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Sample records for genome atlas tcga

  1. TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

    Science.gov (United States)

    Cumbo, Fabio; Fiscon, Giulia; Ceri, Stefano; Masseroli, Marco; Weitschek, Emanuel

    2017-01-03

    Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and miRBase). We also provide and maintain an automatically updated data repository with publicly available Copy Number Variation, DNA-methylation, DNA-seq, miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED format, and their associated clinical and biospecimen meta data in attribute-value text format. The availability of the valuable TCGA data in BED format reduces the time spent in taking advantage of them: it is possible to efficiently and effectively deal with huge amounts of cancer genomic data integratively, and to search, retrieve and extend them with additional information. The BED format facilitates the investigators allowing several knowledge discovery analyses on all tumor types in TCGA with the final aim of understanding pathological mechanisms and aiding cancer treatments.

  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. Molecular characteristics of non-small cell lung cancer with reduced CHFR expression in The Cancer Genome Atlas (TCGA) project.

    Science.gov (United States)

    Brodie, Seth A; Li, Ge; Brandes, Johann C

    2015-01-01

    CHFR expression has previously been established as a powerful predictor for response to taxane based first-line chemotherapy in non-small cell lung cancer. It is currently unknown however, if reduced CHFR expression correlates with certain molecular subtypes of lung cancer. In order to determine which patients may benefit from CHFR biomarker testing we conducted the present study to characterize clinical and molecular characteristics of patients with reduced vs. high CHFR expression. We utilized the extensive molecular and clinical data of the most recent adeno- and squamous cell carcinoma datasets from The Cancer Genome Atlas (TCGA) project. CHFR expression, analyzed by RNA-seq, was classified as high vs. low based on the median CHFR expression level and correlated with the presence or absence of lung cancer specific mutations (EGFR, KRAS, ALK, MET, ERBB2, TP53, STK11, ROS1, RET, NF1, Pik3CA for adenocarcinomas and FGFR1, FGFR2, FGFR3, TP53, STK11, EGFR for squamous cell carcinomas). Reduced CHFR expression was associated with EGFR exon19/21 mutations in adenocarcinoma OR 0.23 (95%CI: 0.06-0.88) and male gender in squamous cell carcinoma (OR 0.46 (95%CI 0.23-0.92), p = 0.02). Published by Elsevier Ltd.

  4. 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.

  5. Biospecimen Core Resource - TCGA

    Science.gov (United States)

    The Cancer Genome Atlas (TCGA) Biospecimen Core Resource centralized laboratory reviews and processes blood and tissue samples and their associated data using optimized standard operating procedures for the entire TCGA Research Network.

  6. Radiogenomics of clear cell renal cell carcinoma: preliminary findings of The Cancer Genome Atlas-Renal Cell Carcinoma (TCGA-RCC) Imaging Research Group.

    Science.gov (United States)

    Shinagare, Atul B; Vikram, Raghu; Jaffe, Carl; Akin, Oguz; Kirby, Justin; Huang, Erich; Freymann, John; Sainani, Nisha I; Sadow, Cheryl A; Bathala, Tharakeswara K; Rubin, Daniel L; Oto, Aytekin; Heller, Matthew T; Surabhi, Venkateswar R; Katabathina, Venkat; Silverman, Stuart G

    2015-08-01

    To investigate associations between imaging features and mutational status of clear cell renal cell carcinoma (ccRCC). This multi-institutional, multi-reader study included 103 patients (77 men; median age 59 years, range 34-79) with ccRCC examined with CT in 81 patients, MRI in 19, and both CT and MRI in three; images were downloaded from The Cancer Imaging Archive, an NCI-funded project for genome-mapping and analyses. Imaging features [size (mm), margin (well-defined or ill-defined), composition (solid or cystic), necrosis (for solid tumors: 0%, 1%-33%, 34%-66% or >66%), growth pattern (endophytic, <50% exophytic, or ≥50% exophytic), and calcification (present, absent, or indeterminate)] were reviewed independently by three readers blinded to mutational data. The association of imaging features with mutational status (VHL, BAP1, PBRM1, SETD2, KDM5C, and MUC4) was assessed. Median tumor size was 49 mm (range 14-162 mm), 73 (71%) tumors had well-defined margins, 98 (95%) tumors were solid, 95 (92%) showed presence of necrosis, 46 (45%) had ≥50% exophytic component, and 18 (19.8%) had calcification. VHL (n = 52) and PBRM1 (n = 24) were the most common mutations. BAP1 mutation was associated with ill-defined margin and presence of calcification (p = 0.02 and 0.002, respectively, Pearson's χ (2) test); MUC4 mutation was associated with an exophytic growth pattern (p = 0.002, Mann-Whitney U test). BAP1 mutation was associated with ill-defined tumor margins and presence of calcification; MUC4 mutation was associated with exophytic growth. Given the known prognostic implications of BAP1 and MUC4 mutations, these results support using radiogenomics to aid in prognostication and management.

  7. TCGA researchers identify potential drug targets, markers for leukemia risk

    Science.gov (United States)

    Investigators for The Cancer Genome Atlas (TCGA) Research Network have detailed and broadly classified the genomic alterations that frequently underlie the development of acute myeloid leukemia (AML), a deadly cancer of the blood and bone marrow. Their wo

  8. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Tiago C. Silva

    2016-12-01

    Full Text Available Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA, The Encyclopedia of DNA Elements (ENCODE, and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap. These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG versus high-grade glioma (glioblastoma multiform or GBM. This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks.

  9. TCGA researchers identify 4 subtypes of stomach cancer

    Science.gov (United States)

    Stomach cancers fall into four distinct molecular subtypes, researchers with The Cancer Genome Atlas (TCGA) Network have found. Scientists report that this discovery could change how researchers think about developing treatments for stomach cancer, also c

  10. 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

  11. TCGA divides gastric cancer into four molecular subtypes:implications for individualized therapeutics

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang

    2014-01-01

    Gastric cancer is a leading cause of cancer deaths in the world. The treatment of gastric cancer is chalenging because of its highly heterogeneous etiology and clinical characteristics. Recent genomic and molecular characterization of gastric cancer, especialy the findings reported by the Cancer Genome Atlas (TCGA), have shed light on the heterogeneity and potential targeted therapeutics for four different subtypes of gastric cancer.

  12. Imaging genomic mapping of an invasive MRI phenotype predicts patient outcome and metabolic dysfunction: a TCGA glioma phenotype research group project.

    Science.gov (United States)

    Colen, Rivka R; Vangel, Mark; Wang, Jixin; Gutman, David A; Hwang, Scott N; Wintermark, Max; Jain, Rajan; Jilwan-Nicolas, Manal; Chen, James Y; Raghavan, Prashant; Holder, Chad A; Rubin, Daniel; Huang, Eric; Kirby, Justin; Freymann, John; Jaffe, Carl C; Flanders, Adam; Zinn, Pascal O

    2014-06-02

    Invasion of tumor cells into adjacent brain parenchyma is a major cause of treatment failure in glioblastoma. Furthermore, invasive tumors are shown to have a different genomic composition and metabolic abnormalities that allow for a more aggressive GBM phenotype and resistance to therapy. We thus seek to identify those genomic abnormalities associated with a highly aggressive and invasive GBM imaging-phenotype. We retrospectively identified 104 treatment-naïve glioblastoma patients from The Cancer Genome Atlas (TCGA) whom had gene expression profiles and corresponding MR imaging available in The Cancer Imaging Archive (TCIA). The standardized VASARI feature-set criteria were used for the qualitative visual assessments of invasion. Patients were assigned to classes based on the presence (Class A) or absence (Class B) of statistically significant invasion parameters to create an invasive imaging signature; imaging genomic analysis was subsequently performed using GenePattern Comparative Marker Selection module (Broad Institute). Our results show that patients with a combination of deep white matter tracts and ependymal invasion (Class A) on imaging had a significant decrease in overall survival as compared to patients with absence of such invasive imaging features (Class B) (8.7 versus 18.6 months, p < 0.001). Mitochondrial dysfunction was the top canonical pathway associated with Class A gene expression signature. The MYC oncogene was predicted to be the top activation regulator in Class A. We demonstrate that MRI biomarker signatures can identify distinct GBM phenotypes associated with highly significant survival differences and specific molecular pathways. This study identifies mitochondrial dysfunction as the top canonical pathway in a very aggressive GBM phenotype. Thus, imaging-genomic analyses may prove invaluable in detecting novel targetable genomic pathways.

  13. Large-scale profiling of microRNAs for The Cancer Genome Atlas.

    Science.gov (United States)

    Chu, Andy; Robertson, Gordon; Brooks, Denise; Mungall, Andrew J; Birol, Inanc; Coope, Robin; Ma, Yussanne; Jones, Steven; Marra, Marco A

    2016-01-01

    The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts.

  14. GWAS meets TCGA to illuminate mechanisms of cancer predisposition.

    Science.gov (United States)

    Kim, Hyun Seok; Minna, John D; White, Michael A

    2013-01-31

    Genome-wide association studies (GWASs) have unraveled a large number of cancer risk alleles. Understanding how these allelic variants predispose to disease is a major bottleneck confronting translational application. In this issue, Li and colleagues combine GWASs with The Cancer Genome Atlas (TCGA) to disambiguate the contributions of germline and somatic variants to tumorigenic gene expression programs. They find that close to half of the known risk alleles for estrogen receptor (ER)-positive breast cancer are expression quantitative trait loci (eQTLs) acting upon major determinants of gene expression in tumors.

  15. 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.

  16. Morphometic analysis of TCGA glioblastoma multiforme

    Directory of Open Access Journals (Sweden)

    Chang Hang

    2011-12-01

    Full Text Available Abstract Background Our goals are to develop a computational histopathology pipeline for characterizing tumor types that are being generated by The Cancer Genome Atlas (TCGA for genomic association. TCGA is a national collaborative program where different tumor types are being collected, and each tumor is being characterized using a variety of genome-wide platforms. Here, we have developed a tumor-centric analytical pipeline to process tissue sections stained with hematoxylin and eosin (H&E for visualization and cell-by-cell quantitative analysis. Thus far, analysis is limited to Glioblastoma Multiforme (GBM and kidney renal clear cell carcinoma tissue sections. The final results are being distributed for subtyping and linking the histology sections to the genomic data. Results A computational pipeline has been designed to continuously update a local image database, with limited clinical information, from an NIH repository. Each image is partitioned into blocks, where each cell in the block is characterized through a multidimensional representation (e.g., nuclear size, cellularity. A subset of morphometric indices, representing potential underlying biological processes, can then be selected for subtyping and genomic association. Simultaneously, these subtypes can also be predictive of the outcome as a result of clinical treatments. Using the cellularity index and nuclear size, the computational pipeline has revealed five subtypes, and one subtype, corresponding to the extreme high cellularity, has shown to be a predictor of survival as a result of a more aggressive therapeutic regime. Further association of this subtype with the corresponding gene expression data has identified enrichment of (i the immune response and AP-1 signaling pathways, and (ii IFNG, TGFB1, PKC, Cytokine, and MAPK14 hubs. Conclusion While subtyping is often performed with genome-wide molecular data, we have shown that it can also be applied to categorizing histology

  17. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular

  18. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular char

  19. 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...

  20. Mining TCGA Data Using Boolean Implications

    Science.gov (United States)

    Sinha, Subarna; Tsang, Emily K.; Zeng, Haoyang; Meister, Michela; Dill, David L.

    2014-01-01

    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/. PMID:25054200

  1. Mining TCGA data using Boolean implications.

    Science.gov (United States)

    Sinha, Subarna; Tsang, Emily K; Zeng, Haoyang; Meister, Michela; Dill, David L

    2014-01-01

    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/.

  2. 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/.

  3. 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.

  4. Feature selection and survival modeling in The Cancer Genome Atlas

    Directory of Open Access Journals (Sweden)

    Kim H

    2013-09-01

    Full Text Available Hyunsoo Kim,1 Markus Bredel2 1Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA; 2Department of Radiation Oncology, and Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, USA Purpose: Personalized medicine is predicated on the concept of identifying subgroups of a common disease for better treatment. Identifying biomarkers that predict disease subtypes has been a major focus of biomedical science. In the era of genome-wide profiling, there is controversy as to the optimal number of genes as an input of a feature selection algorithm for survival modeling. Patients and methods: The expression profiles and outcomes of 544 patients were retrieved from The Cancer Genome Atlas. We compared four different survival prediction methods: (1 1-nearest neighbor (1-NN survival prediction method; (2 random patient selection method and a Cox-based regression method with nested cross-validation; (3 least absolute shrinkage and selection operator (LASSO optimization using whole-genome gene expression profiles; or (4 gene expression profiles of cancer pathway genes. Results: The 1-NN method performed better than the random patient selection method in terms of survival predictions, although it does not include a feature selection step. The Cox-based regression method with LASSO optimization using whole-genome gene expression data demonstrated higher survival prediction power than the 1-NN method, but was outperformed by the same method when using gene expression profiles of cancer pathway genes alone. Conclusion: The 1-NN survival prediction method may require more patients for better performance, even when omitting censored data. Using preexisting biological knowledge for survival prediction is reasonable as a means to understand the biological system of a cancer, unless the analysis goal is to identify completely unknown genes relevant to cancer biology. Keywords: brain, feature selection

  5. Clarifying the biological significance of the CHK2 K373E somatic mutation discovered in The Cancer Genome Atlas database.

    Science.gov (United States)

    Higashiguchi, Masayoshi; Nagatomo, Izumi; Kijima, Takashi; Morimura, Osamu; Miyake, Kotaro; Minami, Toshiyuki; Koyama, Shohei; Hirata, Haruhiko; Iwahori, Kota; Takimoto, Takayuki; Takeda, Yoshito; Kida, Hiroshi; Kumanogoh, Atsushi

    2016-12-01

    We identified CHK2 K373E as a recurrent mutation in The Cancer Genome Atlas (TCGA) database. In this study, we demonstrate that the K373E mutation disrupts CHK2 autophosphorylation as well as kinase activity, thus leading to impairment of CHK2 functions in suppressing cell proliferation and promoting cell survival after ionizing radiation. We propose that K373E impairs p53-independent induction of p21(WAF)(1/)(CIP)(1) by CHK2. Our data implicate the K373E mutation of CHK2 in tumorigenesis. © 2016 Federation of European Biochemical Societies.

  6. Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas.

    Science.gov (United States)

    Wong, Nathan; Khwaja, Shariq S; Baker, Callie M; Gay, Hiram A; Thorstad, Wade L; Daly, Mackenzie D; Lewis, James S; Wang, Xiaowei

    2016-07-01

    Identification of novel prognostic biomarkers typically requires a large dataset which provides sufficient statistical power for discovery research. To this end, we took advantage of the high-throughput data from The Cancer Genome Atlas (TCGA) to identify a set of prognostic biomarkers in head and neck squamous cell carcinomas (HNSCC) including oropharyngeal squamous cell carcinoma (OPSCC) and other subtypes. In this study, we analyzed miRNA-seq data obtained from TCGA patients to identify prognostic biomarkers for OPSCC. The identified miRNAs were further tested with an independent cohort. miRNA-seq data from TCGA was also analyzed to identify prognostic miRNAs in oral cavity squamous cell carcinoma (OSCC) and laryngeal squamous cell carcinoma (LSCC). Our study identified that miR-193b-3p and miR-455-5p were positively associated with survival, and miR-92a-3p and miR-497-5p were negatively associated with survival in OPSCC. A combined expression signature of these four miRNAs was prognostic of overall survival in OPSCC, and more importantly, this signature was validated in an independent OPSCC cohort. Furthermore, we identified four miRNAs each in OSCC and LSCC that were prognostic of survival, and combined signatures were specific for subtypes of HNSCC. A robust 4-miRNA prognostic signature in OPSCC, as well as prognostic signatures in other subtypes of HNSCC, was developed using sequencing data from TCGA as the primary source. This demonstrates the power of using TCGA as a potential resource to develop prognostic tools for improving individualized patient care. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  7. The Cancer Genome Atlas expression profiles of low-grade gliomas.

    Science.gov (United States)

    Gonda, David D; Cheung, Vincent J; Muller, Karra A; Goyal, Amit; Carter, Bob S; Chen, Clark C

    2014-04-01

    Differentiating between low-grade gliomas (LGGs) of astrocytic and oligodendroglial origin remains a major challenge in neurooncology. Here the authors analyzed The Cancer Genome Atlas (TCGA) profiles of LGGs with the goal of identifying distinct molecular characteristics that would afford accurate and reliable discrimination of astrocytic and oligodendroglial tumors. They found that 1) oligodendrogliomas are more likely to exhibit the glioma-CpG island methylator phenotype (G-CIMP), relative to low-grade astrocytomas; 2) relative to oligodendrogliomas, low-grade astrocytomas exhibit a higher expression of genes related to mitosis, replication, and inflammation; and 3) low-grade astrocytic tumors harbor microRNA profiles similar to those previously described for glioblastoma tumors. Orthogonal intersection of these molecular characteristics with existing molecular markers, such as IDH1 mutation, TP53 mutation, and 1p19q status, should facilitate accurate and reliable pathological diagnosis of LGGs.

  8. Using Forensics to Untangle Batch Effects in TCGA Data - TCGA

    Science.gov (United States)

    Rehan Akbani, Ph.D., and colleagues at the University of Texas MD Anderson Cancer Center developed a tool called MBatch to detect, diagnose, and correct batch effects in TCGA data. Read more about batch effects in this Case Study.

  9. 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

  10. Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients.

    Science.gov (United States)

    Nicolasjilwan, Manal; Hu, Ying; Yan, Chunhua; Meerzaman, Daoud; Holder, Chad A; Gutman, David; Jain, Rajan; Colen, Rivka; Rubin, Daniel L; Zinn, Pascal O; Hwang, Scott N; Raghavan, Prashant; Hammoud, Dima A; Scarpace, Lisa M; Mikkelsen, Tom; Chen, James; Gevaert, Olivier; Buetow, Kenneth; Freymann, John; Kirby, Justin; Flanders, Adam E; Wintermark, Max

    2015-07-01

    The purpose of our study was to assess whether a model combining clinical factors, MR imaging features, and genomics would better predict overall survival of patients with glioblastoma (GBM) than either individual data type. The study was conducted leveraging The Cancer Genome Atlas (TCGA) effort supported by the National Institutes of Health. Six neuroradiologists reviewed MRI images from The Cancer Imaging Archive (http://cancerimagingarchive.net) of 102 GBM patients using the VASARI scoring system. The patients' clinical and genetic data were obtained from the TCGA website (http://www.cancergenome.nih.gov/). Patient outcome was measured in terms of overall survival time. The association between different categories of biomarkers and survival was evaluated using Cox analysis. The features that were significantly associated with survival were: (1) clinical factors: chemotherapy; (2) imaging: proportion of tumor contrast enhancement on MRI; and (3) genomics: HRAS copy number variation. The combination of these three biomarkers resulted in an incremental increase in the strength of prediction of survival, with the model that included clinical, imaging, and genetic variables having the highest predictive accuracy (area under the curve 0.679±0.068, Akaike's information criterion 566.7, P<0.001). A combination of clinical factors, imaging features, and HRAS copy number variation best predicts survival of patients with GBM. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  11. Addition of MR Imaging Features and Genetic Biomarkers Strengthen Glioblastoma Survival Prediction in TCGA Patients

    Science.gov (United States)

    Nicolasjilwan, Manal; Hu, Ying; Yan, Chunhua; Meerzaman, Daoud; Holder, Chad A.; Gutman, David; Jain, Rajan; Colen, Rivka; Rubin, Daniel L.; Zinn, Pascal O.; Hwang, Scott N.; Raghavan, Prashant; Hammoud, Dima A; Scarpace, Lisa M; Mikkelsen, Tom; Chen, James; Gevaert, Olivier; Buetow, Kenneth; Freymann, John; Kirby, Justin; Flanders, Adam E.; Wintermark, Max

    2017-01-01

    PURPOSE The purpose of our study was to assess whether a model combining clinical factors, MR imaging features, and genomics would better predict overall survival of patients with glioblastoma (GBM) than either individual data type. METHODS The study was conducted leveraging the Cancer Genome Atlas (TCGA) effort supported by the National Institutes of Health. Six neuroradiologists reviewed MRI images from The Cancer Imaging Archive (http://cancerimagingarchive.net) of 102 GBM patients using the VASARI scoring system. The patients’ clinical and genetic data were obtained from the TCGA website (http://www.cancergenome.nih.gov/). Patient outcome was measured in terms of overall survival time. The association between different categories of biomarkers and survival was evaluated using Cox analysis. RESULTS The features that were significantly associated with survival were: 1) clinical factors: chemotherapy; 2) imaging: proportion of tumor contrast enhancement on MRI, and 3) genomics: HRAS copy number variation. The combination of these three biomarkers resulted in an incremental increase in the strength of prediction of survival, with the model that included clinical, imaging, and genetic variables having the highest predictive accuracy (area under the curve 0.679 ± 0.068, Akaike’s information criterion 566.7, p < 0.001). CONCLUSION A combination of clinical factors, imaging features, and HRAS copy number variation best predicts survival of patients with GBM. PMID:24997477

  12. Expression profile analysis of head and neck squamous cell carcinomas using data from The Cancer Genome Atlas.

    Science.gov (United States)

    Yan, Li; Zhan, Cheng; Wu, Jihong; Wang, Shengzi

    2016-05-01

    Head and neck squamous cell carcinoma (HNSCC) is the major histological type of head and neck cancer and no curative treatments are currently available. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) has produced large‑scale sequencing data, which provide unprecedented opportunities to reveal molecular mechanisms of cancer. The present study analyzed the mRNA and micro (mi)RNA expression data of HNSCC and normal control tissues released by the TCGA database using a bioinformatics approach to explore underlying molecular mechanisms. The mRNA and miRNA expression data were downloaded from the TCGA database and differentially expressed genes (DEGs) and miRNAs (DEMs) between HNSCC and normal head and neck tissues were identified using TwoClassDif. Subsequently, the gene functions and pathways which are significantly altered in HNSCC were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Regulatory networks among DEGs and DEMs were then constructed, and transcription factors (TFs) potentially regulating the DEGs and DEMs were determined and a TF ‑ miRNA ‑ gene network was established. A total of 2,594 significant DEGs (1,087 upregulated and 1,507 downregulated), and 25 DEMs (8 upregulated and 17 downregulated) were identified in HNSCC compared with normal control samples. These DEGs were significantly enriched in GOs and KEGG pathways such as mitosis, cell cycle, Wnt, JAK/STAT and TLR signaling pathway. CPBP, NF‑AT1 and miR‑1 were situated in the central hub of the TF ‑ miRNA ‑ gene network, underlining their central roles in regulatory processes specific for HNSCC. The present study enhanced the current understanding of the molecular mechanisms underlying HNSCC and may offer novel strategies for its prevention, diagnosis and treatment.

  13. CCG Programs with Clinical Data will Build on the Success of TCGA

    Science.gov (United States)

    Though TCGA will wrap up in 2016 with a concluding symposium, cancer genomics projects built upon the success of TCGA will continue to play a major part in the NCI’s mission to better understand and treat cancer in the years to come.

  14. DO CANCER CLINICAL TRIAL POPULATIONS TRULY REPRESENT CANCER PATIENTS? A COMPARISON OF OPEN CLINICAL TRIALS TO THE CANCER GENOME ATLAS.

    Science.gov (United States)

    Geifman, Nophar; Butte, Atul J

    2016-01-01

    Open clinical trial data offer many opportunities for the scientific community to independently verify published results, evaluate new hypotheses and conduct meta-analyses. These data provide a springboard for scientific advances in precision medicine but the question arises as to how representative clinical trials data are of cancer patients overall. Here we present the integrative analysis of data from several cancer clinical trials and compare these to patient-level data from The Cancer Genome Atlas (TCGA). Comparison of cancer type-specific survival rates reveals that these are overall lower in trial subjects. This effect, at least to some extent, can be explained by the more advanced stages of cancer of trial subjects. This analysis also reveals that for stage IV cancer, colorectal cancer patients have a better chance of survival than breast cancer patients. On the other hand, for all other stages, breast cancer patients have better survival than colorectal cancer patients. Comparison of survival in different stages of disease between the two datasets reveals that subjects with stage IV cancer from the trials dataset have a lower chance of survival than matching stage IV subjects from TCGA. One likely explanation for this observation is that stage IV trial subjects have lower survival rates since their cancer is less likely to respond to treatment. To conclude, we present here a newly available clinical trials dataset which allowed for the integration of patient-level data from many cancer clinical trials. Our comprehensive analysis reveals that cancer-related clinical trials are not representative of general cancer patient populations, mostly due to their focus on the more advanced stages of the disease. These and other limitations of clinical trials data should, perhaps, be taken into consideration in medical research and in the field of precision medicine.

  15. Data and analysis of the cancer genome atlas%癌症基因组图谱计划数据及分析

    Institute of Scientific and Technical Information of China (English)

    邓祯祥(综述); 李金明(审校)

    2014-01-01

    Multiple chromosomal aberrations, nucleotide substitutions, and epigenetic modifications may occur in human cancer cells, which drive malignant transformation. The Cancer Genome Atlas (TCGA) project aims to promote large-scale multi-dimensional analysis of these molecular characteristics in human cancer and rapidly provide data to researchers. In this study, we introduce four flow paths of the production of TCGA data, the collections of various cancer types, the data category and level, and the standardized pipeline of data analysis, as well as several existing data analytical tools. We used ovarian cancer as an example to introduce the application of the TCGA data in the analyses of mutation, copy number, analysis, and expression. We summarized the important findings of glioblasto-ma by TCGA teams.%人类癌症细胞中通常藏匿着多种引起恶性病变的染色体变异,核酸替换和表观遗传修饰。癌症基因组图谱(the can-cer genome atlas,TCGA)计划的目标是获取、刻画并分析人类癌症中大规模、多种变异的分子特征,并且为癌症研究者迅速地提供数据。本文对TCGA数据的四个产生流程以及包含的癌症种类、数据类型、数据水平、分析流程和常用的几种分析工具等进行阐述,同时以卵巢癌(ovarian cancer)为例详细介绍了TCGA数据在突变分析、拷贝数分析、表达分析和通路分析等方面的应用,并对TCGA研究团队近几年有关胶质母细胞瘤(glioblastoma,GBM)的研究方法和结果以及已经完成分析的癌症类型进行综述。

  16. Methods for visual mining of genomic and proteomic data atlases.

    Science.gov (United States)

    Boyle, John; Kreisberg, Richard; Bressler, Ryan; Killcoyne, Sarah

    2012-04-23

    As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations

  17. Methods for visual mining of genomic and proteomic data atlases

    Directory of Open Access Journals (Sweden)

    Boyle John

    2012-04-01

    Full Text Available Abstract Background As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. Results This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas and the genomic characterization of cancer (The Cancer Genome Atlas. Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. Conclusions The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make

  18. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.

    Science.gov (United States)

    Guo, Yan; Sheng, Quanhu; Li, Jiang; Ye, Fei; Samuels, David C; Shyr, Yu

    2013-01-01

    RNAseq and microarray methods are frequently used to measure gene expression level. While similar in purpose, there are fundamental differences between the two technologies. Here, we present the largest comparative study between microarray and RNAseq methods to date using The Cancer Genome Atlas (TCGA) data. We found high correlations between expression data obtained from the Affymetrix one-channel microarray and RNAseq (Spearman correlations coefficients of ∼0.8). We also observed that the low abundance genes had poorer correlations between microarray and RNAseq data than high abundance genes. As expected, due to measurement and normalization differences, Agilent two-channel microarray and RNAseq data were poorly correlated (Spearman correlations coefficients of only ∼0.2). By examining the differentially expressed genes between tumor and normal samples we observed reasonable concordance in directionality between Agilent two-channel microarray and RNAseq data, although a small group of genes were found to have expression changes reported in opposite directions using these two technologies. Overall, RNAseq produces comparable results to microarray technologies in term of expression profiling. The RNAseq normalization methods RPKM and RSEM produce similar results on the gene level and reasonably concordant results on the exon level. Longer exons tended to have better concordance between the two normalization methods than shorter exons.

  19. The Cancer Digital Slide Archive - TCGA

    Science.gov (United States)

    Dr. David Gutman and Dr. Lee Cooper developed The Cancer Digital Slide Archive (CDSA), a web platform for accessing pathology slide images of TCGA samples. Find out how they did it and how to use the CDSA website in this Case Study.

  20. Genomic understanding of glioblastoma expanded

    Science.gov (United States)

    Glioblastoma multiforme (GBM) was the first cancer type to be systematically studied by TCGA in 2008. In a new, complementary report, TCGA experts examined more than 590 GBM samples--the largest to date utilizing genomic characterization techniques and ne

  1. TCGA and Its Vital Role in Understanding the Landscape of Somatic Alterations in Cancer - TCGA

    Science.gov (United States)

    Dr. Stephen Chanock, M.D., Director of the Division of Cancer Epidemiology & Genetics at the NCI, discusses how TCGA provides a strong foundation for understanding key biological alterations in cancer.

  2. Stratifying melanoma and breast cancer TCGA datasets on the basis of the CNV of transcription factor binding sites common to proliferation- and apoptosis-effector genes.

    Science.gov (United States)

    Mauro, James A; Yavorski, John M; Blanck, George

    2017-02-28

    Transcription factors that activate both proliferation- and apoptosis-effector genes, along with a number of related observations, have led to a proposal for a feed forward mechanism of activating the two gene classes, whereby a certain concentration of a transcription factor activates the proliferation-effector genes and a higher concentration of the transcription factor activates the apoptosis-effector genes. We reasoned that this paradigm of regulation could lead to, in the cancer setting, a selection for relatively reduced copy numbers of apoptosis-effector gene, transcription factor binding sites (TFBS). Thus, the aim of this investigation was to examine the DNA sequencing read depths of TFBS for a set of proliferation- and apoptosis-effector genes, normalized to the read depths found in matching blood samples, as provided by the cancer genome atlas (TCGA); and thereby document copy number differences among these TFBS. We determined that the melanoma and breast cancer, TCGA datasets could be divided into three categories: (i) no detectable copy number variation for the proliferation- and apoptosis-effector, shared TFBS; (ii) a relative increase in the copy number of proliferation-effector gene TFBS, compared with the copy number of the apoptosis-effector gene TFBS; and (iii) a relative decrease in the number of proliferation-effector gene TFBS. Thus, we conclude that changes in the relative copies of the shared TFBS, for proliferation- and apoptosis-effector genes, have the potential of impacting tumor cell proliferative and apoptotic capacities.

  3. 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.

  4. Follicular cell thyroid neoplasia: insights from genomics and The Cancer Genome Atlas research network.

    Science.gov (United States)

    Giordano, Thomas J

    2016-01-01

    The present review is focused on the recently published study on the genomics of papillary thyroid carcinoma performed by The Cancer Genome Atlas Research Network and its implications for the follicular variant of papillary carcinoma. The Cancer Genome Atlas study of papillary thyroid carcinoma comprehensively examined the cancer genome of nearly 500 primary tumors. Using a highly integrated bioinformatic analysis, papillary carcinoma was shown at the genomic level to consist of two highly distinct classes that reflected both tumor histology and underlying genotype. Tumors with true papillary architecture were dominated by BRAF(V600E) mutations and RET kinase fusions and were designated as BRAF(V600E)-like. Tumors with follicular architecture were conversely dominated by RAS mutations and were designated as RAS-like. Given the strong genotype:phenotype correlation known to be present in thyroid cancer, the separation of BRAF(V600E)-like and RAS-like tumors has profound implications for its classification, especially the follicular variant of papillary carcinoma. The recent genomic characterization of papillary thyroid carcinoma is challenging the established pathological classification of thyroid cancer with significance for the care of patients.

  5. 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.

