandberg, Sa. Jain, S. Fuess, D. Duggan, T. Kurca, Marc Weber, V. V. Tokmenin, G. Facini, J. P. Konrath, T. Kuhl, M. Vesterinen, A. Leflat, M. M. Meijer, Maxim Perfilov, A. Evdokimov, P. Polozov, K. M. Chan, Elemer Nagy, T. Yasuda, B. Penning, R. Otec, H. A. Neal, Reinhard Schwienhorst, Aran Garcia-Bellido, S. Uzunyan, Y. Xie, Amnon Harel, A. Rakitine, M. Jaffré, O. Mundal, K. Yip, Stefan Grünendahl, Harald Fox, Maiko Takahashi, I. A. Vasilyev, D. Buchholz, Aaron Dominguez, A. Das, M. Sosebee, Philip Baringer, B. Gómez, Y. A. Yatsunenko, P. N. Ratoff, Y. Peters, R. Unalan, D. Wicke, J. Warchol, L. Bellantoni, Marvin Johnson, Dennis Stephen Mackin, A. L. Lyon, A. V. Kozelov, Peter Love, L. Stutte, A.S. Dyshkant, J. Piper, S. Banerjee, Viatcheslav Stolin, Emanuela Barberis, S. Hossain, W. Geng, P. M. Tuts, Maksym Titov, Jiri Kvita, E. De La Cruz-Burelo, Carlos Avila, S. Sumowidagdo, P. Verdier, V. A. Kuzmin, Alexander Kupco, Hua-Lei Yin, P. D. Grannis, Andrew Brandt, L. Zivkovic, U. Bassler, I. Katsanos, Suyong Choi, Kirti Ranjan, Carsten Hensel, S. Robinson, Regina Demina, B. Tuchming, S. J. De Jong, J. Sekaric, Samuel Calvet, N. Khalatyan, S. Yacoob, Dorothee Schaile, N. Parua, D. Vilanova, Randy Ruchti, Y. Enari, Anna Goussiou, Sergio F Novaes, T. Moulik, D. N. Brown, M. Hohlfeld, D. Jamin, Grigory Safronov, S. Chakrabarti, P. Skubic, M. Naimuddin, Gregorio Bernardi, D. Denisov, M. P. Sanders, Yurii Maravin, P. Rubinov, G. D. Alexeev, Flera Rizatdinova, Hal Evans, Thomas Ferbel, Vladimir Gavrilov, M. Prewitt, Lars Sonnenschein, Gordon Watts, V. Sirotenko, J. Clutter, George Alverson, S. Beale, Gregory R Snow, Phillip Gutierrez, P. Neustroev, D. Hedin, A. A. Shchukin, Frank Fiedler, E. Kajfasz, Ashok Kumar, Jun Guo, Q. Z. Li, J. A. Parsons, J. Osta, M. Wetstein, Tulika Bose, G. Savage, G. C. Blazey, I. Torchiani, R. Yamada, A. Jonckheere, I. Hall, A. Lobodenko, J. Orduna, P. Jonsson, N. Oshima, Thomas Hebbeker, Florian Lacroix, Daria Zieminska, Pushpalatha C Bhat, R. D. Schamberger, W. Geist, B. Hoeneisen, Lee Sawyer, A. Wenger, G. Sajot, Y. Hu, E. Carrera, M. S. Rangel, D. Lam, M. Demarteau, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, Hakjae Lee, Junjie Zhu, V. Buescher, Richard B. Lipton, Kristian Harder, D. Cutts, Wagner Carvalho, M. Rominsky, Greg Landsberg, K. Herner, O. Atramentov, Pedrame Bargassa, K. Soustruznik, V. M. Podstavkov, R. K. Shivpuri, M. Fortner, Ph Gris, D. R. Claes, P. Houben, M. H. Kirby, Gavin Davies, Philippe Calfayan, S. M. Lietti, M. Padilla, Y. Scheglov, Kaushik De, R. Jesik, Andrew White, Jan Stark, Henry Lubatti, John Hobbs, J. Barreto, J. Cammin, M. R. Adams, Stephen Wimpenny, J. Backusmayes, Martin Grunewald, C. Belanger-Champagne, D. Khatidze, Milos Lokajicek, M. Cooke, V. Kaushik, F. Guo, Darien Wood, T. Dorland, C. P. Buszello, S. Blessing, Scott Snyder, Nikos Varelas, Bing Zhou, Luis Mendoza, K. W. Merritt, J. F. Bartlett, Robert Kehoe, Sergey Burdin, M. Eads, S. P. Denisov, Michael Mulhearn, Marc Escalier, Jeroen Hegeman, G. Alkhazov, D. V. Bandurin, M. Ćwiok, P. A. Kasper, and A. Bellavance
Subjects: Physics, Quantum chromodynamics, Nuclear and High Energy Physics, Particle physics, Large Hadron Collider, 010308 nuclear & particles physics, Astrophysics::High Energy Astrophysical Phenomena, High Energy Physics::Phenomenology, Hadron, Perturbative QCD, Jet (particle physics), 01 natural sciences, 7. Clean energy, Vector boson, Nuclear physics, 0103 physical sciences, Higgs boson, High Energy Physics::Experiment, 010306 general physics, Boson
Abstract: We present the first measurements at a hadron collider of differential cross sections for Z+jet+X production in delta phi(Z, jet), |delta y(Z, jet)| and |y_boost(Z, jet)|. Vector boson production in association with jets is an excellent probe of QCD and constitutes the main background to many small cross section processes, such as associated Higgs production. These measurements are crucial tests of the predictions of perturbative QCD and current event generators, which have varied success in describing the data. Using these measurements as inputs in tuning event generators will increase the experimental sensitivity to rare signals.
Published: 2010

93. Search for pair production of first-generation leptoquarks in pp¯ collisions at s=1.96 TeV

Author: Marco Verzocchi, Theodoros Christoudias, E. G. Zverev, Kristian Harder, A. Patwa, Mark Owen, D. Cutts, Wagner Carvalho, A. Leflat, Marcia Begalli, Meenakshi Narain, G. S. Muanza, Greg Landsberg, K. Herner, A. Evdokimov, J. Haley, Sung Keun Park, S. J. De Jong, Sergio F Novaes, Pedrame Bargassa, K. Soustruznik, M. Naimuddin, D. Edmunds, T. Gadfort, Philip Baringer, M. P. Sanders, Yurii Maravin, A. F. Barfuss, V. A. Bezzubov, J. P. Negret, V. M. Abazov, V. Shary, R. Luna-Garcia, S. Greder, Iain Alexander Bertram, Michael Rijssenbeek, W. M. Van Leeuwen, S. Zelitch, C. Belanger-Champagne, Zhenyu Ye, P. Rich, C. Zeitnitz, Arnulf Quadt, Michael Hildreth, J. Piper, V. N. Evdokimov, S. Banerjee, L. Welty-Rieger, Emanuela Barberis, Elemer Nagy, S. Uzunyan, Yuri Gershtein, Vladimir Gavrilov, R. Magaña-Villalba, G. Obrant, M. Wetstein, Gordon Watts, Y. Xie, Amnon Harel, B. C.K. Casey, V. Sirotenko, G. Alkhazov, D. V. Bandurin, M. Cooke, M. Kirsch, W. L. Prado Da Silva, V. Kaushik, Avto Kharchilava, T. Hoang, Alexander Khanov, P. Polozov, R. Otec, D. Wicke, Dennis Stephen Mackin, M. Arov, Reinhard Schwienhorst, G. D. Alexeev, Ashok Kumar, Flera Rizatdinova, A. A. Shchukin, B. Tiller, Shabnam Jabeen, M. Merkin, J. Clutter, Phillip Gutierrez, P. Haefner, Tae Jeong Kim, P. N. Ratoff, Y. Peters, P. M. Tuts, Maksym Titov, S. Uvarov, Peter Love, W. Geng, Tiefu Zhao, B. Penning, M. C. Cousinou, S. W. Youn, N. Khalatyan, S. Yacoob, Frank Fiedler, George Alverson, J. K. Kraus, Hua-Lei Yin, S. Beale, D. Hedin, David T. Johnston, P. L.M. Podesta-Lerma, Tulika Bose, T. Dorland, E. Kajfasz, M. Ćwiok, L. S. Ancu, S. Fu, Aaron Dominguez, Marvin Johnson, A. L. Lyon, A. V. Kozelov, Markus Wobisch, Stephen Wimpenny, Brad Abbott, G. Sajot, A. Das, M. Sosebee, P. Verdier, J. Backusmayes, Martin Grunewald, Pierre Petroff, P. A. Kasper, Andrew White, J. Orduna, Raymond Brock, Boaz Klima, A. Bellavance, Alexander Grohsjean, M. Buehler, G. Hesketh, R. Beuselinck, Y. Hu, Sergey Burdin, Suyong Choi, S. Cihangir, Milos Lokajicek, P. J. Van Den Berg, Robert Hirosky, Marc Besancon, Michael A. Strauss, Mark Richard James Williams, A. V. Ferapontov, H. E. Fisk, E. Strauss, A. Dubey, M. Eads, S. P. Denisov, B. Sanghi, R. Van Kooten, Y. W. Liu, P. Mättig, Lev Uvarov, V. A. Kuzmin, M. D. Corcoran, M. Padilla, X. B. Bu, B. Quinn, G. Grenier, Chong-Yu Xu, Fabrice Couderc, M. Abolins, F. Guo, R. Illingworth, L. Han, C. Schwanenberger, D. Bauer, M. S. Anzelc, P. Lebrun, Alice Bean, Jovan Mitrevski, G. Gutierrez, Gilvan Alves, Michael Mulhearn, Sarah Catherine Eno, Horst Severini, Darien Wood, S. Hossain, John Hobbs, Marc Escalier, J. Barreto, A. Wenger, Liang Li, Calvin A. Johnson, Sharon Hagopian, Jeroen Hegeman, D. K. Cho, J. P. Konrath, D. N. Brown, C. P. Buszello, Junjie Zhu, T. Scanlon, S. Kermiche, Suman Bala Beri, V. Hynek, Karl Jakobs, Ernest Aguilo, P. Neustroev, Lev Dudko, D. Smirnov, M. A. Strang, E. De La Cruz-Burelo, Maria Elena Pol, S. Desai, A. K.A. Maciel, S. Blessing, Pedro G Mercadante, P. Svoisky, M. Arthaud, V. Buescher, H. Nilsen, Elizaveta Shabalina, Petr Vokac, Timothy Andeen, D. Buchholz, L. S. Vertogradov, Richard B. Lipton, Jun Guo, Q. Z. Li, A. Juste, Todd Adams, Hwi Dong Yoo, Zdenek Hubacek, Scott Snyder, Aran Garcia-Bellido, P. Skubic, A. Jonckheere, I. Hall, J. Snow, N. K. Mondal, Andrew Brandt, L. Zivkovic, H. T. Diehl, T. A. Bolton, R. Jesik, Laurent Duflot, R. G. Wagner, Y. Pogorelov, G. C. Blazey, M. Rominsky, Jonas Strandberg, A. Lobodenko, K. A. Johns, B. Calpas, A. Boehnlein, Y. Arnoud, Anna Goussiou, I. Torchiani, R. K. Shivpuri, K. Peters, R. Yamada, T. Kuhl, M. Jaffré, O. Atramentov, N. Oshima, Dorothee Schaile, Gregorio Bernardi, M. S. Rangel, D. Denisov, Kirti Ranjan, Carsten Hensel, R. Bernhard, W. E. Cooper, K. W. Merritt, Harald Fox, J. A. Parsons, J. Osta, J. Ellison, M. Ahsan, Jean-Francois Grivaz, Gregory R Snow, J. F. Bartlett, Robert Kehoe, M. Hohlfeld, N. Huske, D. R. Claes, Sa. Jain, S. Fuess, Wendy Taylor, Gavin Davies, Philippe Calfayan, Daria Zieminska, V. M. Podstavkov, P. Jonsson, E. E. Boos, Heriberto Castilla-Valdez, T. Kurca, Mikko Voutilainen, Marc Weber, V. Bunichev, D. Onoprienko, Hal Evans, Thomas Ferbel, Lars Sonnenschein, G. Otero y Garzon, Alexander Kupco, M. Fortner, Arnaud Duperrin, Thomas Hebbeker, D. Khatidze, Maiko Takahashi, I. A. Vasilyev, Vipin Bhatnagar, R. D. Schamberger, R. Piegaia, I. Katsanos, Florian Lacroix, Roger Moore, T. R. Wyatt, R. Partridge, D. Duggan, J. M. Hauptman, Cecilia Elena Gerber, Jong-Sung Yu, I. Ripp-Baudot, N. Parua, A. Meyer, Pushpalatha C Bhat, D. Vilanova, Randy Ruchti, Kenneth Bloom, D. Menezes, Benjamin M. Martin, V. L. Malyshev, V. Siccardi, G. Ginther, C. Ochando, F. Badaud, S. M. Lietti, Y. Scheglov, Kaushik De, Suneel Dutt, Jianming Qian, A. Alton, Meng Wang, B. Spurlock, Zeno Dixon Greenwood, W. Geist, Helio Nogima, Cristina Galea, Y. N. Kharzheev, Y. A. Yatsunenko, G. Savage, Jean-Arcady Meyer, L. Bagby, A. Magerkurth, B. Hoeneisen, Lee Sawyer, K. M. Chan, U. Bassler, S. Robinson, Viatcheslav Stolin, Raimund Ströhmer, V. Simak, Sabine Lammers, Regina Demina, P. Vint, A. V. Popov, Y. Enari, Jan Stark, P. Padley, T. Moulik, B. S. Acharya, D. Jamin, Grigory Safronov, S. Chakrabarti, P. Rubinov, E. Carrera, Carlos Avila, S. Sumowidagdo, Mitchell Wayne, H. Schellman, J. M. Kohli, Henry Lubatti, Sabine Crépé-Renaudin, W. M. Lee, D. Lam, Gustaaf Brooijmans, Christophe Royon, Guennadi Borissov, J. Cammin, I. Heredia-De La Cruz, J. Warchol, M. Demarteau, W. C. Fisher, Neeti Parashar, H. D. Wahl, M. Zielinski, J. Hays, Nikos Varelas, Bing Zhou, Luis Mendoza, M. M. Meijer, T. Yasuda, D. A. Stoyanova, C. L. McGivern, Michael Begel, Eduardo De Moraes Gregores, Luiz Mundim, Marc-Andre Pleier, T. H. Burnett, J. A. Benitez, Z. Liu, Ulrich Heintz, P. K. Mal, S. Calvet, Frank Filthaut, M. Diesburg, A. Chandra, T. Nunnemann, B. Baldin, Mansoora Shamim, A. Tanasijczuk, Andre Sopczak, G. Weber, D. Chakraborty, Elliott Cheu, T. Schliephake, V. V. Tokmenin, G. Facini, Don Lincoln, Erich Varnes, H. A. Neal, J. T. Linnemann, O. Mundal, K. Yip, Victor Daniel Elvira, R. Unalan, L. Stutte, Gregory J Pawloski, A.S. Dyshkant, Jiri Kvita, K. Devaughan, Jing Li, Mark Raymond Adams, D. Karmanov, Sudhir Malik, Ia Iashvili, Brajesh C Choudhary, M. A. Carrasco-Lizarraga, P. Renkel, Frederic Deliot, A. Sanchez-Hernandez, Christopher George Tully, V. Zutshi, N. Osman, Andrew Askew, S. Schlobohm, W. C. Yang, Patrick Slattery, Maxim Perfilov, A. Rakitine, H. Greenlee, D. M. Strom, A. Bross, L. Bellantoni, Helena Malbouisson, P. D. Grannis, Serban Protopopescu, M. Aoki, Andy Haas, J. K. Lim, Stefan Grünendahl, B. Gómez, B. Åsman, B. Tuchming, J. Sekaric, A. P. Heinson, R. E. Hall, M. Pangilinan, Ph Gris, P. Houben, M. H. Kirby, Dmitri Tsybychev, R. L. McCarthy, S. Söldner-Rembold, Graham Wilson, D. Gillberg, A. S. Ito, A. Melnitchouk, S. J. Park, V. V. Lipaev, J. Lellouch, and D. Boline
Subjects: Physics, Nuclear and High Energy Physics, Particle physics, 010308 nuclear & particles physics, Branching fraction, Astrophysics::High Energy Astrophysical Phenomena, Scalar (mathematics), Tevatron, D0 experiment, 7. Clean energy, 01 natural sciences, Standard Model, law.invention, Nuclear physics, Pair production, law, 0103 physical sciences, High Energy Physics::Experiment, Fermilab, Nuclear Experiment, 010306 general physics, Collider
Abstract: A search for pair production of first-generation leptoquarks LQ is performed with data collected by the D0 experiment in p pbar collisions at sqrt(s)=1.96 TeV at the Fermilab Tevatron Collider. In a sample of data corresponding to ~1 fb-1, the search has been performed on the final states with two electrons and two jets or one electron, two jets and missing transverse energy. We find our data consistent with standard model expectations. The results are combined with those found in a previous analysis of events with two jets and missing transverse energy to obtain scalar LQ mass limits. We set 95% C.L. lower limits on a scalar LQ mass of 299 GeV, 284 GeV and 216 GeV for beta=1, beta=0.5 and beta=0.02 respectively, where beta is the LQ branching ratio in the eq channel. This improves the results obtained with a lower luminosity sample from Run II of the Tevatron. Lower limits on vector LQ masses with different couplings from 357 GeV to 464 GeV for beta=0.5 are also set using this analysis.
Published: 2009

