WorldWideScience

Sample records for genome atlas tcga

  1. TCGA study identifies genomic features of cervical cancer

    Science.gov (United States)

    Investigators with The Cancer Genome Atlas (TCGA) Research Network have identified novel genomic and molecular characteristics of cervical cancer that will aid in subclassification of the disease and may help target therapies that are most appropriate for each patient.

  2. TCGA Workshop: Genomics and Biology of Glioblastoma Multiforme (GBM) - TCGA

    Science.gov (United States)

    The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) held a workshop entitled, “Genomics and Biology of Glioblastoma Multiforme (GBM),” to review the initial GBM data from the TCGA pilot project.

  3. Cloud Technology May Widen Genomic Bottleneck - TCGA

    Science.gov (United States)

    Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

  4. TCGA head Neck

    Science.gov (United States)

    Investigators with The Cancer Genome Atlas (TCGA) Research Network have discovered genomic differences – with potentially important clinical implications – in head and neck cancers caused by infection with the human papillomavirus (HPV).

  5. Clinical Value of miR-101-3p and Biological Analysis of its Prospective Targets in Breast Cancer: A Study Based on The Cancer Genome Atlas (TCGA) and Bioinformatics.

    Science.gov (United States)

    Li, Chun-Yao; Xiong, Dan-Dan; Huang, Chun-Qin; He, Rong-Quan; Liang, Hai-Wei; Pan, Deng-Hua; Wang, Han-Lin; Wang, Yi-Wen; Zhu, Hua-Wei; Chen, Gang

    2017-04-18

    BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified. The potential genes targeted by miR-101-3p were also predicted. Gene Ontology (GO) and pathway and network analyses were constructed for the DEGs and predicted genes. RESULTS In the TCGA data, a low level of miR-101-2 expression might represent a diagnostic (AUC: 0.63) marker, and the miR-101-1 was a prognostic (HR=1.79) marker. MiR-101-1 was linked to the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), and miR-101-2 was associated with the tumor (T), lymph node (N), and metastasis (M) stages of BC. Moreover, 427 genes were selected from the 921 DEGs in GEO and the 7924 potential target genes from the prediction databases. These genes were related to transcription, metabolism, biosynthesis, and proliferation. The results were also significantly enriched in the VEGF, mTOR, focal adhesion, Wnt, and chemokine signaling pathways. CONCLUSIONS MiR-101-1 and miR-101-2 may be prospective biomarkers for the prognosis and diagnosis of BC, respectively, and are associated with diverse clinical parameters. The target genes of miR-101-3p regulate the development and progression of BC. These results provide insight into the pathogenic mechanism and potential therapies for BC.

  6. TCGA Expedition: A Data Acquisition and Management System for TCGA Data.

    Directory of Open Access Journals (Sweden)

    Uma R Chandran

    Full Text Available The Cancer Genome Atlas Project (TCGA is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS, whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices.TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and

  7. Exposing the cancer genome atlas as a SPARQL endpoint

    Science.gov (United States)

    Deus, Helena F.; Veiga, Diogo F.; Freire, Pablo R.; Weinstein, John N.; Mills, Gordon B.; Almeida, Jonas S.

    2011-01-01

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. PMID:20851208

  8. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

    NARCIS (Netherlands)

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

    2018-01-01

    For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data

  9. TU-CD-BRB-07: Identification of Associations Between Radiologist-Annotated Imaging Features and Genomic Alterations in Breast Invasive Carcinoma, a TCGA Phenotype Research Group Study

    Energy Technology Data Exchange (ETDEWEB)

    Rao, A; Net, J [University of Miami, Miami, Florida (United States); Brandt, K [Mayo Clinic, Rochester, Minnesota (United States); Huang, E [National Cancer Institute, NIH, Bethesda, MD (United States); Freymann, J; Kirby, J [Leidos Biomedical Research Inc., Frederick, MD (United States); Burnside, E [University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States); Morris, E; Sutton, E [Memorial Sloan Kettering Cancer Center, New York, NY (United States); Bonaccio, E [Roswell Park Cancer Institute, Buffalo, NY (United States); Giger, M; Jaffe, C [Univ Chicago, Chicago, IL (United States); Ganott, M; Zuley, M [University of Pittsburgh Medical Center - Magee Womens Hospital, Pittsburgh, Pennsylvania (United States); Le-Petross, H [MD Anderson Cancer Center, Houston, TX (United States); Dogan, B [UT MDACC, Houston, TX (United States); Whitman, G [UTMDACC, Houston, TX (United States)

    2015-06-15

    Purpose: To determine associations between radiologist-annotated MRI features and genomic measurements in breast invasive carcinoma (BRCA) from the Cancer Genome Atlas (TCGA). Methods: 98 TCGA patients with BRCA were assessed by a panel of radiologists (TCGA Breast Phenotype Research Group) based on a variety of mass and non-mass features according to the Breast Imaging Reporting and Data System (BI-RADS). Batch corrected gene expression data was obtained from the TCGA Data Portal. The Kruskal-Wallis test was used to assess correlations between categorical image features and tumor-derived genomic features (such as gene pathway activity, copy number and mutation characteristics). Image-derived features were also correlated with estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2/neu) status. Multiple hypothesis correction was done using Benjamini-Hochberg FDR. Associations at an FDR of 0.1 were selected for interpretation. Results: ER status was associated with rim enhancement and peritumoral edema. PR status was associated with internal enhancement. Several components of the PI3K/Akt pathway were associated with rim enhancement as well as heterogeneity. In addition, several components of cell cycle regulation and cell division were associated with imaging characteristics.TP53 and GATA3 mutations were associated with lesion size. MRI features associated with TP53 mutation status were rim enhancement and peritumoral edema. Rim enhancement was associated with activity of RB1, PIK3R1, MAP3K1, AKT1,PI3K, and PIK3CA. Margin status was associated with HIF1A/ARNT, Ras/ GTP/PI3K, KRAS, and GADD45A. Axillary lymphadenopathy was associated with RB1 and BCL2L1. Peritumoral edema was associated with Aurora A/GADD45A, BCL2L1, CCNE1, and FOXA1. Heterogeneous internal nonmass enhancement was associated with EGFR, PI3K, AKT1, HF/MET, and EGFR/Erbb4/neuregulin 1. Diffuse nonmass enhancement was associated with HGF/MET/MUC20/SHIP

  10. Exposing the cancer genome atlas as a SPARQL endpoint.

    Science.gov (United States)

    Deus, Helena F; Veiga, Diogo F; Freire, Pablo R; Weinstein, John N; Mills, Gordon B; Almeida, Jonas S

    2010-12-01

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. Copyright © 2010 Elsevier Inc. All rights reserved.

  11. Endometrial and acute myeloid leukemia cancer genomes characterized

    Science.gov (United States)

    Two studies from The Cancer Genome Atlas (TCGA) program reveal details about the genomic landscapes of acute myeloid leukemia (AML) and endometrial cancer. Both provide new insights into the molecular underpinnings of these cancers.

  12. Putting TCGA Data to Work - TCGA

    Science.gov (United States)

    Neurosurgeon Cameron Brennan of Memorial Sloan-Kettering Cancer Center used TCGA data to define subgroups of patients with a deadly brain cancer called glioblastoma multiforme. Learn more about his research in this TCGA in Action case study.

  13. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  14. Genomic features of lobular breast carcinoma

    Science.gov (United States)

    Investigators with The Cancer Genome Atlas (TCGA) Research Network have identified molecular characteristics of a type of breast cancer, invasive lobular carcinoma (ILC), that distinguishes it from invasive ductal carcinoma (IDC), the most common invasive breast cancer subtype.

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

    Directory of Open Access Journals (Sweden)

    Gregory P. Way

    2018-04-01

    Full Text Available 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

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

    Directory of Open Access Journals (Sweden)

    Theo A. Knijnenburg

    2018-04-01

    Full Text Available 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

  17. Evaluation of K-ras and p53 expression in pancreatic adenocarcinoma using the cancer genome atlas.

    Directory of Open Access Journals (Sweden)

    Liming Lu

    Full Text Available Genetic alterations in K-ras and p53 are thought to be critical in pancreatic cancer development and progression. However, K-ras and p53 expression in pancreatic adenocarcinoma have not been systematically examined in The Cancer Genome Atlas (TCGA Data Portal. Information regarding K-ras and p53 alterations, mRNA expression data, and protein/protein phosphorylation abundance was retrieved from The Cancer Genome Atlas (TCGA databases, and analyses were performed by the cBioPortal for Cancer Genomics. The mutual exclusivity analysis showed that events in K-ras and p53 were likely to co-occur in pancreatic adenocarcinoma (Log odds ratio = 1.599, P = 0.006. The graphical summary of the mutations showed that there were hotspots for protein activation. In the network analysis, no solid association between K-ras and p53 was observed in pancreatic adenocarcinoma. In the survival analysis, neither K-ras nor p53 were associated with both survival events. As in the data mining study in the TCGA databases, our study provides a new perspective to understand the genetic features of K-ras and p53 in pancreatic adenocarcinoma.

  18. A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data.

    Science.gov (United States)

    Zhang, Zhuo; Li, Hao; Jiang, Shuai; Li, Ruijiang; Li, Wanying; Chen, Hebing; Bo, Xiaochen

    2018-03-29

    The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and discover major cancer-causing genomic alterations with the goal of creating a comprehensive 'atlas' of cancer genomic profiles. The availability of this genome-wide information provides an unprecedented opportunity to expand our knowledge of tumourigenesis. Computational analytics and mining are frequently used as effective tools for exploring this byzantine series of biological and biomedical data. However, some of the more advanced computational tools are often difficult to understand or use, thereby limiting their application by scientists who do not have a strong computational background. Hence, it is of great importance to build user-friendly interfaces that allow both computational scientists and life scientists without a computational background to gain greater biological and medical insights. To that end, this survey was designed to systematically present available Web-based tools and facilitate the use TCGA data for cancer research.

  19. Genetic Alterations in the Molecular Subtypes of Bladder Cancer: Illustration in the Cancer Genome Atlas Dataset.

    Science.gov (United States)

    Choi, Woonyoung; Ochoa, Andrea; McConkey, David J; Aine, Mattias; Höglund, Mattias; Kim, William Y; Real, Francisco X; Kiltie, Anne E; Milsom, Ian; Dyrskjøt, Lars; Lerner, Seth P

    2017-09-01

    Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our overall goal was to determine whether specific DNA mutations and/or copy number variations are enriched in specific molecular subtypes. We used the complete TCGA RNA-seq dataset and three different published classifiers developed by our groups to assign TCGA's bladder cancers to molecular subtypes, and examined the prevalence of the most common DNA alterations within them. We interpreted the results against the background of what was known from the published literature about the prevalence of these alterations in nonmuscle-invasive and muscle-invasive bladder cancers. The results confirmed that alterations involving RB1 and NFE2L2 were enriched in basal cancers, whereas alterations involving FGFR3 and KDM6A were enriched in luminal tumors. The results further reinforce the conclusion that the molecular subtypes of bladder cancer are distinct disease entities with specific genetic alterations. Our observation showed that some of subtype-enriched mutations and copy number aberrations are clinically actionable, which has direct implications for the clinical management of patients with bladder cancer. Copyright © 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.

  20. TopFed: TCGA tailored federated query processing and linking to LOD.

    Science.gov (United States)

    Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

    2014-01-01

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and

  1. Analysis of single nucleotide variants of HFE gene and association to survival in The Cancer Genome Atlas GBM data.

    Science.gov (United States)

    Lee, Sang Y; Zhu, Junjia; Salzberg, Anna C; Zhang, Bo; Liu, Dajiang J; Muscat, Joshua E; Langan, Sara T; Connor, James R

    2017-01-01

    Human hemochromatosis protein (HFE) is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM). However, the effect of other single nucleotide variation (SNV) in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA) GBM (Caucasian only) database. We found 9 SNVs with increased frequency in blood normal of TCGA GBM patients compared to the 1000Genome. Among 9 SNVs, 7 SNVs were located in the intron and 2 SNVs (i.e., H63D, C282Y) in the exon of HFE gene. The statistical analysis demonstrated that blood normal samples of TCGA GBM have more H63D (p = 0.0002, 95% Confidence interval (CI): 0.2119-0.3223) or C282Y (p = 0.0129, 95% CI: 0.0474-0.1159) HFE polymorphisms than 1000Genome. The Kaplan-Meier survival curve for the 264 GBM samples revealed no difference between wild type (WT) HFE and H63D, and WT HFE and C282Y GBM patients. In addition, there was no difference in the survival of male/female GBM patients based on HFE genotype. There was no correlation between HFE expression and survival. In conclusion, the current results suggest that somatic HFE polymorphisms do not impact GBM patients' survival in the TCGA data set of GBM.

  2. Analysis of single nucleotide variants of HFE gene and association to survival in The Cancer Genome Atlas GBM data.

    Directory of Open Access Journals (Sweden)

    Sang Y Lee

    Full Text Available Human hemochromatosis protein (HFE is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM. However, the effect of other single nucleotide variation (SNV in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA GBM (Caucasian only database. We found 9 SNVs with increased frequency in blood normal of TCGA GBM patients compared to the 1000Genome. Among 9 SNVs, 7 SNVs were located in the intron and 2 SNVs (i.e., H63D, C282Y in the exon of HFE gene. The statistical analysis demonstrated that blood normal samples of TCGA GBM have more H63D (p = 0.0002, 95% Confidence interval (CI: 0.2119-0.3223 or C282Y (p = 0.0129, 95% CI: 0.0474-0.1159 HFE polymorphisms than 1000Genome. The Kaplan-Meier survival curve for the 264 GBM samples revealed no difference between wild type (WT HFE and H63D, and WT HFE and C282Y GBM patients. In addition, there was no difference in the survival of male/female GBM patients based on HFE genotype. There was no correlation between HFE expression and survival. In conclusion, the current results suggest that somatic HFE polymorphisms do not impact GBM patients' survival in the TCGA data set of GBM.

  3. Identifying Scientific Project-generated Data Citation from Full-text Articles: An Investigation of TCGA Data Citation

    Directory of Open Access Journals (Sweden)

    Jiao Li

    2016-06-01

    Full Text Available Purpose: In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database. Moreover, scientific publications are preserved in a digital library archive. It is challenging to identify the data usage that is mentioned in literature and associate it with its source. Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA, via a full-text literature analysis. Design/methodology/approach: We focused on identifying articles using the TCGA dataset and constructing linkages between the articles and the specific TCGA dataset. First, we collected 5,372 TCGA-related articles from PubMed Central (PMC. Second, we constructed a benchmark set with 25 full-text articles that truly used the TCGA data in their studies, and we summarized the key features of the benchmark set. Third, the key features were applied to the remaining PMC full-text articles that were collected from PMC. Findings: The amount of publications that use TCGA data has increased significantly since 2011, although the TCGA project was launched in 2005. Additionally, we found that the critical areas of focus in the studies that use the TCGA data were glioblastoma multiforme, lung cancer, and breast cancer; meanwhile, data from the RNA-sequencing (RNA-seq platform is the most preferable for use. Research limitations: The current workflow to identify articles that truly used TCGA data is labor-intensive. An automatic method is expected to improve the performance. Practical implications: This study will help cancer genomics researchers determine the latest advancements in cancer molecular therapy, and it will promote data sharing and data-intensive scientific discovery. Originality/value: Few studies have been conducted to investigate data usage by government-funded projects/programs since their launch. In this preliminary study, we extracted articles that use TCGA data

  4. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

    Science.gov (United States)

    Buckley, Alexandra R; Standish, Kristopher A; Bhutani, Kunal; Ideker, Trey; Lasken, Roger S; Carter, Hannah; Harismendy, Olivier; Schork, Nicholas J

    2017-06-12

    Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples. We demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.

  5. Mining TCGA data using Boolean implications.

    Directory of Open Access Journals (Sweden)

    Subarna Sinha

    Full Text Available Boolean implications (if-then rules provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression from the glioblastoma (GBM and ovarian serous cystadenoma (OV data sets from The Cancer Genome Atlas (TCGA. We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/.

  6. B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

    Science.gov (United States)

    Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

    2017-12-12

    Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

  7. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

    NARCIS (Netherlands)

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

    2018-01-01

    The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the

  8. Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data

    Science.gov (United States)

    Gutman, David A; Cobb, Jake; Somanna, Dhananjaya; Park, Yuna; Wang, Fusheng; Kurc, Tahsin; Saltz, Joel H; Brat, Daniel J; Cooper, Lee A D

    2013-01-01

    Background The integration and visualization of multimodal datasets is a common challenge in biomedical informatics. Several recent studies of The Cancer Genome Atlas (TCGA) data have illustrated important relationships between morphology observed in whole-slide images, outcome, and genetic events. The pairing of genomics and rich clinical descriptions with whole-slide imaging provided by TCGA presents a unique opportunity to perform these correlative studies. However, better tools are needed to integrate the vast and disparate data types. Objective To build an integrated web-based platform supporting whole-slide pathology image visualization and data integration. Materials and methods All images and genomic data were directly obtained from the TCGA and National Cancer Institute (NCI) websites. Results The Cancer Digital Slide Archive (CDSA) produced is accessible to the public (http://cancer.digitalslidearchive.net) and currently hosts more than 20 000 whole-slide images from 22 cancer types. Discussion The capabilities of CDSA are demonstrated using TCGA datasets to integrate pathology imaging with associated clinical, genomic and MRI measurements in glioblastomas and can be extended to other tumor types. CDSA also allows URL-based sharing of whole-slide images, and has preliminary support for directly sharing regions of interest and other annotations. Images can also be selected on the basis of other metadata, such as mutational profile, patient age, and other relevant characteristics. Conclusions With the increasing availability of whole-slide scanners, analysis of digitized pathology images will become increasingly important in linking morphologic observations with genomic and clinical endpoints. PMID:23893318

  9. Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

    Science.gov (United States)

    Ping, Zheng; Siegal, Gene P.; Almeida, Jonas S.; Schnitt, Stuart J.; Shen, Dejun

    2014-01-01

    Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer. PMID:24672738

  10. Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

    Directory of Open Access Journals (Sweden)

    Zheng Ping

    2014-01-01

    Full Text Available Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.

  11. Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Hsu Fang-Han

    2012-10-01

    Full Text Available Abstract Background Despite initial response in adjuvant chemotherapy, ovarian cancer patients treated with the combination of paclitaxel and carboplatin frequently suffer from recurrence after few cycles of treatment, and the underlying mechanisms causing the chemoresistance remain unclear. Recently, The Cancer Genome Atlas (TCGA research network concluded an ovarian cancer study and released the dataset to the public. The TCGA dataset possesses large sample size, comprehensive molecular profiles, and clinical outcome information; however, because of the unknown molecular subtypes in ovarian cancer and the great diversity of adjuvant treatments TCGA patients went through, studying chemotherapeutic response using the TCGA data is difficult. Additionally, factors such as sample batches, patient ages, and tumor stages further confound or suppress the identification of relevant genes, and thus the biological functions and disease mechanisms. Results To address these issues, herein we propose an analysis procedure designed to reduce suppression effect by focusing on a specific chemotherapeutic treatment, and to remove confounding effects such as batch effect, patient's age, and tumor stages. The proposed procedure starts with a batch effect adjustment, followed by a rigorous sample selection process. Then, the gene expression, copy number, and methylation profiles from the TCGA ovarian cancer dataset are analyzed using a semi-supervised clustering method combined with a novel scoring function. As a result, two molecular classifications, one with poor copy number profiles and one with poor methylation profiles, enriched with unfavorable scores are identified. Compared with the samples enriched with favorable scores, these two classifications exhibit poor progression-free survival (PFS and might be associated with poor chemotherapy response specifically to the combination of paclitaxel and carboplatin. Significant genes and biological processes are

  12. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

    NARCIS (Netherlands)

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

    2018-01-01

    The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a

  13. TCGA_LowerGradeGliomas

    Science.gov (United States)

    TCGA researchers analyzed nearly 300 cases of diffuse low- and intermediate-grade gliomas, which together comprise lower-grade gliomas. LGGs occur mainly in adults and include astrocytomas, oligodendrogliomas and oligoastrocytomas.

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

    Directory of Open Access Journals (Sweden)

    Christopher J. Ricketts

    2018-04-01

    Full Text Available 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

  15. A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

    Energy Technology Data Exchange (ETDEWEB)

    Mockler, Todd [Oregon State Univ., Corvallis, OR (United States)

    2017-04-17

    Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes of plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.

  16. Significance of the BRAF mRNA Expression Level in Papillary Thyroid Carcinoma: An Analysis of The Cancer Genome Atlas Data.

    Directory of Open Access Journals (Sweden)

    Young Jun Chai

    Full Text Available BRAFV600E is the most common mutation in papillary thyroid carcinoma (PTC, and it is associated with high-risk prognostic factors. However, the significance of the BRAF mRNA level in PTC remains unknown. We evaluated the significance of BRAF mRNA expression level by analyzing PTC data from The Cancer Genome Atlas (TCGA database.Data from 499 patients were downloaded from the TCGA database. After excluding other PTC variants, we selected 353 cases of classic PTC, including 193 cases with BRAFV600E and 160 cases with the wild-type BRAF. mRNA abundances were measured using RNA-Seq with the Expectation Maximization algorithm.The mean BRAF mRNA level was significantly higher in BRAFV600E patients than in patients with wild-type BRAF (197.6 vs. 179.3, p = 0.031. In wild-type BRAF patients, the mean BRAF mRNA level was higher in cases with a tumor > 2 cm than those with a tumor ≤ 2.0 cm (189.4 vs. 163.8, p = 0.046, and was also higher in cases with lymph node metastasis than in those without lymph node metastasis (188.5 vs. 157.9, p = 0.040. Within BRAFV600E patients, higher BRAF mRNA expression was associated with extrathyroidal extension (186.4 vs. 216.4, p = 0.001 and higher T stage (188.1 vs. 210.2, p = 0.016.A higher BRAF mRNA expression level was associated with tumor aggressiveness in classic PTC regardless of BRAF mutational status. Evaluation of BRAF mRNA level may be helpful in prognostic risk stratification of PTC.

  17. A genomic atlas of human adrenal and gonad development

    Science.gov (United States)

    del Valle, Ignacio; Buonocore, Federica; Duncan, Andrew J.; Lin, Lin; Barenco, Martino; Parnaik, Rahul; Shah, Sonia; Hubank, Mike; Gerrelli, Dianne; Achermann, John C.

    2017-01-01

    Background: In humans, the adrenal glands and gonads undergo distinct biological events between 6-10 weeks post conception (wpc), such as testis determination, the onset of steroidogenesis and primordial germ cell development. However, relatively little is currently known about the genetic mechanisms underlying these processes. We therefore aimed to generate a detailed genomic atlas of adrenal and gonad development across these critical stages of human embryonic and fetal development. Methods: RNA was extracted from 53 tissue samples between 6-10 wpc (adrenal, testis, ovary and control). Affymetrix array analysis was performed and differential gene expression was analysed using Bioconductor. A mathematical model was constructed to investigate time-series changes across the dataset. Pathway analysis was performed using ClueGo and cellular localisation of novel factors confirmed using immunohistochemistry. Results: Using this approach, we have identified novel components of adrenal development (e.g. ASB4, NPR3) and confirmed the role of SRY as the main human testis-determining gene. By mathematical modelling time-series data we have found new genes up-regulated with SOX9 in the testis (e.g. CITED1), which may represent components of the testis development pathway. We have shown that testicular steroidogenesis has a distinct onset at around 8 wpc and identified potential novel components in adrenal and testicular steroidogenesis (e.g. MGARP, FOXO4, MAP3K15, GRAMD1B, RMND2), as well as testis biomarkers (e.g. SCUBE1). We have also shown that the developing human ovary expresses distinct subsets of genes (e.g. OR10G9, OR4D5), but enrichment for established biological pathways is limited. Conclusion: This genomic atlas is revealing important novel aspects of human development and new candidate genes for adrenal and reproductive disorders. PMID:28459107

  18. Expression of the Long Intergenic Non-Protein Coding RNA 665 (LINC00665) Gene and the Cell Cycle in Hepatocellular Carcinoma Using The Cancer Genome Atlas, the Gene Expression Omnibus, and Quantitative Real-Time Polymerase Chain Reaction.

    Science.gov (United States)

    Wen, Dong-Yue; Lin, Peng; Pang, Yu-Yan; Chen, Gang; He, Yun; Dang, Yi-Wu; Yang, Hong

    2018-05-05

    BACKGROUND Long non-coding RNAs (lncRNAs) have a role in physiological and pathological processes, including cancer. The aim of this study was to investigate the expression of the long intergenic non-protein coding RNA 665 (LINC00665) gene and the cell cycle in hepatocellular carcinoma (HCC) using database analysis including The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and quantitative real-time polymerase chain reaction (qPCR). MATERIAL AND METHODS Expression levels of LINC00665 were compared between human tissue samples of HCC and adjacent normal liver, clinicopathological correlations were made using TCGA and the GEO, and qPCR was performed to validate the findings. Other public databases were searched for other genes associated with LINC00665 expression, including The Atlas of Noncoding RNAs in Cancer (TANRIC), the Multi Experiment Matrix (MEM), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) networks. RESULTS Overexpression of LINC00665 in patients with HCC was significantly associated with gender, tumor grade, stage, and tumor cell type. Overexpression of LINC00665 in patients with HCC was significantly associated with overall survival (OS) (HR=1.47795%; CI: 1.046-2.086). Bioinformatics analysis identified 469 related genes and further analysis supported a hypothesis that LINC00665 regulates pathways in the cell cycle to facilitate the development and progression of HCC through ten identified core genes: CDK1, BUB1B, BUB1, PLK1, CCNB2, CCNB1, CDC20, ESPL1, MAD2L1, and CCNA2. CONCLUSIONS Overexpression of the lncRNA, LINC00665 may be involved in the regulation of cell cycle pathways in HCC through ten identified hub genes.

  19. Neil Hayes, M.D., M.P.H., Explains TCGA Findings on GBM Subtypes - TCGA

    Science.gov (United States)

    New findings by researchers at UNC Lineberger Comprehensive Cancer Center suggest that the most common form of malignant brain cancer in adults, glioblastoma multiforme (GBM), is probably not a single disease but a set of diseases, each with a distinct underlying molecular disease process. The study was published by Cell Press in the January issue of the journal Cancer Cell and the researchers are part of the The Cancer Genome Atlas.

  20. MO-DE-207B-05: Predicting Gene Mutations in Renal Cell Carcinoma Based On CT Imaging Features: Validation Using TCGA-TCIA Datasets

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X; Zhou, Z; Thomas, K; Wang, J [UT Southwestern Medical Center, Dallas, TX (United States)

    2016-06-15

    Purpose: The goal of this work is to investigate the use of contrast enhanced computed tomographic (CT) features for the prediction of mutations of BAP1, PBRM1, and VHL genes in renal cell carcinoma (RCC). Methods: For this study, we used two patient databases with renal cell carcinoma (RCC). The first one consisted of 33 patients from our institution (UT Southwestern Medical Center, UTSW). The second one consisted of 24 patients from the Cancer Imaging Archive (TCIA), where each patient is connected by a unique identi?er to the tissue samples from the Cancer Genome Atlas (TCGA). From the contrast enhanced CT image of each patient, tumor contour was first delineated by a physician. Geometry, intensity, and texture features were extracted from the delineated tumor. Based on UTSW dataset, we completed feature selection and trained a support vector machine (SVM) classifier to predict mutations of BAP1, PBRM1 and VHL genes. We then used TCIA-TCGA dataset to validate the predictive model build upon UTSW dataset. Results: The prediction accuracy of gene expression of TCIA-TCGA patients was 0.83 (20 of 24), 0.83 (20 of 24), and 0.75 (18 of 24) for BAP1, PBRM1, and VHL respectively. For BAP1 gene, texture feature was the most prominent feature type. For PBRM1 gene, intensity feature was the most prominent. For VHL gene, geometry, intensity, and texture features were all important. Conclusion: Using our feature selection strategy and models, we achieved predictive accuracy over 0.75 for all three genes under the condition of using patient data from one institution for training and data from other institutions for testing. These results suggest that radiogenomics can be used to aid in prognosis and used as convenient surrogates for expensive and time consuming gene assay procedures.

  1. Atlas2 Cloud: a framework for personal genome analysis in the cloud.

    Science.gov (United States)

    Evani, Uday S; Challis, Danny; Yu, Jin; Jackson, Andrew R; Paithankar, Sameer; Bainbridge, Matthew N; Jakkamsetti, Adinarayana; Pham, Peter; Coarfa, Cristian; Milosavljevic, Aleksandar; Yu, Fuli

    2012-01-01

    Until recently, sequencing has primarily been carried out in large genome centers which have invested heavily in developing the computational infrastructure that enables genomic sequence analysis. The recent advancements in next generation sequencing (NGS) have led to a wide dissemination of sequencing technologies and data, to highly diverse research groups. It is expected that clinical sequencing will become part of diagnostic routines shortly. However, limited accessibility to computational infrastructure and high quality bioinformatic tools, and the demand for personnel skilled in data analysis and interpretation remains a serious bottleneck. To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues. We successfully enabled the Atlas2 Cloud pipeline for personal genome analysis on two different cloud service platforms: a community cloud via the Genboree Workbench, and a commercial cloud via the Amazon Web Services using Software-as-a-Service model. We report a case study of personal genome analysis using our Atlas2 Genboree pipeline. We also outline a detailed cost structure for running Atlas2 Amazon on whole exome capture data, providing cost projections in terms of storage, compute and I/O when running Atlas2 Amazon on a large data set. We find that providing a web interface and an optimized pipeline clearly facilitates usage of cloud computing for personal genome analysis, but for it to be routinely used for large scale projects there needs to be a paradigm shift in the way we develop tools, in standard operating procedures, and in funding mechanisms.

  2. Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data

    Science.gov (United States)

    Wang, Zhaoming; Rajaraman, Preetha; Melin, Beatrice S.; Chung, Charles C.; Zhang, Weijia; McKean-Cowdin, Roberta; Michaud, Dominique; Yeager, Meredith; Ahlbom, Anders; Albanes, Demetrius; Andersson, Ulrika; Beane Freeman, Laura E.; Buring, Julie E.; Butler, Mary Ann; Carreón, Tania; Feychting, Maria; Gapstur, Susan M.; Gaziano, J. Michael; Giles, Graham G.; Hallmans, Goran; Henriksson, Roger; Hoffman-Bolton, Judith; Inskip, Peter D.; Kitahara, Cari M.; Le Marchand, Loic; Linet, Martha S.; Li, Shengchao; Peters, Ulrike; Purdue, Mark P.; Rothman, Nathaniel; Ruder, Avima M.; Sesso, Howard D.; Severi, Gianluca; Stampfer, Meir; Stevens, Victoria L.; Visvanathan, Kala; Wang, Sophia S.; White, Emily; Zeleniuch-Jacquotte, Anne; Hoover, Robert; Fraumeni, Joseph F.; Chatterjee, Nilanjan; Hartge, Patricia; Chanock, Stephen J.

    2016-01-01

    We confirmed strong association of rs78378222:A>C (per allele odds ratio [OR] = 3.14; P = 6.48 × 10−11), a germline rare single-nucleotide polymorphism (SNP) in TP53, via imputation of a genome-wide association study of glioma (1,856 cases and 4,955 controls). We subsequently performed integrative analyses on the Cancer Genome Atlas (TCGA) data for GBM (glioblastoma multiforme) and LUAD (lung adenocarcinoma). Based on SNP data, we imputed genotypes for rs78378222 and selected individuals carrying rare risk allele (C). Using RNA sequencing data, we observed aberrant transcripts with ~3 kb longer than normal for those individuals. Using exome sequencing data, we further showed that loss of haplotype carrying common protective allele (A) occurred somatically in GBM but not in LUAD. Our bioinformatic analysis suggests rare risk allele (C) disrupts mRNA termination, and an allelic loss of a genomic region harboring common protective allele (A) occurs during tumor initiation or progression for glioma. PMID:25907361

  3. ATLAS

    Data.gov (United States)

    Federal Laboratory Consortium — ATLAS is a particle physics experiment at the Large Hadron Collider at CERN, the European Organization for Nuclear Research. Scientists from Brookhaven have played...

  4. Genomics and advances towards precision medicine for head and neck squamous cell carcinoma.

    Science.gov (United States)

    Van Waes, Carter; Musbahi, Omar

    2017-10-01

    To provide a review of emerging knowledge from genomics and related basic science, preclinical, and clinical precision medicine studies in head and neck squamous cell carcinoma (HNSCC). The Cancer Genome Atlas Network (TCGA) publications, PubMed-based literature review, and ClinicalTrials.gov. TCGA publications, PubMed, and ClinicalTrials.gov were queried for genomics and related basic science, preclinical, and developmental clinical precision medicine studies in HNSCC. TCGA reported comprehensive genomic analyses of 279 HNSCC, defining the landscape and frequency of chromosomal copy number alterations, mutations, and expressed genes that contribute to pathogenesis, prognosis, and resistance to therapy. This provides a road map for basic science and preclinical studies to identify key pathways in cancer and cells of the tumor microenvironment affected by these alterations, and candidate targets for new small molecule and biologic therapies. Recurrent chromosomal abnormalities, mutations, and expression of genes affecting HNSCC subsets are associated with differences in prognosis, and define molecules, pathways, and deregulated immune responses as candidates for therapy. Activity of molecularly targeted agents appears to be enhanced by rational combinations of these agents and standard therapies targeting the complex alterations that affect multiple pathways and mechanisms in HNSCC. NA.

  5. ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Brown, Joseph M.; Colby, Sean M.; Overall, Christopher C.; Lee, Joon-Yong; Zucker, Jeremy D.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

    2017-03-02

    ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

  6. TCGA bladder cancer study reveals potential drug targets

    Science.gov (United States)

    Investigators with TCGA have identified new potential therapeutic targets for a major form of bladder cancer, including important genes and pathways that are disrupted in the disease. They also discovered that, at the molecular level, some subtypes of bla

  7. Pan-cancer analysis of TCGA data reveals notable signaling pathways

    International Nuclear Information System (INIS)

    Neapolitan, Richard; Horvath, Curt M.; Jiang, Xia

    2015-01-01

    A signal transduction pathway (STP) is a network of intercellular information flow initiated when extracellular signaling molecules bind to cell-surface receptors. Many aberrant STPs have been associated with various cancers. To develop optimal treatments for cancer patients, it is important to discover which STPs are implicated in a cancer or cancer-subtype. The Cancer Genome Atlas (TCGA) makes available gene expression level data on cases and controls in ten different types of cancer including breast cancer, colon adenocarcinoma, glioblastoma, kidney renal papillary cell carcinoma, low grade glioma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian carcinoma, rectum adenocarcinoma, and uterine corpus endometriod carcinoma. Signaling Pathway Impact Analysis (SPIA) is a software package that analyzes gene expression data to identify whether a pathway is relevant in a given condition. We present the results of a study that uses SPIA to investigate all 157 signaling pathways in the KEGG PATHWAY database. We analyzed each of the ten cancer types mentioned above separately, and we perform a pan-cancer analysis by grouping the data for all the cancer types. In each analysis several pathways were found to be markedly more significant than all the other pathways. We call them notable. Research has already established a connection between many of these pathways and the corresponding cancer type. However, some of our discovered pathways appear to be new findings. Altogether there were 37 notable findings in the separate analyses, 26 of them occurred in 7 pathways. These 7 pathways included the 4 notable pathways discovered in the pan-cancer analysis. So, our results suggest that these 7 pathways account for much of the mechanisms of cancer. Furthermore, by looking at the overlap among pathways, we identified possible regions on the pathways where the aberrant activity is occurring. We obtained 37 notable findings concerning 18 pathways. Some of them appear to be