  6. Pan-cancer analysis of ROS1 genomic aberrations

    OpenAIRE

    Wang, Yidan; 王奕丹

    2015-01-01

    The ROS proto-oncogene 1 (ROS1) encodes the ROS1 receptor kinase. ROS1 rearrangements are known to be oncogenic in glioblastoma, non–small-cell lung carcinoma (NSCLC) and cholangiocarcinoma. The clinical relevance of ROS1 genomic aberrations in other human cancers is largely unexamined. Here, we performed a pan-cancer analysis of ROS1 genomic aberrations across 20 cancer sites by interrogating the whole-exome sequencing data of the Cancer Genome Atlas (TCGA) via the cBioportal (www.cbioportal...

  7. Complete mitochondrial genome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae) and the phylogenetic relationship of Saturniidae species.

    Science.gov (United States)

    Chen, Miao-Miao; Li, Yan; Chen, Mo; Wang, Huan; Li, Qun; Xia, Run-Xi; Zeng, Cai-Yun; Li, Yu-Ping; Liu, Yan-Qun; Qin, Li

    2014-07-15

    Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect with the largest wing surface area of all moths. The mitogenome of A. atlas is a circular molecule of 15,282 bp long, and its nucleotide composition shows heavily biased towards As and Ts, accounting for 79.30%. This genome comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A+T-rich region. It is of note that this genome exhibits a slightly positive AT skew, which is different from the other known Saturniidae species. All PCGs are initiated by ATN codons, except for COI with CGA instead. Only six PCGs use a common stop codon of TAA or TAG, whereas the remaining seven use an incomplete termination codon T or TA. All tRNAs have the typical clover-leaf structure, with an exception for tRNA(Ser)(AGN). The A. atlas A+T-rich region contains non-repetitive sequences, but harbors several features common to the Bombycoidea insects. The phylogenetic relationships based on Maximum Likelihood method provide a well-supported outline of Saturniidae, which is in accordance with the traditional morphological classification and recent molecular works.

  8. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  9. Smoking correlates with increased cytoskeletal protein-related coding region mutations in the lung and head and neck datasets of the cancer genome atlas.

    Science.gov (United States)

    Yavorski, John M; Blanck, George

    2016-12-01

    Cancer from smoking tobacco is considered dependent on mutagens, but significant molecular aspects of smoking-specific, cancer development remain unknown. We defined sets of coding regions for oncoproteins, tumor suppressor proteins, and cytoskeletal-related proteins that were compared between nonsmokers and smokers, for mutation occurrences, in the lung adenocarcinoma (LUAD), head and neck squamous carcinoma (HNSC), bladder carcinoma (BLCA), and pancreatic adenocarcinoma ( PAAD) datasets from the cancer genome atlas (TCGA). We uncovered significant differences in overall mutation rates, and in mutation rates in cytoskeletal protein-related coding regions (CPCRs, including extracellular matrix protein coding regions), between nonsmokers and smokers in LUAD and HNSC (P < 0.001), raising the question of whether the CPCR mutation differences lead to different clinical courses for nonsmoker and smoker cancers. Another important question inspired by these results is, whether high smoker cancer mutation rates would facilitate genotoxicity or neoantigen-based therapies. No significant, mutation-based differences were found in the BLCA or PAAD datasets, between nonsmokers and smokers. However, a significant difference was uncovered for the average number of overall cancer mutations, in LUAD, for persons who stopped smoking more than 15 years ago, compared with more recent smokers (P < 0.032).

  10. 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

  11. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database

    Science.gov (United States)

    Tian, Feng; Zhao, Jinlong; Kang, Zhenxing

    2017-01-01

    Background Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. Methods We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. Results Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. Conclusions The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.

  12. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database.

    Science.gov (United States)

    Tian, Feng; Zhao, Jinlong; Fan, Xinlei; Kang, Zhenxing

    2017-01-01

    Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.

  13. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

    Science.gov (United States)

    Background A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. Results The Bovine Gene...

  14. A Protective Role for Androgen Receptor in Clear Cell Renal Cell Carcinoma Based on Mining TCGA Data.

    Directory of Open Access Journals (Sweden)

    Hongjuan Zhao

    Full Text Available Androgen receptor (AR is expressed in normal murine and human kidneys of both genders, but its physiologic role is uncertain. Several studies showed loss of AR in renal cell carcinoma (RCC in conjunction with increasing clinical stage and pathological grade, but others found that higher AR expression correlated with worse outcomes. Limited functional studies with renal cell lines suggested tumor-promoting activity of AR. In this study, we queried transcriptomic, proteomic, epigenetic and survival data from The Cancer Genome Atlas (TCGA to evaluate AR expression and its association with overall survival in three subtypes of RCC (clear cell [ccRCC], papillary [pRCC], and chromophobe [chRCC]. We found that although there was no significant difference in AR mRNA expression in ccRCC of males vs. females, AR protein expression in ccRCC was significantly higher in male compared to female patients. More importantly, higher expression of AR at both transcript and protein levels was associated with improved overall survival in both genders with ccRCC, but did not predict survival of either gender with pRCC or chRCC. Genes whose transcript levels were associated with AR mRNA levels significantly overlapped between ccRCC and pRCC, but not with chRCC, suggesting a similar transcriptional program mediated by AR in ccRCC and pRCC. Ingenuity pathway analysis also identified overlapping pathways and upstream regulators enriched in AR-associated genes in ccRCC and pRCC. Hypermethylation of CpG sites located in the promoter and first exon of AR was associated with loss of AR expression and poor overall survival. Our findings support a tumor suppressor role for AR in both genders that might be exploited to decrease the incidence or progression of ccRCC.

  15. [Implications of TCGA Network Data on 2nd Generation Immunotherapy Concepts Based on PD-L1 and PD-1 Target Structures].

    Science.gov (United States)

    Peters, I; Tezval, H; Kramer, M W; Wolters, M; Grünwald, V; Kuczyk, M A; Serth, J

    2015-11-01

    The era of cytokines, given to patients with metastatic renal cell carcinoma (mRCC) as part of an unspecific immunomodulatory treatment concept, seems to have ended with the introduction of targeted therapies. However, preliminary data from studies on treatment with checkpoint inhibitors (e. g. anti-PD-1 and anti-PD-L1) may point the way to second-generation immunotherapy. The rationale of such immunomodulatory treatment is to stop or interrupt the tumour from "escaping" the body's immune defence. Thompson et al. report that increased protein expression of PD-L1 (CD274/ B7-H1) in tumour cells and tumour-infiltrating immune cells (TILs; lymphocytes and histiocytes) is associated with unfavourable clinical pathological parameters as well as poor survival. In small pilot groups of mRCC patients it was found that increased PD-L1 protein expression in tumours and TILs may be correlated with the objective response to anti-PD-1 treatment. Sometimes, however, a very wide variety of response rates was observed, which raises the question if this can be explained by individual expression levels of PD-L1 (CD 274) or PD-1 (PDCD1).Recently published data from the Cancer Genome Atlas (TCGA) Kidney Renal Clear Cell Carcinoma (KIRC) Network now provide a genome-wide data base that allows us to review or validate the molecular results obtained in clear cell renal cell carcinomas (ccRCC) to date.In this study, we analysed the TCGA KIRC mRNA expression data for PD-L1 and PD-1 for a possible association with clinical pathological parameters and the survival of 417 ccRCC patients.The mRNA expression of PD-L1 in primary nephrectomy specimens revealed no significant association with unfavourable clinical parameters. Interestingly, though, a positive correlation with patient survival was found (HR=0,59, p=0,006).These results, which partly contradict the concept applied to date, point out the necessity to ascertain the characteristics of PD-L1 and PD-1 expression at mRNA and protein

  16. The genomic landscape of cutaneous melanoma.

    Science.gov (United States)

    Zhang, Tongwu; Dutton-Regester, Ken; Brown, Kevin M; Hayward, Nicholas K

    2016-05-01

    Somatic mutation analysis of melanoma has been performed at the single gene level extensively over the past several decades. This has provided considerable insight into the critical pathways controlling melanoma initiation and progression. During the last 5 yr, next-generation sequencing (NGS) has enabled even more comprehensive mutational screening at the level of multigene panels, exomes and genomes. These studies have uncovered many new and unexpected players in melanoma development. The recent landmark study from The Cancer Genome Atlas (TCGA) consortium describing the genomic architecture of 333 cutaneous melanomas provides the largest and broadest analysis to date on the somatic aberrations underlying melanoma genesis. It thus seems timely to review the mutational landscape of melanoma and highlight the key genes and cellular pathways that appear to drive this cancer.

  17. 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...

  18. 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.

  19. 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

  20. Insights into the Genetic Basis of the Renal Cell Carcinomas from The Cancer Genome Atlas.

    Science.gov (United States)

    Haake, Scott M; Weyandt, Jamie D; Rathmell, W Kimryn

    2016-07-01

    The renal cell carcinomas (RCC), clear cell, papillary, and chromophobe, have recently undergone an unmatched genomic characterization by The Cancer Genome Atlas. This analysis has revealed new insights into each of these malignancies and underscores the unique biology of clear cell, papillary, and chromophobe RCC. Themes that have emerged include distinct mechanisms of metabolic dysregulation and common mutations in chromatin modifier genes. Importantly, the papillary RCC classification encompasses a heterogeneous group of diseases, each with highly distinct genetic and molecular features. In conclusion, this review summarizes RCCs that represent a diverse set of malignancies, each with novel biologic programs that define new paradigms for cancer biology. Mol Cancer Res; 14(7); 589-98. ©2016 AACR. ©2016 American Association for Cancer Research.

  1. ATLAS

    CERN Multimedia

    2002-01-01

    Barrel and END-CAP Toroids In order to produce a powerful magnetic field to bend the paths of the muons, the ATLAS detector uses an exceptionally large system of air-core toroids arranged outside the calorimeter volumes. The large volume magnetic field has a wide angular coverage and strengths of up to 4.7tesla. The toroids system contains over 100km of superconducting wire and has a design current of 20 500 amperes. (ATLAS brochure: The Technical Challenges)

  2. 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

    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...

  3. 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.

  4. The UCSC Cancer Genomics Browser: update 2013.

    Science.gov (United States)

    Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Zhu, Jingchun

    2013-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. The ability to view multiple datasets together allows users to make comparisons across different data and cancer types. Biological pathways, collections of genes, genomic or clinical information can be used to sort, aggregate and zoom into a group of samples. We currently display an expanding set of data from various sources, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and Stand Up To Cancer. New features include a completely redesigned user interface with an interactive tutorial and updated documentation. We have also added data downloads, additional clinical heatmap features, and an updated Tumor Image Browser based on Google Maps. New security features allow authenticated users access to private datasets hosted by several different consortia through the public website.

  5. 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.

  6. Threshold Cryptography-based Group Authentication (TCGA) Scheme for the Internet of Things (IoT)

    DEFF Research Database (Denmark)

    Mahalle, Parikshit N.; Prasad, Neeli R.; Prasad, Ramjee

    2014-01-01

    , and receipt of their authentication request at the same time. Therefore, secure, and efficient group authentication, and authorization scheme is required that authenticates a group of devices at once in the context of resource constrained IoT. This paper presents novel Threshold Cryptography-based Group...... Authentication (TCGA) scheme for the IoT which verifies authenticity of all the devices taking part in the group communication. This paper also presents TCGA framework which is flexible and secure. The proposed TCGA scheme is implemented for WI-FI environment, and the result shows that TCGA scheme is lightweight......Internet of things (IoT) is an emerging paradigm where the devices around us (persistent and non-persistent) are connected to each other to provide seamless communication, and contextual services. In the IoT, each device cannot be authenticated in the short time due to unbounded number of devices...

  7. Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

    Science.gov (United States)

    Mahfouz, Ahmed; Ziats, Mark N.; Rennert, Owen M.; Lelieveldt, Boudewijn P. F.; Reinders, Marcel J. T.

    2014-03-01

    The human brain comprises systems of networks that span the molecular, cellular, anatomic and functional levels. Molecular studies of the developing brain have focused on elucidating networks among gene products that may drive cellular brain development by functioning together in biological pathways. On the other hand, studies of the brain connectome attempt to determine how anatomically distinct brain regions are connected to each other, either anatomically (diffusion tensor imaging) or functionally (functional MRI and EEG), and how they change over development. A global examination of the relationship between gene expression and connectivity in the developing human brain is necessary to understand how the genetic signature of different brain regions instructs connections to other regions. Furthermore, analyzing the development of connectivity networks based on the spatio-temporal dynamics of gene expression provides a new insight into the effect of neurodevelopmental disease genes on brain networks. In this work, we construct connectivity networks between brain regions based on the similarity of their gene expression signature, termed "Genomic Connectivity Networks" (GCNs). Genomic connectivity networks were constructed using data from the BrainSpan Transcriptional Atlas of the Developing Human Brain. Our goal was to understand how the genetic signatures of anatomically distinct brain regions relate to each other across development. We assessed the neurodevelopmental changes in connectivity patterns of brain regions when networks were constructed with genes implicated in the neurodevelopmental disorder autism (autism spectrum disorder; ASD). Using graph theory metrics to characterize the GCNs, we show that ASD-GCNs are relatively less connected later in development with the cerebellum showing a very distinct expression of ASD-associated genes compared to other brain regions.

  8. 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.

  9. Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues.

    Science.gov (United States)

    Chisanga, David; Keerthikumar, Shivakumar; Pathan, Mohashin; Ariyaratne, Dinuka; Kalra, Hina; Boukouris, Stephanie; Mathew, Nidhi Abraham; Al Saffar, Haidar; Gangoda, Lahiru; Ang, Ching-Seng; Sieber, Oliver M; Mariadason, John M; Dasgupta, Ramanuj; Chilamkurti, Naveen; Mathivanan, Suresh

    2016-01-04

    In order to advance our understanding of colorectal cancer (CRC) development and progression, biomedical researchers have generated large amounts of OMICS data from CRC patient samples and representative cell lines. However, these data are deposited in various repositories or in supplementary tables. A database which integrates data from heterogeneous resources and enables analysis of the multidimensional data sets, specifically pertaining to CRC is currently lacking. Here, we have developed Colorectal Cancer Atlas (http://www.colonatlas.org), an integrated web-based resource that catalogues the genomic and proteomic annotations identified in CRC tissues and cell lines. The data catalogued to-date include sequence variations as well as quantitative and non-quantitative protein expression data. The database enables the analysis of these data in the context of signaling pathways, protein-protein interactions, Gene Ontology terms, protein domains and post-translational modifications. Currently, Colorectal Cancer Atlas contains data for >13 711 CRC tissues, >165 CRC cell lines, 62 251 protein identifications, >8.3 million MS/MS spectra, >18 410 genes with sequence variations (404 278 entries) and 351 pathways with sequence variants. Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. 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.

  11. FoldAtlas: a repository for genome-wide RNA structure probing data

    Science.gov (United States)

    Norris, Matthew; Kwok, Chun Kit; Cheema, Jitender; Hartley, Matthew; Morris, Richard J.; Aviran, Sharon; Ding, Yiliang

    2017-01-01

    Summary: Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. Availability and Implementation: The FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. Contact: yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27663500

  12. Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

    Science.gov (United States)

    Robinson, Kelly M; Crabtree, Jonathan; Mattick, John S A; Anderson, Kathleen E; Dunning Hotopp, Julie C

    2017-01-25

    A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.

  13. Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework.

    Science.gov (United States)

    Yang, Hai; Wei, Qiang; Zhong, Xue; Yang, Hushan; Li, Bingshan

    2017-02-15

    Comprehensive catalogue of genes that drive tumor initiation and progression in cancer is key to advancing diagnostics, therapeutics and treatment. Given the complexity of cancer, the catalogue is far from complete yet. Increasing evidence shows that driver genes exhibit consistent aberration patterns across multiple-omics in tumors. In this study, we aim to leverage complementary information encoded in each of the omics data to identify novel driver genes through an integrative framework. Specifically, we integrated mutations, gene expression, DNA copy numbers, DNA methylation and protein abundance, all available in The Cancer Genome Atlas (TCGA) and developed iDriver, a non-parametric Bayesian framework based on multivariate statistical modeling to identify driver genes in an unsupervised fashion. iDriver captures the inherent clusters of gene aberrations and constructs the background distribution that is used to assess and calibrate the confidence of driver genes identified through multi-dimensional genomic data. We applied the method to 4 cancer types in TCGA and identified candidate driver genes that are highly enriched with known drivers. (e.g.: P < 3.40 × 10 -36 for breast cancer). We are particularly interested in novel genes and observed multiple lines of supporting evidence. Using systematic evaluation from multiple independent aspects, we identified 45 candidate driver genes that were not previously known across these 4 cancer types. The finding has important implications that integrating additional genomic data with multivariate statistics can help identify cancer drivers and guide the next stage of cancer genomics research. The C ++ source code is freely available at https://medschool.vanderbilt.edu/cgg/ . hai.yang@vanderbilt.edu or bingshan.li@Vanderbilt.Edu. Supplementary data are available at Bioinformatics online.

  14. Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks

    Directory of Open Access Journals (Sweden)

    Shengda Lin

    2016-01-01

    Full Text Available The advent of the human genome sequence and the resulting ~20,000 genes provide a crucial framework for a transition from traditional biology to an integrative “OMICs” arena (Lander et al., 2001; Venter et al., 2001; Kitano, 2002. This brings in a revolution for cancer research, which now enters a big data era. In the past decade, with the facilitation by next-generation sequencing, there have been a huge number of large-scale sequencing efforts, such as The Cancer Genome Atlas (TCGA, the HapMap, and the 1000 genomes project. As a result, a deluge of genomic information becomes available from patients stricken by a variety of cancer types. The list of cancer-associated genes is ever expanding. New discoveries are made on how frequent and highly penetrant mutations, such as those in the telomerase reverse transcriptase (TERT and TP53, function in cancer initiation, progression, and metastasis. Most genes with relatively frequent but weakly penetrant cancer mutations still remain to be characterized. In addition, genes that harbor rare but highly penetrant cancer-associated mutations continue to emerge. Here, we review recent advances related to cancer genomics, proteomics, and systems biology and suggest new perspectives in targeted therapy and precision medicine.

  15. Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks

    Science.gov (United States)

    Lin, Shengda; Yin, Yi A.; Jiang, Xiaoqian; Sahni, Nidhi; Yi, Song

    2016-01-01

    The advent of the human genome sequence and the resulting ~20,000 genes provide a crucial framework for a transition from traditional biology to an integrative “OMICs” arena (Lander et al., 2001; Venter et al., 2001; Kitano, 2002). This brings in a revolution for cancer research, which now enters a big data era. In the past decade, with the facilitation by next-generation sequencing, there have been a huge number of large-scale sequencing efforts, such as The Cancer Genome Atlas (TCGA), the HapMap, and the 1000 genomes project. As a result, a deluge of genomic information becomes available from patients stricken by a variety of cancer types. The list of cancer-associated genes is ever expanding. New discoveries are made on how frequent and highly penetrant mutations, such as those in the telomerase reverse transcriptase (TERT) and TP53, function in cancer initiation, progression, and metastasis. Most genes with relatively frequent but weakly penetrant cancer mutations still remain to be characterized. In addition, genes that harbor rare but highly penetrant cancer-associated mutations continue to emerge. Here, we review recent advances related to cancer genomics, proteomics, and systems biology and suggest new perspectives in targeted therapy and precision medicine. PMID:27403431

  16. Bioinformatics analyses of the differences between lung adenocarcinoma and squamous cell carcinoma using The Cancer Genome Atlas expression data.

    Science.gov (United States)

    Sun, Fenghao; Yang, Xiaodong; Jin, Yulin; Chen, Li; Wang, Lin; Shi, Mengkun; Zhan, Cheng; Shi, Yu; Wang, Qun

    2017-07-01

    The present study aimed to explore gene and microRNA (miRNA) expression differences between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were identified by analyzing mRNA and miRNA expression data in normal and cancerous lung tissues that were obtained from The Cancer Genome Atlas database. A total of 778 DEGs and 7 DEMs were identified. Altered gene functions and signaling pathways were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, which revealed that DEGs were significantly enriched in extracellular matrix organization, cell differentiation, negative regulation of toll signaling pathway, and several other terms and pathways. Transcription factor (TF)‑miRNA‑gene networks in LUAD and LUSC were predicted using the TargetScan, Miranda, and TRANSFAC databases, which revealed the regulatory links among the TFs, DEMs, and DEGs. The central TFs, i.e., the TFs in the middle of the TF‑miRNA‑gene network, of LUAD and LUSC were similar. Although LUAD and LUSC shared similar miRNAs in the predicted networks, miR‑29b‑3p was demonstrated to be upregulated only in LUAD, whereas miR‑1, miR‑105‑5p, and miR‑193b‑5p were altered in LUSC. These findings may improve our understanding of the different molecular mechanisms in non‑small cell lung cancers and may promote new and accurate strategies for prevention, diagnosis, and treatment.

  17. Interfaces to PeptideAtlas: a case study of standard data access systems.

    Science.gov (United States)

    Killcoyne, Sarah; Handcock, Jeremy; Robinson, Thomas; Deutsch, Eric W; Boyle, John

    2012-09-01

    Access to public data sets is important to the scientific community as a resource to develop new experiments or validate new data. Projects such as the PeptideAtlas, Ensembl and The Cancer Genome Atlas (TCGA) offer both access to public data and a repository to share their own data. Access to these data sets is often provided through a web page form and a web service API. Access technologies based on web protocols (e.g. http) have been in use for over a decade and are widely adopted across the industry for a variety of functions (e.g. search, commercial transactions, and social media). Each architecture adapts these technologies to provide users with tools to access and share data. Both commonly used web service technologies (e.g. REST and SOAP), and custom-built solutions over HTTP are utilized in providing access to research data. Providing multiple access points ensures that the community can access the data in the simplest and most effective manner for their particular needs. This article examines three common access mechanisms for web accessible data: BioMart, caBIG, and Google Data Sources. These are illustrated by implementing each over the PeptideAtlas repository and reviewed for their suitability based on specific usages common to research. BioMart, Google Data Sources, and caBIG are each suitable for certain uses. The tradeoffs made in the development of the technology are dependent on the uses each was designed for (e.g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology.

  18. Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

    Directory of Open Access Journals (Sweden)

    Cameron Brennan

    Full Text Available BACKGROUND: Glioblastoma multiforme (GBM is an umbrella designation that includes a heterogeneous group of primary brain tumors. Several classification strategies of GBM have been reported, some by clinical course and others by resemblance to cell types either in the adult or during development. From a practical and therapeutic standpoint, classifying GBMs by signal transduction pathway activation and by mutation in pathway member genes may be particularly valuable for the development of targeted therapies. METHODOLOGY/PRINCIPAL FINDINGS: We performed targeted proteomic analysis of 27 surgical glioma samples to identify patterns of coordinate activation among glioma-relevant signal transduction pathways, then compared these results with integrated analysis of genomic and expression data of 243 GBM samples from The Cancer Genome Atlas (TCGA. In the pattern of signaling, three subclasses of GBM emerge which appear to be associated with predominance of EGFR activation, PDGFR activation, or loss of the RAS regulator NF1. The EGFR signaling class has prominent Notch pathway activation measured by elevated expression of Notch ligands, cleaved Notch receptor, and downstream target Hes1. The PDGF class showed high levels of PDGFB ligand and phosphorylation of PDGFRbeta and NFKB. NF1-loss was associated with lower overall MAPK and PI3K activation and relative overexpression of the mesenchymal marker YKL40. These three signaling classes appear to correspond with distinct transcriptomal subclasses of primary GBM samples from TCGA for which copy number aberration and mutation of EGFR, PDGFRA, and NF1 are signature events. CONCLUSIONS/SIGNIFICANCE: Proteomic analysis of GBM samples revealed three patterns of expression and activation of proteins in glioma-relevant signaling pathways. These three classes are comprised of roughly equal numbers showing either EGFR activation associated with amplification and mutation of the receptor, PDGF-pathway activation

  19. [HPV-associated head and neck cancer : mutational signature and genomic aberrations].

    Science.gov (United States)

    Wagner, S; Würdemann, N; Hübbers, C; Reuschenbach, M; Prigge, E-S; Wichmann, G; Hess, J; Dietz, A; Dürst, M; Tinhofer, I; von Knebel-Döberitz, M; Wittekindt, C; Klussmann, J P

    2015-11-01

    A significantly increasing proportion of oropharyngeal head and neck carcinomas (OSCC) in North America and Europe are associated with human papillomavirus (HPV) infections. HPV-related OSCC is regarded as a distinct tumor type with regard to its cellular, biologic, and clinical characteristics. Patients with HPV-related OSCC have significantly better local control, but higher rates of regional lymph node and distant metastases as compared to patients with HPV-negative OSCC. Classical molecular genetic investigations demonstrated specific chromosomal aberration signatures in HPV-related OSCC, and recent developments in next generation sequencing (NGS) technology have rendered possible the sequencing of entire genomes, and thus detection of specific mutations, in just a few days. Initial data from The Cancer Genome Atlas (TCGA) project obtained by using genome-wide high throughput methods have confirmed that HPV-related OSCC contain fewer, albeit more specific mutations than HPV-negative tumors. Additionally, these data revealed the presence of specific-potentially therapeutically targetable-activating driver mutations in subgroups of HPV-positive OSCC, some of which have a prognostic impact. Specific targeted NGS technologies provide new possibilities for identification of diagnostic, prognostic, and predictive biomarkers and the development of personalized cancer treatment. Patients with HPV-positive tumors are likely to profit from these developments in the future, since the genetic alterations are relatively homogenous and frequently lead to signal pathway activation. There is an urgent need for network research activities to carry out the necessary basic research in prospective cohort studies.

  20. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma.

    Science.gov (United States)

    Hakimi, A Ari; Reznik, Ed; Lee, Chung-Han; Creighton, Chad J; Brannon, A Rose; Luna, Augustin; Aksoy, B Arman; Liu, Eric Minwei; Shen, Ronglai; Lee, William; Chen, Yang; Stirdivant, Steve M; Russo, Paul; Chen, Ying Bei; Tickoo, Satish K; Reuter, Victor E; Cheng, Emily H; Sander, Chris; Hsieh, James J

    2016-01-11

    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 © 2016 Elsevier Inc. All rights reserved.

  1. Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis

    Science.gov (United States)

    Simeone, Ines; Anjum, Samreen; Mokrab, Younes; Bertucci, François; Finetti, Pascal; Curigliano, Giuseppe; Cerulo, Luigi; Tomei, Sara; Delogu, Lucia Gemma; Maccalli, Cristina; Miller, Lance D.; Ceccarelli, Michele

    2017-01-01

    ABSTRACT Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection. The T helper 1 (Th-1) phenotype (ICR4), which also displays upregulation of immune-regulatory transcripts such as PDL1, PD1, FOXP3, IDO1, and CTLA4, was associated with prolonged patients' survival. We validated these findings in an independent meta-cohort of 1,954 breast cancer gene expression data. Chromosome segment 4q21, which includes genes encoding for the Th-1 chemokines CXCL9-11, was significantly amplified only in the immune favorable phenotype (ICR4). The mutation and neoantigen load progressively decreased from ICR4 to ICR1 but could not fully explain immune phenotypic differences. Mutations of TP53 were enriched in the immune favorable phenotype (ICR4). Conversely, the presence of MAP3K1 and MAP2K4 mutations were tightly associated with an immune-unfavorable phenotype (ICR1). Using both the TCGA and the validation dataset, the degree of MAPK deregulation segregates breast tumors according to their immune disposition. These findings suggest that mutation-driven perturbations of MAPK pathways are linked to the negative regulation of intratumoral immune response in breast cancer. Modulations of MAPK pathways could be experimentally tested to enhance breast cancer immune sensitivity. PMID:28344865

  2. 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

  3. 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

  4. 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

  5. Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia.

    Science.gov (United States)

    Jost, E; Lin, Q; Weidner, C I; Wilop, S; Hoffmann, M; Walenda, T; Schemionek, M; Herrmann, O; Zenke, M; Brümmendorf, T H; Koschmieder, S; Wagner, W

    2014-06-01

    Mutations in the genetic sequence of the DNA de novo methyltransferase DNMT3A (DNA methyltransferase 3A) are found in many patients with acute myeloid leukemia (AML). They lead to dysfunction of DNMT3A protein and represent a marker for poor prognosis. Effects of genetic mutations can be mimicked by epigenetic modifications in the DNA methylation (DNAm) pattern. Using DNAm profiles of the Cancer Genome Atlas Research Network (TCGA), we identified aberrant hypermethylation at an internal promoter region of DNMT3A, which occurred in about 40% of AML patients. Bisulfite pyrosequencing assays designed for this genomic region validated hypermethylation specifically in a subset of our AML samples. High DNAm levels at this site are particularly observed in samples without genetic mutations in DNMT3A. Epimutations and mutations of DNMT3A were associated with related gene expression changes such as upregulation of the homeobox genes in HOXA and HOXB clusters. Furthermore, epimutations in DNMT3A were enriched in patients with poor or intermediate cytogenetic risk, and in patients with shorter event-free survival and overall survival (OS). Taken together, aberrant DNA hypermethylation within the DNMT3A gene, in analogy to DNMT3A mutations, is frequently observed in AML and both modifications seem to be useful for risk stratification or choice of therapeutic regimen.

  6. 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.

  7. A computational method for clinically relevant cancer stratification and driver mutation module discovery using personal genomics profiles.

    Science.gov (United States)

    Wang, Lin; Li, Fuhai; Sheng, Jianting; Wong, Stephen T C

    2015-01-01

    Personalized genomics instability, e.g., somatic mutations, is believed to contribute to the heterogeneous drug responses in patient cohorts. However, it is difficult to discover personalized driver mutations that are predictive of drug sensitivity owing to diverse and complex mutations of individual patients. To circumvent this problem, a novel computational method is presented to discover potential drug sensitivity relevant cancer subtypes and identify driver mutation modules of individual subtypes by coupling differentially expressed genes (DEGs) based subtyping analysis with the driver mutation network analysis. The proposed method was applied to breast cancer and lung cancer samples available from The Cancer Genome Atlas (TCGA). Cancer subtypes were uncovered with significantly different survival rates, and more interestingly, distinct driver mutation modules were also discovered among different subtypes, indicating the potential mechanism of heterogeneous drug sensitivity. The research findings can be used to help guide the repurposing of known drugs and their combinations in order to target these dysfunctional modules and their downstream signaling effectively for achieving personalized or precision medicine treatment.

  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

    2017-07-21

    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.Modern Pathology advance online publication, 21

  9. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    Science.gov (United States)

    2013-07-01

    extending the period of performance soon. The Ivy Center for Advanced Brain Tumor Treatment at the Swedish Neuroscience Institute (SNI) has...Treatment at the Swedish Neuroscience Institute (SNI) has collected potentially eligible tumor tissue from over forty GBM patients. • Primary GBM cell...generated from the TCGA and Allen atlas projects. Promising candidate target proteins will be validated on all 64 patient tumor and blood samples

  10. Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the Cancer Genome Atlas.

    Science.gov (United States)

    Miller, Daniel L; Davis, J Wade; Taylor, Kristen H; Johnson, Jeff; Shi, Zonggao; Williams, Russell; Atasoy, Ulus; Lewis, James S; Stack, M Sharon

    2015-03-01

    High-risk human papillomavirus (HPV) is a causative agent for an increasing subset of oropharyngeal squamous cell carcinomas (OPSCCs), and current evidence supports these tumors as having identifiable risk factors and improved response to therapy. However, the biochemical and molecular alterations underlying the pathobiology of HPV-associated OPSCC (designated HPV(+) OPSCC) remain unclear. Herein, we profile miRNA expression patterns in HPV(+) OPSCC to provide a more detailed understanding of pathologic molecular events and to identify biomarkers that may have applicability for early diagnosis, improved staging, and prognostic stratification. Differentially expressed miRNAs were identified in RNA isolated from an initial clinical cohort of HPV(+/-) OPSCC tumors by quantitative PCR-based miRNA profiling. This oncogenic miRNA panel was validated using miRNA sequencing and clinical data from The Cancer Genome Atlas and miRNA in situ hybridization. The HPV-associated oncogenic miRNA panel has potential utility in diagnosis and disease stratification and in mechanistic elucidation of molecular factors that contribute to OPSCC development, progression, and differential response to therapy. Copyright © 2015 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  11. Anatomy atlases.