94. Search for squark production in events with jets, hadronically decaying tau leptons and missing transverse energy at s=1.96 TeV

Author: A. Wenger, M. C. Cousinou, David T. Johnston, V. Buescher, Raimund Ströhmer, V. Simak, S. Fu, Murilo Rangel, G. Hesketh, P. J. Van Den Berg, Marc Besancon, M. Rominsky, A. Jonckheere, Sung Keun Park, P. Renkel, D. A. Stoyanova, D. Edmunds, T. Gadfort, Zhenyu Ye, Yuri Gershtein, I. Hall, A. Lobodenko, Sabine Lammers, Graham Wilson, Reinhard Schwienhorst, G. C. Blazey, Michael A. Strauss, I. Torchiani, H. E. Fisk, E. Strauss, C. L. McGivern, P. Padley, Chong-Yu Xu, P. Lebrun, N. Oshima, D. K. Cho, Daria Zieminska, T. Scanlon, S. Kermiche, Suman Bala Beri, V. Hynek, A. Juste, Todd Adams, R. Yamada, D. Gillberg, Aran Garcia-Bellido, R. Otec, R. D. Schamberger, S. Schlobohm, Jean-Francois Grivaz, P. N. Ratoff, Michael Begel, Mitchell Wayne, B. Sanghi, Eduardo De Moraes Gregores, A. S. Ito, A. Melnitchouk, T. R. Wyatt, Y. Peters, H. Greenlee, P. Jonsson, D. M. Strom, P. M. Tuts, Maksym Titov, H. Schellman, J. M. Kohli, Thomas Hebbeker, D. Khatidze, Florian Lacroix, Hua-Lei Yin, Pedro G Mercadante, S. J. Park, A. Bross, Andrew White, Luiz Mundim, Marc-Andre Pleier, Serban Protopopescu, Stefan Grünendahl, G. Sajot, Y. Hu, John Hobbs, U. Bassler, E. E. Boos, Emanuela Barberis, J. Barreto, Heriberto Castilla-Valdez, T. H. Burnett, V. V. Lipaev, J. Lellouch, S. Robinson, M. Aoki, Andy Haas, Regina Demina, C. Belanger-Champagne, J. A. Benitez, D. Boline, B. Gómez, Y. Enari, B. Tiller, Ashok Kumar, Z. Liu, M. Cooke, W. L. Prado Da Silva, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, Junjie Zhu, V. Kaushik, T. Moulik, Sergio F Novaes, S. W. Youn, B. Tuchming, R. K. Shivpuri, W. M. Lee, Ulrich Heintz, Richard B. Lipton, D. Jamin, Grigory Safronov, S. Chakrabarti, T. Dorland, M. Naimuddin, M. P. Sanders, J. Sekaric, D. R. Claes, Gavin Davies, Philippe Calfayan, P. K. Mal, Yurii Maravin, Vladimir Gavrilov, Guennadi Borissov, Markus Wobisch, Tulika Bose, I. Heredia-De La Cruz, Frank Filthaut, Sergey Burdin, Gordon Watts, P. Rubinov, S. M. Lietti, M. Diesburg, W. C. Fisher, Robert Hirosky, A. Dubey, Y. Scheglov, G. Grenier, Kaushik De, Y. W. Liu, V. Sirotenko, M. Eads, D. Bauer, W. M. Van Leeuwen, J. Orduna, J. Clutter, Neeti Parashar, Jovan Mitrevski, G. Gutierrez, Gilvan Alves, S. P. Denisov, B. C.K. Casey, Phillip Gutierrez, A. Tanasijczuk, Karl Jakobs, D. Smirnov, Jan Stark, P. Polozov, Henry Lubatti, M. Zielinski, J. Snow, J. Hays, K. Peters, Tae Jeong Kim, J. Cammin, A. Das, M. Sosebee, B. Penning, M. Abolins, P. Haefner, Marvin Johnson, A. L. Lyon, Tiefu Zhao, S. Hossain, J. K. Kraus, A. V. Kozelov, P. Svoisky, P. L.M. Podesta-Lerma, M. Arthaud, E. De La Cruz-Burelo, Michael Mulhearn, Ernest Aguilo, Calvin A. Johnson, S. Desai, Petr Vokac, Brad Abbott, N. K. Mondal, H. T. Diehl, T. A. Bolton, D. Onoprienko, Elizaveta Shabalina, Pierre Petroff, G. Otero y Garzon, Marc Escalier, Y. Pogorelov, Andrew Brandt, L. Zivkovic, Stephen Wimpenny, B. Calpas, Jeroen Hegeman, A. V. Ferapontov, J. Backusmayes, Martin Grunewald, Kirti Ranjan, C. Biscarat, Timothy Andeen, A. Boehnlein, D. Duggan, J. M. Hauptman, Cecilia Elena Gerber, R. Van Kooten, Benjamin M. Martin, G. Ginther, Carsten Hensel, Jianming Qian, M. D. Corcoran, P. Vint, Milos Lokajicek, J. P. Konrath, L. Han, F. Guo, A. V. Popov, J. Ellison, M. Ahsan, Sa. Jain, S. Fuess, N. Huske, Darien Wood, D. Buchholz, O. Atramentov, T. Kurca, W. C. Yang, Maxim Perfilov, C. P. Buszello, V. M. Podstavkov, Gustaaf Brooijmans, Marco Verzocchi, Theodoros Christoudias, E. G. Zverev, S. Blessing, Marc Weber, M. Fortner, Pushpalatha C Bhat, A. Patwa, J. Warchol, Mark Owen, Anna Goussiou, G. Savage, A. Rakitine, A. Leflat, Ph Gris, W. Geist, G. Weber, Scott Snyder, M. A. Strang, P. Houben, M. H. Kirby, Frederic Deliot, D. Chakraborty, Christopher George Tully, Marcia Begalli, Gregory R Snow, L. Bellantoni, Helena Malbouisson, B. Hoeneisen, Lee Sawyer, A. Evdokimov, Meenakshi Narain, Don Lincoln, Erich Varnes, J. Haley, P. D. Grannis, N. Osman, E. Carrera, M. Arov, Patrick Slattery, M. Padilla, D. Lam, A. Chandra, M. Demarteau, S. Calvet, M. Wetstein, Philip Baringer, J. Piper, X. B. Bu, T. Nunnemann, S. Banerjee, B. Baldin, Alexander Grohsjean, Mansoora Shamim, Jing Li, Lev Uvarov, G. D. Alexeev, P. Neustroev, Flera Rizatdinova, R. Jesik, Aaron Dominguez, Laurent Duflot, Kristian Harder, I. Ripp-Baudot, A. Meyer, K. A. Johns, Andre Sopczak, D. Cutts, Elliott Cheu, T. Schliephake, Victor Daniel Elvira, F. Badaud, S. J. De Jong, Avto Kharchilava, T. Hoang, K. W. Merritt, Alexander Khanov, Wagner Carvalho, M. Kirsch, B. Spurlock, Zeno Dixon Greenwood, J. F. Bartlett, Greg Landsberg, K. Herner, Christophe Ochando, A. Sanchez-Hernandez, Robert Kehoe, V. Zutshi, A. A. Shchukin, J. K. Lim, Pedrame Bargassa, Cristina Galea, Frank Fiedler, E. Kajfasz, Andrew Askew, K. Soustruznik, B. Åsman, A. P. Heinson, L. S. Ancu, P. Verdier, P. Mättig, R. E. Hall, R. Illingworth, M. A. Carrasco-Lizarraga, V. A. Kuzmin, Dorothee Schaile, M. Hohlfeld, Wendy Taylor, V. Bunichev, Roger Moore, V. Siccardi, A. Magerkurth, B. S. Acharya, D. N. Brown, G. Alkhazov, D. V. Bandurin, Christophe Royon, H. D. Wahl, M. Ćwiok, P. A. Kasper, A. Bellavance, P. Skubic, M. M. Meijer, T. Yasuda, L. S. Vertogradov, R. G. Wagner, Y. Arnoud, R. Bernhard, W. E. Cooper, Mikko Voutilainen, Arnaud Duperrin, Jong-Sung Yu, R. Magaña-Villalba, G. Obrant, Shabnam Jabeen, M. Merkin, G. S. Muanza, Raymond Brock, Boaz Klima, R. Beuselinck, P. Rich, C. Zeitnitz, Arnulf Quadt, Elemer Nagy, S. Uvarov, D. Wicke, Dennis Stephen Mackin, Y. A. Yatsunenko, Viatcheslav Stolin, V. V. Tokmenin, G. Facini, H. A. Neal, Carlos Avila, S. Sumowidagdo, B. Quinn, J. T. Linnemann, Sabine Crépé-Renaudin, O. Mundal, K. Yip, Suyong Choi, R. Unalan, L. Stutte, M. Buehler, Gregory J Pawloski, A.S. Dyshkant, C. Schwanenberger, Mark Richard James Williams, Alice Bean, Jiri Kvita, Sharon Hagopian, A. F. Barfuss, A. K.A. Maciel, Gregorio Bernardi, D. Denisov, V. A. Bezzubov, J. P. Negret, Nikos Varelas, Bing Zhou, Hal Evans, Thomas Ferbel, R. Luna-Garcia, Luis Mendoza, Lars Sonnenschein, Michael Hildreth, R. Piegaia, L. Welty-Rieger, Jonas Strandberg, S. Uzunyan, T. Kuhl, M. Jaffré, Y. Xie, Amnon Harel, V. M. Abazov, V. Shary, Alexander Kupco, S. Greder, Iain Alexander Bertram, I. Katsanos, N. Parua, Michael Rijssenbeek, S. Zelitch, D. Vilanova, Randy Ruchti, S. Cihangir, Fabrice Couderc, V. N. Evdokimov, D. Menezes, Liang Li, Lev Dudko, H. Nilsen, Hwi Dong Yoo, Zdenek Hubacek, Suneel Dutt, A. Alton, Meng Wang, Helio Nogima, Y. N. Kharzheev, Jean-Arcady Meyer, L. Bagby, Jun Guo, Q. Z. Li, Peter Love, W. Geng, J. A. Parsons, J. Osta, K. M. Chan, N. Khalatyan, S. Yacoob, M. Pangilinan, K. Devaughan, George Alverson, S. Beale, D. Hedin, Dmitri Tsybychev, R. L. McCarthy, Mark Raymond Adams, D. Karmanov, Sudhir Malik, Ia Iashvili, Brajesh C Choudhary, S. Söldner-Rembold, Maria Elena Pol, Harald Fox, Maiko Takahashi, I. A. Vasilyev, Vipin Bhatnagar, R. Partridge, Kenneth Bloom, and V. L. Malyshev
Subjects: Quark, Physics, Nuclear and High Energy Physics, Particle physics, 010308 nuclear & particles physics, Physics beyond the Standard Model, High Energy Physics::Phenomenology, Gaugino, Tevatron, 01 natural sciences, 7. Clean energy, law.invention, Standard Model, Nuclear physics, law, 0103 physical sciences, High Energy Physics::Experiment, Fermilab, 010306 general physics, Collider, Lepton
Abstract: A search for supersymmetric partners of quarks is performed in the topology of multijet events accompanied by at least one tau lepton decaying hadronically and large missing transverse energy. Approximately 1 fb(-1) of p (p) over bar collision data from the Fermilab Tevatron Collider at a center of mass energy of 1.96 TeV recorded by the D detector is analyzed. Results are combined with the previously published DO inclusive search for squarks and gluinos. No evidence of physics beyond the Standard Model is found and lower limits on the squark mass up to 410 GeV are derived in the framework of minimal supergravity with tan beta = 15, A(0) = -2m(0) and mu < 0, in the region where decays to tau leptons dominate. Gaugino masses m(1/2) are excluded up to 172 GeV.
Published: 2009