  8. ATLAS

    CERN Multimedia

    Akhnazarov, V; Canepa, A; Bremer, J; Burckhart, H; Cattai, A; Voss, R; Hervas, L; Kaplon, J; Nessi, M; Werner, P; Ten kate, H; Tyrvainen, H; Vandelli, W; Krasznahorkay, A; Gray, H; Alvarez gonzalez, B; Eifert, T F; Rolando, G; Oide, H; Barak, L; Glatzer, J; Backhaus, M; Schaefer, D M; Maciejewski, J P; Milic, A; Jin, S; Von torne, E; Limbach, C; Medinnis, M J; Gregor, I; Levonian, S; Schmitt, S; Waananen, A; Monnier, E; Muanza, S G; Pralavorio, P; Talby, M; Tiouchichine, E; Tocut, V M; Rybkin, G; Wang, S; Lacour, D; Laforge, B; Ocariz, J H; Bertoli, W; Malaescu, B; Sbarra, C; Yamamoto, A; Sasaki, O; Koriki, T; Hara, K; Da silva gomes, A; Carvalho maneira, J; Marcalo da palma, A; Chekulaev, S; Tikhomirov, V; Snesarev, A; Buzykaev, A; Maslennikov, A; Peleganchuk, S; Sukharev, A; Kaplan, B E; Swiatlowski, M J; Nef, P D; Schnoor, U; Oakham, G F; Ueno, R; Orr, R S; Abouzeid, O; Haug, S; Peng, H; Kus, V; Vitek, M; Temming, K K; Dang, N P; Meier, K; Schultz-coulon, H; Geisler, M P; Sander, H; Schaefer, U; Ellinghaus, F; Rieke, S; Nussbaumer, A; Liu, Y; Richter, R; Kortner, S; Fernandez-bosman, M; Ullan comes, M; Espinal curull, J; Chiriotti alvarez, S; Caubet serrabou, M; Valladolid gallego, E; Kaci, M; Carrasco vela, N; Lancon, E C; Besson, N E; Gautard, V; Bracinik, J; Bartsch, V C; Potter, C J; Lester, C G; Moeller, V A; Rosten, J; Crooks, D; Mathieson, K; Houston, S C; Wright, M; Jones, T W; Harris, O B; Byatt, T J; Dobson, E; Hodgson, P; Hodgkinson, M C; Dris, M; Karakostas, K; Ntekas, K; Oren, D; Duchovni, E; Etzion, E; Oren, Y; Ferrer, L M; Testa, M; Doria, A; Merola, L; Sekhniaidze, G; Giordano, R; Ricciardi, S; Milazzo, A; Falciano, S; De pedis, D; Dionisi, C; Veneziano, S; Cardarelli, R; Verzegnassi, C; Soualah, R; Ochi, A; Ohshima, T; Kishiki, S; Linde, F L; Vreeswijk, M; Werneke, P; Muijs, A; Vankov, P H; Jansweijer, P P M; Dale, O; Lund, E; Bruckman de renstrom, P; Dabrowski, W; Adamek, J D; Wolters, H; Micu, L; Pantea, D; Tudorache, V; Mjoernmark, J; Klimek, P J; Ferrari, A; Abdinov, O; Akhoundov, A; Hashimov, R; Shelkov, G; Khubua, J; Ladygin, E; Lazarev, A; Glagolev, V; Dedovich, D; Lykasov, G; Zhemchugov, A; Zolnikov, Y; Ryabenko, M; Sivoklokov, S; Vasilyev, I; Shalimov, A; Lobanov, M; Paramoshkina, E; Mosidze, M; Bingul, A; Nodulman, L J; Guarino, V J; Yoshida, R; Drake, G R; Calafiura, P; Haber, C; Quarrie, D R; Alonso, J R; Anderson, C; Evans, H; Lammers, S W; Baubock, M; Anderson, K; Petti, R; Suhr, C A; Linnemann, J T; Richards, R A; Tollefson, K A; Holzbauer, J L; Stoker, D P; Pier, S; Nelson, A J; Isakov, V; Martin, A J; Adelman, J A; Paganini, M; Gutierrez, P; Snow, J M; Pearson, B L; Cleland, W E; Savinov, V; Wong, W; Goodson, J J; Li, H; Lacey, R A; Gordeev, A; Gordon, H; Lanni, F; Nevski, P; Rescia, S; Kierstead, J A; Liu, Z; Yu, W W H; Bensinger, J; Hashemi, K S; Bogavac, D; Cindro, V; Hoeferkamp, M R; Coelli, S; Iodice, M; Piegaia, R N; Alonso, F; Wahlberg, H P; Barberio, E L; Limosani, A; Rodd, N L; Jennens, D T; Hill, E C; Pospisil, S; Smolek, K; Schaile, D A; Rauscher, F G; Adomeit, S; Mattig, P M; Wahlen, H; Volkmer, F; Calvente lopez, S; Sanchis peris, E J; Pallin, D; Podlyski, F; Says, L; Boumediene, D E; Scott, W; Phillips, P W; Greenall, A; Turner, P; Gwilliam, C B; Kluge, T; Wrona, B; Sellers, G J; Millward, G; Adragna, P; Hartin, A; Alpigiani, C; Piccaro, E; Bret cano, M; Hughes jones, R E; Mercer, D; Oh, A; Chavda, V S; Carminati, L; Cavasinni, V; Fedin, O; Patrichev, S; Ryabov, Y; Nesterov, S; Grebenyuk, O; Sasso, J; Mahmood, H; Polsdofer, E; Dai, T; Ferretti, C; Liu, H; Hegazy, K H; Benjamin, D P; Zobernig, G; Ban, J; Brooijmans, G H; Keener, P; Williams, H H; Le geyt, B C; Hines, E J; Fadeyev, V; Schumm, B A; Law, A T; Kuhl, A D; Neubauer, M S; Shang, R; Gagliardi, G; Calabro, D; Conta, C; Zinna, M; Jones, G; Li, J; Stradling, A R; Hadavand, H K; Mcguigan, P; Chiu, P; Baldelomar, E; Stroynowski, R A; Kehoe, R L; De groot, N; Timmermans, C; Lach-heb, F; Addy, T N; Nakano, I; Moreno lopez, D; Grosse-knetter, J; Tyson, B; Rude, G D; Tafirout, R; Benoit, P; Danielsson, H O; Elsing, M; Fassnacht, P; Froidevaux, D; Ganis, G; Gorini, B; Lasseur, C; Lehmann miotto, G; Kollar, D; Aleksa, M; Sfyrla, A; Duehrssen-debling, K; Fressard-batraneanu, S; Van der ster, D C; Bortolin, C; Schumacher, J; Mentink, M; Geich-gimbel, C; Yau wong, K H; Lafaye, R; Crepe-renaudin, S; Albrand, S; Hoffmann, D; Pangaud, P; Meessen, C; Hrivnac, J; Vernay, E; Perus, A; Henrot versille, S L; Le dortz, O; Derue, F; Piccinini, M; Polini, A; Terada, S; Arai, Y; Ikeno, M; Fujii, H; Nagano, K; Ukegawa, F; Aguilar saavedra, J A; Conde muino, P; Castro, N F; Eremin, V; Kopytine, M; Sulin, V; Tsukerman, I; Korol, A; Nemethy, P; Bartoldus, R; Glatte, A; Chelsky, S; Van nieuwkoop, J; Bellerive, A; Sinervo, J K; Battaglia, A; Barbier, G J; Pohl, M; Rosselet, L; Alexandre, G B; Prokoshin, F; Pezoa rivera, R A; Batkova, L; Kladiva, E; Stastny, J; Kubes, T; Vidlakova, Z; Esch, H; Homann, M; Herten, L G; Zimmermann, S U; Pfeifer, B; Stenzel, H; Andrei, G V; Wessels, M; Buescher, V; Kleinknecht, K; Fiedler, F M; Schroeder, C D; Fernandez, E; Mir martinez, L; Vorwerk, V; Bernabeu verdu, J; Salt, J; Civera navarrete, J V; Bernard, R; Berriaud, C P; Chevalier, L P; Hubbard, R; Schune, P; Nikolopoulos, K; Batley, J R; Brochu, F M; Phillips, A W; Teixeira-dias, P J; Rose, M B D; Buttar, C; Buckley, A G; Nurse, E L; Larner, A B; Boddy, C; Henderson, J; Costanzo, D; Tarem, S; Maccarrone, G; Laurelli, P F; Alviggi, M; Chiaramonte, R; Izzo, V; Palumbo, V; Fraternali, M; Crosetti, G; Marchese, F; Yamaguchi, Y; Hessey, N P; Mechnich, J M; Liebig, W; Kastanas, K A; Sjursen, T B; Zalieckas, J; Cameron, D G; Banka, P; Kowalewska, A B; Dwuznik, M; Mindur, B; Boldea, V; Hedberg, V; Smirnova, O; Sellden, B; Allahverdiyev, T; Gornushkin, Y; Koultchitski, I; Tokmenin, V; Chizhov, M; Gongadze, A; Khramov, E; Sadykov, R; Krasnoslobodtsev, I; Smirnova, L; Kramarenko, V; Minaenko, A; Zenin, O; Beddall, A J; Ozcan, E V; Hou, S; Wang, S; Moyse, E; Willocq, S; Chekanov, S; Le compte, T J; Love, J R; Ciocio, A; Hinchliffe, I; Tsulaia, V; Gomez, A; Luehring, F; Zieminska, D; Huth, J E; Gonski, J L; Oreglia, M; Tang, F; Shochet, M J; Costin, T; Mcleod, A; Uzunyan, S; Martin, S P; Pope, B G; Schwienhorst, R H; Brau, J E; Ptacek, E S; Milburn, R H; Sabancilar, E; Lauer, R; Saleem, M; Mohamed meera lebbai, M R; Lou, X; Reeves, K B; Rijssenbeek, M; Novakova, P N; Rahm, D; Steinberg, P A; Wenaus, T J; Paige, F; Ye, S; Kotcher, J R; Assamagan, K A; Oliveira damazio, D; Maeno, T; Henry, A; Dushkin, A; Costa, G; Meroni, C; Resconi, S; Lari, T; Biglietti, M; Lohse, T; Gonzalez silva, M L; Monticelli, F G; Saavedra, A F; Patel, N D; Ciodaro xavier, T; Asevedo nepomuceno, A; Lefebvre, M; Albert, J E; Kubik, P; Faltova, J; Turecek, D; Solc, J; Schaile, O; Ebke, J; Losel, P J; Zeitnitz, C; Sturm, P D; Barreiro alonso, F; Modesto alapont, P; Soret medel, J; Garzon alama, E J; Gee, C N; Mccubbin, N A; Sankey, D; Emeliyanov, D; Dewhurst, A L; Houlden, M A; Klein, M; Burdin, S; Lehan, A K; Eisenhandler, E; Lloyd, S; Traynor, D P; Ibbotson, M; Marshall, R; Pater, J; Freestone, J; Masik, J; Haughton, I; Manousakis katsikakis, A; Sampsonidis, D; Krepouri, A; Roda, C; Sarri, F; Fukunaga, C; Nadtochiy, A; Kara, S O; Timm, S; Alam, S M; Rashid, T; Goldfarb, S; Espahbodi, S; Marley, D E; Rau, A W; Dos anjos, A R; Haque, S; Grau, N C; Havener, L B; Thomson, E J; Newcomer, F M; Hansl-kozanecki, G; Deberg, H A; Takeshita, T; Goggi, V; Ennis, J S; Olness, F I; Kama, S; Ordonez sanz, G; Koetsveld, F; Elamri, M; Mansoor-ul-islam, S; Lemmer, B; Kawamura, G; Bindi, M; Schulte, S; Kugel, A; Kretz, M P; Kurchaninov, L; Blanchot, G; Chromek-burckhart, D; Di girolamo, B; Francis, D; Gianotti, F; Nordberg, M Y; Pernegger, H; Roe, S; Boyd, J; Wilkens, H G; Pauly, T; Fabre, C; Tricoli, A; Bertet, D; Ruiz martinez, M A; Arnaez, O L; Lenzi, B; Boveia, A J; Gillberg, D I; Davies, J M; Zimmermann, R; Uhlenbrock, M; Kraus, J K; Narayan, R T; John, A; Dam, M; Padilla aranda, C; Bellachia, F; Le flour chollet, F M; Jezequel, S; Dumont dayot, N; Fede, E; Mathieu, M; Gensolen, F D; Alio, L; Arnault, C; Bouchel, M; Ducorps, A; Kado, M M; Lounis, A; Zhang, Z P; De vivie de regie, J; Beau, T; Bruni, A; Bruni, G; Grafstrom, P; Romano, M; Lasagni manghi, F; Massa, L; Shaw, K; Ikegami, Y; Tsuno, S; Kawanishi, Y; Benincasa, G; Blagov, M; Fedorchuk, R; Shatalov, P; Romaniouk, A; Belotskiy, K; Timoshenko, S; Hooft van huysduynen, L; Lewis, G H; Wittgen, M M; Mader, W F; Rudolph, C J; Gumpert, C; Mamuzic, J; Rudolph, G; Schmid, P; Corriveau, F; Belanger-champagne, C; Yarkoni, S; Leroy, C; Koffas, T; Harack, B D; Weber, M S; Beck, H; Leger, A; Gonzalez sevilla, S; Zhu, Y; Gao, J; Zhang, X; Blazek, T; Rames, J; Sicho, P; Kouba, T; Sluka, T; Lysak, R; Ristic, B; Kompatscher, A E; Von radziewski, H; Groll, M; Meyer, C P; Oberlack, H; Stonjek, S M; Cortiana, G; Werthenbach, U; Ibragimov, I; Czirr, H S; Cavalli-sforza, M; Puigdengoles olive, C; Tallada crespi, P; Marti i garcia, S; Gonzalez de la hoz, S; Guyot, C; Meyer, J; Schoeffel, L O; Garvey, J; Hawkes, C; Hillier, S J; Staley, R J; Salvatore, P F; Santoyo castillo, I; Carter, J; Yusuff, I B; Barlow, N R; Berry, T S; Savage, G; Wraight, K G; Steele, G E; Hughes, G; Walder, J W; Love, P A; Crone, G J; Waugh, B M; Boeser, S; Sarkar, A M; Holmes, A; Massey, R; Pinder, A; Nicholson, R; Korolkova, E; Katsoufis, I; Maltezos, S; Tsipolitis, G; Leontsinis, S; Levinson, L J; Shoa, M; Abramowicz, H E; Bella, G; Gershon, A; Urkovsky, E; Taiblum, N; Gatti, C; Della pietra, M; Lanza, A; Negri, A; Flaminio, V; Lacava, F; Petrolo, E; Pontecorvo, L; Rosati, S; Zanello, L; Pasqualucci, E; Di ciaccio, A; Giordani, M; Yamazaki, Y; Jinno, T; Nomachi, M; De jong, P J; Ferrari, P; Homma, J; Van der graaf, H; Igonkina, O B; Stugu, B S; Buanes, T; Pedersen, M; Turala, M; Olszewski, A J; Koperny, S Z; Onofre, A; Castro nunes fiolhais, M; Alexa, C; Cuciuc, C M; Akesson, T P A; Hellman, S L; Milstead, D A; Bondyakov, A; Pushnova, V; Budagov, Y; Minashvili, I; Romanov, V; Sniatkov, V; Tskhadadze, E; Kalinovskaya, L; Shalyugin, A; Tavkhelidze, A; Rumyantsev, L; Karpov, S; Soloshenko, A; Vostrikov, A; Borissov, E; Solodkov, A; Vorob'ev, A; Sidorov, S; Malyaev, V; Lee, S; Grudzinski, J J; Virzi, J S; Vahsen, S E; Lys, J; Penwell, J W; Yan, Z; Bernard, C S; Barreiro guimaraes da costa, J P; Oliver, J N; Merritt, F S; Brubaker, E M; Kapliy, A; Kim, J; Zutshi, V V; Burghgrave, B O; Abolins, M A; Arabidze, G; Caughron, S A; Frey, R E; Radloff, P T; Schernau, M; Murillo garcia, R; Porter, R A; Mccormick, C A; Karn, P J; Sliwa, K J; Demers konezny, S M; Strauss, M G; Mueller, J A; Izen, J M; Klimentov, A; Lynn, D; Polychronakos, V; Radeka, V; Sondericker, J I I I; Bathe, S; Duffin, S; Chen, H; De castro faria salgado, P E; Kersevan, B P; Lacker, H M; Schulz, H; Kubota, T; Tan, K G; Yabsley, B D; Nunes de moura junior, N; Pinfold, J; Soluk, R A; Ouellette, E A; Leitner, R; Sykora, T; Solar, M; Sartisohn, G; Hirschbuehl, D; Huning, D; Fischer, J; Terron cuadrado, J; Glasman kuguel, C B; Lacasta llacer, C; Lopez-amengual, J; Calvet, D; Chevaleyre, J; Daudon, F; Montarou, G; Guicheney, C; Calvet, S P J; Tyndel, M; Dervan, P J; Maxfield, S J; Hayward, H S; Beck, G; Cox, B; Da via, C; Paschalias, P; Manolopoulou, M; Ragusa, F; Cimino, D; Ezzi, M; Fiuza de barros, N F; Yildiz, H; Ciftci, A K; Turkoz, S; Zain, S B; Tegenfeldt, F; Chapman, J W; Panikashvili, N; Bocci, A; Altheimer, A D; Martin, F F; Fratina, S; Jackson, B D; Grillo, A A; Seiden, A; Watts, G T; Mangiameli, S; Johns, K A; O'grady, F T; Errede, D R; Darbo, G; Ferretto parodi, A; Leahu, M C; Farbin, A; Ye, J; Liu, T; Wijnen, T A; Naito, D; Takashima, R; Sandoval usme, C E; Zinonos, Z; Moreno llacer, M; Agricola, J B; Mcgovern, S A; Sakurai, Y; Trigger, I M; Qing, D; De silva, A S; Butin, F; Dell'acqua, A; Hawkings, R J; Lamanna, M; Mapelli, L; Passardi, G; Rembser, C; Tremblet, L; Andreazza, W; Dobos, D A; Koblitz, B; Bianco, M; Dimitrov, G V; Schlenker, S; Armbruster, A J; Rammensee, M C; Romao rodrigues, L F; Peters, K; Pozo astigarraga, M E; Yi, Y; Desch, K K; Huegging, F G; Muller, K K; Stillings, J A; Schaetzel, S; Xella, S; Hansen, J D; Colas, J; Daguin, G; Wingerter, I; Ionescu, G D; Ledroit, F; Lucotte, A; Clement, B E; Stark, J; Clemens, J; Djama, F; Knoops, E; Coadou, Y; Vigeolas-choury, E; Feligioni, L; Iconomidou-fayard, L; Imbert, P; Schaffer, A C; Nikolic, I; Trincaz-duvoid, S; Warin, P; Camard, A F; Ridel, M; Pires, S; Giacobbe, B; Spighi, R; Villa, M; Negrini, M; Sato, K; Gavrilenko, I; Akimov, A; Khovanskiy, V; Talyshev, A; Voronkov, A; Hakobyan, H; Mallik, U; Shibata, A; Konoplich, R; Barklow, T L; Koi, T; Straessner, A; Stelzer, B; Robertson, S H; Vachon, B; Stoebe, M; Keyes, R A; Wang, K; Billoud, T R V; Strickland, V; Batygov, M; Krieger, P; Palacino caviedes, G D; Gay, C W; Jiang, Y; Han, L; Liu, M; Zenis, T; Lokajicek, M; Staroba, P; Tasevsky, M; Popule, J; Svatos, M; Seifert, F; Landgraf, U; Lai, S T; Schmitt, K H; Achenbach, R; Schuh, N; Kiesling, C; Macchiolo, A; Nisius, R; Schacht, P; Von der schmitt, J G; Kortner, O; Atlay, N B; Segura sole, E; Grinstein, S; Neissner, C; Bruckner, D M; Oliver garcia, E; Boonekamp, M; Perrin, P; Gaillot, F M; Wilson, J A; Thomas, J P; Thompson, P D; Palmer, J D; Falk, I E; Chavez barajas, C A; Sutton, M R; Robinson, D; Kaneti, S A; Wu, T; Robson, A; Shaw, C; Buzatu, A; Qin, G; Jones, R; Bouhova-thacker, E V; Viehhauser, G; Weidberg, A R; Gilbert, L; Johansson, P D C; Orphanides, M; Vlachos, S; Behar harpaz, S; Papish, O; Lellouch, D J H; Turgeman, D; Benary, O; La rotonda, L; Vena, R; Tarasio, A; Marzano, F; Gabrielli, A; Di stante, L; Liberti, B; Aielli, G; Oda, S; Nozaki, M; Takeda, H; Hayakawa, T; Miyazaki, K; Maeda, J; Sugimoto, T; Pettersson, N E; Bentvelsen, S; Groenstege, H L; Lipniacka, A; Vahabi, M; Ould-saada, F; Chwastowski, J J; Hajduk, Z; Kaczmarska, A; Olszowska, J B; Trzupek, A; Staszewski, R P; Palka, M; Constantinescu, S; Jarlskog, G; Lundberg, B L A; Pearce, M; Ellert, M F; Bannikov, A; Fechtchenko, A; Iambourenko, V; Kukhtin, V; Pozdniakov, V; Topilin, N; Vorozhtsov, S; Khassanov, A; Fliaguine, V; Kharchenko, D; Nikolaev, K; Kotenov, K; Kozhin, A; Zenin, A; Ivashin, A; Golubkov, D; Beddall, A; Su, D; Dallapiccola, C J; Cranshaw, J M; Price, L; Stanek, R W; Gieraltowski, G; Zhang, J; Gilchriese, M; Shapiro, M; Ahlen, S; Morii, M; Taylor, F E; Miller, R J; Phillips, F H; Torrence, E C; Wheeler, S J; Benedict, B H; Napier, A; Hamilton, S F; Petrescu, T A; Boyd, G R J; Jayasinghe, A L; Smith, J M; Mc carthy, R L; Adams, D L; Le vine, M J; Zhao, X; Patwa, A M; Baker, M; Kirsch, L; Krstic, J; Simic, L; Filipcic, A; Seidel, S C; Cantore-cavalli, D; Baroncelli, A; Kind, O M; Scarcella, M J; Maidantchik, C L L; Seixas, J; Balabram filho, L E; Vorobel, V; Spousta, M; Strachota, P; Vokac, P; Slavicek, T; Bergmann, B L; Biebel, O; Kersten, S; Srinivasan, M; Trefzger, T; Vazeille, F; Insa, C; Kirk, J; Middleton, R; Burke, S; Klein, U; Morris, J D; Ellis, K V; Millward, L R; Giokaris, N; Ioannou, P; Angelidakis, S; Bouzakis, K; Andreazza, A; Perini, L; Chtcheguelski, V; Spiridenkov, E; Yilmaz, M; Kaya, U; Ernst, J; Mahmood, A; Saland, J; Kutnink, T; Holler, J; Kagan, H P; Wang, C; Pan, Y; Xu, N; Ji, H; Willis, W J; Tuts, P M; Litke, A; Wilder, M; Rothberg, J; Twomey, M S; Rizatdinova, F; Loch, P; Rutherfoord, J P; Varnes, E W; Barberis, D; Osculati-becchi, B; Brandt, A G; Turvey, A J; Benchekroun, D; Nagasaka, Y; Thanakornworakij, T; Quadt, A; Nadal serrano, J; Magradze, E; Nackenhorst, O; Musheghyan, H; Kareem, M; Chytka, L; Perez codina, E; Stelzer-chilton, O; Brunel, B; Henriques correia, A M; Dittus, F; Hatch, M; Haug, F; Hauschild, M; Huhtinen, M; Lichard, P; Schuh-erhard, S; Spigo, G; Avolio, G; Tsarouchas, C; Ahmad, I; Backes, M P; Barisits, M; Gadatsch, S; Cerv, M; Sicoe, A D; Nattamai sekar, L P; Fazio, D; Shan, L; Sun, X; Gaycken, G F; Hemperek, T; Petersen, T C; Alonso diaz, A; Moynot, M; Werlen, M; Hryn'ova, T; Gallin-martel, M; Wu, M; Touchard, F; Menouni, M; Fougeron, D; Le guirriec, E; Chollet, J C; Veillet, J; Barrillon, P; Prat, S; Krasny, M W; Roos, L; Boudarham, G; Lefebvre, G; Boscherini, D; Valentinetti, S; Acharya, B S; Miglioranzi, S; Kanzaki, J; Unno, Y; Yasu, Y; Iwasaki, H; Tokushuku, K; Maio, A; Rodrigues fernandes, B J; Pinto figueiredo raimundo ribeiro, N M; Bot, A; Shmeleva, A; Zaidan, R; Djilkibaev, R; Mincer, A I; Salnikov, A; Aracena, I A; Schwartzman, A G; Silverstein, D J; Fulsom, B G; Anulli, F; Kuhn, D; White, M J; Vetterli, M J; Stockton, M C; Mantifel, R L; Azuelos, G; Shoaleh saadi, D; Savard, P; Clark, A; Ferrere, D; Gaumer, O P; Diaz gutierrez, M A; Liu, Y; Dubnickova, A; Sykora, I; Strizenec, P; Weichert, J; Zitek, K; Naumann, T; Goessling, C; Klingenberg, R; Jakobs, K; Rurikova, Z; Werner, M W; Arnold, H R; Buscher, D; Hanke, P; Stamen, R; Dietzsch, T A; Kiryunin, A; Salihagic, D; Buchholz, P; Pacheco pages, A; Sushkov, S; Porto fernandez, M D C; Cruz josa, R; Vos, M A; Schwindling, J; Ponsot, P; Charignon, C; Kivernyk, O; Goodrick, M J; Hill, J C; Green, B J; Quarman, C V; Bates, R L; Allwood-spiers, S E; Quilty, D; Chilingarov, A; Long, R E; Barton, A E; Konstantinidis, N; Simmons, B; Davison, A R; Christodoulou, V; Wastie, R L; Gallas, E J; Cox, J; Dehchar, M; Behr, J K; Pickering, M A; Filippas, A; Panagoulias, I; Tenenbaum katan, Y D; Roth, I; Pitt, M; Citron, Z H; Benhammou, Y; Amram, N Y N; Soffer, A; Gorodeisky, R; Antonelli, M; Chiarella, V; Curatolo, M; Esposito, B; Nicoletti, G; Martini, A; Sansoni, A; Carlino, G; Del prete, T; Bini, C; Vari, R; Kuna, M; Pinamonti, M; Itoh, Y; Colijn, A P; Klous, S; Garitaonandia elejabarrieta, H; Rosendahl, P L; Taga, A V; Malecki, P; Malecki, P; Wolter, M W; Kowalski, T; Korcyl, G M; Caprini, M; Caprini, I; Dita, P; Olariu, A; Tudorache, A; Lytken, E; Hidvegi, A; Aliyev, M; Alexeev, G; Bardin, D; Kakurin, S; Lebedev, A; Golubykh, S; Chepurnov, V; Gostkin, M; Kolesnikov, V; Karpova, Z; Davkov, K I; Yeletskikh, I; Grishkevich, Y; Rud, V; Myagkov, A; Nikolaenko, V; Starchenko, E; Zaytsev, A; Fakhrutdinov, R; Cheine, I; Istin, S; Sahin, S; Teng, P; Chu, M L; Trilling, G H; Heinemann, B; Richoz, N; Degeorge, C; Youssef, S; Pilcher, J; Cheng, Y; Purohit, M V; Kravchenko, A; Calkins, R E; Blazey, G; Hauser, R; Koll, J D; Reinsch, A; Brost, E C; Allen, B W; Lankford, A J; Ciobotaru, M D; Slagle, K J; Haffa, B; Mann, A; Loginov, A; Cummings, J T; Loyal, J D; Skubic, P L; Boudreau, J F; Lee, B E; Redlinger, G; Wlodek, T; Carcassi, G; Sexton, K A; Yu, D; Deng, W; Metcalfe, J E; Panitkin, S; Sijacki, D; Mikuz, M; Kramberger, G; Tartarelli, G F; Farilla, A; Stanescu, C; Herrberg, R; Alconada verzini, M J; Brennan, A J; Varvell, K; Marroquim, F; Gomes, A A; Do amaral coutinho, Y; Gingrich, D; Moore, R W; Dolejsi, J; Valkar, S; Broz, J; Jindra, T; Kohout, Z; Kral, V; Mann, A W; Calfayan, P P; Langer, T; Hamacher, K; Sanny, B; Wagner, W; Flick, T; Redelbach, A R; Ke, Y; Higon-rodriguez, E; Donini, J N; Lafarguette, P; Adye, T J; Baines, J; Barnett, B; Wickens, F J; Martin, V J; Jackson, J N; Prichard, P; Kretzschmar, J; Martin, A J; Walker, C J; Potter, K M; Kourkoumelis, C; Tzamarias, S; Houiris, A G; Iliadis, D; Fanti, M; Bertolucci, F; Maleev, V; Sultanov, S; Rosenberg, E I; Krumnack, N E; Bieganek, C; Diehl, E B; Mc kee, S P; Eppig, A P; Harper, D R; Liu, C; Schwarz, T A; Mazor, B; Looper, K A; Wiedenmann, W; Huang, P; Stahlman, J M; Battaglia, M; Nielsen, J A; Zhao, T; Khanov, A; Kaushik, V S; Vichou, E; Liss, A M; Gemme, C; Morettini, P; Parodi, F; Passaggio, S; Rossi, L; Kuzhir, P; Ignatenko, A; Ferrari, R; Spairani, M; Pianori, E; Sekula, S J; Firan, A I; Cao, T; Hetherly, J W; Gouighri, M; Vassilakopoulos, V; Long, M C; Shimojima, M; Sawyer, L H; Brummett, R E; Losada, M A; Schorlemmer, A L; Mantoani, M; Bawa, H S; Mornacchi, G; Nicquevert, B; Palestini, S; Stapnes, S; Veness, R; Kotamaki, M J; Sorde, C; Iengo, P; Campana, S; Goossens, L; Zajacova, Z; Pribyl, L; Poveda torres, J; Marzin, A; Conti, G; Carrillo montoya, G D; Kroseberg, J; Gonella, L; Velz, T; Schmitt, S; Lobodzinska, E M; Lovschall-jensen, A E; Galster, G; Perrot, G; Cailles, M; Berger, N; Barnovska, Z; Delsart, P; Lleres, A; Tisserant, S; Grivaz, J; Matricon, P; Bellagamba, L; Bertin, A; Bruschi, M; De castro, S; Semprini cesari, N; Fabbri, L; Rinaldi, L; Quayle, W B; Truong, T N L; Kondo, T; Haruyama, T; Ng, C; Do valle wemans, A; Almeida veloso, F M; Konovalov, S; Ziegler, J M; Su, D; Lukas, W; Prince, S; Ortega urrego, E J; Teuscher, R J; Knecht, N; Pretzl, K; Borer, C; Gadomski, S; Koch, B; Kuleshov, S; Brooks, W K; Antos, J; Kulkova, I; Chudoba, J; Chyla, J; Tomasek, L; Bazalova, M; Messmer, I; Tobias, J; Sundermann, J E; Kuehn, S S; Kluge, E; Scharf, V L; Barillari, T; Kluth, S; Menke, S; Weigell, P; Schwegler, P; Ziolkowski, M; Casado lechuga, P M; Garcia, C; Sanchez, J; Costa mezquita, M J; Valero biot, J A; Laporte, J; Nikolaidou, R; Virchaux, M; Nguyen, V T H; Charlton, D; Harrison, K; Slater, M W; Newman, P R; Parker, A M; Ward, P; Mcgarvie, S A; Kilvington, G J; D'auria, S; O'shea, V; Mcglone, H M; Fox, H; Henderson, R; Kartvelishvili, V; Davies, B; Sherwood, P; Fraser, J T; Lancaster, M A; Tseng, J C; Hays, C P; Apolle, R; Dixon, S D; Parker, K A; Gazis, E; Papadopoulou, T; Panagiotopoulou, E; Karastathis, N; Hershenhorn, A D; Milov, A; Groth-jensen, J; Bilokon, H; Miscetti, S; Canale, V; Rebuzzi, D M; Capua, M; Bagnaia, P; De salvo, A; Gentile, S; Safai tehrani, F; Solfaroli camillocci, E; Sasao, N; Tsunada, K; Massaro, G; Magrath, C A; Van kesteren, Z; Beker, M G; Van den wollenberg, W; Bugge, L; Buran, T; Read, A L; Gjelsten, B K; Banas, E A; Turnau, J; Derendarz, D K; Kisielewska, D; Chesneanu, D; Rotaru, M; Maurer, J B; Wong, M L; Lund-jensen, B; Asman, B; Jon-and, K B; Silverstein, S B; Johansen, M; Alexandrov, I; Iatsounenko, I; Krumshteyn, Z; Peshekhonov, V; Rybaltchenko, K; Samoylov, V; Cheplakov, A; Kekelidze, G; Lyablin, M; Teterine, V; Bednyakov, V; Kruchonak, U; Shiyakova, M M; Demichev, M; Denisov, S P; Fenyuk, A; Djobava, T; Salukvadze, G; Cetin, S A; Brau, B P; Pais, P R; Proudfoot, J; Van gemmeren, P; Zhang, Q; Beringer, J A; Ely, R; Leggett, C; Pengg, F X; Barnett, M R; Quick, R E; Williams, S; Gardner jr, R W; Huston, J; Brock, R; Wanotayaroj, C; Unel, G N; Taffard, A C; Frate, M; Baker, K O; Tipton, P L; Hutchison, A; Walsh, B J; Norberg, S R; Su, J; Tsybyshev, D; Caballero bejar, J; Ernst, M U; Wellenstein, H; Vudragovic, D; Vidic, I; Gorelov, I V; Toms, K; Alimonti, G; Petrucci, F; Kolanoski, H; Smith, J; Jeng, G; Watson, I J; Guimaraes ferreira, F; Miranda vieira xavier, F; Araujo pereira, R; Poffenberger, P; Sopko, V; Elmsheuser, J; Wittkowski, J; Glitza, K; Gorfine, G W; Ferrer soria, A; Fuster verdu, J A; Sanchis lozano, A; Reinmuth, G; Busato, E; Haywood, S J; Mcmahon, S J; Qian, W; Villani, E G; Laycock, P J; Poll, A J; Rizvi, E S; Foster, J M; Loebinger, F; Forti, A; Plano, W G; Brown, G J A; Kordas, K; Vegni, G; Ohsugi, T; Iwata, Y; Cherkaoui el moursli, R; Sahin, M; Akyazi, E; Carlsen, A; Kanwal, B; Cochran jr, J H; Aronnax, M V; Lockner, M J; Zhou, B; Levin, D S; Weaverdyck, C J; Grom, G F; Rudge, A; Ebenstein, W L; Jia, B; Yamaoka, J; Jared, R C; Wu, S L; Banerjee, S; Lu, Q; Hughes, E W; Alkire, S P; Degenhardt, J D; Lipeles, E D; Spencer, E N; Savine, A; Cheu, E C; Lampl, W; Veatch, J R; Roberts, K; Atkinson, M J; Odino, G A; Polesello, G; Martin, T; White, A P; Stephens, R; Grinbaum sarkisyan, E; Vartapetian, A; Yu, J; Sosebee, M; Thilagar, P A; Spurlock, B; Bonde, R; Filthaut, F; Klok, P; Hoummada, A; Ouchrif, M; Pellegrini, G; Rafi tatjer, J M; Navarro, G A; Blumenschein, U; Weingarten, J C; Mueller, D; Graber, L; Gao, Y; Bode, A; Capeans garrido, M D M; Carli, T; Wells, P; Beltramello, O; Vuillermet, R; Dudarev, A; Salzburger, A; Torchiani, C I; Serfon, C L G; Sloper, J E; Duperrier, G; Lilova, P T; Knecht, M O; Lassnig, M; Anders, G; Deviveiros, P; Young, C; Sforza, F; Shaochen, C; Lu, F; Wermes, N; Wienemann, P; Schwindt, T; Hansen, P H; Hansen, J B; Pingel, A M; Massol, N; Elles, S L; Hallewell, G D; Rozanov, A; Vacavant, L; Fournier, D A; Poggioli, L; Puzo, P M; Tanaka, R; Escalier, M A; Makovec, N; Rezynkina, K; De cecco, S; Cavalleri, P G; Massa, I; Zoccoli, A; Tanaka, S; Odaka, S; Mitsui, S; Tomasio pina, J A; Santos, H F; Satsounkevitch, I; Harkusha, S; Baranov, S; Nechaeva, P; Kayumov, F; Kazanin, V; Asai, M; Mount, R P; Nelson, T K; Smith, D; Kenney, C J; Malone, C M; Kobel, M; Friedrich, F; Grohs, J P; Jais, W J; O'neil, D C; Warburton, A T; Vincter, M; Mccarthy, T G; Groer, L S; Pham, Q T; Taylor, W J; La marra, D; Perrin, E; Wu, X; Bell, W H; Delitzsch, C M; Feng, C; Zhu, C; Tokar, S; Bruncko, D; Kupco, A; Marcisovsky, M; Jakoubek, T; Bruneliere, R; Aktas, A; Narrias villar, D I; Tapprogge, S; Mattmann, J; Kroha, H; Crespo, J; Korolkov, I; Cavallaro, E; Cabrera urban, S; Mitsou, V; Kozanecki, W; Mansoulie, B; Pabot, Y; Etienvre, A; Bauer, F; Chevallier, F; Bouty, A R; Watkins, P; Watson, A; Faulkner, P J W; Curtis, C J; Murillo quijada, J A; Grout, Z J; Chapman, J D; Cowan, G D; George, S; Boisvert, V; Mcmahon, T R; Doyle, A T; Thompson, S A; Britton, D; Smizanska, M; Campanelli, M; Butterworth, J M; Loken, J; Renton, P; Barr, A J; Issever, C; Short, D; Crispin ortuzar, M; Tovey, D R; French, R; Rozen, Y; Alexander, G; Kreisel, A; Conventi, F; Raulo, A; Schioppa, M; Susinno, G; Tassi, E; Giagu, S; Luci, C; Nisati, A; Cobal, M; Ishikawa, A; Jinnouchi, O; Bos, K; Verkerke, W; Vermeulen, J; Van vulpen, I B; Kieft, G; Mora, K D; Olsen, F; Rohne, O M; Pajchel, K; Nilsen, J K; Wosiek, B K; Wozniak, K W; Badescu, E; Jinaru, A; Bohm, C; Johansson, E K; Sjoelin, J B R; Clement, C; Buszello, C P; Huseynova, D; Boyko, I; Popov, B; Poukhov, O; Vinogradov, V; Tsiareshka, P; Skvorodnev, N; Soldatov, A; Chuguev, A; Gushchin, V; Yazici, E; Lutz, M S; Malon, D; Vanyashin, A; Lavrijsen, W; Spieler, H; Biesiada, J L; Bahr, M; Kong, J; Tatarkhanov, M; Ogren, H; Van kooten, R J; Cwetanski, P; Butler, J M; Shank, J T; Chakraborty, D; Ermoline, I; Sinev, N; Whiteson, D O; Corso radu, A; Huang, J; Werth, M P; Kastoryano, M; Meirose da silva costa, B; Namasivayam, H; Hobbs, J D; Schamberger jr, R D; Guo, F; Potekhin, M; Popovic, D; Gorisek, A; Sokhrannyi, G; Hofsajer, I W; Mandelli, L; Ceradini, F; Graziani, E; Giorgi, F; Zur nedden, M E G; Grancagnolo, S; Volpi, M; Nunes hanninger, G; Rados, P K; Milesi, M; Cuthbert, C J; Black, C W; Fink grael, F; Fincke-keeler, M; Keeler, R; Kowalewski, R V; Berghaus, F O; Qi, M; Davidek, T; Tas, P; Jakubek, J; Duckeck, G; Walker, R; Mitterer, C A; Harenberg, T; Sandvoss, S A; Del peso, J; Llorente merino, J; Gonzalez millan, V; Irles quiles, A; Crouau, M; Gris, P L Y; Liauzu, S; Romano saez, S M; Gallop, B J; Jones, T J; Austin, N C; Morris, J; Duerdoth, I; Thompson, R J; Kelly, M P; Leisos, A; Garas, A; Pizio, C; Venda pinto, B A; Kudin, L; Qian, J; Wilson, A W; Mietlicki, D; Long, J D; Sang, Z; Arms, K E; Rahimi, A M; Moss, J J; Oh, S H; Parker, S I; Parsons, J; Cunitz, H; Vanguri, R S; Sadrozinski, H; Lockman, W S; Martinez-mc kinney, G; Goussiou, A; Jones, A; Lie, K; Hasegawa, Y; Olcese, M; Gilewsky, V; Harrison, P F; Janus, M; Spangenberg, M; De, K; Ozturk, N; Pal, A K; Darmora, S; Bullock, D J; Oviawe, O; Derkaoui, J E; Rahal, G; Sircar, A; Frey, A S; Stolte, P; Rosien, N; Zoch, K; Li, L; Schouten, D W; Catinaccio, A; Ciapetti, M; Delruelle, N; Ellis, N; Farthouat, P; Hoecker, A; Klioutchnikova, T; Macina, D; Malyukov, S; Spiwoks, R D; Unal, G P; Vandoni, G; Petersen, B A; Pommes, K; Nairz, A M; Wengler, T; Mladenov, D; Solans sanchez, C A; Lantzsch, K; Schmieden, K; Jakobsen, S; Ritsch, E; Sciuccati, A; Alves dos santos, A M; Ouyang, Q; Zhou, M; Brock, I C; Janssen, J; Katzy, J; Anders, C F; Nilsson, B S; Bazan, A; Di ciaccio, L; Yildizkaya, T; Collot, J; Malek, F; Trocme, B S; Breugnon, P; Godiot, S; Adam bourdarios, C; Coulon, J; Duflot, L; Petroff, P G; Zerwas, D; Lieuvin, M; Calderini, G; Laporte, D; Ocariz, J; Gabrielli, A; Ohska, T K; Kurochkin, Y; Kantserov, V; Vasilyeva, L; Speransky, M; Smirnov, S; Antonov, A; Bulekov, O; Tikhonov, Y; Sargsyan, L; Vardanyan, G; Budick, B; Kocian, M L; Luitz, S; Young, C C; Grenier, P J; Kelsey, M; Black, J E; Kneringer, E; Jussel, P; Horton, A J; Beaudry, J; Chandra, A; Ereditato, A; Topfel, C M; Mathieu, R; Bucci, F; Muenstermann, D; White, R M; He, M; Urban, J; Straka, M; Vrba, V; Schumacher, M; Parzefall, U; Mahboubi, K; Sommer, P O; Koepke, L H; Bethke, S; Moser, H; Wiesmann, M; Walkowiak, W A; Fleck, I J; Martinez-perez, M; Sanchez sanchez, C A; Jorgensen roca, S; Accion garcia, E; Sainz ruiz, C A; Valls ferrer, J A; Amoros vicente, G; Vives torrescasana, R; Ouraou, A; Formica, A; Hassani, S; Watson, M F; Cottin buracchio, G F; Bussey, P J; Saxon, D; Ferrando, J E; Collins-tooth, C L; Hall, D C; Cuhadar donszelmann, T; Dawson, I; Duxfield, R; Argyropoulos, T; Brodet, E; Livneh, R; Shougaev, K; Reinherz, E I; Guttman, N; Beretta, M M; Vilucchi, E; Aloisio, A; Patricelli, S; Caprio, M; Cevenini, F; De vecchi, C; Livan, M; Rimoldi, A; Vercesi, V; Ayad, R; Mastroberardino, A; Ciapetti, G; Luminari, L; Rescigno, M; Santonico, R; Salamon, A; Del papa, C; Kurashige, H; Homma, Y; Tomoto, M; Horii, Y; Sugaya, Y; Hanagaki, K; Bobbink, G; Kluit, P M; Koffeman, E N; Van eijk, B; Lee, H; Eigen, G; Dorholt, O; Strandlie, A; Strzempek, P B; Dita, S; Stoicea, G; Chitan, A; Leven, S S; Moa, T; Brenner, R; Ekelof, T J C; Olshevskiy, A; Roumiantsev, V; Chlachidze, G; Zimine, N; Gusakov, Y; Grigalashvili, N; Mineev, M; Potrap, I; Barashkou, A; Shoukavy, D; Shaykhatdenov, B; Pikelner, A; Gladilin, L; Ammosov, V; Abramov, A; Arik, M; Sahinsoy, M; Uysal, Z; Azizi, K; Hotinli, S C; Zhou, S; Berger, E; Blair, R; Underwood, D G; Einsweiler, K; Garcia-sciveres, M A; Siegrist, J L; Kipnis, I; Dahl, O; Holland, S; Barbaro galtieri, A; Smith, P T; Parua, N; Franklin, M; Mercurio, K M; Tong, B; Pod, E; Cole, S G; Hopkins, W H; Guest, D H; Severini, H; Marsicano, J J; Abbott, B K; Wang, Q; Lissauer, D; Ma, H; Takai, H; Rajagopalan, S; Protopopescu, S D; Snyder, S S; Undrus, A; Popescu, R N; Begel, M A; Blocker, C A; Amelung, C; Mandic, I; Macek, B; Tucker, B H; Citterio, M; Troncon, C; Orestano, D; Taccini, C; Romeo, G L; Dova, M T; Taylor, G N; Gesualdi manhaes, A; Mcpherson, R A; Sobie, R; Taylor, R P; Dolezal, Z; Kodys, P; Slovak, R; Sopko, B; Vacek, V; Sanders, M P; Hertenberger, R; Meineck, C; Becks, K; Kind, P; Sandhoff, M; Cantero garcia, J; De la torre perez, H; Castillo gimenez, V; Ros, E; Hernandez jimenez, Y; Chadelas, R; Santoni, C; Washbrook, A J; O'brien, B J; Wynne, B M; Mehta, A; Vossebeld, J H; Landon, M; Teixeira dias castanheira, M; Cerrito, L; Keates, J R; Fassouliotis, D; Chardalas, M; Manousos, A; Grachev, V; Seliverstov, D; Sedykh, E; Cakir, O; Ciftci, R; Edson, W; Prell, S A; Rosati, M; Stroman, T; Jiang, H; Neal, H A; Li, X; Gan, K K; Smith, D S; Kruse, M C; Ko, B R; Leung fook cheong, A M; Cole, B; Angerami, A R; Greene, Z S; Kroll, J I; Van berg, R P; Forbush, D A; Lubatti, H; Raisher, J; Shupe, M A; Wolin, S; Oshita, H; Gaudio, G; Das, R; Konig, A C; Croft, V A; Harvey, A; Maaroufi, F; Melo, I; Greenwood jr, Z D; Shabalina, E; Mchedlidze, G; Drechsler, E; Rieger, J K; Blackston, M; Colombo, T

    2002-01-01

    % ATLAS \\\\ \\\\ ATLAS is a general-purpose experiment for recording proton-proton collisions at LHC. The ATLAS collaboration consists of 144 participating institutions (June 1998) with more than 1750~physicists and engineers (700 from non-Member States). The detector design has been optimized to cover the largest possible range of LHC physics: searches for Higgs bosons and alternative schemes for the spontaneous symmetry-breaking mechanism; searches for supersymmetric particles, new gauge bosons, leptoquarks, and quark and lepton compositeness indicating extensions to the Standard Model and new physics beyond it; studies of the origin of CP violation via high-precision measurements of CP-violating B-decays; high-precision measurements of the third quark family such as the top-quark mass and decay properties, rare decays of B-hadrons, spectroscopy of rare B-hadrons, and $ B ^0 _{s} $-mixing. \\\\ \\\\The ATLAS dectector, shown in the Figure includes an inner tracking detector inside a 2~T~solenoid providing an axial...

  9. Identification of histological correlates of overall survival in lower grade gliomas using a bag-of-words paradigm: A preliminary analysis based on hematoxylin & eosin stained slides from the lower grade glioma cohort of the cancer genome Atlas

    Directory of Open Access Journals (Sweden)

    Reid Trenton Powell

    2017-01-01

    Full Text Available Background: Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO, which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs (WHO Grade II–III have fewer malignant characteristics than high-grade gliomas (WHO Grade IV, and a better clinical prognosis, however, accurate discrimination of overall survival (OS remains a challenge. In this study, we aimed to identify tissue-derived image features using a machine learning approach to predict OS in a mixed histology and grade cohort of lower grade glioma patients. To achieve this aim, we used H and E stained slides from the public LGG cohort of The Cancer Genome Atlas (TCGA to create a machine learned dictionary of “image-derived visual words” associated with OS. We then evaluated the combined efficacy of using these visual words in predicting short versus long OS by training a generalized machine learning model. Finally, we mapped these predictive visual words back to molecular signaling cascades to infer potential drivers of the machine learned survival-associated phenotypes. Methods: We analyzed digitized histological sections downloaded from the LGG cohort of TCGA using a bag-of-words approach. This method identified a diverse set of histological patterns that were further correlated with OS, histology, and molecular signaling activity using Cox regression, analysis of variance, and Spearman correlation, respectively. A support vector machine (SVM model was constructed to discriminate patients into short and long OS groups dichotomized at 24-month. Results: This method identified disease-relevant phenotypes associated with OS, some of which are correlated with disease-associated molecular pathways. From these image

  10. Identification of Histological Correlates of Overall Survival in Lower Grade Gliomas Using a Bag-of-words Paradigm: A Preliminary Analysis Based on Hematoxylin & Eosin Stained Slides from the Lower Grade Glioma Cohort of The Cancer Genome Atlas.

    Science.gov (United States)

    Powell, Reid Trenton; Olar, Adriana; Narang, Shivali; Rao, Ganesh; Sulman, Erik; Fuller, Gregory N; Rao, Arvind

    2017-01-01

    Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO), which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs) (WHO Grade II-III) have fewer malignant characteristics than high-grade gliomas (WHO Grade IV), and a better clinical prognosis, however, accurate discrimination of overall survival (OS) remains a challenge. In this study, we aimed to identify tissue-derived image features using a machine learning approach to predict OS in a mixed histology and grade cohort of lower grade glioma patients. To achieve this aim, we used H and E stained slides from the public LGG cohort of The Cancer Genome Atlas (TCGA) to create a machine learned dictionary of "image-derived visual words" associated with OS. We then evaluated the combined efficacy of using these visual words in predicting short versus long OS by training a generalized machine learning model. Finally, we mapped these predictive visual words back to molecular signaling cascades to infer potential drivers of the machine learned survival-associated phenotypes. We analyzed digitized histological sections downloaded from the LGG cohort of TCGA using a bag-of-words approach. This method identified a diverse set of histological patterns that were further correlated with OS, histology, and molecular signaling activity using Cox regression, analysis of variance, and Spearman correlation, respectively. A support vector machine (SVM) model was constructed to discriminate patients into short and long OS groups dichotomized at 24-month. This method identified disease-relevant phenotypes associated with OS, some of which are correlated with disease-associated molecular pathways. From these image-derived phenotypes, a generalized SVM model which could

  11. A genomic atlas of human adrenal and gonad development [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Ignacio del Valle

    2017-04-01

    Full Text Available Background: In humans, the adrenal glands and gonads undergo distinct biological events between 6-10 weeks post conception (wpc, such as testis determination, the onset of steroidogenesis and primordial germ cell development. However, relatively little is currently known about the genetic mechanisms underlying these processes. We therefore aimed to generate a detailed genomic atlas of adrenal and gonad development across these critical stages of human embryonic and fetal development. Methods: RNA was extracted from 53 tissue samples between 6-10 wpc (adrenal, testis, ovary and control. Affymetrix array analysis was performed and differential gene expression was analysed using Bioconductor. A mathematical model was constructed to investigate time-series changes across the dataset. Pathway analysis was performed using ClueGo and cellular localisation of novel factors confirmed using immunohistochemistry. Results: Using this approach, we have identified novel components of adrenal development (e.g. ASB4, NPR3 and confirmed the role of SRY as the main human testis-determining gene. By mathematical modelling time-series data we have found new genes up-regulated with SOX9 in the testis (e.g. CITED1, which may represent components of the testis development pathway. We have shown that testicular steroidogenesis has a distinct onset at around 8 wpc and identified potential novel components in adrenal and testicular steroidogenesis (e.g. MGARP, FOXO4, MAP3K15, GRAMD1B, RMND2, as well as testis biomarkers (e.g. SCUBE1. We have also shown that the developing human ovary expresses distinct subsets of genes (e.g. OR10G9, OR4D5, but enrichment for established biological pathways is limited. Conclusion: This genomic atlas is revealing important novel aspects of human development and new candidate genes for adrenal and reproductive disorders.

  12. A genomic atlas of human adrenal and gonad development [version 2; referees: 4 approved

    Directory of Open Access Journals (Sweden)

    Ignacio del Valle

    2017-10-01

    Full Text Available Background: In humans, the adrenal glands and gonads undergo distinct biological events between 6-10 weeks post conception (wpc, such as testis determination, the onset of steroidogenesis and primordial germ cell development. However, relatively little is currently known about the genetic mechanisms underlying these processes. We therefore aimed to generate a detailed genomic atlas of adrenal and gonad development across these critical stages of human embryonic and fetal development. Methods: RNA was extracted from 53 tissue samples between 6-10 wpc (adrenal, testis, ovary and control. Affymetrix array analysis was performed and differential gene expression was analysed using Bioconductor. A mathematical model was constructed to investigate time-series changes across the dataset. Pathway analysis was performed using ClueGo and cellular localisation of novel factors confirmed using immunohistochemistry. Results: Using this approach, we have identified novel components of adrenal development (e.g. ASB4, NPR3 and confirmed the role of SRY as the main human testis-determining gene. By mathematical modelling time-series data we have found new genes up-regulated with SOX9 in the testis (e.g. CITED1, which may represent components of the testis development pathway. We have shown that testicular steroidogenesis has a distinct onset at around 8 wpc and identified potential novel components in adrenal and testicular steroidogenesis (e.g. MGARP, FOXO4, MAP3K15, GRAMD1B, RMND2, as well as testis biomarkers (e.g. SCUBE1. We have also shown that the developing human ovary expresses distinct subsets of genes (e.g. OR10G9, OR4D5, but enrichment for established biological pathways is limited. Conclusion: This genomic atlas is revealing important novel aspects of human development and new candidate genes for adrenal and reproductive disorders.

  13. Systemic analysis of different colorectal cancer cell lines and TCGA datasets identified IGF-1R/EGFR-PPAR-CASPASE axis as important indicator for radiotherapy sensitivity.

    Science.gov (United States)

    Chen, Lin; Zhu, Zhe; Gao, Wei; Jiang, Qixin; Yu, Jiangming; Fu, Chuangang

    2017-09-05

    Insulin-like growth factor 1 receptor (IGF-1R) is proved to contribute the development of many types of cancers. But, little is known about its roles in radio-resistance of colorectal cancer (CRC). Here, we demonstrated that low IGF-1R expression value was associated with the better radiotherapy sensitivity of CRC. Besides, through Quantitative Real-time PCR (qRT-PCR), the elevated expression value of epidermal growth factor receptor (EGFR) was observed in CRC cell lines (HT29, RKO) with high radio-sensitivity compared with those with low sensitivity (SW480, LOVO). The irradiation induced apoptosis rates of wild type and EGFR agonist (EGF) or IGF-1R inhibitor (NVP-ADW742) treated HT29 and SW480 cells were quantified by flow cytometry. As a result, the apoptosis rate of EGF and NVP-ADW742 treated HT29 cells was significantly higher than that of those wild type ones, which indicated that high EGFR and low IGF-1R expression level in CRC was associated with the high sensitivity to radiotherapy. We next conducted systemic bioinformatics analysis of genome-wide expression profiles of CRC samples from the Cancer Genome Atlas (TCGA). Differential expression analysis between IGF-1R and EGFR abnormal CRC samples, i.e. CRC samples with higher IGF-1R and lower EGFR expression levels based on their median expression values, and the rest of CRC samples identified potential genes contribute to radiotherapy sensitivity. Functional enrichment of analysis of those differential expression genes (DEGs) in the Database for Annotation, Visualization and Integrated Discovery (DAVID) indicated PPAR signaling pathway as an important pathway for the radio-resistance of CRC. Our study identified the potential biomarkers for the rational selection of radiotherapy for CRC patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.

    Science.gov (United States)

    Nulton, Tara J; Olex, Amy L; Dozmorov, Mikhail; Morgan, Iain M; Windle, Brad

    2017-03-14

    Human papillomavirus (HPV) DNA is detected in up to 80% of oropharyngeal carcinomas (OPC) and this HPV positive disease has reached epidemic proportions. To increase our understanding of the disease, we investigated the status of the HPV16 genome in HPV-positive head and neck cancers (HNC). Raw RNA-Seq and Whole Genome Sequence data from The Cancer Genome Atlas HNC samples were analyzed to gain a full understanding of the HPV genome status for these tumors. Several remarkable and novel observations were made following this analysis. Firstly, there are three main HPV genome states in these tumors that are split relatively evenly: An episomal only state, an integrated state, and a state in which the viral genome exists as a hybrid episome with human DNA. Secondly, none of the tumors expressed high levels of E6; E6*I is the dominant variant expressed in all tumors. The most striking conclusion from this study is that around three quarters of HPV16 positive HNC contain episomal versions of the viral genome that are likely replicating in an E1-E2 dependent manner. The clinical and therapeutic implications of these observations are discussed.

  15. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

    Directory of Open Access Journals (Sweden)

    King Nichole L

    2009-02-01

    Full Text Available Abstract Background Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments. Results In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s in which it was observed. Conclusion PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1 reduction of the complexity inherently associated with performing targeted proteomic studies, (2 designing and accelerating shotgun proteomics experiments, (3 confirming or questioning gene models, and (4 adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.

  16. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

    Science.gov (United States)

    Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

    2014-01-27

    Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available

  17. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies.

    Science.gov (United States)

    Sharma, Deepak K; Solbrig, Harold R; Tao, Cui; Weng, Chunhua; Chute, Christopher G; Jiang, Guoqian

    2017-06-05

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes). We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models. Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

  18. Integration of genomic and medical data into a 3D atlas of human anatomy.

    Science.gov (United States)

    Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Dong, Xiaoli; Stromer, Julie N; Shu, Xueling; Wat, Stephen; Hallgrímsson, Benedikt; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

    2008-01-01

    We have developed a framework for the visual integration and exploration of multi-scale biomedical data, which includes anatomical and molecular components. We have also created a Java-based software system that integrates molecular information, such as gene expression data, into a three-dimensional digital atlas of the male adult human anatomy. Our atlas is structured according to the Terminologia Anatomica. The underlying data-indexing mechanism uses open standards and semantic ontology-processing tools to establish the associations between heterogeneous data types. The software system makes an extensive use of virtual reality visualization.

  19. The mitochondrial genomes of Atlas Geckos (Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets

    OpenAIRE

    Lyra, Mariana L.; Joger, Ulrich; Schulte, Ulrich; Slimani, Tahar; El Mouden, El Hassan; Bouazza, Abdellah; Künzel, Sven; Lemmon, Alan R.; Moriarty Lemmon, Emily; Vences, Miguel

    2017-01-01

    The nearly complete mitogenomes of the two species of North African Atlas geckos, Quedenfeldtia moerens and Q. trachyblepharus were assembled from anchored hybrid enrichment data and RNAseq data. Congruent assemblies were obtained for four samples included in both datasets. We recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for both species, including partial control region. The order of genes agrees with that of other geckos.

  20. Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic and in the United States.

    Directory of Open Access Journals (Sweden)

    Magdalena B Wozniak

    Full Text Available Gene expression microarray and next generation sequencing efforts on conventional, clear cell renal cell carcinoma (ccRCC have been mostly performed in North American and Western European populations, while the highest incidence rates are found in Central/Eastern Europe. We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients recruited within the "K2 Study", using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of this cancer. Differential expression analysis identified 1650 significant probes (fold change ≥2 and false discovery rate <0.05 mapping to 630 up- and 720 down-regulated unique genes. We performed similar statistical analysis on the RNA sequencing data of 65 ccRCC cases from the Cancer Genome Atlas (TCGA project and identified 60% (402 of the downregulated and 74% (469 of the upregulated genes found in the K2 series. The biological characterization of the significantly deregulated genes demonstrated involvement of downregulated genes in metabolic and catabolic processes, excretion, oxidation reduction, ion transport and response to chemical stimulus, while simultaneously upregulated genes were associated with immune and inflammatory responses, response to hypoxia, stress, wounding, vasculature development and cell activation. Furthermore, genome-wide DNA methylation analysis of 317 TCGA ccRCC/adjacent non-tumour renal tissue pairs indicated that deregulation of approximately 7% of genes could be explained by epigenetic changes. Finally, survival analysis conducted on 89 K2 and 464 TCGA cases identified 8 genes associated with differential prognostic outcomes. In conclusion, a large proportion of ccRCC molecular characteristics were common to the two populations and several may have clinical implications when validated further through large clinical cohorts.

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

    Directory of Open Access Journals (Sweden)

    Zhongqi Ge

    2018-04-01

    Full Text Available 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

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

    OpenAIRE

    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

    2018-01-01

    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 sub...

  3. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Ussery, David

    2004-01-01

    , these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...... and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently...... content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues....

  4. Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas.

    Science.gov (United States)

    Mroz, Edmund A; Tward, Aaron D; Tward, Aaron M; Hammon, Rebecca J; Ren, Yin; Rocco, James W

    2015-02-01

    Although the involvement of intra-tumor genetic heterogeneity in tumor progression, treatment resistance, and metastasis is established, genetic heterogeneity is seldom examined in clinical trials or practice. Many studies of heterogeneity have had prespecified markers for tumor subpopulations, limiting their generalizability, or have involved massive efforts such as separate analysis of hundreds of individual cells, limiting their clinical use. We recently developed a general measure of intra-tumor genetic heterogeneity based on whole-exome sequencing (WES) of bulk tumor DNA, called mutant-allele tumor heterogeneity (MATH). Here, we examine data collected as part of a large, multi-institutional study to validate this measure and determine whether intra-tumor heterogeneity is itself related to mortality. Clinical and WES data were obtained from The Cancer Genome Atlas in October 2013 for 305 patients with head and neck squamous cell carcinoma (HNSCC), from 14 institutions. Initial pathologic diagnoses were between 1992 and 2011 (median, 2008). Median time to death for 131 deceased patients was 14 mo; median follow-up of living patients was 22 mo. Tumor MATH values were calculated from WES results. Despite the multiple head and neck tumor subsites and the variety of treatments, we found in this retrospective analysis a substantial relation of high MATH values to decreased overall survival (Cox proportional hazards analysis: hazard ratio for high/low heterogeneity, 2.2; 95% CI 1.4 to 3.3). This relation of intra-tumor heterogeneity to survival was not due to intra-tumor heterogeneity's associations with other clinical or molecular characteristics, including age, human papillomavirus status, tumor grade and TP53 mutation, and N classification. MATH improved prognostication over that provided by traditional clinical and molecular characteristics, maintained a significant relation to survival in multivariate analyses, and distinguished outcomes among patients having

  5. Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes.

    Science.gov (United States)

    Chen, Yang; Gao, Zhen; Wang, Bingcheng; Xu, Rong

    2016-08-22

    Glioblastoma (GBM) is the most common and aggressive brain tumors. It has poor prognosis even with optimal radio- and chemo-therapies. Since GBM is highly heterogeneous, drugs that target on specific molecular profiles of individual tumors may achieve maximized efficacy. Currently, the Cancer Genome Atlas (TCGA) projects have identified hundreds of GBM-associated genes. We develop a drug repositioning approach combining disease genomics and mouse phenotype data towards predicting targeted therapies for GBM. We first identified disease specific mouse phenotypes using the most recently discovered GBM genes. Then we systematically searched all FDA-approved drugs for candidates that share similar mouse phenotype profiles with GBM. We evaluated the ranks for approved and novel GBM drugs, and compared with an existing approach, which also use the mouse phenotype data but not the disease genomics data. We achieved significantly higher ranks for the approved and novel GBM drugs than the earlier approach. For all positive examples of GBM drugs, we achieved a median rank of 9.2 45.6 of the top predictions have been demonstrated effective in inhibiting the growth of human GBM cells. We developed a computational drug repositioning approach based on both genomic and phenotypic data. Our approach prioritized existing GBM drugs and outperformed a recent approach. Overall, our approach shows potential in discovering new targeted therapies for GBM.

  6. Clinical research in small genomically stratified patient populations.

    Science.gov (United States)

    Martin-Liberal, J; Rodon, J

    2017-07-01

    The paradigm of early drug development in cancer is shifting from 'histology-oriented' to 'molecularly oriented' clinical trials. This change can be attributed to the vast amount of tumour biology knowledge generated by large international research initiatives such as The Cancer Genome Atlas (TCGA) and the use of next generation sequencing (NGS) techniques developed in recent years. However, targeting infrequent molecular alterations entails a series of special challenges. The optimal molecular profiling method, the lack of standardised biological thresholds, inter- and intra-tumor heterogeneity, availability of enough tumour material, correct clinical trials design, attrition rate, logistics or costs are only some of the issues that need to be taken into consideration in clinical research in small genomically stratified patient populations. This article examines the most relevant challenges inherent to clinical research in these populations. Moreover, perspectives from the Academia point of view are reviewed as well as initiatives to be taken in forthcoming years. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Expression profiles of pivotal microRNAs and targets in thyroid papillary carcinoma: an analysis of The Cancer Genome Atlas

    Directory of Open Access Journals (Sweden)

    Cong D

    2015-08-01

    Full Text Available Dan Cong,1 Mengzi He,2 Silin Chen,2 Xiaoli Liu,1 Xiaodong Liu,2 Hui Sun11Jilin Provincial Key Laboratory of Surgical Translational Medicine, Department of Thyroid and Parathyroid Surgery, People’s Republic of China–Japan Union Hospital, 2Key Laboratory of Radiobiology (Ministry of Health, School of Public Health, Jilin University, Changchun, Jilin, People’s Republic of ChinaAbstract: In the present study, we analyzed microRNA (miRNA and gene expression profiles using 499 papillary thyroid carcinoma (PTC samples and 58 normal thyroid tissues obtained from The Cancer Genome Atlas database. A pivotal regulatory network of 18 miRNA and 16 targets was identified. Upregulated miRNAs (miR-222, miR-221, miR-146b, miR-181a/b/d, miR-34a, and miR-424 and downregulated miRNAs (miR-9-1, miR-138, miR-363, miR-20b, miR-195, and miR-152 were identified. Among them, the upregulation of miR-424 and downregulation of miR-363, miR-195, and miR-152 were not previously identified. The genes CCNE2 (also known as cyclin E2, E2F1, RARA, CCND1 (cyclin D1, RUNX1, ITGA2, MET, CDKN1A (p21, and COL4A1 were overexpressed, and AXIN2, TRAF6, BCL2, RARB, HSP90B1, FGF7, and PDGFRA were downregulated. Among them, CCNE2, COL4A1, TRAF6, and HSP90B1 were newly identified. Based on receiver operating characteristic curves, several miRNAs (miR-222, miR-221, and miR-34a and genes (CCND1 and MET were ideal diagnostic indicators, with sensitivities and specificities greater than 90%. The combination of inversely expressed miRNAs and targets improved diagnostic accuracy. In a clinical feature analysis, several miRNAs (miR-34a, miR-424, miR-20b, and miR-152 and genes (CCNE2, COL4A1, TRAF6, and HSP90B1 were associated with aggressive clinical features, which have not previously been reported. Our study not only identified a pivotal miRNA regulatory network associated with PTC but also provided evidence that miRNAs and target genes can be used as biomarkers in PTC diagnosis and clinical

  8. Renal cell tumors with clear cell histology and intact VHL and chromosome 3p: a histological review of tumors from the Cancer Genome Atlas database.

    Science.gov (United States)

    Favazza, Laura; Chitale, Dhananjay A; Barod, Ravi; Rogers, Craig G; Kalyana-Sundaram, Shanker; Palanisamy, Nallasivam; Gupta, Nilesh S; Williamson, Sean R

    2017-11-01

    Clear cell renal cell carcinoma is by far the most common form of kidney cancer; however, a number of histologically similar tumors are now recognized and considered distinct entities. The Cancer Genome Atlas published data set was queried (http://cbioportal.org) for clear cell renal cell carcinoma tumors lacking VHL gene mutation and chromosome 3p loss, for which whole-slide images were reviewed. Of the 418 tumors in the published Cancer Genome Atlas clear cell renal cell carcinoma database, 387 had VHL mutation, copy number loss for chromosome 3p, or both (93%). Of the remaining, 27/31 had whole-slide images for review. One had 3p loss based on karyotype but not sequencing, and three demonstrated VHL promoter hypermethylation. Nine could be reclassified as distinct or emerging entities: translocation renal cell carcinoma (n=3), TCEB1 mutant renal cell carcinoma (n=3), papillary renal cell carcinoma (n=2), and clear cell papillary renal cell carcinoma (n=1). Of the remaining, 6 had other clear cell renal cell carcinoma-associated gene alterations (PBRM1, SMARCA4, BAP1, SETD2), leaving 11 specimens, including 2 high-grade or sarcomatoid renal cell carcinomas and 2 with prominent fibromuscular stroma (not TCEB1 mutant). One of the remaining tumors exhibited gain of chromosome 7 but lacked histological features of papillary renal cell carcinoma. Two tumors previously reported to harbor TFE3 gene fusions also exhibited VHL mutation, chromosome 3p loss, and morphology indistinguishable from clear cell renal cell carcinoma, the significance of which is uncertain. In summary, almost all clear cell renal cell carcinomas harbor VHL mutation, 3p copy number loss, or both. Of tumors with clear cell histology that lack these alterations, a subset can now be reclassified as other entities. Further study will determine whether additional entities exist, based on distinct genetic pathways that may have implications for treatment.

  9. Figure 4 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Gene-list view of genomic data. The gene-list view allows users to compare data across a set of loci. The data in this figure includes copy number, mutation, and clinical data from 202 glioblastoma samples from TCGA. Adapted from Figure 7; Thorvaldsdottir H et al. 2012

  10. Figure 2 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Grouping and sorting genomic data in IGV. The IGV user interface displaying 202 glioblastoma samples from TCGA. Samples are grouped by tumor subtype (second annotation column) and data type (first annotation column) and sorted by copy number of the EGFR locus (middle column). Adapted from Figure 1; Robinson et al. 2011

  11. Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers.

    Science.gov (United States)

    Ren, Chao; An, Gaole; Zhao, Chenghui; Ouyang, Zhangyi; Bo, Xiaochen; Shu, Wenjie

    2018-01-30

    Lnc2Catlas ( http://lnc2catlas.bioinfotech.org/ ) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer.

  12. Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma.

    Science.gov (United States)

    Gu, Yunyan; Wang, Hongwei; Qin, Yao; Zhang, Yujing; Zhao, Wenyuan; Qi, Lishuang; Zhang, Yuannv; Wang, Chenguang; Guo, Zheng

    2013-03-01

    The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at the individual pathway level. However, most of these approaches ignore the correlation of alteration events between pathways and miss many genes with rare alterations collectively contributing to carcinogenesis. Here, we devise a network-based approach to capture the cooperative functional modules hidden in genome-wide somatic mutation and copy number alteration profiles of glioblastoma (GBM) from The Cancer Genome Atlas (TCGA), where a module is a set of altered genes with dense interactions in the protein interaction network. We identify 7 pairs of significantly co-altered modules that involve the main pathways known to be altered in GBM (TP53, RB and RTK signaling pathways) and highlight the striking co-occurring alterations among these GBM pathways. By taking into account the non-random correlation of gene alterations, the property of co-alteration could distinguish oncogenic modules that contain driver genes involved in the progression of GBM. The collaboration among cancer pathways suggests that the redundant models and aggravating models could shed new light on the potential mechanisms during carcinogenesis and provide new indications for the design of cancer therapeutic strategies.

  13. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  14. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

    NARCIS (Netherlands)

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

    2018-01-01

    Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic

  15. Radiogenomics of High-Grade Serous Ovarian Cancer: Multireader Multi-Institutional Study from the Cancer Genome Atlas Ovarian Cancer Imaging Research Group.

    Science.gov (United States)

    Vargas, Hebert Alberto; Huang, Erich P; Lakhman, Yulia; Ippolito, Joseph E; Bhosale, Priya; Mellnick, Vincent; Shinagare, Atul B; Anello, Maria; Kirby, Justin; Fevrier-Sullivan, Brenda; Freymann, John; Jaffe, C Carl; Sala, Evis

    2017-11-01

    Purpose To evaluate interradiologist agreement on assessments of computed tomography (CT) imaging features of high-grade serous ovarian cancer (HGSOC), to assess their associations with time-to-disease progression (TTP) and HGSOC transcriptomic profiles (Classification of Ovarian Cancer [CLOVAR]), and to develop an imaging-based risk score system to predict TTP and CLOVAR profiles. Materials and Methods This study was a multireader, multi-institutional, institutional review board-approved, HIPAA-compliant retrospective analysis of 92 patients with HGSOC (median age, 61 years) with abdominopelvic CT before primary cytoreductive surgery available through the Cancer Imaging Archive. Eight radiologists from the Cancer Genome Atlas Ovarian Cancer Imaging Research Group developed and independently recorded the following CT features: characteristics of primary ovarian mass(es), presence of definable mesenteric implants and infiltration, presence of other implants, presence and distribution of peritoneal spread, presence and size of pleural effusions and ascites, lymphadenopathy, and distant metastases. Interobserver agreement for CT features was assessed, as were univariate and multivariate associations with TTP and CLOVAR mesenchymal profile (worst prognosis). Results Interobserver agreement for some features was strong (eg, α = .78 for pleural effusion and ascites) but was lower for others (eg, α = .08 for intraparenchymal splenic metastases). Presence of peritoneal disease in the right upper quadrant (P = .0003), supradiaphragmatic lymphadenopathy (P = .0004), more peritoneal disease sites (P = .0006), and nonvisualization of a discrete ovarian mass (P = .0037) were associated with shorter TTP. More peritoneal disease sites (P = .0025) and presence of pouch of Douglas implants (P = .0045) were associated with CLOVAR mesenchymal profile. Combinations of imaging features contained predictive signal for TTP (concordance index = 0.658; P = .0006) and CLOVAR profile (mean

  16. Integrative genomic approaches to dissect clinically-significant relationships between the VDR cistrome and gene expression in primary colon cancer.