    Science.gov (United States)

    Rosse, C

    1999-01-01

    Anatomy atlases are unlike other knowledge sources in the health sciences in that they communicate knowledge through annotated images without the support of narrative text. An analysis of the knowledge component represented by images and the history of anatomy atlases suggest some distinctions that should be made between atlas and textbook illustrations. Textbook and atlas should synergistically promote the generation of a mental model of anatomy. The objective of such a model is to support anatomical reasoning and thereby replace memorization of anatomical facts. Criteria are suggested for selecting anatomy texts and atlases that complement one another, and the advantages and disadvantages of hard copy and computer-based anatomy atlases are considered.

  12. Integrated transcriptional profiling and genomic analyses reveal RPN2 and HMGB1 as promising biomarkers in colorectal cancer.

    Science.gov (United States)

    Zhang, Jialing; Yan, Bin; Späth, Stephan Stanislaw; Qun, Hu; Cornelius, Shaleeka; Guan, Daogang; Shao, Jiaofang; Hagiwara, Koichi; Van Waes, Carter; Chen, Zhong; Su, Xiulan; Bi, Yongyi

    2015-01-01

    Colorectal cancer (CRC) is a heterogeneous disease that is associated with a gradual accumulation of genetic and epigenetic alterations. Among all CRC stages, stage II tumors are highly heterogeneous with a high relapse rate in about 20-25 % of stage II CRC patients following surgery. Thus, a comprehensive analysis of gene signatures to identify aggressive and metastatic phenotypes in stage II CRC is desired for a more accurate disease classification and outcome prediction. By utilizing a Cancer Array, containing 440 oncogenes and tumor suppressors to profile mRNA expression, we identified a larger number of differentially expressed genes in poorly differentiated stage II colorectal adenocarcinoma tissues, compared to their matched normal tissues. Ontology and Ingenuity Pathway Analysis (IPA) indicated that these genes are involved in functional mechanisms associated with several transcription factors. Genomic alterations of these genes were also investigated through The Cancer Genome Atlas (TCGA) database, utilizing 195 published CRC specimens. The percentage of genomic alterations in these genes was ranked based on their mRNA expression, copy number variations and mutations. This data was further combined with published microarray studies from a large set of CRC tumors classified based on prognostic features. This led to the identification of eight candidate genes including RPN2, HMGB1, AARS, IGFBP3, STAT1, HYOU1, NQO1 and PEA15 that were associated with the progressive phenotype. In particular, RPN2 and HMGB1 displayed a higher genomic alteration frequency in CRC, compared to eight other major solid cancers. Immunohistochemistry was performed on additional 78 stage I-IV CRC samples, where RPN2 protein immunostaining exhibited a significant association with stage III/IV tumors, distant metastasis, and poor differentiation, indicating that RPN2 expression is associated with poor prognosis. Further, our study revealed significant transcriptional regulatory

  13. A time for atlases and atlases for time

    Directory of Open Access Journals (Sweden)

    Yoav Livneh

    2010-02-01

    Full Text Available Advances in neuroanatomy and computational power are leading to the construction of new digital brain atlases. Atlases are rising as indispensable tools for comparing anatomical data as well as being stimulators of new hypotheses and experimental designs. Brain atlases describe nervous systems which are inherently plastic and variable. Thus, the levels of brain plasticity and stereotypy would be important to evaluate as limiting factors in the context of static brain atlases. In this review, we discuss the extent of structural changes which neurons undergo over time, and how these changes would impact the static nature of atlases. We describe the anatomical stereotypy between neurons of the same type, highlighting the differences between invertebrates and vertebrates. We review some recent experimental advances in our understanding of anatomical dynamics in adult neural circuits, and how these are modulated by the organism’s experience. In this respect, we discuss some analogies between brain atlases and the sequenced genome and the emerging epigenome. We argue that variability and plasticity of neurons are substantially high, and should thus be considered as integral features of high-resolution digital brain atlases.

  14. Large scale digital atlases in neuroscience

    Science.gov (United States)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  15. BAP1 is overexpressed in black compared with white patients with Mx-M1 clear cell renal cell carcinoma: A report from the cancer genome atlas.

    Science.gov (United States)

    Paulucci, David J; Sfakianos, John P; Yadav, Shalini Singh; Badani, Ketan K

    2016-06-01

    Incidence of renal cell carcinoma (RCC) is higher in Black patients with disease-specific and overall survival being lower compared with White patients even though renal tumors among Black patients are more likely to be localized. These disparities have been attributed to higher rates of obesity and hypertension, lower rates of nephrectomy, and a lack of access to quality health care. With scant genomic evidence to account for these disparities, the present study sought to compare BAP1 expression between Black and White patients with clear cell RCC (ccRCC); a gene that inhibits tumor progression when overexpressed and results in poor clinical outcomes when silenced. The cancer genome atlas dataset was used to identify 58 (9.9%) Black and 529 (90.9%) White patients with ccRCC with an initial pathologic diagnosis from 1998 to 2013. BAP1 expression was compared using a Mann-Whitney U test. The association between BAP1 expression and pathologic stage, American Joint Committee on Cancer (AJCC) stage, and Fuhrman grade was assessed for the overall cohort and stratified by race. The association between BAP1 expression and overall survival was assessed using Cox proportion hazards models adjusting for Fuhrman grade, pathologic stage, and the presence of pathologic metastases for the overall cohort and stratified by race. The level of BAP1 expression was significantly higher in Black vs. White patients with ccRCC (10.5 vs. 10.3; P<.001). For the overall cohort, increasing BAP1 expression was associated with decreasing pathologic stage (β =-0.25, P = .004) and decreasing AJCC stage (β =-0.029, P = .006). For Black patients, increasing BAP1 expression was associated with decreasing AJCC stage (β =-0.79, P = .016), decreasing Fuhrman grade (β =-0.55, P = .011), and a decreased risk of pathologic metastases (odds ratio [OR] = 0.83, P = .038). For White patients, increasing BAP1 expression was associated with decreasing pathologic stage (β =-0.20, P = .026). BAP1 is

  16. 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

  17. 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

  18. Identification of cancer risk lncRNAs and cancer risk pathways regulated by cancer risk lncRNAs based on genome sequencing data in human cancers.

    Science.gov (United States)

    Li, Yiran; Li, Wan; Liang, Binhua; Li, Liansheng; Wang, Li; Huang, Hao; Guo, Shanshan; Wang, Yahui; He, Yuehan; Chen, Lina; He, Weiming

    2016-12-19

    Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. The complexity of cancer can be reduced to a small number of underlying principles like cancer hallmarks which could govern the transformation of normal cells to cancer. Besides, the growth and metastasis of cancer often relate to combined effects of long non-coding RNAs (lncRNAs). Here, we performed comprehensive analysis for lncRNA expression profiles and clinical data of six types of human cancer patients from The Cancer Genome Atlas (TCGA), and identified six risk pathways and twenty three lncRNAs. In addition, twenty three cancer risk lncRNAs which were closely related to the occurrence or development of cancer had a good classification performance for samples of testing datasets of six cancer datasets. More important, these lncRNAs were able to separate samples in the entire cancer dataset into high-risk group and low-risk group with significantly different overall survival (OS), which was further validated in ten validation datasets. In our study, the robust and effective cancer biomarkers were obtained from cancer datasets which had information of normal-tumor samples. Overall, our research can provide a new perspective for the further study of clinical diagnosis and treatment of cancer.

  19. Gene microarray analysis of ovarian serous cystadenocarcinoma-related genes based on TCGA%基于癌症基因组图谱筛查卵巢浆液性囊腺癌相关基因

    Institute of Scientific and Technical Information of China (English)

    李典鹤; 黄昌男; 李奇

    2016-01-01

    -metrix GeneChip Human Exon 1.0 ST Arrays from The Cancer Genome Atlas ( TCGA) , including 8 OV and 8 normal ovary samples.The function of differential genes was determined by pathway and gene ontology ( GO) analysis.The probable functions of the key genes were predicted according to intergenic signal transduction network .RESULTS:The 1 144 genes were identified as distinctively expressed in OV (P<0.05), 747 of which were up-regulated and 397 were down-regula-ted.The GO analysis results showed that the altered genes were involved in 362 up-regulated and 160 down-regulated sig-nificant functions (P<0.05) related to cell cycle, DNA replication, cell proliferation, cell apoptosis, cell adhesion, etc. The pathways of the different genes were involved in the 59 enrichment-related pathways (P<0.05), 45 of which were up-regulated and 14 were down-regulated.Among the 59 pathways, cell cycle, P53 signaling pathway, DNA replication, path-ways in cancer, PI3K-Akt signaling pathway, ECM-receptor signaling pathway, cell adhesion molecules and cell apoptosis were related to tumor genesis , development and metastasis .As a result, 229 genes with significant functions and pathways in GO and pathway analysis were selected to construct signal transduction network ( Signal-Net), 4 of which, CDK1, PLK1, MCM3 and PGK1, were found to play key roles in OV signal regulation network .CONCLUSION: The OV shows abundant differentially expressed genes that play key roles in cancer-related signal pathways .

  20. 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.

  1. 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.

  2. Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types.

    Science.gov (United States)

    Iglesia, Michael D; Parker, Joel S; Hoadley, Katherine A; Serody, Jonathan S; Perou, Charles M; Vincent, Benjamin G

    2016-11-01

    Immune infiltration of the tumor microenvironment has been associated with improved survival for some patients with solid tumors. The precise makeup and prognostic relevance of immune infiltrates across a broad spectrum of tumors remain unclear. Using mRNA sequencing data from The Cancer Genome Atlas (TCGA) from 11 tumor types representing 3485 tumors, we evaluated lymphocyte and macrophage gene expression by tissue type and by genomic subtypes defined within and across tumor tissue of origin (Cox proportional hazards, Pearson correlation). We investigated clonal diversity of B-cell infiltrates through calculating B-cell receptor (BCR) repertoire sequence diversity. All statistical tests were two-sided. High expression of T-cell and B-cell signatures predicted improved overall survival across many tumor types including breast, lung, and melanoma (breast CD8_T_Cells hazard ratio [HR] = 0.36, 95% confidence interval [CI] = 0.16 to 0.81, P = .01; lung adenocarcinoma B_Cell_60gene HR = 0.71, 95% CI = 0.58 to 0.87, P = 7.80E-04; melanoma LCK HR = 0.86, 95% CI = 0.79 to 0.94, P = 6.75E-04). Macrophage signatures predicted worse survival in GBM, as did B-cell signatures in renal tumors (Glioblastoma Multiforme [GBM]: macrophages HR = 1.62, 95% CI = 1.17 to 2.26, P = .004; renal: B_Cell_60gene HR = 1.17, 95% CI = 1.04 to 1.32, P = .009). BCR diversity was associated with survival beyond gene segment expression in melanoma (HR = 2.67, 95% CI = 1.32 to 5.40, P = .02) and renal cell carcinoma (HR = 0.36, 95% CI = 0.15 to 0.87, P = .006). These data support existing studies suggesting that in diverse tissue types, heterogeneous immune infiltrates are present and typically portend an improved prognosis. In some tumor types, BCR diversity was also associated with survival. Quantitative genomic signatures of immune cells warrant further testing as prognostic markers and potential biomarkers of response to cancer immunotherapy.

  3. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    . 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...

  4. 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.

  5. 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.

  6. NCHHSTP Atlas

    Science.gov (United States)

    ... Sets County-level data on poverty, income, education, housing and other social factors tied to health. Buttons ... HIV STD TB DASH Youth Online Citing AtlasPlus Materials We are pleased to make these materials available, ...

  7. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set.

    Science.gov (United States)

    Li, Hui; Zhu, Yitan; Burnside, Elizabeth S; Huang, Erich; Drukker, Karen; Hoadley, Katherine A; Fan, Cheng; Conzen, Suzanne D; Zuley, Margarita; Net, Jose M; Sutton, Elizabeth; Whitman, Gary J; Morris, Elizabeth; Perou, Charles M; Ji, Yuan; Giger, Maryellen L

    2016-01-01

    Using quantitative radiomics, we demonstrate that computer-extracted magnetic resonance (MR) image-based tumor phenotypes can be predictive of the molecular classification of invasive breast cancers. Radiomics analysis was performed on 91 MRIs of biopsy-proven invasive breast cancers from National Cancer Institute's multi-institutional TCGA/TCIA. Immunohistochemistry molecular classification was performed including estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and for 84 cases, the molecular subtype (normal-like, luminal A, luminal B, HER2-enriched, and basal-like). Computerized quantitative image analysis included: three-dimensional lesion segmentation, phenotype extraction, and leave-one-case-out cross validation involving stepwise feature selection and linear discriminant analysis. The performance of the classifier model for molecular subtyping was evaluated using receiver operating characteristic analysis. The computer-extracted tumor phenotypes were able to distinguish between molecular prognostic indicators; area under the ROC curve values of 0.89, 0.69, 0.65, and 0.67 in the tasks of distinguishing between ER+ versus ER-, PR+ versus PR-, HER2+ versus HER2-, and triple-negative versus others, respectively. Statistically significant associations between tumor phenotypes and receptor status were observed. More aggressive cancers are likely to be larger in size with more heterogeneity in their contrast enhancement. Even after controlling for tumor size, a statistically significant trend was observed within each size group (P = 0.04 for lesions ≤ 2 cm; P = 0.02 for lesions >2 to ≤5 cm) as with the entire data set (P-value = 0.006) for the relationship between enhancement texture (entropy) and molecular subtypes (normal-like, luminal A, luminal B, HER2-enriched, basal-like). In conclusion, computer-extracted image phenotypes show promise for high-throughput discrimination of breast cancer subtypes and may yield a

  8. 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.

  9. 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

  10. 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.

  11. SUSY (ATLAS)

    CERN Document Server

    Sopczak, Andre; The ATLAS collaboration

    2017-01-01

    During the data-taking period at LHC (Run-II), several searches for supersymmetric particles were performed. The results from searches by the ATLAS collaborations are concisely reviewed. Model-independent and model-dependent limits on new particle production are set, and interpretations in supersymmetric models are given.

  12. ATLAS Story

    CERN Multimedia

    AUTHOR|(CDS)2108663

    2012-01-01

    This film produced in July 2012 explains how fundamental research connects to Society and what benefits collaborative way of working can and may generate in the future, using ATLAS Collaboration as a case study. The film is intellectually inspired by the book "Collisions and Collaboration" (OUP) by Max Boisot (ed.), see: collisionsandcollaboration.com. The film is directed by Andrew Millington (OMNI Communications)

  13. 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.

  14. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Binnewies, Tim Terence; Ussery, David

    2008-01-01

    the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context...

  15. Probabilistic liver atlas construction

    OpenAIRE

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

    2017-01-01

    Background 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. Results A new method for probabilistic atlas con...

  16. An anatomically comprehensive atlas of the adult human brain transcriptome

    NARCIS (Netherlands)

    Hawrylycz, M.J.; Beckmann, Christian

    2012-01-01

    Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising

  17. ATLAS Recordings

    CERN Multimedia

    Steven Goldfarb; Mitch McLachlan; Homer A. Neal

    Web Archives of ATLAS Plenary Sessions, Workshops, Meetings, and Tutorials from 2005 until this past month are available via the University of Michigan portal here. Most recent additions include the Trigger-Aware Analysis Tutorial by Monika Wielers on March 23 and the ROOT Workshop held at CERN on March 26-27.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal.Feedback WelcomeOur group is making arrangements now to record plenary sessions, tutorials, and other important ATLAS events for 2007. Your suggestions for potential recording, as well as your feedback on existing archives is always welcome. Please contact us at wlap@umich.edu. Thank you.Enjoy the Lectures!

  18. ATLAS UPGRADES

    CERN Document Server

    Lacasta, C; 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−1 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 ...

  19. 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.

  20. Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas.

    Science.gov (United States)

    Camargo, M Constanza; Bowlby, Reanne; Chu, Andy; Pedamallu, Chandra Sekhar; Thorsson, Vesteinn; Elmore, Sandra; Mungall, Andrew J; Bass, Adam J; Gulley, Margaret L; Rabkin, Charles S

    2016-04-01

    The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole-genome, whole-exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cutoffs of sequencing counts identified 26 (9 %) tumors as EBV positive. EBV positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa = 0.91). EBV-positive gastric tumors can be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.

  1. Expression of lactate/H⁺ symporters MCT1 and MCT4 and their chaperone CD147 predicts tumor progression in clear cell renal cell carcinoma: immunohistochemical and The Cancer Genome Atlas data analyses.

    Science.gov (United States)

    Kim, Younghye; Choi, Jung-Woo; Lee, Ju-Han; Kim, Young-Sik

    2015-01-01

    Clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau protein, leading to the accumulation of hypoxia-inducible factor-α (HIF-α). HIF-1α induces aerobic glycolysis, the Warburg effect, whereas HIF-2α functions as an oncoprotein. Lactate transport through monocarboxylate transporters (MCTs) and the chaperone CD147 is essential for high glycolytic cancer cell survival. To elucidate the clinical significance of MCT1, MCT4, and CD147 expression, we investigated their expressions by immunohistochemistry in ccRCC specimens and validated the results by an open-access The Cancer Genome Atlas data analysis. Overexpression of MCT1, MCT4, and CD147 was observed in 49.4% (89/180), 39.4% (71/180), and 79.4% (143/180) of ccRCC patients, respectively. High MCT1 expression was associated with older age (P = .017), larger tumor size (P = .015), and advanced TNM stage (P = .012). However, MCT4 overexpression was not related to any variables. CD147 overexpression correlated with high grade (P = .005), tumor necrosis (P = .016), and larger tumor size (P = .038). In univariate analysis, high expression of MCT1 (P CD147 (P = .02) was linked to short progression-free survival. In multivariate analysis, high MCT1 expression was associated with worse progression-free survival (P = .001). In conclusion, high expression of MCT1 and CD147 is associated with poor prognostic factors. Overexpression of MCT1, MCT4, and CD147 predicts tumor progression. Reversing the Warburg effect by targeting the lactate transporters may be a useful strategy to prevent ccRCC progression.

  2. [Atlas fractures].

    Science.gov (United States)

    Schären, S; Jeanneret, B

    1999-05-01

    Fractures of the atlas account for 1-2% of all vertebral fractures. We divide atlas fractures into 5 groups: isolated fractures of the anterior arch of the atlas, isolated fractures of the posterior arch, combined fractures of the anterior and posterior arch (so-called Jefferson fractures), isolated fractures of the lateral mass and fractures of the transverse process. Isolated fractures of the anterior or posterior arch are benign and are treated conservatively with a soft collar until the neck pain has disappeared. Jefferson fractures are divided into stable and unstable fracture depending on the integrity of the transverse ligament. Stable Jefferson fractures are treated conservatively with good outcome while unstable Jefferson fractures are probably best treated operatively with a posterior atlanto-axial or occipito-axial stabilization and fusion. The authors preferred treatment modality is the immediate open reduction of the dislocated lateral masses combined with a stabilization in the reduced position using a transarticular screw fixation C1/C2 according to Magerl. This has the advantage of saving the atlanto-occipital joints and offering an immediate stability which makes immobilization in an halo or Minerva cast superfluous. In late instabilities C1/2 with incongruency of the lateral masses occurring after primary conservative treatment, an occipito-cervical fusion is indicated. Isolated fractures of the lateral masses are very rare and may, if the lateral mass is totally destroyed, be a reason for an occipito-cervical fusion. Fractures of the transverse processes may be the cause for a thrombosis of the vertebral artery. No treatment is necessary for the fracture itself.

  3. 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...

  4. ATLAS experimentet

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    Filmen innehåller mycket information om fysik och varför LHC behövs tilsammans med stora detektorer och specielt om behovet av ATLAS Experimentet. Mycket bra film för att förklara det okända- som man undersöker i CERN för att ge svar på frågor som människor har försökt förklara under flere tusen år.

  5. Deep sequencing revealed genome-wide single-nucleotide polymorphism and plasmid content of Erwinia amylovora strains isolated in Middle Atlas, Morocco.

    Science.gov (United States)

    Hannou, Najat; Mondy, Samuel; Planamente, Sara; Moumni, Mohieddine; Llop, Pablo; López, María; Manceau, Charles; Barny, Marie-Anne; Faure, Denis

    2013-10-01

    Erwinia amylovora causes economic losses that affect pear and apple production in Morocco. Here, we report comparative genomics of four Moroccan E. amylovora strains with the European strain CFBP1430 and North-American strain ATCC49946. Analysis of single nucleotide polymorphisms (SNPs) revealed genetic homogeneity of Moroccan's strains and their proximity to the European strain CFBP1430. Moreover, the collected sequences allowed the assembly of a 65 kpb plasmid, which is highly similar to the plasmid pEI70 harbored by several European E. amylovora isolates. This plasmid was found in 33% of the 40 E. amylovora strains collected from several host plants in 2009 and 2010 in Morocco.

  6. Atlases: Complex models of geospace

    Directory of Open Access Journals (Sweden)

    Ikonović Vesna

    2005-01-01

    Full Text Available Atlas is modeled contexture contents of treated thematic of space on optimal map union. Atlases are higher form of cartography. Atlases content composition of maps which are different by projection, scale, format methods, contents, usage and so. Atlases can be classified by multi criteria. Modern classification of atlases by technology of making would be on: 1. classical or traditional (printed on paper and 2. electronic (made on electronic media - computer or computer station. Electronic atlases divided in three large groups: view-only electronic atlases, 2. interactive electronic atlases and 3. analytical electronic atlases.

  7. Developing the eHistology Atlas.

    Science.gov (United States)

    Richardson, Lorna; Graham, Liz; Moss, Julie; Burton, Nick; Roochun, Yogmatee; Armit, Chris; Baldock, Richard A

    2015-01-01

    The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook 'The Atlas of Mouse Development' by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php. © The Author(s) 2015. Published by Oxford University Press.

  8. 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).

  9. ATLAS Data Access Policy

    CERN Document Server

    The ATLAS collaboration

    2015-01-01

    ATLAS has fully supported the principle of open access in its publication policy. This document outlines the policy of ATLAS as regards open access to data at different levels as described in the DPHEP model. The main objective is to make the data available in a usable way to people external to the ATLAS collaboration.

  10. Interactive Atlas of Histology

    Science.gov (United States)

    Goubran, Emile Z.; Vinjamury, Sivarama P.

    2007-01-01

    Purpose: An interactive atlas of histology was developed for online use by chiropractic students to enable them to practice and self-assess their ability to identify various histological structures. This article discusses the steps in the development, implementation, and usefulness of an interactive atlas of histology for students who take histology examinations. Methods: The atlas was developed by digitizing images imported through a video-microscope using actual microscope slides. Leica EWS 2100 and PowerPoint software were used to construct the atlas. The usefulness of the atlas was assessed through a comparison of histology exam scores between four classes before and four classes after the use of the atlas. Analysis of admissions data, including overall grade point average (GPA), science and nonscience GPA, and a number of course units, was done initially to avoid any identifiable differences in the academic competency between the two being compared. A survey of the students was also done to assess atlas usefulness and students' satisfaction with the atlas. Results: Analysis of histology exam scores showed that the average scores in the lab exam were significantly higher for the classes that used the atlas. Survey results showed a high level of student satisfaction with the atlas. Conclusion: The development and use of an online interactive atlas of histology for chiropractic students helped to improve lab exams scores. In addition, students were satisfied with the features and usefulness of this atlas. PMID:18483638

  11. 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.

  12. Report to users of ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Ahmad, I.; Glagola, B. [eds.

    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.

  13. ATLAS Recordings

    CERN Multimedia

    Jeremy Herr; Homer A. Neal; Mitch McLachlan

    The University of Michigan Web Archives for the 2006 ATLAS Week Plenary Sessions, as well as the first of 2007, are now online. In addition, there are a wide variety of Software and Physics Tutorial sessions, recorded over the past couple years, to chose from. All ATLAS-specific archives are accessible here.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal. Shaping Collaboration 2006The Michigan group is happy to announce a complete set of recordings from the Shaping Collaboration conference held last December at the CICG in Geneva.The event hosted a mix of Collaborative Tool experts and LHC Users, and featured presentations by the CERN Deputy Director General, Prof. Jos Engelen, the President of Internet2, and chief developers from VRVS/EVO, WLAP, and other tools...

  14. EnviroAtlas - Green Bay, WI - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Green Bay, WI Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  15. EnviroAtlas - Portland, ME - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Portland, ME Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  16. EnviroAtlas - Portland, OR - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Portland, OR Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  17. EnviroAtlas - Phoenix, AZ - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Phoenix, AZ Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  18. EnviroAtlas - Paterson, NJ - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Paterson, NJ Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  19. EnviroAtlas - Austin, TX - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Austin, TX Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas...

  20. 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.

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

    Science.gov (United States)

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

    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.

  2. 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.

  3. TCGA: Increased oncoprotein coding region mutations correlate with a greater expression of apoptosis-effector genes and a positive outcome for stomach adenocarcinoma.

    Science.gov (United States)

    Yavorski, John M; Blanck, George

    2016-08-17

    Oncogene mutations are primarily thought to facilitate uncontrolled cell growth. However, overexpression of oncoproteins likely leads to apoptosis in a feed forward mechanism, whereby a certain level of oncoprotein leads to the activation of pro-proliferation effector genes and higher levels lead to activation of pro-apoptotic effector genes. TCGA STAD barcodes having no oncoprotein coding region mutations represented reduced expression of the apoptosis-effector genes compared with barcodes with multiple oncoprotein coding region mutations. Furthermore, STAD barcodes in a "no-subsequent tumor" group, representing 224 samples, and in a "positive outcome" group, had more oncoprotein coding regions mutated, on average, than barcodes of the new tumor and negative outcome groups, respectively. BRAF, CTNNB1, KRAS and MTOR coding region mutations (as a group) had the strongest association with the no-subsequent tumor group. Tumor suppressor coding region mutations were also correlated with no-subsequent tumor. These results are consistent with an oncoprotein-mediated, feed-forward mechanism of apoptosis in patients. Importantly, the no-subsequent tumor group also had more overall mutations. This result leads to considerations of unhealthy cells or cells with more neo-antigens for immune rejection. However, a probabilistic aspect of mutagenesis is also consistent with more oncoprotein and tumor suppressor protein mutations, in cases of more overall mutations, and thus a higher likelihood of activation of feed forward apoptosis pathways.

  4. 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...

  5. 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)

  6. 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.

  7. ATLAS inner detector performance

    CERN Document Server

    Gadomski, S

    2001-01-01

    The ATLAS Inner Detector consists of three subsystems using different tracking detector technologies: silicon pixels, silicon strips and straw tubes. The combination gives ATLAS a robust, hermetic and efficient tracking system, able to reconstruct tracks at the highest foreseen LHC luminosities. The inner detector provides vertex and momentum measurements, electron identification and some $K/\\pi$ separation. Since last year the beam pipe of ATLAS was changed, causing a redesign of the first tracking layer and a deterioration of the impact parameter resolutions.

  8. 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

  9. Tumor-specific hypermethylation of epigenetic biomarkers, including SFRP1, predicts for poorer survival in patients from the TCGA Kidney Renal Clear Cell Carcinoma (KIRC project.

    Directory of Open Access Journals (Sweden)

    Christopher J Ricketts

    Full Text Available The recent publication of the TCGA Kidney Renal Clear Cell Carcinoma (KIRC project has provided an immense wealth and breadth of data providing an invaluable tool for confirmation and expansion upon previous observations in a large data set containing multiple data types including DNA methylation, somatic mutation, and clinical information. In clear cell renal cell carcinoma (CCRCC many genes have been demonstrated to be epigenetically inactivated by promoter hypermethylated and in a small number of cases to be associated with clinical outcome. This study created two cohorts based on the Illumina BeadChip array used to confirm the frequency of tumor-specific hypermethylation of these published hypermethylated genes, assess the impact of somatic mutation or chromosomal loss and provide the most comprehensive assessment to date of the association of this hypermethylation with patient survival. Hypermethylation of the Fibrillin 2 (FBN2 gene was the most consistent epigenetic biomarker for CCRCC across both cohorts in 40.2% or 52.5% of tumors respectively. Hypermethylation of the secreted frizzled-related protein 1 (SFRP1 gene and the basonuclin 1 (BNC1 gene were both statistically associated with poorer survival in both cohorts (SFRP1 - p = <0.0001 or 0.0010 and BNC1 - p = <0.0001 or 0.0380 and represented better independent markers of survival than tumor stage, grade or dimension in one cohort and tumor stage or dimension in the other cohort. Loss of the SFRP1 protein can potentially activate the WNT pathway and this analysis highlighted hypermethylation of several other WNT pathway regulating genes and demonstrated a poorer survival outcome for patients with somatic mutation of these genes. The success of demethylating drugs in hematological malignances and the current trials in solid tumors suggest that the identification of clinically relevant hypermethylated genes combined with therapeutic advances may improve the effectiveness and

  10. 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.

  11. 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.

  12. A Slice of ATLAS

    CERN Multimedia

    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.

  13. Higgs Measurement from ATLAS

    CERN Document Server

    Liu, Bo; The ATLAS collaboration

    2015-01-01

    Using run-I data record by ATLAS detector, many searches on the higgs decay modes have been done. Also some properties measurement of the Higgs Boson has been done. This talk will summarise the recent result of Higgs search and measurement from ATLAS.

  14. 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).

  15. 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.

  16. The ATLAS tile calorimeter

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Louis Rose-Dulcina, a technician from the ATLAS collaboration, works on the ATLAS tile calorimeter. Special manufacturing techniques were developed to mass produce the thousands of elements in this detector. Tile detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

  17. 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...

  18. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    Budker Nuclear Physics Institute, Novosibirsk Sequence 1 Shots of aircraft factory where machining for ATLAS is done Shots of aircraft Work on components for ATLAS big wheel Discussions between Tikhonov and Nordberg in workshop Sequence 2 Shots of downtown Novosibirsk, including little church which is mid-point of Russian Federation Sequence 3 Interview of Yuri Tikhonov by Andrew Millington

  19. ATLAS rewards industry

    CERN Multimedia

    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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    La Givrine near St Cergue Cross Country Skiing and Fondue at Basse Ruche with M Nordberg, P Jenni, M Nessi, F Gianotti and Co. ATLAS Management Fondu dinner, reviewing state of play of the experiment Many fun scenes from cross country skiing and after 41 minutes of the film starts the fondue dinner in a nice chalet with many persons working for ATLAS experiment

  6. 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.

  7. 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.

  8. Higgs searches at ATLAS

    CERN Document Server

    Lafaye, R

    2002-01-01

    This proceeding is an overview of ATLAS capabilities on Higgs studies. After a short introduction on LEP and Tevatron searches on this subject, the ATLAS potential on a standard model and a supersymmetric Higgs discovery are summarized. Last, a section presents the Higgs parameters measurement that will be possible at LHC. (6 refs).

  9. Searches in ATLAS

    CERN Document Server

    Kondrashova, Nataliia; The ATLAS collaboration

    2017-01-01

    Many theories beyond the Standard Model predict new phenomena accessible by the LHC. Searches for new physics models are performed using the ATLAS experiment at the LHC. The results reported here use the pp collision data sample collected in 2015 and 2016 by the ATLAS detector at the LHC with a centre-of-mass energy of 13 TeV.

  10. ATLAS Brochure (english version)

    CERN Multimedia

    2004-01-01

    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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. ATLAS-Hadronic Calorimeter

    CERN Multimedia

    2003-01-01

    Hall 180 work on Hadronic Calorimeter The ATLAS hadronic tile calorimeter The Tile Calorimeter, which constitutes the central section of the ATLAS hadronic calorimeter, is a non-compensating sampling device made of iron and scintillating tiles. (IEEE Trans. Nucl. Sci. 53 (2006) 1275-81)

  16. 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.

  17. 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.

  18. 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

  19. 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...

  20. 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...

  1. 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 ...