95. Measurement of the tt¯ production cross section and top quark mass extraction using dilepton events in pp¯ collisions

Author: Andrew White, W. C. Yang, D. Duggan, Maxim Perfilov, A. Rakitine, Stephen Wimpenny, Y. A. Yatsunenko, K. Devaughan, J. Backusmayes, Martin Grunewald, P. Verdier, M. C. Cousinou, Viatcheslav Stolin, Milos Lokajicek, Marco Verzocchi, Theodoros Christoudias, Dugan O'Neil, E. G. Zverev, O. Atramentov, A. Patwa, John Hobbs, K. W. Merritt, F. Guo, Mark Owen, V. A. Kuzmin, J. F. Bartlett, Darien Wood, P. Banerjee, L. Bellantoni, Nicholas John Hadley, C. P. Buszello, Robert Kehoe, Helena Malbouisson, A. F. Barfuss, S. Cihangir, M. Petteni, Marcia Begalli, Jun Guo, Q. Z. Li, Carlos Avila, S. Sumowidagdo, David T. Johnston, J. A. Parsons, J. Osta, S. Blessing, J. Barreto, J. M. Hauptman, Cecilia Elena Gerber, S. Fu, Sabine Crépé-Renaudin, D. Karmanov, R. K. Mommsen, Scott Snyder, P. D. Grannis, D. N. Brown, V. M. Podstavkov, M. Fortner, Fabrice Couderc, Norbert Wermes, Meenakshi Narain, J. Haley, Sudhir Malik, Benjamin M. Martin, G. Ginther, P. Svoisky, M. Arthaud, M. Pangilinan, Ia Iashvili, Brajesh C Choudhary, G. Obrant, W. M. Lee, G. Hesketh, M. H.L.S. Wang, Jianming Qian, P. Skubic, Shabnam Jabeen, G. Alkhazov, A. C.S. Assis Jesus, Guennadi Borissov, D. V. Bandurin, A. Das, M. Sosebee, P. J. Van Den Berg, Marc Besancon, M. Merkin, Ph Gris, Liang Li, M. Arov, M. A. Carrasco-Lizarraga, A. Jonckheere, W. C. Fisher, P. Houben, M. H. Kirby, I. Hall, A. Chandra, A. Lobodenko, L. S. Ancu, C. Belanger-Champagne, Dmitri Tsybychev, R. L. McCarthy, Alexander Grohsjean, T. Nunnemann, B. Baldin, Lev Dudko, P.F. Ermolov, M. Ćwiok, Lev Uvarov, M. Padilla, Neeti Parashar, Nikos Varelas, Freya Blekman, S. Hossain, Bing Zhou, Luis Mendoza, R. K. Shivpuri, Raymond Brock, H. Nilsen, Mansoora Shamim, Emanuela Barberis, B. Åsman, M. Abolins, P. A. Kasper, K. Herner, D. Onoprienko, N. Oshima, D. R. Claes, Robert Hirosky, Daria Zieminska, A. Bellavance, R. D. Schamberger, M. Cooke, E. De La Cruz-Burelo, M. Zielinski, Sergey Burdin, Boaz Klima, M. Eads, I. Katsanos, R. Beuselinck, S. P. Denisov, Gavin Davies, Philippe Calfayan, G. Otero y Garzon, Hwi Dong Yoo, J. Hays, M. Buehler, Zdenek Hubacek, Andrew Brandt, S. M. Lietti, G. Sajot, N. K. Mondal, H. T. Diehl, T. A. Bolton, Suyong Choi, W. L. Prado Da Silva, Mark Richard James Williams, T. R. Wyatt, Y. Scheglov, Kaushik De, Ashok Kumar, U. Bassler, M. Anastasoaie, P. Rich, C. Zeitnitz, Michael Mulhearn, Andre Sopczak, Y. Pogorelov, V. Kaushik, L. Zivkovic, B. Andrieu, A. Boehnlein, M. P. Sanders, P. Mättig, Marc Escalier, S. Söldner-Rembold, Jeroen Hegeman, Y. Hu, Sergio F Novaes, Elliott Cheu, T. Schliephake, Kirti Ranjan, Y. W. Liu, B. Tiller, D. Bauer, Jovan Mitrevski, P. Neustroev, Arnulf Quadt, Victor Daniel Elvira, B. Sanghi, J. Ellison, M. Ahsan, Sa. Jain, S. Fuess, S. Chevalier-Théry, Yvonne Peters, R. Illingworth, T. Kurca, B. G. Pope, M. S. Rangel, S. Robinson, Regina Demina, Jan Stark, Henry Lubatti, S. W. Youn, G. D. Alexeev, Flera Rizatdinova, Samuel Calvet, Sharon Hagopian, Marc Weber, Julia S. Meyer, Y. Enari, Calvin A. Johnson, I. Ripp-Baudot, A. Meyer, L. S. Vertogradov, A. K.A. Maciel, J. Cammin, Tulika Bose, R. Jesik, M. Naimuddin, K. A. Johns, Christophe Ochando, D. Wicke, V. V. Tokmenin, F. Badaud, Yurii Maravin, Vladimir Gavrilov, H. A. Neal, A. Sanchez-Hernandez, C. Hensel, D. Edmunds, T. Gadfort, Graham Wilson, T. Moulik, H. da Motta, Dennis Stephen Mackin, G. Gutierrez, Andre Sznajder, Zhenyu Ye, Gilvan Alves, D. Gillberg, V. Zutshi, J. G.R. Lima, J. T. Linnemann, Grigory Safronov, S. Chakrabarti, M. Wetstein, T. Dorland, B. Spurlock, R. G. Wagner, Elizaveta Shabalina, Y. Arnoud, Zeno Dixon Greenwood, Markus Wobisch, Gregorio Bernardi, Gordon Watts, V. Sirotenko, O. Mundal, K. Yip, A. S. Ito, A. Melnitchouk, S. J. De Jong, J. Clutter, D. Denisov, P. Rubinov, Yuri Gershtein, R. Unalan, L. Stutte, Pushpalatha C Bhat, Cristina Galea, Hal Evans, Thomas Ferbel, Timothy Andeen, R. Bernhard, W. E. Cooper, Karl Jakobs, Mikko Voutilainen, V. Hynek, D. Smirnov, A. Dubey, G. Grenier, Andrew Askew, Brigitte Vachon, Gregory J Pawloski, A.S. Dyshkant, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, Phillip Gutierrez, Jiri Kvita, H. E. Fisk, E. Strauss, V. V. Lipaev, J. Lellouch, M. Kirsch, Lars Sonnenschein, W. Geist, B. Hoeneisen, Lee Sawyer, Arnaud Duperrin, R. Piegaia, F. Villeneuve-Seguier, D. Boline, J. Snow, A. Leflat, Reinhard Schwienhorst, Michael A. Strauss, Chong-Yu Xu, Aran Garcia-Bellido, A. A. Shchukin, Jonas Strandberg, K. Peters, Sung Keun Park, P. Lebrun, Jong-Sung Yu, Frank Fiedler, E. Kajfasz, J. P. Konrath, A. Evdokimov, D. K. Cho, E. Carrera, Pedro G Mercadante, T. Kuhl, Suneel Dutt, A. Alton, Junjie Zhu, D. Buchholz, M. Jaffré, D. Lam, M. Demarteau, Helio Nogima, T. Scanlon, S. Kermiche, S. Strandberg, Anna Goussiou, Suman Bala Beri, Richard B. Lipton, A. Wenger, Kristian Harder, A. Juste, Philip Baringer, J. Piper, S. Banerjee, J. Dyer, Gregory R Snow, Todd Adams, Y. N. Kharzheev, P. Vint, Alexander Kupco, L. Bagby, Carmen García, R. Otec, A. V. Popov, C. De Oliveira Martins, Gustaaf Brooijmans, P. N. Ratoff, K. M. Chan, V. Cuplov, D. Cutts, J. Warchol, P. M. Tuts, Maksym Titov, Hua-Lei Yin, V. Buescher, N. Parua, D. Vilanova, Randy Ruchti, Wagner Carvalho, M. Rominsky, Greg Landsberg, E. E. Boos, Pedrame Bargassa, Heriberto Castilla-Valdez, K. Soustruznik, N. J. Buchanan, G. C. Blazey, I. Torchiani, R. Yamada, Jean-Francois Grivaz, P. Jonsson, Thomas Hebbeker, D. Khatidze, Florian Lacroix, Mary Beth Adams, G.S. Muanza, Raimund Ströhmer, V. Simak, P. Padley, R. F. Rodrigues, Mitchell Wayne, H. Schellman, J. M. Kohli, Stefan Grünendahl, B. Gómez, B. Tuchming, J. Sekaric, Shashikant Dugad, G. Savage, D. A. Stoyanova, G. Weber, Michael Begel, Eduardo De Moraes Gregores, D. Chakraborty, R. Van Kooten, C. Potter, Luiz Mundim, M. D. Corcoran, Marc-Andre Pleier, L. Han, T. H. Burnett, Don Lincoln, Erich Varnes, J. A. Benitez, Z. Liu, Ulrich Heintz, Frank Filthaut, M. Diesburg, A. Tanasijczuk, M. A. Strang, Frederic Deliot, Christopher George Tully, P. Haefner, Aaron Dominguez, Tiefu Zhao, N. Osman, Patrick Slattery, J. K. Kraus, C. Jarvis, P. L.M. Podesta-Lerma, Brad Abbott, Pierre Petroff, A. V. Ferapontov, Dorothee Schaile, M. Hohlfeld, B. Calpas, Avto Kharchilava, Christophe Royon, T. Hoang, H. D. Wahl, M. M. Meijer, T. Yasuda, Wendy Taylor, V. Bunichev, Alexander Khanov, Roger Moore, V. Siccardi, A. Magerkurth, B. S. Acharya, Jing Li, L. Duflot, J. K. Lim, Elemer Nagy, A. P. Heinson, Maria Elena Pol, R. E. Hall, P. Renkel, Harald Fox, S. Schlobohm, H. Greenlee, D. M. Strom, A. Bross, Serban Protopopescu, M. Aoki, Andy Haas, I. A. Vasilyev, Vipin Bhatnagar, R. Partridge, Kenneth Bloom, V. L. Malyshev, S. Uvarov, B. Quinn, C. Schwanenberger, Alice Bean, W. M. Van Leeuwen, B. C.K. Casey, P. Polozov, Tae Jeong Kim, B. Penning, Marvin Johnson, A. L. Lyon, A. V. Kozelov, Ernest Aguilo, S. Desai, Petr Vokac, Prolay Mal, S. Lammers, N. Huske, X. B. Bu, L. Christofek, Peter Love, W. Geng, R. J. Madaras, N. Khalatyan, S. Yacoob, George Alverson, S. Beale, D. Hedin, V. A. Bezzubov, J. P. Negret, R. Luna-Garcia, Michael Hildreth, L. Welty-Rieger, S. Uzunyan, Harrison Prosper, Y. Xie, Amnon Harel, V. M. Abazov, V. Shary, Iain Alexander Bertram, Michael Rijssenbeek, S. Zelitch, V. N. Evdokimov, S. J. Park, and F. Tissandier
Subjects: Quantum chromodynamics, Physics, Nuclear and High Energy Physics, Top quark, Particle physics, Muon, 010308 nuclear & particles physics, High Energy Physics::Phenomenology, Electron, 01 natural sciences, 7. Clean energy, Nuclear physics, Cross section (physics), Pair production, 0103 physical sciences, High Energy Physics::Experiment, 010306 general physics, Lepton, Bar (unit)
Abstract: We present a measurement of the top quark pair production cross section in p (p) over bar collisions at root s = 1.96 TeV using approximately 1 fb(-1) collected with the DO detector. We consider decay channels containing two high p(T) charged leptons where one lepton is identified as an electron or a muon while the other lepton can be an electron, a muon or a hadronically decaying tau lepton. For a mass of the top quark of 170 GeV, the measured cross section is 7.5(-1.0)(+1.0)(stat)(-0.6)(+0.7)(syst)(-0.5)(+0.6)(lumi) pb. Using l tau events only, we measure: sigma(t (t) over bar) x B(t (t) over bar -> l tau b (b) over bar) = 0.13(-0.08)(+0.09)(stat)(-0.06)(+0.06)(syst)(-0.02)(+0.02)(lumi) pb. Comparing the measured cross section as a function of the mass of the top quark with a partial next-to-next-to leading order Quantum Chroniodynamics theoretical prediction, we extract a mass of the top quark of 171.5(-8.8)(+9-9) GeV, in agreement with direct measurements.
Published: 2009