    Science.gov (United States)

    Long, Mark D; Campbell, Moray J

    2017-10-01

    Recently, we undertook a pan-cancer analyses of the nuclear hormone receptor (NR) superfamily in The Cancer Genome Atlas (TCGA), and revealed that the vitamin D receptor (NR1I1/VDR) was commonly and significantly down-regulated specifically in colon adenocarcinoma cohort (COAD). To examine the consequence of down-regulated VDR expression we re-analyzed VDR chromatin immunoprecipitation sequencing (ChIP-Seq) data from LS180 colon cancer cells (GSE31939). This analysis identified 1809 loci that displayed significant (p.adjcolon tumor suppressor, Galactin 4) had significantly shorted disease free survival. These analyses suggest that reduced expression of VDR in colon cancer (but neither loss nor mutation) changes the actions of the VDR by both dampening the expression of tumor suppressors (e.g. LGALS4) whilst either stabilizing or not down-regulating expression of oncogenes (e.g. Carbonic Anhydrase 9 (CA9)). These integrative genomic approaches are relatively generic and applicable to the study of any transcription factor. Copyright © 2016. Published by Elsevier Ltd.

  17. Integrated analysis of epigenomic and genomic changes by DNA methylation dependent mechanisms provides potential novel biomarkers for prostate cancer.

    Science.gov (United States)

    White-Al Habeeb, Nicole M A; Ho, Linh T; Olkhov-Mitsel, Ekaterina; Kron, Ken; Pethe, Vaijayanti; Lehman, Melanie; Jovanovic, Lidija; Fleshner, Neil; van der Kwast, Theodorus; Nelson, Colleen C; Bapat, Bharati

    2014-09-15

    Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated two PCa cell lines, 22Rv1 and DU-145 with the demethylating agent 5-Aza 2'-deoxycitidine (DAC) and global methylation status was analyzed by performing methylation-sensitive restriction enzyme based differential methylation hybridization strategy followed by genome-wide CpG methylation array profiling. In addition, we examined gene expression changes using a custom microarray. Gene Set Enrichment Analysis (GSEA) identified the most significantly dysregulated pathways. In addition, we assessed methylation status of candidate genes that showed reduced CpG methylation and increased gene expression after DAC treatment, in Gleason score (GS) 8 vs. GS6 patients using three independent cohorts of patients; the publically available The Cancer Genome Atlas (TCGA) dataset, and two separate patient cohorts. Our analysis, by integrating methylation and gene expression in PCa cell lines, combined with patient tumor data, identified novel potential biomarkers for PCa patients. These markers may help elucidate the pathogenesis of PCa and represent potential prognostic markers for PCa patients.

  18. Supporting ATLAS

    CERN Multimedia

    maximilien brice

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator.

  19. Supporting ATLAS

    CERN Multimedia

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator. The installation of the feet is scheduled to finish during January 2004 with an installation precision at the 1 mm level despite their height of 5.3 metres. The manufacture was carried out in Russia (Company Izhorskiye Zavody in St. Petersburg), as part of a Russian and JINR Dubna in-kind contribution to ATLAS. Involved in the installation is a team from IHEP-Protvino (Russia), the ATLAS technical co-ordination team at CERN, and the CERN survey team. In all, about 15 people are involved. After the feet are in place, the barrel toroid magnet and the barrel calorimeters will be installed. This will keep the ATLAS team busy for the entire year 2004.

  20. Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.

    Science.gov (United States)

    Rios Velazquez, Emmanuel; Meier, Raphael; Dunn, William D; Alexander, Brian; Wiest, Roland; Bauer, Stefan; Gutman, David A; Reyes, Mauricio; Aerts, Hugo J W L

    2015-11-18

    Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. MRI sets of 109 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA). Spearman's correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Auto-segmented sub-volumes showed moderate to high agreement with manually delineated volumes (range (r): 0.4 - 0.86). Also, the auto and manual volumes showed similar correlation with VASARI features (auto r = 0.35, 0.43 and 0.36; manual r = 0.17, 0.67, 0.41, for contrast-enhancing, necrosis and edema, respectively). The auto-segmented contrast-enhancing volume and post-contrast abnormal volume showed the highest AUC (0.66, CI: 0.55-0.77 and 0.65, CI: 0.54-0.76), comparable to manually defined volumes (0.64, CI: 0.53-0.75 and 0.63, CI: 0.52-0.74, respectively). BraTumIA and manual tumor sub-compartments showed comparable performance in terms of prognosis and correlation with VASARI features. This method can enable more reproducible definition and quantification of imaging based biomarkers and has potential in high-throughput medical imaging research.

  1. Molecular Alterations of TP53 are a Defining Feature of Ovarian High-Grade Serous Carcinoma: A Rereview of Cases Lacking TP53 Mutations in The Cancer Genome Atlas Ovarian Study.

    Science.gov (United States)

    Vang, Russell; Levine, Douglas A; Soslow, Robert A; Zaloudek, Charles; Shih, Ie-Ming; Kurman, Robert J

    2016-01-01

    The Cancer Genome Atlas has reported that 96% of ovarian high-grade serous carcinomas (HGSCs) have TP53 somatic mutations suggesting that mutation of this gene is a defining feature of this neoplasm. In the current study, 5 gynecologic pathologists independently evaluated hematoxylin and eosin slides of 14 available cases from The Cancer Genome Atlas classified as HGSC that lacked a TP53 mutation. The histologic diagnoses rendered by these pathologists and the accompanying molecular genetic data are the subject of this report. Only 1 case (Case 5), which contained a homozygous deletion of TP53, had unanimous interobserver agreement for a diagnosis of pure HGSC. In 1 case (Case 3), all 5 observers (100%) rendered a diagnosis of HGSC; however, 3 observers (60%) noted that the histologic features were not classic for HGSC and suggested this case may have arisen from a low-grade serous carcinoma (arisen from an alternate pathway compared with the usual HGSC). In 2 cases (Cases 4 and 12), only 3 observers (60%) in each case, respectively, interpreted it as having a component of HGSC. In the remaining 10 (71%) of tumors (Cases 1, 2, 6-11, 13, and 14), the consensus diagnosis was not HGSC, with individual diagnoses including low-grade serous carcinoma, high-grade endometrioid carcinoma, HGSC, metastatic carcinoma, clear cell carcinoma, atypical proliferative (borderline) serous tumor, and adenocarcinoma, not otherwise specified. Therefore, 13 (93%) of the tumors (Cases 1-4 and 6-14) were either not a pure HGSC or represented a diagnosis other than HGSC, all with molecular results not characteristic of HGSC. Accordingly, our review of the TP53 wild-type HGSCs reported in The Cancer Genome Atlas suggests that 100% of de novo HGSCs contain TP53 somatic mutations or deletions, with the exception of the rare HGSCs that develop from a low-grade serous tumor precursor. We, therefore, propose that lack of molecular alterations of TP53 are essentially inconsistent with the

  2. Mongolian Atlas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Climatic atlas dated 1985, in Mongolian, with introductory material also in Russian and English. One hundred eight pages in single page PDFs.

  3. Potential targets for lung squamous cell carcinoma

    Science.gov (United States)

    Researchers have identified potential therapeutic targets in lung squamous cell carcinoma, the second most common form of lung cancer. The Cancer Genome Atlas (TCGA) Research Network study comprehensively characterized the lung squamous cell carcinoma gen

  4. Predictors of Chemosensitivity in Triple Negative Breast Cancer: An Integrated Genomic Analysis.

    Directory of Open Access Journals (Sweden)

    Tingting Jiang

    2016-12-01

    Full Text Available Triple negative breast cancer (TNBC is a highly heterogeneous and aggressive disease, and although no effective targeted therapies are available to date, about one-third of patients with TNBC achieve pathologic complete response (pCR from standard-of-care anthracycline/taxane (ACT chemotherapy. The heterogeneity of these tumors, however, has hindered the discovery of effective biomarkers to identify such patients.We performed whole exome sequencing on 29 TNBC cases from the MD Anderson Cancer Center (MDACC selected because they had either pCR (n = 18 or extensive residual disease (n = 11 after neoadjuvant chemotherapy, with cases from The Cancer Genome Atlas (TCGA; n = 144 and METABRIC (n = 278 cohorts serving as validation cohorts. Our analysis revealed that mutations in the AR- and FOXA1-regulated networks, in which BRCA1 plays a key role, are associated with significantly higher sensitivity to ACT chemotherapy in the MDACC cohort (pCR rate of 94.1% compared to 16.6% in tumors without mutations in AR/FOXA1 pathway, adjusted p = 0.02 and significantly better survival outcome in the TCGA TNBC cohort (log-rank test, p = 0.05. Combined analysis of DNA sequencing, DNA methylation, and RNA sequencing identified tumors of a distinct BRCA-deficient (BRCA-D TNBC subtype characterized by low levels of wild-type BRCA1/2 expression. Patients with functionally BRCA-D tumors had significantly better survival with standard-of-care chemotherapy than patients whose tumors were not BRCA-D (log-rank test, p = 0.021, and they had significantly higher mutation burden (p < 0.001 and presented clonal neoantigens that were associated with increased immune cell activity. A transcriptional signature of BRCA-D TNBC tumors was independently validated to be significantly associated with improved survival in the METABRIC dataset (log-rank test, p = 0.009. As a retrospective study, limitations include the small size and potential selection bias in the discovery cohort

  5. Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas

    Directory of Open Access Journals (Sweden)

    Jaegil Kim

    2017-01-01

    Full Text Available Aberrant regulation of microRNA (miRNA machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC, which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC.

  6. Clinical value of miR-452-5p expression in lung adenocarcinoma: A retrospective quantitative real-time polymerase chain reaction study and verification based on The Cancer Genome Atlas and Gene Expression Omnibus databases.

    Science.gov (United States)

    Gan, Xiao-Ning; Luo, Jie; Tang, Rui-Xue; Wang, Han-Lin; Zhou, Hong; Qin, Hui; Gan, Ting-Qing; Chen, Gang

    2017-05-01

    The role and mechanism of miR-452-5p in lung adenocarcinoma remain unclear. In this study, we performed a systematic study to investigate the clinical value of miR-452-5p expression in lung adenocarcinoma. The expression of miR-452-5p in 101 lung adenocarcinoma patients was detected by quantitative real-time polymerase chain reaction. The Cancer Genome Atlas and Gene Expression Omnibus databases were joined to verify the expression level of miR-452-5p in lung adenocarcinoma. Via several online prediction databases and bioinformatics software, pathway and network analyses of miR-452-5p target genes were performed to explore its prospective molecular mechanism. The expression of miR-452-5p in lung adenocarcinoma in house was significantly lower than that in adjacent tissues (p < 0.001). Additionally, the expression level of miR-452-5p was negatively correlated with several clinicopathological parameters including the tumor size (p = 0.014), lymph node metastasis (p = 0.032), and tumor-node-metastasis stage (p = 0.036). Data from The Cancer Genome Atlas also confirmed the low expression of miR-452 in lung adenocarcinoma (p < 0.001). Furthermore, reduced expression of miR-452-5p in lung adenocarcinoma (standard mean deviations = -0.393, 95% confidence interval: -0.774 to -0.011, p = 0.044) was validated by a meta-analysis. Five hub genes targeted by miR-452-5p, including SMAD family member 4, SMAD family member 2, cyclin-dependent kinase inhibitor 1B, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta, were significantly enriched in the cell-cycle pathway. In conclusion, low expression of miR-452-5p tends to play an essential role in lung adenocarcinoma. Bioinformatics analysis might be beneficial to reveal the potential mechanism of miR-452-5p in lung adenocarcinoma.

  7. Systematic Identification and Assessment of Therapeutic Targets for Breast Cancer Based on Genome-Wide RNA Interference Transcriptomes

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2017-02-01

    Full Text Available With accumulating public omics data, great efforts have been made to characterize the genetic heterogeneity of breast cancer. However, identifying novel targets and selecting the best from the sizeable lists of candidate targets is still a key challenge for targeted therapy, largely owing to the lack of economical, efficient and systematic discovery and assessment to prioritize potential therapeutic targets. Here, we describe an approach that combines the computational evaluation and objective, multifaceted assessment to systematically identify and prioritize targets for biological validation and therapeutic exploration. We first establish the reference gene expression profiles from breast cancer cell line MCF7 upon genome-wide RNA interference (RNAi of a total of 3689 genes, and the breast cancer query signatures using RNA-seq data generated from tissue samples of clinical breast cancer patients in the Cancer Genome Atlas (TCGA. Based on gene set enrichment analysis, we identified a set of 510 genes that when knocked down could significantly reverse the transcriptome of breast cancer state. We then perform multifaceted assessment to analyze the gene set to prioritize potential targets for gene therapy. We also propose drug repurposing opportunities and identify potentially druggable proteins that have been poorly explored with regard to the discovery of small-molecule modulators. Finally, we obtained a small list of candidate therapeutic targets for four major breast cancer subtypes, i.e., luminal A, luminal B, HER2+ and triple negative breast cancer. This RNAi transcriptome-based approach can be a helpful paradigm for relevant researches to identify and prioritize candidate targets for experimental validation.

  8. An anatomic transcriptional atlas of human glioblastoma.

    Science.gov (United States)

    Puchalski, Ralph B; Shah, Nameeta; Miller, Jeremy; Dalley, Rachel; Nomura, Steve R; Yoon, Jae-Guen; Smith, Kimberly A; Lankerovich, Michael; Bertagnolli, Darren; Bickley, Kris; Boe, Andrew F; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Chapin, Mike; Datta, Suvro; Dee, Nick; Desta, Tsega; Dolbeare, Tim; Dotson, Nadezhda; Ebbert, Amanda; Feng, David; Feng, Xu; Fisher, Michael; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Hejazinia, Nika; Hohmann, John; Hothi, Parvinder; Howard, Robert; Joines, Kevin; Kriedberg, Ali; Kuan, Leonard; Lau, Chris; Lee, Felix; Lee, Hwahyung; Lemon, Tracy; Long, Fuhui; Mastan, Naveed; Mott, Erika; Murthy, Chantal; Ngo, Kiet; Olson, Eric; Reding, Melissa; Riley, Zack; Rosen, David; Sandman, David; Shapovalova, Nadiya; Slaughterbeck, Clifford R; Sodt, Andrew; Stockdale, Graham; Szafer, Aaron; Wakeman, Wayne; Wohnoutka, Paul E; White, Steven J; Marsh, Don; Rostomily, Robert C; Ng, Lydia; Dang, Chinh; Jones, Allan; Keogh, Bart; Gittleman, Haley R; Barnholtz-Sloan, Jill S; Cimino, Patrick J; Uppin, Megha S; Keene, C Dirk; Farrokhi, Farrokh R; Lathia, Justin D; Berens, Michael E; Iavarone, Antonio; Bernard, Amy; Lein, Ed; Phillips, John W; Rostad, Steven W; Cobbs, Charles; Hawrylycz, Michael J; Foltz, Greg D

    2018-05-11

    Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  9. ATLAS Outreach Highlights

    CERN Document Server

    Cheatham, Susan; The ATLAS collaboration

    2016-01-01

    The ATLAS outreach team is very active, promoting particle physics to a broad range of audiences including physicists, general public, policy makers, students and teachers, and media. A selection of current outreach activities and new projects will be presented. Recent highlights include the new ATLAS public website and ATLAS Open Data, the very recent public release of 1 fb-1 of ATLAS data.

  10. ATLAS Thesis Award 2017

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    Winners of the ATLAS Thesis Award were presented with certificates and glass cubes during a ceremony on 22 February, 2018. They are pictured here with Karl Jakobs (ATLAS Spokesperson), Max Klein (ATLAS Collaboration Board Chair) and Katsuo Tokushuku (ATLAS Collaboration Board Deputy Chair).

  11. EnviroAtlas

    Data.gov (United States)

    City and County of Durham, North Carolina — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  12. Berliner Philarmoniker ATLAS visit

    CERN Multimedia

    ATLAS Collaboration

    2017-01-01

    The Berliner Philarmoniker in on tour through Europe. They stopped on June 27th in Geneva, for a concert at the Victoria Hall. An ATLAS visit was organised the morning after, lead by the ATLAS spokesperson Karl Jakobs (welcome and overview talk) and two ATLAS guides (AVC visit and 3D movie).

  13. Report to users of ATLAS

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1995-05-01

    This report contains discussing in the following areas: Status of the Atlas accelerator; highlights of recent research at Atlas; concept for an advanced exotic beam facility based on Atlas; program advisory committee; Atlas executive committee; and Atlas and ANL physics division on the world wide web

  14. Recent ATLAS Articles on WLAP

    CERN Multimedia

    J. Herr

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Physics Workshop 6-11 June 2005 June 2005 ATLAS Week Plenary Session Click here to browse WLAP for all ATLAS lectures.

  15. ATLAS Distributed Computing Automation

    CERN Document Server

    Schovancova, J; The ATLAS collaboration; Borrego, C; Campana, S; Di Girolamo, A; Elmsheuser, J; Hejbal, J; Kouba, T; Legger, F; Magradze, E; Medrano Llamas, R; Negri, G; Rinaldi, L; Sciacca, G; Serfon, C; Van Der Ster, D C

    2012-01-01

    The ATLAS Experiment benefits from computing resources distributed worldwide at more than 100 WLCG sites. The ATLAS Grid sites provide over 100k CPU job slots, over 100 PB of storage space on disk or tape. Monitoring of status of such a complex infrastructure is essential. The ATLAS Grid infrastructure is monitored 24/7 by two teams of shifters distributed world-wide, by the ATLAS Distributed Computing experts, and by site administrators. In this paper we summarize automation efforts performed within the ATLAS Distributed Computing team in order to reduce manpower costs and improve the reliability of the system. Different aspects of the automation process are described: from the ATLAS Grid site topology provided by the ATLAS Grid Information System, via automatic site testing by the HammerCloud, to automatic exclusion from production or analysis activities.

  16. ERCP atlas

    International Nuclear Information System (INIS)

    Pott, G.; Schrameyer, B.

    1989-01-01

    Endoscopic-retrograde cholangio-pancreatography is a diagnostic tool that has become a routine method also in medical centres other than those specializing in the field of gastroenterology. It is estimated that there are about 1000 hospitals in the Federal Republic of Germany applying cholangio-pancreatography as a diagnostic method. Frequently, data interpretation is difficult, because imaging of subsequently detected lesions is found to have been insufficiently differential, or incomplete. The experienced examiner, who knows the pathological processes involved and hence to be expected, will perform the ERCP examination in a specific manner, i.e. purposefully. The ERCP atlas now presents a selection of typical, frequently found conditions, and of rarely encountered lesions. The material has been chosen from a total of 15 000 retrograde cholangio-pancreatographies. The introductory text is relatively short, as it is not so much intended to enhance experienced readers' skill in endoscopic diagnostics, - there is other literature for this purpose -, but rather as a brief survey for less experienced readers. (orig./MG) With 280 figs [de

  17. TU-CD-BRB-04: Automated Radiomic Features Complement the Prognostic Value of VASARI in the TCGA-GBM Dataset

    Energy Technology Data Exchange (ETDEWEB)

    Velazquez, E Rios [Dana-Farber Cancer Institute | Harvard Medical School, Boston, MA (United States); Narayan, V [Dana-Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medic, Boston, MA (United States); Grossmann, P [Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA (United States); Dunn, W; Gutman, D [Emory University School of Medicine, Atlanta, GA (United States); Aerts, H [Dana-Farber/Brigham Womens Cancer Center, Boston, MA (United States)

    2015-06-15

    Purpose: To compare the complementary prognostic value of automated Radiomic features to that of radiologist-annotated VASARI features in TCGA-GBM MRI dataset. Methods: For 96 GBM patients, pre-operative MRI images were obtained from The Cancer Imaging Archive. The abnormal tumor bulks were manually defined on post-contrast T1w images. The contrast-enhancing and necrotic regions were segmented using FAST. From these sub-volumes and the total abnormal tumor bulk, a set of Radiomic features quantifying phenotypic differences based on the tumor intensity, shape and texture, were extracted from the post-contrast T1w images. Minimum-redundancy-maximum-relevance (MRMR) was used to identify the most informative Radiomic, VASARI and combined Radiomic-VASARI features in 70% of the dataset (training-set). Multivariate Cox-proportional hazards models were evaluated in 30% of the dataset (validation-set) using the C-index for OS. A bootstrap procedure was used to assess significance while comparing the C-Indices of the different models. Results: Overall, the Radiomic features showed a moderate correlation with the radiologist-annotated VASARI features (r = −0.37 – 0.49); however that correlation was stronger for the Tumor Diameter and Proportion of Necrosis VASARI features (r = −0.71 – 0.69). After MRMR feature selection, the best-performing Radiomic, VASARI, and Radiomic-VASARI Cox-PH models showed a validation C-index of 0.56 (p = NS), 0.58 (p = NS) and 0.65 (p = 0.01), respectively. The combined Radiomic-VASARI model C-index was significantly higher than that obtained from either the Radiomic or VASARI model alone (p = <0.001). Conclusion: Quantitative volumetric and textural Radiomic features complement the qualitative and semi-quantitative annotated VASARI feature set. The prognostic value of informative qualitative VASARI features such as Eloquent Brain and Multifocality is increased with the addition of quantitative volumetric and textural features from the

  18. Compassion and Curiosity - TCGA

    Science.gov (United States)

    William Kim, M.D., is motivated by two things: compassion and curiosity. Dr. Kim has taken these dual motivations and created a career in which he cares directly for patients and spearheads research that may lead to improved treatment options.

  19. Probabilistic liver atlas construction.

    Science.gov (United States)

    Dura, Esther; Domingo, Juan; Ayala, Guillermo; Marti-Bonmati, Luis; Goceri, E

    2017-01-13

    Anatomical atlases are 3D volumes or shapes representing an organ or structure of the human body. They contain either the prototypical shape of the object of interest together with other shapes representing its statistical variations (statistical atlas) or a probability map of belonging to the object (probabilistic atlas). Probabilistic atlases are mostly built with simple estimations only involving the data at each spatial location. A new method for probabilistic atlas construction that uses a generalized linear model is proposed. This method aims to improve the estimation of the probability to be covered by the liver. Furthermore, all methods to build an atlas involve previous coregistration of the sample of shapes available. The influence of the geometrical transformation adopted for registration in the quality of the final atlas has not been sufficiently investigated. The ability of an atlas to adapt to a new case is one of the most important quality criteria that should be taken into account. The presented experiments show that some methods for atlas construction are severely affected by the previous coregistration step. We show the good performance of the new approach. Furthermore, results suggest that extremely flexible registration methods are not always beneficial, since they can reduce the variability of the atlas and hence its ability to give sensible values of probability when used as an aid in segmentation of new cases.

  20. Commentary on: "An integrated metabolic atlas of clear cell renal cell carcinoma." Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ.: Cancer Cell. 2016 Jan 11;29(1):104-16.

    Science.gov (United States)

    Lee, Byron H

    2017-09-01

    Dysregulated metabolism is a hallmark of cancer, manifested through alterations in metabolites. We performed metabolomic profiling on 138 matched clear cell renal cell carcinoma (ccRCC)/normal tissue pairs and found that ccRCC is characterized by broad shifts in central carbon metabolism, one-carbon metabolism, and antioxidant response. Tumor progression and metastasis were associated with metabolite increases in glutathione and cysteine/methionine metabolism pathways. We develop an analytic pipeline and visualization tool (metabolograms) to bridge the gap between TCGA transcriptomic profiling and our metabolomic data, which enables us to assemble an integrated pathway-level metabolic atlas and to demonstrate discordance between transcriptome and metabolome. Lastly, expression profiling was performed on a high-glutathione cluster, which corresponds to a poor-survival subgroup in the ccRCC TCGA cohort. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. The ATLAS Analysis Model

    CERN Multimedia

    Amir Farbin

    The ATLAS Analysis Model is a continually developing vision of how to reconcile physics analysis requirements with the ATLAS offline software and computing model constraints. In the past year this vision has influenced the evolution of the ATLAS Event Data Model, the Athena software framework, and physics analysis tools. These developments, along with the October Analysis Model Workshop and the planning for CSC analyses have led to a rapid refinement of the ATLAS Analysis Model in the past few months. This article introduces some of the relevant issues and presents the current vision of the future ATLAS Analysis Model. Event Data Model The ATLAS Event Data Model (EDM) consists of several levels of details, each targeted for a specific set of tasks. For example the Event Summary Data (ESD) stores calorimeter cells and tracking system hits thereby permitting many calibration and alignment tasks, but will be only accessible at particular computing sites with potentially large latency. In contrast, the Analysis...

  2. The Irish Wind Atlas

    Energy Technology Data Exchange (ETDEWEB)

    Watson, R [Univ. College Dublin, Dept. of Electronic and Electrical Engineering, Dublin (Ireland); Landberg, L [Risoe National Lab., Meteorology and Wind Energy Dept., Roskilde (Denmark)

    1999-03-01

    The development work on the Irish Wind Atlas is nearing completion. The Irish Wind Atlas is an updated improved version of the Irish section of the European Wind Atlas. A map of the irish wind resource based on a WA{sup s}P analysis of the measured data and station description of 27 measuring stations is presented. The results of previously presented WA{sup s}P/KAMM runs show good agreement with these results. (au)

  3. Future ATLAS Higgs Studies

    CERN Document Server

    Smart, Ben; The ATLAS collaboration

    2017-01-01

    The High-Luminosity LHC will prove a challenging environment to work in, with for example $=200$ expected. It will however also provide great opportunities for advancing studies of the Higgs boson. The ATLAS detector will be upgraded, and Higgs prospects analyses have been performed to assess the reach of ATLAS Higgs studies in the HL-LHC era. These analyses are presented, as are Run-2 ATLAS di-Higgs analyses for comparison.

  4. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Directory of Open Access Journals (Sweden)

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  5. Report to users of Atlas

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1996-06-01

    This report contains the following topics: Status of the ATLAS Accelerator; Highlights of Recent Research at ATLAS; Program Advisory Committee; ATLAS User Group Executive Committee; FMA Information Available On The World Wide Web; Conference on Nuclear Structure at the Limits; and Workshop on Experiments with Gammasphere at ATLAS

  6. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  7. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S

    2005-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Software Week Plenary 6-10 December 2004 North American ATLAS Physics Workshop (Tucson) 20-21 December 2004 (17 talks) Physics Analysis Tools Tutorial (Tucson) 19 December 2004 Full Chain Tutorial 21 September 2004 ATLAS Plenary Sessions, 17-18 February 2005 (17 talks) Coming soon: ATLAS Tutorial on Electroweak Physics, 14 Feb. 2005 Software Workshop, 21-22 February 2005 Click here to browse WLAP for all ATLAS lectures.

  8. ATLAS Brochure (English version)

    CERN Multimedia

    Lefevre, Christiane

    2011-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  9. ATLAS brochure (Italian version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  10. ATLAS brochure (French version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  11. ATLAS brochure (German version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  12. ATLAS brochure (Danish version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  13. ATLAS Thesis Awards 2015

    CERN Multimedia

    Biondi, Silvia

    2016-01-01

    Winners of the ATLAS Thesis Award were presented with certificates and glass cubes during a ceremony on Thursday 25 February. The winners also presented their work in front of members of the ATLAS Collaboration. Winners: Javier Montejo Berlingen, Barcelona (Spain), Ruth Pöttgen, Mainz (Germany), Nils Ruthmann, Freiburg (Germany), and Steven Schramm, Toronto (Canada).

  14. ATLAS OF EUROPEAN VALUES

    NARCIS (Netherlands)

    M Ed Uwe Krause

    2008-01-01

    Uwe Krause: Atlas of Eurpean Values De Atlas of European Values is een samenwerkingsproject met bijbehorende website van de Universiteit van Tilburg en Fontys Lerarenopleiding in Tilburg, waarbij de wetenschappelijke data van de European Values Study (EVS) voor het onderwijs toegankelijk worden

  15. ATLAS people can run!

    CERN Multimedia

    Claudia Marcelloni de Oliveira; Pauline Gagnon

    It must be all the training we are getting every day, running around trying to get everything ready for the start of the LHC next year. This year, the ATLAS runners were in fine form and came in force. Nine ATLAS teams signed up for the 37th Annual CERN Relay Race with six runners per team. Under a blasting sun on Wednesday 23rd May 2007, each team covered the distances of 1000m, 800m, 800m, 500m, 500m and 300m taking the runners around the whole Meyrin site, hills included. A small reception took place in the ATLAS secretariat a week later to award the ATLAS Cup to the best ATLAS team. For the details on this complex calculation which takes into account the age of each runner, their gender and the color of their shoes, see the July 2006 issue of ATLAS e-news. The ATLAS Running Athena Team, the only all-women team enrolled this year, won the much coveted ATLAS Cup for the second year in a row. In fact, they are so good that Peter Schmid and Patrick Fassnacht are wondering about reducing the women's bonus in...

  16. ATLAS Colouring Book

    CERN Multimedia

    Anthony, Katarina

    2016-01-01

    The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  17. ATLAS brochure (Catalan version)

    CERN Multimedia

    Lefevre, C

    2008-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  18. ATLAS Brochure (french version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  19. ATLAS brochure (Polish version)

    CERN Multimedia

    Lefevre, C

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  20. ATLAS brochure (Norwegian version)

    CERN Multimedia

    Lefevre, C

    2009-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter. Français

  1. ATLAS Brochure (german version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  2. ATLAS Brochure (english version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  3. ATLAS brochure (Spanish version)

    CERN Multimedia

    Lefevre, C

    2008-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  4. ATLAS Visitors Centre

    CERN Multimedia

    claudia Marcelloni

    2009-01-01

    ATLAS Visitors Centre has opened its shiny new doors to the public. Officially launched on Monday February 23rd, 2009, the permanent exhibition at Point 1 was conceived as a tour resource for ATLAS guides, and as a way to preserve the public’s opportunity to get a close-up look at the experiment in action when the cavern is sealed.

  5. A Slice of ATLAS

    CERN Document Server

    2004-01-01

    An entire section of the ATLAS detector is being assembled at Prévessin. Since May the components have been tested using a beam from the SPS, giving the ATLAS team valuable experience of operating the detector as well as an opportunity to debug the system.

  6. ATLAS rewards industry

    CERN Document Server

    Maximilien Brice

    2006-01-01

    For contributing vital pieces to the ATLAS puzzle, three industries were recognized on Friday 5 May during a supplier awards ceremony. After a welcome and overview of the ATLAS experiment by spokesperson Peter Jenni, CERN Secretary-General Maximilian Metzger stressed the importance of industry to CERN's scientific goals. Picture 30 : representatives of the three award-wining companies after the ceremony

  7. ATLAS Open Data project

    CERN Document Server

    The ATLAS collaboration

    2018-01-01

    The current ATLAS model of Open Access to recorded and simulated data offers the opportunity to access datasets with a focus on education, training and outreach. This mandate supports the creation of platforms, projects, software, and educational products used all over the planet. We describe the overall status of ATLAS Open Data (http://opendata.atlas.cern) activities, from core ATLAS activities and releases to individual and group efforts, as well as educational programs, and final web or software-based (and hard-copy) products that have been produced or are under development. The relatively large number and heterogeneous use cases currently documented is driving an upcoming release of more data and resources for the ATLAS Community and anyone interested to explore the world of experimental particle physics and the computer sciences through data analysis.

  8. Dear ATLAS colleagues,

    CERN Multimedia

    PH Department

    2008-01-01

    We are collecting old pairs of glasses to take out to Mali, where they can be re-used by people there. The price for a pair of glasses can often exceed 3 months salary, so they are prohibitively expensive for many people. If you have any old spectacles you can donate, please put them in the special box in the ATLAS secretariat, bldg.40-4-D01 before the Christmas closure on 19 December so we can take them with us when we leave for Africa at the end of the month. (more details in ATLAS e-news edition of 29 September 2008: http://atlas-service-enews.web.cern.ch/atlas-service-enews/news/news_mali.php) many thanks! Katharine Leney co-driver of the ATLAS car on the Charity Run to Mali

  9. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  10. Software Validation in ATLAS

    International Nuclear Information System (INIS)

    Hodgkinson, Mark; Seuster, Rolf; Simmons, Brinick; Sherwood, Peter; Rousseau, David

    2012-01-01

    The ATLAS collaboration operates an extensive set of protocols to validate the quality of the offline software in a timely manner. This is essential in order to process the large amounts of data being collected by the ATLAS detector in 2011 without complications on the offline software side. We will discuss a number of different strategies used to validate the ATLAS offline software; running the ATLAS framework software, Athena, in a variety of configurations daily on each nightly build via the ATLAS Nightly System (ATN) and Run Time Tester (RTT) systems; the monitoring of these tests and checking the compilation of the software via distributed teams of rotating shifters; monitoring of and follow up on bug reports by the shifter teams and periodic software cleaning weeks to improve the quality of the offline software further.

  11. ATLAS' major cooling project

    CERN Multimedia

    2005-01-01

    In 2005, a considerable effort has been put into commissioning the various units of ATLAS' complex cryogenic system. This is in preparation for the imminent cooling of some of the largest components of the detector in their final underground configuration. The liquid helium and nitrogen ATLAS refrigerators in USA 15. Cryogenics plays a vital role in operating massive detectors such as ATLAS. In many ways the liquefied argon, nitrogen and helium are the life-blood of the detector. ATLAS could not function without cryogens that will be constantly pumped via proximity systems to the superconducting magnets and subdetectors. In recent weeks compressors at the surface and underground refrigerators, dewars, pumps, linkages and all manner of other components related to the cryogenic system have been tested and commissioned. Fifty metres underground The helium and nitrogen refrigerators, installed inside the service cavern, are an important part of the ATLAS cryogenic system. Two independent helium refrigerators ...

  12. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    Mortensen, Niels Gylling; Said Said, Usama; Badger, Jake

    2006-01-01

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  13. The ATLAS Pixel Detector

    CERN Document Server

    Huegging, Fabian

    2006-06-26

    The contruction of the ATLAS Pixel Detector which is the innermost layer of the ATLAS tracking system is prgressing well. Because the pixel detector will contribute significantly to the ATLAS track and vertex reconstruction. The detector consists of identical sensor-chip-hybrid modules, arranged in three barrels in the centre and three disks on either side for the forward region. The position of the detector near the interaction point requires excellent radiation hardness, mechanical and thermal robustness, good long-term stability for all parts, combined with a low material budget. The final detector layout, new results from production modules and the status of assembly are presented.

  14. Integrating Networking into ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; The ATLAS collaboration

    2018-01-01

    Networking is foundational to the ATLAS distributed infrastructure and there are many ongoing activities related to networking both within and outside of ATLAS. We will report on the progress in a number of areas exploring ATLAS's use of networking and our ability to monitor the network, analyze metrics from the network, and tune and optimize application and end-host parameters to make the most effective use of the network. Specific topics will include work on Open vSwitch for production systems, network analytics, FTS testing and tuning, and network problem alerting and alarming.

  15. The Latest from ATLAS

    CERN Multimedia

    2009-01-01

    Since November 2008, ATLAS has undertaken detailed maintenance, consolidation and repair work on the detector (see Bulletin of 20 July 2009). Today, the fraction of the detector that is operational has increased compared to last year: less than 1% of dead channels for most of the sub-systems. "We are going to start taking data this year with a detector which is even more efficient than it was last year," agrees ATLAS Spokesperson, Fabiola Gianotti. By mid-September the detector was fully closed again, and the cavern sealed. The magnet system has been operated at nominal current for extensive periods over recent months. Once the cavern was sealed, ATLAS began two weeks of combined running. Right now, subsystems are joining the run incrementally until the point where the whole detector is integrated and running as one. In the words of ATLAS Technical Coordinator, Marzio Nessi: "Now we really start physics." In parallel, the analysis ...

  16. ATLAS soft QCD results

    CERN Document Server

    Sykora, Tomas; The ATLAS collaboration

    2018-01-01

    Recent results of soft QCD measurements performed by the ATLAS collaboration are reported. The measurements include total, elastic and inelastic cross sections, inclusive spectra, underlying event and particle correlations in p-p and p-Pb collisions.

  17. PeptideAtlas

    Data.gov (United States)

    U.S. Department of Health & Human Services — PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass...

  18. Apollo Image Atlas

    Data.gov (United States)

    National Aeronautics and Space Administration — The Apollo Image Atlas is a comprehensive collection of Apollo-Saturn mission photography. Included are almost 25,000 lunar images, both from orbit and from the...

  19. Consolidated Lunar Atlas

    Data.gov (United States)

    National Aeronautics and Space Administration — The Consolidated Lunar Atlas is a collection of the best photographic images of the moon, including low-oblique photography, full-moon photography, and tabular and...

  20. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    2012-11-16

    Nov 16, 2012 ... laboration has set up a framework to automatically process the ... ing (FPM) is complementary to data quality monitoring as problems may ... the full power of the ATLAS software framework Athena [4] and the availability of the.

  1. Printed circuit for ATLAS

    CERN Multimedia

    Laurent Guiraud

    1999-01-01

    A printed circuit board made by scientists in the ATLAS collaboration for the transition radiaton tracker (TRT). This will read data produced when a high energy particle crosses the boundary between two materials with different electrical properties.

  2. ATLAS Distributed Computing

    CERN Document Server

    Schovancova, J; The ATLAS collaboration

    2011-01-01

    The poster details the different aspects of the ATLAS Distributed Computing experience after the first year of LHC data taking. We describe the performance of the ATLAS distributed computing system and the lessons learned during the 2010 run, pointing out parts of the system which were in a good shape, and also spotting areas which required improvements. Improvements ranged from hardware upgrade on the ATLAS Tier-0 computing pools to improve data distribution rates, tuning of FTS channels between CERN and Tier-1s, and studying data access patterns for Grid analysis to improve the global processing rate. We show recent software development driven by operational needs with emphasis on data management and job execution in the ATLAS production system.

  3. ATLAS Metadata Task Force

    Energy Technology Data Exchange (ETDEWEB)

    ATLAS Collaboration; Costanzo, D.; Cranshaw, J.; Gadomski, S.; Jezequel, S.; Klimentov, A.; Lehmann Miotto, G.; Malon, D.; Mornacchi, G.; Nemethy, P.; Pauly, T.; von der Schmitt, H.; Barberis, D.; Gianotti, F.; Hinchliffe, I.; Mapelli, L.; Quarrie, D.; Stapnes, S.

    2007-04-04

    This document provides an overview of the metadata, which are needed to characterizeATLAS event data at different levels (a complete run, data streams within a run, luminosity blocks within a run, individual events).

  4. California Ocean Uses Atlas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset is a result of the California Ocean Uses Atlas Project: a collaboration between NOAA's National Marine Protected Areas Center and Marine Conservation...

  5. ATLAS accelerator laboratory report

    International Nuclear Information System (INIS)

    Den Hartog, P.

    1986-01-01

    The operation of the ATLAS Accelerator is reported. Modifications are reported, including the installation of conductive tires for the Pelletron chain pulleys, installation of a new high frequency sweeper system at the entrance to the linac, and improvements to the rf drive ports of eight resonators to correct failures in the thermally conductive ceramic insulators. Progress is reported on the positive-ion injector upgrade for ATLAS. Also reported are building modifications and possible new uses for the tandem injector

  6. The ATLAS electromagnetic calorimeter

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Michel Mathieu, a technician for the ATLAS collaboration, is cabling the ATLAS electromagnetic calorimeter's first end-cap, before insertion into its cryostat. Millions of wires are connected to the electromagnetic calorimeter on this end-cap that must be carefully fed out from the detector so that data can be read out. Every element on the detector will be attached to one of these wires so that a full digital map of the end-cap can be recreated.

  7. Budker INP in ATLAS

    CERN Multimedia

    2001-01-01

    The Novosibirsk group has proposed a new design for the ATLAS liquid argon electromagnetic end-cap calorimeter with a constant thickness of absorber plates. This design has signifi- cant advantages compared to one in the Technical Proposal and it has been accepted by the ATLAS Collaboration. The Novosibirsk group is responsible for the fabrication of the precision aluminium structure for the e.m.end-cap calorimeter.

  8. ATLAS construction status

    International Nuclear Information System (INIS)

    Jenni, P.

    2006-01-01

    The ATLAS detector is being constructed at the LHC, in view of a data-taking startup in 2007. This report concentrates on the progress and the technical challenges of the detector construction, and summarizes the status of the work as of August 2004. The project is on track to allow the highly motivated ATLAS Collaboration to enter into a new exploratory domain of high-energy physics in 2007. (author)

  9. ATLAS Facility Description Report

    International Nuclear Information System (INIS)

    Kang, Kyoung Ho; Moon, Sang Ki; Park, Hyun Sik; Cho, Seok; Choi, Ki Yong

    2009-04-01

    A thermal-hydraulic integral effect test facility, ATLAS (Advanced Thermal-hydraulic Test Loop for Accident Simulation), has been constructed at KAERI (Korea Atomic Energy Research Institute). The ATLAS has the same two-loop features as the APR1400 and is designed according to the well-known scaling method suggested by Ishii and Kataoka to simulate the various test scenarios as realistically as possible. It is a half-height and 1/288-volume scaled test facility with respect to the APR1400. The fluid system of the ATLAS consists of a primary system, a secondary system, a safety injection system, a break simulating system, a containment simulating system, and auxiliary systems. The primary system includes a reactor vessel, two hot legs, four cold legs, a pressurizer, four reactor coolant pumps, and two steam generators. The secondary system of the ATLAS is simplified to be of a circulating loop-type. Most of the safety injection features of the APR1400 and the OPR1000 are incorporated into the safety injection system of the ATLAS. In the ATLAS test facility, about 1300 instrumentations are installed to precisely investigate the thermal-hydraulic behavior in simulation of the various test scenarios. This report describes the scaling methodology, the geometric data of the individual component, and the specification and the location of the instrumentations in detail

  10. ATLAS-AWS

    International Nuclear Information System (INIS)

    Gehrcke, Jan-Philip; Stonjek, Stefan; Kluth, Stefan

    2010-01-01

    We show how the ATLAS offline software is ported on the Amazon Elastic Compute Cloud (EC2). We prepare an Amazon Machine Image (AMI) on the basis of the standard ATLAS platform Scientific Linux 4 (SL4). Then an instance of the SLC4 AMI is started on EC2 and we install and validate a recent release of the ATLAS offline software distribution kit. The installed software is archived as an image on the Amazon Simple Storage Service (S3) and can be quickly retrieved and connected to new SL4 AMI instances using the Amazon Elastic Block Store (EBS). ATLAS jobs can then configure against the release kit using the ATLAS configuration management tool (cmt) in the standard way. The output of jobs is exported to S3 before the SL4 AMI is terminated. Job status information is transferred to the Amazon SimpleDB service. The whole process of launching instances of our AMI, starting, monitoring and stopping jobs and retrieving job output from S3 is controlled from a client machine using python scripts implementing the Amazon EC2/S3 API via the boto library working together with small scripts embedded in the SL4 AMI. We report our experience with setting up and operating the system using standard ATLAS job transforms.

  11. Genomic and Functional Approaches to Understanding Cancer Aneuploidy

    NARCIS (Netherlands)

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

    2018-01-01

    Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was

  12. Report to users of ATLAS

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1997-03-01

    This report covers the following topics: (1) status of the ATLAS accelerator; (2) progress in R and D towards a proposal for a National ISOL Facility; (3) highlights of recent research at ATLAS; (4) the move of gammasphere from LBNL to ANL; (5) Accelerator Target Development laboratory; (6) Program Advisory Committee; (7) ATLAS User Group Executive Committee; and (8) ATLAS user handbook available in the World Wide Web. A brief summary is given for each topic

  13. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S.

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: June ATLAS Plenary Meeting Tutorial on Physics EDM and Tools (June) Freiburg Overview Week Ketevi Assamagan's Tutorial on Analysis Tools Click here to browse WLAP for all ATLAS lectures.

  14. Baby brain atlases.

    Science.gov (United States)

    Oishi, Kenichi; Chang, Linda; Huang, Hao

    2018-04-03

    The baby brain is constantly changing due to its active neurodevelopment, and research into the baby brain is one of the frontiers in neuroscience. To help guide neuroscientists and clinicians in their investigation of this frontier, maps of the baby brain, which contain a priori knowledge about neurodevelopment and anatomy, are essential. "Brain atlas" in this review refers to a 3D-brain image with a set of reference labels, such as a parcellation map, as the anatomical reference that guides the mapping of the brain. Recent advancements in scanners, sequences, and motion control methodologies enable the creation of various types of high-resolution baby brain atlases. What is becoming clear is that one atlas is not sufficient to characterize the existing knowledge about the anatomical variations, disease-related anatomical alterations, and the variations in time-dependent changes. In this review, the types and roles of the human baby brain MRI atlases that are currently available are described and discussed, and future directions in the field of developmental neuroscience and its clinical applications are proposed. The potential use of disease-based atlases to characterize clinically relevant information, such as clinical labels, in addition to conventional anatomical labels, is also discussed. Copyright © 2018. Published by Elsevier Inc.

  15. ATLAS Review Office

    CERN Multimedia

    Szeless, B

    The ATLAS internal reviews, be it the mandatory Production Readiness Reviews, the now newly installed Production Advancement Reviews, or the more and more requested different Design Reviews, have become a part of our ATLAS culture over the past years. The Activity Systems Status Overviews are, for the time being, a one in time event and should be held for each system as soon as possible to have some meaning. There seems to a consensus that the reviews have become a useful project tool for the ATLAS management but even more so for the sub-systems themselves making achievements as well as possible shortcomings visible. One other recognized byproduct is the increasing cross talk between the systems, a very important ingredient to make profit all the systems from the large collective knowledge we dispose of in ATLAS. In the last two months, the first two PARs were organized for the MDT End Caps and the TRT Barrel Modules, both part of the US contribution to the ATLAS Project. Furthermore several different design...

  16. ATLAS MPGD production status

    CERN Document Server

    Schioppa, Marco; The ATLAS collaboration

    2018-01-01

    Micromegas (MICRO MEsh GAseous Structure) chambers are Micro-Pattern Gaseous Detectors designed to provide a high spatial resolution and reasonable good time resolution in highly irradiated environments. In 2007 an ambitious long-term R\\&D activity was started in the context of the ATLAS experiment, at CERN: the Muon ATLAS Micromegas Activity (MAMMA). After years of tests on prototypes and technology breakthroughs, Micromegas chambers were chosen as tracking detectors for an upgrade of the ATLAS Muon Spectrometer. These novel detectors will be installed in 2020 at the end of the second long shutdown of the Large Hadron Collider, and will serve mainly as precision detectors in the innermost part of the forward ATLAS Muon Spectrometer. Four different types of Micromegas modules, eight layers each, up to $3 m^2$ area (of unprecedented size), will cover a surface of $150 m^2$ for a total active area of about $1200 m^2$. With this upgrade the ATLAS muon system will maintain the full acceptance of its excellent...

  17. ATLAS: Exceeding all expectations

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    “One year ago it would have been impossible for us to guess that the machine and the experiments could achieve so much so quickly”, says Fabiola Gianotti, ATLAS spokesperson. The whole chain – from collision to data analysis – has worked remarkably well in ATLAS.   The first LHC proton run undoubtedly exceeded expectations for the ATLAS experiment. “ATLAS has worked very well since the beginning. Its overall data-taking efficiency is greater than 90%”, says Fabiola Gianotti. “The quality and maturity of the reconstruction and simulation software turned out to be better than we expected for this initial stage of the experiment. The Grid is a great success, and right from the beginning it has allowed members of the collaboration all over the world to participate in the data analysis in an effective and timely manner, and to deliver physics results very quickly”. In just a few months of data taking, ATLAS has observed t...

  18. AGIS: The ATLAS Grid Information System

    CERN Document Server

    Anisenkov, A; The ATLAS collaboration; Klimentov, A; Senchenko, A

    2012-01-01

    The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configuration and status information about resources, services and topology of whole ATLAS Grid needed by ATLAS Distributed Computing applications and services.

  19. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  20. ATLAS production system

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration; De, Kaushik; Klimentov, Alexei; Golubkov, Dmitry; Maeno, Tadashi; Mashinistov, Ruslan; Wenaus, Torre; Padolski, Siarhei

    2016-01-01

    The second generation of the ATLAS production system called ProdSys2 is a distributed workload manager which used by thousands of physicists to analyze the data remotely, with the volume of processed data is beyond the exabyte scale, across a more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criterias, such as input and output size, memory requirements and CPU consumption with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteering computers. Besides jobs definition Production System also includes flexible web user interface, which implements user-friendly environment for main ATLAS workflows, e.g. simple way of combining different data flows, and real-time monitoring, optimised for using with huge amount of information to present. We present an overview of the ATLAS Production System major components: job and task definition, workflow manager web user i...

  1. Event visualization in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00211497; The ATLAS collaboration; Boudreau, Joseph; Konstantinidis, Nikolaos; Martyniuk, Alex; Moyse, Edward; Thomas, Juergen; Waugh, Ben; Yallup, David

    2017-01-01

    At the beginning, HEP experiments made use of photographical images both to record and store experimental data and to illustrate their findings. Then the experiments evolved and needed to find ways to visualize their data. With the availability of computer graphics, software packages to display event data and the detector geometry started to be developed. Here, an overview of the usage of event display tools in HEP is presented. Then the case of the ATLAS experiment is considered in more detail and two widely used event display packages are presented, Atlantis and VP1, focusing on the software technologies they employ, as well as their strengths, differences and their usage in the experiment: from physics analysis to detector development, and from online monitoring to outreach and communication. Towards the end, the other ATLAS visualization tools will be briefly presented as well. Future development plans and improvements in the ATLAS event display packages will also be discussed.

  2. The ATLAS Inner Detector

    CERN Document Server

    Gray, HM; The ATLAS collaboration

    2012-01-01

    The ATLAS experiment at the LHC is equipped with a charged particle tracking system, the Inner Detector, built on three subdetectors, which provide high precision measurements made from a fine detector granularity. The Pixel and microstrip (SCT) subdetectors, which use the silicon technology, are complemented with the Transition Radiation Tracker. Since the LHC startup in 2009, the ATLAS inner tracker has played a central role in many ATLAS physics analyses. Rapid improvements in the calibration and alignment of the detector allowed it to reach nearly the nominal performance in the timespan of a few months. The tracking performance proved to be stable as the LHC luminosity increased by five orders of magnitude during the 2010 proton run, New developments in the offline reconstruction for the 2011 run will improve the tracking performance in high pile-up conditions as well as in highly boosted jets will be discussed.

  3. ATLAS rewards industry

    CERN Multimedia

    2006-01-01

    Showing excellence in mechanics, electronics and cryogenics, three industries are honoured for their contributions to the ATLAS experiment. Representatives of the three award-wining companies after the ceremony. For contributing vital pieces to the ATLAS puzzle, three industries were recognized on Friday 5 May during a supplier awards ceremony. After a welcome and overview of the ATLAS experiment by spokesperson Peter Jenni, CERN Secretary-General Maximilian Metzger stressed the importance of industry to CERN's scientific goals. Close interaction with CERN was a key factor in the selection of each rewarded company, in addition to the high-quality products they delivered to the experiment. Alu Menziken Industrie AG, of Switzerland, was honoured for the production of 380,000 aluminium tubes for the Monitored Drift Tube Chambers (MDT). As Giora Mikenberg, the Muon System Project Leader stressed, the aluminium tubes were delivered on time with an extraordinary quality and precision. Between October 2000 and Jan...

  4. Two ATLAS suppliers honoured

    CERN Multimedia

    2007-01-01

    The ATLAS experiment has recognised the outstanding contribution of two firms to the pixel detector. Recipients of the supplier award with Peter Jenni, ATLAS spokesperson, and Maximilian Metzger, CERN Secretary-General.At a ceremony held at CERN on 28 November, the ATLAS collaboration presented awards to two of its suppliers that had produced sensor wafers for the pixel detector. The CiS Institut für Mikrosensorik of Erfurt in Germany has supplied 655 sensor wafers containing a total of 1652 sensor tiles and the firm ON Semiconductor has supplied 515 sensor wafers (1177 sensor tiles) from its foundry at Roznov in the Czech Republic. Both firms have successfully met the very demanding requirements. ATLAS’s huge pixel detector is very complicated, requiring expertise in highly specialised integrated microelectronics and precision mechanics. Pixel detector project leader Kevin Einsweiler admits that when the project was first propo...

  5. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2014-01-01

    Physics processes involving tau leptons play a crucial role in understanding particle physics at the high energy frontier. The ability to efficiently trigger on events containing hadronic tau decays is therefore of particular importance to the ATLAS experiment. During the 2012 run, the Large Hadronic Collder (LHC) reached instantaneous luminosities of nearly $10^{34} cm^{-2}s^{-1}$ with bunch crossings occurring every $50 ns$. This resulted in a huge event rate and a high probability of overlapping interactions per bunch crossing (pile-up). With this in mind it was necessary to design an ATLAS tau trigger system that could reduce the event rate to a manageable level, while efficiently extracting the most interesting physics events in a pile-up robust manner. In this poster the ATLAS tau trigger is described, its performance during 2012 is presented, and the outlook for the LHC Run II is briefly summarized.