  2. ATLAS Virtual Visits

    CERN Document Server

    Goldfarb, Steven; The ATLAS collaboration

    2015-01-01

    ATLAS Virtual Visits is a project initiated in 2011 for the Education & Outreach program of the ATLAS Experiment at CERN. Its goal is to promote public appreciation of the LHC physics program and particle physics, in general, through direct dialogue between ATLAS physicists and remote audiences. A Virtual Visit is an IP-based videoconference, coupled with a public webcast and video recording, between ATLAS physicists and remote locations around the world, that typically include high school or university classrooms, Masterclasses, science fairs, or other special events, usually hosted by collaboration members. Over the past two years, more than 10,000 people, from all of the world’s continents, have actively participated in ATLAS Virtual Visits, with many more enjoying the experience from the publicly available webcasts and recordings. We present an overview of our experience and discuss potential development for the future.

  3. [Research on Atlas of Viscera].

    Science.gov (United States)

    Jin, S

    1994-01-01

    Chinese ancient visceral atlas, or anatomical illustrations were derived from Taoist and medical schools through observation in cadavers. During the period from Five-Dynasties to Song, there were several works on visceral atlas, including Yanluo illustration, Atlas of Ou Xifan's visceral atlas of fidelity, Li Jung's Atlas. Among them, there exist relations of transmission-heredity, with gradual improvement. It seems likely that the visceral illustrations in Japanese Wan'an Prescription is the extant illustration of Ou's. After the advent of Atlas of Fidelity visceral atlas was differentiated into 3 different kinds of illustrations, as the Inner Picture (Neijing) of Mingtang Atlas; Neizhao Picture in pulsological works and visceral picture in physical Shenxing picture. Chinese visceral atlas was transmitted to Japan, Korea, Persia, and Europe and exerted some influence on cosmopolitan medicine.

  4. Integrated genomic analyses of ovarian carcinoma

    NARCIS (Netherlands)

    Bell, D.; Berchuck, A.; Birrer, M.; Chien, J.; Dao, F.; Dhir, R.; DiSaia, P.; Gabra, H.; Glenn, P.; Godwin, A. K.; Gross, J.; Hartmann, L.; Huang, M.; Huntsman, D. G.; Iacocca, M.; Imielinski, M.; Kalloger, S.; Karlan, B. Y.; Levine, D. A.; Mills, G. B.; Morrison, C.; Mutch, D.; Olvera, N.; Orsulic, S.; Park, K.; Petrelli, N.; Rabeno, B.; Rader, J. S.; Sikic, B. I.; Smith-McCune, K.; Sood, A. K.; Bowtell, D.; Penny, R.; Testa, J. R.; Chang, K.; Dinh, H. H.; Drummond, J. A.; Fowler, G.; Gunaratne, P.; Hawes, A. C.; Kovar, C. L.; Lewis, L. R.; Morgan, M. B.; Newsham, I. F.; Santibanez, J.; Reid, J. G.; Trevino, L. R.; Wu, Y. -Q.; Wang, M.; Muzny, D. M.; Wheeler, D. A.; Gibbs, R. A.; Getz, G.; Lawrence, M. S.; Cibulskis, K.; Sivachenko, A. Y.; Sougnez, C.; Voet, D.; Wilkinson, J.; Bloom, T.; Ardlie, K.; Fennell, T.; Baldwin, J.; Gabriel, S.; Lander, E. S.; Ding, L.; Fulton, R. S.; Koboldt, D. C.; McLellan, M. D.; Wylie, T.; Walker, J.; O'Laughlin, M.; Dooling, D. J.; Fulton, L.; Abbott, R.; Dees, N. D.; Zhang, Q.; Kandoth, C.; Wendl, M.; Schierding, W.; Shen, D.; Harris, C. C.; Schmidt, H.; Kalicki, J.; Delehaunty, K. D.; Fronick, C. C.; Demeter, R.; Cook, L.; Wallis, J. W.; Lin, L.; Magrini, V. J.; Hodges, J. S.; Eldred, J. M.; Smith, S. M.; Pohl, C. S.; Vandin, F.; Raphael, B. J.; Weinstock, G. M.; Mardis, R.; Wilson, R. K.; Meyerson, M.; Winckler, W.; Getz, G.; Verhaak, R. G. W.; Carter, S. L.; Mermel, C. H.; Saksena, G.; Nguyen, H.; Onofrio, R. C.; Lawrence, M. S.; Hubbard, D.; Gupta, S.; Crenshaw, A.; Ramos, A. H.; Ardlie, K.; Chin, L.; Protopopov, A.; Zhang, Juinhua; Kim, T. M.; Perna, I.; Xiao, Y.; Zhang, H.; Ren, G.; Sathiamoorthy, N.; Park, R. W.; Lee, E.; Park, P. J.; Kucherlapati, R.; Absher, D. M.; Waite, L.; Sherlock, G.; Brooks, J. D.; Li, J. Z.; Xu, J.; Myers, R. M.; Laird, P. W.; Cope, L.; Herman, J. G.; Shen, H.; Weisenberger, D. J.; Noushmehr, H.; Pan, F.; Triche, T.; Berman, B. P.; Van den Berg, D. J.; Buckley, J.; Baylin, S. B.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Jakkula, L. R.; Durinck, S.; Han, J.; Dorton, S.; Marr, H.; Choi, Y. G.; Wang, V.; Wang, N. J.; Ngai, J.; Conboy, J. G.; Parvin, B.; Feiler, H. S.; Speed, T. P.; Gray, J. W.; Levine, D. A.; Socci, N. D.; Liang, Y.; Taylor, B. S.; Schultz, N.; Borsu, L.; Lash, A. E.; Brennan, C.; Viale, A.; Sander, C.; Ladanyi, M.; Hoadley, K. A.; Meng, S.; Du, Y.; Shi, Y.; Li, L.; Turman, Y. J.; Zang, D.; Helms, E. B.; Balu, S.; Zhou, X.; Wu, J.; Topal, M. D.; Hayes, D. N.; Perou, C. M.; Getz, G.; Voet, D.; Saksena, G.; Zhang, Junihua; Zhang, H.; Wu, C. J.; Shukla, S.; Cibulskis, K.; Lawrence, M. S.; Sivachenko, A.; Jing, R.; Park, R. W.; Liu, Y.; Park, P. J.; Noble, M.; Chin, L.; Carter, H.; Kim, D.; Karchin, R.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Durinck, S.; Han, J.; Korkola, J. E.; Heiser, L. M.; Cho, R. J.; Hu, Z.; Parvin, B.; Speed, T. P.; Gray, J. W.; Schultz, N.; Cerami, E.; Taylor, B. S.; Olshen, A.; Reva, B.; Antipin, Y.; Shen, R.; Mankoo, P.; Sheridan, R.; Ciriello, G.; Chang, W. K.; Bernanke, J. A.; Borsu, L.; Levine, D. A.; Ladanyi, M.; Sander, C.; Haussler, D.; Benz, C. C.; Stuart, J. M.; Benz, S. C.; Sanborn, J. Z.; Vaske, C. J.; Zhu, J.; Szeto, C.; Scott, G. K.; Yau, C.; Hoadley, K. A.; Du, Y.; Balu, S.; Hayes, D. N.; Perou, C. M.; Wilkerson, M. D.; Zhang, N.; Akbani, R.; Baggerly, K. A.; Yung, W. K.; Mills, G. B.; Weinstein, J. N.; Penny, R.; Shelton, T.; Grimm, D.; Hatfield, M.; Morris, S.; Yena, P.; Rhodes, P.; Sherman, M.; Paulauskis, J.; Millis, S.; Kahn, A.; Greene, J. M.; Sfeir, R.; Jensen, M. A.; Chen, J.; Whitmore, J.; Alonso, S.; Jordan, J.; Chu, A.; Zhang, Jinghui; Barker, A.; Compton, C.; Eley, G.; Ferguson, M.; Fielding, P.; Gerhard, D. S.; Myles, R.; Schaefer, C.; Shaw, K. R. Mills; Vaught, J.; Vockley, J. B.; Good, P. J.; Guyer, M. S.; Ozenberger, B.; Peterson, J.; Thomson, E.; Cramer, D.W.

    2011-01-01

    A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade

  5. ATLAS Forward Detectors and Physics

    CERN Document Server

    Soni, N

    2010-01-01

    In this communication I describe the ATLAS forward physics program and the detectors, LUCID, ZDC and ALFA that have been designed to meet this experimental challenge. In addition to their primary role in the determination of ATLAS luminosity these detectors - in conjunction with the main ATLAS detector - will be used to study soft QCD and diffractive physics in the initial low luminosity phase of ATLAS running. Finally, I will briefly describe the ATLAS Forward Proton (AFP) project that currently represents the future of the ATLAS forward physics program.

  6. Full genome sequence of a Danish isolate of Mycobacterium avium subspecies paratuberculosis, strain Ejlskov2007

    DEFF Research Database (Denmark)

    Afzal, Mamuna; Abidi, Soad; Mikkelsen, Heidi

    , consisting of 4317 unique gene families. Comparison with M. avium paratuberculosis strain K10 revealed only 3436 genes in common (~70%). We have used GenomeAtlases to show conserved (and unique) regions along the Ejlskov2007 chromosome, compared to 2 other Mycobacterium avium sequenced genomes. Pan-genome...

  7. 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

  8. Ceremony for ATLAS cavern

    CERN Multimedia

    2003-01-01

    Wednesday 4 June will be a special day for CERN. The President of the Swiss Confederation, Pascal Couchepin, will officially inaugurate the huge ATLAS cavern now that the civil engineering works have ended. The inauguration ceremony will be held in the ATLAS surface building, with speeches by Pascal Couchepin and CERN, ATLAS and civil engineering personalities. This ceremony will be Webcast live. To access the Webcast on 4 June at 18h00 go to CERN Intranet home page or the following address : http://webcast.cern.ch/live.php

  9. Highlights from ATLAS

    CERN Document Server

    Charlton, D; The ATLAS collaboration

    2013-01-01

    Highlights of recent results from ATLAS were presented. The data collected to date, the detector and physics performance, and measurements of previously established Standard Model processes were reviewed briefly before summarising the latest ATLAS results in the Brout-Englert-Higgs sector, where big progress has been made in the year since the discovery. Finally, selected prospects for measurements including the data from the HL-LHC luminosity upgrade were presented, for both ATLAS and CMS. Many of the results mentioned are preliminary. These proceedings reflect only a brief summary of the material presented, and the status at the time of the conference is reported.

  10. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  11. EnviroAtlas - Des Moines, IA - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Des Moines, IA EnviroAtlas Community. It represents the outside edge of all the block groups included in the...

  12. EnviroAtlas - Cleveland, OH - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Cleveland, OH EnviroAtlas Community. It represents the outside edge of all the block groups included in the...

  13. ATLAS Event - First Splash of Particles in ATLAS

    CERN Multimedia

    ATLAS Outreach

    2008-01-01

    A simulated event. September 10, 2008 - The ATLAS detector lit up as a flood of particles traversed the detector when the beam was occasionally directed at a target near ATLAS. This allowed ATLAS physicists to study how well the various components of the detector were functioning in preparation for the forthcoming collisions. The first ATLAS data recorded on September 10, 2008 is seen here. Running time 24 seconds

  14. Atlas Skills for Learning Rather than Learning Atlas Skills.

    Science.gov (United States)

    Carswell, R. J. B.

    1986-01-01

    Presents a model for visual learning and describes an approach to skills instruction which aids students in using atlases. Maintains that teachers must help students see atlases as tools capable of providing useful information rather than experiencing atlas learning as an empty exercise with little relevance to their lives. (JDH)

  15. 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.

  16. ATLAS Cavern baseplate

    CERN Multimedia

    2002-01-01

    This video shows the incredible amounth of iron used for ATLAS cavern. Please look at the related links and also videos that are concerning the civil engineering where you can see even more detailed cavern excavation work.

  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. ATLAS TV PROJECT

    CERN Multimedia

    2006-01-01

    CERN, Building 40 Interview with theorist Mr. Philip Hinchliffe (Berkeley) as well an interview with his wife Mrs. Hinchliffe who is also Physics Department head at Berkeley. They are both working in ATLAS Experiment.

  19. Russian wind atlas

    Energy Technology Data Exchange (ETDEWEB)

    Starkov, A.N.; Bezroukikh, P.P.; Borisenko, M.M. (Russian Danish Institute of Energy Efficiency (RDIEE), Moscow (RU)); Landberg, L. (Risoe National Lab., Roskilde (DK))

    2000-07-01

    The Atlas provides the assessment of wind energy potential in the near-surface 200 metres of the atmospheric boundary layer. It is based on numerical modeling of wind flows according to hydrodynamic laws and takes into account the effects of roughness, orography and sheltering. The primary information is derived from long-term data series from 332 meteorological stations in Russia. The regional climatologies are calculated in the Atlas for five standard heights (10, 30, 50, 100, 200 m) and four roughness classes of flat and homogeneous terrain. Besides, the Atlas provides the maps of wind energy potential in Russia at 50 metres above ground level, the most important height for wind energy applications. The maps show mean wind speeds and mean wind power densities for any region and any of the five basic types of landscape. The Atlas gives recommendations and examples of wind energy resource assessment and siting of wind turbines. (LN)

  20. Vermont Natural Resources Atlas

    Data.gov (United States)

    Vermont Center for Geographic Information — The purpose of the Natural Resources Atlas is to provide geographic information about environmental features and sites that the Vermont Agency of Natural Resources...

  1. Lunar Sample Atlas

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sample Atlas provides pictures of the Apollo samples taken in the Lunar Sample Laboratory, full-color views of the samples in microscopic thin-sections,...

  2. Overview of ATLAS results

    CERN Document Server

    Di Ciaccio, Anna; The ATLAS collaboration

    2012-01-01

    This talk presents recent ATLAS results on performances and physics concerning in particular: di-boson, single top cross-section measurements, Higgs measurement, SUSY and beyond Standard model searches.

  3. Higgs measurements with ATLAS

    CERN Document Server

    Queitsch-Maitland, Michaela; The ATLAS collaboration

    2017-01-01

    The final Run 1 and first Run 2 results with the ATLAS detector on the measurement of the cross sections, couplings and properties of the Higgs boson in individual final states and their combination are presented.

  4. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    ATLAS Physics Workshop at the University of Roma Tre held from Monday 06 June 2005 to Saturday 11 June 2005. Experts establishing workshop, poster, people milling Shots of Peter Jenni introduction Many audience shots Sequences from various talks

  5. ATLAS DAQ Configuration Databases

    Institute of Scientific and Technical Information of China (English)

    I.Alexandrov; A.Amorim; 等

    2001-01-01

    The configuration databases are an important part of the Trigger/DAQ system of the future ATLAS experiment .This paper describes their current status giving details of architecture,implementation,test results and plans for future work.

  6. 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 ...

  7. 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...

  8. 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.

  9. Recent results from ATLAS experiment

    CERN Document Server

    Smirnov, Sergei; The ATLAS collaboration

    2016-01-01

    The 2nd LHC run has started in 2015 with a pp centre-of-mass collision energy of 13 TeV and ATLAS has taken more than 20 fb-1 of data at the new energy by 2016 summer. In this talk, an overview is given on the ATLAS data taking and the improvements made to the ATLAS experiment during the 2-year shutdown 2013/2014. Selected new results from the recent data analysis from ATLAS is also presented.

  10. 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

  11. ATLAS physics results

    CERN Document Server

    AUTHOR|(CDS)2074312

    2015-01-01

    The ATLAS experiment at the Large Hadron Collider at CERN has been successfully taking data since the end of 2009 in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV, and in heavy ion collisions. In these lectures, some of the most recent ATLAS results will be given on Standard Model measurements, the discovery of the Higgs boson, searches for supersymmetry and exotics and on heavy-ion results.

  12. ATLAS construction status

    CERN Document Server

    Jenni, P

    2006-01-01

    The ATLAS detector is being constructed at the LHC, in view of a data-taking start-up 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.

  13. ATLAS Transitional Radiation Tracker

    CERN Multimedia

    ATLAS Outreach

    2006-01-01

    This colorful 3D animation is an excerpt from the film "ATLAS-Episode II, The Particles Strike Back." Shot with a bug's eye view of the inside of the detector. The viewer is taken on a tour of the inner workings of the transitional radiation tracker within the ATLAS detector. Subjects covered include what the tracker is used to measure, its structure, what happens when particles pass through the tracker, how it distinguishes between different types of particles within it.

  14. 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.

  15. 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.

  16. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    1999-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are ever so busy to finish the different infrastructures for ATLAS. Real underground video. The film has original working sound.

  17. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

    Science.gov (United States)

    Ewing, Adam D; Houlahan, Kathleen E; Hu, Yin; Ellrott, Kyle; Caloian, Cristian; Yamaguchi, Takafumi N; Bare, J Christopher; P'ng, Christine; Waggott, Daryl; Sabelnykova, Veronica Y; Kellen, Michael R; Norman, Thea C; Haussler, David; Friend, Stephen H; Stolovitzky, Gustavo; Margolin, Adam A; Stuart, Joshua M; Boutros, Paul C

    2015-07-01

    The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.

  18. EnviroAtlas - Metrics for Cleveland, OH

    Data.gov (United States)

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

  19. EnviroAtlas - Metrics for Austin, TX

    Data.gov (United States)

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

  20. EnviroAtlas Community Boundaries Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundaries of all EnviroAtlas Communities. It represents the outside edge of all the block groups included in each EnviroAtlas...

  1. Distributed analysis in ATLAS

    CERN Document Server

    Legger, Federica; The ATLAS collaboration

    2015-01-01

    The ATLAS experiment accumulated more than 140 PB of data during the first run of the Large Hadron Collider (LHC) at CERN. The analysis of such an amount of data for the distributed physics community is a challenging task. The Distributed Analysis (DA) system of the ATLAS experiment is an established and stable component of the ATLAS distributed computing operations. About half a million user jobs are daily running on DA resources, submitted by more than 1500 ATLAS physicists. The reliability of the DA system during the first run of the LHC and the following shutdown period has been high thanks to the continuous automatic validation of the distributed analysis sites and the user support provided by a dedicated team of expert shifters. During the LHC shutdown, the ATLAS computing model has undergone several changes to improve the analysis workflows, including the re-design of the production system, a new analysis data format and event model, and the development of common reduction and analysis frameworks. We r...

  2. 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...

  3. 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...

  4. OCCIPITALIZATION OF ATLAS

    Directory of Open Access Journals (Sweden)

    Sween Walia

    2014-12-01

    Full Text Available Occipitalization of atlas is an osseous anomaly of the craniovertebral junction which occurs at the base of the skull in the region of the foramen magnum. The knowledge of such a fusion is important because skeletal abnormalities at the craniocervical junction may result in sudden death. During bone cleaning procedure and routine undergraduate osteology teaching, three skulls with Occipitalization of atlas were encountered in the department of Anatomy at MMIMSR, Mullana, India. In one skull, both anterior and posterior arch were completely fused with occipital bone while the transverse process on the right side was not fused whereas left transverse process was fused with occipital bone. Both anterior and posterior arch were completely fused whereas transverse process on both sides were not fused in other skull. In another skull, partial and asymmetrical Occipitalization of atlas vertebra with occipital bone was found with bifid posterior arch of atlas at the level of posterior tubercle. Anterior arch was completely fused with basilar part of occipital bone but both the transverse processes were not fused. Reduced diameter of foramen magnum due to the atlanto-occipital fusion might cause neurological complications due to compression of spinal cord or medulla oblongata, vertebral vessels, 1st cervical nerve, thus, knowledge of occipitalization of the atlas may be of substantial importance to orthopaedicians, neurosurgeons, physicians and radiologists dealing with abnormalities of the cervical spine.

  5. New format for ATLAS e-news

    CERN Document Server

    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.

  6. 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.

  7. 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

  8. 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.

  9. Event visualization in ATLAS

    CERN Document Server

    Bianchi, Riccardo-Maria; The ATLAS collaboration

    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.

  10. The Tomato Expression Atlas.

    Science.gov (United States)

    Fernandez-Pozo, Noe; Zheng, Yi; Snyder, Stephen I; Nicolas, Philippe; Shinozaki, Yoshihito; Fei, Zhangjun; Catala, Carmen; Giovannoni, James J; Rose, Jocelyn K C; Mueller, Lukas A

    2017-08-01

    With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal context of expression data and help elucidate gene function. Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing in addition to candidate gene identification. This atlas can be adapted to different types of expression data from diverse multicellular species. The Tomato Expression Atlas is available at http://tea.solgenomics.net/ . Source code is available at https://github.com/solgenomics/Tea . jr286@cornell.edu or lam87@cornell.edu. Supplementary data are available at Bioinformatics online.

  11. 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...

  12. 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.

  13. 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...

  14. 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...

  15. 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...

  16. 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

  17. ATLAS forward physics program

    CERN Document Server

    HELLER, M; The ATLAS collaboration

    2010-01-01

    The variety of forward detectors installed in the vicinity of the ATLAS experiment allows to look over a wide range of forward physics topics. They ensure a good information about rapidity gaps, and the installation of very forward detectors (ALFA and AFP) will allow to tag the leading proton(s) remaining from the different processes studied. Most of the studies have to be done at low luminosity to avoid pile-up, but the AFP project offers a really exiting future for the ATLAS forward physics program. We also present how these forward detectors can be used to measure the relative and absolute luminosity.