96. Search for admixture of scalar top quarks in the tt¯ lepton + jets final state at s=1.96 TeV

Author: J. M. Hauptman, Cecilia Elena Gerber, Stephen Wimpenny, Emanuela Barberis, J. Backusmayes, Martin Grunewald, L. S. Vertogradov, R. G. Wagner, Benjamin M. Martin, Milos Lokajicek, G. Ginther, M. Abolins, Ashok Kumar, F. Guo, Sergio F Novaes, Jianming Qian, Darien Wood, Tulika Bose, Nicholas John Hadley, C. P. Buszello, C. Belanger-Champagne, A. Leflat, P. Svoisky, M. Arthaud, M. C. Cousinou, R. K. Shivpuri, D. R. Claes, Gavin Davies, Philippe Calfayan, M. Naimuddin, S. M. Lietti, Y. Scheglov, Kaushik De, Jan Stark, Henry Lubatti, J. Cammin, S. Blessing, Scott Snyder, Yurii Maravin, G. Weber, D. Chakraborty, Y. Arnoud, M. Cooke, W. L. Prado Da Silva, Vladimir Gavrilov, Gordon Watts, Don Lincoln, Erich Varnes, N. K. Mondal, H. T. Diehl, Christophe Ochando, A. Evdokimov, Raimund Ströhmer, V. Simak, V. Sirotenko, Graham Wilson, H. da Motta, D. Gillberg, T. A. Bolton, Y. Pogorelov, J. Clutter, V. Kaushik, T. H. Burnett, P. Padley, R. F. Rodrigues, R. Bernhard, W. E. Cooper, A. Boehnlein, Philip Baringer, A. Sanchez-Hernandez, V. Zutshi, A. Wenger, Phillip Gutierrez, David T. Johnston, A. S. Ito, A. Melnitchouk, G. S. Muanza, M. Padilla, Adam L. Lyon, J. Piper, F. Villeneuve-Seguier, Nikos Varelas, Mitchell Wayne, Bing Zhou, Marco Verzocchi, Luis Mendoza, B. Sanghi, Mikko Voutilainen, P. A. Kasper, S. Banerjee, Kristian Harder, H. Schellman, J. M. Kohli, Theodoros Christoudias, K. Herner, J. Ellison, M. Ahsan, Stefan Grünendahl, S. Fu, D. Duggan, P. Neustroev, V. Hynek, V. Buescher, D. Onoprienko, M. Anastasoaie, J. A. Benitez, Dugan O'Neil, E. G. Zverev, G. Otero y Garzon, Z. Liu, A. Patwa, H. E. Fisk, Mark Owen, E. Strauss, Jing Li, Arnaud Duperrin, Sa. Jain, P. Rich, S. Fuess, Jonas Strandberg, Christophe Royon, Jong-Sung Yu, B. G. Pope, Calvin A. Johnson, Arnulf Quadt, Andrew Askew, T. Kurca, Marc Weber, B. Gómez, Peter Love, R. Jesik, Laurent Duflot, K. A. Johns, P. Renkel, W. Geng, Sung Keun Park, V. V. Lipaev, J. Lellouch, T. Dorland, G. Hesketh, Suneel Dutt, T. Kuhl, D. Boline, Elemer Nagy, Aran Garcia-Bellido, M. Jaffré, M. H.L.S. Wang, A. Alton, Elizaveta Shabalina, M. Rominsky, Brigitte Vachon, A. Chandra, J. Sekaric, Shashikant Dugad, P. J. Van Den Berg, Marc Besancon, M. Pangilinan, Helio Nogima, O. Atramentov, Marcia Begalli, F. Tissandier, Ulrich Heintz, D. Wicke, D. Cutts, Norbert Wermes, S. Schlobohm, Dennis Stephen Mackin, K. W. Merritt, P. Haefner, Tiefu Zhao, Timothy Andeen, M. Arov, S. Calvet, Pedro G Mercadante, M. Buehler, T. Nunnemann, B. Baldin, K. Devaughan, G. Obrant, P. Vint, H. Greenlee, D. M. Strom, V. M. Podstavkov, Andrew White, Dmitri Tsybychev, R. L. McCarthy, Meenakshi Narain, J. Haley, A. V. Popov, Alexander Kupco, B. Tiller, A. Bross, Y. N. Kharzheev, P. Verdier, Shabnam Jabeen, H. D. Wahl, M. Fortner, Alexander Grohsjean, Mansoora Shamim, M. Merkin, V. A. Kuzmin, J. F. Bartlett, P. Banerjee, R. J. Madaras, Michael A. Strauss, U. Bassler, Serban Protopopescu, Chong-Yu Xu, Gustaaf Brooijmans, S. Robinson, N. Khalatyan, S. Yacoob, S. W. Youn, V. Cuplov, Y. A. Yatsunenko, J. K. Kraus, L. Bagby, Wagner Carvalho, Robert Kehoe, N. Parua, D. Vilanova, Randy Ruchti, Lev Uvarov, P. L.M. Podesta-Lerma, M. Petteni, Ph Gris, Regina Demina, B. Åsman, I. Ripp-Baudot, Frank Filthaut, K. M. Chan, Christian Zeitnitz, M. Diesburg, M. Aoki, Andy Haas, J. Warchol, P. Lebrun, Greg Landsberg, A. Meyer, L. S. Ancu, Viatcheslav Stolin, Markus Wobisch, Raymond Brock, Boaz Klima, Y. Enari, D. N. Brown, S. Söldner-Rembold, Andre Sopczak, Jun Guo, Q. Z. Li, B. Andrieu, Elliott Cheu, T. Schliephake, Victor Daniel Elvira, F. Badaud, John Hobbs, S. J. De Jong, Pedrame Bargassa, C. Hensel, P. Mättig, B. Spurlock, Zeno Dixon Greenwood, A. Dubey, G. Grenier, K. Soustruznik, N. J. Buchanan, R. Illingworth, E. E. Boos, Heriberto Castilla-Valdez, D. K. Cho, T. Scanlon, S. Kermiche, S. Strandberg, Carlos Avila, W. C. Yang, Maxim Perfilov, T. Moulik, J. G.R. Lima, Grigory Safronov, S. Chakrabarti, A. Tanasijczuk, D. Karmanov, R. K. Mommsen, A. Das, M. Sosebee, Freya Blekman, S. Hossain, Suman Bala Beri, J. K. Lim, P. Rubinov, G. Alkhazov, A. Rakitine, D. A. Stoyanova, D. V. Bandurin, J. A. Parsons, J. Osta, Brad Abbott, Pierre Petroff, M. Kirsch, Cristina Galea, E. De La Cruz-Burelo, S. Cihangir, Fabrice Couderc, A. P. Heinson, G. Sajot, Sudhir Malik, Ia Iashvili, Brajesh C Choudhary, A. Juste, R. Otec, M. M. Meijer, S. Sumowidagdo, Sabine Crépé-Renaudin, W. M. Lee, Y. Hu, M. S. Rangel, A. V. Ferapontov, R. Van Kooten, Mark Richard James Williams, Todd Adams, T. Yasuda, R. E. Hall, A. A. Shchukin, I. Katsanos, R. Beuselinck, H. Yin, Julia S. Meyer, V. V. Tokmenin, Andrew Brandt, L. Zivkovic, L. Bellantoni, Helena Malbouisson, Liang Li, M. D. Corcoran, C. De Oliveira Martins, P. N. Ratoff, M. Ćwiok, Kirti Ranjan, A. C.S. Assis Jesus, Guennadi Borissov, H. A. Neal, Frank Fiedler, L. Han, E. Kajfasz, Michael Begel, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, Lev Dudko, A. Bellavance, Eduardo De Moraes Gregores, P. D. Grannis, Sharon Hagopian, J. T. Linnemann, A. K.A. Maciel, Sergey Burdin, M. Eads, O. Mundal, W. C. Fisher, P. M. Tuts, Maksym Titov, H. Nilsen, Junjie Zhu, Richard B. Lipton, S. P. Denisov, Boris Tuchming, K. Yip, Hwi Dong Yoo, C. Potter, Luiz Mundim, Zdenek Hubacek, G. Savage, G. C. Blazey, D. Edmunds, I. Torchiani, Michael Mulhearn, M. P. Sanders, Marc Escalier, Marc-Andre Pleier, Neeti Parashar, R. Unalan, R. Yamada, Jeroen Hegeman, T. Gadfort, Robert Hirosky, L. Stutte, Gregory J Pawloski, R. Piegaia, M. A. Strang, M. Zielinski, A.S. Dyshkant, J. Hays, Y. W. Liu, Andre Sznajder, Zhenyu Ye, Jiri Kvita, Frederic Deliot, D. Bauer, Suyong Choi, Yuri Gershtein, Christopher George Tully, Jovan Mitrevski, G. Gutierrez, N. Osman, Gilvan Alves, Patrick Slattery, Avto Kharchilava, T. Hoang, Alexander Khanov, M. A. Carrasco-Lizarraga, Karl Jakobs, Reinhard Schwienhorst, D. Smirnov, Gregorio Bernardi, D. Denisov, J. Snow, Hal Evans, K. Peters, Thomas Ferbel, Lars Sonnenschein, Yvonne Peters, J. P. Konrath, D. Buchholz, A. Jonckheere, I. Hall, A. Lobodenko, Anna Goussiou, N. Oshima, Daria Zieminska, R. D. Schamberger, Jean-Francois Grivaz, T. R. Wyatt, Pushpalatha C Bhat, J. Dyer, Gregory R Snow, P. Jonsson, W. Geist, P. Skubic, J. Barreto, B. Hoeneisen, P. Houben, Lee Sawyer, Thomas Hebbeker, D. Khatidze, George Alverson, Florian Lacroix, E. Carrera, S. Beale, D. Hedin, V. M. Abazov, V. Shary, Iain Alexander Bertram, Michael Rijssenbeek, S. Zelitch, V. N. Evdokimov, S. J. Park, A. F. Barfuss, V. A. Bezzubov, J. P. Negret, R. Luna-Garcia, Michael Hildreth, L. Welty-Rieger, Mary Beth Adams, D. Lam, M. Demarteau, Carmen García, G. D. Alexeev, Flera Rizatdinova, P.F. Ermolov, M. Wetstein, W. M. Van Leeuwen, B. C.K. Casey, P. Polozov, Tae Jeong Kim, B. Penning, Marvin Johnson, A. V. Kozelov, X. B. Bu, L. Christofek, Ernest Aguilo, S. Desai, Petr Vokac, Prolay Mal, B. Calpas, S. Lammers, S. Uvarov, N. Huske, B. Quinn, Aaron Dominguez, C. Jarvis, C. Schwanenberger, Alice Bean, Viacheslav Bunichev, Dorothee Schaile, Maria Elena Pol, M. Hohlfeld, Wendy Taylor, Roger Moore, M. H. Kirby, Harald Fox, V. Siccardi, I. A. Vasilyev, Vipin Bhatnagar, R. Partridge, Kenneth Bloom, V. L. Malyshev, A. Magerkurth, B. S. Acharya, S. Uzunyan, Harrison Prosper, Y. Xie, and Amnon Harel
Subjects: Physics, Quark, Nuclear and High Energy Physics, Top quark, Particle physics, Stop squark, 010308 nuclear & particles physics, High Energy Physics::Lattice, High Energy Physics::Phenomenology, Tevatron, Top quark condensate, 7. Clean energy, 01 natural sciences, Bottom quark, Nuclear physics, Nonlinear Sciences::Exactly Solvable and Integrable Systems, 0103 physical sciences, Physics::Atomic and Molecular Clusters, High Energy Physics::Experiment, B meson, 010306 general physics, Minimal Supersymmetric Standard Model
Abstract: A search for pair production of the lightest supersymmetric partner of the top quark is performed in the lepton+jets channel using 0.9 fb-1 of data collected by the D0 experiment. Kinematic differences between scalar top quark pair production and the dominant top quark pair production background are used to separate the two processes. First limits from Run II of the Fermilab Tevatron Collider for the scalar top quark decaying to a chargino and a b quark are obtained for scalar top quark masses of 130-190 GeV and chargino masses of 90-150 GeV.
Published: 2009