  6. Calorimetry triggering in ATLAS

    CERN Document Server

    Igonkina, O; Adragna, P; Aharrouche, M; Alexandre, G; Andrei, V; Anduaga, X; Aracena, I; Backlund, S; Baines, J; Barnett, B M; Bauss, B; Bee, C; Behera, P; Bell, P; Bendel, M; Benslama, K; Berry, T; Bogaerts, A; Bohm, C; Bold, T; Booth, J R A; Bosman, M; Boyd, J; Bracinik, J; Brawn, I, P; Brelier, B; Brooks, W; Brunet, S; Bucci, F; Casadei, D; Casado, P; Cerri, A; Charlton, D G; Childers, J T; Collins, N J; Conde Muino, P; Coura Torres, R; Cranmer, K; Curtis, C J; Czyczula, Z; Dam, M; Damazio, D; Davis, A O; De Santo, A; Degenhardt, J; Delsart, P A; Demers, S; Demirkoz, B; Di Mattia, A; Diaz, M; Djilkibaev, R; Dobson, E; Dova, M, T; Dufour, M A; Eckweiler, S; Ehrenfeld, W; Eifert, T; Eisenhandler, E; Ellis, N; Emeliyanov, D; Enoque Ferreira de Lima, D; Faulkner, P J W; Ferland, J; Flacher, H; Fleckner, J E; Flowerdew, M; Fonseca-Martin, T; Fratina, S; Fhlisch, F; Gadomski, S; Gallacher, M P; Garitaonandia Elejabarrieta, H; Gee, C N P; George, S; Gillman, A R; Goncalo, R; Grabowska-Bold, I; Groll, M; Gringer, C; Hadley, D R; Haller, J; Hamilton, A; Hanke, P; Hauser, R; Hellman, S; Hidvgi, A; Hillier, S J; Hryn'ova, T; Idarraga, J; Johansen, M; Johns, K; Kalinowski, A; Khoriauli, G; Kirk, J; Klous, S; Kluge, E-E; Koeneke, K; Konoplich, R; Konstantinidis, N; Kwee, R; Landon, M; LeCompte, T; Ledroit, F; Lei, X; Lendermann, V; Lilley, J N; Losada, M; Maettig, S; Mahboubi, K; Mahout, G; Maltrana, D; Marino, C; Masik, J; Meier, K; Middleton, R P; Mincer, A; Moa, T; Monticelli, F; Moreno, D; Morris, J D; Mller, F; Navarro, G A; Negri, A; Nemethy, P; Neusiedl, A; Oltmann, B; Olvito, D; Osuna, C; Padilla, C; Panes, B; Parodi, F; Perera, V J O; Perez, E; Perez Reale, V; Petersen, B; Pinzon, G; Potter, C; Prieur, D P F; Prokishin, F; Qian, W; Quinonez, F; Rajagopalan, S; Reinsch, A; Rieke, S; Riu, I; Robertson, S; Rodriguez, D; Rogriquez, Y; Rhr, F; Saavedra, A; Sankey, D P C; Santamarina, C; Santamarina Rios, C; Scannicchio, D; Schiavi, C; Schmitt, K; Schultz-Coulon, H C; Schfer, U; Segura, E; Silverstein, D; Silverstein, S; Sivoklokov, S; Sjlin, J; Staley, R J; Stamen, R; Stelzer, J; Stockton, M C; Straessner, A; Strom, D; Sushkov, S; Sutton, M; Tamsett, M; Tan, C L A; Tapprogge, S; Thomas, J P; Thompson, P D; Torrence, E; Tripiana, M; Urquijo, P; Urrejola, P; Vachon, B; Vercesi, V; Vorwerk, V; Wang, M; Watkins, P M; Watson, A; Weber, P; Weidberg, T; Werner, P; Wessels, M; Wheeler-Ellis, S; Whiteson, D; Wiedenmann, W; Wielers, M; Wildt, M; Winklmeier, F; Wu, X; Xella, S; Zhao, L; Zobernig, H; de Seixas, J M; dos Anjos, A; Asman, B; Özcan, E

    2009-01-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 105 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  7. ATLAS TDAQ System Administration:

    CERN Document Server

    Lee, Christopher Jon; The ATLAS collaboration; Bogdanchikov, Alexander; Ballestrero, Sergio; Contescu, Alexandru Cristian; Dubrov, Sergei; Fazio, Daniel; Korol, Aleksandr; Scannicchio, Diana; Twomey, Matthew Shaun; Voronkov, Artem

    2015-01-01

    The ATLAS Trigger and Data Acquisition (TDAQ) system is responsible for the online processing of live data, streaming from the ATLAS experiment at the Large Hadron Collider (LHC) at CERN. The online farm is composed of ̃3000 servers, processing the data readout from ̃100 million detector channels through multiple trigger levels. During the two years of the first Long Shutdown (LS1) there has been a tremendous amount of work done by the ATLAS TDAQ System Administrators, implementing numerous new software applications, upgrading the OS and the hardware, changing some design philosophies and exploiting the High Level Trigger farm with different purposes. During the data taking only critical security updates are applied and broken hardware is replaced to ensure a stable operational environment. The LS1 provided an excellent opportunity to look into new technologies and applications that would help to improve and streamline the daily tasks of not only the System Administrators, but also of the scientists who wil...

  8. Calorimetry triggering in ATLAS

    International Nuclear Information System (INIS)

    Igonkina, O; Achenbach, R; Andrei, V; Adragna, P; Aharrouche, M; Bauss, B; Bendel, M; Alexandre, G; Anduaga, X; Aracena, I; Backlund, S; Bogaerts, A; Baines, J; Barnett, B M; Bee, C; P, Behera; Bell, P; Benslama, K; Berry, T; Bohm, C

    2009-01-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 | 10 5 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  9. Calorimetry Triggering in ATLAS

    International Nuclear Information System (INIS)

    Igonkina, O.; Achenbach, R.; Adragna, P.; Aharrouche, M.; Alexandre, G.; Andrei, V.; Anduaga, X.; Aracena, I.; Backlund, S.; Baines, J.; Barnett, B.M.; Bauss, B.; Bee, C.; Behera, P.; Bell, P.; Bendel, M.; Benslama, K.; Berry, T.; Bogaerts, A.; Bohm, C.; Bold, T.; Booth, J.R.A.; Bosman, M.; Boyd, J.; Bracinik, J.; Brawn, I.P.; Brelier, B.; Brooks, W.; Brunet, S.; Bucci, F.; Casadei, D.; Casado, P.; Cerri, A.; Charlton, D.G.; Childers, J.T.; Collins, N.J.; Conde Muino, P.; Coura Torres, R.; Cranmer, K.; Curtis, C.J.; Czyczula, Z.; Dam, M.; Damazio, D.; Davis, A.O.; De Santo, A.; Degenhardt, J.

    2011-01-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2/10 5 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  10. Calorimetry triggering in ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Igonkina, O [Nikhef National Institute for Subatomic Physics, Amsterdam (Netherlands); Achenbach, R; Andrei, V [Kirchhoff Institut fuer Physik, Universitaet Heidelberg, Heidelberg (Germany); Adragna, P [Physics Department, Queen Mary, University of London, London (United Kingdom); Aharrouche, M; Bauss, B; Bendel, M [Institut fr Physik, Universitt Mainz, Mainz (Germany); Alexandre, G [Section de Physique, Universite de Geneve, Geneva (Switzerland); Anduaga, X [Universidad Nacional de La Plata, La Plata (Argentina); Aracena, I [Stanford Linear Accelerator Center (SLAC), Stanford (United States); Backlund, S; Bogaerts, A [European Laboratory for Particle Physics (CERN), Geneva (Switzerland); Baines, J; Barnett, B M [STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon (United Kingdom); Bee, C [Centre de Physique des Particules de Marseille, IN2P3-CNRS, Marseille (France); P, Behera [Iowa State University, Ames, Iowa (United States); Bell, P [School of Physics and Astronomy, University of Manchester, Manchester (United Kingdom); Benslama, K [University of Regina, Regina (Canada); Berry, T [Department of Physics, Royal Holloway and Bedford New College, Egham (United Kingdom); Bohm, C [Fysikum, Stockholm University, Stockholm (Sweden)

    2009-04-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 | 10{sup 5} to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  11. The ATLAS Simulation Infrastructure

    CERN Document Server

    Aad, G.; Abdallah, J.; Abdelalim, A.A.; Abdesselam, A.; Abdinov, O.; Abi, B.; Abolins, M.; Abramowicz, H.; Abreu, H.; Acharya, B.S.; Adams, D.L.; Addy, T.N.; Adelman, J.; Adorisio, C.; Adragna, P.; Adye, T.; Aefsky, S.; Aguilar-Saavedra, J.A.; Aharrouche, M.; Ahlen, S.P.; Ahles, F.; Ahmad, A.; Ahmed, H.; Ahsan, M.; Aielli, G.; Akdogan, T.; Akesson, T.P.A.; Akimoto, G.; Akimov, A.V.; Aktas, A.; Alam, M.S.; Alam, M.A.; Albrand, S.; Aleksa, M.; Aleksandrov, I.N.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Aliev, M.; Alimonti, G.; Alison, J.; Aliyev, M.; Allport, P.P.; Allwood-Spiers, S.E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alviggi, M.G.; Amako, K.; Amelung, C.; Amorim, A.; Amoros, G.; Amram, N.; Anastopoulos, C.; Andeen, T.; Anders, C.F.; Anderson, K.J.; Andreazza, A.; Andrei, V.; Anduaga, X.S.; Angerami, A.; Anghinolfi, F.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonelli, S.; Antos, J.; Antunovic, B.; Anulli, F.; Aoun, S.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A.T.H.; Archambault, J.P.; Arfaoui, S.; Arguin, J-F.; Argyropoulos, T.; Arik, M.; Armbruster, A.J.; Arnaez, O.; Arnault, C.; Artamonov, A.; Arutinov, D.; Asai, M.; Asai, S.; Asfandiyarov, R.; Ask, S.; Asman, B.; Asner, D.; Asquith, L.; Assamagan, K.; Astbury, A.; Astvatsatourov, A.; Atoian, G.; Auerbach, B.; Augsten, K.; Aurousseau, M.; Austin, N.; Avolio, G.; Avramidou, R.; Axen, D.; Ay, C.; Azuelos, G.; Azuma, Y.; Baak, M.A.; Bach, A.M.; Bachacou, H.; Bachas, K.; Backes, M.; Badescu, E.; Bagnaia, P.; Bai, Y.; Bain, T.; Baines, J.T.; Baker, O.K.; Baker, M.D.; Baker, S; Baltasar Dos Santos Pedrosa, F.; Banas, E.; Banerjee, P.; Banerjee, S.; Banfi, D.; Bangert, A.; Bansal, V.; Baranov, S.P.; Baranov, S.; Barashkou, A.; Barber, T.; Barberio, E.L.; Barberis, D.; Barbero, M.; Bardin, D.Y.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B.M.; Barnett, R.M.; Baroncelli, A.; Barr, A.J.; Barreiro, F.; Barreiro Guimaraes da Costa, J.; Barrillon, P.; Bartoldus, R.; Bartsch, D.; Bates, R.L.; Batkova, L.; Batley, J.R.; Battaglia, A.; Battistin, M.; Bauer, F.; Bawa, H.S.; Bazalova, M.; Beare, B.; Beau, T.; Beauchemin, P.H.; Beccherle, R.; Becerici, N.; Bechtle, P.; Beck, G.A.; Beck, H.P.; Beckingham, M.; Becks, K.H.; Beddall, A.J.; Beddall, A.; Bednyakov, V.A.; Bee, C.; Begel, M.; Behar Harpaz, S.; Behera, P.K.; Beimforde, M.; Belanger-Champagne, C.; Bell, P.J.; Bell, W.H.; Bella, G.; Bellagamba, L.; Bellina, F.; Bellomo, M.; Belloni, A.; Belotskiy, K.; Beltramello, O.; Ben Ami, S.; Benary, O.; Benchekroun, D.; Bendel, M.; Benedict, B.H.; Benekos, N.; Benhammou, Y.; Benincasa, G.P.; Benjamin, D.P.; Benoit, M.; Bensinger, J.R.; Benslama, K.; Bentvelsen, S.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernat, P.; Bernhard, R.; Bernius, C.; Berry, T.; Bertin, A.; Besana, M.I.; Besson, N.; Bethke, S.; Bianchi, R.M.; Bianco, M.; Biebel, O.; Biesiada, J.; Biglietti, M.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Biscarat, C.; Bitenc, U.; Black, K.M.; Blair, R.E.; Blanchard, J-B; Blanchot, G.; Blocker, C.; Blondel, A.; Blum, W.; Blumenschein, U.; Bobbink, G.J.; Bocci, A.; Boehler, M.; Boek, J.; Boelaert, N.; Boser, S.; Bogaerts, J.A.; Bogouch, A.; Bohm, C.; Bohm, J.; Boisvert, V.; Bold, T.; Boldea, V.; Bondarenko, V.G.; Bondioli, M.; Boonekamp, M.; Bordoni, S.; Borer, C.; Borisov, A.; Borissov, G.; Borjanovic, I.; Borroni, S.; Bos, K.; Boscherini, D.; Bosman, M.; Boterenbrood, H.; Bouchami, J.; Boudreau, J.; Bouhova-Thacker, E.V.; Boulahouache, C.; Bourdarios, C.; Boveia, A.; Boyd, J.; Boyko, I.R.; Bozovic-Jelisavcic, I.; Bracinik, J.; Braem, A.; Branchini, P.; Brandenburg, G.W.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J.E.; Braun, H.M.; Brelier, B.; Bremer, J.; Brenner, R.; Bressler, S.; Britton, D.; Brochu, F.M.; Brock, I.; Brock, R.; Brodet, E.; Bromberg, C.; Brooijmans, G.; Brooks, W.K.; Brown, G.; Bruckman de Renstrom, P.A.; Bruncko, D.; Bruneliere, R.; Brunet, S.; Bruni, A.; Bruni, G.; Bruschi, M.; Bucci, F.; Buchanan, J.; Buchholz, P.; Buckley, A.G.; Budagov, I.A.; Budick, B.; Buscher, V.; Bugge, L.; Bulekov, O.; Bunse, M.; Buran, T.; Burckhart, H.; Burdin, S.; Burgess, T.; Burke, S.; Busato, E.; Bussey, P.; Buszello, C.P.; Butin, F.; Butler, B.; Butler, J.M.; Buttar, C.M.; Butterworth, J.M.; Byatt, T.; Caballero, J.; Cabrera Urban, S.; Caforio, D.; Cakir, O.; Calafiura, P.; Calderini, G.; Calfayan, P.; Calkins, R.; Caloba, L.P.; Calvet, D.; Camarri, P.; Cameron, D.; Campana, S.; Campanelli, M.; Canale, V.; Canelli, F.; Canepa, A.; Cantero, J.; Capasso, L.; Capeans Garrido, M.D.M.; Caprini, I.; Caprini, M.; Capua, M.; Caputo, R.; Caramarcu, C.; Cardarelli, R.; Carli, T.; Carlino, G.; Carminati, L.; Caron, B.; Caron, S.; Carrillo Montoya, G.D.; Carron Montero, S.; Carter, A.A.; Carter, J.R.; Carvalho, J.; Casadei, D.; Casado, M.P.; Cascella, M.; Castaneda Hernandez, A.M.; Castaneda-Miranda, E.; Castillo Gimenez, V.; Castro, N.F.; Cataldi, G.; Catinaccio, A.; Catmore, J.R.; Cattai, A.; Cattani, G.; Caughron, S.; Cauz, D.; Cavalleri, P.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Ceradini, F.; Cerqueira, A.S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cetin, S.A.; Chafaq, A.; Chakraborty, D.; Chan, K.; Chapman, J.D.; Chapman, J.W.; Chareyre, E.; Charlton, D.G.; Chavda, V.; Cheatham, S.; Chekanov, S.; Chekulaev, S.V.; Chelkov, G.A.; Chen, H.; Chen, S.; Chen, X.; Cheplakov, A.; Chepurnov, V.F.; Cherkaoui El Moursli, R.; Tcherniatine, V.; Chesneanu, D.; Cheu, E.; Cheung, S.L.; Chevalier, L.; Chevallier, F.; Chiarella, V.; Chiefari, G.; Chikovani, L.; Childers, J.T.; Chilingarov, A.; Chiodini, G.; Chizhov, V.; Choudalakis, G.; Chouridou, S.; Christidi, I.A.; Christov, A.; Chromek-Burckhart, D.; Chu, M.L.; Chudoba, J.; Ciapetti, G.; Ciftci, A.K.; Ciftci, R.; Cinca, D.; Cindro, V.; Ciobotaru, M.D.; Ciocca, C.; Ciocio, A.; Cirilli, M.; Citterio, M.; Clark, A.; Clark, P.J.; Cleland, W.; Clemens, J.C.; Clement, B.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coggeshall, J.; Cogneras, E.; Colijn, A.P.; Collard, C.; Collins, N.J.; Collins-Tooth, C.; Collot, J.; Colon, G.; Conde Muino, P.; Coniavitis, E.; Consonni, M.; Constantinescu, S.; Conta, C.; Conventi, F.; Cooke, M.; Cooper, B.D.; Cooper-Sarkar, A.M.; Cooper-Smith, N.J.; Copic, K.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Corso-Radu, A.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M.J.; Costanzo, D.; Costin, T.; Cote, D.; Coura Torres, R.; Courneyea, L.; Cowan, G.; Cowden, C.; Cox, B.E.; Cranmer, K.; Cranshaw, J.; Cristinziani, M.; Crosetti, G.; Crupi, R.; Crepe-Renaudin, S.; Cuenca Almenar, C.; Cuhadar Donszelmann, T.; Curatolo, M.; Curtis, C.J.; Cwetanski, P.; Czyczula, Z.; D'Auria, S.; D'Onofrio, M.; D'Orazio, A.; Da Via, C; Dabrowski, W.; Dai, T.; Dallapiccola, C.; Dallison, S.J.; Daly, C.H.; Dam, M.; Danielsson, H.O.; Dannheim, D.; Dao, V.; Darbo, G.; Darlea, G.L.; Davey, W.; Davidek, T.; Davidson, N.; Davidson, R.; Davies, M.; Davison, A.R.; Dawson, I.; Daya, R.K.; De, K.; de Asmundis, R.; De Castro, S.; De Castro Faria Salgado, P.E.; De Cecco, S.; de Graat, J.; De Groot, N.; de Jong, P.; De Mora, L.; De Oliveira Branco, M.; De Pedis, D.; De Salvo, A.; De Sanctis, U.; De Santo, A.; De Vivie De Regie, J.B.; De Zorzi, G.; Dean, S.; Dedovich, D.V.; Degenhardt, J.; Dehchar, M.; Del Papa, C.; Del Peso, J.; Del Prete, T.; Dell'Acqua, A.; Dell'Asta, L.; Della Pietra, M.; della Volpe, D.; Delmastro, M.; Delsart, P.A.; Deluca, C.; Demers, S.; Demichev, M.; Demirkoz, B.; Deng, J.; Deng, W.; Denisov, S.P.; Derkaoui, J.E.; Derue, F.; Dervan, P.; Desch, K.; Deviveiros, P.O.; Dewhurst, A.; DeWilde, B.; Dhaliwal, S.; Dhullipudi, R.; Di Ciaccio, A.; Di Ciaccio, L.; Di Domenico, A.; Di Girolamo, A.; Di Girolamo, B.; Di Luise, S.; Di Mattia, A.; Di Nardo, R.; Di Simone, A.; Di Sipio, R.; Diaz, M.A.; Diblen, F.; Diehl, E.B.; Dietrich, J.; Dietzsch, T.A.; Diglio, S.; Dindar Yagci, K.; Dingfelder, J.; Dionisi, C.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djilkibaev, R.; Djobava, T.; do Vale, M.A.B.; Do Valle Wemans, A.; Doan, T.K.O.; Dobos, D.; Dobson, E.; Dobson, M.; Doglioni, C.; Doherty, T.; Dolejsi, J.; Dolenc, I.; Dolezal, Z.; Dolgoshein, B.A.; Dohmae, T.; Donega, M.; Donini, J.; Dopke, J.; Doria, A.; Dos Anjos, A.; Dotti, A.; Dova, M.T.; Doxiadis, A.; Doyle, A.T.; Drasal, Z.; Dris, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Dudarev, A.; Dudziak, F.; Duhrssen, M.; Duflot, L.; Dufour, M-A.; Dunford, M.; Duran Yildiz, H.; Dushkin, A.; Duxfield, R.; Dwuznik, M.; Duren, M.; Ebenstein, W.L.; Ebke, J.; Eckweiler, S.; Edmonds, K.; Edwards, C.A.; Egorov, K.; Ehrenfeld, W.; Ehrich, T.; Eifert, T.; Eigen, G.; Einsweiler, K.; Eisenhandler, E.; Ekelof, T.; El Kacimi, M.; Ellert, M.; Elles, S.; Ellinghaus, F.; Ellis, K.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Engelmann, R.; Engl, A.; Epp, B.; Eppig, A.; Erdmann, J.; Ereditato, A.; Eriksson, D.; Ermoline, I.; Ernst, J.; Ernst, M.; Ernwein, J.; Errede, D.; Errede, S.; Ertel, E.; Escalier, M.; Escobar, C.; Espinal Curull, X.; Esposito, B.; Etienvre, A.I.; Etzion, E.; Evans, H.; Fabbri, L.; Fabre, C.; Facius, K.; Fakhrutdinov, R.M.; Falciano, S.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farley, J.; Farooque, T.; Farrington, S.M.; Farthouat, P.; Fassnacht, P.; Fassouliotis, D.; Fatholahzadeh, B.; Fayard, L.; Fayette, F.; Febbraro, R.; Federic, P.; Fedin, O.L.; Fedorko, W.; Feligioni, L.; Felzmann, C.U.; Feng, C.; Feng, E.J.; Fenyuk, A.B.; Ferencei, J.; Ferland, J.; Fernandes, B.; Fernando, W.; Ferrag, S.; Ferrando, J.; Ferrara, V.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferrer, A.; Ferrer, M.L.; Ferrere, D.; Ferretti, C.; Fiascaris, M.; Fiedler, F.; Filipcic, A.; Filippas, A.; Filthaut, F.; Fincke-Keeler, M.; Fiolhais, M.C.N.; Fiorini, L.; Firan, A.; Fischer, G.; Fisher, M.J.; Flechl, M.; Fleck, I.; Fleckner, J.; Fleischmann, P.; Fleischmann, S.; Flick, T.; Flores Castillo, L.R.; Flowerdew, M.J.; Fonseca Martin, T.; Formica, A.; Forti, A.; Fortin, D.; Fournier, D.; Fowler, A.J.; Fowler, K.; Fox, H.; Francavilla, P.; Franchino, S.; Francis, D.; Franklin, M.; Franz, S.; Fraternali, M.; Fratina, S.; Freestone, J.; French, S.T.; Froeschl, R.; Froidevaux, D.; Frost, J.A.; Fukunaga, C.; Fullana Torregrosa, E.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gadfort, T.; Gadomski, S.; Gagliardi, G.; Gagnon, P.; Galea, C.; Gallas, E.J.; Gallo, V.; Gallop, B.J.; Gallus, P.; Galyaev, E.; Gan, K.K.; Gao, Y.S.; Gaponenko, A.; Garcia-Sciveres, M.; Garcia, C.; Garcia Navarro, J.E.; Gardner, R.W.; Garelli, N.; Garitaonandia, H.; Garonne, V.; Gatti, C.; Gaudio, G.; Gautard, V.; Gauzzi, P.; Gavrilenko, I.L.; Gay, C.; Gaycken, G.; Gazis, E.N.; Ge, P.; Gee, C.N.P.; Geich-Gimbel, Ch.; Gellerstedt, K.; Gemme, C.; Genest, M.H.; Gentile, S.; Georgatos, F.; George, S.; Gershon, A.; Ghazlane, H.; Ghodbane, N.; Giacobbe, B.; Giagu, S.; Giakoumopoulou, V.; Giangiobbe, V.; Gianotti, F.; Gibbard, B.; Gibson, A.; Gibson, S.M.; Gilbert, L.M.; Gilchriese, M.; Gilewsky, V.; Gingrich, D.M.; Ginzburg, J.; Giokaris, N.; Giordani, M.P.; Giordano, R.; Giorgi, F.M.; Giovannini, P.; Giraud, P.F.; Girtler, P.; Giugni, D.; Giusti, P.; Gjelsten, B.K.; Gladilin, L.K.; Glasman, C.; Glazov, A.; Glitza, K.W.; Glonti, G.L.; Godfrey, J.; Godlewski, J.; Goebel, M.; Gopfert, T.; Goeringer, C.; Gossling, C.; Gottfert, T.; Goggi, V.; Goldfarb, S.; Goldin, D.; Golling, T.; Gomes, A.; Gomez Fajardo, L.S.; Goncalo, R.; Gonella, L.; Gong, C.; Gonzalez de la Hoz, S.; Gonzalez Silva, M.L.; Gonzalez-Sevilla, S.; Goodson, J.J.; Goossens, L.; Gordon, H.A.; Gorelov, I.; Gorfine, G.; Gorini, B.; Gorini, E.; Gorisek, A.; Gornicki, E.; Gosdzik, B.; Gosselink, M.; Gostkin, M.I.; Gough Eschrich, I.; Gouighri, M.; Goujdami, D.; Goulette, M.P.; Goussiou, A.G.; Goy, C.; Grabowska-Bold, I.; Grafstrom, P.; Grahn, K-J.; Grancagnolo, S.; Grassi, V.; Gratchev, V.; Grau, N.; Gray, H.M.; Gray, J.A.; Graziani, E.; Green, B.; Greenshaw, T.; Greenwood, Z.D.; Gregor, I.M.; Grenier, P.; Griesmayer, E.; Griffiths, J.; Grigalashvili, N.; Grillo, A.A.; Grimm, K.; Grinstein, S.; Grishkevich, Y.V.; Groh, M.; Groll, M.; Gross, E.; Grosse-Knetter, J.; Groth-Jensen, J.; Grybel, K.; Guicheney, C.; Guida, A.; Guillemin, T.; Guler, H.; Gunther, J.; Guo, B.; Gupta, A.; Gusakov, Y.; Gutierrez, A.; Gutierrez, P.; Guttman, N.; Gutzwiller, O.; Guyot, C.; Gwenlan, C.; Gwilliam, C.B.; Haas, A.; Haas, S.; Haber, C.; Hadavand, H.K.; Hadley, D.R.; Haefner, P.; Hartel, R.; Hajduk, Z.; Hakobyan, H.; Haller, J.; Hamacher, K.; Hamilton, A.; Hamilton, S.; Han, L.; Hanagaki, K.; Hance, M.; Handel, C.; Hanke, P.; Hansen, J.R.; Hansen, J.B.; Hansen, J.D.; Hansen, P.H.; Hansl-Kozanecka, T.; Hansson, P.; Hara, K.; Hare, G.A.; Harenberg, T.; Harrington, R.D.; Harris, O.M.; Harrison, K; Hartert, J.; Hartjes, F.; Harvey, A.; Hasegawa, S.; Hasegawa, Y.; Hashemi, K.; Hassani, S.; Haug, S.; Hauschild, M.; Hauser, R.; Havranek, M.; Hawkes, C.M.; Hawkings, R.J.; Hayakawa, T.; Hayward, H.S.; Haywood, S.J.; Head, S.J.; Hedberg, V.; Heelan, L.; Heim, S.; Heinemann, B.; Heisterkamp, S.; Helary, L.; Heller, M.; Hellman, S.; Helsens, C.; Hemperek, T.; Henderson, R.C.W.; Henke, M.; Henrichs, A.; Henriques Correia, A.M.; Henrot-Versille, S.; Hensel, C.; Henss, T.; Hernandez Jimenez, Y.; Hershenhorn, A.D.; Herten, G.; Hertenberger, R.; Hervas, L.; Hessey, N.P.; Higon-Rodriguez, E.; Hill, J.C.; Hiller, K.H.; Hillert, S.; Hillier, S.J.; Hinchliffe, I.; Hines, E.; Hirose, M.; Hirsch, F.; Hirschbuehl, D.; Hobbs, J.; Hod, N.; Hodgkinson, M.C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M.R.; Hoffman, J.; Hoffmann, D.; Hohlfeld, M.; Holy, T.; Holzbauer, J.L.; Homma, Y.; Horazdovsky, T.; Hori, T.; Horn, C.; Horner, S.; Horvat, S.; Hostachy, J-Y.; Hou, S.; Hoummada, A.; Howe, T.; Hrivnac, J.; Hryn'ova, T.; Hsu, P.J.; Hsu, S.C.; Huang, G.S.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Hughes, E.W.; Hughes, G.; Hurwitz, M.; Husemann, U.; Huseynov, N.; Huston, J.; Huth, J.; Iacobucci, G.; Iakovidis, G.; Ibragimov, I.; Iconomidou-Fayard, L.; Idarraga, J.; Iengo, P.; Igonkina, O.; Ikegami, Y.; Ikeno, M.; Ilchenko, Y.; Iliadis, D.; Ince, T.; Ioannou, P.; Iodice, M.; Irles Quiles, A.; Ishikawa, A.; Ishino, M.; Ishmukhametov, R.; Isobe, T.; Issakov, V.; Issever, C.; Istin, S.; Itoh, Y.; Ivashin, A.V.; Iwanski, W.; Iwasaki, H.; Izen, J.M.; Izzo, V.; Jackson, B.; Jackson, J.N.; Jackson, P.; Jaekel, M.R.; Jain, V.; Jakobs, K.; Jakobsen, S.; Jakubek, J.; Jana, D.K.; Jansen, E.; Jantsch, A.; Janus, M.; Jared, R.C.; Jarlskog, G.; Jeanty, L.; Jen-La Plante, I.; Jenni, P.; Jez, P.; Jezequel, S.; Ji, W.; Jia, J.; Jiang, Y.; Jimenez Belenguer, M.; Jin, S.; Jinnouchi, O.; Joffe, D.; Johansen, M.; Johansson, K.E.; Johansson, P.; Johnert, S; Johns, K.A.; Jon-And, K.; Jones, G.; Jones, R.W.L.; Jones, T.J.; Jorge, P.M.; Joseph, J.; Juranek, V.; Jussel, P.; Kabachenko, V.V.; Kaci, M.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kaiser, S.; Kajomovitz, E.; Kalinin, S.; Kalinovskaya, L.V.; Kalinowski, A.; Kama, S.; Kanaya, N.; Kaneda, M.; Kantserov, V.A.; Kanzaki, J.; Kaplan, B.; Kapliy, A.; Kaplon, J.; Kar, D.; Karagounis, M.; Karagoz Unel, M.; Kartvelishvili, V.; Karyukhin, A.N.; Kashif, L.; Kasmi, A.; Kass, R.D.; Kastanas, A.; Kastoryano, M.; Kataoka, M.; Kataoka, Y.; Katsoufis, E.; Katzy, J.; Kaushik, V.; Kawagoe, K.; Kawamoto, T.; Kawamura, G.; Kayl, M.S.; Kayumov, F.; Kazanin, V.A.; Kazarinov, M.Y.; Keates, J.R.; Keeler, R.; Keener, P.T.; Kehoe, R.; Keil, M.; Kekelidze, G.D.; Kelly, M.; Kenyon, M.; Kepka, O.; Kerschen, N.; Kersevan, B.P.; Kersten, S.; Kessoku, K.; Khakzad, M.; Khalil-zada, F.; Khandanyan, H.; Khanov, A.; Kharchenko, D.; Khodinov, A.; Khomich, A.; Khoriauli, G.; Khovanskiy, N.; Khovanskiy, V.; Khramov, E.; Khubua, J.; Kim, H.; Kim, M.S.; Kim, P.C.; Kim, S.H.; Kind, O.; Kind, P.; King, B.T.; Kirk, J.; Kirsch, G.P.; Kirsch, L.E.; Kiryunin, A.E.; Kisielewska, D.; Kittelmann, T.; Kiyamura, H.; Kladiva, E.; Klein, M.; Klein, U.; Kleinknecht, K.; Klemetti, M.; Klier, A.; Klimentov, A.; Klingenberg, R.; Klinkby, E.B.; Klioutchnikova, T.; Klok, P.F.; Klous, S.; Kluge, E.E.; Kluge, T.; Kluit, P.; Klute, M.; Kluth, S.; Knecht, N.S.; Kneringer, E.; Ko, B.R.; Kobayashi, T.; Kobel, M.; Koblitz, B.; Kocian, M.; Kocnar, A.; Kodys, P.; Koneke, K.; Konig, A.C.; Koenig, S.; Kopke, L.; Koetsveld, F.; Koevesarki, P.; Koffas, T.; Koffeman, E.; Kohn, F.; Kohout, Z.; Kohriki, T.; Kolanoski, H.; Kolesnikov, V.; Koletsou, I.; Koll, J.; Kollar, D.; Kolos, S.; Kolya, S.D.; Komar, A.A.; Komaragiri, J.R.; Kondo, T.; Kono, T.; Konoplich, R.; Konovalov, S.P.; Konstantinidis, N.; Koperny, S.; Korcyl, K.; Kordas, K.; Korn, A.; Korolkov, I.; Korolkova, E.V.; Korotkov, V.A.; Kortner, O.; Kostka, P.; Kostyukhin, V.V.; Kotov, S.; Kotov, V.M.; Kotov, K.Y.; Kourkoumelis, C.; Koutsman, A.; Kowalewski, R.; Kowalski, H.; Kowalski, T.Z.; Kozanecki, W.; Kozhin, A.S.; Kral, V.; Kramarenko, V.A.; Kramberger, G.; Krasny, M.W.; Krasznahorkay, A.; Kreisel, A.; Krejci, F.; Kretzschmar, J.; Krieger, N.; Krieger, P.; Kroeninger, K.; Kroha, H.; Kroll, J.; Kroseberg, J.; Krstic, J.; Kruchonak, U.; Kruger, H.; Krumshteyn, Z.V.; Kubota, T.; Kuehn, S.; Kugel, A.; Kuhl, T.; Kuhn, D.; Kukhtin, V.; Kulchitsky, Y.; Kuleshov, S.; Kummer, C.; Kuna, M.; Kunkle, J.; Kupco, A.; Kurashige, H.; Kurata, M.; Kurchaninov, L.L.; Kurochkin, Y.A.; Kus, V.; Kwee, R.; La Rotonda, L.; Labbe, J.; Lacasta, C.; Lacava, F.; Lacker, H.; Lacour, D.; Lacuesta, V.R.; Ladygin, E.; Lafaye, R.; Laforge, B.; Lagouri, T.; Lai, S.; Lamanna, M.; Lampen, C.L.; Lampl, W.; Lancon, E.; Landgraf, U.; Landon, M.P.J.; Lane, J.L.; Lankford, A.J.; Lanni, F.; Lantzsch, K.; Lanza, A.; Laplace, S.; Lapoire, C.; Laporte, J.F.; Lari, T.; Larner, A.; Lassnig, M.; Laurelli, P.; Lavrijsen, W.; Laycock, P.; Lazarev, A.B.; Lazzaro, A.; Le Dortz, O.; Le Guirriec, E.; Le Menedeu, E.; Le Vine, M.; Lebedev, A.; Lebel, C.; LeCompte, T.; Ledroit-Guillon, F.; Lee, H.; Lee, J.S.H.; Lee, S.C.; Lefebvre, M.; Legendre, M.; LeGeyt, B.C.; Legger, F.; Leggett, C.; Lehmacher, M.; Lehmann Miotto, G.; Lei, X.; Leitner, R.; Lellouch, D.; Lellouch, J.; Lendermann, V.; Leney, K.J.C.; Lenz, T.; Lenzen, G.; Lenzi, B.; Leonhardt, K.; Leroy, C.; Lessard, J-R.; Lester, C.G.; Leung Fook Cheong, A.; Leveque, J.; Levin, D.; Levinson, L.J.; Leyton, M.; Li, H.; Li, S.; Li, X.; Liang, Z.; Liang, Z.; Liberti, B.; Lichard, P.; Lichtnecker, M.; Lie, K.; Liebig, W.; Lilley, J.N.; Lim, H.; Limosani, A.; Limper, M.; Lin, S.C.; Linnemann, J.T.; Lipeles, E.; Lipinsky, L.; Lipniacka, A.; Liss, T.M.; Lissauer, D.; Lister, A.; Litke, A.M.; Liu, C.; Liu, D.; Liu, H.; Liu, J.B.; Liu, M.; Liu, T.; Liu, Y.; Livan, M.; Lleres, A.; Lloyd, S.L.; Lobodzinska, E.; Loch, P.; Lockman, W.S.; Lockwitz, S.; Loddenkoetter, T.; Loebinger, F.K.; Loginov, A.; Loh, C.W.; Lohse, T.; Lohwasser, K.; Lokajicek, M.; Long, R.E.; Lopes, L.; Lopez Mateos, D.; Losada, M.; Loscutoff, P.; Lou, X.; Lounis, A.; Loureiro, K.F.; Lovas, L.; Love, J.; Love, P.A.; Lowe, A.J.; Lu, F.; Lubatti, H.J.; Luci, C.; Lucotte, A.; Ludwig, A.; Ludwig, D.; Ludwig, I.; Luehring, F.; Luisa, L.; Lumb, D.; Luminari, L.; Lund, E.; Lund-Jensen, B.; Lundberg, B.; Lundberg, J.; Lundquist, J.; Lynn, D.; Lys, J.; Lytken, E.; Ma, H.; Ma, L.L.; Macana Goia, J.A.; Maccarrone, G.; Macchiolo, A.; Macek, B.; Machado Miguens, J.; Mackeprang, R.; Madaras, R.J.; Mader, W.F.; Maenner, R.; Maeno, T.; Mattig, P.; Mattig, S.; Magalhaes Martins, P.J.; Magradze, E.; Mahalalel, Y.; Mahboubi, K.; Mahmood, A.; Maiani, C.; Maidantchik, C.; Maio, A.; Majewski, S.; Makida, Y.; Makouski, M.; Makovec, N.; Malecki, Pa.; Malecki, P.; Maleev, V.P.; Malek, F.; Mallik, U.; Malon, D.; Maltezos, S.; Malyshev, V.; Malyukov, S.; Mambelli, M.; Mameghani, R.; Mamuzic, J.; Mandelli, L.; Mandic, I.; Mandrysch, R.; Maneira, J.; Mangeard, P.S.; Manjavidze, I.D.; Manning, P.M.; Manousakis-Katsikakis, A.; Mansoulie, B.; Mapelli, A.; Mapelli, L.; March, L.; Marchand, J.F.; Marchese, F.; Marchiori, G.; Marcisovsky, M.; Marino, C.P.; Marroquim, F.; Marshall, Z.; Marti-Garcia, S.; Martin, A.J.; Martin, A.J.; Martin, B.; Martin, B.; Martin, F.F.; Martin, J.P.; Martin, T.A.; Martin dit Latour, B.; Martinez, M.; Martinez Outschoorn, V.; Martini, A.; Martyniuk, A.C.; Marzano, F.; Marzin, A.; Masetti, L.; Mashimo, T.; Mashinistov, R.; Masik, J.; Maslennikov, A.L.; Massa, I.; Massol, N.; Mastroberardino, A.; Masubuchi, T.; Matricon, P.; Matsunaga, H.; Matsushita, T.; Mattravers, C.; Maxfield, S.J.; Mayne, A.; Mazini, R.; Mazur, M.; Mazzanti, M.; Mc Donald, J.; Mc Kee, S.P.; McCarn, A.; McCarthy, R.L.; McCubbin, N.A.; McFarlane, K.W.; McGlone, H.; Mchedlidze, G.; McMahon, S.J.; McPherson, R.A.; Meade, A.; Mechnich, J.; Mechtel, M.; Medinnis, M.; Meera-Lebbai, R.; Meguro, T.M.; Mehlhase, S.; Mehta, A.; Meier, K.; Meirose, B.; Melachrinos, C.; Mellado Garcia, B.R.; Mendoza Navas, L.; Meng, Z.; Menke, S.; Meoni, E.; Mermod, P.; Merola, L.; Meroni, C.; Merritt, F.S.; Messina, A.M.; Metcalfe, J.; Mete, A.S.; Meyer, J-P.; Meyer, J.; Meyer, J.; Meyer, T.C.; Meyer, W.T.; Miao, J.; Michal, S.; Micu, L.; Middleton, R.P.; Migas, S.; Mijovic, L.; Mikenberg, G.; Mikestikova, M.; Mikuz, M.; Miller, D.W.; Mills, W.J.; Mills, C.M.; Milov, A.; Milstead, D.A.; Milstein, D.; Minaenko, A.A.; Minano, M.; Minashvili, I.A.; Mincer, A.I.; Mindur, B.; Mineev, M.; Ming, Y.; Mir, L.M.; Mirabelli, G.; Misawa, S.; Miscetti, S.; Misiejuk, A.; Mitrevski, J.; Mitsou, V.A.; Miyagawa, P.S.; Mjornmark, J.U.; Mladenov, D.; Moa, T.; Moed, S.; Moeller, V.; Monig, K.; Moser, N.; Mohr, W.; Mohrdieck-Mock, S.; Moles-Valls, R.; Molina-Perez, J.; Monk, J.; Monnier, E.; Montesano, S.; Monticelli, F.; Moore, R.W.; Mora Herrera, C.; Moraes, A.; Morais, A.; Morel, J.; Morello, G.; Moreno, D.; Moreno Llacer, M.; Morettini, P.; Morii, M.; Morley, A.K.; Mornacchi, G.; Morozov, S.V.; Morris, J.D.; Moser, H.G.; Mosidze, M.; Moss, J.; Mount, R.; Mountricha, E.; Mouraviev, S.V.; Moyse, E.J.W.; Mudrinic, M.; Mueller, F.; Mueller, J.; Mueller, K.; Muller, T.A.; Muenstermann, D.; Muir, A.; Munwes, Y.; Murillo Garcia, R.; Murray, W.J.; Mussche, I.; Musto, E.; Myagkov, A.G.; Myska, M.; Nadal, J.; Nagai, K.; Nagano, K.; Nagasaka, Y.; Nairz, A.M.; Nakamura, K.; Nakano, I.; Nakatsuka, H.; Nanava, G.; Napier, A.; Nash, M.; Nation, N.R.; Nattermann, T.; Naumann, T.; Navarro, G.; Nderitu, S.K.; Neal, H.A.; Nebot, E.; Nechaeva, P.; Negri, A.; Negri, G.; Nelson, A.; Nelson, T.K.; Nemecek, S.; Nemethy, P.; Nepomuceno, A.A.; Nessi, M.; Neubauer, M.S.; Neusiedl, A.; Neves, R.N.; Nevski, P.; Newcomer, F.M.; Nickerson, R.B.; Nicolaidou, R.; Nicolas, L.; Nicoletti, G.; Nicquevert, B.; Niedercorn, F.; Nielsen, J.; Nikiforov, A.; Nikolaev, K.; Nikolic-Audit, I.; Nikolopoulos, K.; Nilsen, H.; Nilsson, P.; Nisati, A.; Nishiyama, T.; Nisius, R.; Nodulman, L.; Nomachi, M.; Nomidis, I.; Nordberg, M.; Nordkvist, B.; Notz, D.; Novakova, J.; Nozaki, M.; Nozicka, M.; Nugent, I.M.; Nuncio-Quiroz, A.E.; Nunes Hanninger, G.; Nunnemann, T.; Nurse, E.; O'Neil, D.C.; O'Shea, V.; Oakham, F.G.; Oberlack, H.; Ochi, A.; Oda, S.; Odaka, S.; Odier, J.; Ogren, H.; Oh, A.; Oh, S.H.; Ohm, C.C.; Ohshima, T.; Ohshita, H.; Ohsugi, T.; Okada, S.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olchevski, A.G.; Oliveira, M.; Oliveira Damazio, D.; Oliver, J.; Oliver Garcia, E.; Olivito, D.; Olszewski, A.; Olszowska, J.; Omachi, C.; Onofre, A.; Onyisi, P.U.E.; Oram, C.J.; Oreglia, M.J.; Oren, Y.; Orestano, D.; Orlov, I.; Oropeza Barrera, C.; Orr, R.S.; Ortega, E.O.; Osculati, B.; Ospanov, R.; Osuna, C.; Ottersbach, J.P; Ould-Saada, F.; Ouraou, A.; Ouyang, Q.; Owen, M.; Owen, S.; Oyarzun, A; Ozcan, V.E.; Ozone, K.; Ozturk, N.; Pacheco Pages, A.; Padilla Aranda, C.; Paganis, E.; Pahl, C.; Paige, F.; Pajchel, K.; Palestini, S.; Pallin, D.; Palma, A.; Palmer, J.D.; Pan, Y.B.; Panagiotopoulou, E.; Panes, B.; Panikashvili, N.; Panitkin, S.; Pantea, D.; Panuskova, M.; Paolone, V.; Papadopoulou, Th.D.; Park, S.J.; Park, W.; Parker, M.A.; Parker, S.I.; Parodi, F.; Parsons, J.A.; Parzefall, U.; Pasqualucci, E.; Passeri, A.; Pastore, F.; Pastore, Fr.; Pasztor, G.; Pataraia, S.; Pater, J.R.; Patricelli, S.; Patwa, A.; Pauly, T.; Peak, L.S.; Pecsy, M.; Pedraza Morales, M.I.; Peleganchuk, S.V.; Peng, H.; Penson, A.; Penwell, J.; Perantoni, M.; Perez, K.; Perez Codina, E.; Perez Garcia-Estan, M.T.; Perez Reale, V.; Perini, L.; Pernegger, H.; Perrino, R.; Persembe, S.; Perus, P.; Peshekhonov, V.D.; Petersen, B.A.; Petersen, T.C.; Petit, E.; Petridou, C.; Petrolo, E.; Petrucci, F.; Petschull, D; Petteni, M.; Pezoa, R.; Phan, A.; Phillips, A.W.; Piacquadio, G.; Piccinini, M.; Piegaia, R.; Pilcher, J.E.; Pilkington, A.D.; Pina, J.; Pinamonti, M.; Pinfold, J.L.; Pinto, B.; Pizio, C.; Placakyte, R.; Plamondon, M.; Pleier, M.A.; Poblaguev, A.; Poddar, S.; Podlyski, F.; Poffenberger, P.; Poggioli, L.; Pohl, M.; Polci, F.; Polesello, G.; Policicchio, A.; Polini, A.; Poll, J.; Polychronakos, V.; Pomeroy, D.; Pommes, K.; Ponsot, P.; Pontecorvo, L.; Pope, B.G.; Popeneciu, G.A.; Popovic, D.S.; Poppleton, A.; Popule, J.; Portell Bueso, X.; Porter, R.; Pospelov, G.E.; Pospisil, S.; Potekhin, M.; Potrap, I.N.; Potter, C.J.; Potter, C.T.; Potter, K.P.; Poulard, G.; Poveda, J.; Prabhu, R.; Pralavorio, P.; Prasad, S.; Pravahan, R.; Pribyl, L.; Price, D.; Price, L.E.; Prichard, P.M.; Prieur, D.; Primavera, M.; Prokofiev, K.; Prokoshin, F.; Protopopescu, S.; Proudfoot, J.; Prudent, X.; Przysiezniak, H.; Psoroulas, S.; Ptacek, E.; Puigdengoles, C.; Purdham, J.; Purohit, M.; Puzo, P.; Pylypchenko, Y.; Qi, M.; Qian, J.; Qian, W.; Qin, Z.; Quadt, A.; Quarrie, D.R.; Quayle, W.B.; Quinonez, F.; Raas, M.; Radeka, V.; Radescu, V.; Radics, B.; Rador, T.; Ragusa, F.; Rahal, G.; Rahimi, A.M.; Rajagopalan, S.; Rammensee, M.; Rammes, M.; Rauscher, F.; Rauter, E.; Raymond, M.; Read, A.L.; Rebuzzi, D.M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reeves, K.; Reinherz-Aronis, E.; Reinsch, A; Reisinger, I.; Reljic, D.; Rembser, C.; Ren, Z.L.; Renkel, P.; Rescia, S.; Rescigno, M.; Resconi, S.; Resende, B.; Reznicek, P.; Rezvani, R.; Richards, A.; Richards, R.A.; Richter, R.; Richter-Was, E.; Ridel, M.; Rijpstra, M.; Rijssenbeek, M.; Rimoldi, A.; Rinaldi, L.; Rios, R.R.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Roa Romero, D.A.; Robertson, S.H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, JEM; Robinson, M.; Robson, A.; Rocha de Lima, J.G.; Roda, C.; Roda Dos Santos, D.; Rodriguez, D.; Rodriguez Garcia, Y.; Roe, S.; Rohne, O.; Rojo, V.; Rolli, S.; Romaniouk, A.; Romanov, V.M.; Romeo, G.; Romero Maltrana, D.; Roos, L.; Ros, E.; Rosati, S.; Rosenbaum, G.A.; Rosselet, L.; Rossetti, V.; Rossi, L.P.; Rotaru, M.; Rothberg, J.; Rousseau, D.; Royon, C.R.; Rozanov, A.; Rozen, Y.; Ruan, X.; Ruckert, B.; Ruckstuhl, N.; Rud, V.I.; Rudolph, G.; Ruhr, F.; Ruggieri, F.; Ruiz-Martinez, A.; Rumyantsev, L.; Rurikova, Z.; Rusakovich, N.A.; Rutherfoord, J.P.; Ruwiedel, C.; Ruzicka, P.; Ryabov, Y.F.; Ryan, P.; Rybkin, G.; Rzaeva, S.; Saavedra, A.F.; Sadrozinski, H.F-W.; Sadykov, R.; Sakamoto, H.; Salamanna, G.; Salamon, A.; Saleem, M.S.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvachua Ferrando, B.M.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sampsonidis, D.; Samset, B.H.; Sandaker, H.; Sander, H.G.; Sanders, M.P.; Sandhoff, M.; Sandhu, P.; Sandstroem, R.; Sandvoss, S.; Sankey, D.P.C.; Sanny, B.; Sansoni, A.; Santamarina Rios, C.; Santoni, C.; Santonico, R.; Saraiva, J.G.; Sarangi, T.; Sarkisyan-Grinbaum, E.; Sarri, F.; Sasaki, O.; Sasao, N.; Satsounkevitch, I.; Sauvage, G.; Savard, P.; Savine, A.Y.; Savinov, V.; Sawyer, L.; Saxon, D.H.; Says, L.P.; Sbarra, C.; Sbrizzi, A.; Scannicchio, D.A.; Schaarschmidt, J.; Schacht, P.; Schafer, U.; Schaetzel, S.; Schaffer, A.C.; Schaile, D.; Schamberger, R.D.; Schamov, A.G.; Schegelsky, V.A.; Scheirich, D.; Schernau, M.; Scherzer, M.I.; Schiavi, C.; Schieck, J.; Schioppa, M.; Schlenker, S.; Schmidt, E.; Schmieden, K.; Schmitt, C.; Schmitz, M.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schreiner, A.; Schroeder, C.; Schroer, N.; Schroers, M.; Schultes, J.; Schultz-Coulon, H.C.; Schumacher, J.W.; Schumacher, M.; Schumm, B.A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schwemling, Ph.; Schwienhorst, R.; Schwierz, R.; Schwindling, J.; Scott, W.G.; Searcy, J.; Sedykh, E.; Segura, E.; Seidel, S.C.; Seiden, A.; Seifert, F.; Seixas, J.M.; Sekhniaidze, G.; Seliverstov, D.M.; Sellden, B.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Seuster, R.; Severini, H.; Sevior, M.E.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L.Y.; Shank, J.T.; Shao, Q.T.; Shapiro, M.; Shatalov, P.B.; Shaw, K.; Sherman, D.; Sherwood, P.; Shibata, A.; Shimojima, M.; Shin, T.; Shmeleva, A.; Shochet, M.J.; Shupe, M.A.; Sicho, P.; Sidoti, A.; Siegert, F; Siegrist, J.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S.B.; Simak, V.; Simic, Lj.; Simion, S.; Simmons, B.; Simonyan, M.; Sinervo, P.; Sinev, N.B.; Sipica, V.; Siragusa, G.; Sisakyan, A.N.; Sivoklokov, S.Yu.; Sjoelin, J.; Sjursen, T.B.; Skovpen, K.; Skubic, P.; Slater, M.; Slavicek, T.; Sliwa, K.; Sloper, J.; Sluka, T.; Smakhtin, V.; Smirnov, S.Yu.; Smirnov, Y.; Smirnova, L.N.; Smirnova, O.; Smith, B.C.; Smith, D.; Smith, K.M.; Smizanska, M.; Smolek, K.; Snesarev, A.A.; Snow, S.W.; Snow, J.; Snuverink, J.; Snyder, S.; Soares, M.; Sobie, R.; Sodomka, J.; Soffer, A.; Solans, C.A.; Solar, M.; Solc, J.; Solfaroli Camillocci, E.; Solodkov, A.A.; Solovyanov, O.V.; Soluk, R.; Sondericker, J.; Sopko, V.; Sopko, B.; Sosebee, M.; Soukharev, A.; Spagnolo, S.; Spano, F.; Spencer, E.; Spighi, R.; Spigo, G.; Spila, F.; Spiwoks, R.; Spousta, M.; Spreitzer, T.; Spurlock, B.; St. Denis, R.D.; Stahl, T.; Stahlman, J.; Stamen, R.; Stancu, S.N.; Stanecka, E.; Stanek, R.W.; Stanescu, C.; Stapnes, S.; Starchenko, E.A.; Stark, J.; Staroba, P.; Starovoitov, P.; Stastny, J.; Stavina, P.; Steele, G.; Steinbach, P.; Steinberg, P.; Stekl, I.; Stelzer, B.; Stelzer, H.J.; Stelzer-Chilton, O.; Stenzel, H.; Stevenson, K.; Stewart, G.A.; Stockton, M.C.; Stoerig, K.; Stoicea, G.; Stonjek, S.; Strachota, P.; Stradling, A.R.; Straessner, A.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strauss, M.; Strizenec, P.; Strohmer, R.; Strom, D.M.; Stroynowski, R.; Strube, J.; Stugu, B.; Soh, D.A.; Su, D.; Sugaya, Y.; Sugimoto, T.; Suhr, C.; Suk, M.; Sulin, V.V.; Sultansoy, S.; Sumida, T.; Sun, X.H.; Sundermann, J.E.; Suruliz, K.; Sushkov, S.; Susinno, G.; Sutton, M.R.; Suzuki, T.; Suzuki, Y.; Sykora, I.; Sykora, T.; Szymocha, T.; Sanchez, J.; Ta, D.; Tackmann, K.; Taffard, A.; Tafirout, R.; Taga, A.; Takahashi, Y.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Talby, M.; Talyshev, A.; Tamsett, M.C.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tapprogge, S.; Tardif, D.; Tarem, S.; Tarrade, F.; Tartarelli, G.F.; Tas, P.; Tasevsky, M.; Tassi, E.; Tatarkhanov, M.; Taylor, C.; Taylor, F.E.; Taylor, G.N.; Taylor, R.P.; Taylor, W.; Teixeira-Dias, P.; Ten Kate, H.; Teng, P.K.; Tennenbaum-Katan, Y.D.; Terada, S.; Terashi, K.; Terron, J.; Terwort, M.; Testa, M.; Teuscher, R.J.; Thioye, M.; Thoma, S.; Thomas, J.P.; Thompson, E.N.; Thompson, P.D.; Thompson, P.D.; Thompson, R.J.; Thompson, A.S.; Thomson, E.; Thun, R.P.; Tic, T.; Tikhomirov, V.O.; Tikhonov, Y.A.; Tipton, P.; Tique Aires Viegas, F.J.; Tisserant, S.; Toczek, B.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokar, S.; Tokushuku, K.; Tollefson, K.; Tomasek, L.; Tomasek, M.; Tomoto, M.; Tompkins, L.; Toms, K.; Tonoyan, A.; Topfel, C.; Topilin, N.D.; Torrence, E.; Torro Pastor, E.; Toth, J.; Touchard, F.; Tovey, D.R.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I.M.; Trincaz-Duvoid, S.; Trinh, T.N.; Tripiana, M.F.; Triplett, N.; Trischuk, W.; Trivedi, A.; Trocme, B.; Troncon, C.; Trzupek, A.; Tsarouchas, C.; Tseng, J.C-L.; Tsiakiris, M.; Tsiareshka, P.V.; Tsionou, D.; Tsipolitis, G.; Tsiskaridze, V.; Tskhadadze, E.G.; Tsukerman, I.I.; Tsulaia, V.; Tsung, J.W.; Tsuno, S.; Tsybychev, D.; Tuggle, J.M.; Turecek, D.; Turk Cakir, I.; Turlay, E.; Tuts, P.M.; Twomey, M.S.; Tylmad, M.; Tyndel, M.; Uchida, K.; Ueda, I.; Ugland, M.; Uhlenbrock, M.; Uhrmacher, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Unno, Y.; Urbaniec, D.; Urkovsky, E.; Urquijo, P.; Urrejola, P.; Usai, G.; Uslenghi, M.; Vacavant, L.; Vacek, V.; Vachon, B.; Vahsen, S.; Valente, P.; Valentinetti, S.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J.A.; Van Berg, R.; van der Graaf, H.; van der Kraaij, E.; van der Poel, E.; van der Ster, D.; van Eldik, N.; van Gemmeren, P.; van Kesteren, Z.; van Vulpen, I.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Vari, R.; Varnes, E.W.; Varouchas, D.; Vartapetian, A.; Varvell, K.E.; Vasilyeva, L.; Vassilakopoulos, V.I.; Vazeille, F.; Vellidis, C.; Veloso, F.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J.C.; Vetterli, M.C.; Vichou, I.; Vickey, T.; Viehhauser, G.H.A.; Villa, M.; Villani, E.G.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M.G.; Vinek, E.; Vinogradov, V.B.; Viret, S.; Virzi, J.; Vitale, A.; Vitells, O.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vlasak, M.; Vlasov, N.; Vogel, A.; Vokac, P.; Volpi, M.; von der Schmitt, H.; von Loeben, J.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorwerk, V.; Vos, M.; Voss, R.; Voss, T.T.; Vossebeld, J.H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vu Anh, T.; Vudragovic, D.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Walbersloh, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Wang, C.; Wang, H.; Wang, J.; Wang, S.M.; Warburton, A.; Ward, C.P.; Warsinsky, M.; Wastie, R.; Watkins, P.M.; Watson, A.T.; Watson, M.F.; Watts, G.; Watts, S.; Waugh, A.T.; Waugh, B.M.; Weber, M.D.; Weber, M.; Weber, M.S.; Weber, P.; Weidberg, A.R.; Weingarten, J.; Weiser, C.; Wellenstein, H.; Wells, P.S.; Wen, M.; Wenaus, T.; Wendler, S.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Werth, M.; Werthenbach, U.; Wessels, M.; Whalen, K.; White, A.; White, M.J.; White, S.; Whitehead, S.R.; Whiteson, D.; Whittington, D.; Wicek, F.; Wicke, D.; Wickens, F.J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik, L.A.M.; Wildauer, A.; Wildt, M.A.; Wilkens, H.G.; Williams, E.; Williams, H.H.; Willocq, S.; Wilson, J.A.; Wilson, M.G.; Wilson, A.; Wingerter-Seez, I.; Winklmeier, F.; Wittgen, M.; Wolter, M.W.; Wolters, H.; Wosiek, B.K.; Wotschack, J.; Woudstra, M.J.; Wraight, K.; Wright, C.; Wright, D.; Wrona, B.; Wu, S.L.; Wu, X.; Wulf, E.; Wynne, B.M.; Xaplanteris, L.; Xella, S.; Xie, S.; Xu, D.; Xu, N.; Yamada, M.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamaoka, J.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, U.K.; Yang, Z.; Yao, W-M.; Yao, Y.; Yasu, Y.; Ye, J.; Ye, S.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Young, C.; Youssef, S.P.; Yu, D.; Yu, J.; Yuan, L.; Yurkewicz, A.; Zaidan, R.; Zaitsev, A.M.; Zajacova, Z.; Zambrano, V.; Zanello, L.; Zaytsev, A.; Zeitnitz, C.; Zeller, M.; Zemla, A.; Zendler, C.; Zenin, O.; Zenis, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; Zevi della Porta, G.; Zhan, Z.; Zhang, H.; Zhang, J.; Zhang, Q.; Zhang, X.; Zhao, L.; Zhao, T.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, N.; Zhou, Y.; Zhu, C.G.; Zhu, H.; Zhu, Y.; Zhuang, X.; Zhuravlov, V.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Ziolkowski, M.; Zivkovic, L.; Zobernig, G.; Zoccoli, A.; zur Nedden, M.; Zutshi, V.