  18. The ATLAS Simulation Infrastructure

    CERN Document Server

    Aad, Georges; Abdallah, Jalal; Abdelalim, Ahmed Ali; Abdesselam, Abdelouahab; Abdinov, Ovsat; Abi, Babak; Abolins, Maris; Abramowicz, Halina; Abreu, Henso; Acharya, Bobby Samir; Adams, David; Addy, Tetteh; Adelman, Jahred; Adorisio, Cristina; Adragna, Paolo; Adye, Tim; Aefsky, Scott; Aguilar-Saavedra, Juan Antonio; Aharrouche, Mohamed; Ahlen, Steven; Ahles, Florian; Ahmad, Ashfaq; Ahmed, Hossain; Ahsan, Mahsana; Aielli, Giulio; Akdogan, Taylan; Åkesson, Torsten Paul Ake; Akimoto, Ginga; Akimov , Andrei; Aktas, Adil; Alam, Mohammad; Alam, Muhammad Aftab; Albrand, Solveig; Aleksa, Martin; Aleksandrov, Igor; Alexa, Calin; Alexander, Gideon; Alexandre, Gauthier; Alexopoulos, Theodoros; Alhroob, Muhammad; Aliev, Malik; Alimonti, Gianluca; Alison, John; Aliyev, Magsud; Allport, Phillip; Allwood-Spiers, Sarah; Almond, John; Aloisio, Alberto; Alon, Raz; Alonso, Alejandro; Alviggi, Mariagrazia; Amako, Katsuya; Amelung, Christoph; Amorim, Antonio; Amorós, Gabriel; Amram, Nir; Anastopoulos, Christos; Andeen, Timothy; Anders, Christoph Falk; Anderson, Kelby; Andreazza, Attilio; Andrei, George Victor; Anduaga, Xabier; Angerami, Aaron; Anghinolfi, Francis; Anjos, Nuno; Annovi, Alberto; Antonaki, Ariadni; Antonelli, Mario; Antonelli, Stefano; Antos, Jaroslav; Antunovic, Bijana; Anulli, Fabio; Aoun, Sahar; Arabidze, Giorgi; Aracena, Ignacio; Arai, Yasuo; Arce, Ayana; Archambault, John-Paul; Arfaoui, Samir; Arguin, Jean-Francois; Argyropoulos, Theodoros; Arik, Metin; Armbruster, Aaron James; Arnaez, Olivier; Arnault, Christian; Artamonov, Andrei; Arutinov, David; Asai, Makoto; Asai, Shoji; Silva, José; Asfandiyarov, Ruslan; Ask, Stefan; Åsman, Barbro; Asner, David; Asquith, Lily; Assamagan, Ketevi; Astbury, Alan; Astvatsatourov, Anatoli; Atoian, Grigor; Auerbach, Benjamin; Augsten, Kamil; Aurousseau, Mathieu; Austin, Nicholas; Avolio, Giuseppe; Avramidou, Rachel Maria; Axen, David; Ay, Cano; Azuelos, Georges; Azuma, Yuya; Baak, Max; Bach, Andre; Bachacou, Henri; Bachas, Konstantinos; Backes, Moritz; Badescu, Elisabeta; Bagnaia, Paolo; Bai, Yu; Bain, Travis; Baines, John; Baker, Mark; Baker, Oliver Keith; Baker, Sarah; Baltasar Dos Santos Pedrosa, Fernando; Banas, Elzbieta; Banerjee, Piyali; Banerjee, Swagato; Banfi, Danilo; Bangert, Andrea Michelle; Bansal, Vikas; Baranov, Sergey; Baranov, Sergei; Barashkou, Andrei; Barber, Tom; Barberio, Elisabetta Luigia; Barberis, Dario; Barbero, Marlon; Bardin, Dmitri; Barillari, Teresa; Barisonzi, Marcello; Barklow, Timothy; Barlow, Nick; Barnett, Bruce; Barnett, Michael; Baroncelli, Antonio; Barr, Alan; Barreiro, Fernando; Barreiro Guimarães da Costa, João; Barrillon, Pierre; Bartoldus, Rainer; Bartsch, Detlef; Bates, Richard; Batkova, Lucia; Batley, Richard; Battaglia, Andreas; Battistin, Michele; Bauer, Florian; Bawa, Harinder Singh; Bazalova, Magdalena; Beare, Brian; Beau, Tristan; Beauchemin, Pierre-Hugues; Beccherle, Roberto; Becerici, Neslihan; Bechtle, Philip; Beck, Graham; Beck, Hans Peter; Beckingham, Matthew; Becks, Karl-Heinz; Beddall, Ayda; 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Chekanov, Sergei; Chekulaev, Sergey; Chelkov, Gueorgui; Chen, Hucheng; Chen, Shenjian; Chen, Xin; Cheplakov, Alexander; Chepurnov, Vladimir; Cherkaoui El Moursli, Rajaa; Tcherniatine, Valeri; Chesneanu, Daniela; Cheu, Elliott; Cheung, Sing-Leung; Chevalier, Laurent; Chevallier, Florent; Chiarella, Vitaliano; Chiefari, Giovanni; Chikovani, Leila; Childers, John Taylor; Chilingarov, Alexandre; Chiodini, Gabriele; Chizhov, Mihail; Choudalakis, Georgios; Chouridou, Sofia; Christidi, Illectra-Athanasia; Christov, Asen; Chromek-Burckhart, Doris; Chu, Ming-Lee; Chudoba, Jiri; Ciapetti, Guido; Ciftci, Abbas Kenan; Ciftci, Rena; Cinca, Diane; Cindro, Vladimir; Ciobotaru, Matei Dan; Ciocca, Claudia; Ciocio, Alessandra; Cirilli, Manuela; Citterio, Mauro; Clark, Allan G.; Clark, Philip James; Cleland, Bill; Clemens, Jean-Claude; Clement, Benoit; Clement, Christophe; Coadou, Yann; Cobal, Marina; Coccaro, Andrea; Cochran, James H.; Coggeshall, James; Cogneras, Eric; Colijn, Auke-Pieter; Collard, Caroline; Collins, Neil; Collins-Tooth, Christopher; Collot, Johann; Colon, German; Conde Muiño, Patricia; Coniavitis, Elias; Consonni, Michele; Constantinescu, Serban; Conta, Claudio; Conventi, Francesco; Cooke, Mark; Cooper, Ben; Cooper-Sarkar, Amanda; Cooper-Smith, Neil; Copic, Katherine; Cornelissen, Thijs; Corradi, Massimo; Corriveau, Francois; Corso-Radu, Alina; Cortes-Gonzalez, Arely; Cortiana, Giorgio; Costa, Giuseppe; Costa, María José; Costanzo, Davide; Costin, Tudor; Côté, David; Coura Torres, Rodrigo; Courneyea, Lorraine; Cowan, Glen; Cowden, Christopher; Cox, Brian; Cranmer, Kyle; Cranshaw, Jack; Cristinziani, Markus; Crosetti, Giovanni; Crupi, Roberto; Crépé-Renaudin, Sabine; Cuenca Almenar, Cristóbal; Cuhadar Donszelmann, Tulay; Curatolo, Maria; Curtis, Chris; Cwetanski, Peter; Czyczula, Zofia; D'Auria, Saverio; D'Onofrio, Monica; D'Orazio, Alessia; Da Via, Cinzia; Dabrowski, Wladyslaw; Dai, Tiesheng; Dallapiccola, Carlo; Dallison, Steve; Daly, Colin; Dam, Mogens; Danielsson, Hans Olof; Dannheim, Dominik; Dao, Valerio; Darbo, Giovanni; Darlea, Georgiana Lavinia; Davey, Will; Davidek, Tomas; Davidson, Nadia; Davidson, Ruth; Davies, Merlin; Davison, Adam; Dawson, Ian; Daya, Rozmin; De, Kaushik; de Asmundis, Riccardo; De Castro, Stefano; De Castro Faria Salgado, Pedro; De Cecco, Sandro; de Graat, Julien; De Groot, Nicolo; de Jong, Paul; De Mora, Lee; De Oliveira Branco, Miguel; De Pedis, Daniele; De Salvo, Alessandro; De Sanctis, Umberto; De Santo, Antonella; De Vivie De Regie, Jean-Baptiste; De Zorzi, Guido; Dean, Simon; Dedovich, Dmitri; Degenhardt, James; Dehchar, Mohamed; Del Papa, Carlo; Del Peso, Jose; Del Prete, Tarcisio; Dell'Acqua, Andrea; Dell'Asta, Lidia; Della Pietra, Massimo; della Volpe, Domenico; Delmastro, Marco; Delsart, Pierre-Antoine; Deluca, Carolina; Demers, Sarah; Demichev, Mikhail; Demirkoz, Bilge; Deng, Jianrong; Deng, Wensheng; Denisov, Sergey; Derkaoui, Jamal Eddine; Derue, Frederic; Dervan, Paul; Desch, Klaus Kurt; Deviveiros, Pier-Olivier; Dewhurst, Alastair; DeWilde, Burton; Dhaliwal, Saminder; Dhullipudi, Ramasudhakar; Di Ciaccio, Anna; Di Ciaccio, Lucia; Di Domenico, Antonio; Di Girolamo, Alessandro; Di Girolamo, Beniamino; Di Luise, Silvestro; Di Mattia, Alessandro; Di Nardo, Roberto; Di Simone, Andrea; Di Sipio, Riccardo; Diaz, Marco Aurelio; Diblen, Faruk; Diehl, Edward; Dietrich, Janet; Dietzsch, Thorsten; Diglio, Sara; Dindar Yagci, Kamile; Dingfelder, Jochen; Dionisi, Carlo; Dita, Petre; Dita, Sanda; Dittus, Fridolin; Djama, Fares; Djilkibaev, Rashid; Djobava, Tamar; do Vale, Maria Aline Barros; Do Valle Wemans, André; Doan, Thi Kieu Oanh; Dobos, Daniel; Dobson, Ellie; Dobson, Marc; Doglioni, Caterina; Doherty, Tom; Dolejsi, Jiri; Dolenc, Irena; Dolezal, Zdenek; Dolgoshein, Boris; Dohmae, Takeshi; Donega, Mauro; Donini, Julien; Dopke, Jens; Doria, Alessandra; Dos Anjos, Andre; Dotti, Andrea; Dova, Maria-Teresa; Doxiadis, Alexander; Doyle, Tony; Drasal, Zbynek; Dris, Manolis; Dubbert, Jörg; Duchovni, Ehud; Duckeck, Guenter; Dudarev, Alexey; Dudziak, Fanny; Dührssen , Michael; Duflot, Laurent; Dufour, Marc-Andre; Dunford, Monica; Duran Yildiz, Hatice; Dushkin, Andrei; Duxfield, Robert; Dwuznik, Michal; Düren, Michael; Ebenstein, William; Ebke, Johannes; Eckweiler, Sebastian; Edmonds, Keith; Edwards, Clive; Egorov, Kirill; Ehrenfeld, Wolfgang; Ehrich, Thies; Eifert, Till; Eigen, Gerald; Einsweiler, Kevin; Eisenhandler, Eric; Ekelof, Tord; El Kacimi, Mohamed; Ellert, Mattias; Elles, Sabine; Ellinghaus, Frank; Ellis, Katherine; Ellis, Nicolas; Elmsheuser, Johannes; Elsing, Markus; Emeliyanov, Dmitry; Engelmann, Roderich; Engl, Albert; Epp, Brigitte; Eppig, Andrew; Erdmann, Johannes; Ereditato, Antonio; Eriksson, Daniel; Ermoline, Iouri; Ernst, Jesse; Ernst, Michael; Ernwein, Jean; Errede, Deborah; Errede, Steven; Ertel, Eugen; Escalier, Marc; Escobar, Carlos; Espinal Curull, Xavier; Esposito, Bellisario; Etienvre, Anne-Isabelle; Etzion, Erez; Evans, Hal; Fabbri, Laura; Fabre, Caroline; Facius, Katrine; Fakhrutdinov, Rinat; Falciano, Speranza; Fang, Yaquan; Fanti, Marcello; Farbin, Amir; Farilla, Addolorata; Farley, Jason; Farooque, Trisha; Farrington, Sinead; Farthouat, Philippe; Fassnacht, Patrick; Fassouliotis, Dimitrios; Fatholahzadeh, Baharak; Fayard, Louis; Fayette, Florent; Febbraro, Renato; Federic, Pavol; Fedin, Oleg; Fedorko, Woiciech; Feligioni, Lorenzo; Felzmann, Ulrich; Feng, Cunfeng; Feng, Eric; Fenyuk, Alexander; Ferencei, Jozef; Ferland, Jonathan; Fernandes, Bruno; Fernando, Waruna; Ferrag, Samir; Ferrando, James; Ferrara, Valentina; Ferrari, Arnaud; Ferrari, Pamela; Ferrari, Roberto; Ferrer, Antonio; Ferrer, Maria Lorenza; Ferrere, Didier; Ferretti, Claudio; Fiascaris, Maria; Fiedler, Frank; Filipčič, Andrej; Filippas, Anastasios; Filthaut, Frank; Fincke-Keeler, Margret; Fiolhais, Miguel; Fiorini, Luca; Firan, Ana; Fischer, Gordon; Fisher, Matthew; Flechl, Martin; Fleck, Ivor; Fleckner, Johanna; Fleischmann, Philipp; Fleischmann, Sebastian; Flick, Tobias; Flores Castillo, Luis; Flowerdew, Michael; Fonseca Martin, Teresa; Formica, Andrea; Forti, Alessandra; Fortin, Dominique; Fournier, Daniel; Fowler, Andrew; Fowler, Ken; Fox, Harald; Francavilla, Paolo; Franchino, Silvia; Francis, David; Franklin, Melissa; Franz, Sebastien; Fraternali, Marco; Fratina, Sasa; Freestone, Julian; French, Sky; Froeschl, Robert; Froidevaux, Daniel; Frost, James; Fukunaga, Chikara; Fullana Torregrosa, Esteban; Fuster, Juan; Gabaldon, Carolina; Gabizon, Ofir; Gadfort, Thomas; Gadomski, Szymon; Gagliardi, Guido; Gagnon, Pauline; Galea, Cristina; Gallas, Elizabeth; Gallas, Manuel; Gallo, Valentina Santina; Gallop, Bruce; Gallus, Petr; Galyaev, Eugene; Gan, K K; Gao, Yongsheng; Gaponenko, Andrei; Garcia-Sciveres, Maurice; García, Carmen; García Navarro, José Enrique; Gardner, Robert; Garelli, Nicoletta; Garitaonandia, Hegoi; Garonne, Vincent; Gatti, Claudio; Gaudio, Gabriella; Gautard, Valerie; Gauzzi, Paolo; Gavrilenko, Igor; Gay, Colin; Gaycken, Goetz; Gazis, Evangelos; Ge, Peng; Gee, Norman; Geich-Gimbel, Christoph; Gellerstedt, Karl; Gemme, Claudia; Genest, Marie-Hélène; Gentile, Simonetta; Georgatos, Fotios; George, Simon; Gershon, Avi; Ghazlane, Hamid; Ghodbane, Nabil; Giacobbe, Benedetto; Giagu, Stefano; Giakoumopoulou, Victoria; Giangiobbe, Vincent; Gianotti, Fabiola; Gibbard, Bruce; Gibson, Adam; Gibson, Stephen; Gilbert, Laura; Gilchriese, Murdock; Gilewsky, Valentin; Gingrich, Douglas; Ginzburg, Jonatan; Giokaris, Nikos; Giordani, MarioPaolo; Giordano, Raffaele; Giorgi, Francesco Michelangelo; Giovannini, Paola; Giraud, Pierre-Francois; Girtler, Peter; Giugni, Danilo; Giusti, Paolo; Gjelsten, Børge Kile; Gladilin, Leonid; Glasman, Claudia; Glazov, Alexandre; Glitza, Karl-Walter; Glonti, George; Godfrey, Jennifer; Godlewski, Jan; Goebel, Martin; Göpfert, Thomas; Goeringer, Christian; Gössling, Claus; Göttfert, Tobias; Goggi, Virginio; Goldfarb, Steven; Goldin, Daniel; Golling, Tobias; Gomes, Agostinho; Gomez Fajardo, Luz Stella; Gonçcalo, Ricardo; Gonella, Laura; Gong, Chenwei; González de la Hoz, Santiago; Gonzalez Silva, Laura; Gonzalez-Sevilla, Sergio; Goodson, Jeremiah Jet; Goossens, Luc; Gordon, Howard; Gorelov, Igor; Gorfine, Grant; Gorini, Benedetto; Gorini, Edoardo; Gorišek, Andrej; Gornicki, Edward; Gosdzik, Bjoern; Gosselink, Martijn; Gostkin, Mikhail Ivanovitch; Gough Eschrich, Ivo; Gouighri, Mohamed; Goujdami, Driss; Goulette, Marc Phillippe; Goussiou, Anna; Goy, Corinne; Grabowska-Bold, Iwona; Grafström, Per; Grahn, Karl-Johan; Grancagnolo, Sergio; Grassi, Valerio; Gratchev, Vadim; Grau, Nathan; Gray, Heather; Gray, Julia Ann; Graziani, Enrico; Green, Barry; Greenshaw, Timothy; Greenwood, Zeno Dixon; Gregor, Ingrid-Maria; Grenier, Philippe; Griesmayer, Erich; Griffiths, Justin; Grigalashvili, Nugzar; Grillo, Alexander; Grimm, Kathryn; Grinstein, Sebastian; Grishkevich, Yaroslav; Groh, Manfred; Groll, Marius; Gross, Eilam; Grosse-Knetter, Joern; Groth-Jensen, Jacob; Grybel, Kai; Guicheney, Christophe; Guida, Angelo; Guillemin, Thibault; Guler, Hulya; Gunther, Jaroslav; Guo, Bin; Gupta, Ambreesh; Gusakov, Yury; Gutierrez, Andrea; Gutierrez, Phillip; Guttman, Nir; Gutzwiller, Olivier; Guyot, Claude; Gwenlan, Claire; Gwilliam, Carl; Haas, Andy; Haas, Stefan; Haber, Carl; Hadavand, Haleh Khani; Hadley, David; Haefner, Petra; Härtel, Roland; Hajduk, Zbigniew; Hakobyan, Hrachya; Haller, Johannes; Hamacher, Klaus; Hamilton, Andrew; Hamilton, Samuel; Han, Liang; Hanagaki, Kazunori; Hance, Michael; Handel, Carsten; Hanke, Paul; Hansen, Jørgen Beck; Hansen, Jorn Dines; Hansen, John Renner; Hansen, Peter Henrik; Hansl-Kozanecka, Traudl; Hansson, Per; Hara, Kazuhiko; Hare, Gabriel; Harenberg, Torsten; Harrington, Robert; Harris, Orin; Harrison, Karl; Hartert, Jochen; Hartjes, Fred; Harvey, Alex; Hasegawa, Satoshi; Hasegawa, Yoji; Hashemi, Kevan; Hassani, Samira; Haug, Sigve; Hauschild, Michael; Hauser, Reiner; Havranek, Miroslav; Hawkes, Christopher; Hawkings, Richard John; Hayakawa, Takashi; Hayward, Helen; Haywood, Stephen; Head, Simon; Hedberg, Vincent; Heelan, Louise; Heim, Sarah; Heinemann, Beate; Heisterkamp, Simon; Helary, Louis; Heller, Mathieu; Hellman, Sten; Helsens, Clement; Hemperek, Tomasz; Henderson, Robert; Henke, Michael; Henrichs, Anna; Henriques Correia, Ana Maria; Henrot-Versille, Sophie; Hensel, Carsten; Henß, Tobias; Hernández Jiménez, Yesenia; Hershenhorn, Alon David; Herten, Gregor; Hertenberger, Ralf; Hervas, Luis; Hessey, Nigel; Higón-Rodriguez, Emilio; Hill, John; Hiller, Karl Heinz; Hillert, Sonja; Hillier, Stephen; Hinchliffe, Ian; Hines, Elizabeth; Hirose, Minoru; Hirsch, Florian; Hirschbuehl, Dominic; Hobbs, John; Hod, Noam; Hodgkinson, Mark; Hodgson, Paul; Hoecker, Andreas; Hoeferkamp, Martin; Hoffman, Julia; Hoffmann, Dirk; Hohlfeld, Marc; Holy, Tomas; Holzbauer, Jenny; Homma, Yasuhiro; Horazdovsky, Tomas; Hori, Takuya; Horn, Claus; Horner, Stephan; Hostachy, Jean-Yves; Hou, Suen; Hoummada, Abdeslam; Howe, Travis; Hrivnac, Julius; Hryn'ova, Tetiana; Hsu, Pai-hsien Jennifer; Hsu, Shih-Chieh; Huang, Guang Shun; Hubacek, Zdenek; Hubaut, Fabrice; Huegging, Fabian; Hughes, Emlyn; Hughes, Gareth; Hurwitz, Martina; Husemann, Ulrich; Huseynov, Nazim; Huston, Joey; Huth, John; Iacobucci, Giuseppe; Iakovidis, Georgios; Ibragimov, Iskander; Iconomidou-Fayard, Lydia; Idarraga, John; Iengo, Paolo; Igonkina, Olga; Ikegami, Yoichi; Ikeno, Masahiro; Ilchenko, Yuri; Iliadis, Dimitrios; Ince, Tayfun; Ioannou, Pavlos; Iodice, Mauro; Irles Quiles, Adrian; Ishikawa, Akimasa; Ishino, Masaya; Ishmukhametov, Renat; Isobe, Tadaaki; Issakov, Vladimir; Issever, Cigdem; Istin, Serhat; Itoh, Yuki; Ivashin, Anton; Iwanski, Wieslaw; Iwasaki, Hiroyuki; Izen, Joseph; Izzo, Vincenzo; Jackson, Brett; Jackson, John; Jackson, Paul; Jaekel, Martin; Jain, Vivek; Jakobs, Karl; Jakobsen, Sune; Jakubek, Jan; Jana, Dilip; Jansen, Eric; Jantsch, Andreas; Janus, Michel; Jared, Richard; Jarlskog, Göran; Jeanty, Laura; Jen-La Plante, Imai; Jenni, Peter; Jež, Pavel; Jézéquel, Stéphane; Ji, Weina; Jia, Jiangyong; Jiang, Yi; Jimenez Belenguer, Marcos; Jin, Shan; Jinnouchi, Osamu; Joffe, David; Johansen, Marianne; Johansson, Erik; Johansson, Per; Johnert, Sebastian; Johns, Kenneth; Jon-And, Kerstin; Jones, Graham; Jones, Roger; Jones, Tim; Jorge, Pedro; Joseph, John; Juranek, Vojtech; Jussel, Patrick; Kabachenko, Vasily; Kaci, Mohammed; Kaczmarska, Anna; Kado, Marumi; Kagan, Harris; Kagan, Michael; Kaiser, Steffen; Kajomovitz, Enrique; Kalinin, Sergey; Kalinovskaya, Lidia; Kalinowski, Artur; Kama, Sami; Kanaya, Naoko; Kaneda, Michiru; Kantserov, Vadim; Kanzaki, Junichi; Kaplan, Benjamin; Kapliy, Anton; Kaplon, Jan; Kar, Deepak; Karagounis, Michael; Karagoz, Muge; Kartvelishvili, Vakhtang; Karyukhin, Andrey; Kashif, Lashkar; Kasmi, Azzedine; Kass, Richard; Kastanas, Alex; Kastoryano, Michael; Kataoka, Mayuko; Kataoka, Yousuke; Katsoufis, Elias; Katzy, Judith; Kaushik, Venkatesh; Kawagoe, Kiyotomo; Kawamoto, Tatsuo; Kawamura, Gen; Kayl, Manuel; Kayumov, Fred; Kazanin, Vassili; Kazarinov, Makhail; Keates, James Robert; Keeler, Richard; Keener, Paul; Kehoe, Robert; Keil, Markus; Kekelidze, George; Kelly, Marc; Kenyon, Mike; Kepka, Oldrich; Kerschen, Nicolas; Kerševan, Borut Paul; Kersten, Susanne; Kessoku, Kohei; Khakzad, Mohsen; Khalil-zada, Farkhad; Khandanyan, Hovhannes; Khanov, Alexander; Kharchenko, Dmitri; Khodinov, Alexander; Khomich, Andrei; Khoriauli, Gia; Khovanskiy, Nikolai; Khovanskiy, Valery; Khramov, Evgeniy; Khubua, Jemal; Kim, Hyeon Jin; Kim, Min Suk; Kim, Peter; Kim, Shinhong; Kind, Oliver; Kind, Peter; King, Barry; Kirk, Julie; Kirsch, Guillaume; Kirsch, Lawrence; Kiryunin, Andrey; Kisielewska, Danuta; Kittelmann, Thomas; Kiyamura, Hironori; Kladiva, Eduard; Klein, Max; Klein, Uta; Kleinknecht, Konrad; Klemetti, Miika; Klier, Amit; Klimentov, Alexei; Klingenberg, Reiner; Klinkby, Esben; Klioutchnikova, Tatiana; Klok, Peter; Klous, Sander; Kluge, Eike-Erik; Kluge, Thomas; Kluit, Peter; Klute, Markus; Kluth, Stefan; Knecht, Neil; Kneringer, Emmerich; Ko, Byeong Rok; Kobayashi, Tomio; Kobel, Michael; Koblitz, Birger; Kocian, Martin; Kocnar, Antonin; Kodys, Peter; Köneke, Karsten; König, Adriaan; Koenig, Sebastian; Köpke, Lutz; Koetsveld, Folkert; Koevesarki, Peter; Koffas, Thomas; Koffeman, Els; Kohn, Fabian; Kohout, Zdenek; Kohriki, Takashi; Kolanoski, Hermann; Kolesnikov, Vladimir; Koletsou, Iro; Koll, James; Kollar, Daniel; Kolos, Serguei; Kolya, Scott; Komar, Aston; Komaragiri, Jyothsna Rani; Kondo, Takahiko; Kono, Takanori; Konoplich, Rostislav; Konovalov, Serguei; Konstantinidis, Nikolaos; Koperny, Stefan; Korcyl, Krzysztof; Kordas, Kostantinos; Korn, Andreas; Korolkov, Ilya; Korolkova, Elena; Korotkov, Vladislav; Kortner, Oliver; Kortner, Sandra; Kostka, Peter; Kostyukhin, Vadim; Kotov, Serguei; Kotov, Vladislav; Kotov, Konstantin; Kourkoumelis, Christine; Koutsman, Alex; Kowalewski, Robert Victor; Kowalski, Henri; Kowalski, Tadeusz; Kozanecki, Witold; Kozhin, Anatoly; Kral, Vlastimil; Kramarenko, Viktor; Kramberger, Gregor; Krasny, Mieczyslaw Witold; Krasznahorkay, Attila; Kreisel, Arik; Krejci, Frantisek; Kretzschmar, Jan; Krieger, Nina; Krieger, Peter; Kroeninger, Kevin; Kroha, Hubert; Kroll, Joe; Kroseberg, Juergen; Krstic, Jelena; Kruchonak, Uladzimir; Krüger, Hans; Krumshteyn, Zinovii; Kubota, Takashi; Kuehn, Susanne; Kugel, Andreas; Kuhl, Thorsten; Kuhn, Dietmar; Kukhtin, Victor; Kulchitsky, Yuri; Kuleshov, Sergey; Kummer, Christian; Kuna, Marine; Kunkle, Joshua; Kupco, Alexander; Kurashige, Hisaya; Kurata, Masakazu; Kurchaninov, Leonid; Kurochkin, Yurii; Kus, Vlastimil; Kwee, Regina; La Rotonda, Laura; Labbe, Julien; Lacasta, Carlos; Lacava, Francesco; Lacker, Heiko; Lacour, Didier; Lacuesta, Vicente Ramón; Ladygin, Evgueni; Lafaye, Rémi; Laforge, Bertrand; Lagouri, Theodota; Lai, Stanley; Lamanna, Massimo; Lampen, Caleb; Lampl, Walter; Lancon, Eric; Landgraf, Ulrich; Landon, Murrough; Lane, Jenna; Lankford, Andrew; Lanni, Francesco; Lantzsch, Kerstin; Lanza, Agostino; Laplace, Sandrine; Lapoire, Cecile; Laporte, Jean-Francois; Lari, Tommaso; Larner, Aimee; Lassnig, Mario; Laurelli, Paolo; Lavrijsen, Wim; Laycock, Paul; Lazarev, Alexandre; Lazzaro, Alfio; Le Dortz, Olivier; Le Guirriec, Emmanuel; Le Menedeu, Eve; Le Vine, Micheal; Lebedev, Alexander; Lebel, Céline; LeCompte, Thomas; Ledroit-Guillon, Fabienne Agnes Marie; Lee, Hurng-Chun; Lee, Jason; Lee, Shih-Chang; Lefebvre, Michel; Legendre, Marie; LeGeyt, Benjamin; Legger, Federica; Leggett, Charles; Lehmacher, Marc; Lehmann Miotto, Giovanna; Lei, Xiaowen; Leitner, Rupert; Lellouch, Daniel; Lellouch, Jeremie; Lendermann, Victor; Leney, Katharine; Lenz, Tatiana; Lenzen, Georg; Lenzi, Bruno; Leonhardt, Kathrin; Leroy, Claude; Lessard, Jean-Raphael; Lester, Christopher; Leung Fook Cheong, Annabelle; Levêque, Jessica; Levin, Daniel; Levinson, Lorne; Leyton, Michael; Li, Haifeng; Li, Shumin; Li, Xuefei; Liang, Zhihua; Liang, Zhijun; Liberti, Barbara; Lichard, Peter; Lichtnecker, Markus; Lie, Ki; Liebig, Wolfgang; Lilley, Joseph; Lim, Heuijin; Limosani, Antonio; Limper, Maaike; Lin, Simon; Linnemann, James; Lipeles, Elliot; Lipinsky, Lukas; Lipniacka, Anna; Liss, Tony; Lissauer, David; Lister, Alison; Litke, Alan; Liu, Chuanlei; Liu, Dong; Liu, Hao; Liu, Jianbei; Liu, Minghui; Liu, Tiankuan; Liu, Yanwen; Livan, Michele; Lleres, Annick; Lloyd, Stephen; Lobodzinska, Ewelina; Loch, Peter; Lockman, William; Lockwitz, Sarah; Loddenkoetter, Thomas; Loebinger, Fred; Loginov, Andrey; Loh, Chang Wei; Lohse, Thomas; Lohwasser, Kristin; Lokajicek, Milos; Long, Robin Eamonn; Lopes, Lourenco; Lopez Mateos, David; Losada, Marta; Loscutoff, Peter; Lou, Xinchou; Lounis, Abdenour; Loureiro, Karina; Lovas, Lubomir; Love, Jeremy; Love, Peter; Lowe, Andrew; Lu, Feng; Lubatti, Henry; Luci, Claudio; Lucotte, Arnaud; Ludwig, Andreas; Ludwig, Dörthe; Ludwig, Inga; Luehring, Frederick; Luisa, Luca; Lumb, Debra; Luminari, Lamberto; Lund, Esben; Lund-Jensen, Bengt; Lundberg, Björn; Lundberg, Johan; Lundquist, Johan; Lynn, David; Lys, Jeremy; Lytken, Else; Ma, Hong; Ma, Lian Liang; Macana Goia, Jorge Andres; Maccarrone, Giovanni; Macchiolo, Anna; Maček, Boštjan; Machado Miguens, Joana; Mackeprang, Rasmus; Madaras, Ronald; Mader, Wolfgang; Maenner, Reinhard; Maeno, Tadashi; Mättig, Peter; Mättig, Stefan; Magalhaes Martins, Paulo Jorge; Magradze, Erekle; Mahalalel, Yair; Mahboubi, Kambiz; Mahmood, A.; Maiani, Camilla; Maidantchik, Carmen; Maio, Amélia; Majewski, Stephanie; Makida, Yasuhiro; Makouski, Mikhail; Makovec, Nikola; Malecki, Piotr; Malecki, Pawel; Maleev, Victor; Malek, Fairouz; Mallik, Usha; Malon, David; Maltezos, Stavros; Malyshev, Vladimir; Malyukov, Sergei; Mambelli, Marco; Mameghani, Raphael; Mamuzic, Judita; Mandelli, Luciano; Mandić, Igor; Mandrysch, Rocco; Maneira, José; Mangeard, Pierre-Simon; Manjavidze, Ioseb; Manning, Peter; Manousakis-Katsikakis, Arkadios; Mansoulie, Bruno; Mapelli, Alessandro; Mapelli, Livio; March , Luis; Marchand, Jean-Francois; Marchese, Fabrizio; Marchiori, Giovanni; Marcisovsky, Michal; Marino, Christopher; Marroquim, Fernando; Marshall, Zach; Marti-Garcia, Salvador; Martin, Alex; Martin, Andrew; Martin, Brian; Martin, Brian; Martin, Franck Francois; Martin, Jean-Pierre; Martin, Tim; Martin dit Latour, Bertrand; Martinez, Mario; Martinez Outschoorn, Verena; Martini, Agnese; Martyniuk, Alex; Marzano, Francesco; Marzin, Antoine; Masetti, Lucia; Mashimo, Tetsuro; Mashinistov, Ruslan; Masik, Jiri; Maslennikov, Alexey; Massa, Ignazio; Massol, Nicolas; Mastroberardino, Anna; Masubuchi, Tatsuya; Matricon, Pierre; Matsunaga, Hiroyuki; Matsushita, Takashi; Mattravers, Carly; Maxfield, Stephen; Mayne, Anna; Mazini, Rachid; Mazur, Michael; Mazzanti, Marcello; Mc Donald, Jeffrey; Mc Kee, Shawn Patrick; McCarn, Allison; McCarthy, Robert; McCubbin, Norman; McFarlane, Kenneth; McGlone, Helen; Mchedlidze, Gvantsa; McMahon, Steve; McPherson, Robert; Meade, Andrew; Mechnich, Joerg; Mechtel, Markus; Medinnis, Mike; Meera-Lebbai, Razzak; Meguro, Tatsuma; Mehlhase, Sascha; Mehta, Andrew; Meier, Karlheinz; Meirose, Bernhard; Melachrinos, Constantinos; Mellado Garcia, Bruce Rafael; Mendoza Navas, Luis; Meng, Zhaoxia; Menke, Sven; Meoni, Evelin; Mermod, Philippe; Merola, Leonardo; Meroni, Chiara; Merritt, Frank; Messina, Andrea; Metcalfe, Jessica; Mete, Alaettin Serhan; Meyer, Jean-Pierre; Meyer, Jochen; Meyer, Joerg; Meyer, Thomas Christian; Meyer, W. Thomas; Miao, Jiayuan; Michal, Sebastien; Micu, Liliana; Middleton, Robin; Migas, Sylwia; Mijović, Liza; Mikenberg, Giora; Mikestikova, Marcela; Mikuž, Marko; Miller, David; Mills, Corrinne; Mills, Bill; Milov, Alexander; Milstead, David; Milstein, Dmitry; Minaenko, Andrey; Miñano, Mercedes; Minashvili, Irakli; Mincer, Allen; Mindur, Bartosz; Mineev, Mikhail; Ming, Yao; Mir, Lluisa-Maria; Mirabelli, Giovanni; Misawa, Shigeki; Miscetti, Stefano; Misiejuk, Andrzej; Mitrevski, Jovan; Mitsou, Vasiliki A.; Miyagawa, Paul; Mjörnmark, Jan-Ulf; Mladenov, Dimitar; Moa, Torbjoern; Moed, Shulamit; Moeller, Victoria; Mönig, Klaus; Möser, Nicolas; Mohr, Wolfgang; Mohrdieck-Möck, Susanne; Moles-Valls, Regina; Molina-Perez, Jorge; Monk, James; Monnier, Emmanuel; Montesano, Simone; Monticelli, Fernando; Moore, Roger; Mora Herrera, Clemencia; Moraes, Arthur; Morais, Antonio; Morel, Julien; Morello, Gianfranco; Moreno, Deywis; Moreno Llácer, María; Morettini, Paolo; Morii, Masahiro; Morley, Anthony Keith; Mornacchi, Giuseppe; Morozov, Sergey; Morris, John; Moser, Hans-Guenther; Mosidze, Maia; Moss, Josh; Mount, Richard; Mountricha, Eleni; Mouraviev, Sergei; Moyse, Edward; Mudrinic, Mihajlo; Mueller, Felix; Mueller, James; Mueller, Klemens; Müller, Thomas; Muenstermann, Daniel; Muir, Alex; Munwes, Yonathan; Murillo Garcia, Raul; Murray, Bill; Mussche, Ido; Musto, Elisa; Myagkov, Alexey; Myska, Miroslav; Nadal, Jordi; Nagai, Koichi; Nagano, Kunihiro; Nagasaka, Yasushi; Nairz, Armin Michael; Nakamura, Koji; Nakano, Itsuo; Nakatsuka, Hiroki; Nanava, Gizo; Napier, Austin; Nash, Michael; Nation, Nigel; Nattermann, Till; Naumann, Thomas; Navarro, Gabriela; Nderitu, Simon Kirichu; Neal, Homer; Nebot, Eduardo; Nechaeva, Polina; Negri, Andrea; Negri, Guido; Nelson, Andrew; Nelson, Timothy Knight; Nemecek, Stanislav; Nemethy, Peter; Nepomuceno, Andre Asevedo; Nessi, Marzio; Neubauer, Mark; Neusiedl, Andrea; Neves, Ricardo; Nevski, Pavel; Newcomer, Mitchel; Nickerson, Richard; Nicolaidou, Rosy; Nicolas, Ludovic; Nicoletti, Giovanni; Nicquevert, Bertrand; Niedercorn, Francois; Nielsen, Jason; Nikiforov, Andriy; Nikolaev, Kirill; Nikolic-Audit, Irena; Nikolopoulos, Konstantinos; Nilsen, Henrik; Nilsson, Paul; Nisati, Aleandro; Nishiyama, Tomonori; Nisius, Richard; Nodulman, Lawrence; Nomachi, Masaharu; Nomidis, Ioannis; Nordberg, Markus; Nordkvist, Bjoern; Notz, Dieter; Novakova, Jana; Nozaki, Mitsuaki; Nožička, Miroslav; Nugent, Ian Michael; Nuncio-Quiroz, Adriana-Elizabeth; Nunes Hanninger, Guilherme; Nunnemann, Thomas; Nurse, Emily; O'Neil, Dugan; O'Shea, Val; Oakham, Gerald; Oberlack, Horst; Ochi, Atsuhiko; Oda, Susumu; Odaka, Shigeru; Odier, Jerome; Ogren, Harold; Oh, Alexander; Oh, Seog; Ohm, Christian; Ohshima, Takayoshi; Ohshita, Hidetoshi; Ohsugi, Takashi; Okada, Shogo; Okawa, Hideki; Okumura, Yasuyuki; Okuyama, Toyonobu; Olchevski, Alexander; Oliveira, Miguel Alfonso; Oliveira Damazio, Denis; Oliver, John; Oliver Garcia, Elena; Olivito, Dominick; Olszewski, Andrzej; Olszowska, Jolanta; Omachi, Chihiro; Onofre, António; Onyisi, Peter; Oram, Christopher; Oreglia, Mark; Oren, Yona; Orestano, Domizia; Orlov, Iliya; Oropeza Barrera, Cristina; Orr, Robert; Ortega, Eduardo; Osculati, Bianca; Ospanov, Rustem; Osuna, Carlos; Ottersbach, John; Ould-Saada, Farid; Ouraou, Ahmimed; Ouyang, Qun; Owen, Mark; Owen, Simon; Oyarzun, Alejandro; Ozcan, Veysi Erkcan; Ozone, Kenji; Ozturk, Nurcan; Pacheco Pages, Andres; Padilla Aranda, Cristobal; Paganis, Efstathios; Pahl, Christoph; Paige, Frank; Pajchel, Katarina; Palestini, Sandro; Pallin, Dominique; Palma, Alberto; Palmer, Jody; Pan, Yibin; Panagiotopoulou, Evgenia; Panes, Boris; Panikashvili, Natalia; Panitkin, Sergey; Pantea, Dan; Panuskova, Monika; Paolone, Vittorio; Papadopoulou, Theodora; Park, Su-Jung; Park, Woochun; Parker, Andy; Parker, Sherwood; Parodi, Fabrizio; Parsons, John; Parzefall, Ulrich; Pasqualucci, Enrico; Passeri, Antonio; Pastore, Fernanda; Pastore, Francesca; Pásztor , Gabriella; Pataraia, Sophio; Pater, Joleen; Patricelli, Sergio; Patwa, Abid; Pauly, Thilo; Peak, Lawrence; Pecsy, Martin; Pedraza Morales, Maria Isabel; Peleganchuk, Sergey; Peng, Haiping; Penson, Alexander; Penwell, John; Perantoni, Marcelo; Perez, Kerstin; Perez Codina, Estel; Pérez García-Estañ, María Teresa; Perez Reale, Valeria; Perini, Laura; Pernegger, Heinz; Perrino, Roberto; Persembe, Seda; Perus, Antoine; Peshekhonov, Vladimir; Petersen, Brian; Petersen, Troels; Petit, Elisabeth; Petridou, Chariclia; Petrolo, Emilio; Petrucci, Fabrizio; Petschull, Dennis; Petteni, Michele; Pezoa, Raquel; Phan, Anna; Phillips, Alan; Piacquadio, Giacinto; Piccinini, Maurizio; Piegaia, Ricardo; Pilcher, James; Pilkington, Andrew; Pina, João Antonio; Pinamonti, Michele; Pinfold, James; Pinto, Belmiro; Pizio, Caterina; Placakyte, Ringaile; Plamondon, Mathieu; Pleier, Marc-Andre; Poblaguev, Andrei; Poddar, Sahill; Podlyski, Fabrice; Poffenberger, Paul; Poggioli, Luc; Pohl, Martin; Polci, Francesco; Polesello, Giacomo; Policicchio, Antonio; Polini, Alessandro; Poll, James; Polychronakos, Venetios; Pomeroy, Daniel; Pommès, Kathy; Ponsot, Patrick; Pontecorvo, Ludovico; Pope, Bernard; Popeneciu, Gabriel Alexandru; Popovic, Dragan; Poppleton, Alan; Popule, Jiri; Portell Bueso, Xavier; Porter, Robert; Pospelov, Guennady; Pospisil, Stanislav; Potekhin, Maxim; Potrap, Igor; Potter, Christina; Potter, Christopher; Potter, Keith; Poulard, Gilbert; Poveda, Joaquin; Prabhu, Robindra; Pralavorio, Pascal; Prasad, Srivas; Pravahan, Rishiraj; Pribyl, Lukas; Price, Darren; Price, Lawrence; Prichard, Paul; Prieur, Damien; Primavera, Margherita; Prokofiev, Kirill; Prokoshin, Fedor; Protopopescu, Serban; Proudfoot, James; Prudent, Xavier; Przysiezniak, Helenka; Psoroulas, Serena; Ptacek, Elizabeth; Puigdengoles, Carles; Purdham, John; Purohit, Milind; Puzo, Patrick; Pylypchenko, Yuriy; Qi, Ming; Qian, Jianming; Qian, Weiming; Qin, Zhonghua; Quadt, Arnulf; Quarrie, David; Quayle, William; Quinonez, Fernando; Raas, Marcel; Radeka, Veljko; Radescu, Voica; Radics, Balint; Rador, Tonguc; Ragusa, Francesco; Rahal, Ghita; Rahimi, Amir; Rajagopalan, Srinivasan; Rammensee, Michael; Rammes, Marcus; Rauscher, Felix; Rauter, Emanuel; Raymond, Michel; Read, Alexander Lincoln; Rebuzzi, Daniela; Redelbach, Andreas; Redlinger, George; Reece, Ryan; Reeves, Kendall; Reinherz-Aronis, Erez; Reinsch, Andreas; Reisinger, Ingo; Reljic, Dusan; Rembser, Christoph; Ren, Zhongliang; Renkel, Peter; Rescia, Sergio; Rescigno, Marco; Resconi, Silvia; Resende, Bernardo; Reznicek, Pavel; Rezvani, Reyhaneh; Richards, Alexander; Richards, Ronald; Richter, Robert; Richter-Was, Elzbieta; Ridel, Melissa; Rijpstra, Manouk; Rijssenbeek, Michael; Rimoldi, Adele; Rinaldi, Lorenzo; Rios, Ryan Randy; Riu, Imma; Rizatdinova, Flera; Rizvi, Eram; Roa Romero, Diego Alejandro; Robertson, Steven; Robichaud-Veronneau, Andree; Robinson, Dave; Robinson, James; Robinson, Mary; Robson, Aidan; Rocha de Lima, Jose Guilherme; Roda, Chiara; Roda Dos Santos, Denis; Rodriguez, Diego; Rodriguez Garcia, Yohany; Roe, Shaun; Røhne, Ole; Rojo, Victoria; Rolli, Simona; Romaniouk, Anatoli; Romanov, Victor; Romeo, Gaston; Romero Maltrana, Diego; Roos, Lydia; Ros, Eduardo; Rosati, Stefano; Rosenbaum, Gabriel; Rosselet, Laurent; Rossetti, Valerio; Rossi, Leonardo Paolo; Rotaru, Marina; Rothberg, Joseph; Rousseau, David; Royon, Christophe; Rozanov, Alexander; Rozen, Yoram; Ruan, Xifeng; Ruckert, Benjamin; Ruckstuhl, Nicole; Rud, Viacheslav; Rudolph, Gerald; Rühr, Frederik; Ruggieri, Federico; Ruiz-Martinez, Aranzazu; Rumyantsev, Leonid; Rurikova, Zuzana; Rusakovich, Nikolai; Rutherfoord, John; Ruwiedel, Christoph; Ruzicka, Pavel; Ryabov, Yury; Ryan, Patrick; Rybkin, Grigori; Rzaeva, Sevda; Saavedra, Aldo; Sadrozinski, Hartmut; Sadykov, Renat; Sakamoto, Hiroshi; Salamanna, Giuseppe; Salamon, Andrea; Saleem, Muhammad; Salihagic, Denis; Salnikov, Andrei; Salt, José; Salvachua Ferrando, Belén; Salvatore, Daniela; Salvatore, Pasquale Fabrizio; Salvucci, Antonio; Salzburger, Andreas; Sampsonidis, Dimitrios; Samset, Björn Hallvard; Sandaker, Heidi; Sander, Heinz Georg; Sanders, Michiel; Sandhoff, Marisa; Sandhu, Pawan; Sandstroem, Rikard; Sandvoss, Stephan; Sankey, Dave; Sanny, Bernd; Sansoni, Andrea; Santamarina Rios, Cibran; Santoni, Claudio; Santonico, Rinaldo; Saraiva, João; Sarangi, Tapas; Sarkisyan-Grinbaum, Edward; Sarri, Francesca; Sasaki, Osamu; Sasao, Noboru; Satsounkevitch, Igor; Sauvage, Gilles; Savard, Pierre; Savine, Alexandre; Savinov, Vladimir; Sawyer, Lee; Saxon, David; Says, Louis-Pierre; Sbarra, Carla; Sbrizzi, Antonio; Scannicchio, Diana; Schaarschmidt, Jana; Schacht, Peter; Schäfer, Uli; Schaetzel, Sebastian; Schaffer, Arthur; Schaile, Dorothee; Schamberger, R.~Dean; Schamov, Andrey; Schegelsky, Valery; Scheirich, Daniel; Schernau, Michael; Scherzer, Max; Schiavi, Carlo; Schieck, Jochen; Schioppa, Marco; Schlenker, Stefan; Schmidt, Evelyn; Schmieden, Kristof; Schmitt, Christian; Schmitz, Martin; Schott, Matthias; Schouten, Doug; Schovancova, Jaroslava; Schram, Malachi; Schreiner, Alexander; Schroeder, Christian; Schroer, Nicolai; Schroers, Marcel; Schultes, Joachim; Schultz-Coulon, Hans-Christian; Schumacher, Jan; Schumacher, Markus; Schumm, Bruce; Schune, Philippe; Schwanenberger, Christian; Schwartzman, Ariel; Schwemling, Philippe; Schwienhorst, Reinhard; Schwierz, Rainer; Schwindling, Jerome; Scott, Bill; Searcy, Jacob; Sedykh, Evgeny; Segura, Ester; Seidel, Sally; Seiden, Abraham; Seifert, Frank; Seixas, José; Sekhniaidze, Givi; Seliverstov, Dmitry; Sellden, Bjoern; Semprini-Cesari, Nicola; Serfon, Cedric; Serin, Laurent; Seuster, Rolf; Severini, Horst; Sevior, Martin; Sfyrla, Anna; Shabalina, Elizaveta; Shamim, Mansoora; Shan, Lianyou; Shank, James; Shao, Qi Tao; Shapiro, Marjorie; Shatalov, Pavel; Shaw, Kate; Sherman, Daniel; Sherwood, Peter; Shibata, Akira; Shimojima, Makoto; Shin, Taeksu; Shmeleva, Alevtina; Shochet, Mel; Shupe, Michael; Sicho, Petr; Sidoti, Antonio; Siegert, Frank; Siegrist, James; Sijacki, Djordje; Silbert, Ohad; Silver, Yiftah; Silverstein, Daniel; Silverstein, Samuel; Simak, Vladislav; Simic, Ljiljana; Simion, Stefan; Simmons, Brinick; Simonyan, Margar; Sinervo, Pekka; Sinev, Nikolai; Sipica, Valentin; Siragusa, Giovanni; Sisakyan, Alexei; Sivoklokov, Serguei; Sjölin, Jörgen; Sjursen, Therese; Skovpen, Kirill; Skubic, Patrick; Slater, Mark; Slavicek, Tomas; Sliwa, Krzysztof; Sloper, John erik; Sluka, Tomas; Smakhtin, Vladimir; Smirnov, Sergei; Smirnov, Yuri; Smirnova, Lidia; Smirnova, Oxana; Smith, Ben Campbell; Smith, Douglas; Smith, Kenway; Smizanska, Maria; Smolek, Karel; Snesarev, Andrei; Snow, Steve; Snow, Joel; Snuverink, Jochem; Snyder, Scott; Soares, Mara; Sobie, Randall; Sodomka, Jaromir; Soffer, Abner; Solans, Carlos; Solar, Michael; Solc, Jaroslav; Solfaroli Camillocci, Elena; Solodkov, Alexander; Solovyanov, Oleg; Soluk, Richard; Sondericker, John; Sopko, Vit; Sopko, Bruno; Sosebee, Mark; Soukharev, Andrey; Spagnolo, Stefania; Spanò, Francesco; Spencer, Edwin; Spighi, Roberto; Spigo, Giancarlo; Spila, Federico; Spiwoks, Ralf; Spousta, Martin; Spreitzer, Teresa; Spurlock, Barry; St. Denis, Richard Dante; Stahl, Thorsten; Stahlman, Jonathan; Stamen, Rainer; Stancu, Stefan Nicolae; Stanecka, Ewa; Stanek, Robert; Stanescu, Cristian; Stapnes, Steinar; Starchenko, Evgeny; Stark, Jan; Staroba, Pavel; Starovoitov, Pavel; Stastny, Jan; Stavina, Pavel; Stavropoulos, Georgios; Steele, Genevieve; Steinbach, Peter; Steinberg, Peter; Stekl, Ivan; Stelzer, Bernd; Stelzer, Harald Joerg; Stelzer-Chilton, Oliver; Stenzel, Hasko; Stevenson, Kyle; Stewart, Graeme; Stockton, Mark; Stoerig, Kathrin; Stoicea, Gabriel; Stonjek, Stefan; Strachota, Pavel; Stradling, Alden; Straessner, Arno; Strandberg, Jonas; Strandberg, Sara; Strandlie, Are; Strauss, Michael; Strizenec, Pavol; Ströhmer, Raimund; Strom, David; Stroynowski, Ryszard; Strube, Jan; Stugu, Bjarne; Su, Dong; Soh, Dart-yin; Sugaya, Yorihito; Sugimoto, Takuya; Suhr, Chad; Suk, Michal; Sulin, Vladimir; Sultansoy, Saleh; Sumida, Toshi; Sun, Xiaohu; Sundermann, Jan Erik; Suruliz, Kerim; Sushkov, Serge; Susinno, Giancarlo; Sutton, Mark; Suzuki, Takuya; Suzuki, Yu; Sykora, Ivan; Sykora, Tomas; Szymocha, Tadeusz; Sánchez, Javier; Ta, Duc; Tackmann, Kerstin; Taffard, Anyes; Tafirout, Reda; Taga, Adrian; Takahashi, Yuta; Takai, Helio; Takashima, Ryuichi; Takeda, Hiroshi; Takeshita, Tohru; Talby, Mossadek; Talyshev, Alexey; Tamsett, Matthew; Tanaka, Junichi; Tanaka, Reisaburo; Tanaka, Satoshi; Tanaka, Shuji; Tapprogge, Stefan; Tardif, Dominique; Tarem, Shlomit; Tarrade, Fabien; Tartarelli, Giuseppe Francesco; Tas, Petr; Tasevsky, Marek; Tassi, Enrico; Tatarkhanov, Mous; Taylor, Christopher; Taylor, Frank; Taylor, Geoffrey; Taylor, Ryan P.; Taylor, Wendy; Teixeira-Dias, Pedro; Ten Kate, Herman; Teng, Ping-Kun; Tennenbaum-Katan, Yaniv-David; Terada, Susumu; Terashi, Koji; Terron, Juan; Terwort, Mark; Testa, Marianna; Teuscher, Richard; Thioye, Moustapha; Thoma, Sascha; Thomas, Juergen; Thompson, Stan; Thompson, Emily; Thompson, Peter; Thompson, Paul; Thompson, Ray; Thomson, Evelyn; Thun, Rudolf; Tic, Tomas; Tikhomirov, Vladimir; Tikhonov, Yury; Tipton, Paul; Tique Aires Viegas, Florbela De Jes; Tisserant, Sylvain; Toczek, Barbara; Todorov, Theodore; Todorova-Nova, Sharka; Toggerson, Brokk; Tojo, Junji; Tokár, Stanislav; Tokushuku, Katsuo; Tollefson, Kirsten; Tomasek, Lukas; Tomasek, Michal; Tomoto, Makoto; Tompkins, Lauren; Toms, Konstantin; Tonoyan, Arshak; Topfel, Cyril; Topilin, Nikolai; Torrence, Eric; Torró Pastor, Emma; Toth, Jozsef; Touchard, Francois; Tovey, Daniel; Trefzger, Thomas; Tremblet, Louis; Tricoli, Alesandro; Trigger, Isabel Marian; Trincaz-Duvoid, Sophie; Trinh, Thi Nguyet; Tripiana, Martin; Triplett, Nathan; Trischuk, William; Trivedi, Arjun; Trocmé, Benjamin; Troncon, Clara; Trzupek, Adam; Tsarouchas, Charilaos; Tseng, Jeffrey; Tsiakiris, Menelaos; Tsiareshka, Pavel; Tsionou, Dimitra; Tsipolitis, Georgios; Tsiskaridze, Vakhtang; Tskhadadze, Edisher; Tsukerman, Ilya; Tsulaia, Vakhtang; Tsung, Jieh-Wen; Tsuno, Soshi; Tsybychev, Dmitri; Tuggle, Joseph; Turecek, Daniel; Turk Cakir, Ilkay; Turlay, Emmanuel; Tuts, Michael; Twomey, Matthew Shaun; Tylmad, Maja; Tyndel, Mike; Uchida, Kirika; Ueda, Ikuo; Ugland, Maren; Uhlenbrock, Mathias; Uhrmacher, Michael; Ukegawa, Fumihiko; Unal, Guillaume; Undrus, Alexander; Unel, Gokhan; Unno, Yoshinobu; Urbaniec, Dustin; Urkovsky, Evgeny; Urquijo, Phillip; Urrejola, Pedro; Usai, Giulio; Uslenghi, Massimiliano; Vacavant, Laurent; Vacek, Vaclav; Vachon, Brigitte; Vahsen, Sven; Valente, Paolo; Valentinetti, Sara; Valkar, Stefan; Valladolid Gallego, Eva; Vallecorsa, Sofia; Valls Ferrer, Juan Antonio; Van Berg, Richard; van der Graaf, Harry; van der Kraaij, Erik; van der Poel, Egge; van der Ster, Daniel; van Eldik, Niels; van Gemmeren, Peter; van Kesteren, Zdenko; van Vulpen, Ivo; Vandelli, Wainer; Vaniachine, Alexandre; Vankov, Peter; Vannucci, Francois; Vari, Riccardo; Varnes, Erich; Varouchas, Dimitris; Vartapetian, Armen; Varvell, Kevin; Vasilyeva, Lidia; Vassilakopoulos, Vassilios; Vazeille, Francois; Vellidis, Constantine; Veloso, Filipe; Veneziano, Stefano; Ventura, Andrea; Ventura, Daniel; Venturi, Manuela; Venturi, Nicola; Vercesi, Valerio; Verducci, Monica; Verkerke, Wouter; Vermeulen, Jos; Vetterli, Michel; Vichou, Irene; Vickey, Trevor; Viehhauser, Georg; Villa, Mauro; Villani, Giulio; Villaplana Perez, Miguel; Vilucchi, Elisabetta; Vincter, Manuella; Vinek, Elisabeth; Vinogradov, Vladimir; Viret, Sébastien; Virzi, Joseph; Vitale , Antonio; Vitells, Ofer; Vivarelli, Iacopo; Vives Vaque, Francesc; Vlachos, Sotirios; Vlasak, Michal; Vlasov, Nikolai; Vogel, Adrian; Vokac, Petr; Volpi, Matteo; von der Schmitt, Hans; von Loeben, Joerg; von Radziewski, Holger; von Toerne, Eckhard; Vorobel, Vit; Vorwerk, Volker; Vos, Marcel; Voss, Rudiger; Voss, Thorsten Tobias; Vossebeld, Joost; Vranjes, Nenad; Vranjes Milosavljevic, Marija; Vrba, Vaclav; Vreeswijk, Marcel; Vu Anh, Tuan; Vudragovic, Dusan; Vuillermet, Raphael; Vukotic, Ilija; Wagner, Peter; Walbersloh, Jorg; Walder, James; Walker, Rodney; Walkowiak, Wolfgang; Wall, Richard; Wang, Chiho; Wang, Haichen; Wang, Jin; Wang, Song-Ming; Warburton, Andreas; Ward, Patricia; Warsinsky, Markus; Wastie, Roy; Watkins, Peter; Watson, Alan; Watson, Miriam; Watts, Gordon; Watts, Stephen; Waugh, Anthony; Waugh, Ben; Weber, Marc; Weber, Manuel; Weber, Michele; Weber, Pavel; Weidberg, Anthony; Weingarten, Jens; Weiser, Christian; Wellenstein, Hermann; Wells, Phillippa; Wen, Mei; Wenaus, Torre; Wendler, Shanti; Wengler, Thorsten; Wenig, Siegfried; Wermes, Norbert; Werner, Matthias; Werner, Per; Werth, Michael; Werthenbach, Ulrich; Wessels, Martin; Whalen, Kathleen; White, Andrew; White, Martin; White, Sebastian; Whitehead, Samuel Robert; Whiteson, Daniel; Whittington, Denver; Wicek, Francois; Wicke, Daniel; Wickens, Fred; Wiedenmann, Werner; Wielers, Monika; Wienemann, Peter; Wiglesworth, Craig; Wiik, Liv Antje Mari; Wildauer, Andreas; Wildt, Martin Andre; Wilkens, Henric George; Williams, Eric; Williams, Hugh; Willocq, Stephane; Wilson, John; Wilson, Michael Galante; Wilson, Alan; Wingerter-Seez, Isabelle; Winklmeier, Frank; Wittgen, Matthias; Wolter, Marcin Wladyslaw; Wolters, Helmut; Wosiek, Barbara; Wotschack, Jorg; Woudstra, Martin; Wraight, Kenneth; Wright, Catherine; Wright, Dennis; Wrona, Bozydar; Wu, Sau Lan; Wu, Xin; Wulf, Evan; Wynne, Benjamin; Xaplanteris, Leonidas; Xella, Stefania; Xie, Song; Xu, Da; Xu, Neng; Yamada, Miho; Yamamoto, Akira; Yamamoto, Kyoko; Yamamoto, Shimpei; Yamamura, Taiki; Yamaoka, Jared; Yamazaki, Takayuki; Yamazaki, Yuji; Yan, Zhen; Yang, Haijun; Yang, Un-Ki; Yang, Zhaoyu; Yao, Weiming; Yao, Yushu; Yasu, Yoshiji; Ye, Jingbo; Ye, Shuwei; Yilmaz, Metin; Yoosoofmiya, Reza; Yorita, Kohei; Yoshida, Riktura; Young, Charles; Youssef, Saul; Yu, Dantong; Yu, Jaehoon; Yuan, Li; Yurkewicz, Adam; Zaidan, Remi; Zaitsev, Alexander; Zajacova, Zuzana; Zambrano, Valentina; Zanello, Lucia; Zaytsev, Alexander; Zeitnitz, Christian; Zeller, Michael; Zemla, Andrzej; Zendler, Carolin; Zenin, Oleg; Ženiš, Tibor; Zenonos, Zenonas; Zenz, Seth; Zerwas, Dirk; Zevi della Porta, Giovanni; Zhan, Zhichao; Zhang, Huaqiao; Zhang, Jinlong; Zhang, Qizhi; Zhang, Xueyao; Zhao, Long; Zhao, Tianchi; Zhao, Zhengguo; Zhemchugov, Alexey; Zhong, Jiahang; Zhou, Bing; Zhou, Ning; Zhou, Yue; Zhu, Cheng Guang; Zhu, Hongbo; Zhu, Yingchun; Zhuang, Xuai; Zhuravlov, Vadym; Zimmermann, Robert; Zimmermann, Simone; Zimmermann, Stephanie; Ziolkowski, Michael; Živković, Lidija; Zobernig, Georg; Zoccoli, Antonio; zur Nedden, Martin; Zutshi, Vishnu