97. Measurement of σ(pp¯→Z+X)Br(Z→τ+τ−) at s=1.96 TeV

Author: G. Obrant, A. Das, M. Sosebee, P. Renkel, W. M. Van Leeuwen, Jonas Strandberg, Shabnam Jabeen, M. Merkin, R. Luna, B. C.K. Casey, T. Kuhl, P. Polozov, M. C. Cousinou, G. C. Blazey, B. Tiller, S. W. Youn, S. Schlobohm, M. Jaffré, Markus Wobisch, A. Dubey, G. Grenier, N. A. Naumann, Tae Jeong Kim, Raymond Brock, Boaz Klima, I. Katsanos, Freya Blekman, S. Hossain, M. Buehler, Mark Richard James Williams, B. Penning, Pushpalatha C Bhat, W. Geist, R. Beuselinck, H. Greenlee, D. M. Strom, Wendy Taylor, V. Bunichev, Roger Moore, M. H. Kirby, Robert Hirosky, David T. Johnston, I. Torchiani, R. Yamada, Avto Kharchilava, Marvin Johnson, A. Bross, S. Chakrabarti, Peter Love, W. Geng, Alexander Kupco, A. V. Kozelov, Y. W. Liu, S. Fu, Alexander Khanov, D. Bauer, Serban Protopopescu, E. De La Cruz-Burelo, Sharon Hagopian, A. K.A. Maciel, B. Hoeneisen, Lee Sawyer, R. J. Madaras, V. Siccardi, Adam L. Lyon, Jean-Francois Grivaz, Julia S. Meyer, N. Khalatyan, S. Yacoob, G. Hesketh, J. P. Konrath, N. Parua, D. Vilanova, Randy Ruchti, B. Sanghi, M. Aoki, Andy Haas, Jovan Mitrevski, G. Gutierrez, Gilvan Alves, X. B. Bu, H. Dong, F. Chevallier, P. J. Van Den Berg, Marc Besancon, George Alverson, L. S. Vertogradov, Sergio F Novaes, S. Beale, G. Weber, D. Hedin, D. Chakraborty, M. Anastasoaie, Pedro G Mercadante, R. G. Wagner, Michael A. Strauss, P. Haefner, P. Rich, M. Naimuddin, H. E. Fisk, E. Strauss, L. Christofek, Karl Jakobs, D. Buchholz, Arnulf Quadt, A. F. Barfuss, Tiefu Zhao, V. A. Bezzubov, D. Smirnov, J. P. Negret, Don Lincoln, Erich Varnes, Yurii Maravin, Elemer Nagy, Vladimir Gavrilov, Y. Arnoud, P. Lebrun, Gordon Watts, R. Bernhard, Ernest Aguilo, S. Desai, W. E. Cooper, Michael Hildreth, D. Kau, Petr Vokac, J. K. Kraus, V. Sirotenko, L. Welty-Rieger, Prolay Mal, J. Clutter, S. Uzunyan, D. K. Cho, D. Wicke, P. Tamburello, T. Scanlon, Mikko Voutilainen, J. Snow, Phillip Gutierrez, S. Kermiche, S. Strandberg, Dennis Stephen Mackin, K. Peters, Sung Keun Park, Harrison Prosper, Anna Goussiou, E. E. Boos, Heriberto Castilla-Valdez, Y. Xie, Amnon Harel, Arnaud Duperrin, Aran Garcia-Bellido, Suman Bala Beri, Vivian O'Dell, S. Lammers, D. Duggan, T. H. Burnett, Jong-Sung Yu, P. Svoisky, J. A. Benitez, Z. Liu, A. Juste, P. Verdier, L. S. Ancu, V. M. Abazov, V. Shary, V. V. Tokmenin, H. A. Neal, Jing Li, P. L.M. Podesta-Lerma, M. Abolins, Todd Adams, L. Duflot, J. K. Lim, Vipin Bhatnagar, R. Partridge, Iain Alexander Bertram, V. A. Kuzmin, Michael Rijssenbeek, S. Zelitch, J. Dyer, Gregory R Snow, D. Edmunds, T. Gadfort, M. Petteni, Andrew Brandt, L. Zivkovic, E. Carrera, D. Lam, P. Jonsson, Thomas Hebbeker, D. Khatidze, Florian Lacroix, R. Otec, J. T. Linnemann, O. Mundal, K. Yip, J. M. Kalk, N. K. Mondal, H. T. Diehl, T. A. Bolton, Kenneth Bloom, M. Arthaud, C. De Oliveira Martins, P. N. Ratoff, A. P. Heinson, V. N. Evdokimov, A. Wenger, S. Cihangir, Andre Sznajder, V. L. Malyshev, S. J. Park, Y. Pogorelov, G. S. Muanza, Deidre Brown, Kirti Ranjan, K. Herner, D. Onoprienko, M. Demarteau, U. Bassler, Carmen García, Mary Beth Adams, A. Magerkurth, Brad Abbott, Y. A. Yatsunenko, Ulrich Heintz, P.F. Ermolov, S. Robinson, A. Boehnlein, A. Chandra, P. M. Tuts, Maksym Titov, Fabrice Couderc, Hua-Lei Yin, Nikos Varelas, R. E. Hall, P. A. Kasper, Regina Demina, R. Piegaia, P. Mättig, Pierre Petroff, R. Unalan, B. S. Acharya, Viatcheslav Stolin, Samuel Calvet, P. Skubic, J. Ellison, Y. Enari, M. Ahsan, Bing Zhou, Luis Mendoza, R. K. Shivpuri, R. Illingworth, C. Belanger-Champagne, T. Moulik, Liang Li, Sa. Jain, S. Fuess, T. Kurca, Marc Weber, F. Villeneuve-Seguier, A. Jonckheere, I. Hall, A. Lobodenko, Aaron Dominguez, T. Nunnemann, B. Baldin, C. Jarvis, D. R. Claes, Carlos Avila, S. Sumowidagdo, Frank Filthaut, A. V. Ferapontov, J. G.R. Lima, Grigory Safronov, Gavin Davies, Philippe Calfayan, V. Buescher, Lev Dudko, S. Uvarov, I. Ripp-Baudot, A. Leflat, H. Nilsen, A. Meyer, N. Oshima, Marco Verzocchi, C. Magass, Daria Zieminska, Theodoros Christoudias, R. D. Schamberger, T. R. Wyatt, M. Wetstein, Sabine Crépé-Renaudin, L. Stutte, G. Sajot, Dugan O'Neil, E. G. Zverev, Gregory J Pawloski, A.S. Dyshkant, Y. Hu, Jiri Kvita, P. Rubinov, M. Diesburg, Suyong Choi, M. S. Rangel, J. M. Hauptman, R. Van Kooten, Cecilia Elena Gerber, Hwi Dong Yoo, Zdenek Hubacek, S. M. Lietti, M. D. Corcoran, Y. Scheglov, Kaushik De, B. Quinn, F. Badaud, A. Patwa, Mark Owen, C. Biscarat, C. Hensel, A. Evdokimov, A. Alton, Mansoora Shamim, G. Ginther, M. Cooke, Jianming Qian, M. S. Anzelc, Sarah Catherine Eno, C. Schwanenberger, Alice Bean, Marcia Begalli, Horst Severini, B. Spurlock, Zeno Dixon Greenwood, M. Rominsky, P. Vint, Helio Nogima, G. D. Alexeev, Flera Rizatdinova, A. V. Popov, J. Rieger, W. L. Prado Da Silva, A. Tanasijczuk, V. Kaushik, Philip Baringer, G. J. Otero Y Garzón, Norbert Wermes, Meenakshi Narain, J. Haley, Junjie Zhu, L. Han, A. Zieminski, L. Bagby, Cristina Galea, J. Piper, Emanuela Barberis, Dorothee Schaile, Jan Stark, S. Banerjee, Henry Lubatti, M. Hohlfeld, Maria Elena Pol, N. Gollub, Richard B. Lipton, Gregorio Bernardi, D. Denisov, J. D. Degenhardt, Kristian Harder, D. Cutts, M. H.L.S. Wang, K. M. Chan, Christian Zeitnitz, Gustaaf Brooijmans, B. G. Pope, Ariel Schwartzman, Christophe Royon, Ashok Kumar, Calvin A. Johnson, Hal Evans, Wagner Carvalho, Thomas Ferbel, Lars Sonnenschein, Greg Landsberg, V. Cuplov, M. Arov, J. Cammin, J. Warchol, Stephen Wimpenny, M. A. Strang, H. D. Wahl, Harald Fox, Elizaveta Shabalina, W. M. Lee, Pedrame Bargassa, K. Devaughan, Andre Sopczak, B. Andrieu, Alexander Grohsjean, Timothy Andeen, A. C.S. Assis Jesus, H. Hoeth, Guennadi Borissov, K. Soustruznik, N. J. Buchanan, Elliott Cheu, T. Schliephake, I. A. Vasilyev, Lev Uvarov, B. Åsman, W. C. Fisher, Tulika Bose, Frederic Deliot, Victor Daniel Elvira, Christopher George Tully, Martin Grunewald, T. Yasuda, Milos Lokajicek, S. J. De Jong, Neeti Parashar, D. Karmanov, R. K. Mommsen, M. Zielinski, T. Dorland, N. Osman, Y. M. Kharzheev, Patrick Slattery, J. Hays, M. Kirsch, Sudhir Malik, Ia Iashvili, D. A. Stoyanova, Brajesh C Choudhary, F. Guo, A. A. Shchukin, Christophe Ochando, Darien Wood, Frank Fiedler, E. Kajfasz, A. Sanchez-Hernandez, V. Zutshi, Michael Begel, Eduardo De Moraes Gregores, Nicholas John Hadley, F. Tissandier, Boris Tuchming, C. Potter, Luiz Mundim, C. P. Buszello, Marc-Andre Pleier, S. Blessing, Scott Snyder, Yvonne Peters, Andrew White, O. Atramentov, P. Neustroev, Andrew Askew, Brigitte Vachon, W. C. Yang, R. Jesik, Maxim Perfilov, K. A. Johns, A. Rakitine, L. Bellantoni, Helena Malbouisson, J. N. Butler, P. D. Grannis, V. M. Podstavkov, J. Steele, John Hobbs, J. Barreto, M. Fortner, Ph Gris, P. Houben, G. Alkhazov, D. V. Bandurin, Yuri Gershtein, Reinhard Schwienhorst, M. Ćwiok, A. Bellavance, Sergey Burdin, M. Eads, S. P. Denisov, Raimund Ströhmer, V. Simak, P. Padley, R. F. Rodrigues, Mitchell Wayne, H. Schellman, J. M. Kohli, Stefan Grünendahl, Michael Mulhearn, B. Gómez, M. P. Sanders, J. Sekaric, Shashikant Dugad, Jeroen Hegeman, G. Savage, Jun Guo, Q. Z. Li, J. A. Parsons, J. Osta, K. W. Merritt, J. F. Bartlett, P. Banerjee, Robert Kehoe, M. Pangilinan, Dmitri Tsybychev, R. L. McCarthy, S. Söldner-Rembold, Graham Wilson, H. da Motta, D. Gillberg, Brian Thomas Martin, A. S. Ito, A. Melnitchouk, V. Hynek, V. V. Lipaev, J. Lellouch, and D. Boline
Subjects: Physics, Nuclear and High Energy Physics, Particle physics, Muon, Physics::Instrumentation and Detectors, 010308 nuclear & particles physics, Branching fraction, High Energy Physics::Phenomenology, Tevatron, 01 natural sciences, 7. Clean energy, Standard Model, law.invention, Luminosity, Nuclear physics, law, 0103 physical sciences, High Energy Physics::Experiment, Neutrino, 010306 general physics, Collider, Lepton
Abstract: We present a measurement of the cross section for Z boson production times the branching fraction to tau lepton pairs sigma(p (p) over bar -> Z + X)Br(Z -> tau(+)tau(-)) in p (p) over bar collisions at root s = 1.96 TeV. The measurement is performed in the channel in which one tau lepton decays into a muon and neutrinos. and the other tau lepton decays hadronically or into an electron and neutrinos. The data sample corresponds to an integrated luminosity of 1.0 fb(-1) collected with the DO detector at the Fermilab Tevatron Collider. The sample contains 1511 candidate events with an estimated 20% background from jets or muons misidentified as tau leptons. We obtain sigma . Br = 240 +/- 8 (star) +/- 12 (sys) +/- 15 (lum) pb, which is consistent with the standard model prediction.
Published: 2009