    2010-01-01

    The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.

  12. Atlas of Yellowstone

    Science.gov (United States)

    Pierce, Kenneth L.; Marcus, A. W.; Meachan, J. E.; Rodman, A. W.; Steingisser, A. Y.; Allan, Stuart; West, Ross

    2012-01-01

    Established in 1872, Yellowstone National Park was the world’s first national park. In a fitting tribute to this diverse and beautiful region, the Atlas of Yellowstone is a compelling visual guide to this unique national park and its surrounding area. Ranging from art to wolves, from American Indians to the Yellowstone Volcano, and from geysers to population, each page explains something new about the dynamic forces shaping Yellowstone. Equal parts reference and travel guide, the Atlas of Yellowstone is an unsurpassed resource.

  13. ATLAS-Canada Network

    Energy Technology Data Exchange (ETDEWEB)

    Gable, I; Sobie, R J [HEPnet/Canada, Victoria, BC (Canada); Bedinelli, M; Butterworth, S; Groer, L; Kupchinsky, V [University of Toronto, Toronto, ON (Canada); Caron, B; McDonald, S; Payne, C [TRIUMF Laboratory, Vancouver, BC (Canada); Chambers, R [University of Alberta, Edmonton, AB (Canada); Fitzgerald, B [University of Victoria, Victoria, BC (Canada); Hatem, R; Marshall, P; Pobric, D [CANARIE Inc., Ottawa, ON (Canada); Maddalena, P; Mercure, P; Robertson, S; Rochefort, M [McGill University, Montreal, QC (Canada); McWilliam, D [BCNet, Vancouver, BC (Canada); Siegert, M [Simon Fraser University, Burnaby, BC (Canada)], E-mail: igable@uvic.ca (and others)

    2008-12-15

    The ATLAS-Canada computing model consists of a WLCG Tier-1 computing centre located at the TRIUMF Laboratory in Vancouver, Canada, and two distributed Tier-2 computing centres in eastern and western Canadian universities. The TRIUMF Tier-1 is connected to the CERN Tier-0 via a 10G dedicated circuit provided by CANARIE. The Canadian institutions hosting Tier-2 facilities are connected to TRIUMF via 1G lightpaths, and routing between Tier-2s occurs through TRIUMF. This paper discusses the architecture of the ATLAS-Canada network, the challenges of building the network, and the future plans.

  14. LUCID in ATLAS

    CERN Document Server

    Groth-Jensen, J; The ATLAS collaboration

    2009-01-01

    This talk is to be given at the workshop DIFF2010 : Diffractive and electromagnetic processes at the LHC , early January next year. The aim of the talk is to give a overview/status update of the LUCID detector in ATLAS. As such the presentation will be focused on the design and current layout of the detector - with emphasis on the hardware side. The first few slides will be used to give an overview of the location, design and layout LUCID with respect to ATLAS. Afterwards some hardware issues will be address and finally some results from first LHC data will be shown.

  15. ATLAS Forward Proton Detector

    CERN Document Server

    Grieco, Chiara; The ATLAS collaboration

    2018-01-01

    The aim of the ATLAS Forward Proton (AFP) detector system is the measurement of protons scattered diffractively or electromagnetically at very small angles. The full two-arm setup was installed during the 2016/2017 EYETS. This allows measurements of processes with two forward protons: central diffraction, exclusive production, and two-photon processes. In 2017, AFP participated in the ATLAS high-luminosity data taking on the day-by-day basis. In addition, several special runs with reduced luminosity were taken. The poster will present the AFP detectors and the lessons learned from the last year operation and some performance from 2016 and 2017.

  16. The Herschel ATLAS

    Science.gov (United States)

    Eales, S.; Dunne, L.; Clements, D.; Cooray, A.; De Zotti, G.; Dye, S.; Ivison, R.; Jarvis, M.; Lagache, G.; Maddox, S.; hide

    2010-01-01

    The Herschel ATLAS is the largest open-time key project that will be carried out on the Herschel Space Observatory. It will survey 570 sq deg of the extragalactic sky, 4 times larger than all the other Herschel extragalactic surveys combined, in five far-infrared and submillimeter bands. We describe the survey, the complementary multiwavelength data sets that will be combined with the Herschel data, and the six major science programs we are undertaking. Using new models based on a previous submillimeter survey of galaxies, we present predictions of the properties of the ATLAS sources in other wave bands.

  17. Multiple brain atlas database and atlas-based neuroimaging system.

    Science.gov (United States)

    Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

    1997-01-01

    For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

  18. The observer's sky atlas

    CERN Document Server

    Karkoschka, E

    2007-01-01

    This title includes a short introduction to observing, a thorough description of the star charts and tables, a glossary and much more. It is perfect for both the beginner and seasoned observer. It is fully revised edition of a best-selling and highly-praised sky atlas.

  19. ATLAS solenoid operates underground

    CERN Multimedia

    2006-01-01

    A new phase for the ATLAS collaboration started with the first operation of a completed sub-system: the Central Solenoid. Teams monitoring the cooling and powering of the ATLAS solenoid in the control room. The solenoid was cooled down to 4.5 K from 17 to 23 May. The first current was established the same evening that the solenoid became cold and superconductive. 'This makes the ATLAS Central Solenoid the very first cold and superconducting magnet to be operated in the LHC underground areas!', said Takahiko Kondo, professor at KEK. Though the current was limited to 1 kA, the cool-down and powering of the solenoid was a major milestone for all of the control, cryogenic, power and vacuum systems-a milestone reached by the hard work and many long evenings invested by various teams from ATLAS, all of CERN's departments and several large and small companies. Since the Central Solenoid and the barrel liquid argon (LAr) calorimeter share the same cryostat vacuum vessel, this achievement was only possible in perfe...

  20. The ATLAS event filter

    CERN Document Server

    Beck, H P; Boissat, C; Davis, R; Duval, P Y; Etienne, F; Fede, E; Francis, D; Green, P; Hemmer, F; Jones, R; MacKinnon, J; Mapelli, Livio P; Meessen, C; Mommsen, R K; Mornacchi, Giuseppe; Nacasch, R; Negri, A; Pinfold, James L; Polesello, G; Qian, Z; Rafflin, C; Scannicchio, D A; Stanescu, C; Touchard, F; Vercesi, V

    1999-01-01

    An overview of the studies for the ATLAS Event Filter is given. The architecture and the high level design of the DAQ-1 prototype is presented. The current status if the prototypes is briefly given. Finally, future plans and milestones are given. (11 refs).

  1. Tema-atlas

    DEFF Research Database (Denmark)

    Jensen, Ole Michael; Olsen, S.

    I dette tema-atlas viser forskere på By og Byg, hvordan registre over befolkning, bygninger og forbrug kan overføres til kort ved hjælp af GIS-teknologi. Atlasset er samtidig en illustration af de muligheder, som tegner sig i kommunerne for at udnytte eksisterende registre i forbindelse med...

  2. Taus at ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Demers, Sarah M. [Yale Univ., New Haven, CT (United States). Dept. of Physics

    2017-12-06

    The grant "Taus at ATLAS" supported the group of Sarah Demers at Yale University over a period of 8.5 months, bridging the time between her Early Career Award and her inclusion on Yale's grant cycle within the Department of Energy's Office of Science. The work supported the functioning of the ATLAS Experiment at CERN's Large Hadron Collider and the analysis of ATLAS data. The work included searching for the Higgs Boson in a particular mode of its production (with a W or Z boson) and decay (to a pair of tau leptons.) This was part of a broad program of characterizing the Higgs boson as we try to understand this recently discovered particle, and whether or not it matches our expectations within the current standard model of particle physics. In addition, group members worked with simulation to understand the physics reach of planned upgrades to the ATLAS experiment. Supported group members include postdoctoral researcher Lotte Thomsen and graduate student Mariel Pettee.

  3. ATLAS Experiment Brochure - French

    CERN Multimedia

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  4. ATLAS Experiment Brochure - Turkish

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  5. ATLAS Experiment Brochure - Hebrew

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  6. ATLAS Experiment Brochure - Italian

    CERN Multimedia

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  7. ATLAS Experiment Brochure - German

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  8. ATLAS Experiment Brochure - Japanese

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  9. ATLAS Experiment Brochure - Portuguese

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  10. ATLAS Experiment Brochure - Czech

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  11. ATLAS Experiment Brochure - Dutch

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  12. ATLAS Experiment Brochure - Romanian

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  13. ATLAS Experiment Brochure - Serbian

    CERN Multimedia

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  14. ATLAS Pixel Detector Upgrade

    CERN Document Server

    Flick, T; The ATLAS collaboration

    2009-01-01

    The first upgrade for higher luminosity at LHC for the ATLAS pixel detector is the insertion of a forth layer, the IBL. The talk gives an overview about what the IBL is and how it will be set up, as well as to give a status of the research and develoment work.

  15. Prime wires for ATLAS

    CERN Multimedia

    2003-01-01

    In an award ceremony on 3 September, ATLAS honoured the French company Axon Cable for its special coaxial cables, which were purpose-built for the Liquid Argon calorimeter modules. Working for CERN since the 1970s, Axon' Cable received the ATLAS supplier award last week for its contribution to the liquid argon calorimeter cables of ATLAS (LAL/Orsay, France and University of Victoria, Canada), started in 1996. Its two sets of minicoaxial cables, called harnesses "A" and "B", are designed to function in the harsh conditions in the liquid argon (at 90 Kelvin or -183°C) and under extreme radiation (up to several Mrads). The cables are mainly used for the readout of the calorimeters, and are connected to the outside world by 114 signal feedthroughs with 1920 channels each. The signal from the detectors is transmitted directly without any amplification, which imposes tight restrictions on the impedance and on the signal propagation time of the cables. Peter Jenni, ATLAS spokesperson, gives the award for best s...

  16. ATLAS Detector Upgrade Prospects

    International Nuclear Information System (INIS)

    Dobre, M

    2017-01-01

    After the successful operation at the centre-of-mass energies of 7 and 8 TeV in 2010-2012, the LHC was ramped up and successfully took data at the centre-of-mass energies of 13 TeV in 2015 and 2016. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, which will deliver of the order of five times the LHC nominal instantaneous luminosity along with luminosity levelling. The ultimate goal is to extend the dataset from about few hundred fb −1 expected for LHC running by the end of 2018 to 3000 fb −1 by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of extensions to larger pseudorapidity, particularly in tracking and muon systems. This report summarizes various improvements to the ATLAS detector required to cope with the anticipated evolution of the LHC luminosity during this decade and the next. A brief overview is also given on physics prospects with a pp centre-of-mass energy of 14 TeV. (paper)

  17. ATLAS Experiment Brochure

    CERN Multimedia

    AUTHOR|(INSPIRE)INSPIRE-00085461

    2016-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  18. ATLAS starts moving in

    CERN Multimedia

    2004-01-01

    The first large active detector component was lowered into the ATLAS cavern on 1 March. It consisted of the 8 modules forming the lower part of the central barrel of the tile hadronic calorimeter. The work of assembling the barrel, which comprises 64 modules, started the following day.

  19. A thermosiphon for ATLAS

    CERN Multimedia

    Rosaria Marraffino

    2013-01-01

    A new thermosiphon cooling system, designed for the ATLAS silicon detectors by CERN’s EN-CV team in collaboration with the experiment, will replace the current system in the next LHC run in 2015. Using the basic properties of density difference and making gravity do the hard work, the thermosiphon promises to be a very reliable solution that will ensure the long-term stability of the whole system.   Former compressor-based cooling system of the ATLAS inner detectors. The system is currently being replaced by the innovative thermosiphon. (Photo courtesy of Olivier Crespo-Lopez). Reliability is the major issue for the present cooling system of the ATLAS silicon detectors. The system was designed 13 years ago using a compressor-based cooling cycle. “The current cooling system uses oil-free compressors to avoid fluid pollution in the delicate parts of the silicon detectors,” says Michele Battistin, EN-CV-PJ section leader and project leader of the ATLAS thermosiphon....

  20. South Baltic Wind Atlas

    DEFF Research Database (Denmark)

    Pena Diaz, Alfredo; Hahmann, Andrea N.; Hasager, Charlotte Bay

    A first version of a wind atlas for the South Baltic Sea has been developed using the WRF mesoscale model and verified by data from tall Danish and German masts. Six different boundary-layer parametrization schemes were evaluated by comparing the WRF results to the observed wind profiles at the m...

  1. Prototype ATLAS straw tracker

    CERN Multimedia

    Laurent Guiraud

    1998-01-01

    This is an early prototype of the straw tracking device for the ATLAS detector at CERN. This detector will be part of the LHC project, scheduled to start operation in 2008. The straw tracker will consist of thousands of gas-filled straws, each containing a wire, allowing the tracks of particles to be followed.

  2. Top Physics at Atlas

    CERN Document Server

    Romano, M; The ATLAS collaboration

    2013-01-01

    This talk is an overview of recent results on top-quark physics obtained by the ATLAS collaboration from the analysis of p-p collisions at 7 and 8 TeV at the Large Hadron Collider. Total and differential top pair cross section, single top cross section and mass measurements are presented.

  3. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    The ATLAS Collaboration has set up a framework to automatically process the rapidly growing dataset and produce performance and physics plots for the most interesting analyses. The system is designed to give fast feedback. The histograms are produced within hours of data reconstruction (2–3 days after data taking).

  4. Genomics technologies to study structural variations in the grapevine genome

    Directory of Open Access Journals (Sweden)

    Cardone Maria Francesca

    2016-01-01

    Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

  5. ATLAS. LHC experiments

    International Nuclear Information System (INIS)

    Anon.

    1995-01-01

    In Greek mythology, Atlas was a Titan who had to hold up the heavens with his hands as a punishment for having taken part in a revolt against the Olympians. For LHC, the ATLAS detector will also have an onerous physics burden to bear, but this is seen as a golden opportunity rather than a punishment. The major physics goal of CERN's LHC proton-proton collider is the quest for the long-awaited£higgs' mechanism which drives the spontaneous symmetry breaking of the electroweak Standard Model picture. The large ATLAS collaboration proposes a large general-purpose detector to exploit the full discovery potential of LHC's proton collisions. LHC will provide proton-proton collision luminosities at the aweinspiring level of 1034 cm2 s~1, with initial running in at 1033. The ATLAS philosophy is to handle as many signatures as possible at all luminosity levels, with the initial running providing more complex possibilities. The ATLAS concept was first presented as a Letter of Intent to the LHC Committee in November 1992. Following initial presentations at the Evian meeting (Towards the LHC Experimental Programme') in March of that year, two ideas for generalpurpose detectors, the ASCOT and EAGLE schemes, merged, with Friedrich Dydak (MPI Munich) and Peter Jenni (CERN) as ATLAS cospokesmen. Since the initial Letter of Intent presentation, the ATLAS design has been optimized and developed, guided by physics performance studies and the LHC-oriented detector R&D programme (April/May, page 3). The overall detector concept is characterized by an inner superconducting solenoid (for inner tracking) and large superconducting air-core toroids outside the calorimetry. This solution avoids constraining the calorimetry while providing a high resolution, large acceptance and robust detector. The outer magnet will extend over a length of 26 metres, with an outer diameter of almost 20 metres. The total weight of the detector is 7,000 tonnes. Fitted with its end

  6. New format for ATLAS e-news

    CERN Multimedia

    Pauline Gagnon

    ATLAS e-news got a new look! As of November 30, 2007, we have a new format for ATLAS e-news. Please go to: http://atlas-service-enews.web.cern.ch/atlas-service-enews/index.html . ATLAS e-news will now be published on a weekly basis. If you are not an ATLAS colaboration member but still want to know how the ATLAS experiment is doing, we will soon have a version of ATLAS e-news intended for the general public. Information will be sent out in due time.

  7. Networks in ATLAS

    Science.gov (United States)

    McKee, Shawn; ATLAS Collaboration

    2017-10-01

    Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks. We will report on a number of networking initiatives in ATLAS including participation in the global perfSONAR network monitoring and measuring efforts of WLCG and OSG, the collaboration with the LHCOPN/LHCONE effort, the integration of network awareness into PanDA, the use of the evolving ATLAS analytics framework to better understand our networks and the changes in our DDM system to allow remote access to data. We will also discuss new efforts underway that are exploring the inclusion and use of software defined networks (SDN) and how ATLAS might benefit from: • Orchestration and optimization of distributed data access and data movement. • Better control of workflows, end to end. • Enabling prioritization of time-critical vs normal tasks • Improvements in the efficiency of resource usage

  8. TU-AB-BRA-11: Evaluation of Fully Automatic Volumetric GBM Segmentation in the TCGA-GBM Dataset: Prognosis and Correlation with VASARI Features

    International Nuclear Information System (INIS)

    Rios Velazquez, E; Meier, R; Dunn, W; Gutman, D; Alexander, B; Wiest, R; Reyes, M; Bauer, S; Aerts, H

    2015-01-01

    Purpose: Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. Methods: MRI sets of 67 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA), including necrosis, edema, contrast enhancing and non-enhancing tumor. Spearman’s correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Results: Auto-segmented sub-volumes showed high agreement with manually delineated volumes (range (r): 0.65 – 0.91). Also showed higher correlation with VASARI features (auto r = 0.35, 0.60 and 0.59; manual r = 0.29, 0.50, 0.43, for contrast-enhancing, necrosis and edema, respectively). The contrast-enhancing volume and post-contrast abnormal volume showed the highest C-index (0.73 and 0.72), comparable to manually defined volumes (p = 0.22 and p = 0.07, respectively). The non-enhancing region defined by BraTumIA showed a significantly higher prognostic value (CI = 0.71) than the edema (CI = 0.60), both of which could not be distinguished by manual delineation. Conclusion: BraTumIA tumor sub-compartments showed higher correlation with VASARI data, and equivalent performance in terms of prognosis compared to manual sub-volumes. This method can enable more reproducible definition and quantification of imaging based biomarkers and has a large potential in high-throughput medical imaging research

  9. TU-AB-BRA-11: Evaluation of Fully Automatic Volumetric GBM Segmentation in the TCGA-GBM Dataset: Prognosis and Correlation with VASARI Features

    Energy Technology Data Exchange (ETDEWEB)

    Rios Velazquez, E [Dana-Farber Cancer Institute | Harvard Medical School, Boston, MA (United States); Meier, R [Institute for Surgical Technology and Biomechanics, Bern, NA (Switzerland); Dunn, W; Gutman, D [Emory University School of Medicine, Atlanta, GA (United States); Alexander, B [Dana- Farber Cancer Institute, Brigham and Womens Hospital, Harvard Medic, Boston, MA (United States); Wiest, R; Reyes, M [Institute for Surgical Technology and Biomechanics, University of Bern, Bern, NA (Switzerland); Bauer, S [Institute for Surgical Technology and Biomechanics, Support Center for Adva, Bern, NA (Switzerland); Aerts, H [Dana-Farber/Brigham Womens Cancer Center, Boston, MA (United States)

    2015-06-15

    Purpose: Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. Methods: MRI sets of 67 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA), including necrosis, edema, contrast enhancing and non-enhancing tumor. Spearman’s correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Results: Auto-segmented sub-volumes showed high agreement with manually delineated volumes (range (r): 0.65 – 0.91). Also showed higher correlation with VASARI features (auto r = 0.35, 0.60 and 0.59; manual r = 0.29, 0.50, 0.43, for contrast-enhancing, necrosis and edema, respectively). The contrast-enhancing volume and post-contrast abnormal volume showed the highest C-index (0.73 and 0.72), comparable to manually defined volumes (p = 0.22 and p = 0.07, respectively). The non-enhancing region defined by BraTumIA showed a significantly higher prognostic value (CI = 0.71) than the edema (CI = 0.60), both of which could not be distinguished by manual delineation. Conclusion: BraTumIA tumor sub-compartments showed higher correlation with VASARI data, and equivalent performance in terms of prognosis compared to manual sub-volumes. This method can enable more reproducible definition and quantification of imaging based biomarkers and has a large potential in high-throughput medical imaging research.

  10. ATLAS B-physics potential

    International Nuclear Information System (INIS)

    Smizanska, M.

    2001-01-01

    Studies since 1993 have demonstrated the ability of ATLAS to pursue a wide B physics program. This document presents the latest performance studies with special stress on lepton identification. B-decays containing several leptons in ATLAS statistically dominate the high-precision measurements. We present new results on physics simulations of CP violation measurements in the B s 0 → J/Ψphi decay and on a novel ATLAS programme on beauty production in central proton-proton collisions of LHC

  11. The ATLAS distributed analysis system

    OpenAIRE

    Legger, F.

    2014-01-01

    In the LHC operations era, analysis of the multi-petabyte ATLAS data sample by globally distributed physicists is a challenging task. To attain the required scale the ATLAS Computing Model was designed around the concept of grid computing, realized in the Worldwide LHC Computing Grid (WLCG), the largest distributed computational resource existing in the sciences. The ATLAS experiment currently stores over 140 PB of data and runs about 140,000 concurrent jobs continuously at WLCG sites. During...

  12. The ATLAS hadronic tau trigger

    International Nuclear Information System (INIS)

    Shamim, Mansoora

    2012-01-01

    The extensive tau physics programs of the ATLAS experiment relies heavily on trigger to select hadronic decays of tau lepton. Such a trigger is implemented in ATLAS to efficiently collect signal events, while keeping the rate of multi-jet background within the allowed bandwidth. This contribution summarizes the performance of the ATLAS hadronic tau trigger system during 2011 data taking period and improvements implemented for the 2012 data collection.

  13. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

    NARCIS (Netherlands)

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

    2018-01-01

    We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations

  14. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

    NARCIS (Netherlands)

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

    2018-01-01

    We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA

  15. Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk

    DEFF Research Database (Denmark)

    Guo, Xingyi; Long, Jirong; Zeng, Chenjie

    2015-01-01

    or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150...

  16. Rare kidney tumor provides insight on metabolic changes

    Science.gov (United States)

    Researchers in The Cancer Genome Atlas (TCGA) Network have uncovered a number of new findings about the biology and development of a rare form of kidney cancer. They found that the disease – chromophobe renal cell carcinoma – stems in part from alteratio

  17. MBAT: A scalable informatics system for unifying digital atlasing workflows

    Directory of Open Access Journals (Sweden)

    Sane Nikhil

    2010-12-01

    Full Text Available Abstract Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context

  18. Taking ATLAS to new heights

    CERN Document Server

    Abha Eli Phoboo, ATLAS experiment

    2013-01-01

    Earlier this month, 51 members of the ATLAS collaboration trekked up to the highest peak in the Atlas Mountains, Mt. Toubkal (4,167m), in North Africa.    The physicists were in Marrakech, Morocco, attending the ATLAS Overview Week (7 - 11 October), which was held for the first time on the African continent. Around 300 members of the collaboration met to discuss the status of the LS1 upgrades and plans for the next run of the LHC. Besides the trek, 42 ATLAS members explored the Saharan sand dunes of Morocco on camels.  Photos courtesy of Patrick Jussel.

  19. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.

    Science.gov (United States)

    Zaslavsky, Ilya; Baldock, Richard A; Boline, Jyl

    2014-01-01

    Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.

  20. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

    Directory of Open Access Journals (Sweden)

    Ilya eZaslavsky

    2014-09-01

    Full Text Available Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today’s data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI. A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS, a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML: XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POIs, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas

  1. The Human Cell Atlas.

    Science.gov (United States)

    Regev, Aviv; Teichmann, Sarah A; Lander, Eric S; Amit, Ido; Benoist, Christophe; Birney, Ewan; Bodenmiller, Bernd; Campbell, Peter; Carninci, Piero; Clatworthy, Menna; Clevers, Hans; Deplancke, Bart; Dunham, Ian; Eberwine, James; Eils, Roland; Enard, Wolfgang; Farmer, Andrew; Fugger, Lars; Göttgens, Berthold; Hacohen, Nir; Haniffa, Muzlifah; Hemberg, Martin; Kim, Seung; Klenerman, Paul; Kriegstein, Arnold; Lein, Ed; Linnarsson, Sten; Lundberg, Emma; Lundeberg, Joakim; Majumder, Partha; Marioni, John C; Merad, Miriam; Mhlanga, Musa; Nawijn, Martijn; Netea, Mihai; Nolan, Garry; Pe'er, Dana; Phillipakis, Anthony; Ponting, Chris P; Quake, Stephen; Reik, Wolf; Rozenblatt-Rosen, Orit; Sanes, Joshua; Satija, Rahul; Schumacher, Ton N; Shalek, Alex; Shapiro, Ehud; Sharma, Padmanee; Shin, Jay W; Stegle, Oliver; Stratton, Michael; Stubbington, Michael J T; Theis, Fabian J; Uhlen, Matthias; van Oudenaarden, Alexander; Wagner, Allon; Watt, Fiona; Weissman, Jonathan; Wold, Barbara; Xavier, Ramnik; Yosef, Nir

    2017-12-05

    The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

  2. ATLAS Upgrade Programme

    CERN Document Server

    Hillier, S J; The ATLAS collaboration

    2012-01-01

    With the already outstanding LHC luminosity performance, and planned LHC upgrades in the upcoming shutdowns, it is expected that within a short time-scale, the general purpose LHC experiments will have to cope with luminosities beyond their original design. In order to maintain detector performance and sensitivity to expected and new physics processes, ATLAS has defined a continuous upgrade programme which foresees staged enhancements during the next 10 years of operation, and then more widespread changes before the transition to the highest luminosities after 2022. This talk will describe several components of the ATLAS upgrade, focusing in particular on the Inner Detector and Trigger. The Inner Detector faces two challenges in the higher luminosity environment: high particle multiplicities and increased radiation dose. These will be addressed in the short term by a new layer of Pixel detectors, and in the long term by a complete replacement. The Trigger faces an increasingly difficult task of distinguishing...

  3. ATLAS IBL operational experience

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00237659; The ATLAS collaboration

    2017-01-01

    The Insertable B-Layer (IBL) is the inner most pixel layer in the ATLAS experiment, which was installed at 3.3 cm radius from the beam axis in 2014 to improve the tracking performance. To cope with the high radiation and hit occupancy due to proximity to the interaction point, a new read-out chip and two different silicon sensor technologies (planar and 3D) have been developed for the IBL. After the long shut-down period over 2013 and 2014, the ATLAS experiment started data-taking in May 2015 for Run-2 of the Large Hadron Collider (LHC). The IBL has been operated successfully since the beginning of Run-2 and shows excellent performance with the low dead module fraction, high data-taking efficiency and improved tracking capability. The experience and challenges in the operation of the IBL is described as well as its performance.

  4. Networks in ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; The ATLAS collaboration

    2016-01-01

    Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks....

  5. Networks in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00260714; The ATLAS collaboration

    2017-01-01

    Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks....

  6. The ATLAS Tau Trigger

    International Nuclear Information System (INIS)

    Rados, Petar Kevin

    2013-06-01

    The tau lepton plays a crucial role in understanding particle physics at the Tera scale. One of the most promising probes of the Higgs boson coupling to fermions is with detector signatures involving taus. In addition, many theories beyond the Standard Model, such as supersymmetry and exotic particles (W' and Z'), predict new physics with large couplings to taus. The ability to trigger on hadronic tau decays is therefore critical to achieving the physics goals of the ATLAS experiment. The higher instantaneous luminosities of proton-proton collisions achieved by the Large Hadron Collider (LHC) in 2012 resulted in a larger probability of overlap (pile-up) between bunch crossings, and so it was critical for ATLAS to have an effective tau trigger strategy. The details of this strategy are summarized in this paper, and the results of the latest performance measurements are presented. (authors)

  7. Analysis Streamlining in ATLAS

    CERN Document Server

    Heinrich, Lukas; The ATLAS collaboration

    2018-01-01

    We present recent work within the ATLAS collaboration centrally provide tools to facilitate analysis management and highly automated container-based analysis execution in order to both enable non-experts to benefit from these best practices as well as the collaboration to track and re-execute analyses indpendently, e.g. during their review phase. Through integration with the ATLAS GLANCE system, users can request a pre-configured, but customizable version control setup, including continuous integration for automated build and testing as well as continuous Linux Container image building for software preservation purposes. As analyses typically require many individual steps, analysis workflow pipelines can then be defined using such images and the yadage workflow description language. The integration into the workflow exection service REANA allows the interactive or automated reproduction of the main analysis results by orchestrating a large number of container jobs using the Kubernetes. For long-term archival,...

  8. Jet physics in ATLAS

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    Measurements of hadronic jets provide tests of strong interactions which are interesting both in their own right and as backgrounds to many New Physics searches. It is also through tests of Quantum Chromodynamics that new physics may be discovered. The extensive dataset recorded with the ATLAS detector throughout the 7 TeV centre-of-mass LHC operation period allows QCD to be probed at distances never reached before. We present a review of selected ATLAS jet performance and physics measurements, together with results from new physics searches using the 2011 dataset. They include studies of the underlying event and fragmentation models, measurements of the inclusive jet, dijet and multijet cross sections, parton density functions, heavy flavours, jet shape, mass and substructure. Searches for new physics in monojet, dijet and photon-jet final states are also presented.

  9. Jet substructure in ATLAS

    CERN Document Server

    Miller, David W

    2011-01-01

    Measurements are presented of the jet invariant mass and substructure in proton-proton collisions at $\\sqrt{s} = 7$ TeV with the ATLAS detector using an integrated luminosity of 37 pb$^{-1}$. These results exercise the tools for distinguishing the signatures of new boosted massive particles in the hadronic final state. Two "fat" jet algorithms are used, along with the filtering jet grooming technique that was pioneered in ATLAS. New jet substructure observables are compared for the first time to data at the LHC. Finally, a sample of candidate boosted top quark events collected in the 2010 data is analyzed in detail for the jet substructure properties of hadronic "top-jets" in the final state. These measurements demonstrate not only our excellent understanding of QCD in a new energy regime but open the path to using complex jet substructure observables in the search for new physics.

  10. Teaching atlas of mammography

    International Nuclear Information System (INIS)

    Tabar, L.; Dean, P.B.

    1985-01-01

    The illustrated case reports in this teaching atlas cover practically the entire range of possible pathological changes and are based on in-patient case material and 80,000 screening documents. The two basic approaches, - detection and analysis of changes -, are taught comprehensively and in great detail. A systematic procedure for analysing the mammographies, in order to detect even the very least changes, and its practical application is explained using mammographies showing unclear findings at first sight. A system of coordinates is presented which allows precise localisation of the changes. Exercises for practising the technique of identifying the pathological changes round up the methodolical chapters. Additional imaging technical enhancements and detail enlargements are of great help in interpreting the findings. The specific approach adopted for this teaching atlas is a 'reverse procedure', which leaves the beaten track and starts with analysing the mammographies and evaluating the radiographic findings, in order to finally derive the diagnosis. (orig./CB) [de

  11. An integrated expression atlas of miRNAs and their promoters in human and mouse

    DEFF Research Database (Denmark)

    de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir

    2017-01-01

    MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libr...

  12. Boosted tops at ATLAS

    CERN Document Server

    Villaplana, M; The ATLAS collaboration

    2011-01-01

    A sample of candidate events for highly boosted top quarks is selected following the standard ATLAS selection for semi-leptonic ttbar events plus a requirement that the invariant mass of the reconstructed ttbar pair is greater than 700 GeV. Event displays are presented for the most promising candidates, as well as quantitative results for observables designed to isolate a boosted top quark signal.

  13. The ATLAS simulation infrastructure

    Czech Academy of Sciences Publication Activity Database

    Aad, G.; Abbott, B.; Abdallah, J.; Bazalová, Magdalena; Böhm, Jan; Chudoba, Jiří; Gallus, Petr; Gunther, Jaroslav; Havránek, Miroslav; Hruška, I.; Jahoda, M.; Juránek, Vojtěch; Kepka, Oldřich; Kupčo, Alexander; Kůs, Vlastimil; Kvasnička, Jiří; Lipinský, L.; Lokajíček, Miloš; Marčišovský, Michal; Mikeštíková, Marcela; Myška, Miroslav; Němeček, Stanislav; Panušková, M.; Popule, Jiří; Růžička, Pavel; Schovancová, Jaroslava; Šícho, Petr; Staroba, Pavel; Šťastný, Jan; Taševský, Marek; Tic, Tomáš; Tomášek, Lukáš; Tomášek, Michal; Valenta, J.; Vrba, Václav

    2010-01-01

    Roč. 70, č. 3 (2010), s. 823-874 ISSN 1434-6044 R&D Projects: GA MŠk LC527; GA MŠk LA08015; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : ATLAS * simulation Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 3.248, year: 2010 http://arxiv.org/pdf/1005.4568

  14. The atlas detector

    International Nuclear Information System (INIS)

    Perrodo, P.

    2001-01-01

    The ATLAS detector, one of the two multi-purpose detectors at the Large Hadron Collider at CERN, is currently being built in order to meet the first proton-proton collisions in time. A description of the detector components will be given, corresponding to the most up to date design and status of construction, completed with test beam results and performances of the first serial modules. (author)

  15. Exotics searches in ATLAS

    CERN Document Server

    Wang, Renjie; The ATLAS collaboration

    2017-01-01

    Many theories beyond the Standard Model predict new physics accessible by the LHC. The ATLAS experiment all have rigorous search programs ongoing with the aim to find indications for new physics involving state of the art analysis techniques. This talk reports on new results obtained using the pp collision data sample collected in 2015 and 2016 at the LHC with a centre-of-mass energy of 13 TeV.

  16. Higgs results from ATLAS

    International Nuclear Information System (INIS)

    Chen, Xin

    2016-01-01

    The updated Higgs measurements in various search channels with ATLAS Run 1 data are reviewed. Both the Standard Model (SM) Higgs results, such as H → γγ, ZZ, WW, ττ, μμ, bb-bar, and Beyond Standard Model (BSM) results, such as the charged Higgs, Higgs invisible decay and tensor couplings, are summarized. Prospects for future Higgs searches are briefly discussed

  17. The ATLAS TRT electronics

    OpenAIRE

    Çetin, Serkant Ali; ATLAS Collaboration

    2008-01-01

    The ATLAS inner detector consists of three sub-systems: the pixel detector spanning the radius range 4cm-20cm, the semiconductor tracker at radii from 30 to 52 cm, and the transition radiation tracker (TRT), tracking from 56 to 107 cm. The TRT provides a combination of continuous tracking with many projective measurements based on individual drift tubes (or straws) and of electron identification based on transition radiation from fibres or foils interleaved between the straws themselves. This...

  18. The ATLAS Analysis Architecture

    International Nuclear Information System (INIS)

    Cranmer, K.S.

    2008-01-01

    We present an overview of the ATLAS analysis architecture including the relevant aspects of the computing model and the major architectural aspects of the Athena framework. Emphasis will be given to the interplay between the analysis use cases and the technical aspects of the architecture including the design of the event data model, transient-persistent separation, data reduction strategies, analysis tools, and ROOT interoperability

  19. Atlas de fitoplancton marino.

    OpenAIRE

    Amaya, Oscar; Alvarado, Yaneth; Chávez, Isaias; Ruíz, Gerrado; Lopez, Douglas

    2014-01-01

    En El Salvador existe un fenómeno natural que afecta a las costas marítimas que son los fitoplancton; mediante el cual se expone el Atlas de fitoplancton marino que contiene 100 p. con imágenes, mapas, etc., con el fin de dar a conocer más de 200 especies de fitoplancton identificada hasta el momento, algunos son tóxicas, inocuas y nocivas.

  20. ATLAS Detector Upgrade Prospects

    CERN Document Server

    Dobre, Monica; The ATLAS collaboration

    2016-01-01

    After the successful operation at the center-of-mass energies of 7 and 8 TeV in 2010 - 2012, the LHC is ramped up and successfully took data at the center-of-mass energies of 13 TeV in 2015. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity leveling. The ultimate goal is to extend the dataset from about few hundred fb−1 expected for LHC running to 3000 fb−1 by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of extens...

  1. ATLAS detector upgrade prospects

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00184940; The ATLAS collaboration

    2017-01-01

    After the successful operation at the centre-of-mass energies of 7 and 8 TeV in 2010-2012, the LHC is ramped up and successfully took data at the centre-of-mass energies of 13 TeV in 2015. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity levelling. The ultimate goal is to extend the dataset from about few hundred fb$^{-1}$ expected for LHC running to 3000 fb $^{-1}$ by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of ...

  2. ATLAS Upgrade Plans

    CERN Document Server

    Hopkins, W; The ATLAS collaboration

    2014-01-01

    After the successful LHC operation at the center-of-mass energies of 7 and 8 TeV in 2010-2012, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity leveling. The final goal is to extend the dataset from about few hundred fb−1 expected for LHC running to 3000/fb by around 2035 for ATLAS and CMS. In parallel, the experiments need to be keep lockstep with the accelerator to accommodate running beyond the nominal luminosity this decade. Current planning in ATLAS envisions significant upgrades to the detector during the consolidation of the LHC to reach full LHC energy and further upgrades. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new...

  3. ATLAS Job Transforms

    CERN Document Server

    Stewart, G A; The ATLAS collaboration; Maddocks, H J; Harenberg, T; Sandhoff, M; Sarrazin, B

    2013-01-01

    The need to run complex workflows for a high energy physics experiment such as ATLAS has always been present. However, as computing resources have become even more constrained, compared to the wealth of data generated by the LHC, the need to use resources efficiently and manage complex workflows within a single grid job have increased. In ATLAS, a new Job Transform framework has been developed that we describe in this paper. This framework manages the multiple execution steps needed to `transform' one data type into another (e.g., RAW data to ESD to AOD to final ntuple) and also provides a consistent interface for the ATLAS production system. The new framework uses a data driven workflow definition which is both easy to manage and powerful. After a transform is defined, jobs are expressed simply by specifying the input data and the desired output data. The transform infrastructure then executes only the necessary substeps to produce the final data products. The global execution cost of running the job is mini...

  4. ATLAS Job Transforms

    CERN Document Server

    Stewart, G A; The ATLAS collaboration; Maddocks, H J; Harenberg, T; Sandhoff, M; Sarrazin, B

    2013-01-01

    The need to run complex workflows for a high energy physics experiment such as ATLAS has always been present. However, as computing resources have become even more constrained, compared to the wealth of data generated by the LHC, the need to use resources efficiently and manage complex workflows within a single grid job have increased. In ATLAS, a new Job Transform framework has been developed that we describe in this paper. This framework manages the multiple execution steps needed to 'transform' one data type into another (e.g., RAW data to ESD to AOD to final ntuple) and also provides a consistent interface for the ATLAS production system. The new framework uses a data driven workflow definition which is both easy to manage and powerful. After a transform is defined, jobs are expressed simply by specifying the input data and the desired output data. The transform infrastructure then executes only the necessary substeps to produce the final data products. The global execution cost of running the job is mini...

  5. ATLAS overview week highlights

    CERN Multimedia

    D. Froidevaux

    2005-01-01

    A warm and early October afternoon saw the beginning of the 2005 ATLAS overview week, which took place Rue de La Montagne Sainte-Geneviève in the heart of the Quartier Latin in Paris. All visitors had been warned many times by the ATLAS management and the organisers that the premises would be the subject of strict security clearance because of the "plan Vigipirate", which remains at some level of alert in all public buildings across France. The public building in question is now part of the Ministère de La Recherche, but used to host one of the so-called French "Grandes Ecoles", called l'Ecole Polytechnique (in France there is only one Ecole Polytechnique, whereas there are two in Switzerland) until the end of the seventies, a little while after it opened its doors also to women. In fact, the setting chosen for this ATLAS overview week by our hosts from LPNHE Paris has turned out to be ideal and the security was never an ordeal. For those seeing Paris for the first time, there we...

  6. Clean tracks for ATLAS

    CERN Multimedia

    2006-01-01

    First cosmic ray tracks in the integrated ATLAS barrel SCT and TRT tracking detectors. A snap-shot of a cosmic ray event seen in the different layers of both the SCT and TRT detectors. The ATLAS Inner Detector Integration Team celebrated a major success recently, when clean tracks of cosmic rays were detected in the completed semiconductor tracker (SCT) and transition radiation tracker (TRT) barrels. These tracking tests come just months after the successful insertion of the SCT into the TRT (See Bulletin 09/2006). The cosmic ray test is important for the experiment because, after 15 years of hard work, it is the last test performed on the fully assembled barrel before lowering it into the ATLAS cavern. The two trackers work together to provide millions of channels so that particles' tracks can be identified and measured with great accuracy. According to the team, the preliminary results were very encouraging. After first checks of noise levels in the final detectors, a critical goal was to study their re...

  7. ATLAS Silicon Microstrip Tracker

    CERN Document Server

    Haefner, Petra; The ATLAS collaboration

    2010-01-01

    The SemiConductor Tracker (SCT), made up from silicon micro-strip detectors is the key precision tracking device in ATLAS, one of the experiments at CERN LHC. The completed SCT is in very good shape: 99.3% of the SCT strips are operational, noise occupancy and hit efficiency exceed the design specifications. In the talk the current status of the SCT will be reviewed. We will report on the operation of the detector and observed problems, with stress on the sensor and electronics performance. TWEPP Summary In December 2009 the ATLAS experiment at the CERN Large Hadron Collider (LHC) recorded the first proton- proton collisions at a centre-of-mass energy of 900 GeV and this was followed by the unprecedented energy of 7 TeV in March 2010. The SemiConductor Tracker (SCT) is the key precision tracking device in ATLAS, made up from silicon micro-strip detectors processed in the planar p-in-n technology. The signal from the strips is processed in the front-end ASICS ABCD3TA, working in the binary readout mode. Data i...

  8. ATLAS end-cap detector

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Three scientists from the Institute of Nuclear Phyiscs at Novossibirsk with one of the end-caps of the ATLAS detector. The end-caps will be used to detect particles produced in the proton-proton collisions at the heart of the ATLAS experiment that are travelling close to the axis of the two beams.

  9. Lowering the first ATLAS toroid

    CERN Document Server

    Maximilien Brice

    2004-01-01

    The ATLAS detector on the LHC at CERN will consist of eight toroid magnets, the first of which was lowered into the cavern in these images on 26 October 2004. The coils are supported on platforms where they will be attached to form a giant torus. The platforms will hold about 300 tonnes of ATLAS' muon chambers and will envelop the inner detectors.

  10. ATLAS recognises its best suppliers

    CERN Multimedia

    2002-01-01

    The ATLAS Collaboration has recently rewarded two of its suppliers in the construction of very major detector components, fabricated in Japan. The ATLAS Supplier Award in recognition of excellent supplier performance has just been attributed to Kawasaki Heavy Industries, while Toshiba Corporation received the award two months ago at their headquarters in Japan.

  11. ATLAS DDM integration in ARC

    DEFF Research Database (Denmark)

    Behrmann, Gerd; Cameron, David; Ellert, Mattias

    by the DQ2 software. Managing ATLAS data within NDGF and between NDGF and other Grids used by ATLAS (the LHC Computing Grid and the Open Science Grid) presents a unique challenge for several reasons. Firstly, the entry point for data, the Tier 1 centre, is physically distributed among heterogeneous...

  12. ATLAS Grid Workflow Performance Optimization

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration

    2018-01-01

    The CERN ATLAS experiment grid workflow system manages routinely 250 to 500 thousand concurrently running production and analysis jobs to process simulation and detector data. In total more than 300 PB of data is distributed over more than 150 sites in the WLCG. At this scale small improvements in the software and computing performance and workflows can lead to significant resource usage gains. ATLAS is reviewing together with CERN IT experts several typical simulation and data processing workloads for potential performance improvements in terms of memory and CPU usage, disk and network I/O. All ATLAS production and analysis grid jobs are instrumented to collect many performance metrics for detailed statistical studies using modern data analytics tools like ElasticSearch and Kibana. This presentation will review and explain the performance gains of several ATLAS simulation and data processing workflows and present analytics studies of the ATLAS grid workflows.

  13. The ATLAS Experiment Laboratory - Overview

    International Nuclear Information System (INIS)

    Malecki, P.

    1999-01-01

    Full text: ATLAS Experiment Laboratory has been created by physicists and engineers preparing a research programme and detector for the LHC collider. This group is greatly supported by members of other Departments taking also part (often full time) in the ATLAS project. These are: J. Blocki, J. Godlewski, Z. Hajduk, P. Kapusta, B. Kisielewski, W. Ostrowicz, E. Richter-Was, and M. Turala. Our ATLAS Laboratory realizes its programme in very close collaboration with the Faculty of Physics and Nuclear Technology of the University of Mining and Metallurgy. ATLAS, A Toroidal LHC ApparatuS Collaboration groups about 1700 experimentalists from about 150 research institutes. This apparatus, a huge system of many detectors, which are technologically very advanced, is going to be ready by 2005. With the start of the 2 x 7 TeV LHC collider ATLAS and CMS (the sister experiment at LHC) will begin their fascinating research programme at beam energies and intensities which have never been exploited. (author)

  14. ATLAS Award for Difficult Task

    CERN Multimedia

    2004-01-01

    Two Russian companies were honoured with an ATLAS Award, for supply of the ATLAS Inner Detector barrel support structure elements, last week. On 23 March the Russian company ORPE Technologiya and its subcontractor, RSP Khrunitchev, were jointly presented with an ATLAS Supplier Award. Since 1998, ORPE Technologiya has been actively involved in the development of the carbon-fibre reinforced plastic elements of the ATLAS Inner Detector barrel support structure. After three years of joint research and development, CERN and ORPE Technologiya launched the manufacturing contract. It had a tight delivery schedule and very demanding specifications in terms of mechanical tolerance and stability. The contract was successfully completed with the arrival of the last element of the structure at CERN on 8 January 2004. The delivery of this key component of the Inner Detector deserves an ATLAS Award given the difficulty of manufacturing the end-frames, which very few companies in the world would have been able to do at an ...

  15. A genetic atlas of human admixture history

    Science.gov (United States)

    Hellenthal, Garrett; Busby, George B.J.; Band, Gavin; Wilson, James F.; Capelli, Cristian

    2014-01-01

    Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations. PMID:24531965

  16. A genetic atlas of human admixture history.

    Science.gov (United States)

    Hellenthal, Garrett; Busby, George B J; Band, Gavin; Wilson, James F; Capelli, Cristian; Falush, Daniel; Myers, Simon

    2014-02-14

    Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

  17. 17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

    CERN Multimedia

    Mona Schweizer

    2008-01-01

    17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

  18. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  19. ATLAS parameter study

    International Nuclear Information System (INIS)

    Adler, R.J.

    1994-01-01

    The purpose of this study is to make an independent assessment on the parameters chosen for the ATLAS capacitor bank at LANL. The contractor will perform a study of the basic pulsed power parameters of the ATLAS device with baseline functional parameters of >25 MA implosion current and <2.5 microsecond current risetime. Nominal circuit parameters held fixed will be the 14 nH from the vacuum interface to the load, and the nominal load impedances of 1 milliohm for slow loads and 10 milliohms for fast loads. Single Ended designs, as opposed to bipolar designs, will be studied in detail. The ATLAS pulsed power design problem is about inductance. The reason that a 36 MJ bank is required is that such a bank has enough individual capacitors so that the parallel inductance is acceptably low. Since about half the inductance is in the bank, and the inductance and time constant of the submodules is fixed, the variation of output with a given parameter will generally be a weak one. In general, the dl/dt calculation demonstrates that for the real system inductances, 700 kV is the optimum voltage for the bank to drive X-ray loads. The optimum is broad, and there is little reduction in performance at voltages as low as 450 kV. The direct drive velocity analysis also shows that the optimum velocity is between 480 and 800 kV for a variety of assumptions, and that there is less than a 10% variation in velocity over this range. Voltages in the 120 kV--600 kV range are desirable for driving heavy liners. A compromise optimum operating point might be 480 kV, at which all X-ray operation scenarios are within 10% of their velocity optimum, and heavy liners can be configured to be near optimum if small enough. Based on very preliminary studies the author believes that the choice of a single operating voltage point (say, 480 kV) is unnecessary, and that a bank engineered for dual operation at 480 and 240 kV will be the best solution to the ATLAS problem

  20. ATLAS Exotic Searches

    CERN Document Server

    Bousson, Nicolas

    2012-01-01

    Thanks to the outstanding performance of the Large Hadron Collider (LHC) that delivered more than 2 fb^-1 of proton-proton collision data at center-of-mass energy of 7 TeV, the ATLAS experiment has been able to explore a wide range of exotic models trying to address the questions unanswered by the Standard Model of particle physics. Searches for leptoquarks, new heavy quarks, vector-like quarks, black holes, hidden valley and contact interactions are reviewed in these proceedings.

  1. Commissioning of ATLAS

    CERN Document Server

    Thomas, J

    2008-01-01

    The status of the commissioning of the ATLAS experiment as of May 2008 is presented. The subdetector integration in recent milestone weeks is described, especially the cosmic commissioning in milestone week M6, focussing on combined running and track analysis of the muon detector and inner detector. The liquid argon and tile calorimeters have achieved near-full operation, and are integrated with the calorimeter trigger. The High-Level-Trigger infrastructure is installed and algorithms tested in technical runs. Problems with the inner detector cooling compressors are being fixed.

  2. Surveying the ATLAS cavern

    CERN Multimedia

    Laurent Guiraud

    2000-01-01

    The cathedral-like cavern into which the ATLAS experiment will be lowered and installed forms a vital part of the engineering work at CERN in preparation for the new LHC accelerator. This cavern, being measured by surveyors in these images, will have one of the largest spans of any man-made underground structure. The massive 46X25X25 cubic metre detector will be the largest of its type in the world when it is completed for the LHC start-up in 2008.

  3. Atlas of liver imaging

    International Nuclear Information System (INIS)

    1989-05-01

    This atlas is an outcome of an IAEA co-ordinated research programme. In addition to Japan, nine other Asian countries participated in the project and 293 liver scintigrams (116 from Japanese institutions and 177 from seven Asian countries) were evaluated by physicians from the participating Asian countries. The computer analysis of the scan findings of the individual physicians was carried out and individual scores have been separately tabulated for: (a) scan abnormality; (b) space occupying lesions; (c) cirrhosis and (d) diffuse liver diseases like hepatitis. Refs, figs and tabs

  4. SUSY Searches at ATLAS

    CERN Document Server

    Mamuzic, Judita; The ATLAS collaboration

    2017-01-01

    Supersymmetry (SUSY) is considered one of the best motivated extensions of the Standard Model. It postulates a fundamental symmetry between fermions and bosons, and introduces a set of new supersymmetric particles at the electroweak scale. It addresses the hierarchy and naturalness problem, gives a solution to the gauge coupling unification, and offers a cold dark matter candidate. Different aspects of SUSY searches, using strong, electroweak, third generation production, and R-parity violation and long lived particles are being studied at the LHC. An overview of most recent SUSY searches results using the 13 TeV ATLAS RUN2 data will be presented.