    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.

  19. ATLAS SCT Commissioning

    CERN Document Server

    Limper, Maaike

    2007-01-01

    The Barrel and End-Cap SCT detectors are installed in the ATLAS cavern. This paper will focus on the assembly, installation and first tests of the SCT in-situ. The thermal, electrical and optical services were tested and the results will be reviewed. Problems with the cooling have led to a modification for the heaters on the cooling return lines. The first tests of the SCT in-situ will be described using the calibration scans. The performance of the SCT, in particular the fraction of working channels and the noise performance, is well within the ATLAS specification.

  20. 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.; Negrello, M.; Serjeant, S.; Thompson, M. A.; Van Kampen, E.; Amblard, A.; Andreani, P.; Baes, M.; Beelen, A.; Bendo, G. J.; Bertoldi, F.; Benford, D.; Bock, J.

    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.

  1. The ATLAS Detector Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Clark, P.J. [University of Edinburgh, School of Physics and Astronomy, James Clerk Maxwell Building, The Kings Buildings, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom)

    2011-06-15

    We present the simulation software for the ATLAS experiment [G. Aad et al., The ATLAS Experiment at the CERN Large Hadron Collider, JINST 3 (2008), S08003] at the Large Hadron Collider [L. Evans and P. Bryant, LHC Machine, JINST 3 (2008), S08001]. The overall infrastructure and some selected features are discussed. In particular, the detector description, the interface to Geant4, event generator support, magnetic field integration improvements, pile-up and digitisation of overlapping events and fast simulation. Also described are performance studies, large scale production and the validation of the simulated output against recent data.

  2. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    CAMERA ON TOROID The ATLAS barrel toroid system consists of eight coils, each of axial length 25.3 m, assembled radially and symmetrically around the beam axis. The coils are of a flat racetrack type with two double-pancake windings made of 20.5 kA aluminium-stabilized niobium-titanium superconductor. The video is about the slow lowering of the toroid down to the cavern of ATLAS. It is very demanding task. The camera is placed on top of the toroid.

  3. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    Karsten Köneke; on behalf of the ATLAS Collaboration

    2012-11-01

    The ATLAS experiment at the Large Hadron Collider is recording data from proton–proton collisions at a centre-of-mass energy of 7 TeV since the spring of 2010. The integrated luminosity has grown nearly exponentially since then and continues to rise fast. 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). Hints of potentially interesting physics signals obtained this way are followed up by physics groups.

  4. Improving ATLAS reprocessing software

    CERN Document Server

    Novak, Tadej

    2014-01-01

    For my CERN Summer Student programme I have been working with ATLAS reprocessing group. Data taken at ATLAS experiment is not only processed after being taken, but is also reprocessed multiple times afterwards. This allows applying new alignments, calibration of detector and using improved or faster algorithms. Reprocessing is usually done in campaigns for different periods of data or for different interest groups. The idea of my project was to simplify the definition of tasks and monitoring of their progress. I created a LIST configuration files generator script in Python and a monitoring webpage for tracking current reprocessing tasks.

  5. Jet Physics in ATLAS

    CERN Document Server

    Sandoval, C; The ATLAS collaboration

    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 physics measurements. These measurements constitute precision tests of QCD in a new energy regime, and show sensitivity to the parton densities in the proton and to the value of the strong coupling, alpha_s.

  6. ATLAS/CMS Upgrades

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00370685; The ATLAS collaboration

    2016-01-01

    Precision studies of the Standard Model (SM) and the searches of the physics beyond the SM are ongoing at the ATLAS and CMS experiments at the Large Hadron Collider (LHC). A luminosity upgrade of LHC is planned, which provides a significant challenge for the experiments. In this report, the plans of the ATLAS and CMS upgrades are introduced. Physics prospects for selected topics, including Higgs coupling measurements, Bs,d -> mumu decays, and top quark decays through flavor changing neutral current, are also shown.

  7. The ATLAS Simulation Infrastructure

    Science.gov (United States)

    Aad, G.; Abbott, B.; 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.; Åkesson, 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.; Amorós, 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.; Åsman, 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 Guimarães 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.; Böser, 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.; Büscher, 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 Urbán, 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. 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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.; McDonald, J.; McKee, 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.; Mijović, L.; Mikenberg, G.; Mikestikova, M.; Mikuž, M.; Miller, D. W.; Mills, W. J.; Mills, C. M.; Milov, A.; Milstead, D. A.; Milstein, D.; Minaenko, A. A.; Miñano, 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.; Mjörnmark, J. U.; Mladenov, D.; Moa, T.; Moed, S.; Moeller, V.; Mönig, K.; Möser, N.; Mohr, W.; Mohrdieck-Möck, 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 Llácer, 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.; Müller, 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. M.; 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.; Nožička, 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.; Oliveira 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.; Pásztor, 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.; Pérez García-Estañ, 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.; Pommès, 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, J. E. M.; Robinson, M.; Robson, A.; Rocha de Lima, J. G.; Roda, C.; Roda Dos Santos, D.; Rodriguez, D.; Rodriguez Garcia, Y.; Roe, S.; Røhne, 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.; Rühr, 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.; Schäfer, 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.; Spanò, F.; Spencer, E.; Spighi, R.; Spigo, G.; Spila, F.; Spiwoks, R.; Spousta, M.; Spreitzer, T.; Spurlock, B.; Denis, R. D. St.; 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.; Stavropoulos, G.; 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.; Ströhmer, 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.; Sánchez, 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.; Tokár, S.; Tokushuku, K.; Tollefson, K.; Tomasek, L.; Tomasek, M.; Tomoto, M.; Tompkins, L.; Toms, K.; Tonoyan, A.; Topfel, C.; Topilin, N. D.; Torrence, E.; Torró 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.; Trocmé, 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.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zur Nedden, M.; Zutshi, V.

    2010-12-01

    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.

  8. Local atlas selection for discrete multi-atlas segmentation

    OpenAIRE

    Alchatzidis, Stavros; Sotiras, Aristeidis; Paragios, Nikos

    2015-01-01

    International audience; Multi-atlas segmentation is commonly performed in two separate steps: i) multiple pairwise registrations, and ii) fusion of the deformed segmentation masks towards labeling objects of interest. In this paper we propose an approach for integrated volume segmentation through multi-atlas registration. To tackle this problem, we opt for a graphical model where registration and segmentation nodes are coupled. The aim is to recover simultaneously all atlas deformations along...

  9. The UCSC Cancer Genomics Browser: update 2011.

    Science.gov (United States)

    Sanborn, J Zachary; Benz, Stephen C; Craft, Brian; Szeto, Christopher; Kober, Kord M; Meyer, Laurence; Vaske, Charles J; Goldman, Mary; Smith, Kayla E; Kuhn, Robert M; Karolchik, Donna; Kent, W James; Stuart, Joshua M; Haussler, David; Zhu, Jingchun

    2011-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

  10. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    2000-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are ever so busy to finish the different infrastructures for ATLAS. Real underground video. When passing throw the walls the succeeding can be heard and seen. The film has original working sound.

  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. ATLAS Detector Upgrade Prospects

    Science.gov (United States)

    Dobre, M.; 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 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.

  13. ATLAS Supersymmetry Searches

    CERN Document Server

    Ughetto, Michael; The ATLAS collaboration

    2016-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles, with focus on those obtained using proton-proton collisions at a centre of mass energy of 13 TeV.

  14. HWW in ATLAS

    CERN Document Server

    Rados, Pere; The ATLAS collaboration

    2016-01-01

    The H-->WW channel plays an important role in Higgs boson property measurements, searches for rare decay modes, and searches for possible extended Higgs sectors. In this talk the latest H-->WW results from ATLAS will be briefly summarised.

  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 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.

  17. Hard Probes at ATLAS

    CERN Document Server

    Citron, Z; The ATLAS collaboration

    2014-01-01

    The ATLAS collaboration has measured several hard probe observables in Pb+Pb and p+Pb collisions at the LHC. These measurements include jets which show modification in the hot dense medium of heavy ion collisions as well as color neutral electro-weak bosons. Together, they elucidate the nature of heavy ion collisions.

  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. 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. ATLAS solenoid operates underground

    CERN Document Server

    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...

  1. Higgs searches with ATLAS

    CERN Document Server

    Price, J D; The ATLAS collaboration

    2013-01-01

    Summary of the ATLAS analyses for the rarer SM Higgs decay channels, and the limits of the SM Higgs invisible decay width. Analyses included are the VH->Vbb, H->tautau, VH->VWW, H->Zy, H->mumu, ttH->ttyy and ZH->ll+inv.

  2. An Icelandic wind atlas

    Science.gov (United States)

    Nawri, Nikolai; Nína Petersen, Gudrun; Bjornsson, Halldór; Arason, Þórður; Jónasson, Kristján

    2013-04-01

    While Iceland has ample wind, its use for energy production has been limited. Electricity in Iceland is generated from renewable hydro- and geothermal source and adding wind energy has not be considered practical or even necessary. However, adding wind into the energy mix is becoming a more viable options as opportunities for new hydro or geothermal power installation become limited. In order to obtain an estimate of the wind energy potential of Iceland a wind atlas has been developed as a part of the Nordic project "Improved Forecast of Wind, Waves and Icing" (IceWind). The atlas is based on mesoscale model runs produced with the Weather Research and Forecasting (WRF) Model and high-resolution regional analyses obtained through the Wind Atlas Analysis and Application Program (WAsP). The wind atlas shows that the wind energy potential is considerable. The regions with the strongest average wind are nevertheless impractical for wind farms, due to distance from road infrastructure and power grid as well as harsh winter climate. However, even in easily accessible regions wind energy potential in Iceland, as measured by annual average power density, is among the highest in Western Europe. There is a strong seasonal cycle, with wintertime power densities throughout the island being at least a factor of two higher than during summer. Calculations show that a modest wind farm of ten medium size turbines would produce more energy throughout the year than a small hydro power plants making wind energy a viable additional option.

  3. 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...

  4. 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.

  5. 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.

  6. Exotic searches at ATLAS

    CERN Document Server

    Turra, Ruggero; The ATLAS collaboration

    2016-01-01

    The ATLAS detector has collected 3.2 fb^-1 of proton-proton collisions at 13 TeV centre of mass energy during the 2015 LHC run. A selected review of the recent result are presented in the context of the direct search for BSM, not SUSY, not BSM Higgs.

  7. Atlas of NATO.

    Science.gov (United States)

    Young, Harry F.

    This atlas provides basic information about the North Atlantic Treaty Organization (NATO). Formed in response to growing concern for the security of Western Europe after World War II, NATO is a vehicle for Western efforts to reduce East-West tensions and the level of armaments. NATO promotes political and economic collaboration as well as military…

  8. Taking ATLAS to new heights

    CERN Multimedia

    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.

  9. 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.

  10. Atlas of genetics and cytogenetics in oncology and haematology in 2013.

    Science.gov (United States)

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians.

  11. Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013

    Science.gov (United States)

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians. PMID:23161685

  12. Improving atlas methodology

    Science.gov (United States)

    Robbins, C.S.; Dowell, B.A.; O'Brien, J.

    1987-01-01

    We are studying a sample of Maryland (2 %) and New Hampshire (4 %) Atlas blocks and a small sample in Maine. These three States used different sampling methods and block sizes. We compare sampling techniques, roadside with off-road coverage, our coverage with that of the volunteers, and different methods of quantifying Atlas results. The 7 1/2' (12-km) blocks used in the Maine Atlas are satisfactory for coarse mapping, but are too large to enable changes to be detected in the future. Most states are subdividing the standard 7 1/2' maps into six 5-km blocks. The random 1/6 sample of 5-km blocks used in New Hampshire, Vermont (published 1985), and many other states has the advantage of permitting detection of some changes in the future, but the disadvantage of leaving important habitats unsampled. The Maryland system of atlasing all 1,200 5-km blocks and covering one out of each six by quarterblocks (2 1/2-km) is far superior if enough observers can be found. A good compromise, not yet attempted, would be to Atlas a 1/6 random sample of 5-km blocks and also one other carefully selected (non-random) block on the same 7 1/2' map--the block that would include the best sample of habitats or elevations not in the random block. In our sample the second block raised the percentage of birds found from 86% of the birds recorded in the 7 1/2' quadrangle to 93%. It was helpful to list the expected species in each block and to revise this list annually. We estimate that 90-100 species could be found with intensive effort in most Maryland blocks; perhaps 95-105 in New Hampshire. It was also helpful to know which species were under-sampled so we could make a special effort to search for these. A total of 75 species per block (or 75% of the expected species in blocks with very restricted habitat diversity) is considered a practical and adequate goal in these States. When fewer than 60 species are found per block, a high proportion of the rarer species are missed, as well as some of

  13. ATLAS: civil engineering Point 1

    CERN Multimedia

    2000-01-01

    The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are busy to finish the different infrastructures for ATLAS. Real underground video. Nice view from the surface to the cavern from the pit side - all the big machines looked very small. The film has original working sound.