98. Measurement of differential Z/γ∗+jet+X cross sections in pp¯ collisions at s=1.96 TeV

Author: M. Abolins, Yvonne Peters, N. K. Mondal, W. M. Lee, Christophe Royon, C. Biscarat, P. Vint, C. Belanger-Champagne, A. V. Popov, H. T. Diehl, T. A. Bolton, B. Tiller, Y. Pogorelov, A. C.S. Assis Jesus, H. Hoeth, Guennadi Borissov, P. Haefner, A. Boehnlein, S. W. Youn, H. D. Wahl, Gustaaf Brooijmans, Tiefu Zhao, M. Buehler, Mark Richard James Williams, J. K. Kraus, J. Ellison, J. M. Hauptman, Cecilia Elena Gerber, M. Ahsan, Sa. Jain, S. Fuess, V. Cuplov, M. Cooke, W. L. Prado Da Silva, V. Kaushik, T. Kurca, W. C. Fisher, Marc Weber, L. S. Vertogradov, Markus Wobisch, J. Warchol, G. Ginther, P. L.M. Podesta-Lerma, Ariel Schwartzman, Ernest Aguilo, Neeti Parashar, Sharon Hagopian, Raimund Ströhmer, R. G. Wagner, Sung Keun Park, Jianming Qian, A. Dubey, A. K.A. Maciel, V. Simak, G. Grenier, N. A. Naumann, S. Desai, Petr Vokac, T. Dorland, V. V. Tokmenin, P. Padley, R. F. Rodrigues, Prolay Mal, Y. Arnoud, T. Yasuda, Brad Abbott, M. Zielinski, Pierre Petroff, B. G. Pope, Mitchell Wayne, F. Tissandier, R. Bernhard, H. A. Neal, Jonas Strandberg, H. Schellman, J. M. Kohli, W. E. Cooper, J. Hays, Andrew White, S. Lammers, A. V. Ferapontov, R. Piegaia, Calvin A. Johnson, Stefan Grünendahl, O. Mundal, K. Yip, Mikko Voutilainen, R. Unalan, B. Gómez, R. Otec, L. Stutte, Gregory J Pawloski, A.S. Dyshkant, Jiri Kvita, Elizaveta Shabalina, B. Tuchming, J. Sekaric, Arnaud Duperrin, T. Kuhl, Suyong Choi, C. De Oliveira Martins, P. N. Ratoff, R. Jesik, I. Ripp-Baudot, A. Meyer, S. J. De Jong, Timothy Andeen, John Hobbs, J. Barreto, M. R. Adams, G. Alkhazov, Jong-Sung Yu, Aaron Dominguez, G. D. Alexeev, Flera Rizatdinova, P. Svoisky, F. Badaud, K. Devaughan, H. E. Fisk, E. Strauss, P. M. Tuts, Maksym Titov, Hua-Lei Yin, C. Jarvis, M. Jaffré, Marco Verzocchi, C. Magass, Theodoros Christoudias, Dugan O'Neil, A. Patwa, Mark Owen, A. A. Shchukin, Frank Fiedler, E. Kajfasz, Graham Wilson, C. Hensel, H. da Motta, B. Spurlock, Zeno Dixon Greenwood, W. M. Van Leeuwen, R. Luna, M. Arthaud, B. C.K. Casey, Emanuela Barberis, D. V. Bandurin, Aran Garcia-Bellido, S. R. Dugad, F. Villeneuve-Seguier, G. Obrant, Marcia Begalli, Avto Kharchilava, P. Verdier, J. Rieger, D. Karmanov, R. K. Mommsen, D. Gillberg, Brian Thomas Martin, P. Polozov, Tae Jeong Kim, Sudhir Malik, E. G. Zverev, Ia Iashvili, B. Penning, Shabnam Jabeen, M. Ćwiok, Robert Hirosky, Christophe Ochando, Dorothee Schaile, Alexander Khanov, Brajesh C Choudhary, Cristina Galea, M. Merkin, Jun Guo, Norbert Wermes, Meenakshi Narain, J. Haley, Y. W. Liu, D. Bauer, L. S. Ancu, Q. Z. Li, Alexander Kupco, Marvin Johnson, A. L. Lyon, P. A. Kasper, A. Sanchez-Hernandez, A. V. Kozelov, U. Bassler, K. Herner, D. Onoprienko, B. Sanghi, A. Bellavance, R. Van Kooten, A. S. Ito, A. Melnitchouk, A. Alton, M. Hohlfeld, Gregorio Bernardi, Jovan Mitrevski, G. Gutierrez, Gilvan Alves, Raymond Brock, V. Hynek, Boaz Klima, I. Katsanos, Helio Nogima, Ashok Kumar, Wendy Taylor, V. Bunichev, S. Robinson, M. D. Corcoran, D. Denisov, V. A. Kuzmin, Regina Demina, Samuel Calvet, J. A. Parsons, J. D. Degenhardt, Sergey Burdin, J. Osta, V. Zutshi, M. Eads, R. Beuselinck, X. B. Bu, M. H.L.S. Wang, S. P. Denisov, Roger Moore, Y. Enari, K. A. Johns, G. Sajot, Karl Jakobs, Y. Hu, Stephen Wimpenny, T. Moulik, N. Parua, D. Vilanova, Randy Ruchti, P. Mättig, G. Weber, D. Chakraborty, Martin Grunewald, L. Han, M. Kirsch, D. Smirnov, J. G.R. Lima, V. V. Lipaev, J. Lellouch, R. Illingworth, M. Arov, Michael Mulhearn, V. Siccardi, Julia S. Meyer, Grigory Safronov, L. Christofek, M. S. Rangel, Hal Evans, Thomas Ferbel, A. Leflat, M. P. Sanders, Jeroen Hegeman, L. Bagby, Milos Lokajicek, K. M. Chan, Pushpalatha C Bhat, Lars Sonnenschein, A. Zieminski, A. Das, M. Sosebee, J. Snow, K. Peters, M. Petteni, P. Rubinov, A. Evdokimov, Pedro G Mercadante, Alexander Grohsjean, D. Boline, J. M. Kalk, Lev Uvarov, W. Geist, F. Guo, Tulika Bose, A. Magerkurth, Frederic Deliot, Christopher George Tully, G. Savage, Sergio F Novaes, B. S. Acharya, D. Duggan, Andrew Askew, Brigitte Vachon, Darien Wood, B. Åsman, Freya Blekman, S. Hossain, M. A. Strang, Don Lincoln, Erich Varnes, M. Pangilinan, A. Chandra, K. W. Merritt, Nicholas John Hadley, C. P. Buszello, B. Hoeneisen, Lee Sawyer, J. F. Bartlett, Deidre Brown, Philip Baringer, P. Banerjee, Robert Kehoe, E. De La Cruz-Burelo, J. Piper, S. Banerjee, E. E. Boos, M. S. Anzelc, M. Naimuddin, Sarah Catherine Eno, Horst Severini, Yurii Maravin, Vladimir Gavrilov, Gordon Watts, Andrew Brandt, L. Zivkovic, Heriberto Castilla-Valdez, S. Blessing, Kirti Ranjan, T. Nunnemann, B. Baldin, E. Carrera, Dmitri Tsybychev, R. L. McCarthy, Y. A. Yatsunenko, N. Osman, P. Skubic, Y. M. Kharzheev, Scott Snyder, Viatcheslav Stolin, V. Sirotenko, J. Clutter, S. Söldner-Rembold, Phillip Gutierrez, D. Lam, Mansoora Shamim, M. Demarteau, O. Atramentov, Carlos Avila, S. Sumowidagdo, Patrick Slattery, Sabine Crépé-Renaudin, Carmen García, G. J. Otero Y Garzón, P. Neustroev, S. Cihangir, R. K. Shivpuri, A. Jonckheere, I. Hall, A. Lobodenko, N. Oshima, Junjie Zhu, Fabrice Couderc, M. Anastasoaie, P. Rich, C. Zeitnitz, Daria Zieminska, Arnulf Quadt, T. H. Burnett, Andre Sopczak, D. R. Claes, Gavin Davies, Philippe Calfayan, Liang Li, B. Andrieu, N. Gollub, Richard B. Lipton, Elliott Cheu, T. Schliephake, Lev Dudko, H. Nilsen, Victor Daniel Elvira, V. M. Podstavkov, Elemer Nagy, Hwi Dong Yoo, W. C. Yang, Maxim Perfilov, Zdenek Hubacek, A. Rakitine, D. Wicke, L. Bellantoni, Helena Malbouisson, G. C. Blazey, Dennis Stephen Mackin, S. M. Lietti, Y. Scheglov, Kaushik De, M. Fortner, J. N. Butler, P. D. Grannis, I. Torchiani, J. Steele, R. Yamada, Ph Gris, J. A. Benitez, P. Houben, M. H. Kirby, Jan Stark, Henry Lubatti, P. Jonsson, Z. Liu, J. Cammin, Thomas Hebbeker, D. Khatidze, Florian Lacroix, R. D. Schamberger, A. Wenger, Ulrich Heintz, Kristian Harder, V. Buescher, Jing Li, Frank Filthaut, M. Diesburg, Nikos Varelas, D. Cutts, Wagner Carvalho, M. Rominsky, L. Duflot, Greg Landsberg, Bing Zhou, A. Tanasijczuk, Luis Mendoza, D. A. Stoyanova, J. K. Lim, Michael Begel, Eduardo De Moraes Gregores, Pedrame Bargassa, K. Soustruznik, N. J. Buchanan, C. Potter, Luiz Mundim, Marc-Andre Pleier, A. P. Heinson, G. S. Muanza, R. E. Hall, Terry Richard Wyatt, P. Renkel, S. Schlobohm, H. Greenlee, D. M. Strom, A. Bross, Serban Protopopescu, M. Aoki, Andy Haas, Maria Elena Pol, Harald Fox, I. A. Vasilyev, Vipin Bhatnagar, R. Partridge, Kenneth Bloom, V. L. Malyshev, D. Edmunds, T. Gadfort, Andre Sznajder, S. Uvarov, Yuri Gershtein, Reinhard Schwienhorst, Michael A. Strauss, B. Quinn, C. Schwanenberger, Alice Bean, P. Lebrun, D. K. Cho, T. Scanlon, S. Kermiche, S. Strandberg, Suman Bala Beri, Vivian O'Dell, A. Juste, Todd Adams, M. C. Cousinou, David T. Johnston, S. Fu, G. Hesketh, P. J. Van Den Berg, Marc Besancon, P.F. Ermolov, M. Wetstein, J. P. Konrath, H. Dong, D. Buchholz, P. Tamburello, Anna Goussiou, J. Dyer, Gregory R Snow, A. F. Barfuss, V. A. Bezzubov, J. P. Negret, Michael Hildreth, D. Kau, L. Welty-Rieger, S. Uzunyan, Harrison Prosper, Y. Xie, Amnon Harel, V. M. Abazov, V. Shary, Iain Alexander Bertram, Michael Rijssenbeek, S. Zelitch, Jean-Francois Grivaz, V. N. Evdokimov, S. J. Park, J. T. Linnemann, S. Chakrabarti, Peter Love, W. Geng, R. J. Madaras, N. Khalatyan, S. Yacoob, F. Chevallier, George Alverson, S. Beale, and D. Hedin
Subjects: Quantum chromodynamics, Physics, Nuclear and High Energy Physics, Jet (fluid), Particle physics, Proton, 010308 nuclear & particles physics, Astrophysics::High Energy Astrophysical Phenomena, Perturbative QCD, Parton, 01 natural sciences, Nuclear physics, 0103 physical sciences, High Energy Physics::Experiment, Rapidity, Nuclear Experiment, 010306 general physics, Parton shower, Event generator
Abstract: We present new measurements of differential cross sections for Z/gamma*(->mumu)+jet+X production in a 1 fb-1 data sample collected with the D0 detector in proton anti-proton collisions at sqrt{s}=1.96 TeV. Results include the first measurements differential in the Z/gamma* transverse momentum and rapidity, as well as new measurements differential in the leading jet transverse momentum and rapidity. Next-to-leading order perturbative QCD predictions are compared to the measurements, and reasonable agreement is observed, except in the region of low Z/gamma* transverse momentum. Predictions from two event generators based on matrix elements and parton showers, and one pure parton shower event generator are also compared to the measurements. These show significant overall normalization differences to the data and have varied success in describing the shape of the distributions.
Published: 2008