  5. Computational and mathematical methods in brain atlasing.

    Science.gov (United States)

    Nowinski, Wieslaw L

    2017-12-01

    Brain atlases have a wide range of use from education to research to clinical applications. Mathematical methods as well as computational methods and tools play a major role in the process of brain atlas building and developing atlas-based applications. Computational methods and tools cover three areas: dedicated editors for brain model creation, brain navigators supporting multiple platforms, and atlas-assisted specific applications. Mathematical methods in atlas building and developing atlas-aided applications deal with problems in image segmentation, geometric body modelling, physical modelling, atlas-to-scan registration, visualisation, interaction and virtual reality. Here I overview computational and mathematical methods in atlas building and developing atlas-assisted applications, and share my contribution to and experience in this field.

  6. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  7. Atlas C++ Coding Standard Specification

    CERN Document Server

    Albrand, S; Barberis, D; Bosman, M; Jones, B; Stavrianakou, M; Arnault, C; Candlin, D; Candlin, R; Franck, E; Hansl-Kozanecka, Traudl; Malon, D; Qian, S; Quarrie, D; Schaffer, R D

    2001-01-01

    This document defines the ATLAS C++ coding standard, that should be adhered to when writing C++ code. It has been adapted from the original "PST Coding Standard" document (http://pst.cern.ch/HandBookWorkBook/Handbook/Programming/programming.html) CERN-UCO/1999/207. The "ATLAS standard" comprises modifications, further justification and examples for some of the rules in the original PST document. All changes were discussed in the ATLAS Offline Software Quality Control Group and feedback from the collaboration was taken into account in the "current" version.

  8. ATLAS B-physics potential

    CERN Document Server

    Smizanska, M

    2001-01-01

    Studies since 1993 have demonstrated the ability of ATLAS to pursue a wide B physics program. This document presents the latest performance studies with special stress on lepton identification. B-decays containing several leptons in ATLAS statistically dominate the high- precision measurements. We present new results on physics simulations of CP violation measurements in the B/sub s//sup 0/ to J/ psi phi decay and on a novel ATLAS programme on beauty production in central proton-proton collisions at the LHC. (7 refs).

  9. Hidden Valley Searches at ATLAS

    CERN Document Server

    Ventura, D; The ATLAS collaboration

    2011-01-01

    A number of extensions of the Standard Model result in neutral and weakly-coupled particles that decay to multi hadrons or multi leptons with macroscopic decay lengths. These particles with decay paths that can be comparable with ATLAS detector dimensions represent, from an experimental point of view, a challenge both for the trigger and for the reconstruction capabilities of the ATLAS detector. We will present a set of signature driven triggers for the ATLAS detector that target such displaced decays and evaluate their performances for some benchmark models.

  10. Automated Loads Analysis System (ATLAS)

    Science.gov (United States)

    Gardner, Stephen; Frere, Scot; O’Reilly, Patrick

    2013-01-01

    ATLAS is a generalized solution that can be used for launch vehicles. ATLAS is used to produce modal transient analysis and quasi-static analysis results (i.e., accelerations, displacements, and forces) for the payload math models on a specific Shuttle Transport System (STS) flight using the shuttle math model and associated forcing functions. This innovation solves the problem of coupling of payload math models into a shuttle math model. It performs a transient loads analysis simulating liftoff, landing, and all flight events between liftoff and landing. ATLAS utilizes efficient and numerically stable algorithms available in MSC/NASTRAN.

  11. The Medicago truncatula gene expression atlas web server

    Directory of Open Access Journals (Sweden)

    Tang Yuhong

    2009-12-01

    Full Text Available Abstract Background Legumes (Leguminosae or Fabaceae play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible

  12. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  13. CRISPR/Cas9 Genome Editing of Epidermal Growth Factor Receptor Sufficiently Abolished Oncogenicity in Anaplastic Thyroid Cancer

    Directory of Open Access Journals (Sweden)

    Li-Chi Huang

    2018-01-01

    Full Text Available Anaplastic carcinoma of the thyroid (ATC, also called undifferentiated thyroid cancer, is the least common but most aggressive and deadly thyroid gland malignancy of all thyroid cancers. The aim of this study is to explore essential biomarker and use CRISPR/Cas9 with lentivirus delivery to establish a gene-target therapeutic platform in ATC cells. At the beginning, the gene expression datasets from 1036 cancers from CCLE and 8215 tumors from TCGA were collected and analyzed, showing EGFR is predominantly overexpressed in thyroid cancers than other type of cancers (P=0.017 in CCLE and P=0.001 in TCGA. Using CRISPR/Cas9 genomic edit system, ATC cells with EGFR sgRNA lentivirus transfection obtained great disruptions on gene and protein expression, resulting in cell cycle arrest, cell growth inhibition, and most importantly metastasis turn-off ability. In addition, the FDA-approved TKI of afatinib for EGFR targeting also illustrates great anticancer activity on cancer cell death occurrence, cell growth inhibition, and cell cycle arrest in SW579 cells, an EGFR expressing human ATC cell line. Furthermore, off-target effect of using EGFR sgRNAs was measured and found no genomic editing can be detected in off-target candidate gene. To conclude, this study provides potential ATC therapeutic strategies for current and future clinical needs, which may be possible in increasing the survival rate of ATC patients by translational medicine.

  14. The Atlas upgrade project

    International Nuclear Information System (INIS)

    Bollinger, L.M.

    1988-01-01

    ATLAS is a heavy-ion accelerator system consisting of a 9-MV tandem electrostatic injector coupled to a superconducting linac. A project now well advanced will upgrade the capabilities of ATLAS immensely by replacing the tandem and its negative-ion source with a positive-ion injector that consists of an electron-cyclotron resonance (ECR) ion source and a 12-MV superconducting injector linac of novel design. This project will increase the beam intensity 100 fold and will extend the projectile-mass range up to uranium. Phase 1 of the work, which is nearing completion in late 1988, will provide an injector comprising the ECR source and its 350-kV voltage platform, beam analysis and bunching systems, beam lines, and a prototype 3-MV linac. The ECR source and its voltage platform are operational, development of the new class of low-frequency interdigital superconducting resonators required for the injector linac has been completed, and assembly of the whole system is in progress. Test runs and then routine use of the Phase 1 injector systems are planned for early 1989, and the final 12-MV injector linac will be commissioned in 1990. 12 refs., 6 figs

  15. ATLAS Solenoid Integration

    CERN Multimedia

    Ruber, R

    Last month the central solenoid was installed in the barrel cryostat, which it shares with the liquid argon calorimeter. Figure 1: Some members of the solenoid and liquid argon teams proudly pose in front of the barrel cryosat, complete with detector and magnet. Some two years ago the central solenoid arrived at CERN after being manufactured and tested in Japan. It was kept in storage until last October when it was finally moved to the barrel cryostat integration area. Here a position survey of the solenoid (with respect to the cryostat's inner warm vessel) was performed. Figure 2: The alignment survey by Dirk Mergelkuhl and Aude Wiart. (EST-SU) At the start of the New Year the solenoid was moved to the cryostat insertion stand. Figure 3: The solenoid on the insertion stand, with Akira Yamamoto the solenoid designer and project leader. Figure 4: Taka Kondo, ATLAS Japan spokesperson, and Shoichi Mizumaki, Toshiba project engineer for the ATLAS solenoid, celebrate the insertion. Aft...

  16. ATLAS construction schedule

    CERN Multimedia

    Kotamaki, M

    The goal during the last few months has been to freeze and baseline as much as possible the schedules of various ATLAS systems and activities. The main motivations for the re-baselining of the schedules have been the new LHC schedule aiming at first collisions in early 2006 and the encountered delays in civil engineering as well as in the production of some of the detectors. The process was started by first preparing a new installation schedule that takes into account all the new external constraints and the new ATLAS staging scenario. The installation schedule version 3 was approved in the March EB and it provides the Ready For Installation (RFI) milestones for each system, i.e. the date when the system should be available for the start of the installation. TCn is now interacting with the systems aiming at a more realistic and resource loaded version 4 before the end of the year. Using the new RFI milestones as driving dates a new summary schedule has been prepared, or is under preparation, for each system....

  17. ATLAS Christmas lunch

    CERN Document Server

    Francois Butin; Markus Nordberg

    The end of the year ATLAS pit lunch is now a well established tradition: the 4th edition took place in the most prestigious place at CERN; the "Globe de l'innovation", or simply "the Globe". This end-of-year event is the opportunity to thank all those working so hard at Point 1. The first event took place in December 2003. At that time, there was no Globe yet, and the party took place in SX1 building, at the top of the shafts leading to the ATLAS cavern, with some 100 guests. In December 2004, we had the privilege to be the first to organize a lunch in the Globe with some 200 guests. Since then, many have followed our example! Well, almost: we were requested to refrain from serving "Tartiflette" again in there (a Savoyard specialty, using vast amounts of Reblochon, a smelly cheese...). It was said to have left a poignant odour for following events throughout 2004... Long queues formed for this special event. In December 2005, we were authorized to party in the Globe again (once we promised we would b...

  18. ATLAS muon detector

    CERN Multimedia

    Muon detectors from the outer layer of the ATLAS experiment at the Large Hadron Collider. Over a million individual detectors combine to make up the outer layer of ATLAS. All of this is exclusively to track the muons, the only detectable particles to make it out so far from the collision point. How the muon’s path curves in the magnetic field depends on how fast it is travelling. A fast muon curves only a very little, a slower one curves a lot. Together with the calorimeters, the muon detectors play an essential role in deciding which collisions to store and which to ignore. Certain signals from muons are a sure sign of exciting discoveries. To make sure the data from these collisions is not lost, some of the muon detectors react very quickly and trigger the electronics to record. The other detectors take a little longer, but are much more precise. Their job is to measure exactly where the muons have passed, calculating the curvature of their tracks in the magnetic field to the nearest five hundredths of a ...

  19. The ATLAS Fast Tracker

    CERN Document Server

    Volpi, Guido; The ATLAS collaboration

    2015-01-01

    The use of tracking information at the trigger level in the LHC Run II period is crucial for the trigger an data acquisition (TDAQ) system. The tracking precision is in fact important to identify specific decay products of the Higgs boson or new phenomena, a well as to distinguish the contributions coming from many contemporary collisions that occur at every bunch crossing. However, the track reconstruction is among the most demanding tasks performed by the TDAQ computing farm; in fact, full reconstruction at full Level-1 trigger accept rate (100 KHz) is not possible. In order to overcome this limitation, the ATLAS experiment is planning the installation of a specific processor: the Fast Tracker (FTK), which is aimed at achieving this goal. The FTK is a pipeline of high performance electronic, based on custom and commercial devices, which is expected to reconstruct, with high resolution, the trajectories of charged tracks with a transverse momentum above 1 GeV, using the ATLAS inner tracker information. Patte...

  20. ATLAS Physicist in Space

    CERN Multimedia

    Bengt Lund-Jensen

    2007-01-01

    On December 9, the former ATLAS physicist Christer Fuglesang was launched into space onboard the STS-116 Space Shuttle flight from Kennedy Space Center in Florida. Christer worked on the development of the accordion-type liquid argon calorimeter and SUSY simulations in what eventually became ATLAS until summer 1992 when he became one out of six astronaut trainees with the European Space Agency (ESA). His selection out of a very large number of applicants from all over the ESA member states involved a number of tests in order to choose the most suitable candidates. As ESA astronaut Christer trained with the Russian Soyuz programme in Star City outside of Moscow from 1993 until 1996, when he moved to Houston to train for space shuttle missions with NASA. Christer belonged to the backup crew for the Euromir95 mission. After additional training in Russia, Christer qualified as ‘Soyuz return commander’ in 1998. Christer rerouting cables during his second space walk. (Photo: courtesy NASA) During...

  1. Spring comes for ATLAS

    CERN Multimedia

    Butin, F.

    2004-01-01

    (First published in the CERN weekly bulletin 24/2004, 7 June 2004.) A short while ago the ATLAS cavern underwent a spring clean, marking the end of the installation of the detector's support structures and the cavern's general infrastructure. The list of infrastructure to be installed in the ATLAS cavern from September 2003 was long: a thousand tonnes of mechanical structures spread over 13 storeys, two lifts, two 65-tonne overhead travelling cranes 25 metres above cavern floor, with a telescopic boom and cradle to access the remaining 10 metres of the cavern, a ventilation system for the 55 000 cubic metre cavern, a drainage system, a standard sprinkler system and an innovative foam fire-extinguishing system, as well as the external cryogenic system for the superconducting magnets and the liquid argon calorimeters (comprising, amongst other things, two helium refrigeration units, a nitrogen refrigeration unit and 5 km of piping for gaseous or liquid helium and nitrogen), not to mention the handling eq...

  2. ATLAS starts moving in

    CERN Multimedia

    Della Mussia, S

    2004-01-01

    The first large active detector component was lowered into the ATLAS cavern on 1st March. It consisted of the 8 modules forming the lower part of the central barrel of the tile hadronic calorimeter. The work of assembling the barrel, which comprises 64 modules, started the following day. Two road trailers each with 64 wheels, positioned side by side. This was the solution chosen to transport the lower part of the central barrel of ATLAS' tile hadronic calorimeter from Building 185 to the PX16 shaft at Point 1 (see Figure 1). The transportation, and then the installation of the component in the experimental cavern, which took place over three days were, to say the least, rather spectacular. On 25 February, the component, consisting of eight 6-metre modules, was loaded on to the trailers. The segment of the barrel was transported on a steel support so that it wouldn't move an inch during the journey. On 26 February, once all the necessary safety checks had been carried out, the convoy was able to leave Buildi...

  3. ATLAS Distributed Analysis Tools

    CERN Document Server

    Gonzalez de la Hoz, Santiago; Liko, Dietrich

    2008-01-01

    The ATLAS production system has been successfully used to run production of simulation data at an unprecedented scale. Up to 10000 jobs were processed in one day. The experiences obtained operating the system on several grid flavours was essential to perform a user analysis using grid resources. First tests of the distributed analysis system were then performed. In the preparation phase data was registered in the LHC File Catalog (LFC) and replicated in external sites. For the main test, few resources were used. All these tests are only a first step towards the validation of the computing model. The ATLAS management computing board decided to integrate the collaboration efforts in distributed analysis in only one project, GANGA. The goal is to test the reconstruction and analysis software in a large scale Data production using Grid flavors in several sites. GANGA allows trivial switching between running test jobs on a local batch system and running large-scale analyses on the Grid; it provides job splitting a...

  4. ATLAS DBM Module Qualification

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gorisek, Andrej [J. Stefan Inst., Ljubljana (Slovenia); Zavrtanik, Marko [J. Stefan Inst., Ljubljana (Slovenia); Sokhranyi, Grygorii [J. Stefan Inst., Ljubljana (Slovenia); McGoldrick, Garrin [Univ. of Toronto, ON (Canada); Cerv, Matevz [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2014-06-18

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of Jozef Stefan Institute, CERN, and University of Toronto who have committed to participate in beam tests to be carried out during the 2014 Fermilab Test Beam Facility program. Chemical Vapour Deposition (CVD) diamond has a number of properties that make it attractive for high energy physics detector applications. Its large band-gap (5.5 eV) and large displacement energy (42 eV/atom) make it a material that is inherently radiation tolerant with very low leakage currents and high thermal conductivity. CVD diamond is being investigated by the RD42 Collaboration for use very close to LHC interaction regions, where the most extreme radiation conditions are found. This document builds on that work and proposes a highly spatially segmented diamond-based luminosity monitor to complement the time-segmented ATLAS Beam Conditions Monitor (BCM) so that, when Minimum Bias Trigger Scintillators (MTBS) and LUCID (LUminosity measurement using a Cherenkov Integrating Detector) have difficulty functioning, the ATLAS luminosity measurement is not compromised.

  5. AGIS: The ATLAS Grid Information System

    CERN Document Server

    Anisenkov, Alexey; Di Girolamo, Alessandro; Gayazov, Stavro; Klimentov, Alexei; Oleynik, Danila; Senchenko, Alexander

    2012-01-01

    ATLAS is a particle physics experiment at the Large Hadron Collider at CERN. The experiment produces petabytes of data annually through simulation production and tens petabytes of data per year from the detector itself. The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configuration and status information about resources, services and topology of whole ATLAS Grid needed by ATLAS Distributed Computing applications and services.

  6. CERN Open Days 2013, Point 1 - ATLAS: ATLAS Experiment

    CERN Multimedia

    CERN Photolab

    2013-01-01

    Stand description: The ATLAS Experiment at CERN is one of the largest and most complex scientific endeavours ever assembled. The detector, located at collision point 1 of the LHC, is designed to explore the fundamental components of nature and to study the forces that shape our universe. The past year’s discovery of a Higgs boson is one of the most important scientific achievements of our time, yet this is only one of many key goals of ATLAS. During a brief break in their journey, some of the 3000-member ATLAS collaboration will be taking time to share the excitement of this exploration with you. On surface no restricted access  The exhibit at Point 1 will give visitors a chance to meet these modern-day explorers and to learn from them how answers to the most fundamental questions of mankind are being sought. Activities will include a visit to the ATLAS detector, located 80m below ground; watching the prize-winning ATLAS movie in the ATLAS cinema; seeing real particle tracks in a cloud chamber and discussi...

  7. NATIONAL ATLAS OF THE ARCTIC

    Directory of Open Access Journals (Sweden)

    Nikolay S. Kasimov

    2018-01-01

    Full Text Available The National Atlas of the Arctic is a set of spatio-temporal information about the geographic, ecological, economic, historical-ethnographic, cultural, and social features of theArcticcompiled as a cartographic model of the territory. The Atlas is intended for use in a wide range of scientific, management, economic, defense, educational, and public activities. The state policy of theRussian Federationin the Arctic for the period until 2020 and beyond, states that the Arctic is of strategic importance forRussiain the 21st century. A detailed description of all sections of the Atlas is given. The Atlas can be used as an information-reference and educational resource or as a gift edition.

  8. Two new wheels for ATLAS

    CERN Multimedia

    2002-01-01

    Juergen Zimmer (Max Planck Institute), Roy Langstaff (TRIUMF/Victoria) and Sergej Kakurin (JINR), in front of one of the completed wheels of the ATLAS Hadronic End Cap Calorimeter. A decade of careful preparation and construction by groups in three continents is nearing completion with the assembly of two of the four 4 m diameter wheels required for the ATLAS Hadronic End Cap Calorimeter. The first two wheels have successfully passed all their mechanical and electrical tests, and have been rotated on schedule into the vertical position required in the experiment. 'This is an important milestone in the completion of the ATLAS End Cap Calorimetry' explains Chris Oram, who heads the Hadronic End Cap Calorimeter group. Like most experiments at particle colliders, ATLAS consists of several layers of detectors in the form of a 'barrel' and two 'end caps'. The Hadronic Calorimeter layer, which measures the energies of particles such as protons and pions, uses two techniques. The barrel part (Tile Calorimeter) cons...

  9. National Transportation Atlas Databases : 2013.

    Science.gov (United States)

    2013-01-01

    The National Transportation Atlas Databases 2013 (NTAD2013) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  10. National Transportation Atlas Databases : 2015.

    Science.gov (United States)

    2015-01-01

    The National Transportation Atlas Databases 2015 (NTAD2015) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  11. National Transportation Atlas Databases : 2012.

    Science.gov (United States)

    2012-01-01

    The National Transportation Atlas Databases 2012 (NTAD2012) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  12. National Transportation Atlas Databases : 2011.

    Science.gov (United States)

    2011-01-01

    The National Transportation Atlas Databases 2011 (NTAD2011) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  13. National Transportation Atlas Databases : 2009.

    Science.gov (United States)

    2009-01-01

    The National Transportation Atlas Databases 2009 (NTAD2009) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  14. National Transportation Atlas Databases : 2014.

    Science.gov (United States)

    2014-01-01

    The National Transportation Atlas Databases 2014 (NTAD2014) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  15. National Transportation Atlas Databases : 2010.

    Science.gov (United States)

    2010-01-01

    The National Transportation Atlas Databases 2010 (NTAD2010) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  16. World Ocean Atlas 2005, Temperature

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — World Ocean Atlas 2005 (WOA05) is a set of objectively analyzed (1° grid) climatological fields of in situ temperature, salinity, dissolved oxygen, Apparent Oxygen...

  17. Wheels lining up for ATLAS

    CERN Multimedia

    2003-01-01

    On 30 October, the mechanics test assembly of the central barrel of the ATLAS tile hadronic calorimeter was completed in building 185. It is the second wheel for the Tilecal completely assembled this year.

  18. World Ocean Atlas 2005, Salinity

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — World Ocean Atlas 2005 (WOA05) is a set of objectively analyzed (1° grid) climatological fields of in situ temperature, salinity, dissolved oxygen, Apparent Oxygen...

  19. Dartmouth Atlas of Health Care

    Data.gov (United States)

    U.S. Department of Health & Human Services — For more than 20 years, the Dartmouth Atlas Project has documented glaring variations in how medical resources are distributed and used in the United States. The...

  20. ATLAS DDM integration in ARC

    DEFF Research Database (Denmark)

    Behrmann, Gerd; Cameron, David; Ellert, Mattias

    2008-01-01

    The Nordic Data Grid Facility (NDGF) consists of Grid resources running ARC middleware in Denmark, Finland, Norway and Sweden. These resources serve many virtual organisations and contribute a large fraction of total worldwide resources for the ATLAS experiment, whose data is distributed and mana......The Nordic Data Grid Facility (NDGF) consists of Grid resources running ARC middleware in Denmark, Finland, Norway and Sweden. These resources serve many virtual organisations and contribute a large fraction of total worldwide resources for the ATLAS experiment, whose data is distributed...... and managed by the DQ2 software. Managing ATLAS data within NDGF and between NDGF and other Grids used by ATLAS (the Enabling Grids for E-sciencE Grid and the Open Science Grid) presents a unique challenge for several reasons. Firstly, the entry point for data, the Tier 1 centre, is physically distributed...

  1. ATLAS Software Installation on Supercomputers

    CERN Document Server

    Undrus, Alexander; The ATLAS collaboration

    2018-01-01

    PowerPC and high performance computers (HPC) are important resources for computing in the ATLAS experiment. The future LHC data processing will require more resources than Grid computing, currently using approximately 100,000 cores at well over 100 sites, can provide. Supercomputers are extremely powerful as they use resources of hundreds of thousands CPUs joined together. However their architectures have different instruction sets. ATLAS binary software distributions for x86 chipsets do not fit these architectures, as emulation of these chipsets results in huge performance loss. This presentation describes the methodology of ATLAS software installation from source code on supercomputers. The installation procedure includes downloading the ATLAS code base as well as the source of about 50 external packages, such as ROOT and Geant4, followed by compilation, and rigorous unit and integration testing. The presentation reports the application of this procedure at Titan HPC and Summit PowerPC at Oak Ridge Computin...

  2. ATLAS recognises its best suppliers

    CERN Multimedia

    Jenni, P

    The ATLAS Collaboration has recently rewarded two of its suppliers in the construction of very major detector components, fabricated in Japan. The ATLAS Supplier Award in recognition of excellent supplier performance was attributed on 2nd September 2002 during a ceremony in Hall 180 to Kawasaki Heavy Industries, while Toshiba Corporation received the award two months before at their headquarters in Japan. The ATLAS experiment will become a reality thanks to a large international collaboration partnership. The industrial suppliers for the components all over the world play a major role in the construction of this gigantic jigsaw for the LHC. And sometimes they perform so well, that their work deserves specially to be recognised. This is the case for Kawasaki Heavy Industries and Toshiba Corporation, producers of the Liquid Argon Barrel Cryostat and of the Superconducting Central Solenoid, respectively. With these awards, the ATLAS Collaboration wants to congratulate Kawasaki and Toshiba for fulfilling the hi...

  3. Hidden Valley Search at ATLAS

    CERN Document Server

    Verducci, M

    2011-01-01

    A number of extensions of the Standard Model result in neutral and weakly-coupled particles that decay to multi hadrons or multi leptons with macroscopic decay lengths. These particles with decay paths that can be comparable with ATLAS detector dimensions represent, from an experimental point of view, a challenge both for the trigger and for the reconstruction capabilities of the ATLAS detector. We will present a set of signature driven triggers for the ATLAS detector that target such displaced decays and evaluate their performances for some benchmark models and describe analysis strategies and limits on the production of such long-lived particles. A first estimation of the Hidden Valley trigger rates has been evaluated with 6 pb-1 of data collected at ATLAS during the data taking of 2010.

  4. Nuclear Receptor Signaling Atlas (NURSA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Nuclear Receptor Signaling Atlas (NURSA) is designed to foster the development of a comprehensive understanding of the structure, function, and role in disease...

  5. The ATLAS detector simulation application

    International Nuclear Information System (INIS)

    Rimoldi, A.

    2007-01-01

    The simulation program for the ATLAS experiment at CERN is currently in a full operational mode and integrated into the ATLAS common analysis framework, Athena. The OO approach, based on GEANT4, has been interfaced within Athena and to GEANT4 using the LCG dictionaries and Python scripting. The robustness of the application was proved during the test productions since 2004. The Python interface has added the flexibility, modularity and interactivity that the simulation tool requires in order to be able to provide a common implementation of different full ATLAS simulation setups, test beams and cosmic ray applications. Generation, simulation and digitization steps were exercised for performance and robustness tests. The comparison with real data has been possible in the context of the ATLAS Combined Test Beam (2004-2005) and cosmic ray studies (2006)

  6. The ATLAS Forward Physics Program

    OpenAIRE

    Royon, C

    2010-01-01

    After a brief review of the approved ATLAS forward detector system we describe the main ATLAS forward physics program. This program currently includes such topics as soft and hard diffraction, double pomeron exchange, central exclusive production, rapidity gap survival, two photon physics, the determination of the total cross-section and the determination of the absolute luminosity A possible high luminosity upgrade program involving new forward proton detectors is also briefly reviewed. This...

  7. Searches for Supersymmetry in ATLAS

    CERN Document Server

    Cervelli, Alberto; The ATLAS collaboration

    2017-01-01

    After the discovery of the Higgs boson in ATLAS first run of data taking, and due to the lack of observation of new physics, searches for new particles such as Supersymmetric states are one of the main area of interest for the general purpose detectors operating at LHC. In this talk we will present a review of the searches for Supersymmetric particles, performed by the ATLAS experiment

  8. ATLAS cloud R and D

    International Nuclear Information System (INIS)

    Panitkin, Sergey; Bejar, Jose Caballero; Hover, John; Zaytsev, Alexander; Megino, Fernando Barreiro; Girolamo, Alessandro Di; Kucharczyk, Katarzyna; Llamas, Ramon Medrano; Benjamin, Doug; Gable, Ian; Paterson, Michael; Sobie, Randall; Taylor, Ryan; Hendrix, Val; Love, Peter; Ohman, Henrik; Walker, Rodney

    2014-01-01

    The computing model of the ATLAS experiment was designed around the concept of grid computing and, since the start of data taking, this model has proven very successful. However, new cloud computing technologies bring attractive features to improve the operations and elasticity of scientific distributed computing. ATLAS sees grid and cloud computing as complementary technologies that will coexist at different levels of resource abstraction, and two years ago created an R and D working group to investigate the different integration scenarios. The ATLAS Cloud Computing R and D has been able to demonstrate the feasibility of offloading work from grid to cloud sites and, as of today, is able to integrate transparently various cloud resources into the PanDA workload management system. The ATLAS Cloud Computing R and D is operating various PanDA queues on private and public resources and has provided several hundred thousand CPU days to the experiment. As a result, the ATLAS Cloud Computing R and D group has gained a significant insight into the cloud computing landscape and has identified points that still need to be addressed in order to fully utilize this technology. This contribution will explain the cloud integration models that are being evaluated and will discuss ATLAS' learning during the collaboration with leading commercial and academic cloud providers.

  9. ATLAS Award for Shield Supplier

    CERN Multimedia

    2004-01-01

    ATLAS technical coordinator Dr. Marzio Nessi presents the ATLAS supplier award to Vojtech Novotny, Director General of Skoda Hute.On 3 November, the ATLAS experiment honoured one of its suppliers, Skoda Hute s.r.o., of Plzen, Czech Republic, for their work on the detector's forward shielding elements. These huge and very massive cylinders surround the beampipe at either end of the detector to block stray particles from interfering with the ATLAS's muon chambers. For the shields, Skoda Hute produced 10 cast iron pieces with a total weight of 780 tonnes at a cost of 1.4 million CHF. Although there are many iron foundries in the CERN member states, there are only a limited number that can produce castings of the necessary size: the large pieces range in weight from 59 to 89 tonnes and are up to 1.5 metres thick.The forward shielding was designed by the ATLAS Technical Coordination in close collaboration with the ATLAS groups from the Czech Technical University and Charles University in Prague. The Czech groups a...

  10. ATLAS Cloud R&D

    Science.gov (United States)

    Panitkin, Sergey; Barreiro Megino, Fernando; Caballero Bejar, Jose; Benjamin, Doug; Di Girolamo, Alessandro; Gable, Ian; Hendrix, Val; Hover, John; Kucharczyk, Katarzyna; Medrano Llamas, Ramon; Love, Peter; Ohman, Henrik; Paterson, Michael; Sobie, Randall; Taylor, Ryan; Walker, Rodney; Zaytsev, Alexander; Atlas Collaboration

    2014-06-01

    The computing model of the ATLAS experiment was designed around the concept of grid computing and, since the start of data taking, this model has proven very successful. However, new cloud computing technologies bring attractive features to improve the operations and elasticity of scientific distributed computing. ATLAS sees grid and cloud computing as complementary technologies that will coexist at different levels of resource abstraction, and two years ago created an R&D working group to investigate the different integration scenarios. The ATLAS Cloud Computing R&D has been able to demonstrate the feasibility of offloading work from grid to cloud sites and, as of today, is able to integrate transparently various cloud resources into the PanDA workload management system. The ATLAS Cloud Computing R&D is operating various PanDA queues on private and public resources and has provided several hundred thousand CPU days to the experiment. As a result, the ATLAS Cloud Computing R&D group has gained a significant insight into the cloud computing landscape and has identified points that still need to be addressed in order to fully utilize this technology. This contribution will explain the cloud integration models that are being evaluated and will discuss ATLAS' learning during the collaboration with leading commercial and academic cloud providers.

  11. AGIS: The ATLAS Grid Information System

    CERN Document Server

    Anisenkov, A; The ATLAS collaboration; Klimentov, A; Oleynik, D; Petrosyan, A

    2014-01-01

    In this paper we describe ATLAS Grid Information System (AGIS), the system designed to integrate configuration and status information about resources, services and topology of the computing infrastructure used by ATLAS Distributed Computing applications and services.

  12. AGIS: The ATLAS Grid Information System

    OpenAIRE

    Anisenkov, A; Di Girolamo, A; Klimentov, A; Oleynik, D; Petrosyan, A

    2013-01-01

    In this paper we describe ATLAS Grid Information System (AGIS), the system designed to integrate configuration and status information about resources, services and topology of the computing infrastructure used by ATLAS Distributed Computing applications and services.

  13. EnviroAtlas - Durham, NC - Demo (Parent)

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset is the base layer for the Durham, NC EnviroAtlas Area. The block groups are from the US Census Bureau and are included/excluded based on...

  14. EnviroAtlas - Phoenix, AZ - Block Groups

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset is the base layer for the Phoenix, AZ EnviroAtlas area. The block groups are from the US Census Bureau and are included/excluded based on...

  15. EnviroAtlas - Fresno, CA - Block Groups

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset is the base layer for the Fresno, CA EnviroAtlas area. The block groups are from the US Census Bureau and are included/excluded based on...

  16. Argonne Tandem Linac Accelerator System (ATLAS)

    Data.gov (United States)

    Federal Laboratory Consortium — ATLAS is a national user facility at Argonne National Laboratory in Argonne, Illinois. The ATLAS facility is a leading facility for nuclear structure research in the...

  17. Women of ATLAS - International Women's Day 2016

    CERN Multimedia

    Biondi, Silvia

    2016-01-01

    Women play key roles in the ATLAS Experiment: from young physicists at the start of their careers to analysis group leaders and spokespersons of the collaboration. Celebrate International Women's Day by meeting a few of these inspiring ATLAS researchers.

  18. EnviroAtlas - Cleveland, OH - Block Groups

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset is the base layer for the Cleveland, OH EnviroAtlas community. The block groups are from the US Census Bureau and are included/excluded...

  19. Atlas of neutron resonances

    CERN Document Server

    Mughabghab, Said

    2018-01-01

    Atlas of Neutron Resonances: Resonance Properties and Thermal Cross Sections Z= 1-60, Sixth Edition, contains an extensive list of detailed individual neutron resonance parameters for Z=1-60, as well as thermal cross sections, capture resonance integrals, average resonance parameters and a short survey of the physics of thermal and resonance neutrons. The long introduction contains: nuclear physics formulas aimed at neutron physicists; topics of special interest such as valence neutron capture, nuclear level density parameters, and s-, p-, and d-wave neutron strength functions; and various comparisons of measured quantities with the predictions of nuclear models, such as the optical model. As in the last edition, additional features have been added to appeal to a wider spectrum of users. These include: spin-dependent scattering lengths that are of interest to solid-state physicists, nuclear physicists and neutron evaluators; calculated and measured Maxwellian average 5-keV and 30-keV capture cross sections o...

  20. The ATLAS Tile Calorimeter

    CERN Document Server

    Henriques Correia, Ana Maria

    2015-01-01

    TileCal is the Hadronic calorimeter covering the most central region of the ATLAS experiment at the LHC. It uses iron plates as absorber and plastic scintillating tiles as the active material. Scintillation light produced in the tiles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). The resulting electronic signals from the approximately 10000 PMTs are measured and digitised every 25 ns before being transferred to off-detector data-acquisition systems. This contribution will review in a first part the performances of the calorimeter during run 1, obtained from calibration data, and from studies of the response of particles from collisions. In a second part it will present the solutions being investigated for the ongoing and future upgrades of the calorimeter electronics.

  1. The ATLAS Tile Calorimeter

    International Nuclear Information System (INIS)

    Henriques, A.

    2015-01-01

    TileCal is the Hadronic calorimeter covering the most central region of the ATLAS experiment at the LHC. It uses iron plates as absorber and plastic scintillating tiles as the active material. Scintillation light produced in the tiles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). The resulting electronic signals from the approximately 10000 PMTs are measured and digitised every 25 ns before being transferred to off-detector data-acquisition systems. This contribution will review in a first part the performances of the calorimeter during run 1, obtained from calibration data, and from studies of the response of particles from collisions. In a second part it will present the solutions being investigated for the ongoing and future upgrades of the calorimeter electronics. (authors)

  2. ATLAS ITk Pixel detector

    CERN Document Server

    Gemme, Claudia; The ATLAS collaboration

    2016-01-01

    The high luminosity upgrade of the LHC (HL-LHC) in 2026 will provide new challenge to the ATLAS tracker. The current inner detector will be replaced with a whole silicon tracker which will consist of a five barrel layer Pixel detector surrounded by a four barrel layer Strip detector. The expected high radiation level are requiring the development of upgraded silicon sensors as well as new a front-end chip. The dense tracking environment will require finer granularity detectors. The data rates will require new technologies for high bandwidth data transmission and handling. The current status of the HL-LHC ATLA Pixel detector developments as well as the various layout options will be reviewed.

  3. The ATLAS Tau Trigger

    CERN Document Server

    Dam, M; The ATLAS collaboration

    2009-01-01

    The ATLAS experiment at CERN’s LHC has implemented a dedicated tau trigger system to select hadronically decaying tau leptons from the enormous background of QCD jets. This promises a significant increase in the discovery potential to the Higgs boson and in searches for physics beyond the Standard Model. The three level trigger system has been optimised for effciency and good background rejection. The first level uses information from the calorimeters only, while the two higher levels include also information from the tracking detectors. Shower shape variables and the track multiplicity are important variables to distinguish taus from QCD jets. At the initial lumonosity of 10^31 cm^−2 s^−1, single tau triggers with a transverse energy threshold of 50 GeV or higher can be run standalone. Below this level, the tau signatures will be combined with other event signature

  4. Atlas of Nuclear Isomers

    International Nuclear Information System (INIS)

    Jain, Ashok Kumar; Maheshwari, Bhoomika; Garg, Swati; Patial, Monika; Singh, Balraj

    2015-01-01

    We present an atlas of nuclear isomers containing the experimental data for the isomers with a half-life ≥ 10 ns together with their various properties such as excitation-energy, half-life, decay mode(s), spin-parity, energies and multipolarities of emitted gamma transitions, etc. The ENSDF database complemented by the XUNDL database has been extensively used in extracting the relevant data. Recent literature from primary nuclear physics journals, and the NSR bibliographic database have been searched to ensure that the compiled data Table is as complete and current as possible. The data from NUBASE-12 have also been checked for completeness, but as far as possible original references have been cited. Many interesting systematic features of nuclear isomers emerge, some of them new; these are discussed and presented in various graphs and figures. The cutoff date for the extraction of data from the literature is August 15, 2015

  5. Atlas of Nuclear Isomers

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Ashok Kumar, E-mail: ajainfph@iitr.ac.in [Department of Physics, Indian Institute of Technology, Roorkee-247667 (India); Maheshwari, Bhoomika; Garg, Swati; Patial, Monika [Department of Physics, Indian Institute of Technology, Roorkee-247667 (India); Singh, Balraj [Department of Physics and Astronomy, McMaster University, Hamilton, Ontario-L8S 4M1 (Canada)

    2015-09-15

    We present an atlas of nuclear isomers containing the experimental data for the isomers with a half-life ≥ 10 ns together with their various properties such as excitation-energy, half-life, decay mode(s), spin-parity, energies and multipolarities of emitted gamma transitions, etc. The ENSDF database complemented by the XUNDL database has been extensively used in extracting the relevant data. Recent literature from primary nuclear physics journals, and the NSR bibliographic database have been searched to ensure that the compiled data Table is as complete and current as possible. The data from NUBASE-12 have also been checked for completeness, but as far as possible original references have been cited. Many interesting systematic features of nuclear isomers emerge, some of them new; these are discussed and presented in various graphs and figures. The cutoff date for the extraction of data from the literature is August 15, 2015.

  6. Atlas of Astronomical Discoveries

    CERN Document Server

    Schilling, Govert

    2011-01-01

    Four hundred years ago in Middelburg, in the Netherlands, the telescope was invented. The invention unleashed a revolution in the exploration of the universe. Galileo Galilei discovered mountains on the Moon, spots on the Sun, and moons around Jupiter. Christiaan Huygens saw details on Mars and rings around Saturn. William Herschel discovered a new planet and mapped binary stars and nebulae. Other astronomers determined the distances to stars, unraveled the structure of the Milky Way, and discovered the expansion of the universe. And, as telescopes became bigger and more powerful, astronomers delved deeper into the mysteries of the cosmos. In his Atlas of Astronomical Discoveries, astronomy journalist Govert Schilling tells the story of 400 years of telescopic astronomy. He looks at the 100 most important discoveries since the invention of the telescope. In his direct and accessible style, the author takes his readers on an exciting journey encompassing the highlights of four centuries of astronomy. Spectacul...

  7. The human cell atlas

    DEFF Research Database (Denmark)

    Regev, Aviv; Teichmann, Sarah A.; Lander, Eric S.

    2017-01-01

    The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international...... collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells...... in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early...

  8. Consumer Energy Atlas

    Energy Technology Data Exchange (ETDEWEB)

    1980-06-01

    This first edition of the Atlas provides, in reference form, a central source of information to consumers on key contacts concerned with energy in the US. Energy consumers need information appropriate to local climates and characteristics - best provided by state and local governments. The Department of Energy recognizes the authority of state and local governments to manage energy programs on their own. Therefore, emphasis has been given to government organizations on both the national and state level that influence, formulate, or administer policies affecting energy production, distribution, and use, or that provide information of interest to consumers and non-specialists. In addition, hundreds of non-government energy-related membership organizations, industry trade associations, and energy publications are included.

  9. The ATLAS experiment

    CERN Document Server

    Dunford, Monica Lynn

    2014-01-01

    In particle physics experiments, the discovery of increasingly more massive particles has brought deep understanding of the basic constituents of matter and of the fundamental forces among them. In order to explore Nature in its deepest elementary secrets, the Large Hadron Collider (LHC) was built at CERN, Geneva. The LHC provides the highest energy collisions in a laboratory, at very high rates to allow one to study very rare reactions. Two independent sophisticated huge instruments, called ATLAS and CMS detectors, are operated to explore in a most broad way the physics of these collisions. In addition to these two general-purpose detectors, smaller specialized experiments (LHCb, ALICE and some others) are collecting collision data as well.

  10. AGIS: The ATLAS Grid Information System

    OpenAIRE

    Anisenkov, Alexey; Belov, Sergey; Di Girolamo, Alessandro; Gayazov, Stavro; Klimentov, Alexei; Oleynik, Danila; Senchenko, Alexander

    2012-01-01

    ATLAS is a particle physics experiment at the Large Hadron Collider at CERN. The experiment produces petabytes of data annually through simulation production and tens petabytes of data per year from the detector itself. The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configurat...

  11. Soft QCD at CMS and ATLAS

    CERN Document Server

    Starovoitov, Pavel; The ATLAS collaboration

    2018-01-01

    A short overview of the recent soft QCD results from the ATLAS and CMS collaborations is presented. The inelastic cross section measurement by CMS at 13 TeV is summarised. The contribution of the diffractive processes to the very forward photon spectra studied by ATLAS and LHCf is discussed. The ATLAS measurements of the exclusive two-photon production of the muon pairs is presented and compared to the previous ATLAS and CMS results.

  12. Report to users of ATLAS, January 1998

    International Nuclear Information System (INIS)

    Ahmad, I.; Hofman, D.

    1998-01-01

    This report is aimed at informing users about the operating schedule, user policies, and recent changes in research capabilities. It covers the following subjects: (1) status of the Argonne Tandem-Linac Accelerator System (ATLAS) accelerator; (2) the move of Gammasphere from LBNL to ANL; (3) commissioning of the CPT mass spectrometer at ATLAS; (4) highlights of recent research at ATLAS; (5) Program Advisory Committee; and (6) ATLAS User Group Executive Committee

  13. CP violation in ATLAS

    International Nuclear Information System (INIS)

    Saavedra, A.F.

    1995-01-01

    Full text: In the standard model CP violation is generated by a non trivial complex phase in the CKM matrix. The Standard Model does not predict the elements of the CKM matrix, they need to be experimentally measured. This will show if all the CP violation phenomena can be accounted by the complex phase or there are other contributing mechanisms which lie beyond the scope of Standard Model. It is of interest to overconstraint the so called unitary triangle by measuring each angle (α, β and γ) from the CP asymmetry that occurs in different decay modes. During the initial low luminosity period of the LHC a large effort will be concentrated in studying B physics, especially CP violation in the B 0 - B-bar 0 system, with the ATLAS detector. The features of the detector which are important for CP studies are: sharp trigger from the muon spectrometer (muons will be identify down to p T ≅ 5GeV, be able to distinguish electrons from hadrons (down to p T ≅ 1 GeV) with the Straw Tracker and Transition detector and high resolution of tracks, secondary vertices with the Semiconductor Tracker (resolution of 10-90 μm. For some decays modes ATLAS is expected to obtain larger sample of events than the B-factories that are being proposed. It has been calculated that the systematic error σ sin (2 α) = 0.06 and σ sin ( 2 β) = 0.027 which is comparable with other future experiments

  14. ATLAS Silicon Microstrip Tracker Operation and Performance

    CERN Document Server

    Rosendahl, P L; The ATLAS collaboration

    2012-01-01

    The Semi-Conductor Tracker (SCT) is a silicon microstrip detector part of the ATLAS experiment at the CERN Large Hadron Collider (LHC). Together with the rest for the ATLAS Inner Detector (ID) it provides vital precision tracking information of charged particles. In this paper the performance and operational status of the SCT in the last two years of ATLAS data taking are reviewed.

  15. ATLAS Cloud R&D

    CERN Document Server

    Panitkin, S; The ATLAS collaboration; Caballero Bejar, J; Benjamin, D; DiGirolamo, A; Gable, I; Hendrix, V; Hover, J; Kucharczuk, K; Medrano LLamas, R; Love, P; Ohman, H; Paterson, M; Sobie, R; Taylor, R; Walker, R; Zaytsev, A

    2014-01-01

    The computing model of the ATLAS experiment was designed around the concept of grid computing and, since the start of data taking, this model has proven very successful. However, new cloud computing technologies bring attractive features to improve the operations and elasticity of scientific distributed computing. ATLAS sees grid and cloud computing as complementary technologies that will coexist at different levels of resource abstraction, and two years ago created an R&D working group to investigate the different integration scenarios. The ATLAS Cloud Computing R&D has been able to demonstrate the feasibility of offloading work from grid to cloud sites and, as of today, is able to integrate transparently various cloud resources into the PanDA workload management system. The ATLAS Cloud Computing R&D is operating various PanDA queues on private and public resources and has provided several hundred thousand CPU days to the experiment. As a result, the ATLAS Cloud Computing R&D group has gained...

  16. First ATLAS Events Recorded Underground

    CERN Multimedia

    Teuscher, R

    As reported in the CERN Bulletin, Issue No.30-31, 25 July 2005 The ATLAS barrel Tile calorimeter has recorded its first events underground using a cosmic ray trigger, as part of the detector commissioning programme. This is not a simulation! A cosmic ray muon recorded by the barrel Tile calorimeter of ATLAS on 21 June 2005 at 18:30. The calorimeter has three layers and a pointing geometry. The light trapezoids represent the energy deposited in the tiles of the calorimeter depicted as a thick disk. On the evening of June 21, the ATLAS detector, now being installed in the underground experimental hall UX15, reached an important psychological milestone: the barrel Tile calorimeter recorded the first cosmic ray events in the underground cavern. An estimated million cosmic muons enter the ATLAS cavern every 3 minutes, and the ATLAS team decided to make good use of some of them for the commissioning of the detector. Although only 8 of the 128 calorimeter slices ('superdrawers') were included in the trigg...

  17. The ATLAS distributed analysis system

    International Nuclear Information System (INIS)

    Legger, F

    2014-01-01

    In the LHC operations era, analysis of the multi-petabyte ATLAS data sample by globally distributed physicists is a challenging task. To attain the required scale the ATLAS Computing Model was designed around the concept of Grid computing, realized in the Worldwide LHC Computing Grid (WLCG), the largest distributed computational resource existing in the sciences. The ATLAS experiment currently stores over 140 PB of data and runs about 140,000 concurrent jobs continuously at WLCG sites. During the first run of the LHC, the ATLAS Distributed Analysis (DA) service has operated stably and scaled as planned. More than 1600 users submitted jobs in 2012, with 2 million or more analysis jobs per week, peaking at about a million jobs per day. The system dynamically distributes popular data to expedite processing and maximally utilize resources. The reliability of the DA service is high and steadily improving; Grid sites are continually validated against a set of standard tests, and a dedicated team of expert shifters provides user support and communicates user problems to the sites. Both the user support techniques and the direct feedback of users have been effective in improving the success rate and user experience when utilizing the distributed computing environment. In this contribution a description of the main components, activities and achievements of ATLAS distributed analysis is given. Several future improvements being undertaken will be described.

  18. Cassini Tour Atlas Automated Generation

    Science.gov (United States)

    Grazier, Kevin R.; Roumeliotis, Chris; Lange, Robert D.

    2011-01-01

    During the Cassini spacecraft s cruise phase and nominal mission, the Cassini Science Planning Team developed and maintained an online database of geometric and timing information called the Cassini Tour Atlas. The Tour Atlas consisted of several hundreds of megabytes of EVENTS mission planning software outputs, tables, plots, and images used by mission scientists for observation planning. Each time the nominal mission trajectory was altered or tweaked, a new Tour Atlas had to be regenerated manually. In the early phases of Cassini s Equinox Mission planning, an a priori estimate suggested that mission tour designers would develop approximately 30 candidate tours within a short period of time. So that Cassini scientists could properly analyze the science opportunities in each candidate tour quickly and thoroughly so that the optimal series of orbits for science return could be selected, a separate Tour Atlas was required for each trajectory. The task of manually generating the number of trajectory analyses in the allotted time would have been impossible, so the entire task was automated using code written in five different programming languages. This software automates the generation of the Cassini Tour Atlas database. It performs with one UNIX command what previously took a day or two of human labor.

  19. The ATLAS distributed analysis system

    Science.gov (United States)

    Legger, F.; Atlas Collaboration

    2014-06-01

    In the LHC operations era, analysis of the multi-petabyte ATLAS data sample by globally distributed physicists is a challenging task. To attain the required scale the ATLAS Computing Model was designed around the concept of Grid computing, realized in the Worldwide LHC Computing Grid (WLCG), the largest distributed computational resource existing in the sciences. The ATLAS experiment currently stores over 140 PB of data and runs about 140,000 concurrent jobs continuously at WLCG sites. During the first run of the LHC, the ATLAS Distributed Analysis (DA) service has operated stably and scaled as planned. More than 1600 users submitted jobs in 2012, with 2 million or more analysis jobs per week, peaking at about a million jobs per day. The system dynamically distributes popular data to expedite processing and maximally utilize resources. The reliability of the DA service is high and steadily improving; Grid sites are continually validated against a set of standard tests, and a dedicated team of expert shifters provides user support and communicates user problems to the sites. Both the user support techniques and the direct feedback of users have been effective in improving the success rate and user experience when utilizing the distributed computing environment. In this contribution a description of the main components, activities and achievements of ATLAS distributed analysis is given. Several future improvements being undertaken will be described.

  20. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  1. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  2. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  3. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  4. AGIS: The ATLAS Grid Information System

    Science.gov (United States)

    Anisenkov, A.; Di Girolamo, A.; Klimentov, A.; Oleynik, D.; Petrosyan, A.; Atlas Collaboration

    2014-06-01

    ATLAS, a particle physics experiment at the Large Hadron Collider at CERN, produced petabytes of data annually through simulation production and tens of petabytes of data per year from the detector itself. The ATLAS computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we describe the ATLAS Grid Information System (AGIS), designed to integrate configuration and status information about resources, services and topology of the computing infrastructure used by the ATLAS Distributed Computing applications and services.

  5. ATLAS Maintenance and Operation management system

    CERN Document Server

    Copy, B

    2007-01-01

    The maintenance and operation of the ATLAS detector will involve thousands of contributors from 170 physics institutes. Planning and coordinating the action of ATLAS members, ensuring their expertise is properly leveraged and that no parts of the detector are understaffed or overstaffed will be a challenging task. The ATLAS Maintenance and Operation application (referred to as Operation Task Planner inside the ATLAS experiment) offers a fluent web based interface that combines the flexibility and comfort of a desktop application, intuitive data visualization and navigation techniques, with a lightweight service oriented architecture. We will review the application, its usage within the ATLAS experiment, its underlying design and implementation.

  6. Last piece of the puzzle for ATLAS

    CERN Multimedia

    Clare Ryan

    At around 15.40 on Friday 29th February the ATLAS collaboration cracked open the champagne as the second of the small wheels was lowered into the cavern. Each of ATLAS' small wheels are 9.3 metres in diameter and weigh 100 tonnes including the massive shielding elements. They are the final parts of ATLAS' muon spectrometer. The first piece of ATLAS was installed in 2003 and since then many detector elements have journeyed down the 100 metre shaft into the ATLAS underground cavern. This last piece completes this gigantic puzzle.

  7. ATLAS experiment : mapping the secrets of the universe

    CERN Multimedia

    ATLAS Outreach

    2010-01-01

    This 4 page color brochure describes ATLAS and the LHC, the ATLAS inner detector, calorimeters, muon spectrometer, magnet system, a short definition of the terms "particles," "dark matter," "mass," "antimatter." It also explains the ATLAS collaboration and provides the ATLAS website address with some images of the detector and the ATLAS collaboration at work.

  8. ProstAtlas: A digital morphologic atlas of the prostate

    International Nuclear Information System (INIS)

    Betrouni, N.; Iancu, A.; Puech, P.; Mordon, S.; Makni, N.

    2012-01-01

    Computer-aided medical interventions and medical robotics for prostate cancer have known an increasing interest and research activity. However before the routine deployment of these procedures in clinical practice becomes a reality, in vivo and in silico validations must be undertaken. In this study, we developed a digital morphologic atlas of the prostate. We were interested by the gland, the peripheral zone and the central gland. Starting from an image base collected from 30 selected patients, a mean shape and most important deformations for each structure were deduced using principal component analysis. The usefulness of this atlas was highlighted in two applications: image simulation and physical phantom design

  9. The ATLAS positive ion injector

    International Nuclear Information System (INIS)

    Shepard, K.W.; Bollinger, L.M.; Pardo, R.C.

    1990-01-01

    This paper reviews the design, construction status, and beam tests to date of the positive ion injector (PII) which is replacing the tandem injector for the ATLAS heavy-ion facility. PII consists of an ECR ion source on a 350 KV platform injecting a very low velocity superconducting linac. The linac is composed of an independently-phased array of superconducting four-gap interdigital resonators which accelerate over a velocity range of .006 to .05c. In finished form, PII will be able to inject ions as heavy as uranium into the existing ATLAS linac. Although at the present time little more than 50% of the linac is operational, the indenpently-phased array is sufficiently flexible that ions in the lower half of the periodic table can be accelerated and injected into ATLAS. Results of recent operational experience will be discussed. 5 refs

  10. The ATLAS Detector Control System

    CERN Document Server

    Schlenker, S; Kersten, S; Hirschbuehl, D; Braun, H; Poblaguev, A; Oliveira Damazio, D; Talyshev, A; Zimmermann, S; Franz, S; Gutzwiller, O; Hartert, J; Mindur, B; Tsarouchas, CA; Caforio, D; Sbarra, C; Olszowska, J; Hajduk, Z; Banas, E; Wynne, B; Robichaud-Veronneau, A; Nemecek, S; Thompson, PD; Mandic, I; Deliyergiyev, M; Polini, A; Kovalenko, S; Khomutnikov, V; Filimonov, V; Bindi, M; Stanecka, E; Martin, T; Lantzsch, K; Hoffmann, D; Huber, J; Mountricha, E; Santos, HF; Ribeiro, G; Barillari, T; Habring, J; Arabidze, G; Boterenbrood, H; Hart, R; Marques Vinagre, F; Lafarguette, P; Tartarelli, GF; Nagai, K; D'Auria, S; Chekulaev, S; Phillips, P; Ertel, E; Brenner, R; Leontsinis, S; Mitrevski, J; Grassi, V; Karakostas, K; Iakovidis, G.; Marchese, F; Aielli, G

    2011-01-01

    The ATLAS experiment is one of the multi-purpose experiments at the Large Hadron Collider (LHC), constructed to study elementary particle interactions in collisions of high-energy proton beams. Twelve different sub-detectors as well as the common experimental infrastructure are supervised by the Detector Control System (DCS). The DCS enables equipment supervision of all ATLAS sub-detectors by using a system of >130 server machines running the industrial SCADA product PVSS. This highly distributed system reads, processes and archives of the order of 106 operational parameters. Higher level control system layers allow for automatic control procedures, efficient error recognition and handling, and manage the communication with external systems such as the LHC. This contribution firstly describes the status of the ATLAS DCS and the experience gained during the LHC commissioning and the first physics data taking operation period. Secondly, the future evolution and maintenance constraints for the coming years an...

  11. ATLAS Muon Drift Tube Electronics

    Energy Technology Data Exchange (ETDEWEB)

    Arai, Y [KEK, High Energy Accelerator Research Organisation, Tsukuba (Japan); Ball, B; Chapman, J W; Dai, T; Ferretti, C; Gregory, J [University of Michigan, Department of Physics, Ann Arbor, MI (United States); Beretta, M [INFN Laboratori Nazionali di Frascati, Frascati (Italy); Boterenbrood, H; Jansweijer, P P M [Nikhef National Institute for Subatomic Physics, Amsterdam (Netherlands); Brandenburg, G W; Fries, T; Costa, J Guimaraes da; Harder, S; Huth, J [Harvard University, Laboratory for Particle Physics and Cosmology, Cambridge, MA (United States); Ceradini, F [INFN Roma Tre and Universita Roma Tre, Dipartimento di Fisica, Roma (Italy); Hazen, E [Boston University, Physics Department, Boston, MA (United States); Kirsch, L E [Brandeis University, Department of Physics, Waltham, MA (United States); Koenig, A C [Radboud University Nijmegen/Nikhef, Dept. of Exp. High Energy Physics, Nijmegen (Netherlands); Lanza, A [INFN Pavia, Pavia (Italy); Mikenberg, G [Weizmann Institute of Science, Department of Particle Physics, Rehovot (Israel)], E-mail: brandenburg@physics.harvard.edu (and others)

    2008-09-15

    This paper describes the electronics used for the ATLAS monitored drift tube (MDT) chambers. These chambers are the main component of the precision tracking system in the ATLAS muon spectrometer. The MDT detector system consists of 1,150 chambers containing a total of 354,000 drift tubes. It is capable of measuring the sagitta of muon tracks to an accuracy of 60 {mu}m, which corresponds to a momentum accuracy of about 10% at p{sub T}= 1 TeV. The design and performance of the MDT readout electronics as well as the electronics for controlling, monitoring and powering the detector will be discussed. These electronics have been extensively tested under simulated running conditions and have undergone radiation testing certifying them for more than 10 years of LHC operation. They are now installed on the ATLAS detector and are operating during cosmic ray commissioning runs.

  12. ATLAS Muon Drift Tube Electronics

    CERN Document Server

    Arai, Y; Beretta, M; Boterenbrood, H; Brandenburg, G W; Ceradini, F; Chapman, J W; Dai, T; Ferretti, C; Fries, T; Gregory, J; Guimarães da Costa, J; Harder, S; Hazen, E; Huth, J; Jansweijer, P P M; Kirsch, L E; König, A C; Lanza, A; Mikenberg, G; Oliver, J; Posch, C; Richter, R; Riegler, W; Spiriti, E; Taylor, F E; Vermeulen, J; Wadsworth, B; Wijnen, T A M

    2008-01-01

    This paper describes the electronics used for the ATLAS monitored drift tube (MDT) chambers. These chambers are the main component of the precision tracking system in the ATLAS muon spectrometer. The MDT detector system consists of 1,150 chambers containing a total of 354,000 drift tubes. It is capable of measuring the sagitta of muon tracks to an accuracy of 60 microns, which corresponds to a momentum accuracy of about 10% at pT = 1 TeV. The design and performance of the MDT readout electronics as well as the electronics for controlling, monitoring and powering the detector will be discussed. These electronics have been extensively tested under simulated running conditions and have undergone radiation testing certifying them for more than 10 years of LHC operation. They are now installed on the ATLAS detector and are operating during cosmic ray commissioning runs.

  13. Top quark properties at ATLAS

    CERN Document Server

    Dilip, Jana

    2008-01-01

    The ATLAS potential for the study of the top quark properties and physics beyond the Standard Model in the top quark sector, is described. The measurements of the top quark charge, the spin and spin correlations, the Standard Model decay (t-> bW), rare top quark decays associated to flavour changing neutral currents (t-> qX with X = gluon, Z, photon) and ttbar resonances are discussed. The sensitivity of the ATLAS experiment is estimated for an expected luminosity of 1fb-1 at the LHC. The full simulation of the ATLAS detector is used. For the Standard Model measurements the expected precision is presented. For the tests of physics beyond the Standard Model, the 5 sigma discovery potential (in the presence of a signal) and the 95% Confidence Level (CL) limit (in the absence of a signal) are given.

  14. ATLAS honours two Swiss companies

    CERN Document Server

    2003-01-01

    On 18 June 2003, ATLAS presented awards to two Swiss companies, Cicorel SA and Isola Composites AG, the suppliers of the electrodes and the composite bars for the electromagnetic calorimeter. "Physicists' dreams could not become reality without industry's active participation and creativity", said Peter Jenni, ATLAS spokesman, congratulating two of the collaboration's suppliers, to which it presented awards on 18 June. Swiss quality was the order of the day, since the two companies, Cicorel SA and Isola Composites AG, which are both involved in the production of components for the electromagnetic calorimeter, are located in Switzerland's Jura region. "You have taken up and met a challenge that bordered on the impossible", added Peter Jenni. The suppliers who received the ATLAS award: Hans Wyss from Cicorel SA (left) and Constant Gentile from Isola Composites (right).Circorel SA produced enough electrodes to cover an entire football pitch. Each electrode, measuring 2 square metres, consists of three layers of...

  15. ATLAS Pixel Detector Operational Experience

    CERN Document Server

    Di Girolamo, B; The ATLAS collaboration

    2011-01-01

    The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 96.9% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

  16. New ATLAS Software & Computing Organization

    CERN Multimedia

    Barberis, D

    Following the election by the ATLAS Collaboration Board of Dario Barberis (Genoa University/INFN) as Computing Coordinator and David Quarrie (LBNL) as Software Project Leader, it was considered necessary to modify the organization of the ATLAS Software & Computing ("S&C") project. The new organization is based upon the following principles: separation of the responsibilities for computing management from those of software development, with the appointment of a Computing Coordinator and a Software Project Leader who are both members of the Executive Board; hierarchical structure of responsibilities and reporting lines; coordination at all levels between TDAQ, S&C and Physics working groups; integration of the subdetector software development groups with the central S&C organization. A schematic diagram of the new organization can be seen in Fig.1. Figure 1: new ATLAS Software & Computing organization. Two Management Boards will help the Computing Coordinator and the Software Project...

  17. Two ATLAS trackers become one

    CERN Multimedia

    2006-01-01

    The ATLAS inner detector barrel comes one step closer to completion as the semiconductor tracker is merged with the transition radiation tracker. ATLAS collaborators prepare for the insertion of the semiconductor tracker (SCT, behind) into the transition radiation tracker (TRT, in front). Some had hoped it would fall on Valentine's Day. But despite the slight delay, Friday 17 February was lovingly embraced as 'Conception Day,' when dozens of physicists and engineers from the international collaboration gathered to witness the insertion of the ATLAS semiconductor tracker into the transition radiation tracker, a major milestone in the assembly of the experiment's inner detector. With just millimeters of room for error, the cylindrical trackers were slid into each other as inner detector integration coordinator Heinz Pernegger issued commands and scientists held out flashlights, lay on their backs and stood on ladders to take careful measurements. Each tracker is the result of about 10 years of international ...

  18. The ATLAS Glasgow Overview Week

    CERN Multimedia

    Richard Hawkings

    2007-01-01

    The ATLAS Overview Weeks always provide a good opportunity to see the status and progress throughout the experiment, and the July week at Glasgow University was no exception. The setting, amidst the traditional buildings of one of the UK's oldest universities, provided a nice counterpoint to all the cutting-edge research and technology being discussed. And despite predictions to the contrary, the weather at these northern latitudes was actually a great improvement on the previous few weeks in Geneva. The meeting sessions comprehensively covered the whole ATLAS project, from the subdetector and TDAQ systems and their commissioning, through to offline computing, analysis and physics. As a long-time ATLAS member who remembers plenary meetings in 1991 with 30 people drawing detector layouts on a whiteboard, the hardware and installation sessions were particularly impressive - to see how these dreams have been translated into 7000 tons of reality (and with attendant cabling, supports and services, which certainly...

  19. Hidden Valley Search at ATLAS

    CERN Document Server

    Verducci, M; The ATLAS collaboration

    2011-01-01

    A number of extensions of the Standard Model result in neutral and weakly-coupled particles that decay to multi hadrons or multi leptons with macroscopic decay lengths. These particles with decay paths that can be comparable with ATLAS detector dimensions represent, from an experimental point of view, a challenge both for the trigger and for the reconstruction capabilities of the ATLAS detector. We will present a set of signature driven triggers for the ATLAS detector that target such displaced decays and evaluate their performances for some benchmark models. and describe analysis strategies and limits on the production of such long-lived particles that can be achieved with the first 100 pb-1.

  20. ATLAS DQ2 Deletion Service

    International Nuclear Information System (INIS)

    Oleynik, Danila; Petrosyan, Artem; Garonne, Vincent; Campana, Simone

    2012-01-01

    The ATLAS Distributed Data Management project DQ2 is responsible for the replication, access and bookkeeping of ATLAS data across more than 100 distributed grid sites. It also enforces data management policies decided on by the collaboration and defined in the ATLAS computing model. The DQ2 Deletion Service is one of the most important DDM services. This distributed service interacts with 3rd party grid middleware and the DQ2 catalogues to serve data deletion requests on the grid. Furthermore, it also takes care of retry strategies, check-pointing transactions, load management and fault tolerance. In this paper special attention is paid to the technical details which are used to achieve the high performance of service, accomplished without overloading either site storage, catalogues or other DQ2 components. Special attention is also paid to the deletion monitoring service that allows operators a detailed view of the working system.

  1. The ATLAS positive ion injector

    Energy Technology Data Exchange (ETDEWEB)

    Shepard, K.W.; Bollinger, L.M.; Pardo, R.C.

    1990-01-01

    This paper reviews the design, construction status, and beam tests to date of the positive ion injector (PII) which is replacing the tandem injector for the ATLAS heavy-ion facility. PII consists of an ECR ion source on a 350 KV platform injecting a very low velocity superconducting linac. The linac is composed of an independently-phased array of superconducting four-gap interdigital resonators which accelerate over a velocity range of .006 to .05c. In finished form, PII will be able to inject ions as heavy as uranium into the existing ATLAS linac. Although at the present time little more than 50% of the linac is operational, the indenpently-phased array is sufficiently flexible that ions in the lower half of the periodic table can be accelerated and injected into ATLAS. Results of recent operational experience will be discussed. 5 refs.

  2. The Pig PeptideAtlas

    DEFF Research Database (Denmark)

    Hesselager, Marianne Overgaard; Codrea, Marius; Sun, Zhi

    2016-01-01

    Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data...... repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been...... underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within...

  3. ATLAS Detector Interface Group

    CERN Multimedia

    Mapelli, L

    Originally organised as a sub-system in the DAQ/EF-1 Prototype Project, the Detector Interface Group (DIG) was an information exchange channel between the Detector systems and the Data Acquisition to provide critical detector information for prototype design and detector integration. After the reorganisation of the Trigger/DAQ Project and of Technical Coordination, the necessity to provide an adequate context for integration of detectors with the Trigger and DAQ lead to organisation of the DIG as one of the activities of Technical Coordination. Such an organisation emphasises the ATLAS wide coordination of the Trigger and DAQ exploitation aspects, which go beyond the domain of the Trigger/DAQ project itself. As part of Technical Coordination, the DIG provides the natural environment for the common work of Trigger/DAQ and detector experts. A DIG forum for a wide discussion of all the detector and Trigger/DAQ integration issues. A more restricted DIG group for the practical organisation and implementation o...

  4. Diphoton searches in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00213273; The ATLAS collaboration

    2016-01-01

    Searches for new resonances decaying into two photons in the ATLAS experiment at the LHC are described. The analysis is based on $pp$ collision data corresponding to an integrated luminosity of 3.2 fb$^{-1}$ at $\\sqrt{s}$ = 13 TeV recorded in 2015. Two different searches are performed, one targeted for a spin-2 particle, using Randall-Sundrum graviton states as a benchmark model, and one optimized for a spin-0 particle. The most significant deviation from the background predictions is observed at a diphoton invariant mass around 750 GeV with local significances of 3.6 and 3.9 standard deviations in the searches optimized for a spin-2 and spin-0 particle, respectively. The global significances are estimated to be 1.8 and 2.0 standard deviations. The consistency between the data collected at 13 TeV and 8 TeV is also evaluated. Limits on the production cross-section for the two benchmark resonances are reported.

  5. ATLAS Tau Trigger

    CERN Document Server

    Belanger-Champagne, C; Bosman, M; Brenner, R; Casado, MP; Czyczula, Z; Dam, M; Demers, S; Farrington, S; Igonkina, O; Kalinowski, A; Kanaya, N; Osuna, C; Pérez, E; Ptacek, E; Reinsch, A; Saavedra, A; Sopczak, A; Strom, D; Torrence, E; Tsuno, S; Vorwerk, V; Watson, A; Xella, S

    2008-01-01

    Moving to the high energy scale of the LHC, the identification of tau leptons will become a necessary and very powerful tool, allowing a discovery of physics beyond Standard Model. Many models, among them light SM Higgs and various SUSY models, predict an abundant production of taus with respect to other leptons. The reconstruction of hadronic tau decays, although a very challenging task in hadronic enviroments, allows to increase a signal efficiency by at least of factor 2, and provides an independent control sample to disantangle lepton tau decays from prompt electrons and muons. Thanks to the advanced calorimetry and tracking, the ATLAS experiment has developed tools to efficiently identify hadronic taus at the trigger level. In this presentation we will review the characteristics of taus and the methods to suppress low-multiplicity, low-energy jets contributions as well as we will address the tau trigger chain which provide a rejection rate of 10^5. We will further present plans for commissioning the ATLA...

  6. ATLAS TRT 2002 Workshop

    CERN Multimedia

    Capeans, M.

    Starting on 17th May, the ATLAS TRT 2002 Workshop was organised by Ken MacFarlane and his team at Hampton University, Virginia, USA. During a welcome break in the very dense workshop programme, the group enjoyed a half-day long boat trip along the waterways, offering a first-hand look at the history and heritage of this part of America. The attendance during the six-day workshop was about 50 people representing most of the collaborating institutes, although many Russian colleagues had stayed in their institutes to pursue the start-up of end-cap wheel production at PNPI and DUBNA. The meeting clearly showed that, during the year 2002, the TRT community is focusing on final design issues and module/wheel construction, while moving at the same time towards acceptance testing and integration, including the front-end electronics. The two main topics treated at the workshop were the preparation for beginning full production of the FE electronics, and the wire-joint problem that the US barrel colleagues have been fa...

  7. Electroweak probes with ATLAS

    CERN Document Server

    Milov, Alexander; The ATLAS collaboration

    2018-01-01

    Measuring electroweak bosons in relativistic heavy ion collisions at high energy provide an opportunity to understand temporal evolution of the quark-gluon plasma created in such collisions by constraining the initial state of the interaction. Due to lack of colour charges the bosons and or particles produced in their leptonic decays are unaffected by the quark-gluon plasma and therefore preserve the information about the very early stage of the collision when they were born. This singles EW bosons as a unique and very interesting class of observables in HI collisions. The ATLAS experiment at LHC measures production of electroweak bosons in $pp$, $p$+Pb and Pb+Pb collisions systems. A review of the existing results is given in this proceeding that includes studies made with isolated photons to constraint kinematic properties and flavour composition of associated jets, measurements of $W$ and $Z$ bosons used to estimate nuclear modification of PDF and the production rates of the bosons used to verify geometric...

  8. Radon atlas of Finland

    International Nuclear Information System (INIS)

    Voutilainen, A.; Maekelaeinen, I.; Pennanen, M.; Reisbacka, H.; Castren, O.

    1997-11-01

    The most efficient means of reducing indoor radon exposure is to locate and mitigate dwellings with radon concentration exceeding the action level of 400 Bq/m 3 and to build new houses so that radon concentrations do not exceed 200 Bq/m 3 . The maps and tables in this report are useful tools for those who plan and decide what kind of radon mitigation measures are needed in municipalities. STUK (The Radiation and Nuclear Safety Authority) has an indoor radon database of 52 000 dwellings, for which the indoor radon concentration and construction details are known. The building site soil type of about 38 000 dwellings is known. This atlas is a summary of all indoor radon measurements made by STUK in lowrise dwellings and in first-floor flats. The results are shown as arithmetic means of 5- or 10-km squares on maps of the provinces. Three radon maps have been made for each province. On one map the data consist of all measurements the position coordinates of which are known. On the two other maps the building sites of houses are classified into permeable and low-permeable soil types. The tables show statistics for all indoor radon measurements by municipality and building site soil type. (orig.)

  9. ATLAS Data Challenge 1

    CERN Document Server

    Poulard, G

    2003-01-01

    In 2002 the ATLAS experiment started a series of Data Challenges (DC) of which the goals are the validation of the Computing Model, of the complete software suite, of the data model, and to ensure the correctness of the technical choices to be made. A major feature of the first Data Challenge (DC1) was the preparation and the deployment of the software required for the production of large event samples for the High Level Trigger (HLT) and physics communities, and the production of those samples as a world-wide distributed activity. The first phase of DC1 was run during summer 2002, and involved 39 institutes in 18 countries. More than 10 million physics events and 30 million single particle events were fully simulated. Over a period of about 40 calendar days 71000 CPU-days were used producing 30 Tbytes of data in about 35000 partitions. In the second phase the next processing step was performed with the participation of 56 institutes in 21 countries (~ 4000 processors used in parallel). The basic elements of ...

  10. Argonne's atlas control system upgrade

    International Nuclear Information System (INIS)

    Munson, F.; Quock, D.; Chapin, B.; Figueroa, J.

    1999-01-01

    The ATLAS facility (Argonne Tandem-Linac Accelerator System) is located at the Argonne National Laboratory. The facility is a tool used in nuclear and atomic physics research, which focuses primarily on heavy-ion physics. The accelerator as well as its control system are evolutionary in nature, and consequently, continue to advance. In 1998 the most recent project to upgrade the ATLAS control system was completed. This paper briefly reviews the upgrade, and summarizes the configuration and features of the resulting control system

  11. ATLAS computing on CSCS HPC

    Science.gov (United States)

    Filipcic, A.; Haug, S.; Hostettler, M.; Walker, R.; Weber, M.

    2015-12-01

    The Piz Daint Cray XC30 HPC system at CSCS, the Swiss National Supercomputing centre, was the highest ranked European system on TOP500 in 2014, also featuring GPU accelerators. Event generation and detector simulation for the ATLAS experiment have been enabled for this machine. We report on the technical solutions, performance, HPC policy challenges and possible future opportunities for HEP on extreme HPC systems. In particular a custom made integration to the ATLAS job submission system has been developed via the Advanced Resource Connector (ARC) middleware. Furthermore, a partial GPU acceleration of the Geant4 detector simulations has been implemented.

  12. ATLAS computing on CSCS HPC

    CERN Document Server

    Hostettler, Michael Artur; The ATLAS collaboration; Haug, Sigve; Walker, Rodney; Weber, Michele

    2015-01-01

    The Piz Daint Cray XC30 HPC system at CSCS, the Swiss National Supercomputing centre, was in 2014 the highest ranked European system on TOP500, also featuring GPU accelerators. Event generation and detector simulation for the ATLAS experiment have been enabled for this machine. We report on the technical solutions, performance, HPC policy challenges and possible future opportunities for HEP on extreme HPC systems. In particular a custom made integration to the ATLAS job submission system has been developed via the Advanced Resource Connector (ARC) middleware. Furthermore, some GPU acceleration of the Geant4 detector simulations has been implemented to justify the allocation request for this machine.

  13. ATLAS computing on CSCS HPC

    CERN Document Server

    Filipcic, Andrej; The ATLAS collaboration; Weber, Michele; Walker, Rodney; Hostettler, Michael Artur

    2015-01-01

    The Piz Daint Cray XC30 HPC system at CSCS, the Swiss National Supercomputing centre, is in 2014 the highest ranked European system on TOP500, also featuring GPU accelerators. Event generation and detector simulation for the ATLAS experiment has been enabled for this machine. We report on the technical solutions, performance, HPC policy challenges and possible future opportunities for HEP on extreme HPC systems. In particular a custom made integration to the ATLAS job submission system has been developed via the Advanced Resource Connector (ARC) middleware. Further, some GPU acceleration of the Geant4 detector simulations were implemented to justify the allocation request for this machine.

  14. LUCID: the ATLAS Luminosity Detector

    CERN Document Server

    Fabbri, Laura; The ATLAS collaboration

    2018-01-01

    A precise measurement of luminosity is a key component of the ATLAS program: its uncertainty is a systematics for all cross-section measurements, from Standard Model processes to new discoveries, and for some precise measurements it can be dominant. To be predictive a precision compatible with PDF uncertainty ( 1-2%) is desired. LUCID (LUminosity Cherenkov Integrating Detector) is sensitive to charged particles generated by the pp collisions. It is the only ATLAS dedicated detector for this purpose and the referred one during the second run of LHC data taking.

  15. Pocket atlas of radiographic anatomy

    International Nuclear Information System (INIS)

    Moeller, T.B.; Reif, E.; Stark, P.

    1993-01-01

    The 'Pocket Atlas of Radiographic Anatomy' presents 170 radiographs of the various body regions of adults, showing only the normal radiographic anatomy. Each radiograph is supplemented on the opposite page by a drawing of the particular body region. There is no commenting text, but the drawings are provided with captions in English. The atlas is a useful guide for interpreting radiographs. The pictures are arranged in chapters entitled as follows: Skeletal Imaging (skull, spine, upper extremity), lower extremity; Miscellaneous Plain Films (chest, mammogram, trachea, lung tomograms); Contrast Examinations (gastrointestinal tract, intravenous contrast examinations, arthrography, angiography); Special Examinations (myelograms, lymphangiograms, bronchograms, sialograms). (UWA). 348 figs [de

  16. Dissecting DNA repair in adult high grade gliomas for patient stratification in the post-genomic era

    Science.gov (United States)

    Perry, Christina; Agarwal, Devika; Abdel-Fatah, Tarek M.A.; Lourdusamy, Anbarasu; Grundy, Richard; Auer, Dorothee T.; Walker, David; Lakhani, Ravi; Scott, Ian S.; Chan, Stephen; Ball, Graham; Madhusudan, Srinivasan

    2014-01-01

    Deregulation of multiple DNA repair pathways may contribute to aggressive biology and therapy resistance in gliomas. We evaluated transcript levels of 157 genes involved in DNA repair in an adult glioblastoma Test set (n=191) and validated in ‘The Cancer Genome Atlas’ (TCGA) cohort (n=508). A DNA repair prognostic index model was generated. Artificial neural network analysis (ANN) was conducted to investigate global gene interactions. Protein expression by immunohistochemistry was conducted in 61 tumours. A fourteen DNA repair gene expression panel was associated with poor survival in Test and TCGA cohorts. A Cox multivariate model revealed APE1, NBN, PMS2, MGMT and PTEN as independently associated with poor prognosis. A DNA repair prognostic index incorporating APE1, NBN, PMS2, MGMT and PTEN stratified patients in to three prognostic sub-groups with worsening survival. APE1, NBN, PMS2, MGMT and PTEN also have predictive significance in patients who received chemotherapy and/or radiotherapy. ANN analysis of APE1, NBN, PMS2, MGMT and PTEN revealed interactions with genes involved in transcription, hypoxia and metabolic regulation. At the protein level, low APE1 and low PTEN remain associated with poor prognosis. In conclusion, multiple DNA repair pathways operate to influence biology and clinical outcomes in adult high grade gliomas. PMID:25026297

  17. EnviroAtlas Proximity to Parks Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset shows...

  18. EnviroAtlas Near Road Tree Buffer Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset...

  19. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  20. The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

    OpenAIRE

    Willnow, TE; Antignac, C; Brändli, AW; Christensen, EI; Cox, RD; Davidson, D; Davies, JA; Devuyst, O; Eichele, G; Hastie, ND; Verroust, PJ; Schedl, A; Meij, IC

    2005-01-01

    Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a thr...

  1. Oncogenic Signaling Pathways in The Cancer Genome Atlas

    NARCIS (Netherlands)

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

    2018-01-01

    Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number

  2. Heavy ion results from ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00241915; The ATLAS collaboration

    2017-01-01

    These proceedings provide an overview of the new results obtained with the ATLAS Detector at the LHC, which are presented in the Quark Matter 2017 conference. These results are covered in twelve parallel talks, one flash talk and eleven posters, and they are grouped into five areas: initial state, jet quenching, quarkonium production, longitudinal flow dynamics, and collectivity in small systems.

  3. New ATLAS Higgs physics results

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    New Higgs physics results from the ATLAS experiment using the full Run-1 LHC dataset, corresponding to an integrated luminosity of approximately 25 fb-1, of proton-proton collisions at 7 TeV and 8 TeV, will be presented.

  4. Atlas of the Soviet Union.

    Science.gov (United States)

    Young, Harry F.

    This atlas consists of 20 maps, tables, charts, and graphs with complementary text illustrating Soviet government machinery, trade and political relations, and military stance. Some topics depicted by charts and graphs include: (1) Soviet foreign affairs machinery; (2) Soviet intelligence and security services; (4) Soviet position in the United…

  5. ATLAS Experiment Brochure - Chinese (Traditional)

    CERN Multimedia

    AUTHOR|(CDS)2081027

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  6. ATLAS Experiment Brochure - Chinese (Simplified)

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  7. ATLAS: Now under new management

    CERN Multimedia

    Katarina Anthony

    2013-01-01

    On 1 March, the ATLAS Collaboration welcomed a new spokesperson, Dave Charlton (University of Birmingham), and two new deputy spokespersons, Thorsten Wengler (CERN) and Beate Heinemann (University of California, Berkeley and LBNL). The Bulletin takes a look at what’s in store for one of the world’s largest scientific collaborations.   ATLAS members at the 2010 collaboration meeting in Copenhagen. Image: Rune Johansen and Troels Petersen. ATLAS spokesperson Dave Charlton has seen the collaboration through countless milestones: from construction to start-up to the 4 July 2012 announcement, he’s been an integral part of the team. Now, after twelve years with the collaboration, Dave is moving into the main office for the next two years. “2012 was a landmark year for ATLAS,” says Dave. “We spent a lot of time in the limelight and, in many ways, all eyes are still on us. But with the shutdown now under way, our focus is ...

  8. Higgs boson properties in ATLAS

    CERN Document Server

    Mansoulie, Bruno; The ATLAS collaboration

    2017-01-01

    The measurement by the ATLAS collaboration of Higgs boson properties is presented, in terms of production cross-sections, simplified template cross-sections, couplings. The measurements are based on the analysis of the H decay channels to diphoton and 4 leptons, using 36.1 fb-1 of 13 TeV data recorded in 2015 and 2016.

  9. The ATLAS Distributed Analysis System

    CERN Document Server

    Legger, F; The ATLAS collaboration; Pacheco Pages, A; Stradling, A

    2013-01-01

    In the LHC operations era, analysis of the multi-petabyte ATLAS data sample by globally distributed physicists is a challenging task. To attain the required scale the ATLAS Computing Model was designed around the concept of grid computing, realized in the Worldwide LHC Computing Grid (WLCG), the largest distributed computational resource existing in the sciences. The ATLAS experiment currently stores over 140 PB of data and runs about 140,000 concurrent jobs continuously at WLCG sites. During the first run of the LHC, the ATLAS Distributed Analysis (DA) service has operated stably and scaled as planned. More than 1600 users submitted jobs in 2012, with 2 million or more analysis jobs per week, peaking at about a million jobs per day. The system dynamically distributes popular data to expedite processing and maximally utilize resources. The reliability of the DA service is high but steadily improving; grid sites are continually validated against a set of standard tests, and a dedicated team of expert shifters ...

  10. The ATLAS Distributed Analysis System

    CERN Document Server

    Legger, F; The ATLAS collaboration

    2014-01-01

    In the LHC operations era, analysis of the multi-petabyte ATLAS data sample by globally distributed physicists is a challenging task. To attain the required scale the ATLAS Computing Model was designed around the concept of grid computing, realized in the Worldwide LHC Computing Grid (WLCG), the largest distributed computational resource existing in the sciences. The ATLAS experiment currently stores over 140 PB of data and runs about 140,000 concurrent jobs continuously at WLCG sites. During the first run of the LHC, the ATLAS Distributed Analysis (DA) service has operated stably and scaled as planned. More than 1600 users submitted jobs in 2012, with 2 million or more analysis jobs per week, peaking at about a million jobs per day. The system dynamically distributes popular data to expedite processing and maximally utilize resources. The reliability of the DA service is high but steadily improving; grid sites are continually validated against a set of standard tests, and a dedicated team of expert shifters ...

  11. ATLAS Assembly Hall Open Day

    CERN Multimedia

    Patrice Loiez

    2004-01-01

    To mark the 50th Anniversary of the founding of CERN, a day of tours, displays and presentations was held in October 2004. The assembly halls for the experiments that were waiting to be installed on the LHC, such as ATLAS shown here, were transformed into display areas and cafés.

  12. A Lego version of ATLAS

    CERN Multimedia

    Laëtitia Pedroso

    2010-01-01

    There's nothing very unusual about a small child making simple objects out of Lego. But wouldn't you be surprised to learn that one six-year old has just made a life-like model of the ATLAS detector?   Bastian with his Lego ATLAS detector. © Photo provided by Kai Nicklas, Bastian's father. It all began a month ago when the boy's father was watching a video about the construction of the ATLAS detector on the Internet. He hadn't noticed that his son was watching it over his shoulder. The small boy was fascinated by what he was seeing on the computer screen and his first reaction was to exclaim: "Wow! That's a terrific machine! I think the people who built it must be really clever." The detector must have really fired his imagination because, after asking his father a few questions, he decided to make a Lego model of it. Look at the photo and you will see how closely the model he produced resembles the actual ATLAS detector. Is the little boy in question, Bastia...

  13. Inside the ATLAS solenoid cryostat

    CERN Multimedia

    Claudia Marcelloni

    2006-01-01

    Scientists are seen working on the inside of the ATLAS cryostat, which will be used to cool liquid argon to 90 K in the electromagnetic calorimeter. Thin lead plates immersed in the cooled liquid will produce electromagnetic showers of particles when an electron, positron or photon enter the detector. This causes the argon to glow, allowing the initial particle energy to be measured.

  14. The ATLAS semiconductor tracker (SCT)

    International Nuclear Information System (INIS)

    Jackson, J.N.

    2005-01-01

    The ATLAS detector (CERN,LHCC,94-43 (1994)) is designed to study a wide range of physics at the CERN Large Hadron Collider (LHC) at luminosities up to 10 34 cm -2 s -1 with a bunch-crossing rate of 40 MHz. The Semiconductor Tracker (SCT) forms a key component of the Inner Detector (vol. 1, ATLAS TDR 4, CERN,LHCC 97-16 (1997); vol. 2, ATLAS TDR 5, CERN,LHCC 97-17 (1997)) which is situated inside a 2 T solenoid field. The ATLAS Semiconductor Tracker (SCT) utilises 4088 silicon modules with binary readout mounted on carbon fibre composite structures arranged in the forms of barrels in the central region and discs in the forward region. The construction of the SCT is now well advanced. The design of the SCT modules, services and support structures will be briefly outlined. A description of the various stages in the construction process will be presented with examples of the performance achieved and the main difficulties encountered. Finally, the current status of the construction is reviewed

  15. Hunting New Physics with ATLAS

    CERN Document Server

    Mitsou, Vasiliki A.; The ATLAS collaboration

    2017-01-01

    Highlights from recent new physics searches with the ATLAS detector at the CERN LHC will be presented. They include searches for supersymmetry, extra-dimension models, compositeness, new gauge bosons, leptoquarks, among others. Results are based on analysis of pp collision data recorded at a centre-of-mass energy of 13 TeV.

  16. Getting ATLAS ready for Physics

    CERN Multimedia

    CERN. Geneva

    2007-01-01

    The ATLAS detector is reaching completion and all subsystems are being commissioned into global operation. Periodic runs with cosmics allow tuning of the entire chain of controls and data taking up to physics analysis. The scenario of early physics reach will also be presented.

  17. ATLAS results on soft diffraction

    CERN Document Server

    Monzani, Simone

    2013-01-01

    The measurements of the total inelastic cross section and the differential inelastic cross section as a function of rapidity gap are presented. The data used for these studies were collected in $pp$ collisions at a center-of-mass energy of 7 TeV with the ATLAS detector at the LHC in 2010.

  18. ATLAS DDM integration in ARC

    International Nuclear Information System (INIS)

    Behrmann, G; Cameron, D; Ellert, M; Kleist, J; Taga, A

    2008-01-01

    The Nordic Data Grid Facility (NDGF) consists of Grid resources running ARC middleware in Denmark, Finland, Norway and Sweden. These resources serve many virtual organisations and contribute a large fraction of total worldwide resources for the ATLAS experiment, whose data is distributed and managed by the DQ2 software. Managing ATLAS data within NDGF and between NDGF and other Grids used by ATLAS (the Enabling Grids for E-sciencE Grid and the Open Science Grid) presents a unique challenge for several reasons. Firstly, the entry point for data, the Tier 1 centre, is physically distributed among heterogeneous resources in several countries and yet must present a single access point for all data stored within the centre. The middleware framework used in NDGF differs significantly from other Grids, specifically in the way that all data movement and registration is performed by services outside the worker node environment. Also, the service used for cataloging the location of data files is different from other Grids but must still be useable by DQ2 and ATLAS users to locate data within NDGF. This paper presents in detail how we solve these issues to allow seamless access worldwide to data within NDGF

  19. The Atlas load protection switch

    CERN Document Server

    Davis, H A; Dorr, G; Martínez, M; Gribble, R F; Nielsen, K E; Pierce, D; Parsons, W M

    1999-01-01

    Atlas is a high-energy pulsed-power facility under development to study materials properties and hydrodynamics experiments under extreme conditions. Atlas will implode heavy liner loads (m~45 gm) with a peak current of 27-32 MA delivered in 4 mu s, and is energized by 96, 240 kV Marx generators storing a total of 23 MJ. A key design requirement for Atlas is obtaining useful data for 95601130f all loads installed on the machine. Materials response calculations show current from a prefire can damage the load requiring expensive and time consuming replacement. Therefore, we have incorporated a set of fast-acting mechanical switches in the Atlas design to reduce the probability of a prefire damaging the load. These switches, referred to as the load protection switches, short the load through a very low inductance path during system charge. Once the capacitors have reached full charge, the switches open on a time scale short compared to the bank charge time, allowing current to flow to the load when the trigger pu...

  20. Hunting New Physics with ATLAS

    CERN Document Server

    Mitsou, Vasiliki A.; The ATLAS collaboration

    2017-01-01

    Highlights from recent new physics searches with the ATLAS detector at the CERN LHC are presented in this paper. They include searches for extra-dimension models, compositeness, new gauge bosons, supersymmetry, among others. Results are based on analyses of pp collision data recorded at a centre-of-mass energy of 13 TeV.

  1. Highlights from the ATLAS experiment

    CERN Document Server

    Grabowska-Bold, Iwona; The ATLAS collaboration

    2018-01-01

    An overview of the heavy-ion results from the ATLAS experiment is given. It includes a discussion of measurements with non-UPC dimuons in Pb+Pb collisions, dijet asymmetry, charged-hadron Raa and flow harmonics in the Xe+Xe collisions, vn-pt correlations in Pb+Pb collisions, symmetric and asymmetric cumulants in small systems and many more.

  2. Superconducting rf development at ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Shepard, K.W.; Kedzie, M.; Clifft, B.E. [Argonne National Lab., IL (United States); Roy, A.; Potukuchi, P. [Nuclear Science Centre, New Delhi (India); Givens, J.; Potter, J.; Crandall, K. [AccSys Technology, Inc., Pleasanton, CA (United States); Added, N. [Sao Paulo Univ., SP (Brazil)

    1993-12-31

    The ATLAS superconducting heavy-ion linac began operation in 1978 and has operated nearly continuously since that time, while undergoing a series of upgrades and expansions, the most recent being the ``uranium upgrade`` completed earlier this year and described below. In its present configuration the ATLAS linac consists of an array of 64 resonant cavities operating from 48 to 145 MHz, which match a range of particle velocities .007 < {beta} = v/c < .2. The linac provides approximately 50 MV of effective accelerating potential for ions of q/m > 1/10 over the entire periodic table. Delivered beams include 5 {minus} 7 pnA of {sup 238}U{sup 39+} at 1535 MeV. At present more than 10{sup 6} cavity-hours of operation at surface electric fields of 15 MV/m have been accumulated. Superconducting structure development at ATLAS is aimed at improving the cost/performance of existing low velocity structures both for possible future ATLAS upgrades, and also for heavy-ion linacs at other institutions. An application of particular current interest is to develop structures suitable for accelerating radioactive ion beams. Such structures must accelerate very low charge to mass ratio beams and must also have very large transverse acceptance.

  3. Radiography atlas of domestic animals

    International Nuclear Information System (INIS)

    Ruebel, G.A.; Isenbuegel, E.; Wolvekamp, P.; Gabrisch, K.; Grimm, F.; Koblik, P.; Paul-Murphy, J.; Oschwald, C.P.; Schildger, B.J.

    1991-01-01

    The 370 radiographs presented in the atlas together with notes and explanations give information on normal roentgenographic findings, physiological variations, and important pathological findings observed in small mammals, birds, reptilia and amphibia. Introductory notes to each chapter explain the principles of exposure techniques and the handling of the animals. (VHE) [de

  4. The effect of morphometric atlas selection on multi-atlas-based automatic brachial plexus segmentation

    International Nuclear Information System (INIS)

    Van de Velde, Joris; Wouters, Johan; Vercauteren, Tom; De Gersem, Werner; Achten, Eric; De Neve, Wilfried; Van Hoof, Tom

    2015-01-01

    The present study aimed to measure the effect of a morphometric atlas selection strategy on the accuracy of multi-atlas-based BP autosegmentation using the commercially available software package ADMIRE® and to determine the optimal number of selected atlases to use. Autosegmentation accuracy was measured by comparing all generated automatic BP segmentations with anatomically validated gold standard segmentations that were developed using cadavers. Twelve cadaver computed tomography (CT) atlases were included in the study. One atlas was selected as a patient in ADMIRE®, and multi-atlas-based BP autosegmentation was first performed with a group of morphometrically preselected atlases. In this group, the atlases were selected on the basis of similarity in the shoulder protraction position with the patient. The number of selected atlases used started at two and increased up to eight. Subsequently, a group of randomly chosen, non-selected atlases were taken. In this second group, every possible combination of 2 to 8 random atlases was used for multi-atlas-based BP autosegmentation. For both groups, the average Dice similarity coefficient (DSC), Jaccard index (JI) and Inclusion index (INI) were calculated, measuring the similarity of the generated automatic BP segmentations and the gold standard segmentation. Similarity indices of both groups were compared using an independent sample t-test, and the optimal number of selected atlases was investigated using an equivalence trial. For each number of atlases, average similarity indices of the morphometrically selected atlas group were significantly higher than the random group (p < 0,05). In this study, the highest similarity indices were achieved using multi-atlas autosegmentation with 6 selected atlases (average DSC = 0,598; average JI = 0,434; average INI = 0,733). Morphometric atlas selection on the basis of the protraction position of the patient significantly improves multi-atlas-based BP autosegmentation accuracy

  5. Damage Atlas for Photographic materials

    Directory of Open Access Journals (Sweden)

    Kristel Van Camp

    2010-11-01

    Full Text Available La conservation des documents photographiques peut nécessiter des interventions préventives ou curatives. Ce choix est guidé par leur état de conservation. Une meilleure connaissance des détériorations est donc cruciale. Le répertoire présenté ici essaie de les classifier selon des caractéristiques spécifiques et leur niveau de gravité. Les différents types de dégradation sont illustrés et décrits avec une terminologie précise. L’auteur propose en regard de ceux-ci l’intervention qui semble la plus appropriée. Ce répertoire s’adresse à toutes les personnes concernées par la photographie, qu’ils soient dans le milieu de la conservation ou dans le domaine artistique, dans les musées ou dans les archives. In order to rescue a damaged photographic object, preventive or conservative actions are needed. Knowing the specific characteristics of different types of damage is crucial. A damage atlas can provide these characteristics. With this atlas the damage can be recognised and appropriate actions can be taken. This damage atlas offers a first attempt to such a characterisation in the field of photography. The damage atlas contains images and the necessary information about damage on photographic material. The atlas with special annotations about the terminology and the grade of the damage is meant for everybody who works with photographic material, as well in museums as in archives.

  6. ATLAS & Google - The Data Ocean Project

    CERN Document Server

    Lassnig, Mario; The ATLAS collaboration

    2018-01-01

    With the LHC High Luminosity upgrade the workload and data management systems are facing new major challenges. To address those challenges ATLAS and Google agreed to cooperate on a project to connect Google Cloud Storage and Compute Engine to the ATLAS computing environment. The idea is to allow ATLAS to explore the use of different computing models, to allow ATLAS user analysis to benefit from the Google infrastructure, and to give Google real science use cases to improve their cloud platform. Making the output of a distributed analysis from the grid quickly available to the analyst is a difficult problem. Redirecting the analysis output to Google Cloud Storage can provide an alternative, faster solution for the analyst. First, Google's Cloud Storage will be connected to the ATLAS Data Management System Rucio. The second part aims to let jobs run on Google Compute Engine, accessing data from either ATLAS storage or Google Cloud Storage. The third part involves Google implementing a global redirection between...

  7. Shedding genomic light on Aristotle's lantern.

    Science.gov (United States)

    Sodergren, Erica; Shen, Yufeng; Song, Xingzhi; Zhang, Lan; Gibbs, Richard A; Weinstock, George M

    2006-12-01

    Sea urchins have proved fascinating to biologists since the time of Aristotle who compared the appearance of their bony mouth structure to a lantern in The History of Animals. Throughout modern times it has been a model system for research in developmental biology. Now, the genome of the sea urchin Strongylocentrotus purpuratus is the first echinoderm genome to be sequenced. A high quality draft sequence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with sequences from a collection of BACs selected to form a minimal tiling path along the genome. A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. This was overcome by use of the BAC tiling path backbone, in which each BAC represents a single haplotype, as well as by improvements in the Atlas software. Another innovation introduced in this project was the sequencing of pools of tiling path BACs rather than individual BAC sequencing. The Clone-Array Pooled Shotgun Strategy greatly reduced the cost and time devoted to preparing shotgun libraries from BAC clones. The genome sequence was analyzed with several gene prediction methods to produce a comprehensive gene list that was then manually refined and annotated by a volunteer team of sea urchin experts. This latter annotation community edited over 9000 gene models and uncovered many unexpected aspects of the sea urchin genetic content impacting transcriptional regulation, immunology, sensory perception, and an organism's development. Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development.

  8. Heavy ion collisions with the ATLAS detector

    International Nuclear Information System (INIS)

    Nevski, Pavel

    2004-01-01

    The ATLAS detector is designed to study high-p T physics in proton-proton collisions at the LHC design luminosity. The detector capabilities for heavy-ion physics are now being evaluated. This paper reports on a preliminary assessment of the baseline ATLAS detector potential for heavy-ion physics. The ATLAS sensitivity to some of the expected signatures from the quark-gluon plasma (e.g. jet quenching, Υ suppression) is discussed. (orig.)

  9. Mindboggle: Automated brain labeling with multiple atlases

    International Nuclear Information System (INIS)

    Klein, Arno; Mensh, Brett; Ghosh, Satrajit; Tourville, Jason; Hirsch, Joy

    2005-01-01

    To make inferences about brain structures or activity across multiple individuals, one first needs to determine the structural correspondences across their image data. We have recently developed Mindboggle as a fully automated, feature-matching approach to assign anatomical labels to cortical structures and activity in human brain MRI data. Label assignment is based on structural correspondences between labeled atlases and unlabeled image data, where an atlas consists of a set of labels manually assigned to a single brain image. In the present work, we study the influence of using variable numbers of individual atlases to nonlinearly label human brain image data. Each brain image voxel of each of 20 human subjects is assigned a label by each of the remaining 19 atlases using Mindboggle. The most common label is selected and is given a confidence rating based on the number of atlases that assigned that label. The automatically assigned labels for each subject brain are compared with the manual labels for that subject (its atlas). Unlike recent approaches that transform subject data to a labeled, probabilistic atlas space (constructed from a database of atlases), Mindboggle labels a subject by each atlas in a database independently. When Mindboggle labels a human subject's brain image with at least four atlases, the resulting label agreement with coregistered manual labels is significantly higher than when only a single atlas is used. Different numbers of atlases provide significantly higher label agreements for individual brain regions. Increasing the number of reference brains used to automatically label a human subject brain improves labeling accuracy with respect to manually assigned labels. Mindboggle software can provide confidence measures for labels based on probabilistic assignment of labels and could be applied to large databases of brain images

  10. ATLAS End-cap Part II

    CERN Multimedia

    2007-01-01

    The epic journey of the ATLAS magnets is drawing to an end. On Thursday 12 July, the second end-cap of the ATLAS toroid magnet was lowered into the cavern of the experiment with the same degree of precision as the first (see Bulletin No. 26/2007). This spectacular descent of the 240-tonne component, is one of the last transport to be completed for ATLAS.

  11. The ATLAS Level-1 Calorimeter Trigger

    International Nuclear Information System (INIS)

    Achenbach, R; Andrei, V; Adragna, P; Apostologlou, P; Barnett, B M; Brawn, I P; Davis, A O; Edwards, J P; Asman, B; Bohm, C; Ay, C; Bauss, B; Bendel, M; Dahlhoff, A; Eckweiler, S; Booth, J R A; Thomas, P Bright; Charlton, D G; Collins, N J; Curtis, C J

    2008-01-01

    The ATLAS Level-1 Calorimeter Trigger uses reduced-granularity information from all the ATLAS calorimeters to search for high transverse-energy electrons, photons, τ leptons and jets, as well as high missing and total transverse energy. The calorimeter trigger electronics has a fixed latency of about 1 μs, using programmable custom-built digital electronics. This paper describes the Calorimeter Trigger hardware, as installed in the ATLAS electronics cavern

  12. The ATLAS Level-1 Calorimeter Trigger

    Energy Technology Data Exchange (ETDEWEB)

    Achenbach, R; Andrei, V [Kirchhoff-Institut fuer Physik, University of Heidelberg, D-69120 Heidelberg (Germany); Adragna, P [Physics Department, Queen Mary, University of London, London E1 4NS (United Kingdom); Apostologlou, P; Barnett, B M; Brawn, I P; Davis, A O; Edwards, J P [STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom); Asman, B; Bohm, C [Fysikum, Stockholm University, SE-106 91 Stockholm (Sweden); Ay, C; Bauss, B; Bendel, M; Dahlhoff, A; Eckweiler, S [Institut fuer Physik, University of Mainz, D-55099 Mainz (Germany); Booth, J R A; Thomas, P Bright; Charlton, D G; Collins, N J; Curtis, C J [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom)], E-mail: e.eisenhandler@qmul.ac.uk (and others)

    2008-03-15

    The ATLAS Level-1 Calorimeter Trigger uses reduced-granularity information from all the ATLAS calorimeters to search for high transverse-energy electrons, photons, {tau} leptons and jets, as well as high missing and total transverse energy. The calorimeter trigger electronics has a fixed latency of about 1 {mu}s, using programmable custom-built digital electronics. This paper describes the Calorimeter Trigger hardware, as installed in the ATLAS electronics cavern.

  13. Commissioning of the ATLAS pixel detector

    International Nuclear Information System (INIS)

    Golling, Tobias

    2008-01-01

    The ATLAS pixel detector is a high precision silicon tracking device located closest to the LHC interaction point. It belongs to the first generation of its kind in a hadron collider experiment. It will provide crucial pattern recognition information and will largely determine the ability of ATLAS to precisely track particle trajectories and find secondary vertices. It was the last detector to be installed in ATLAS in June 2007, has been fully connected and tested in-situ during spring and summer 2008, and is ready for the imminent LHC turn-on. The highlights of the past and future commissioning activities of the ATLAS pixel system are presented

  14. Report to users of ATLAS, December 1995

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1995-12-01

    This report covers the following: status of ATLAS accelerator; highlights of recent research at ATLAS; research related concept for an Advanced Exotic Beam Facility on ATLAS; program advisory committee; and ATLAS user group executive committee. Research highlights are given for the following: APEX progress report; transport efficiency of the Argonne Fragment Mass Analyzer; collective motion in light polonium isotopes; angular correlation measurements for 12 C(g.s.) + 12 C(3-,9.64MeV) inelastic scattering; and the AYE-ball (Argonne-Yale-European gamma spectrometer) used to study the structure of nuclei far from stability

  15. Brief retrospection on Hungarian school atlases

    Science.gov (United States)

    Klinghammer, István; Jesús Reyes Nuñez, José

    2018-05-01

    The first part of this article is dedicated to the history of Hungarian school atlases to the end of the 1st World War. Although the first maps included in a Hungarian textbook were probably made in 1751, the publication of atlases for schools is dated almost 50 years later, when professor Ézsáiás Budai created his "New School Atlas for elementary pupils" in 1800. This was followed by a long period of 90 years, when the school atlases were mostly translations and adaptations of foreign atlases, the majority of which were made in German-speaking countries. In those years, a school atlas made by a Hungarian astronomer, Antal Vállas, should be highlighted as a prominent independent piece of work. In 1890, a talented cartographer, Manó Kogutowicz founded the Hungarian Geographical Institute, which was the institution responsible for producing school atlases for the different types of schools in Hungary. The professional quality of the school atlases published by his institute was also recognized beyond the Hungarian borders by prizes won in international exhibitions. Kogutowicz laid the foundations of the current Hungarian school cartography: this statement is confirmed in the second part of this article, when three of his school atlases are presented in more detail to give examples of how the pupils were introduced to the basic cartographic and astronomic concepts as well as how different innovative solutions were used on the maps.

  16. The forward Detectors of the ATLAS experiment

    CERN Document Server

    Vittori, Camilla; The ATLAS collaboration

    2017-01-01

    In this poster, a review of the ATLAS forward detectors operating in the 2015-2016 data taking is given. This includes a description of LUCID, the preferred ATLAS luminosity provider; of the ALFA detector, aimed to measure elastically scattered protons at small angle for the total proton-proton cross section measurement; of the ATLAS Forward Proton project AFP, which was partially installed and took the first data in 2015, and of the Zero Degree Calorimeter ZDC built for the ATLAS Heavy Ions physics program. The near future plans for these detectors will also be addressed.

  17. Glance Information System for ATLAS Management

    International Nuclear Information System (INIS)

    Grael, F F; Maidantchik, C; Évora, L H R A; Karam, K; Moraes, L O F; Cirilli, M; Nessi, M; Pommès, K

    2011-01-01

    ATLAS Experiment is an international collaboration where more than 37 countries, 172 institutes and laboratories, 2900 physicists, engineers, and computer scientists plus 700 students participate. The management of this teamwork involves several aspects such as institute contribution, employment records, members' appointment, authors' list, preparation and publication of papers and speakers nomination. Previously, most of the information was accessible by a limited group and developers had to face problems such as different terminology, diverse data modeling, heterogeneous databases and unlike users needs. Moreover, the systems were not designed to handle new requirements. The maintenance has to be an easy task due to the long lifetime experiment and professionals turnover. The Glance system, a generic mechanism for accessing any database, acts as an intermediate layer isolating the user from the particularities of each database. It retrieves, inserts and updates the database independently of its technology and modeling. Relying on Glance, a group of systems were built to support the ATLAS management and operation aspects: ATLAS Membership, ATLAS Appointments, ATLAS Speakers, ATLAS Analysis Follow-Up, ATLAS Conference Notes, ATLAS Thesis, ATLAS Traceability and DSS Alarms Viewer. This paper presents the overview of the Glance information framework and describes the privilege mechanism developed to grant different level of access for each member and system.

  18. Glance Information System for ATLAS Management

    Science.gov (United States)

    Grael, F. F.; Maidantchik, C.; Évora, L. H. R. A.; Karam, K.; Moraes, L. O. F.; Cirilli, M.; Nessi, M.; Pommès, K.; ATLAS Collaboration

    2011-12-01

    ATLAS Experiment is an international collaboration where more than 37 countries, 172 institutes and laboratories, 2900 physicists, engineers, and computer scientists plus 700 students participate. The management of this teamwork involves several aspects such as institute contribution, employment records, members' appointment, authors' list, preparation and publication of papers and speakers nomination. Previously, most of the information was accessible by a limited group and developers had to face problems such as different terminology, diverse data modeling, heterogeneous databases and unlike users needs. Moreover, the systems were not designed to handle new requirements. The maintenance has to be an easy task due to the long lifetime experiment and professionals turnover. The Glance system, a generic mechanism for accessing any database, acts as an intermediate layer isolating the user from the particularities of each database. It retrieves, inserts and updates the database independently of its technology and modeling. Relying on Glance, a group of systems were built to support the ATLAS management and operation aspects: ATLAS Membership, ATLAS Appointments, ATLAS Speakers, ATLAS Analysis Follow-Up, ATLAS Conference Notes, ATLAS Thesis, ATLAS Traceability and DSS Alarms Viewer. This paper presents the overview of the Glance information framework and describes the privilege mechanism developed to grant different level of access for each member and system.

  19. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  20. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

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

    DEFF Research Database (Denmark)

    Farshidfar, Farshad; Zheng, Siyuan; Gingras, Marie-Claude

    2017-01-01

    Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahep...

  2. The ATLAS Track Extrapolation Package

    CERN Document Server

    Salzburger, A

    2007-01-01

    The extrapolation of track parameters and their associated covariances to destination surfaces of different types is a very frequent process in the event reconstruction of high energy physics experiments. This is amongst other reasons due to the fact that most track and vertex fitting techniques are based on the first and second momentum of the underlying probability density distribution. The correct stochastic or deterministic treatment of interactions with the traversed detector material is hereby crucial for high quality track reconstruction throughout the entire momentum range of final state particles that are produced in high energy physics collision experiments. This document presents the main concepts, the algorithms and the implementation of the newly developed, powerful ATLAS track extrapolation engine. It also emphasises on validation procedures, timing measurements and the integration into the ATLAS offline reconstruction software.

  3. Upgrading the ATLAS control system

    International Nuclear Information System (INIS)

    Munson, F.H.; Ferraretto, M.

    1993-01-01

    Heavy-ion accelerators are tools used in the research of nuclear and atomic physics. The ATLAS facility at the Argonne National Laboratory is one such tool. The ATLAS control system serves as the primary operator interface to the accelerator. A project to upgrade the control system is presently in progress. Since this is an upgrade project and not a new installation, it was imperative that the development work proceed without interference to normal operations. An additional criteria for the development work was that the writing of additional ''in-house'' software should be kept to a minimum. This paper briefly describes the control system being upgraded, and explains some of the reasons for the decision to upgrade the control system. Design considerations and goals for the new system are described, and the present status of the upgrade is discussed

  4. The ATLAS hadronic tau trigger

    CERN Document Server

    Black, C; The ATLAS collaboration

    2012-01-01

    With the high luminosities of proton-proton collisions achieved at the LHC, the strategies for triggering have become more important than ever for physics analysis. The naive inclusive single tau lepton triggers now suffer from severe rate limitations. To allow for a large program of physics analyses with taus, the development of topological triggers that combine tau signatures with other measured quantities in the event is required. These combined triggers open many opportunities to study new physics beyond the Standard Model and to search for the Standard Model Higgs. We present the status and performance of the hadronic tau trigger in ATLAS. We demonstrate that the ATLAS tau trigger ran remarkably well over 2011, and how the lessons learned from 2011 led to numerous improvements in the preparation of the 2012 run. These improvements include the introduction of tau selection criteria that are robust against varying pileup scenarios, and the implementation of multivariate selection techniques in the tau trig...

  5. The ATLAS hadronic tau trigger

    CERN Document Server

    Black, C; The ATLAS collaboration

    2012-01-01

    With the high luminosities of proton-proton collisions achieved at the LHC, the strategies for triggering have become more important than ever for physics analysis. The naïve inclusive single tau lepton triggers now suffer from severe rate limitations. To allow for a large program of physics analyses with taus, the development of topological triggers that combine tau signatures with other measured quantities in the event is required. These combined triggers open many opportunities to study new physics beyond the Standard Model and to search for the Standard Model Higgs. We present the status and performance of the hadronic tau trigger in ATLAS. We demonstrate that the ATLAS tau trigger ran remarkably well over 2011, and how the lessons learned from 2011 led to numerous improvements in the preparation of the 2012 run. These improvements include the introduction of tau selection criteria that are robust against varying pileup scenarios, and the implementation of multivariate selection techniques in the tau tri...

  6. ATLAS Live: Collaborative Information Streams

    Energy Technology Data Exchange (ETDEWEB)

    Goldfarb, Steven [Department of Physics, University of Michigan, Ann Arbor, MI 48109 (United States); Collaboration: ATLAS Collaboration

    2011-12-23

    I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using digital signage software. The system is robust and flexible, utilizing scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intra-screen divisibility. Information is published via the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video tool. Authorisation is enforced at the level of the streaming and at the web portals, using the CERN SSO system.

  7. ATLAS Live: Collaborative Information Streams

    International Nuclear Information System (INIS)

    Goldfarb, Steven

    2011-01-01

    I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using digital signage software. The system is robust and flexible, utilizing scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intra-screen divisibility. Information is published via the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video tool. Authorisation is enforced at the level of the streaming and at the web portals, using the CERN SSO system.

  8. ATLAS Live: Collaborative Information Streams

    CERN Document Server

    Goldfarb, S; The ATLAS collaboration

    2011-01-01

    I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using digital signage software. The system is robust and flexible, utilizing scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intra-screen divisibility. Information is published via the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video tool. Authorisation is enforced at the level of the streaming and at th...

  9. ATLAS Live: Collaborative Information Streams

    CERN Document Server

    Goldfarb, S; The ATLAS collaboration

    2010-01-01

    I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using the SCALA digital signage software system. The system is robust and flexible, allowing for the usage of scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intrascreen divisibility. The video is made available to the collaboration or public through the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video t...

  10. The ATLAS Production System Evolution

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration

    2017-01-01

    The second generation of the ATLAS Production System called ProdSys2 is a distributed workload manager that runs daily hundreds of thousands of jobs, from dozens of different ATLAS-specific workflows, across more than a hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based upon many criteria, such as input and output size, memory requirements and CPU consumption, with manageable scheduling policies and by supporting different kinds of computational resources, such as GRID, clouds, supercomputers and volunteer computers. The system dynamically assigns a group of jobs (task) to a group of geographically distributed computing resources. Dynamic assignment and resource utilization is one of the major features of the system. The Production System has a sophisticated job fault recovery mechanism, which efficiently allows running multi-terabyte tasks without human intervention. We have implemented new features which allow automatic task submission and chaining of differe...

  11. The Equine PeptideAtlas

    DEFF Research Database (Denmark)

    Bundgaard, Louise; Jacobsen, Stine; Sørensen, Mette Aamand

    2014-01-01

    Progress in MS-based methods for veterinary research and diagnostics is lagging behind compared to the human research, and proteome data of domestic animals is still not well represented in open source data repositories. This is particularly true for the equine species. Here we present a first...... Equine PeptideAtlas encompassing high-resolution tandem MS analyses of 51 samples representing a selection of equine tissues and body fluids from healthy and diseased animals. The raw data were processed through the Trans-Proteomic Pipeline to yield high quality identification of proteins and peptides....... The current release comprises 24 131 distinct peptides representing 2636 canonical proteins observed at false discovery rates of 0.2% at the peptide level and 1.4% at the protein level. Data from the Equine PeptideAtlas are available for experimental planning, validation of new datasets, and as a proteomic...

  12. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology[1]. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary service...

  13. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services a...

  14. ATLAS facility fabrication and assembly

    CERN Document Server

    Ballard, E O; Davis, H A; Nielsen, K E; Parker, G V; Parsons, W M

    2001-01-01

    Summary form only given. Atlas is a pulsed-power facility recently completed at Los Alamos National Laboratory to drive hydrodynamic experiments. This new generation pulsed-power machine consists of a radial array of 24, 240-kV Marx modules and transmission lines supplying current to the load region at the machine center. The transmission lines, powered by the Marx modules, consist of cable headers, load protection switches and tri-plates interfacing to the center transition section through detachable current joints. A conical power-flow-channel attaches to the transition section providing an elevated interface to attach the experimental loads for diagnostic access. Fabrication and assembly of all components for the Atlas machine was completed in August 2000. The machine has also progressed through a test phase where the Marx module/transmission line units were fired, individually, into a test load. Progression continued with eight and sixteen lines being fired. Subsequently, an overall machine test was condu...

  15. The ATLAS Detector Control System

    International Nuclear Information System (INIS)

    Lantzsch, K; Braun, H; Hirschbuehl, D; Kersten, S; Arfaoui, S; Franz, S; Gutzwiller, O; Schlenker, S; Tsarouchas, C A; Mindur, B; Hartert, J; Zimmermann, S; Talyshev, A; Oliveira Damazio, D; Poblaguev, A; Martin, T; Thompson, P D; Caforio, D; Sbarra, C; Hoffmann, D

    2012-01-01

    The ATLAS experiment is one of the multi-purpose experiments at the Large Hadron Collider (LHC) at CERN, constructed to study elementary particle interactions in collisions of high-energy proton beams. Twelve different sub detectors as well as the common experimental infrastructure are controlled and monitored by the Detector Control System (DCS) using a highly distributed system of 140 server machines running the industrial SCADA product PVSS. Higher level control system layers allow for automatic control procedures, efficient error recognition and handling, manage the communication with external systems such as the LHC controls, and provide a synchronization mechanism with the ATLAS data acquisition system. Different databases are used to store the online parameters of the experiment, replicate a subset used for physics reconstruction, and store the configuration parameters of the systems. This contribution describes the computing architecture and software tools to handle this complex and highly interconnected control system.

  16. The ATLAS Detector Control System

    Science.gov (United States)

    Lantzsch, K.; Arfaoui, S.; Franz, S.; Gutzwiller, O.; Schlenker, S.; Tsarouchas, C. A.; Mindur, B.; Hartert, J.; Zimmermann, S.; Talyshev, A.; Oliveira Damazio, D.; Poblaguev, A.; Braun, H.; Hirschbuehl, D.; Kersten, S.; Martin, T.; Thompson, P. D.; Caforio, D.; Sbarra, C.; Hoffmann, D.; Nemecek, S.; Robichaud-Veronneau, A.; Wynne, B.; Banas, E.; Hajduk, Z.; Olszowska, J.; Stanecka, E.; Bindi, M.; Polini, A.; Deliyergiyev, M.; Mandic, I.; Ertel, E.; Marques Vinagre, F.; Ribeiro, G.; Santos, H. F.; Barillari, T.; Habring, J.; Huber, J.; Arabidze, G.; Boterenbrood, H.; Hart, R.; Iakovidis, G.; Karakostas, K.; Leontsinis, S.; Mountricha, E.; Ntekas, K.; Filimonov, V.; Khomutnikov, V.; Kovalenko, S.; Grassi, V.; Mitrevski, J.; Phillips, P.; Chekulaev, S.; D'Auria, S.; Nagai, K.; Tartarelli, G. F.; Aielli, G.; Marchese, F.; Lafarguette, P.; Brenner, R.

    2012-12-01

    The ATLAS experiment is one of the multi-purpose experiments at the Large Hadron Collider (LHC) at CERN, constructed to study elementary particle interactions in collisions of high-energy proton beams. Twelve different sub detectors as well as the common experimental infrastructure are controlled and monitored by the Detector Control System (DCS) using a highly distributed system of 140 server machines running the industrial SCADA product PVSS. Higher level control system layers allow for automatic control procedures, efficient error recognition and handling, manage the communication with external systems such as the LHC controls, and provide a synchronization mechanism with the ATLAS data acquisition system. Different databases are used to store the online parameters of the experiment, replicate a subset used for physics reconstruction, and store the configuration parameters of the systems. This contribution describes the computing architecture and software tools to handle this complex and highly interconnected control system.

  17. ATLAS construction: A status report

    CERN Document Server

    Sfyrla, Anna

    2006-01-01

    ATLAS is a general purpose p-p collider detector being constructed for the CERN Large Hadron Collider (LHC). It is located in one of the two high luminosity bunch crossing points (peak luminosity of 1 0 3 4 c m - 2 s _ 1 ) of the LHC. It consists of 3 main sections. Located close to the beam axis, the tracking system employs pixel detectors, silicon microstrip modules and transition radiation straws, all within a 2 Tesla superconducting solenoid. The tracker is surrounded by the electromagnetic and hadronic calorimeters. In the outer part of the detector, 8 superconducting coils define an open toroidal magnetic field for muon detection. The construction status of the ATLAS detector towards being ready for the first collisions in 2007 will be presented, with particular emphasis on the construction and projected performance of the tracking system.

  18. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  19. MRI atlas of MS lesions

    Energy Technology Data Exchange (ETDEWEB)

    Sahraian, Mohammad Ali [Tehran Univ. of Medical Sciences Sina Hospital (Iran). Dept. of Neurology; Radue, Ernst-Wilhelm [Univ. Hospital Basel (Switzerland). Dept. of Neuroradiology

    2008-07-01

    MRI has become the main paraclinical test in the diagnosis and management of multiple sclerosis. We have demonstrated more than 400 pictures of different typical and atypical MS lesions in this atlas. Each image has a teaching point. New diagnostic criteria and differential diagnosis are discussed and the book is supported by a teaching DVD where the reader can see MS lesions in different slices and sequences. (orig.)

  20. The ATLAS Beam Conditions Monitor

    International Nuclear Information System (INIS)

    Cindro, V; Dolenc, I; Kramberger, G; Macek, B; Mandic, I; Mikuz', M; Zavrtanik, M; Dobos, D; Gorisek, A; Pernegger, H; Weilhammer, P; Frais-Koelbl, H; Griesmayer, E; Niegl, M; Kagan, H; Tardif, D; Trischuk, W

    2008-01-01

    Beam conditions and the potential detector damage resulting from their anomalies have pushed the LHC experiments to build their own beam monitoring devices. The ATLAS Beam Conditions Monitor (BCM) consists of two stations (forward and backward) of detectors each with four modules. The sensors are required to tolerate doses up to 500 kGy and in excess of 10 15 charged particles per cm 2 over the lifetime of the experiment. Each module includes two diamond sensors read out in parallel. The stations are located symmetrically around the interaction point, positioning the diamond sensors at z = ±184 cm and r = 55 mm (a pseudo- rapidity of about 4.2). Equipped with fast electronics (2 ns rise time) these stations measure time-of-flight and pulse height to distinguish events resulting from lost beam particles from those normally occurring in proton-proton interactions. The BCM also provides a measurement of bunch-by-bunch luminosities in ATLAS by counting in-time and out-of-time collisions. Eleven detector modules have been fully assembled and tested. Tests performed range from characterisation of diamond sensors to full module tests with electron sources and in proton testbeams. Testbeam results from the CERN SPS show a module median-signal to noise of 11:1 for minimum ionising particles incident at a 45-degree angle. The best eight modules were installed on the ATLAS pixel support frame that was inserted into ATLAS in the summer of 2007. This paper describes the full BCM detector system along with simulation studies being used to develop the logic in the back-end FPGA coincidence hardware

  1. The ATLAS Beam Conditions Monitor

    Energy Technology Data Exchange (ETDEWEB)

    Cindro, V; Dolenc, I; Kramberger, G; Macek, B; Mandic, I; Mikuz' , M; Zavrtanik, M [Jozef Stefan Institute and Department of Physics, University of Ljubljana, Ljubljana (Slovenia); Dobos, D; Gorisek, A; Pernegger, H; Weilhammer, P [CERN, Geneva (Switzerland); Frais-Koelbl, H; Griesmayer, E; Niegl, M [University of Applied Sciences Wiener Neustadt and Fotec, Wiener Neustadt (Austria); Kagan, H [Ohio State University, Columbus (United States); Tardif, D; Trischuk, W [University of Toronto, Toronto (Canada)], E-mail: william@physics.utoronto.ca

    2008-02-15

    Beam conditions and the potential detector damage resulting from their anomalies have pushed the LHC experiments to build their own beam monitoring devices. The ATLAS Beam Conditions Monitor (BCM) consists of two stations (forward and backward) of detectors each with four modules. The sensors are required to tolerate doses up to 500 kGy and in excess of 10{sup 15} charged particles per cm{sup 2} over the lifetime of the experiment. Each module includes two diamond sensors read out in parallel. The stations are located symmetrically around the interaction point, positioning the diamond sensors at z = {+-}184 cm and r = 55 mm (a pseudo- rapidity of about 4.2). Equipped with fast electronics (2 ns rise time) these stations measure time-of-flight and pulse height to distinguish events resulting from lost beam particles from those normally occurring in proton-proton interactions. The BCM also provides a measurement of bunch-by-bunch luminosities in ATLAS by counting in-time and out-of-time collisions. Eleven detector modules have been fully assembled and tested. Tests performed range from characterisation of diamond sensors to full module tests with electron sources and in proton testbeams. Testbeam results from the CERN SPS show a module median-signal to noise of 11:1 for minimum ionising particles incident at a 45-degree angle. The best eight modules were installed on the ATLAS pixel support frame that was inserted into ATLAS in the summer of 2007. This paper describes the full BCM detector system along with simulation studies being used to develop the logic in the back-end FPGA coincidence hardware.

  2. ATLAS insertable B-layer

    Czech Academy of Sciences Publication Activity Database

    Marčišovský, Michal

    2011-01-01

    Roč. 633, č. 1 (2011), "S224"-"S225" ISSN 0168-9002. [International workshop on radiation imaging detectors /11./. Praha, 26.06.2009-02.07.2009] R&D Projects: GA MŠk LA08015; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : ATLAS * pixel detector * insertable B-layer Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.207, year: 2011

  3. The ATLAS Open Data project

    CERN Document Server

    Doglioni, Caterina; The ATLAS collaboration; Sanchez Pineda, Arturo Rodolfo

    2018-01-01

    The ATLAS Open Data project is a collection of high-level LHC collision data and tools to be used for education, training, outreach and citizen science. These resources are meant to be platform-independent, and are available on the web and on digital supports, such as USB drives. The project includes a Community hub where users can interact and actively participate in discussions.

  4. Upgrading ATLAS Fast Calorimeter Simulation

    CERN Document Server

    Heath, Matthew Peter; The ATLAS collaboration

    2017-01-01

    Producing the very large samples of simulated events required by many physics and performance studies with the ATLAS detector using the full GEANT4 detector simulation is highly CPU intensive. Fast simulation tools are a useful way of reducing CPU requirements when detailed detector simulations are not needed. During the LHC Run-1, a fast calorimeter simulation (FastCaloSim) was successfully used in ATLAS. FastCaloSim provides a simulation of the particle energy response at the calorimeter read-out cell level, taking into account the detailed particle shower shapes and the correlations between the energy depositions in the various calorimeter layers. It is interfaced to the standard ATLAS digitization and reconstruction software, and it can be tuned to data more easily than Geant4. Now an improved version of FastCaloSim is in development, incorporating the experience with the version used during Run-1. The new FastCaloSim aims to overcome some limitations of the first version by improving the description of s...

  5. The ATLAS detector control system

    International Nuclear Information System (INIS)

    Schlenker, S.; Arfaoui, S.; Franz, S.

    2012-01-01

    The ATLAS experiment is one of the multi-purpose experiments at the Large Hadron Collider (LHC), constructed to study elementary particle interactions in collisions of high-energy proton beams. Twelve different sub-detectors as well as the common experimental infrastructure are supervised by the Detector Control System (DCS). The DCS enables equipment supervision of all ATLAS sub-detectors by using a system of more that 130 server machines running the industrial SCADA product PVSS. This highly distributed system reads, processes and archives of the order of 10 6 operational parameters. Higher level control system layers allow for automatic control procedures, efficient error recognition and handling, and manage the communication with external systems such as the LHC. First, this contribution describes the status of the ATLAS DCS and the experience gained during the LHC commissioning and the first physics data taking operation period. Secondly, the future evolution and maintenance constraints for the coming years and the LHC high luminosity upgrades are outlined. (authors)

  6. The ATLAS Silicon Microstrip Tracker

    CERN Document Server

    Haefner, Petra

    2010-01-01

    In December 2009 the ATLAS experiment at the CERN Large Hadron Collider (LHC) recorded the first proton-proton collisions at a centre-of-mass energy of 900 GeV. This was followed by collisions at the unprecedented energy of 7 TeV in March 2010. The SemiConductor Tracker (SCT) is a precision tracking device in ATLAS made up from silicon micro-strip detectors processed in the planar p-in-n technology. The signal from the strips is processed in the front-end ASICs working in binary readout mode. Data is transferred to the off-detector readout electronics via optical fibers. The completed SCT has been installed inside the ATLAS experiment. Since then the detector was operated for two years under realistic conditions. Calibration data has been taken and analysed to determine the performance of the system. In addition, extensive commissioning with cosmic ray events has been performed both with and without magnetic field. The sensor behaviour in magnetic field was studied by measurements of the Lorentz angle. After ...

  7. ATLAS diamond Beam Condition Monitor

    Energy Technology Data Exchange (ETDEWEB)

    Gorisek, A. [CERN (Switzerland)]. E-mail: andrej.gorisek@cern.ch; Cindro, V. [J. Stefan Institute (Slovenia); Dolenc, I. [J. Stefan Institute (Slovenia); Frais-Koelbl, H. [Fotec (Austria); Griesmayer, E. [Fotec (Austria); Kagan, H. [Ohio State University, OH (United States); Korpar, S. [J. Stefan Institute (Slovenia); Kramberger, G. [J. Stefan Institute (Slovenia); Mandic, I. [J. Stefan Institute (Slovenia); Meyer, M. [CERN (Switzerland); Mikuz, M. [J. Stefan Institute (Slovenia); Pernegger, H. [CERN (Switzerland); Smith, S. [Ohio State University, OH (United States); Trischuk, W. [University of Toronto (Canada); Weilhammer, P. [CERN (Switzerland); Zavrtanik, M. [J. Stefan Institute (Slovenia)

    2007-03-01

    The ATLAS experiment has chosen to use diamond for its Beam Condition Monitor (BCM) given its radiation hardness, low capacitance and short charge collection time. In addition, due to low leakage current diamonds do not require cooling. The ATLAS Beam Condition Monitoring system is based on single beam bunch crossing measurements rather than integrating the accumulated particle flux. Its fast electronics will allow separation of LHC collisions from background events such as beam gas interactions or beam accidents. There will be two stations placed symmetrically about the interaction point along the beam axis at z=+/-183.8cm. Timing of signals from the two stations will provide almost ideal separation of beam-beam interactions and background events. The ATLAS BCM module consists of diamond pad detectors of 1cm{sup 2} area and 500{mu}m thickness coupled to a two-stage RF current amplifier. The production of the final detector modules is almost done. A S/N ratio of 10:1 has been achieved with minimum ionizing particles (MIPs) in the test beam setup at KEK. Results from the test beams and bench measurements are presented.

  8. ATLAS diamond Beam Condition Monitor

    International Nuclear Information System (INIS)

    Gorisek, A.; Cindro, V.; Dolenc, I.; Frais-Koelbl, H.; Griesmayer, E.; Kagan, H.; Korpar, S.; Kramberger, G.; Mandic, I.; Meyer, M.; Mikuz, M.; Pernegger, H.; Smith, S.; Trischuk, W.; Weilhammer, P.; Zavrtanik, M.

    2007-01-01

    The ATLAS experiment has chosen to use diamond for its Beam Condition Monitor (BCM) given its radiation hardness, low capacitance and short charge collection time. In addition, due to low leakage current diamonds do not require cooling. The ATLAS Beam Condition Monitoring system is based on single beam bunch crossing measurements rather than integrating the accumulated particle flux. Its fast electronics will allow separation of LHC collisions from background events such as beam gas interactions or beam accidents. There will be two stations placed symmetrically about the interaction point along the beam axis at z=+/-183.8cm. Timing of signals from the two stations will provide almost ideal separation of beam-beam interactions and background events. The ATLAS BCM module consists of diamond pad detectors of 1cm 2 area and 500μm thickness coupled to a two-stage RF current amplifier. The production of the final detector modules is almost done. A S/N ratio of 10:1 has been achieved with minimum ionizing particles (MIPs) in the test beam setup at KEK. Results from the test beams and bench measurements are presented

  9. 2001, the ATLAS Cryostat Odyssey

    CERN Multimedia

    2001-01-01

    After a journey of several thousand kilometres, over sea and land, by canal and highway, the cryogenics barrel of the ATLAS electromagnetic calorimeter finally arrived at CERN last week. Installed in Hall 180, the cryogenics barrel of the ATLAS electromagnetic calorimeter will be fitted out to take the central superconducting solenoid and the electromagnetic calorimeter. On Monday 2 July, different French police units and EDF officials were once again keeping careful watch around the hairpin bends of the road twisting down from the Col de la Faucille: a special load weighing 100 tonnes, 7 metres high, 5.8 metres wide and 7.2 metres long was being brought down into the Pays de Gex to the Meyrin site of CERN. This time the destination was the ATLAS experiment. A huge blue tarpaulin cover concealed the cryogenics barrel of the experiment's liquid argon electromagnetic calorimeter. The cryostat consists of a vacuum chamber, a cylinder that is 5.5 metres in diameter, 7 metres long, and a concentric cold chamber ...

  10. ATLAS diamond Beam Condition Monitor

    CERN Document Server

    Gorišek, A; Dolenc, I; Frais-Kölbl, H; Griesmayer, E; Kagan, H; Korpar, S; Kramberger, G; Mandic, I; Meyer, M; Mikuz, M; Pernegger, H; Smith, S; Trischuk, W; Weilhammer, P; Zavrtanik, M

    2007-01-01

    The ATLAS experiment has chosen to use diamond for its Beam Condition Monitor (BCM) given its radiation hardness, low capacitance and short charge collection time. In addition, due to low leakage current diamonds do not require cooling. The ATLAS Beam Condition Monitoring system is based on single beam bunch crossing measurements rather than integrating the accumulated particle flux. Its fast electronics will allow separation of LHC collisions from background events such as beam gas interactions or beam accidents. There will be two stations placed symmetrically about the interaction point along the beam axis at . Timing of signals from the two stations will provide almost ideal separation of beam–beam interactions and background events. The ATLAS BCM module consists of diamond pad detectors of area and thickness coupled to a two-stage RF current amplifier. The production of the final detector modules is almost done. A S/N ratio of 10:1 has been achieved with minimum ionizing particles (MIPs) in the test bea...

  11. Fast Calorimeter Simulation in ATLAS

    CERN Document Server

    Schaarschmidt, Jana; The ATLAS collaboration

    2017-01-01

    Producing the very large samples of simulated events required by many physics and performance studies with the ATLAS detector using the full GEANT4 detector simulation is highly CPU intensive. Fast simulation tools are a useful way of reducing CPU requirements when detailed detector simulations are not needed. During the LHC Run-1, a fast calorimeter simulation (FastCaloSim) was successfully used in ATLAS. FastCaloSim provides a simulation of the particle energy response at the calorimeter read-out cell level, taking into account the detailed particle shower shapes and the correlations between the energy depositions in the various calorimeter layers. It is interfaced to the standard ATLAS digitization and reconstruction software, and it can be tuned to data more easily than GEANT4. It is 500 times faster than full simulation in the calorimeter system. Now an improved version of FastCaloSim is in development, incorporating the experience with the version used during Run-1. The new FastCaloSim makes use of mach...

  12. Learning with the ATLAS Experiment at CERN

    Science.gov (United States)

    Barnett, R. M.; Johansson, K. E.; Kourkoumelis, C.; Long, L.; Pequenao, J.; Reimers, C.; Watkins, P.

    2012-01-01

    With the start of the LHC, the new particle collider at CERN, the ATLAS experiment is also providing high-energy particle collisions for educational purposes. Several education projects--education scenarios--have been developed and tested on students and teachers in several European countries within the Learning with ATLAS@CERN project. These…

  13. ATLAS: First rehearsal for the tile calorimeter

    CERN Multimedia

    2003-01-01

    The dry run assembly of the first barrel of the ATLAS tile hadron calorimeter has been successfully completed. It is now being dismantled again so that it can be lowered into the ATLAS cavern where it will be reassembled in October 2004.

  14. ATLAS Experiment Colouring Book in Arabic

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    Language: Arabic - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  15. ATLAS detector records its first curved muon

    CERN Multimedia

    2007-01-01

    The barrel muon spectrometer of the ATLAS detector has acquired its first cosmic event in a magnetic field produced by the barrel toroid magnet. This was an important test of the chambers in their final configurations, and marked the first triggering and measurement of curved cosmic ray muons in ATLAS.

  16. search of extra space dimensions with ATLAs

    Indian Academy of Sciences (India)

    search of extra space dimensions with ATLAs. AMBREEsH GUPTA (for the ATLAs Collaboration). 5640 South Ellis Avenue, Enrico Fermi Institute, University of Chicago, Chicago,. IL 60637, USA. Abstract. If extra spatial dimensions were to exist, they could provide a solution to the hierarchy problem. The studies done by the ...

  17. A system for managing information at ATLAS

    International Nuclear Information System (INIS)

    Tilbrook, I.R.

    1993-01-01

    In response to a need for better management of maintenance and document information at the Argonne Tandem-Linear Accelerating System (ATLAS), the ATLAS Information Management System (AIMS) has been created. The system is based on the relational database model. The system's applications use the Alpha-4 relational database management system, a commercially available software package. The system's function and design are described

  18. Das Ausmalbuch zum ATLAS-Experiment

    CERN Multimedia

    Anthony, Katarina

    2017-01-01

    Deutsche Fassung - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  19. Status of the AFP Project in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00224260; The ATLAS collaboration

    2017-01-01

    Status of the AFP project in the ATLAS experiment is given. In 2016 one arm of the AFP detector was installed and first data have been taken. In parallel with integration of the AFP subdetector into the ATLAS TDAQ nad DCS, beam tests and preparations for the installation of the 2nd arm are performed.

  20. Philippines Wind Energy Resource Atlas Development

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, D.

    2000-11-29

    This paper describes the creation of a comprehensive wind energy resource atlas for the Philippines. The atlas was created to facilitate the rapid identification of good wind resource areas and understanding of the salient wind characteristics. Detailed wind resource maps were generated for the entire country using an advanced wind mapping technique and innovative assessment methods recently developed at the National Renewable Energy Laboratory.

  1. ATLAS@Home looks for CERN volunteers

    CERN Multimedia

    Rosaria Marraffino

    2014-01-01

    ATLAS@Home is a CERN volunteer computing project that runs simulated ATLAS events. As the project ramps up, the project team is looking for CERN volunteers to test the system before planning a bigger promotion for the public.   The ATLAS@home outreach website. ATLAS@Home is a large-scale research project that runs ATLAS experiment simulation software inside virtual machines hosted by volunteer computers. “People from all over the world offer up their computers’ idle time to run simulation programmes to help physicists extract information from the large amount of data collected by the detector,” explains Claire Adam Bourdarios of the ATLAS@Home project. “The ATLAS@Home project aims to extrapolate the Standard Model at a higher energy and explore what new physics may look like. Everything we’re currently running is preparation for next year's run.” ATLAS@Home became an official BOINC (Berkeley Open Infrastructure for Network ...

  2. Development, deployment and operations of ATLAS databases

    International Nuclear Information System (INIS)

    Vaniachine, A. V.; von der Schmitt, J. G.

    2008-01-01

    In preparation for ATLAS data taking, a coordinated shift from development towards operations has occurred in ATLAS database activities. In addition to development and commissioning activities in databases, ATLAS is active in the development and deployment (in collaboration with the WLCG 3D project) of the tools that allow the worldwide distribution and installation of databases and related datasets, as well as the actual operation of this system on ATLAS multi-grid infrastructure. We describe development and commissioning of major ATLAS database applications for online and offline. We present the first scalability test results and ramp-up schedule over the initial LHC years of operations towards the nominal year of ATLAS running, when the database storage volumes are expected to reach 6.1 TB for the Tag DB and 1.0 TB for the Conditions DB. ATLAS database applications require robust operational infrastructure for data replication between online and offline at Tier-0, and for the distribution of the offline data to Tier-1 and Tier-2 computing centers. We describe ATLAS experience with Oracle Streams and other technologies for coordinated replication of databases in the framework of the WLCG 3D services

  3. Brain transcriptome atlases : A computational perspective

    NARCIS (Netherlands)

    Mahfouz, A.M.E.T.A.; Huisman, S.M.H.; Lelieveldt, B.P.F.; Reinders, M.J.T.

    2017-01-01

    The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases

  4. Translating the cancer genome: Going beyond p values

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Lynda; Chin, Lynda; Gray, Joe W.

    2008-04-03

    Cancer cells are endowed with diverse biological capabilities driven by myriad inherited and somatic genetic and epigenetic aberrations that commandeer key cancer-relevant pathways. Efforts to elucidate these aberrations began with Boveri's hypothesis of aberrant mitoses causing cancer and continue today with a suite of powerful high-resolution technologies that enable detailed catalogues of genomic aberrations and epigenomic modifications. Tomorrow will likely bring the complete atlas of reversible and irreversible alteration in individual cancers. The challenge now is to discern causal molecular abnormalities from genomic and epigenomic 'noise', to understand how the ensemble of these aberrations collaborate to drive cancer pathophysiology. Here, we highlight lessons learned from now classical examples of successful translation of genomic discoveries into clinical practice, lessons that may be used to guide and accelerate translation of emerging genomic insights into practical clinical endpoints that can impact on practice of cancer medicine.

  5. Mycobacterial species as case-study of comparative genome analysis

    DEFF Research Database (Denmark)

    Zakham, F.; Belayachi, L.; Ussery, David

    2011-01-01

    . Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR—1, For this purpose a comparison has been done based on their length...... defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene...... the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str...

  6. Draft genome sequence of the Algerian bee Apis mellifera intermissa

    Directory of Open Access Journals (Sweden)

    Nizar Jamal Haddad

    2015-06-01

    Full Text Available Apis mellifera intermissa is the native honeybee subspecies of Algeria. A. m. intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts. This bee is very important due to its high ability to adapt to great variations in climatic conditions and due to its preferable cleaning behavior. Here we report the draft genome sequence of this honey bee, its Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JSUV00000000. The 240-Mb genome is being annotated and analyzed. Comparison with the genome of other Apis mellifera sub-species promises to yield insights into the evolution of adaptations to high temperature and resistance to Varroa parasite infestation.

  7. Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

    Science.gov (United States)

    Taylor, Alison M; Shih, Juliann; Ha, Gavin; Gao, Galen F; Zhang, Xiaoyang; Berger, Ashton C; Schumacher, Steven E; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J; Cherniack, Andrew D; Beroukhim, Rameen; Meyerson, Matthew

    2018-04-09

    Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. We applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  8. The High-Resolution IRAS Galaxy Atlas

    Science.gov (United States)

    Cao, Yu; Terebey, Susan; Prince, Thomas A.; Beichman, Charles A.; Oliversen, R. (Technical Monitor)

    1997-01-01

    An atlas of the Galactic plane (-4.7 deg is less than b is less than 4.7 deg), along with the molecular clouds in Orion, rho Oph, and Taurus-Auriga, has been produced at 60 and 100 microns from IRAS data. The atlas consists of resolution-enhanced co-added images with 1 min - 2 min resolution and co-added images at the native IRAS resolution. The IRAS Galaxy Atlas, together with the Dominion Radio Astrophysical Observatory H(sub I) line/21 cm continuum and FCRAO CO (1-0) Galactic plane surveys, which both have similar (approx. 1 min) resolution to the IRAS atlas, provides a powerful tool for studying the interstellar medium, star formation, and large-scale structure in our Galaxy. This paper documents the production and characteristics of the atlas.

  9. Analytics Platform for ATLAS Computing Services

    CERN Document Server

    Vukotic, Ilija; The ATLAS collaboration; Bryant, Lincoln

    2016-01-01

    Big Data technologies have proven to be very useful for storage, processing and visualization of derived metrics associated with ATLAS distributed computing (ADC) services. Log file data and database records, and metadata from a diversity of systems have been aggregated and indexed to create an analytics platform for ATLAS ADC operations analysis. Dashboards, wide area data access cost metrics, user analysis patterns, and resource utilization efficiency charts are produced flexibly through queries against a powerful analytics cluster. Here we explore whether these techniques and analytics ecosystem can be applied to add new modes of open, quick, and pervasive access to ATLAS event data so as to simplify access and broaden the reach of ATLAS public data to new communities of users. An ability to efficiently store, filter, search and deliver ATLAS data at the event and/or sub-event level in a widely supported format would enable or significantly simplify usage of machine learning tools like Spark, Jupyter, R, S...

  10. The ATLAS IBL CO2 Cooling System

    CERN Document Server

    Verlaat, Bartholomeus; The ATLAS collaboration

    2016-01-01

    The Atlas Pixel detector has been equipped with an extra B-layer in the space obtained by a reduced beam pipe. This new pixel detector called the ATLAS Insertable B-Layer (IBL) is installed in 2014 and is operational in the current ATLAS data taking. The IBL detector is cooled with evaporative CO2 and is the first of its kind in ATLAS. The ATLAS IBL CO2 cooling system is designed for lower temperature operation (<-35⁰C) than the previous developed CO2 cooling systems in High Energy Physics experiments. The cold temperatures are required to protect the pixel sensors for the high expected radiation dose up to 550 fb^-1 integrated luminosity. This paper describes the design, development, construction and commissioning of the IBL CO2 cooling system. It describes the challenges overcome and the important lessons learned for the development of future systems which are now under design for the Phase-II upgrade detectors.

  11. Renewable Energy Atlas of the United States

    Energy Technology Data Exchange (ETDEWEB)

    Kuiper, J. [Environmental Science Division; Hlava, K. [Environmental Science Division; Greenwood, H. [Environmentall Science Division; Carr, A. [Environmental Science Division

    2013-12-13

    The Renewable Energy Atlas (Atlas) of the United States is a compilation of geospatial data focused on renewable energy resources, federal land ownership, and base map reference information. This report explains how to add the Atlas to your computer and install the associated software. The report also includes: A description of each of the components of the Atlas; Lists of the Geographic Information System (GIS) database content and sources; and A brief introduction to the major renewable energy technologies. The Atlas includes the following: A GIS database organized as a set of Environmental Systems Research Institute (ESRI) ArcGIS Personal GeoDatabases, and ESRI ArcReader and ArcGIS project files providing an interactive map visualization and analysis interface.

  12. Support system for ATLAS distributed computing operations

    CERN Document Server

    Kishimoto, Tomoe; The ATLAS collaboration

    2018-01-01

    The ATLAS distributed computing system has allowed the experiment to successfully meet the challenges of LHC Run 2. In order for distributed computing to operate smoothly and efficiently, several support teams are organized in the ATLAS experiment. The ADCoS (ATLAS Distributed Computing Operation Shifts) is a dedicated group of shifters who follow and report failing jobs, failing data transfers between sites, degradation of ATLAS central computing services, and more. The DAST (Distributed Analysis Support Team) provides user support to resolve issues related to running distributed analysis on the grid. The CRC (Computing Run Coordinator) maintains a global view of the day-to-day operations. In this presentation, the status and operational experience of the support system for ATLAS distributed computing in LHC Run 2 will be reported. This report also includes operations experience from the grid site point of view, and an analysis of the errors that create the biggest waste of wallclock time. The report of oper...

  13. The Next Generation ATLAS Production System

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration; Golubkov, Dmitry; Klimentov, Alexei; Maeno, Tadashi; Mashinistov, Ruslan; Vaniachine, Alexandre

    2015-01-01

    The ATLAS experiment at LHC data processing and simulation grows continuously, as more data and more use cases emerge. For data processing the ATLAS experiment adopted the data transformation approach, where software applications transform the input data into outputs. In the ATLAS production system, each data transformation is represented by a task, a collection of many jobs, dynamically submitted by the ATLAS workload management system (PanDA/JEDI) and executed on the Grid, clouds and supercomputers. Patterns in ATLAS data transformation workflows composed of many tasks provided a scalable production system framework for template definitions of the many-tasks workflows. User interface and system logic of these workflows are being implemented in the Database Engine for Tasks (DEFT). Such development required using modern computing technologies and approaches. We report technical details of this development: database implementation, server logic and Web user interface technologies.

  14. The ATLAS IBL CO2 Cooling System

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00237783; The ATLAS collaboration; Zwalinski, L.; Bortolin, C.; Vogt, S.; Godlewski, J.; Crespo-Lopez, O.; Van Overbeek, M.; Blaszcyk, T.

    2017-01-01

    The ATLAS Pixel detector has been equipped with an extra B-layer in the space obtained by a reduced beam pipe. This new pixel detector called the ATLAS Insertable B-Layer (IBL) is installed in 2014 and is operational in the current ATLAS data taking. The IBL detector is cooled with evaporative CO2 and is the first of its kind in ATLAS. The ATLAS IBL CO2 cooling system is designed for lower temperature operation (<-35⁰C) than the previous developed CO2 cooling systems in High Energy Physics experiments. The cold temperatures are required to protect the pixel sensors for the high expected radiation dose up to 550 fb^-1 integrated luminosity.

  15. Luminosity Monitoring in ATLAS with MPX Detectors

    CERN Document Server

    AUTHOR|(CDS)2086061

    2013-01-01

    The ATLAS-MPX detectors are based on the Medipix2 silicon devices designed by CERN for the detection of multiple types of radiation. Sixteen such detectors were successfully operated in the ATLAS detector at the LHC and collected data independently of the ATLAS data-recording chain from 2008 to 2013. Each ATLAS-MPX detector provides separate measurements of the bunch-integrated LHC luminosity. An internal consistency for luminosity monitoring of about 2% was demonstrated. In addition, the MPX devices close to the beam are sensitive enough to provide relative-luminosity measurements during van der Meer calibration scans, in a low-luminosity regime that lies below the sensitivity of the ATLAS calorimeter-based bunch-integrating luminometers. Preliminary results from these luminosity studies are presented for 2012 data taken at $\\sqrt{s}=8$ TeV proton-proton collisions.

  16. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  17. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  18. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

    Directory of Open Access Journals (Sweden)

    Severin Andrew J

    2010-08-01

    Full Text Available Abstract Background Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. Results The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. Conclusions This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.

  19. Preparing a new book on ATLAS

    CERN Multimedia

    Claudia Marcelloni de Oliveira

    A book about the ATLAS project and the ATLAS collaboration is going to be published and available for sale in mid 2008. The book is intended to be a symbol of appreciation for all the people from ATLAS institutes, triggering fond memories through photos, interviews, short commentaries and anecdotes about the daily life and milestones encountered while designing, constructing and completing ATLAS. We would like to give you the opportunity to collaborate with this project in two different ways: Firstly, please send us the best anecdotes related to ATLAS that you remember. To submit anecdotes, send an email to Claudia.Marcelloni@cern.ch. Secondly, you are invited to participate in our PHOTO COMPETITION. Please send the best photos you have of ATLAS attached with a description, the location, and date taken. The categories are: Milestones in the process of designing and building the detector, People at work and Important gatherings. To submit photos you should go to the CDS page and select ATLAS Photo Competi...

  20. A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

    Directory of Open Access Journals (Sweden)

    Graciana Diez-Roux

    Full Text Available Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function. It is, therefore, crucial to determine on a genome-wide level, the spatio-temporal gene expression profiles at cellular resolution. This information is provided by colorimetric RNA in situ hybridization that can elucidate expression of genes in their native context and does so at cellular resolution. We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org, consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.

  1. ATLAS Fact Sheet : To raise awareness of the ATLAS detector and collaboration on the LHC

    CERN Multimedia

    ATLAS Outreach

    2010-01-01

    Facts on the Detector, Calorimeters, Muon System, Inner Detector, Pixel Detector, Semiconductor Tracker, Transition Radiation Tracker,, Surface hall, Cavern, Detector, Magnet system, Solenoid, Toroid, Event rates, Physics processes, Supersymmetric particles, Comparing LHC with Cosmic rays, Heavy ion collisions, Trigger and Data Acquisition TDAQ, Computing, the LHC and the ATLAS collaboration. This fact sheet also contains images of ATLAS and the collaboration as well as a short list of videos on ATLAS available for viewing.

  2. Dark matter searches at ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00220289; The ATLAS collaboration

    2015-01-01

    The large excess of Dark Matter observed in the Universe and its particle nature is one of the key problems yet to be solved in particle physics. Despite the extensive success of the Standard Model, it is not able to explain this excess, which instead might be due to yet unknown particles, such as Weakly Interacting Massive Particles, that could be produced at the Large Hadron Collider. This contribution will give an overview of different approaches to finding evidence for Dark Matter with the ATLAS experiment in $\\sqrt{s}=8~\\mathrm{TeV}$ Run-1 data.

  3. Neutralino spin measurement with ATLAS

    CERN Document Server

    Ventura, A

    2007-01-01

    One of the goals of the ATLAS experiment at the LHC is to search for evidence of Supersymmetry (SUSY) signals and to measure, if discovered, the main properties of the new particles, like the spin. Left-handed squark cascade decay to second lightest neutralino which further decays to slepton represents a good opportunity for SUSY particles' spin measurement. The observability of charge asymmetries in invariant mass distributions of some final products is investigated to prove that neutralino spin is 1/2. The criteria used to select signal events and to reject background are described, together with the applied cut efficiencies. Results on charge asymmetry are then shown and discussed.

  4. Dark Matter Searches at ATLAS

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The astrophysical evidence of dark matter provides some of the most compelling clues to the nature of physics beyond the Standard Model. From these clues, ATLAS has developed a broad and systematic search program for dark matter production in LHC collisions. These searches are now entering their prime, with the LHC now colliding protons at the increased 13 TeV centre-of-mass energy and set to deliver much larger datasets than ever before. The results of these searches on the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  5. Recent QCD results from ATLAS

    CERN Document Server

    Meyer, C; The ATLAS collaboration

    2014-01-01

    The ATLAS collaboration has performed studies of a wide range of QCD phenomena, from soft particle to hard photon and jet production. Recent soft-QCD measurements include studies of underlying event and vector meson production. Differential measurements of inclusive and dijet production provide stringent tests of high-order QCD predictions and provide input for determination of parton density functions. Measurements of isolated inclusive and di-photons cross sections for high transverse momentum photons test theoretical predictions of perturbative QCD and constrain parton density functions. An overview of these results is given.

  6. Commissioning of the ATLAS Experiment

    CERN Document Server

    AUTHOR|(CDS)2069446

    2008-01-01

    The status of the commissioning of the ATLAS experiment as of May 2008 is presented. The subdetector integration in recent milestone weeks is described, especially the cosmic commissioning in milestone week M6, focusing on simultaneous running and combined track analysis of the muon detector and inner detector. The liquid argon and tile calorimeters have achieved near-full operation, and are integrated with the calorimeter trigger. The High-Level-Trigger infrastructure is installed and algorithms tested in technical runs. Problems with the inner detector cooling compressors are being fixed.

  7. Constraining Dark Matter with ATLAS

    CERN Document Server

    Czodrowski, Patrick; The ATLAS collaboration

    2017-01-01

    The presence of a non-baryonic dark matter component in the Universe is inferred from the observation of its gravitational interaction. If dark matter interacts weakly with the Standard Model it would be produced at the LHC, escaping the detector and leaving a large missing transverse momentum as their signature. The ATLAS detector has developed a broad and systematic search program for dark matter production in LHC collisions. The results of these searches on the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  8. Physics with Photons in ATLAS

    CERN Multimedia

    CERN. Geneva

    2011-01-01

    The fine granularity ATLAS electromagnetic calorimeter provides a precise measurement of the photon energy and direction, as well as efficient rejection of background from fake photons, while the high precision inner detector allows also the reconstruction of photons that convert into electron-positron pairs.Isolated photons are measured using well-defined infrared-safe isolation criteria corrected for underlying event and the effects of additional proton-proton collisions. Differential cross sections for inclusive photons and diphotons are presented, and the spectrum of diphoton production is used to search for the Higgs boson in this decay channel.

  9. The new European wind atlas

    DEFF Research Database (Denmark)

    Lundtang Petersen, Erik; Troen, Ib; Ejsing Jørgensen, Hans

    2014-01-01

    , from insufficient input data to deficient physics and resolution in any of the models, model linking issues, insufficient resolution or errors in surface topographical data such as terrain heights, land cover data etc. Therefore it has been decided on a European Union level to launch a project “The New...... European Wind Atlas” aiming at reducing overall uncertainties in determining wind conditions; standing on three legs: A data bank from a series of intensive measuring campaigns; a thorough examination and redesign of the model chain from global, mesoscale to microscale models and creation of the wind atlas...

  10. SEARCHES FOR SUPERSYMMETRY IN ATLAS

    CERN Document Server

    Xu, Da; The ATLAS collaboration

    2017-01-01

    A wide range of supersymmetric searches are presented. All searches are based on the proton- proton collision dataset collected by the ATLAS experiment during the 2015 and 2016 (before summer) run with a center-of-mass energy of 13 TeV, corresponding to an integrated lumi- nosity of 36.1 (36.7) fb-1. The searches are categorized into inclusive gluino and squark search, third generation search, electroweak search, prompt RPV search and long-lived par- ticle search. No evidence of new physics is observed. The results are intepreted in various models and expressed in terms of limits on the masses of new particles.

  11. The ATLAS multithreaded offline framework

    CERN Document Server

    Snyder, Scott; The ATLAS collaboration

    2018-01-01

    In preparation for Run 3 of the LHC, scheduled to start in 2021, the ATLAS experiment is revising its offline software so as to better take advantage of machines with many cores. A major part of this effort is migrating the software to run as a fully multithreaded application, as this has been shown to significantly improve the memory scaling behavior. This talk will outline changes made to the software framework to support this migration, as well as describe a static code checker used to assist in locating violations of thread-safety rules. Preliminary experiences in migrating reconstruction algorithms will also be discussed.

  12. LUCID: The ATLAS Luminosity Detector

    CERN Document Server

    Cabras, Grazia; The ATLAS collaboration

    2018-01-01

    After the long shut-down, the LHC Run2 has started with new running conditions with respect to Run1: in particular the centre of mass energy has reached 13 TeV and the bunch-spacing is now 25 ns. In order to cope with these changes, the ATLAS luminosity monitor LUCID and its electronics have been completely rebuilt. This note describes the new detector and electronics, the new luminosity algorithms and the new calibration systems, with a brief review of the first results about the stability of the measurement and evaluation of systematic uncertainties for the 2015 data-taking.

  13. Recent photon results from ATLAS

    CERN Document Server

    Glasman, Claudia; The ATLAS collaboration

    2017-01-01

    The production of prompt isolated photons at hadron colliders provides a stringent test of perturbative QCD and can be used to probe the gluon density function of the proton. The ATLAS collaboration has performed precise measurements of the inclusive production o f isolated prompt photons at a center-of-mass energy of 13 TeV, differential in both rap idity and the photon transverse momentum. In addition, the integrated and differential c ross sections for isolated photon pair production 8 TeV have been measured. The results are compared with state-of-the-art theory predictions at NLO in QCD and with predictions of several MC generators.

  14. Radiation atlas of Poland 1997

    International Nuclear Information System (INIS)

    Jagielak, J.; Biernacka, M.; Henschke, J.; Sosinska, A.

    1998-01-01

    The Central Laboratory for Radiological Protection with support and commitment of the State Inspectorate for Environmental Protection carried out necessary surveys and collected materials which allowed to elaborate present edition of the Radiation Atlas of Poland (1997). Data presented in the form of maps provide readers with the information on the 137 Cs and natural radionuclides concentration in the environment. The average annual doses to the public from various sources of the ionizing radiation, e.g. doses from X-ray apparatus and radionuclides used in medical diagnostics or from the internal contamination of the human organism are also presented in the publication

  15. Distributed analysis challenges in ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Duckeck, Guenter; Legger, Federica; Mitterer, Christoph Anton; Walker, Rodney [Ludwig-Maximilians-Universitaet Muenchen (Germany)

    2016-07-01

    The ATLAS computing model has undergone massive changes to meet the high luminosity challenge of the second run of the Large Hadron Collider (LHC) at CERN. The production system and distributed data management have been redesigned, a new data format and event model for analysis have been introduced, and common reduction and derivation frameworks have been developed. We report on the impact these changes have on the distributed analysis system, study the various patterns of grid usage for user analysis, focusing on the differences between the first and th e second LHC runs, and measure performances of user jobs.

  16. B-physics with ATLAS

    International Nuclear Information System (INIS)

    Smizanska, M.

    1997-01-01

    The large cross section for b-quark production at LHC will allow a necessary precision for a complete program of beauty physics. ATLAS detector capabilities in this field are described. After the introduction outlining the relevant detector features, the status of triggering studies devoted to beauty physics is presented. There follows a description of methods and expected precisions for measurements of CP violation in B-decays, beauty baryon polarization, B s mixing parameter, and expected limits for FCNC B-decays measurement. At the end future plans are mentioned. (orig.)

  17. The geosystems of complex geographical atlases

    Directory of Open Access Journals (Sweden)

    Jovanović Jasmina

    2012-01-01

    Full Text Available Complex geographical atlases represent geosystems of different hierarchical rank, complexity and diversity, scale and connection. They represent a set of large number of different pieces of information about geospace. Also, they contain systematized, correlative and in the apparent form represented pieces of information about space. The degree of information revealed in the atlas is precisely explained by its content structure and the form of presentation. The quality of atlas depends on the method of visualization of data and the quality of geodata. Cartographic visualization represents cognitive process. The analysis converts geospatial data into knowledge. A complex geographical atlas represents information complex of spatial - temporal coordinated database on geosystems of different complexity and territorial scope. Each geographical atlas defines a concrete geosystem. Systemic organization (structural and contextual determines its complexity and concreteness. In complex atlases, the attributes of geosystems are modeled and pieces of information are given in systematized, graphically unique form. The atlas can be considered as a database. In composing a database, semantic analysis of data is important. The result of semantic modeling is expressed in structuring of data information, in emphasizing logic connections between phenomena and processes and in defining their classes according to the degree of similarity. Accordingly, the efficiency of research of needed pieces of information in the process of the database use is enabled. An atlas map has a special power to integrate sets of geodata and present information contents in user - friendly and understandable visual and tactile way using its visual ability. Composing an atlas by systemic cartography requires the pieces of information on concrete - defined geosystems of different hierarchical level, the application of scientific methods and making of adequate number of analytical, synthetic

  18. A practical workflow for making anatomical atlases for biological research.

    Science.gov (United States)

    Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

    2012-01-01

    The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

  19. Encoding atlases by randomized classification forests for efficient multi-atlas label propagation.

    Science.gov (United States)

    Zikic, D; Glocker, B; Criminisi, A

    2014-12-01

    We propose a method for multi-atlas label propagation (MALP) based on encoding the individual atlases by randomized classification forests. Most current approaches perform a non-linear registration between all atlases and the target image, followed by a sophisticated fusion scheme. While these approaches can achieve high accuracy, in general they do so at high computational cost. This might negatively affect the scalability to large databases and experimentation. To tackle this issue, we propose to use a small and deep classification forest to encode each atlas individually in reference to an aligned probabilistic atlas, resulting in an Atlas Forest (AF). Our classifier-based encoding differs from current MALP approaches, which represent each point in the atlas either directly as a single image/label value pair, or by a set of corresponding patches. At test time, each AF produces one probabilistic label estimate, and their fusion is done by averaging. Our scheme performs only one registration per target image, achieves good results with a simple fusion scheme, and allows for efficient experimentation. In contrast to standard forest schemes, in which each tree would be trained on all atlases, our approach retains the advantages of the standard MALP framework. The target-specific selection of atlases remains possible, and incorporation of new scans is straightforward without retraining. The evaluation on four different databases shows accuracy within the range of the state of the art at a significantly lower running time. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. O Livro de Colorir da Experiência ATLAS - ATLAS Experiment Colouring Book in Portuguese

    CERN Multimedia

    Anthony, Katarina

    2017-01-01

    Language: Portuguese - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration. Língua: Português - O Livro de Colorir da Experiência ATLAS é um livro educacional gratuito para descarregar, ideal para crianças dos 5 aos 9 anos de idade. Este livro procura introduzir as crianças ao estudo da Física de Alta-Energia, bem como ao trabalho desenvolvido pela Colaboração ATLAS.