  14. 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.

  15. Lowering the first ATLAS toroid

    CERN Multimedia

    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.

  16. 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 ...

  17. 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.

  18. ATLAS Transition Radiation Tracker

    CERN Multimedia

    2006-01-01

    The ATLAS transition radiation tracker is made of 300'000 straw tubes, up to 144cm long. Filled with a gas mixture and threaded with a wire, each straw is a complete mini-detector in its own right. An electric field is applied between the wire and the outside wall of the straw. As particles pass through, they collide with atoms in the gas, knocking out electrons. The avalanche of electrons is detected as an electrical signal on the wire in the centre. The tracker plays two important roles. Firstly, it makes more position measurements, giving more dots for the computers to join up to recreate the particle tracks. Also, together with the ATLAS calorimeters, it distinguishes between different types of particles depending on whether they emit radiation as they make the transition from the surrounding foil into the straws.

  19. ATLAS IBL operational experience

    CERN Document Server

    Takubo, Yosuke; The ATLAS collaboration

    2016-01-01

    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.

  20. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    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 (Wʹ′ and Zʹ′), 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 poster, and the latest performance measurements are presented.

  1. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    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 (Wʹ and Zʹ), 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.

  2. ATLAS software packaging

    CERN Document Server

    Rybkin, G

    2012-01-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages - platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis pro...

  3. Jet Physics in ATLAS

    CERN Document Server

    Sandoval, C; The ATLAS collaboration

    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 and 8 TeV centre-of-mass LHC operation periods allows QCD to be probed at distances never reached before. We present a review of selected ATLAS jet physics measurements. These measurements constitute precision tests of QCD in a new energy regime, and show sensitivity to the parton densities in the proton and to the value of the strong coupling, alpha_s.

  4. Networks in ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; 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....

  5. 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....

  6. Supersymmetry searches in ATLAS

    CERN Document Server

    Torro Pastor, Emma; The ATLAS collaboration

    2016-01-01

    Weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  7. SUSY searches in ATLAS

    CERN Document Server

    ATLAS, C; The ATLAS collaboration

    2014-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  8. Supersymmetry Searches in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00237280; The ATLAS collaboration

    2015-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  9. SUSY Searches in ATLAS

    CERN Document Server

    Zhuang, Xuai; The ATLAS collaboration

    2016-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles, with focus on those obtained using proton-proton collisions at a centre of mass energy of 13 TeV using 2015+2016 data. The searches with final states including jets, missing transverse momentum, light leptons will be presented.

  10. Supersymmetry Searches with ATLAS

    CERN Document Server

    Hill, Ewan; The ATLAS collaboration

    2015-01-01

    Supersymmetry is one of the best motivated and studied theories of physics beyond the Standard Model. This talk summarises recent ATLAS results on searches for supersymmetric particles. Weak and strong production Supersymmetry scenarios are considered, along with direct production of third generation supersymmtric particles. The searches involve final states including jets, missing transverse momentum, leptons, and long lived particles. Sensitivity projections for the 13 TeV data are also presented.

  11. Overview of ATLAS results

    CERN Document Server

    Grabowska-Bold, Iwona; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the Large Hadron Collider has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This talk presents recent results based on Run 2 data on production of jet, electroweak bosons and quarkonium, electromagnetic processes in ultra-peripheral collisions, and bulk particle collectivity from PbPb, pPb and pp collisions.

  12. ATLAS reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bartsch, R.R.

    1995-09-01

    Key elements of the 36 MJ ATLAS capacitor bank have been evaluated for individual probabilities of failure. These have been combined to estimate system reliability which is to be greater than 95% on each experimental shot. This analysis utilizes Weibull or Weibull-like distributions with increasing probability of failure with the number of shots. For transmission line insulation, a minimum thickness is obtained and for the railgaps, a method for obtaining a maintenance interval from forthcoming life tests is suggested.

  13. ATLAS support rails

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    These supports will hold the 7000 tonne ATLAS detector in its cavern at the LHC. The huge toroid will be assembled from eight coils that will house some of the muon chambers. Supported within the toroid will be the inner detector, containing tracking devices, as well as devices to measure the energies of the particles produced in the 14 TeV proton-proton collisions at the LHC.

  14. The ATLAS Experiment Movie

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  15. Top physics at ATLAS

    CERN Document Server

    Romano, M

    2016-01-01

    This paper is an overview of recent results on top-quark physics obtained by the ATLAS Collaboration from the analysis of pp collisions at $\\sqrt s$= 7 and 8TeV at the Large Hadron Collider. Total and differential top-quark pair (t$\\overline t$), single top and t$\\overline t$+$\\gamma$ cross-sections and top properties measurements are presented.

  16. Hybrid Atlas Models

    CERN Document Server

    Ichiba, Tomoyuki; Banner, Adrian; Karatzas, Ioannis; Fernholz, Robert

    2009-01-01

    We study Atlas-type models of equity markets with local characteristics that depend on both name and rank, and in ways that induce a stability of the capital distribution. Ergodic properties and rankings of processes are examined with reference to the theory of reflected Brownian motions in polyhedral domains. In the context of such models, we discuss properties of various investment strategies, including the so-called growth-optimal and universal portfolios.

  17. Higgs results from ATLAS

    Directory of Open Access Journals (Sweden)

    Chen Xin

    2016-01-01

    Full Text Available 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, bb̄, 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.

  18. El experimento ATLAS

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  19. L'esperimento ATLAS

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  20. 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...

  1. ATLAS Detector Upgrade Prospects

    CERN Document Server

    Dobre, Monica; The ATLAS collaboration

    2016-01-01

    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 f b −1 expected for LHC running to 3000 f b −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 ext...

  2. 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...

  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 du Liban

    Directory of Open Access Journals (Sweden)

    Ramez Philippe Maalouf

    2008-11-01

    Full Text Available Compte-rendu de l’ouvrage Atlas du Liban: territoires et société, sous la direction d’Éric Verdeil, Ghaleb Faour et Sébastien Velut, édition franco-libanaise de l’IFPO (Institut Français du Proche-Orient et du CNRS Liban (Conseil National de la Recherche Scientifique – Liban, Beyrouth 2007.Resenha do livro Atlas du Liban: territoires et société, sob a direção de Éric Verdeil, Ghaleb Faour e Sébastien Velut, editado por iniciativa franco-libanesa do IFPO (Institut Français du Proche-Orient e pelo CNRS Liban (Conseil National de la Recherche Scientifique – Liban, Beirute, 2007.Review of Atlas du Liban: territoires et société, edited by Éric Verdeil, Ghaleb Faour and Sébastien Velut, french-lebanese edition by IFPO (Institut Français du Proche-Orient and CNRS Liban (Conseil National de la Recherche Scientifique – Liban Beirut, 2007.

  5. 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...

  6. 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...

  7. 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...

  8. ATLAS: Forecasting Falling Rocks

    Science.gov (United States)

    Heinze, Aren; Tonry, John L.; Denneau, Larry; Stalder, Brian; Sherstyuk, Andrei

    2016-10-01

    The Asteroid Terrestrial-impact Last Alert System (ATLAS) is a new asteroid survey aimed at detecting small (10-100 meter) asteroids inbound for impact with Earth. Relative to the larger objects targeted by most surveys, these small asteroids pose very different threats to our planet. Large asteroids can be seen at great distances and measured over many years, resulting in precise orbits that enable long-term impact predictions. If an impact were predicted, a costly deflection mission would be warranted to avert global catastrophe -- but a large asteroid impact is very unlikely in the next century. By contrast, impacts from small asteroids are inevitable. Such objects can be detected only during close encounters with Earth -- encounters too brief to yield long-term predictions. Only a few days' warning could be expected for an impactor in the 10-100 meter range, but fortunately the impact of such an asteroid would cause only regional damage. As in the case of a hurricane, a quixotic attempt to deflect or destroy it would be more expensive than the damage from its impact. A better response is to save human lives by evacuating the impact zone, and then rebuild. Only a few days warning are needed for this purpose, and ATLAS is unique among asteroid surveys in being optimized to provide it. While the optimization has many facets, the most important is rapidly surveying the entire accessible sky. A small asteroid could come from any direction and go from invisibility to impact in less than a week: ATLAS must look everywhere, all the time. Sky coverage is more important than exquisite sensitivity to faint objects, because asteroids inbound for impact will eventually become quite bright. This makes ATLAS complementary to other surveys, which scan the sky at a more leisurely pace but are able to detect asteroids at greater distances. We report on ATLAS' first year of survey operations, including the maturing of robotic observation and detection strategies, and asteroid and

  9. 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

  10. 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...

  11. The Pig PeptideAtlas

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM...

  12. 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.

  13. The new European wind atlas

    DEFF Research Database (Denmark)

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

    2014-01-01

    database. Although the project participants will come from the 27 member states it is envisioned that the project will be opened for global participation through test benches for model development and sharing of data – climatologically as well as experimental. Experiences from national wind atlases...... will be utilized, such as the Indian, the South African, the Finnish, the German, the Canadian atlases and others....... 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...

  14. Jet energy calibration in ATLAS

    CERN Document Server

    Schouten, Doug

    A correct energy calibration for jets is essential to the success of the ATLAS experi- ment. In this thesis I study a method for deriving an in situ jet energy calibration for the ATLAS detector. In particular, I show the applicability of the missing transverse energy projection fraction method. This method is shown to set the correct mean energy for jets. Pileup effects due to the high luminosities at ATLAS are also stud- ied. I study the correlations in lateral distributions of pileup energy, as well as the luminosity dependence of the in situ calibration metho

  15. 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.

  16. Electrons and Photons at ATLAS

    CERN Document Server

    Heim, Sarah; The ATLAS collaboration

    2016-01-01

    The performance of the reconstruction, calibration and identification of electrons and photons with the ATLAS detector at the LHC is a key component to realize the ATLAS full physics potential, both in the searches for new physics and in precision measurements. The algorithms used for the reconstruction and identification of electrons and photons with the ATLAS detector during LHC run 2 are presented. Measurements of the identification efficiencies are derived from data. The results from the 2015 pp collision data set at sqrt(s)=13 TeV are reported. The electron and photon energy calibration procedure and its performance are also discussed.

  17. Common atlas format and 3D brain atlas reconstructor: infrastructure for constructing 3D brain atlases.

    Science.gov (United States)

    Majka, Piotr; Kublik, Ewa; Furga, Grzegorz; Wójcik, Daniel Krzysztof

    2012-04-01

    One of the challenges of modern neuroscience is integrating voluminous data of diferent modalities derived from a variety of specimens. This task requires a common spatial framework that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume. The 3D atlases available so far have been created using frameworks which make it difficult for other researchers to replicate the results. To facilitate reproducible research and data sharing in the field we propose an SVG-based Common Atlas Format (CAF) to store 2D atlas delineations or other compatible data and 3D Brain Atlas Reconstructor (3dBAR), software dedicated to automated reconstruction of three-dimensional brain structures from 2D atlas data. The basic functionality is provided by (1) a set of parsers which translate various atlases from a number of formats into the CAF, and (2) a module generating 3D models from CAF datasets. The whole reconstruction process is reproducible and can easily be configured, tracked and reviewed, which facilitates fixing errors. Manual corrections can be made when automatic reconstruction is not sufficient. The software was designed to simplify interoperability with other neuroinformatics tools by using open file formats. The content can easily be exchanged at any stage of data processing. The framework allows for the addition of new public or proprietary content.

  18. ATLAS software packaging

    Science.gov (United States)

    Rybkin, Grigory

    2012-12-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages—platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis projects (currently 6) used by particular physics groups on top of the full release. The tools provide an installation test for the full distribution kit. Packaging is done in two formats for use with the Pacman and RPM package managers. The tools are functional on the platforms supported by ATLAS—GNU/Linux and Mac OS X. The packaged software is used for software deployment on all ATLAS computing resources from the detector and trigger computing farms, collaboration laboratories computing centres, grid sites, to physicist laptops, and CERN VMFS and covers the use cases of running all applications as well as of software development.

  19. 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

  20. 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...

  1. Forward Physics at the ATLAS experiment

    CERN Document Server

    The ATLAS collaboration

    2009-01-01

    Poster summarize forward physics at the ATLAS experiment. It aims to AFP project which is the project to install forward detectors at 220m (AFP220) and 420m (AFP420) around ATLAS for measurements at high luminosity.

  2. EnviroAtlas - Portland, OR - Block Groups

    Data.gov (United States)

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

  3. 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...

  4. EnviroAtlas - Metrics for Memphis, TN

    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). The layers in this web service...

  5. The ATLAS Trigger Muon "Vertical Slice"

    CERN Document Server

    Sidoti, A; Biglietti, M; Carlino, G; Cataldi, G; Conventi, F; Del Prete, T; Di Mattia, A; Falciano, S; Gorini, S; Kanaya, N; Kohno, T; Krasznahorkay, A; Lagouri, T; Luci, C; Luminari, L; Marzano, F; Nagano, K; Nisati, A; Panikashvili, N; Pasqualucci, E; Primavera, M; Scannicchio, D A; Spagnolo, S; Tarem, S; Tarem, Z; Tokushuku, K; Usai, G; Ventura, A; Vercesi, V; Yamazaki, Y; 10th Pisa Meeting on Advanced Detectors : Frontier Detectors For Frontier Physics

    2007-01-01

    The muon trigger system is a fundamental component of the ATLAS detector at the LHC collider. In this paper we describe the ATLAS multi-level trigger selecting events with muons: the Muon Trigger Slice.

  6. 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...

  7. EnviroAtlas - Metrics for Phoenix, AZ

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  8. EnviroAtlas - Metrics for Paterson, NJ

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  9. 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.

  10. EnviroAtlas - Metrics for Fresno, CA

    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). The layers in this web service...

  11. EnviroAtlas - Milwaukee, WI - Block Groups

    Data.gov (United States)

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

  12. EnviroAtlas - Metrics for Woodbine, IA

    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). The layers in this web service...

  13. EnviroAtlas - Metrics for Pittsburgh, PA

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  14. EnviroAtlas - Metrics for Milwaukee, WI

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (http://www.epa.gov/enviroatlas). The layers in these web...

  15. ATLAS : civil engineering at Point 1

    CERN Multimedia

    2002-01-01

    The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are ever so busy to finish the different infrastructures for ATLAS. Real underground video.

  16. 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...

  17. 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...

  18. EnviroAtlas - Metrics for Portland, OR

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (http://www.epa.gov/enviroatlas). The layers in these web...

  19. EnviroAtlas - Metrics for Portland, ME

    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). The layers in this web service...

  20. EnviroAtlas - Metrics for Tampa, FL

    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). The layers in this web service...

  1. EnviroAtlas - Metrics for Durham, NC

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The layers in these web...

  2. EnviroAtlas - Paterson, NJ - Block Groups

    Data.gov (United States)

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

  3. EnviroAtlas - Memphis, TN - Block Groups

    Data.gov (United States)

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

  4. 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...

  5. Supersymmetry searches in ATLAS

    CERN Document Server

    Kuwertz, Emma Sian; The ATLAS collaboration

    2015-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, including those those tagged as originating from b-quark decays, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures. An overview of the constraints on supersymmetry from the run1 results is presented, as well as sensitivity projections for the data that will be collected in 2015.

  6. Supersymmetry searches in ATLAS

    CERN Document Server

    Meloni, Federico; The ATLAS collaboration

    2015-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures. Sensitivity projections for the data that will be collected in 2015 are also presented.

  7. 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.

  8. ATLAS Exotic Searches

    Directory of Open Access Journals (Sweden)

    Bousson Nicolas

    2012-06-01

    Full Text Available 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.

  9. The ATLAS Simulation Software

    CERN Document Server

    Marshall, Z

    2008-01-01

    We present the status of the ATLAS Simulation Pro ject. Recent detector description improvements have focussed on commissioning layouts, implementation of inert material, and comparisons to the as-built detector. Core Simulation is reviewed with a focus on parameter optimizations, physics list choices, visualization, large-scale production, and validation. A fast simulation is also briefly described, and its performance is evaluated with respect to the full Simulation. Digitization, the last step of the Monte Carlo chain, is described, including developments in pile up and data overlay.

  10. 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.

  11. VH WW in ATLAS

    CERN Document Server

    Kinghorn-taenzer, Joseph Peter; The ATLAS collaboration

    2015-01-01

    A search for Higgs boson production in association with a W or Z boson, in the H -> WW decay channel, is performed with a data sample collected with the ATLAS detector at the LHC in proton– proton collisions at centre-of-mass energies sqrt(s) = 7 TeV and 8 TeV, corresponding to integrated luminosities of 4.5 fb-1 and 20.3 fb-1, respectively. The WH production mode is studied in two-lepton and three-lepton final states, while two-lepton and four-lepton final states are used to search for the ZH production mode.

  12. Overview of ATLAS results

    CERN Document Server

    Grabowska-Bold, Iwona; The ATLAS collaboration

    2016-01-01

    The heavy-ion programme in the ATLAS experiment at the Large Hadron Collider aims to probe and characterise hot and dense matter created in relativistic lead-lead collisions. Moreover, smaller collision systems involving nuclei and hadrons are of interest to disentangle initial- from final-state effects. This report presents new results based on lead-lead and proton-proton data collected at √sNN = 5.02 TeV in 2015, including measurements of bulk collectivity, charged-particle production, electroweak bosons, photon-jet correlations, and quarkonium suppression. First attempts to measure electromagnetic processes in ultra-peripheral collisions are also discussed.

  13. Supersymmetry searches in ATLAS

    CERN Document Server

    Meloni, Federico; The ATLAS collaboration

    2015-01-01

    This document summarises recent ATLAS results for searches for supersymmetric particles using LHC proton-proton collision data. Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. We consider both R-Parity conserving and R-Parity violating SUSY scenarios. The searches involve final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures. Sensitivity projections for the data that will be collected in 2015 are also presented.

  14. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    Budker Nuclear Physics Institute, Novosibirsk Sequence 1 Reception for Markus Nordberg and Andrew Millington by about 20 physicists from the Budker Nuclear Physics Institute Host: Yuri Tikhonov Various short talks and exchanges, with coffee Sequence 2 Visit to BINP Facilities Tikhonov and Nordberg walking and talking Visit to electron accelerator, old solar detector Sequence 3 Visit to BNIP workshops Work on big wheel segments shots over-exposed Work on Atlas coils LHC Magnets Men playing chess, exterior shots of Tikhonov, Nordberg arriving Sequence 4 Shots from car of journey from workshop to main BNIP building.

  15. ATLAS Style Guide

    CERN Document Server

    Eisenhandler, E F

    2008-01-01

    This is a compendium of rules, recommendations, information and advice for writing papers and notes within the ATLAS Experiment at the CERN Large Hadron Collider. It covers what to include in the paper, and some general guidelines and specific points about writing a scientific paper. There are sections on the use of English (though it is not a guide to grammar), punctuation, and typography. Advice about the use of LATEX is given in the main text, and there is an appendix on software tools containing general comments about LATEX and information on using Microsoft Word. Currently on version 2.6, 3 March 2017, 47pp.

  16. Dark Matter in ATLAS

    CERN Document Server

    Resconi, Silvia; The ATLAS collaboration

    2016-01-01

    Results of Dark Matter searches in mono-X analysis with the ATLAS experiment at the Large Hadron Collider are reported. The data were collected in proton–proton collisions at a centre-of-mass energy of 13 TeV and correspond to an integrated luminosity of 3.2 fb-1. A description of the main characteristics of each analysis and how the main backgrounds are estimated is shown. The observed data are in agreement with the expected Standard Model backgrounds for all analysis described. Exclusion limits are presented for Dark Matter models including pair production of dark matter candidates.

  17. ATLAS Muon Detector Commissioning

    CERN Document Server

    Diehl, E

    2009-01-01

    The ATLAS muon spectrometer consists of several major components: Monitored Drift Tubes (MDTs) for precision measurements in the bending plane of the muons, supplemented by Cathode Strip Chambers (CSC) in the high eta region; Resistive Plate Chambers (RPCs) and Thin Gap Chambers (TGCs) for trigger and second coordinate measurement in the barrel and endcap regions, respectively; an optical alignment system to track the relative positions of all chambers; and, finally, the world's largest air-core magnetic toroid system. We will describe the status and commissioning of the muon system with cosmic rays and plans for commissioning with early beams.

  18. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    CPPM Laboratory Marseille Starting with the Workshop- adding modules to the strip 00:09:19 Exterior-entering the lab site by car, Sascha Rosanov and a PR lady walking, Lab sign on building -Physique des Particules de Marseille 00:20:00 Interviews of the ATLAS pixel work for bio-mediacal research 00:34:00 Interview of Roy Aleksov, Head of CPPM Laboratory, Working in international team, working with CERN and GRID The rest of the film inclusdes lab testingand some exterior shots.

  19. ATLAS top quark results

    CERN Document Server

    Menke, Sven; The ATLAS collaboration

    2017-01-01

    The top quark is the heaviest known fundamental particle. As it is the only quark that decays before it hadronises, analyses of events containing top quarks allow to probe the properties of bare quarks and to test perturbative QCD. This talk will focus on recent precision top-quark measurements by the ATLAS Collaboration: Single top-quark and top-quark pair production cross sections including differential distributions will be presented, as well as measurements of top-quark pair production in association with a W or Z boson and measurements of top quark properties such as the spin correlation and W boson helicity in top quark pair events.

  20. 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...

  1. ATLAS DDM integration in ARC

    DEFF Research Database (Denmark)

    Behrmann, Gerd; Cameron, David; Ellert, Mattias;

    The Nordic Data Grid Facility (NDGF) consists of Grid resources running ARC middleware in Scandinavia and other countries. 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 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...... 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....

  2. 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...

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. ATLAS Civil Engineering Point 1

    CERN Multimedia

    2001-01-01

    Different phases of realisation to Point 1: zone of the ATLAS experiment 14-02-2001Realising anchorage, isolations and scaffoldings at UX 15 18-04-2001Concreting the arch and posing the metal reinforcements at UX 15

  9. 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...

  10. 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...

  11. The atlas of endangered species

    National Research Council Canada - National Science Library

    Mackay, R

    2009-01-01

    Vividly illustrated with full-color maps and detailed graphics, The Atlas of Endangered Species catalogs the inhabitants of a wide variety of ecosystems, including forests, mangroves, and coral reefs...

  12. ATLAS online data quality monitoring

    CERN Document Server

    Cuenca Almenar, C; The ATLAS collaboration; Hadavand, H; Ilchenko, Y; Kolos, S; Slagle, K; Taffard, A

    2010-01-01

    Every minute the ATLAS detector is taking data, the monitoring framework serves several thousands physics events to monitoring data analysis applications, handles millions of histogram updates coming from thousands applications, executes over forty thousand advanced data quality checks for a subset of those histograms, displays histograms and results of these checks on several dozens of monitors installed in main and satellite ATLAS control rooms. The online data quality monitoring system has been of great help in providing quick feedback to the subsystems about the functioning and performance of the different parts of ATLAS by providing a configurable easy and fast visualization of all this information. The Data Quality Monitoring Display (DQMD) is a visualization tool for the automatic data quality assessment of the ATLAS experiment. It is the interface through which the shift crew and experts can validate the quality of the data being recorded or processed, be warned of problems related to data quality, an...

  13. BioFuels Atlas (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, K.

    2011-02-01

    Presentation for biennial merit review of Biofuels Atlas, a first-pass visualization tool that allows users to explore the potential of biomass-to-biofuels conversions at various locations and scales.

  14. ATLAS discoveries of optical transients

    Science.gov (United States)

    Tonry, J.; Denneau, L.; Stalder, B.; Heinze, A.; Sherstyuk, A.; Rest, A.; Smith, K. W.; Smartt, S. J.

    2016-09-01

    We report the following transients found by the ATLAS survey (see Tonry et al. ATel #8680). ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is operational on Haleakala is robotically surveying the sky. Two filters are used, cyan and orange (denoted c and o, all mags in AB system), more information is on http://www.fallingstar.com.

  15. Composition of the ATLAS Collaboration

    CERN Document Server

    Pater, Joleen; The ATLAS collaboration

    2016-01-01

    The ATLAS collaboration consists of about 5,000 members from 178 institutes in 38 countries. About half of the members of the collaboration are scientific authors of the papers, and there are about 1,200 students in the collaboration. This note presents data showing aspects of the composition of the collaboration; in particular the relative fraction of women is described at several levels within the hierarchy of the ATLAS experiment.

  16. ATLAS discoveries of optical transients

    Science.gov (United States)

    Tonry, J.; Denneau, L.; Stalder, B.; Heinze, A.; Sherstyuk, A.; Rest, A.; Smith, K. W.; Smartt, S. J.

    2016-10-01

    We report the following transients found by the ATLAS survey (see Tonry et al. ATel #8680). ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is operational on Haleakala is robotically surveying the sky. Two filters are used, cyan and orange (denoted c and o, all mags in AB system), more information is on http://www.fallingstar.com.

  17. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    2000-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment The film is about the excavation work in the cavern and tunnels of ATLAS experiment in the point 1. You can see people working for iron mounting at the side of the pit where the parts of the detector will be lowered in the future. Partly the film concentrates the USA 15 and the work done there.

  18. ATLAS Overview Week 2009 Barcelona

    CERN Multimedia

    Claudia Marcelloni

    2009-01-01

    From October 5th to October 9th about 400 physicists from the ATLAS Collaboration met in Barcelona (Catalonia) to discuss the status of the experiment. The event was organized by the Institut de Física d'Altes Energies (IFAE), a member of the ATLAS Collaboration. Besides the Scientific program, few social events were organized, such as Reception at the Palau de Pedralbes, a visit to the Fundacio Joan Miro and a social dinner at Maremagnunm hall.

  19. Higgs boson measurements at ATLAS

    CERN Document Server

    Hays, Chris; The ATLAS collaboration

    2016-01-01

    A comprehensive set of Higgs boson measurements has been performed in pp collisions produced by the Large Hadron Collider at centre-of-mass energies of 7 and 8 TeV, and the results combined between the ATLAS and CMS experiments. Recent results from ATLAS at a centre-of-mass energy of 13 TeV are consistent with expectations. With more data available, additional Higgs boson processes are on the cusp of observation, while measured processes promise improved precision.

  20. Other Exotic States in ATLAS

    CERN Document Server

    Tu, Yanjun; The ATLAS collaboration

    2017-01-01

    Many theories beyond the Standard Model (BSM) predict new phenomena accessible by the LHC. Searches for new physics models are performed using the ATLAS experiment at the LHC focusing on exotic signatures that can cover serval BSM theories. The results reported here use the pp collision data sample collected in 2015 and 2016 by the ATLAS detector at the LHC with a centre-of-mass energy of 13 TeV.

  1. Transporting the first ATLAS toroid

    CERN Multimedia

    Maximilien Brice

    2004-01-01

    The first coil for the ATLAS toroid magnet is transported from its assembly hall at the CERN Meyrin site to the storage hall above the ATLAS cavern. This involves driving the massive transportation vehicle first through the Meyrin site and then across a main road only metres from the France-Swiss border. Eight magnets in total will be transported in this way before being lowered into the experimental cavern where they will be mounted in a huge ring surrounding the detector.

  2. Neonatal atlas construction using sparse representation.

    Science.gov (United States)

    Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H; Lin, Weili; Shen, Dinggang

    2014-09-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases.

  3. 27 CFR 9.140 - Atlas Peak.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Atlas Peak. 9.140 Section... THE TREASURY LIQUORS AMERICAN VITICULTURAL AREAS Approved American Viticultural Areas § 9.140 Atlas Peak. (a) Name. The name of the viticultural area described in this section is “Atlas Peak.”...

  4. 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...

  5. 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.

  6. 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.

  7. Reconstructing cancer genomes from paired-end sequencing data

    Directory of Open Access Journals (Sweden)

    Oesper Layla

    2012-04-01

    Full Text Available Abstract Background A cancer genome is derived from the germline genome through a series of somatic mutations. Somatic structural variants - including duplications, deletions, inversions, translocations, and other rearrangements - result in a cancer genome that is a scrambling of intervals, or "blocks" of the germline genome sequence. We present an efficient algorithm for reconstructing the block organization of a cancer genome from paired-end DNA sequencing data. Results By aligning paired reads from a cancer genome - and a matched germline genome, if available - to the human reference genome, we derive: (i a partition of the reference genome into intervals; (ii adjacencies between these intervals in the cancer genome; (iii an estimated copy number for each interval. We formulate the Copy Number and Adjacency Genome Reconstruction Problem of determining the cancer genome as a sequence of the derived intervals that is consistent with the measured adjacencies and copy numbers. We design an efficient algorithm, called Paired-end Reconstruction of Genome Organization (PREGO, to solve this problem by reducing it to an optimization problem on an interval-adjacency graph constructed from the data. The solution to the optimization problem results in an Eulerian graph, containing an alternating Eulerian tour that corresponds to a cancer genome that is consistent with the sequencing data. We apply our algorithm to five ovarian cancer genomes that were sequenced as part of The Cancer Genome Atlas. We identify numerous rearrangements, or structural variants, in these genomes, analyze reciprocal vs. non-reciprocal rearrangements, and identify rearrangements consistent with known mechanisms of duplication such as tandem duplications and breakage/fusion/bridge (B/F/B cycles. Conclusions We demonstrate that PREGO efficiently identifies complex and biologically relevant rearrangements in cancer genome sequencing data. An implementation of the PREGO algorithm is

  8. 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...

  9. 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...

  10. ATLAS Christmas lunch

    CERN Multimedia

    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...

  11. 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.

  12. 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...

  13. 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....

  14. 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.

  15. 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...

  16. 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...

  17. 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...

  18. The ATLAS Event Builder

    CERN Document Server

    Vandelli, W; Battaglia, A; Beck, H P; Blair, R; Bogaerts, A; Bosman, M; Ciobotaru, M; Cranfield, R; Crone, G; Dawson, J; Dobinson, Robert W; Dobson, M; Dos Anjos, A; Drake, G; Ermoline, Y; Ferrari, R; Ferrer, M L; Francis, D; Gadomski, S; Gameiro, S; Gorini, B; Green, B; Haberichter, W; Haberli, C; Hauser, R; Hinkelbein, C; Hughes-Jones, R; Joos, M; Kieft, G; Klous, S; Korcyl, K; Kordas, K; Kugel, A; Leahu, L; Lehmann, G; Martin, B; Mapelli, L; Meessen, C; Meirosu, C; Misiejuk, A; Mornacchi, G; Müller, M; Nagasaka, Y; Negri, A; Pasqualucci, E; Pauly, T; Petersen, J; Pope, B; Schlereth, J L; Spiwoks, R; Stancu, S; Strong, J; Sushkov, S; Szymocha, T; Tremblet, L; Ünel, G; Vermeulen, J; Werner, P; Wheeler-Ellis, S; Wickens, F; Wiedenmann, W; Yu, M; Yasu, Y; Zhang, J; Zobernig, H; 2007 IEEE Nuclear Science Symposium and Medical Imaging Conference

    2008-01-01

    Event data from proton-proton collisions at the LHC will be selected by the ATLAS experiment in a three-level trigger system, which, at its first two trigger levels (LVL1+LVL2), reduces the initial bunch crossing rate of 40~MHz to $sim$3~kHz. At this rate, the Event Builder collects the data from the readout system PCs (ROSs) and provides fully assembled events to the Event Filter (EF). The EF is the third trigger level and its aim is to achieve a further rate reduction to $sim$200~Hz on the permanent storage. The Event Builder is based on a farm of O(100) PCs, interconnected via a Gigabit Ethernet to O(150) ROSs. These PCs run Linux and multi-threaded software applications implemented in C++. All the ROSs, and substantial fractions of the Event Builder and Event Filter PCs have been installed and commissioned. We report on performance tests on this initial system, which is capable of going beyond the required data rates and bandwidths for Event Building for the ATLAS experiment.

  19. ATLAS Future Upgrade

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00225024; 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. In parallel, the experiments need to be keep lockstep with the accelerator to accommodate running beyond the nominal luminosity this decade. Along with maintenance and consolidation of the detector in the past few years, ATLAS has added inner b-layer to its tracking system. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requir...

  20. The Origin of the Term 'Atlas'

    Directory of Open Access Journals (Sweden)

    Miljenko Lapaine

    2008-05-01

    Full Text Available In this paper the origin of the term 'atlas', as a bound collection of maps, is considered. It is usually thought to derive from the name of the Titan, Atlas, who was punished by being forced to bear the entire celestial sphere or universe on his shoulders. However, on the basis of research into and translation of the original Preface of Mercator's Atlas sive cosmographicae meditationes de fabrica mvndi et fabricati figvra, it has been determined that Mercator did not refer to this legend, but named his atlas for the completely different characteristics, such as wisdom, erudition and humanity, of another Atlas.

  1. 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.

  2. ATLAS Maintenance and Operation management system

    CERN Multimedia

    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.

  3. 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...

  4. EnviroAtlas - Metrics for Des Moines, IA

    Data.gov (United States)

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

  5. 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...

  6. EnviroAtlas - Metrics for Minneapolis/St. Paul, MN

    Data.gov (United States)

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

  7. Association of cancer mortality with postdiagnosis overweight and obesity using body mass index

    OpenAIRE

    Xu, Xinsen; Zhou, Lei; Miao, Runchen; Chen, Wei; Zhou, Yanyan; Pang, Qing; Qu, Kai; Liu, Chang

    2015-01-01

    Although overweight and obesity increase cancer risk, it is still controversial with respect to cancer mortality. In the current study, we enrolled 2670 patients of 14 tumor types from the Cancer Genome Atlas (TCGA) project, to identify the prognostic role of overweight and obesity in cancer patients. After dividing the patients into different groups by the body mass index (BMI), we found significant lower mortality in the obesity group. In addition, we also treat BMI value as a binary catego...

  8. Genomic characterization of Campylobacter jejuni strain M1.

    Directory of Open Access Journals (Sweden)

    Carsten Friis

    Full Text Available Campylobacter jejuni strain M1 (laboratory designation 99/308 is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C. jejuni strain M1, and compared this to 12 other C. jejuni sequenced genomes currently publicly available. Compared to these, M1 is closest to strain 81116. Based on the 13 genome sequences, we have identified the C. jejuni pan-genome, as well as the core genome, the auxiliary genes, and genes unique between strains M1 and 81116. The pan-genome contains 2,427 gene families, whilst the core genome comprised 1,295 gene families, or about two-thirds of the gene content of the average of the sequenced C. jejuni genomes. Various comparison and visualization tools were applied to the 13 C. jejuni genome sequences, including a species pan- and core genome plot, a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1.

  9. A gene expression atlas of the domestic pig

    Directory of Open Access Journals (Sweden)

    Freeman Tom C

    2012-11-01

    Full Text Available Abstract Background This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering. Results The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development. Conclusions As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.

  10. 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 masts. The WRF modeling was done in a nested domain of high spatial resolution for 4 years. In addition the longterm wind statistics using the NCAR-NCEP reanalysis data were performed during 30 years to provide basis for a long-term adjustment of the results and the final WRF results include a weighting...... for the long-term trends variability in the South Baltic Sea. Observations from Earth observing satellites were used to evaluate the spatial resolution of the WRF model results near the surface. The QuikSCAT and the WRF results compared well whereas the Envisat ASAR mean wind map showed some variation...

  11. Exotic Physics at ATLAS

    Directory of Open Access Journals (Sweden)

    Meehan Samuel

    2014-04-01

    Full Text Available A number of proposed explanations to observed phenomena predict new physics that will be directly observable at the LHC. Each new theory is manifested in the experiments as an experimental signature that sets it apart from the many well understood Standard Model processes. Presented here is a summary of a selection of such searches performed using 8 TeV center of mass energy data produced by the LHC and collected with the ATLAS detector. As no significant deviations from the standard model are observed in any search channel presented here, the results are interpreted in terms of constraints on new physics in a number of scenarios including dark matter, sequential standard model extensions, and model independent interpretations depending on the given search channel.

  12. 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.

  13. ATLAS Top Quark Results

    CERN Document Server

    Black, Kevin; The ATLAS collaboration

    2017-01-01

    The top quark is the heaviest known fundamental particle. As it is the only quark that decays before it hadronizes, this gives us the unique opportunity to probe the properties of bare quarks at the Large Hadron Collider. This talk will present highlights of a few recent precision measurements by the ATLAS Collaboration of the top quark using 13 TeV and 8 TeV collision data: top-quark pair and single top production cross sections including differential distributions will be presented alongside top quark properties measurements. These measurements, including results using boosted top quarks, probe our understanding of top quark production in the TeV regime. Measurements of the top quark mass and searches for rare top quark decays are also presented.

  14. BSM searches in ATLAS

    CERN Document Server

    Policicchio, Antonio

    2015-01-01

    Results are presented for searches beyond the Standard Model (SM) at the LHC by the ATLAS collaboration. The minimal supersymmetric extension of the SM has been investigated in various configurations at 8TeV center of mass energy at LHC and lower limits are set on the sparticle masses. The searches for other scenarios of physics beyond the SM are also presented. The data are found to be consistent with the Standard Model. The non-observation of a signal is converted to limits at the 95% confidence level (CL) on the production cross section times branching ratio and/or on the masses of the hypothezed new particles for appropriate benchmark models.

  15. ATLAS IBL sensor qualifiaction

    CERN Document Server

    Weingarten, J; The ATLAS collaboration

    2011-01-01

    The upgrade for the ATLAS detector will undergo different phases towards HL-LHC. The first upgrade for the Pixel Detector will consist in the construction of a new pixel layer which will be installed during the first shutdown of the LHC machine (foreseen for 2013-14). The new detector, called Insertable B-Layer (IBL), will be inserted between the existing pixel detector and a new (smaller radius) beam-pipe at a radius of 3.2 cm. The IBL will require the development of several new technologies to cope with increase of radiation or pixel occupancy and also to improve the physics performance which will be achieved by reduction of the pixel size and of the material budget. Two different promising Silicon sensor technologies (Planar n-in-n and 3D) are currently under investigation for the pixel detector. An overview of the sensor technologies qualification with particular emphasis on irradiation and beam tests will be presented.

  16. ATLAS IBL Sensor Qualification

    CERN Document Server

    Weingarten, J; The ATLAS collaboration

    2011-01-01

    The upgrade for the ATLAS detector will undergo different phases towards HL-LHC. The first upgrade for the Pixel Detector will consist in the construction of a new pixel layer which will be installed during the first shutdown of the LHC machine (foreseen for 2013-14). The new detector, called Insertable B-Layer (IBL), will be inserted between the existing pixel detector and a new (smaller radius) beam-pipe at a radius of 3.2 cm. The IBL will require the development of several new technologies to cope with increase of radiation or pixel occupancy and also to improve the physics performance which will be achieved by reduction of the pixel size and of the material budget. Two different promising Silicon sensor technologies (Planar n-in-n and 3D) are currently under investigation for the pixel detector. An overview of the sensor technologies qualification with particular emphasis on irradiation and beam tests will be presented.

  17. 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...

  18. Electroweak results from ATLAS

    CERN Document Server

    Glazov, S

    2012-01-01

    Measurements of single W and Z as well as diboson WW , WZ and ZZ production at the LHC performed by the ATLAS collaboration in 2010 and 2011 are presented. The data provide accurate tests of the theory in a wide kinematic range. A QCD analysis of the W and Z boson differential distributions reveals a novel sensitivity to the strange-quark density which is found to be large compared to previous expectations. Studies of W+b and Z+b jet production and W polarisation test NLO QCD calculations and proton PDFs. The diboson cross- section measurements are used to determine limits on the anomalous couplings. No deviation from the standard model is observed.

  19. The ATLAS central solenoid

    CERN Document Server

    Yamamoto, A; Ruber, R; Doi, Y; Haruyama, T; Haug, F; ten Kate, H; Kawai, M; Kondo, T; Kondo, Y; Metselaar, J; Mizumaki, S; Olesen, G; Pavlov, O; Ravat, S; Sbrissa, E; Tanaka, K; Taylor, T; Yamaoka, H

    2008-01-01

    The ATLAS detector at the CERN LHC is equipped with a superconducting magnet system consisting of three large toroids and a solenoid. The 2.3 m diameter, 5.3 m long solenoid is located at the heart of the experiment where it provides a 2 T field for spectrometry of the particles emanating from the interaction of the counter-rotating beams of hadrons. As the electromagnetic calorimeter of the experiment is situated outside the solenoid, the coil must be as transparent as possible to traversing particles. The magnet, which was designed at KEK, incorporates progress in technology coming from the development of previous solenoids of this type, in particular that of a new type of reinforced superconductor addressing the requirement of transparency. Special attention has been paid to ensuring reliability and ease of operation of the magnet, through the application of sufficiently conservative guidelines for the mechanical and electrical design, stringent testing during manufacture, and a comprehensive commissioning...

  20. ATLAS TRT barrel

    CERN Multimedia

    CERN Video Productions

    2005-01-01

    On 3 February 2005, members of the US-TRT team proceeded to the installation of the last TRT barrel module for the Transition Radiation Tracker, which will be used for tracking in the Atlas detector. The TRT barrel is made of 96 modules containing around 52 000 4-mm straws, each of them equipped with a 20 microns sense wire. The modules were first designed at CERN, then built in the USA between 1996 and 2003. Duke, Hampton and Indiana Universities, tested in details at CERN between 2003 and 2005 by members of the US-TRT group, and mounted on the support structure in the SR-1 building where this video was taken. During assembly of the last module, one can see Kirill Egorov (PNPI, Gatchina, Russia), Chuck Mahlong (Hampton) as well as John Callahan and Pauline Gagnon (Indiana). (Written by Pauline Gagnon)

  1. 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.

  2. 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.

  3. ATLAS IBL Pixel Upgrade

    CERN Document Server

    La Rosa, A

    2011-01-01

    The upgrade for ATLAS detector will undergo different phase towards super-LHC. The first upgrade for the Pixel detector will consist of the construction of a new pixel layer which will be installed during the first shutdown of the LHC machine (LHC phase-I upgrade). The new detector, called Insertable B-Layer (IBL), will be inserted between the existing pixel detector and a new (smaller radius) beam-pipe at a radius of 3.3 cm. The IBL will require the development of several new technologies to cope with increase of radiation or pixel occupancy and also to improve the physics performance which will be achieved by reducing the pixel size and of the material budget. Three different promising sensor technologies (planar-Si, 3D-Si and diamond) are currently under investigation for the pixel detector. An overview of the project with particular emphasis on pixel module is presented in this paper

  4. GenoMetric Query Language: a novel approach to large-scale genomic data management.

    Science.gov (United States)

    Masseroli, Marco; Pinoli, Pietro; Venco, Francesco; Kaitoua, Abdulrahman; Jalili, Vahid; Palluzzi, Fernando; Muller, Heiko; Ceri, Stefano

    2015-06-15

    Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art 'big data' computing strategies, with abstraction levels beyond available tool capabilities. We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic 'big data' analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets. The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. 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...

  6. 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...... outside the worker node environment. Also, the service used for cataloging the location of data files is different from otherGrids 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...

  7. 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...

  8. 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.

  9. EnviroAtlas - Des Moines, IA - EnviroAtlas Community Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Des Moines, IA EnviroAtlas Community. It represents the outside edge of all the block groups included in the...

  10. EnviroAtlas - Minneapolis/St. Paul, MN - EnviroAtlas Community Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Minneapolis/St. Paul, MN EnviroAtlas Community. It represents the outside edge of all the block groups included in...

  11. 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...

  12. 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...

  13. 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.

  14. 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...

  15. ATLAS honours two Swiss companies

    CERN Multimedia

    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...

  16. The Cambridge double star atlas

    CERN Document Server

    MacEvoy, Bruce; Mullaney, James; Tirion, Wil; Mullaney, James

    2015-01-01

    The Cambridge Double Star Atlas is back! It is the first and only atlas of physical double stars that can be viewed with amateur astronomical instruments. Completely rewritten, this new edition explains the latest research into double stars, and looks at the equipment, techniques and opportunities that will enable you to discover, observe and measure them. The target list has been completely revised and extended to 2500 binary or multiple systems. Each system is described with the most recent and accurate data from the authoritative Washington Double Star Catalog, including the HD and SAO numbers that are most useful in our digital age. Hundreds of remarks explain the attributes of local, rapidly changing, often measured or known orbital systems. The color atlas charts by Wil Tirion have been updated to help you easily find and identify the target systems, as well as other deep-sky objects. This is an essential reference for double star observers..

  17. European Atlas of Soil Biodiversity

    DEFF Research Database (Denmark)

    Krogh (contributor), Paul Henning

    on Earth, life within the soil is often hidden away and suffers by being 'out of sight and out of mind'. What kind of life is there in soil? What do we mean by soil biodiversity? What is special about soil biology? How do our activities affect soil ecosystems? What are the links between soil biota...... and climate change? The first ever European Atlas of Soil Biodiversity uses informative texts, stunning photographs and maps to answer these questions and other issues. The European Atlas of Soil Biodiversity functions as a comprehensive guide allowing non-specialists to access information about this unseen...... Biodiversity'. Starting with the smallest organisms such as the bacteria, this segment works through a range of taxonomic groups such as fungi, nematodes, insects and macro-fauna to illustrate the astonishing levels of heterogeneity of life in soil. The European Atlas of Soil Biodiversity is more than just...

  18. ATLAS Nightly Build System Upgrade

    CERN Document Server

    Dimitrov, G; The ATLAS collaboration; Simmons, B; Undrus, A

    2014-01-01

    The ATLAS Nightly Build System is a facility for automatic production of software releases. Being the major component of ATLAS software infrastructure, it supports more than 50 multi-platform branches of nightly releases and provides ample opportunities for testing new packages, for verifying patches to existing software, and for migrating to new platforms and compilers. The Nightly System testing framework runs several hundred integration tests of different granularity and purpose. The nightly releases are distributed and validated, and some are transformed into stable releases used for data processing worldwide. The first LHC long shutdown (2013-2015) activities will elicit increased load on the Nightly System as additional releases and builds are needed to exploit new programming techniques, languages, and profiling tools. This paper describes the plan of the ATLAS Nightly Build System Long Shutdown upgrade. It brings modern database and web technologies into the Nightly System, improves monitoring of nigh...

  19. ATLAS Nightly Build System Upgrade

    CERN Document Server

    Dimitrov, G; The ATLAS collaboration; Simmons, B; Undrus, A

    2013-01-01

    The ATLAS Nightly Build System is a facility for automatic production of software releases. Being the major component of ATLAS software infrastructure, it supports more than 50 multi-platform branches of nightly releases and provides ample opportunities for testing new packages, for verifying patches to existing software, and for migrating to new platforms and compilers. The Nightly System testing framework runs several hundred integration tests of different granularity and purpose. The nightly releases are distributed and validated, and some are transformed into stable releases used for data processing worldwide. The first LHC long shutdown (2013-2015) activities will elicit increased load on the Nightly System as additional releases and builds are needed to exploit new programming techniques, languages, and profiling tools. This paper describes the plan of the ATLAS Nightly Build System Long Shutdown upgrade. It brings modern database and web technologies into the Nightly System, improves monitoring of nigh...

  20. ATLAS online data quality monitoring

    CERN Document Server

    Cuenca Almenar, C; The ATLAS collaboration

    2010-01-01

    With the delivery of the first proton-proton collisions by the LHC, the ATLAS collaboration had the opportunity to operate the detector under the environment it was designed for. These first events have been of great interest not only for the high energy physics outcome, but also as a means to perform a general commissioning of system. A highly scalable distributed monitoring framework assesses the quality of the data and the operational conditions of the detector, trigger and data acquisition system. Every minute of an ATLAS data taking session the monitoring framework serves several thousands physics events to monitoring data analysis applications, handles millions of histogram updates coming from thousands applications, executes over forty thousand advanced data quality checks for a subset of those histograms, displays histograms and results of these checks on several dozens of monitors installed in main and satellite ATLAS control rooms. The online data quality monitoring system has been of great help in ...

  1. 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 ...

  2. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  3. The ATLAS Forward Physics Program

    CERN Document Server

    Pinfold, J L

    2009-01-01

    The ATLAS forward physics program is discussed in the light of the future detector upgrades under study. These developments will enhance the overall physics potential of the experiment. The physics topics presented include: luminosity determination using the LUCID and ALFA detectors; diffractive measurements that should be possible with early data; and, the AFP project which plans to deploy proton taggers at 220 and 420 m from the ATLAS IP. The AFP program includes such physics topics as hard diffraction; diffractive Higgs production,two photon physics; and, new physics in the forward region.

  4. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    1998-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment After watching this film you can get the view of the civil engineering work at POINT1 where the ATLAS will be built. 03-11-1998 The video starts with the view of the POINT1 taken from the roof of the building 33. 04-11-1998 View of the installation of the entrance of the SDX1 18/19-11-1998 Installation of the rafters to the building PX15

  5. 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.

  6. 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.

  7. 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...

  8. Continental Atlas of Poland for Automobilists – the first road atlas in the independent Poland

    Directory of Open Access Journals (Sweden)

    Rutkowski Jan

    2015-07-01

    Full Text Available The 90th anniversary of the appearance of Atlas Polski Continental dla automobilistów (Continental Atlas of Poland for Automobilists published by Continental Caoutchouc Compagnie Ltd Warsaw is nearing. The Atlas was the first publication of its kind after Poland had regained its independence in 1918.

  9. Evolution of the ATLAS Nightly Build System

    CERN Document Server

    Undrus, A

    2012-01-01

    The ATLAS Nightly Build System is a major component in the ATLAS collaborative software organization, validation, and code approval scheme. For over 10 years of development it has evolved into a factory for automatic release production and grid distribution. The 50 multi-platform branches of ATLAS releases provide vast opportunities for testing new packages, verification of patches to existing software, and migration to new platforms and compilers for ATLAS code that currently contains 2200 packages with 4 million C++ and 1.4 million python scripting lines written by about 1000 developers. Recent development was focused on the integration of ATLAS Nightly Builds and Installation systems. The nightly releases are distributed and validated and some are transformed into stable releases used for data processing worldwide. The ATLAS Nightly System is managed by the NICOS control tool on a computing farm with 50 powerful multiprocessor nodes. NICOS provides the fully automated framework for the release builds, test...

  10. Luminosity measurements in ATLAS with MPX detectors

    Energy Technology Data Exchange (ETDEWEB)

    Sopczak, Andre; Benes, Petr; Bergmann, Benedikt; Biskup, Bartolomej; Jakubek, Jan; Pospisil, Stanislav; Solc, Jaroslav; Sopko, Vit; Suk, Michal; Turecek, Daniel; Vykydal, Zdenek [IEAP CTU Prague (Czech Republic); Asbah, Nedaa; Leroy, Claude; Soueid, Paul [Universite de Montreal (Canada)

    2013-07-01

    The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are successfully operating in the ATLAS detector at 16 places and collect data independent of the ATLAS data-recording chain. Recently it has been recognized that these detectors are well suited for luminosity measurements. Results from these studies are presented.

  11. Inauguration of the ATLAS cavern, June 2003.

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Before the inauguration, Pascal Couchepin visited the ATLAS cavern. From left to right: Peter Jenni, ATLAS spokesman; Maurice Bourquin, President of the CERN Council; Carlo Lamprecht, State councillor, Canton of Geneva; Pascal Couchepin, President of the Swiss Confederation; Luciano Maiani, CERN Director-General; Marzio Nessi, ATLAS technical coordinator; Arturo Henniger, ZSCHOKKE-LOCHER AG Director; Benno Baettig, personal advisor of President Couchepin; Jean-Luc Baldy, head of CERN Civil Engineering Group.

  12. The constellation observing Atlas

    CERN Document Server

    Privett, Grant

    2013-01-01

    Designed for anyone who wishes to learn the constellations or observe the best and brightest deep sky objects and double stars, this book contains an alphabetical list of constellations complete with star maps, historical background, and highlights of deep sky objects. Each entry contains position and physical information on enough stars to support astronomers in star-hopping, swinging the telescope from star to star to star to arrive at a faint target. It provides a carefully selected list of accessible and rewarding deep sky objects. Full-color maps show the constellations, with star types (spectral and physical) indicated by the colors used on the map. Extended objects such as galaxies and nebulae are shown with the approximate apparent size in the sky. With unmatched thoroughness and accessibility, this is a constellation atlas that makes the ideal companion to a night's telescope viewing, for novices and expert amateur astronomers alike. Easy to navigate and refer to, it is the key that unlocks the do...

  13. News from the ATLAS

    CERN Document Server

    Beauchemin, P; The ATLAS collaboration

    2015-01-01

    The LHC has been running for over 2 years and the different experiments have accumulated enough data to find a new particle which could well be the Higgs boson, achieve Standard Model measurements with precision at the percent level, and seriously constrain a large variety of new physics scenarios, giving important hints on what the physics beyond the Standard Model can be and what it cannot be. This presentation will focus on ATLAS latest searches for new physics in events featuring signatures relevant to theories of quantum gravity. Will be presented the results on searches for large extra dimensions (direct graviton emission, virtual graviton propagation, Kaluza-Klein Randall-Sundrum resonances, etc.) and other TeV-scale gravity phenomena such as black holes (rotating and non-rotating) and string balls production and decay. Results will be reported on each of the various final states investigated for each signals. The results of some searches that are not typically interpreted into bounds on quantum gravit...

  14. The ATLAS tau trigger

    CERN Document Server

    Tsuno, S; The ATLAS collaboration

    2009-01-01

    The ATLAS tau trigger has three levels: the first one (L1) is hardware based and uses FPGAs, while the second (L2) and third levels (EF -Event Filter-) are software based and use commodity computers (2 x Intel Harpertown quad-core 2.5 GHz), running scientific linux 4. In this contribution we discuss both the physics characteristics of tau leptons and the technical solutions to quick data access and fast algorithms. We show that L1 selects narrow jets in the calorimeter with an overall rejection against QCD jets of 300, whilst L2 and EF (referred together as High Level Trigger -HLT-) use all the detectors with full granularity and apply a typical rejection of 15 within the stringent timing requirements of the LHC. In the HLT there are two complementary approaches: specialized, fast algorithms are used at L2, while more refined and sophisticated algorithms, imported from the offline, are utilized in the EF.

  15. 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...

  16. 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.

  17. 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 ...

  18. ATLAS Data Challenge 1

    CERN Document Server

    DC1 TaskForce

    2003-01-01

    The ATLAS Collaboration at CERN is preparing for the data taking and analysis at LHC that will start in 2007. Therefore, in 2002 a series of Data Challenges (DC's) was started whose 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 and Physics communities, and the production of those large data samples as a worldwide distributed activity. It should be noted that it was not an option to "run everything at CERN" even if we had wanted to; the resources were not available at CERN to carry out the production on a reasonable time-scale. We were therefore faced with the great challenge of organising and then carrying out this large-scale production at a significant number of sites around the world. However, the benefits o...

  19. 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...

  20. 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...

  1. ATLAS Visit of Indian President

    CERN Multimedia

    2005-01-01

    Welcomed by CERN's Director General, Robert Aymar, the President of India Dr. A.P.J. Abdul Kalam visited the LHC tunnel, the ATLAS experimental cavern and the test facility for the LHC magnets. There the President had the chance to meet Indian scientists working at CERN.

  2. 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 ...

  3. ATLAS Civil Engineering Point 1

    CERN Multimedia

    2000-01-01

    Different phases of realisation to Point 1: zone of the ATLAS experiment 18-10-2000 UX 15 cavern and PX16 15-12-2000 USA 15 - UX 15 concreting the arch 14-02-2001 UX 15 - ancrages, isolation and scaffolding

  4. ATLAS Fast Tracker Simulation Challenges

    CERN Document Server

    Adelman, Jahred; The ATLAS collaboration; Borodin, Mikhail; Chakraborty, Dhiman; García Navarro, José Enrique; Golubkov, Dmitry; Kama, Sami; Panitkin, Sergey; Smirnov, Yuri; Stewart, Graeme; Tompkins, Lauren; Vaniachine, Alexandre; Volpi, Guido

    2015-01-01

    To deal with Big Data flood from the ATLAS detector most events have to be rejected in the trigger system. the trigger rejection is complicated by the presence of a large number of minimum-bias events – the pileup. To limit pileup effects in the high luminosity environment of the LHC Run-2, ATLAS relies on full tracking provided by the Fast TracKer (FTK) implemented with custom electronics. The FTK data processing pipeline has to be simulated in preparation for LHC upgrades to support electronics design and develop trigger strategies at high luminosity. The simulation of the FTK - a highly parallelized system - has inherent performance bottlenecks on general-purpose CPUs. To take advantage of the Grid Computing power, the FTK simulation is integrated with Monte Carlo simulations at the Production System level above the ATLAS workload management system PanDA. We report on ATLAS experience with FTK simulations on the Grid and next steps for accommodating the growing requirements for resources during the LHC R...

  5. 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...

  6. A Lego version of ATLAS

    CERN Document Server

    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...

  7. 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.

  8. ATLAS Detector : Performance and Upgrades

    CERN Document Server

    Oliveira Damazio, Denis; The ATLAS collaboration

    2016-01-01

    Describe the ATLAS detector and summarize most relevant and recent information about the detector performance in 2016 with LHC colliding bunches at sqrt(s)=13 TeV with luminosity above the nominal value. Describe the different upgrade phases previewed for the detector and main activities already ongoing.

  9. 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 ...

  10. 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 ...

  11. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    1998-01-01

    Different phases of the PX 15 realisation to Point 1: zone of the ATLAS experiment 19-11-1998 Realisation of the Walkway for PX 15 and the putting up scaffolds 15-01-1999 Film from the surface of Point 1 and descent in the well of PX 15

  12. 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.

  13. Heavy Ion Results from ATLAS

    CERN Document Server

    Jia, Jiangyong; 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.

  14. 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.

  15. The ATLAS semiconductor tracker (SCT)

    CERN Document Server

    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**3**4 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.

  16. Searched for exotics at ATLAS

    CERN Document Server

    Turra, Ruggero; The ATLAS collaboration

    2016-01-01

    This note presents a selected subset of the analyses made by ATLAS using data from Run2 at 13 TeV searching for exotic New Physics. The choice of the analyses has been motivated by the connection with the $\\gamma\\gamma$ search where a modest excess has been found.

  17. ATLAS Assembly Hall Open Day

    CERN Document Server

    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.

  18. 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.

  19. 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.

  20. Commissioning of the ATLAS pixel detector

    Energy Technology Data Exchange (ETDEWEB)

    ATLAS Collaboration; Golling, Tobias

    2008-09-01

    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.

  1. The latest results of the ATLAS experiment

    CERN Document Server

    Samset, BH; The ATLAS collaboration

    2010-01-01

    The ATLAS experiment at the LHC has recorded proton-proton collisions at three energies. This talk reviews the early performance and physics results from ATLAS. Topics include tracking and reconstruction of resonances, electron, jet and tau reconstruction, early b-tagging, and observation of J/Psi, W and Z particles. ATLAS studies of charged particle production at 0.9 TeV and 7 TeV are shown, together with an investigation of the underlying event and an associated tuning of PYTHIA parameters. General ATLAS talk for PASCOS 2010. 20 minutes, including questions.

  2. Mini-atlas of the marmoset brain.

    Science.gov (United States)

    Senoo, Aya; Tokuno, Hironobu; Watson, Charles

    2015-04-01

    A mini-atlas of the brain is designed to help students and young researchers who are not familiar with neuroanatomy. In the mini-atlas, a limited number of important nuclei and fiber tracts are shown on a small number of brain sections from posterior end to the anterior end of the brain. The first mini-atlas was introduced for the rat brain (Watson et al., 2010). Here we present a mini-atlas of the common marmoset (Callithrix jaccus), which is one of representative experimental primates for modern neuroscience. We further discuss the differences of brain structures between rodents and primates.

  3. Image database for digital hand atlas

    Science.gov (United States)

    Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente; Dey, Partha S.; Gertych, Arkadiusz; Pospiech-Kurkowska, Sywia

    2003-05-01

    Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A commonly used method is atlas matching by a visual comparison of a hand radiograph with a small reference set of old Greulich-Pyle atlas. We have developed a new digital hand atlas with a large set of clinically normal hand images of diverse ethnic groups. In this paper, we will present our system design and implementation of the digital atlas database to support the computer-aided atlas matching for bone age assessment. The system consists of a hand atlas image database, a computer-aided diagnostic (CAD) software module for image processing and atlas matching, and a Web user interface. Users can use a Web browser to push DICOM images, directly or indirectly from PACS, to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas image database to assess the bone age. The digital atlas method built on a large image database and current Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.

  4. Protein - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available otein information on other websites. Data file File name: tp_atlas_protein.zip Fi...le URL: ftp://ftp.biosciencedbc.jp/archive/tp_atlas/LATEST/tp_atlas_protein.zip File size: 49.8 KB Simple se...arch URL http://togodb.biosciencedbc.jp/togodb/view/tp_atlas_protein#en Data acquisition method - Data analy

  5. Protein - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available eins Research Program (TPRP). Data file File name: at_atlas_protein.zip File URL:... ftp://ftp.biosciencedbc.jp/archive/at_atlas/LATEST/at_atlas_protein.zip File size: 1.13 KB Simple search UR...L http://togodb.biosciencedbc.jp/togodb/view/at_atlas_protein#en Data acquisition method - Data analysis met

  6. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  7. EnviroAtlas - Des Moines, IA - Demographics by Block Group 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://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas...

  8. EnviroAtlas - Minneapolis/St. Paul, MN - Demographics by Block Group 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://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas...

  9. EnviroAtlas - Cleveland, OH - Demographics by Block Group 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://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas...

  10. EnviroAtlas - Austin, TX - Tree Cover Configuration and Connectivity, Water Background 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://enviroatlas.epa.gov/EnviroAtlas). The EnviroAtlas...

  11. EnviroAtlas - Memphis, TN - Tree Cover Configuration and Connectivity, Water Background 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://enviroatlas.epa.gov/EnviroAtlas). The EnviroAtlas...

  12. EnviroAtlas - New York, NY - Tree Cover Configuration and Connectivity 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://enviroatlas.epa.gov/EnviroAtlas). The EnviroAtlas New...

  13. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  14. 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.

  15. A fast atlas pre-selection procedure for multi-atlas based brain segmentation.

    Science.gov (United States)

    Ma, Jingbo; Ma, Heather T; Li, Hengtong; Ye, Chenfei; Wu, Dan; Tang, Xiaoying; Miller, Michael; Mori, Susumu

    2015-01-01

    Multi-atlas based MR image segmentation has been recognized as a quantitative analysis approach for brain. For such purpose, atlas databases keep increasing to include various anatomical characteristics of human brain. Atlas pre-selection becomes a necessary step for efficient and accurate automated segmentation of human brain images. In this study, we proposed a method of atlas pre-selection for target image segmentation on the MriCloud platform, which is a state-of-the-art multi-atlas based segmentation tool. In the MRIcloud pipeline, segmentation of lateral ventricle (LV) label is generated as an additional input in the segmentation pipeline. Under this circumstance, similarity of the LV label between target image and atlases was adopted as the atlas ranking scheme. Dice overlap coefficient was calculated and taken as the quantitative measure for atlas ranking. Segmentation results based on the proposed method were compared with that based on atlas pre-selection by mutual information (MI) between images. The final segmentation results showed a comparable accuracy of the proposed method with that from MI based atlas pre-selection. However, the computation load for the atlas pre-selection was speeded up by about 20 times compared to MI based pre-selection. The proposed method provides a promising assistance for quantitative analysis of brain images.

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Haddad, Nizar Jamal; Loucif-Ayad, Wahida; Adjlane, Noureddine; Saini, Deepti; Manchiganti, Rushiraj; Krishnamurthy, Venkatesh; AlShagoor, Banan; Batainh, Ahmed Mahmud; Mugasimangalam, Raja

    2015-06-01

    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.

  19. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  20. 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...