99. Search for scalar leptoquarks and T-odd quarks in the acoplanar jet topology using of collision data at

Author: M. Naimuddin, Yurii Maravin, G. Weber, D. Chakraborty, Vladimir Gavrilov, Gordon Watts, A. Jonckheere, V. Sirotenko, Don Lincoln, J. Clutter, I. Hall, A. Lobodenko, Erich Varnes, Phillip Gutierrez, N. Oshima, Daria Zieminska, K. Devaughan, Y. Tschudi, P. Neustroev, J. P. Konrath, H. Dong, D. Edmunds, R. D. Schamberger, A. Wenger, D. Karmanov, R. K. Mommsen, Jing Li, T. Gadfort, Vipin Bhatnagar, D. Buchholz, C. Belanger-Champagne, P. Tamburello, Anna Goussiou, Andre Sznajder, R. Partridge, V. Buescher, Sudhir Malik, E. G. Zverev, Ia Iashvili, J. Dyer, Gregory R Snow, Yuri Gershtein, Kenneth Bloom, P.F. Ermolov, Brajesh C Choudhary, M. Wetstein, V. L. Malyshev, Graham Wilson, H. da Motta, D. Gillberg, S. Cihangir, Sung Keun Park, P. Renkel, B. Sanghi, M. Cooke, Nikos Varelas, M. Rominsky, W. M. Van Leeuwen, Bing Zhou, Luis Mendoza, W. L. Prado Da Silva, V. Kaushik, O. Atramentov, Fabrice Couderc, I. Ripp-Baudot, A. Meyer, Reinhard Schwienhorst, V. V. Tokmenin, F. Villeneuve-Seguier, S. Schlobohm, A. S. Ito, A. Melnitchouk, V. M. Podstavkov, R. K. Shivpuri, Ariel Schwartzman, M. Fortner, G. D. Alexeev, Flera Rizatdinova, Liang Li, H. Greenlee, V. M. Abazov, D. R. Claes, V. Shary, M. Arthaud, D. M. Strom, F. Badaud, Michael A. Strauss, R. Luna, B. C.K. Casey, H. A. Neal, O. Mundal, K. Yip, P. Lebrun, A. Bross, V. Hynek, Christophe Royon, Marco Verzocchi, C. Magass, Theodoros Christoudias, Dugan O'Neil, Gavin Davies, Philippe Calfayan, Ph Gris, Lev Dudko, H. Nilsen, R. Otec, S. M. Lietti, Y. Scheglov, C. Hensel, P. Houben, M. H. Kirby, B. Spurlock, A. Patwa, Mark Owen, H. D. Wahl, R. Unalan, Kaushik De, Zeno Dixon Greenwood, Avto Kharchilava, Serban Protopopescu, Pedro G Mercadante, L. Stutte, Gregory J Pawloski, W. M. Lee, D. K. Cho, S. Uvarov, A.S. Dyshkant, V. V. Lipaev, J. Lellouch, M. Aoki, Andy Haas, T. Dorland, G. Alkhazov, C. De Oliveira Martins, P. N. Ratoff, Jiri Kvita, J. K. Lim, J. Rieger, D. V. Bandurin, P. M. Tuts, Maksym Titov, Marcia Begalli, K. Herner, D. Onoprienko, D. Boline, Norbert Wermes, Meenakshi Narain, J. Haley, Hua-Lei Yin, Emanuela Barberis, Jan Stark, Hwi Dong Yoo, Ashok Kumar, A. P. Heinson, Cristina Galea, M. Merkin, B. Quinn, Robert Hirosky, Y. W. Liu, D. Bauer, F. Tissandier, Henry Lubatti, S. R. Dugad, M. Abolins, Alexander Khanov, P. Polozov, K. A. Johns, T. Scanlon, S. Kermiche, S. Strandberg, Suman Bala Beri, Vivian O'Dell, F. Chevallier, G. S. Muanza, M. Ćwiok, Tae Jeong Kim, B. Penning, Iain Alexander Bertram, Michael Rijssenbeek, S. Zelitch, A. Juste, B. Tiller, J. Cammin, J. D. Degenhardt, C. Schwanenberger, Alice Bean, Pushpalatha C Bhat, Andrew White, P. Haefner, Zdenek Hubacek, Tulika Bose, D. A. Stoyanova, R. E. Hall, Jovan Mitrevski, G. Gutierrez, Gilvan Alves, W. Geist, C. Biscarat, Terry Richard Wyatt, Todd Adams, Tiefu Zhao, P. A. Kasper, A. Bellavance, E. E. Boos, Heriberto Castilla-Valdez, S. W. Youn, P. Vint, A. C.S. Assis Jesus, H. Hoeth, Guennadi Borissov, Stephen Wimpenny, A. Das, M. Sosebee, M. C. Cousinou, T. Yasuda, Wendy Taylor, Marvin Johnson, A. L. Lyon, B. Hoeneisen, Lee Sawyer, N. K. Mondal, Jonas Strandberg, H. T. Diehl, T. A. Bolton, M. Pangilinan, A. V. Popov, Karl Jakobs, A. Alton, Helio Nogima, M. Kirsch, Martin Grunewald, W. C. Fisher, J. K. Kraus, Y. Pogorelov, Neeti Parashar, T. Kuhl, V. N. Evdokimov, K. W. Merritt, V. Bunichev, Yvonne Peters, Milos Lokajicek, Markus Wobisch, Freya Blekman, D. Smirnov, E. Carrera, A. V. Kozelov, S. J. Park, A. Boehnlein, J. T. Linnemann, J. F. Bartlett, P. Banerjee, Gustaaf Brooijmans, M. Jaffré, F. Guo, Maria Elena Pol, V. Cuplov, S. Hossain, J. Ellison, P. L.M. Podesta-Lerma, Jun Guo, E. De La Cruz-Burelo, David T. Johnston, Roger Moore, Q. Z. Li, Dmitri Tsybychev, R. L. McCarthy, Robert Kehoe, A. Dubey, G. Grenier, Darien Wood, L. Bagby, N. A. Naumann, V. Siccardi, John Hobbs, A. F. Barfuss, D. Lam, J. Snow, K. Peters, M. Demarteau, J. Barreto, M. Ahsan, Sa. Jain, S. Fuess, J. Warchol, V. A. Bezzubov, Nicholas John Hadley, C. P. Buszello, J. P. Negret, T. Kurca, Marc Weber, Andrew Brandt, L. Zivkovic, S. Fu, Alexander Kupco, M. Zielinski, S. Blessing, M. R. Adams, Michael Begel, Carmen García, Eduardo De Moraes Gregores, K. M. Chan, M. H.L.S. Wang, Scott Snyder, Brad Abbott, Kirti Ranjan, S. Söldner-Rembold, X. B. Bu, Pierre Petroff, Sergey Burdin, M. Eads, A. Magerkurth, S. P. Denisov, G. Hesketh, Harald Fox, M. Arov, M. Buehler, Michael Hildreth, J. Hays, P. J. Van Den Berg, A. V. Ferapontov, D. Kau, Suyong Choi, Michael Mulhearn, Marc Besancon, C. Potter, Luiz Mundim, Mark Richard James Williams, L. Welty-Rieger, M. P. Sanders, N. Parua, D. Vilanova, Randy Ruchti, R. Van Kooten, Jeroen Hegeman, Alexander Grohsjean, J. A. Parsons, B. S. Acharya, M. D. Corcoran, J. Osta, Lev Uvarov, Aaron Dominguez, B. Åsman, Sharon Hagopian, C. Jarvis, S. Uzunyan, L. Han, Raimund Ströhmer, Marc-Andre Pleier, A. K.A. Maciel, A. Zieminski, I. A. Vasilyev, L. Christofek, Harrison Prosper, V. Simak, R. Piegaia, Ernest Aguilo, T. H. Burnett, J. A. Benitez, Z. Liu, M. A. Strang, S. Desai, Petr Vokac, P. Padley, R. F. Rodrigues, Prolay Mal, Y. Xie, Amnon Harel, Ulrich Heintz, G. Obrant, Dorothee Schaile, S. Lammers, Frank Filthaut, M. Diesburg, M. Hohlfeld, Shabnam Jabeen, A. Tanasijczuk, Mitchell Wayne, H. Schellman, J. M. Kohli, R. Jesik, Frederic Deliot, Christopher George Tully, Laurent Duflot, N. Osman, Y. M. Kharzheev, S. Chakrabarti, Peter Love, Patrick Slattery, Stefan Grünendahl, Raymond Brock, Boaz Klima, W. Geng, Gregorio Bernardi, D. Denisov, I. Katsanos, R. Beuselinck, S. J. De Jong, B. Gómez, B. Tuchming, R. J. Madaras, Julia S. Meyer, Hal Evans, Thomas Ferbel, Lars Sonnenschein, L. S. Vertogradov, N. Khalatyan, S. Yacoob, R. G. Wagner, Y. Arnoud, J. Sekaric, R. Bernhard, W. E. Cooper, Mikko Voutilainen, Arnaud Duperrin, D. Duggan, Jong-Sung Yu, George Alverson, S. Beale, A. A. Shchukin, D. Hedin, Frank Fiedler, E. Kajfasz, Y. A. Yatsunenko, G. Savage, Viatcheslav Stolin, Carlos Avila, S. Sumowidagdo, Sabine Crépé-Renaudin, Christophe Ochando, A. Sanchez-Hernandez, B. G. Pope, V. Zutshi, Calvin A. Johnson, Andrew Askew, Brigitte Vachon, A. Chandra, S. Calvet, T. Nunnemann, B. Baldin, Elizaveta Shabalina, Mansoora Shamim, Timothy Andeen, Andre Sopczak, B. Andrieu, Elliott Cheu, T. Schliephake, Victor Daniel Elvira, W. C. Yang, Maxim Perfilov, A. Rakitine, L. Bellantoni, Helena Malbouisson, J. N. Butler, P. D. Grannis, J. Steele, L. S. Ancu, P. Mättig, R. Illingworth, A. Leflat, A. Evdokimov, Philip Baringer, J. Piper, S. Banerjee, U. Bassler, S. Robinson, Regina Demina, Y. Enari, T. Moulik, J. G.R. Lima, Grigory Safronov, P. Rubinov, H. E. Fisk, E. Strauss, Aran Garcia-Bellido, J. M. Hauptman, Cecilia Elena Gerber, Benjamin M. Martin, G. Ginther, Jianming Qian, M. Anastasoaie, P. Rich, C. Zeitnitz, Arnulf Quadt, Elemer Nagy, D. Wicke, Dennis Stephen Mackin, P. Svoisky, P. Verdier, Kristian Harder, D. Cutts, V. A. Kuzmin, Wagner Carvalho, M. Petteni, Greg Landsberg, J. M. Kalk, Deidre Brown, P. Skubic, Pedrame Bargassa, K. Soustruznik, N. J. Buchanan, G. C. Blazey, I. Torchiani, R. Yamada, Jean-Francois Grivaz, P. Jonsson, Thomas Hebbeker, D. Khatidze, Florian Lacroix, G. Sajot, Y. Hu, M. S. Rangel, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, G. J. Otero Y Garzón, Junjie Zhu, N. Gollub, Richard B. Lipton, and Sergio F Novaes
Subjects: Quark, Physics, Nuclear and High Energy Physics, Particle physics, 010308 nuclear & particles physics, Physics beyond the Standard Model, High Energy Physics::Phenomenology, Tevatron, Elementary particle, Little Higgs, Topology, 01 natural sciences, Nuclear physics, 0103 physical sciences, High Energy Physics::Experiment, Leptoquark, Fermilab, Neutrino, 010306 general physics
Abstract: A search for new physics in the acoplanar jet topology has been performed in 2.5 fb(-1) of data from p (p) over bar collisions at root s = 1.96 TeV, recorded by the DO detector at the Fermilab Tevatron Collider. The numbers of events with exactly two acoplanar jets and missing transverse energy are in good agreement with the Standard Model expectations. The result of this search has been used to set a lower mass limit of 205 GeV at the 95% C.L. on the mass of a scalar leptoquark when this particle decays exclusively into a quark and a neutrino. In the framework of the Little Higgs model with T-parity, limits have also been obtained on the T-odd quark mass as a function of the T-odd photon mass.
Published: 2008

100. Measurement of B(t→Wb)/B(t→Wq) at s=1.96TeV

Author: V. Simak, F. Villeneuve-Seguier, Vipin Bhatnagar, E. De La Cruz-Burelo, R. Partridge, Christian Autermann, V. L. Malyshev, V. V. Tokmenin, P. Padley, H. S. Mao, R. F. Rodrigues, B. Åsman, R. Van Kooten, V. M. Abazov, M. D. Corcoran, G. Obrant, V. Shary, Mitchell Wayne, H. Schellman, J. M. Kohli, A. C.S. Assis Jesus, Guennadi Borissov, H. A. Neal, D. Meder, J. T. Linnemann, K. Yip, N. Xuan, Stefan Grünendahl, D. Brown, Christian Schmitt, S. Nelson, M. H.G. Souza, W. C. Fisher, P. Verdier, K. J. Rani, A. Alton, M. Merkin, Robert Hirosky, K. W. Merritt, J. F. Bartlett, P. Banerjee, Armen Vartapetian, A. P. Heinson, G. S. Muanza, Stephen Wimpenny, Iain Alexander Bertram, R. Gelhaus, Michael Rijssenbeek, D. V. Bandurin, D. A. Stoyanova, Robert Kehoe, M. C. Cousinou, Marco Verzocchi, C. Magass, Dugan O'Neil, E. G. Zverev, A. Patwa, Mark Owen, Denis Gelé, Raymond Brock, Boaz Klima, M. Das, Sascha Caron, R. Unalan, L. Stutte, Gregory J Pawloski, L. Han, A. Zieminski, A.S. Dyshkant, Dmitri Tsybychev, R. L. McCarthy, I. Katsanos, N. M. Cason, M. Agelou, A. M. Magnan, M. Yan, S. Fu, R. Beuselinck, F. Borcherding, R. W. Moore, F. Lehner, T. Edwards, Martin Grunewald, A. M. Kalinin, Mossadek Talby, R. E. Hall, B. Gómez, Shashikant Dugad, A. Yurkewicz, Jiri Kvita, P. A. Rapidis, S. Burke, D. A. Wijngaarden, Marcia Begalli, M. Zielinski, Milos Lokajicek, L. Bagby, Christophe Royon, N. Gollub, A. Evdokimov, Terry Richard Wyatt, P. K. Mal, V. N. Evdokimov, I. Hall, M. Kopal, A. Chandra, Jovan Mitrevski, M. A. Strang, G. Hesketh, Norbert Wermes, Julia S. Meyer, Meenakshi Narain, Sherry Towers, J. Haley, Suyong Choi, Emily Nurse, G. Sajot, Elizabeth Gallas, V. I. Rud, S. Söldner-Rembold, Darien Wood, V. A. Bezzubov, M. Strovink, R. A. Sidwell, J. P. Negret, G. Gutierrez, R. P. Smith, P. J. Van Den Berg, Jessica Levêque, K. Bos, Marc Besancon, J. Temple, L. S. Vertogradov, Michael Begel, Sergey Burdin, M. Eads, K. M. Chan, Christian Zeitnitz, Lev Uvarov, Y. Hu, Gilvan Alves, Emanuela Barberis, M. Abolins, Sophie Trincaz-Duvoid, Nicholas John Hadley, C. P. Buszello, Kazunori Hanagaki, Dongliang Zhang, H. D. Wahl, Nikola Makovec, Rupinder Kaur, Bradley Cox, S. P. Denisov, J. D. Degenhardt, S. Lammers, Y. Arnoud, B. Davies, H. Weerts, J. Kozminski, S. Blessing, P. Renkel, Michael Hildreth, Eduardo De Moraes Gregores, S. E.K. Mattingly, Graham Wilson, Heriberto Castilla-Valdez, H. da Motta, S. Krzywdzinski, M. Petteni, J. Lazoflores, D. Edmunds, M. Binder, W. E. Cooper, Scott Snyder, D. Bauer, F. Badaud, Kevin Black, Cris W. Barnes, Yann Coadou, D. Kau, P.F. Ermolov, D. Gillberg, K. Stevenson, N. K. Mondal, P. Schieferdecker, H. T. Diehl, T. A. Bolton, Lev Dudko, Mikko Voutilainen, W. D. Shephard, R. McCroskey, Andre Sznajder, M. Cooke, Y. Pogorelov, S. Uzunyan, Karl Jakobs, R. K. Shivpuri, C. Noeding, A. S. Ito, A. Melnitchouk, A. Sanchez-Hernandez, A. Boehnlein, M. Sosebee, J. M. Kalk, Arnaud Duperrin, Yuri Gershtein, G. A. Davis, Boris Tuchming, Sharon Hagopian, Gregorio Bernardi, Emmanuelle Perez, A. K.A. Maciel, D. Denisov, W. L. Prado Da Silva, S. Greder, V. M. Korablev, Harrison Prosper, Y. Xie, Amnon Harel, S. Desai, V. Hynek, Jeroen Hegeman, J. Ellison, Jong-Sung Yu, Hwi Dong Yoo, B. Vachon, D. R. Claes, V. Zutshi, Gavin Davies, W. M. Van Leeuwen, C. Schwanenberger, M. Ahsan, J. M. Heinmiller, Sa. Jain, S. Fuess, Jun Guo, Q. Z. Li, Hal Evans, Thomas Ferbel, H. Greenlee, D. M. Strom, S. Doulas, L. Berntzon, Ashok Kumar, T. Kurca, S. Sengupta, Freya Blekman, Luiz Mundim, V. V. Lipaev, Lars Sonnenschein, M. S. Anzelc, Sarah Catherine Eno, Horst Severini, Marc Weber, S. Chakrabarti, Peter Love, E. Galyaev, B. C.K. Casey, V. Lesne, I. Ripp-Baudot, A. Meyer, S. J. Hong, Jonas Strandberg, N. Parua, Y. Scheglov, Kaushik De, M. H. Kirby, Reinhard Schwienhorst, R. Piegaia, Ariel Schwartzman, Michael A. Strauss, R. Bernhard, Limin Wang, A. Bross, Marc-Andre Pleier, P. Lewis, Ashok Das, Christos Leonidopoulos, T. Kuhl, G. Alkhazov, A. Jenkins, R. J. Madaras, S. Yacoob, J. A. Parsons, Paul Telford, V. White, I. Blackler, Avto Kharchilava, P. Lebrun, J. Snow, Christophe Clement, F. Charles, Andrew Brandt, N. Parashar, Serban Protopopescu, M. Jaffré, Tae Jeong Kim, Marcel Vreeswijk, B. Spurlock, O. Boeriu, F. Chevallier, T. Yasuda, Alexander Khanov, Sung Keun Park, Jan Stark, Wendy Taylor, J. Womersley, Zeno Dixon Greenwood, Kirti Ranjan, H.E. Miettinen, Carsten Hensel, Junjie Zhu, Henry Lubatti, Y. A. Yatsunenko, D. K. Cho, A. Stone, George Alverson, Johannes Elmsheuser, P. Neustroev, Tobias Golling, T. Scanlon, Andy Haas, S. Kermiche, M. Wobisch, Alexey Ferapontov, A. Pompoš, J. Cammin, Viatcheslav Stolin, Richard B. Lipton, Tulika Bose, Suman Bala Beri, D. Hedin, J. Kasper, K. Gounder, J. R. Kalk, P. Haefner, Vivian O'Dell, Mark Raymond Adams, Emmanuel Busato, M. Ćwiok, Cristina Galea, Alexander Kupco, D. Karmanov, Marvin Johnson, J. Molina, Carlos Avila, S. Sumowidagdo, Kristian Harder, S. Kesisoglou, O. Atramentov, Tiefu Zhao, V. Siccardi, A. Juste, Todd Adams, M. Wetstein, Sudhir Malik, A. V. Kozelov, Ia Iashvili, P. Skubic, Sabine Crépé-Renaudin, D. Cutts, Ulrike Blumenschein, Frederic Deliot, Christopher George Tully, Jean-Roch Vlimant, Brajesh C Choudhary, J. P. Konrath, H. Dong, Andrew White, D. Buchholz, Wagner Carvalho, M. Michaut, P. L.M. Podesta-Lerma, Jean-Laurent Agram, R. Otec, Randy Ruchti, D. Chakraborty, Greg Landsberg, Adam L. Lyon, G. Savage, Brad Abbott, A. Magerkurth, A. Zatserklyaniy, Y. M. Kharzheev, Sergio F Novaes, R. Jesik, Michael Martens, P. Tamburello, Juan Estrada, C. Ay, Pierre Petroff, B. S. Acharya, C. De Oliveira Martins, P. N. Ratoff, Nikos Varelas, Bing Zhou, Luis Mendoza, Patrick Slattery, G. J. Otero y Garzón, M. Ford, Andrew Askew, Zhengguo Zhao, Anna Goussiou, Abdenour Lounis, D. Shpakov, Pedrame Bargassa, P. M. Tuts, Maksym Titov, T. H. Burnett, Hyun-Chul Kim, Yurii Maravin, Don Lincoln, Erich Varnes, Vladimir Gavrilov, M. Anastasoaie, K. Soustruznik, K. A. Johns, Andrei Nomerotski, C. Jarvis, Gordon Watts, V. Sirotenko, S. N. Fatakia, Robert Harrington, Arnulf Quadt, J. Dyer, N. J. Buchanan, A. Mendes, Gregory R Snow, Elemer Nagy, J. A. Benitez, A. C. Le Bihan, V. M. Podstavkov, J. Monk, John Hobbs, A. Baden, J. Barreto, Ulrich Heintz, Md. Naimuddin, A. S. Turcot, Phillip Gutierrez, M. Fortner, B. Clement, G. C. Blazey, Y. Yen, I. Torchiani, M. Buehler, Frank Filthaut, T. Gadfort, M. Diesburg, M. Lynker, R. Hooper, D. Wicke, R. Yamada, X. F. Song, L. Lobo, T. Nunnemann, Ph Gris, B. Baldin, P. Houben, Lorenzo Feligioni, Jean-Francois Grivaz, S. H. Ahn, P. de Jong, M. Arov, Dorothee Schaile, V. Oguri, A. Koubarovsky, P. Jonsson, Mansoora Shamim, Jing Li, A. V. Popov, M. Hohlfeld, Thomas Hebbeker, D. Khatidze, M. Mulders, J. Hays, Gustaaf Brooijmans, J. Warchol, V. Buescher, S. J. De Jong, B. Kothari, A. A. Shchukin, Andre Sopczak, Frank Fiedler, E. Kajfasz, H. E. Fisk, Aran Garcia-Bellido, M. P. Sanders, J. M. Hauptman, Cecilia Elena Gerber, G. Ginther, Jianming Qian, M. Doidge, B. Andrieu, Elliott Cheu, Victor Daniel Elvira, U. Bassler, S. Robinson, Regina Demina, T. Moulik, Alberto Santoro, J. G.R. Lima, W. M. Lee, P. Rubinov, L. Christofek, Helena Malbouisson, D. Chapin, J. N. Butler, P. D. Grannis, J. Steele, B. Tiller, S. W. Youn, E. Von Toerne, P. Demine, D. Coppage, G. Grenier, N. A. Naumann, Pushpalatha C Bhat, S. Reucroft, Reiner Hauser, D. Käfer, A. Bellavance, B. Hoeneisen, Lee Sawyer, B. G. Pope, Calvin A. Johnson, S. Calvet, Elizaveta Shabalina, Timothy Andeen, A. Kryemadhi, Shuichi Kunori, P. Mättig, R. Illingworth, A. Leflat, S.A. Kahn, Philip Baringer, S. Jabeen, S. Banerjee, M. Demarteau, Carmen García, T. Toole, S. Lager, S. Uvarov, Ivor Fleck, B. Quinn, Thomas Trefzger, Makoto Tomoto, Alice Bean, N. Oliveira, Maria Elena Pol, J. Gardner, J. Kotcher, S. Anderson, Harald Fox, M. Vaupel, Y. D. Mutaf, I. A. Vasilyev, P. M. Perea, G. D. Alexeev, Flera Rizatdinova, C. Biscarat, A. Jonckheere, A. Lobodenko, N. Oshima, Daniel Bloch, Daria Zieminska, R. D. Schamberger, Raimund Ströhmer, and L. Duflot
Subjects: Physics, Nuclear and High Energy Physics, Particle physics, Top quark, Muon, 010308 nuclear & particles physics, High Energy Physics::Phenomenology, Tevatron, Electron, 7. Clean energy, 01 natural sciences, Lower limit, Standard Model, law.invention, Nuclear physics, law, 0103 physical sciences, High Energy Physics::Experiment, Fermilab, 010306 general physics, Collider
Abstract: We present the measurement of R = B(t -> Wb)/B(t -> Wq) in pp collisions at root s = 1.96 TeV, using 230 pb(-1) of data collected by the DO experiment at the Fermilab Tevatron Collider. We fit simultaneously R and the number (N-tt) of selected top quark pairs (tt), to the number of identified b-quark jets in events with one electron or one muon, three or more jets, and high transverse energy imbalance. To improve sensitivity, kinematical properties of events with no identified b-quark jets are included in the fit. We measure R = 1.03(-0.17)(0.19) (stat + syst), in good agreement with the standard model. We set lower limits of R > 0.61 and vertical bar V-tb vertical bar > 0.78 at 95% confidence level.
Published: 2006

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

241 results on '"P. J. van den Berg"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources