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.

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

Directory of Open Access Journals (Sweden)

Gregory P. Way

2018-04-01

Full Text Available Summary: Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these “hidden responders” may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders. : Way et al. develop a machine-learning approach using PanCanAtlas data to detect Ras activation in cancer. Integrating mutation, copy number, and expression data, the authors show that their method detects Ras-activating variants in tumors and sensitivity to MEK inhibitors in cell lines. Keywords: Gene expression, machine learning, Ras, NF1, KRAS, NRAS, HRAS, pan-cancer, TCGA, drug sensitivity

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

Science.gov (United States)

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

2017-04-18

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

TCGA bladder cancer study reveals potential drug targets

Science.gov (United States)

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-15

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

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.

The Education and Outreach Program of ATLAS

CERN Multimedia

Barnett, M.

2006-01-01

The ATLAS Education and Outreach (E&O) program began in 1997, but the advent of LHC has placed a new urgency in our efforts. Even a year away, we can feel the approaching impact of starting an experiment that could make revolutionary discoveries. The public and teachers are beginning to turn their attention our way, and the newsmedia are showing growing interest in ATLAS. When datataking begins, the interest will peak, and the demands on us are likely to be substantial. The collaboration is responding to this challenge in a number of ways. ATLAS management has begun consultation with experts. The official budget for the E&O group has been growing as have the contributions of many ATLAS institutions. The number of collaboration members joining these efforts has grown, and their time and effort is increasing. We are in ongoing consultation with the CERN Public Affairs Office, as well as the other LHC experiments and the European Particle Physics Outreach Group. The E&O group has expanded the scope...

Recent results from the ATLAS heavy ion program

CERN Document Server

Havener, Laura Brittany; The ATLAS collaboration

2018-01-01

The heavy-ion program in the ATLAS experiment at the LHC originated as an extensive program to probe and characterize the hot, dense matter created in relativistic lead-lead collisions. In recent years, the program has also broadened to a detailed study of collective behavior in smaller systems. In particular, the techniques used to study larger systems are also applied to proton-proton and proton-lead collisions over a wide range of particle multiplicities, to try and understand the early-time dynamics which lead to similar flow-like features in all of the systems. Another recent development is a program studying ultra-peripheral collisions, which provide gamma-gamma and photonuclear processes over a wide range of CM energy, to probe the nuclear wavefunction. This talk presents a subset of the the most recent results from the ATLAS experiment based on Run 1 and Run 2 data, including measurements of collectivity over a wide range of collision systems, potential nPDF modifications — using electroweak bosons,...

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

The implementation of full ATLAS detector simulation program

International Nuclear Information System (INIS)

Rimoldi, A.; Dell'Acqua, A.; Stavrianakou, M.; Amako, K.; Kanzaki, J.; Morita, Y.; Murakami, K.; Sasaki, T.; Saeki, T.; Ueda, I.; Tanaka, S.; Yoshida, H.

2001-01-01

The ATLAS detector is one of the most sophisticated and huge detectors ever designed up to now. A detailed, flexible and complete simulation program is needed in order to study the characteristics and possible problems of such a challenging apparatus and to answer to all raising questions in terms of physics, design optimization, etc. To cope with these needs the authors are implementing an application based on the simulation framework FADS/Goofy (Framework for ATLAS Detector Simulation /Geant4-based Object-Oriented Folly) in the Geant4 environment. The user's specific code implementation is presented in details for the different applications implemented until now, from the various components of the ATLAS spectrometer to some particular testbeam facilities. Particular emphasis is put in describing the simulation of the Muon Spectrometer and its subsystems as a test case for the implementation of the whole detector simulation program: the intrinsic complexity in the geometry description of the Muon System is one of the more demanding problems that are faced. The magnetic field handling, the physics impact in the event processing in presence of backgrounds from different sources and the implementation of different possible generators (including Pythia) are also discussed

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

Report to users of ATLAS

International Nuclear Information System (INIS)

Ahmad, I.; Glagola, B.

1995-05-01

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

ATLAS Virtual Visits bringing the world into the ATLAS control room

CERN Document Server

AUTHOR|(CDS)2051192; The ATLAS collaboration; Yacoob, Sahal

2016-01-01

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.

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

Science.gov (United States)

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

2017-01-01

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

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

Directory of Open Access Journals (Sweden)

Sang Y Lee

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

Future of the ATLAS heavy ion program

CERN Document Server

ATLAS-Collaboration, The; The ATLAS collaboration

2012-01-01

The primary goal of the heavy ion program at the LHC is to study the properties of deconfined strongly interacting matter, often referred to as ``quark-gluon plasma'' (QGP), created in ultra-relativistic nuclear collisions. That matter is found to be strongly coupled with a viscosity to entropy ratio near a conjectured quantum lower bound. ATLAS foresees a rich program of studies using jets, Upsilons, measurements of global event properties and measurements in proton-nucleus collisions that will measure fundamental transport properties of the QGP, probe the nature of the interactions between constituents of the QGP, elucidate the origin of the strong coupling, and provide insight on the initial state of nuclear collisions. The heavy ion program through the third long shutdown should provide one inverse nb of 5.5~TeV Pb+Pb data. That data will provide more than an order of magnitude increase in statistics over currently available data for high-pT observables such as gamma-jet and Z-jet pairs. However, potentia...

Report to users of Atlas

International Nuclear Information System (INIS)

Ahmad, I.; Glagola, B.

1996-06-01

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

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.

Pan-cancer analysis of TCGA data reveals notable signaling pathways

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Science.gov (United States)

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

2017-09-01

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

ATLAS Tile Calorimeter Readout Electronics Upgrade Program for the High Luminosity LHC

CERN Document Server

Cerqueira, A S

2013-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the most central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The ATLAS upgrade program is divided in three phases: The Phase~0 occurs during 2013-2014, Phase~1 during 2018-1019 and finally Phase~2, which is foreseen for 2022-2023, whereafter the peak luminosity will reach 5-7 x 10$^{34}$ cm$^2$s$^{-1}$ (HL-LHC). The main TileCal upgrade is focused on the Phase~2 period. The upgrade aims at replacing the majority of the on- and off-detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. All new electronics must be able to cope with the increased radiation levels. An ambitious upgrade development program is pursued to study different electronics options. Three options are presently being investigated for the front-end electronic upgrade. The first option is an improved version of the present system built using comm...

Report to users of ATLAS

International Nuclear Information System (INIS)

Ahmad, I.; Glagola, B.

1997-03-01

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

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

Science.gov (United States)

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

EnviroAtlas - Ecosystem Services Market-Based Programs Web Service, U.S., 2016, Forest Trends' Ecosystem Marketplace

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas web service contains layers depicting market-based programs and projects addressing ecosystem services protection in the United States. Layers...

ATLAS B-physics potential

International Nuclear Information System (INIS)

Smizanska, M.

2001-01-01

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

ATLAS Open Data project

CERN Document Server

The ATLAS collaboration

2018-01-01

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

The ATLAS hadronic tau trigger

International Nuclear Information System (INIS)

Shamim, Mansoora

2012-01-01

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

Conference Report: The First ATLAS.ti User Conference

Directory of Open Access Journals (Sweden)

Jeanine C. Evers

2014-01-01

Full Text Available This report on the First ATLAS.ti User Conference shares our impressions and experiences as longstanding ATLAS.ti users and trainers about the First ATLAS.ti User Conference in Berlin 2013. The origins, conceptual principles and development of the program are outlined, the conference themes discussed and experiences shared. Finally, the future of the program is discussed. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs1401197

ATLAS B-physics potential

CERN Document Server

Smizanska, M

2001-01-01

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

Report to users of ATLAS, January 1998

International Nuclear Information System (INIS)

Ahmad, I.; Hofman, D.

1998-01-01

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

ATLAS note ATL-COM-PHYS-2009

International Nuclear Information System (INIS)

Chekanov, S.; Boomsma, J.

2009-01-01

The program InvMass has been developed to perform a general model-independent search for new particles using the ATLAS detector at the Large Hadron Collider (LHC), a proton-proton collider at CERN. The search is performed by examining statistically significant variations from the Standard Model predictions in exclusive event classes classified according to the number of identified objects. The program, called InvMass, finds all relevant particle groups identified with the ATLAS detector and analyzes their production rates, invariant masses and the total transverse momenta. The generic code of InvMass can easily be adapted for any particle types identified with the ATLAS detector. Several benchmark tests are presented.

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

Directory of Open Access Journals (Sweden)

Theo A. Knijnenburg

2018-04-01

Full Text Available Summary: DNA damage repair (DDR pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy. : Knijnenburg et al. present The Cancer Genome Atlas (TCGA Pan-Cancer analysis of DNA damage repair (DDR deficiency in cancer. They use integrative genomic and molecular analyses to identify frequent DDR alterations across 33 cancer types, correlate gene- and pathway-level alterations with genome-wide measures of genome instability and impaired function, and demonstrate the prognostic utility of DDR deficiency scores. Keywords: The Cancer Genome Atlas PanCanAtlas project, DNA damage repair, somatic mutations, somatic copy-number alterations, epigenetic silencing, DNA damage footprints, mutational signatures, integrative statistical analysis, protein structure analysis

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.

Preparation of Northern Mid-Continent Petroleum Atlas

Energy Technology Data Exchange (ETDEWEB)

Lee C. Gerhard; Timothy R. Carr; W. Lynn Watney

1998-05-01

As proposed, the third year program will continue and expand upon the Kansas elements of the original program, and provide improved on-line access to the prototype atlas. The third year of the program will result in a digital atlas sufficient to provide a permanent improvement in data access to Kansas operators. The ultimate goal of providing an interactive history-matching interface with a regional database will be demonstrated as the program covers more geographic territory and the database expands. The atlas will expand to include significant reservoirs representing the major plays in Kansas, and North Dakota. Primary products of the third year prototype atlas will be on-line accessible digital databases and technical publications covering two additional petroleum plays in Kansas and one in North Dakota. Regional databases will be supplemented with geological field studies of selected fields in each play. Digital imagery, digital mapping, relational data queries, and geographical information systems will be integral to the field studies and regional data sets. Data sets will have relational links to provide opportunity for history-matching, feasibility, and risk analysis tests on contemplated exploration and development projects. The flexible "web-like" design of the atlas provides ready access to data, and technology at a variety of scales from regional, to field, to lease, and finally to the individual well bore. The digital structure of the atlas permits the operator to access comprehensive reservoir data and customize the interpretative products (e.g., maps and cross-sections) to their needs. The atlas will be accessible in digital form on-line using a World-Wide-Web browser as the graphical user interface. Regional data sets and field studies will be freestanding entities that will be made available on-line through the Internet to users as they are completed. Technology transfer activities will be ongoing from the earliest part of this project, providing

Report to users of ATLAS, December 1995

International Nuclear Information System (INIS)

Ahmad, I.; Glagola, B.

1995-12-01

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

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.

Recent Results from the ATLAS UPC Program

CERN Document Server

Cole, Brian; The ATLAS collaboration

2018-01-01

Recent results from ATLAS measurements of ultra-peripheral Pb+Pb collisions are presented. Measurements include gamma+gamma -> dimuon, photo-nuclear production of di/multi-jets, and light-by-light scattering.

Taus at ATLAS

Energy Technology Data Exchange (ETDEWEB)

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

2017-12-06

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

The ATLAS detector simulation application

International Nuclear Information System (INIS)

Rimoldi, A.

2007-01-01

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

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

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.;

A new program for particle physics: ATLAS in CERN

International Nuclear Information System (INIS)

Hubaut, F.

2004-01-01

LHC (large hadron collider) is being built in CERN and will enter into service in 2007. LHC is a proton collider: the 2 proton beams moving in opposite direction along a 27 km long circle will collide in 4 places and the maximum energy reached will be 14 TeV (in the mass center frame). 4 huge detectors (ATLAS, CMS, LHC-B, and ALICE) are being designed through important international collaborations, each one will fit a colliding site. ATLAS and CMS are all-particles detectors while LHC-B is dedicated to the physics of b-hadrons and ALICE will deal with heavy ions. LHC is expected to produce 40 million collisions every second and each collision will generate thousands of particles, so the huge amount of data generated requires the use of an efficient and reliable data acquisition system. Moreover the article describes the different parts of the ATLAS detector: the track detector, the calorimeter, the muon spectrometer and the superconducting central solenoid. (A.C.)

ATLAS Tile Calorimeter Readout Electronics Upgrade Program for the High Luminosity LHC

CERN Document Server

Cerqueira, A S; The ATLAS collaboration

2013-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the most central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The ATLAS upgrade program is divided in three phases: The Phase 0 occurs during 2013-2014 and prepares the LHC to reach peak luminosities of 1034 cm2s-1; Phase 1, foreseen for 2018-1019, prepares the LHC for peak luminosity up to 2-3 x 1034 cm2s-1, corresponding to 55 to 80 interactions per bunch-crossing with 25 ns bunch interval; and Phase 2 is foreseen for 2022-2023, whereafter the peak luminosity will reach 5-7 x 1034 cm2s-1 (HL-LHC). With luminosity leveling, the average luminosity will increase with a factor 10. The main TileCal upgrade is focused on the HL-LHC period. The upgrade aims at replacing the majority of the on- and off-detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. All new electronics must be able to cope with the increased rad...

Genomic features of lobular breast carcinoma

Science.gov (United States)

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

Heavy Ion Physics with the ATLAS Detector at the LHC

International Nuclear Information System (INIS)

Trzupek, A.

2009-01-01

The heavy-ion program at LHC will be pursued by three experiments including ATLAS, a multipurpose detector to study p + p collisions. A report on the potential of the ATLAS detector to uncover new physics in Pb + Pb collisions at energies thirty times larger than energy available at RHIC will be presented. Key aspects of the heavy-ion program of the ATLAS experiment, implied by measurements at RHIC, will be discussed. They include measurement capability of high-p T hadronic and electromagnetic probes, quarkonia as well as elliptic flow and other bulk phenomena. Measurements by the ATLAS experiment will provide crucial information about the formation of a quark-gluon plasma at the new energy scale accessible at the LHC. (author)

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

Science.gov (United States)

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

2018-05-05

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

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

Science.gov (United States)

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

2018-01-30

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

EnviroAtlas - Acres of USDA Farm Service Agency Conservation Reserve Program land by 12-Digit HUC for the Conterminous United States.

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the acres of land enrolled in the US Department of Agriculture (USDA)'s Conservation Reserve Program (CRP). The CRP is administered by...

ATLAS and ultra high energy cosmic ray physics

Directory of Open Access Journals (Sweden)

Pinfold James

2017-01-01

Full Text Available After a brief introduction to extended air shower cosmic ray physics the current and future deployment of forward detectors at ATLAS is discussed along with the various aspects of the current and future ATLAS programs to explore hadronic physics. The emphasis is placed on those results and future plans that have particular relevance for high-energy, and ultra high-energy, cosmic ray physics. The possible use of ATLAS as an “underground” cosmic muon observatory is briefly considered.

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

NARCIS (Netherlands)

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

2018-01-01

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

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

NARCIS (Netherlands)

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

2018-01-01

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

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

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.

Development of the ATLAS simulation framework

International Nuclear Information System (INIS)

DellAcqua, A.; Stavrianakou, M.; Amako, K.; Kanzaki, J.; Morita, Y.; Murakami, K.; Sasaki; Kurashige, H.; Rimoldi, A.; Saeki, T.; Ueda, I.; Tanaka, S.; Yoshida, H.

2001-01-01

Object-oriented (OO) approach is the key technology to develop a software system in the LHC/ATLAS experiment. The authors developed a OO simulation framework based on the Geant4 general-purpose simulation toolkit. Because of complexity of simulation in ATLAS, the authors paid most attention to the scalability in the design. Although the first target to apply this framework is to implement the ATLAS full detector simulation program, there is no experiment-specific code in it, therefore it can be utilized for the development of any simulation package, not only for HEP experiments but also for various different research domains. The authors discuss our approach of design and implementation of the framework

Model Stellar Atmospheres and Real Stellar Atmospheres and Status of the ATLAS12 Opacity Sampling Program and of New Programs for Rosseland and for Distribution Function Opacity

Science.gov (United States)

Kurucz, Robert L.

1996-01-01

I discuss errors in theory and in interpreting observations that are produced by the failure to consider resolution in space, time, and energy. I discuss convection in stellar model atmospheres and in stars. Large errors in abundances are possible such as the factor of ten error in the Li abundance for extreme Population II stars. Finally I discuss the variation of microturbulent velocity with depth, effective temperature, gravity, and abundance. These variations must be dealt with in computing models and grids and in any type of photometric calibration. I have also developed a new opacity-sampling version of my model atmosphere program called ATLAS12. It recognizes more than 1000 atomic and molecular species, each in up to 10 isotopic forms. It can treat all ions of the elements up through Zn and the first 5 ions of heavier elements up through Es. The elemental and isotopic abundances are treated as variables with depth. The fluxes predicted by ATLAS12 are not accurate in intermediate or narrow bandpass intervals because the sample size is too small. A special stripped version of the spectrum synthesis program SYNTHE is used to generate the surface flux for the converged model using the line data on CD-ROMs 1 and 15. ATLAS12 can be used to produce improved models for Am and Ap stars. It should be very useful for investigating diffusion effects in atmospheres. It can be used to model exciting stars for H II regions with abundances consistent with those of the H II region. These programs and line files will be distributed on CD-ROMs.

Search for exotic physics with ATLAS

CERN Document Server

Delsart, Pierre-Antoine

2006-01-01

At the LHC, the program of research in particle physics beyond the Standard Model is extremely rich. With the ATLAS detector, besides SUSY mainstream studies, many exotic theoretical models will be investigated. They range from compositeness of fundamental fermions to extra dimension scenarii through GUT models and include many variants. I shall review some selected typical studies by the ATLAS collaboration on exotic physics, highlighting the discovery prospects and the recent analyses using the latest full detector simulations.

LUCID: the ATLAS Luminosity Detector

CERN Document Server

Fabbri, Laura; The ATLAS collaboration

2018-01-01

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

A Nuclear Physics Program at the ATLAS Experiment at the CERN Large Hadron Collider

CERN Document Server

Aronson, S H; Gordon, H; Leite, M; Le Vine, M J; Nevski, P; Takai, H; White, S; Cole, B; Nagle, J L

2002-01-01

The ATLAS collaboration has significant interest in the physics of ultra-relativistic heavy ion collisions. We submitted a Letter of Intent to the United States Department of Energy in March 2002. The following document is a slightly modified version of that LOI. More details are available at: http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/SM/ions

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.

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

NARCIS (Netherlands)

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

2018-01-01

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

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

DEFF Research Database (Denmark)

Guo, Xingyi; Long, Jirong; Zeng, Chenjie

2015-01-01

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

Calorimetry triggering in ATLAS

International Nuclear Information System (INIS)

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

2009-01-01

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

Calorimetry Triggering in ATLAS

International Nuclear Information System (INIS)

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

2011-01-01

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

Calorimetry triggering in ATLAS

Energy Technology Data Exchange (ETDEWEB)

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

2009-04-01

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

TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.

Science.gov (United States)

Iwayanagi, Takao; Miyamoto, Sei; Konno, Takeshi; Mizutani, Hisashi; Hirai, Tomohiro; Shigemoto, Yasumasa; Gojobori, Takashi; Sugawara, Hideaki

2012-09-01

The Targeted Proteins Research Program (TPRP) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan is the phase II of structural biology project (2007-2011) following the Protein 3000 Project (2002-2006) in Japan. While the phase I Protein 3000 Project put partial emphasis on the construction and maintenance of pipelines for structural analyses, the TPRP is dedicated to revealing the structures and functions of the targeted proteins that have great importance in both basic research and industrial applications. To pursue this objective, 35 Targeted Proteins (TP) Projects selected in the three areas of fundamental biology, medicine and pharmacology, and food and environment are tightly collaborated with 10 Advanced Technology (AT) Projects in the four fields of protein production, structural analyses, chemical library and screening, and information platform. Here, the outlines and achievements of the 35 TP Projects are summarized in the system named TP Atlas. Progress in the diversified areas is described in the modules of Graphical Summary, General Summary, Tabular Summary, and Structure Gallery of the TP Atlas in the standard and unified format. Advances in TP Projects owing to novel technologies stemmed from AT Projects and collaborative research among TP Projects are illustrated as a hallmark of the Program. The TP Atlas can be accessed at http://net.genes.nig.ac.jp/tpatlas/index_e.html .

Physics with Tau Lepton Final States in ATLAS

Directory of Open Access Journals (Sweden)

Pingel Almut M.

2013-05-01

Full Text Available The ATLAS detector records collisions from two high-energetic proton beams circulating in the LHC. An integral part of the ATLAS physics program are analyses with tau leptons in the final state. Here an overview is given over the studies done in ATLAS with hadronically-decaying final state tau leptons: Standard Model cross-section measurements of Z → ττ, W → τν and tt̅ → bb̅ e/μν τhadν; τ polarization measurements in W → τν decays; Higgs searches and various searches for physics beyond the Standard Model.

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

Science.gov (United States)

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

2014-01-27

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

Design and implementation of the object-oriented fast simulation program for the ATLAS experiment and its use to determine the discovery potential of the Higgs Boson via the channel h- > ZZ- > bbl+l-

CERN Document Server

Steward, Richard M

2004-01-01

The design and implementation of the object-oriented fast simulation program Atlfast is described for the ATLAS experiment at the CERN particle physics laboratory in Switzerland. Fast simulations use parametrised energy and momentum smearing in order to recreate the detection efficiency and particle identification of a real experimental detector, without the time-consuming computation required for full detector simulation. Additionally, an object-oriented program for performing user-defined physics analyses is described. This program is released for general use by the ATLAS collaboration and is designed for use with, but not restricted to, physics output from the Atlfast fast simulation program. These programs are demonstrated in a physics study of the feasibility of discovering the Higgs boson at the ATLAS experiment, using the discovery channel ho > Z Z * > bb l+l via weak vector boson fusion in the mass range 150 GeV - 200 GeV. It is found that this channel does not significantly increase the discovery pot...

Digital atlas of fetal brain MRI

Energy Technology Data Exchange (ETDEWEB)

Chapman, Teresa; Weinberger, E. [Department of Radiology, Seattle Children' s Hospital, Seattle, WA (United States); Matesan, Manuela [University of Washington, Department of Radiology, Seattle, WA (United States); Bulas, Dorothy I. [Division of Diagnostic Imaging and Radiology, Children' s National Medical Center, Washington, DC (United States)

2010-02-15

Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download. Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development. (orig.)

Digital atlas of fetal brain MRI

International Nuclear Information System (INIS)

Chapman, Teresa; Weinberger, E.; Matesan, Manuela; Bulas, Dorothy I.

2010-01-01

Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download. Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development. (orig.)

Multiple brain atlas database and atlas-based neuroimaging system.

Science.gov (United States)

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

1997-01-01

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

ATLAS @ LHC: status and recent results

CERN Document Server

McPherson, Robert; The ATLAS collaboration

2017-01-01

The status and data taking summary of the ATLAS experiment at the CERN Large Hadron Collider is reviewed. Recent physics analysis results are presented, and the detector upgrade program is briefly summarized.

Networks in ATLAS

Science.gov (United States)

McKee, Shawn; ATLAS Collaboration

2017-10-01

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

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.

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

NARCIS (Netherlands)

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

2018-01-01

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

Jet calibration in the ATLAS experiment at LHC

CERN Document Server

Francavilla, P

2009-01-01

Jets produced in the hadronisation of quarks and gluons play a central role in the rich physics program that will be covered by the ATLAS experiment at the LHC, and are central elements of the signature for many physics channels. A well understood energy scale, which for some processes demands an uncertainty in the energy scale of order 1%, is a prerequisite. Moreover, in early data we face the challenge of dealing with the unexpected issues of a brand new detector in an unexplored energy domain. The ATLAS collaboration is carrying out a program to revisit the jet calibration strategies used in earlier hadron-collider experiments and develop a strategy which takes into account the new experimental problems introduced from higher measurement precision and from the LHC environment. The ATLAS calorimeter is intrinsically non-compensating and we will discuss the use of different offline approaches based on cell energy density and jet topology to correct the linearity response while improving the resolution. In ad...

Heavy Ion Physics with the ATLAS Detector

CERN Document Server

Nevski, P

2006-01-01

The ATLAS experiment at the LHC plans to study the bulk matter formed in heavy ion collisions, already being studied at RHIC, as well as crucial reference data from p+p and p+A collisions. ATLAS is designed to perform optimally at the nominal machine luminosity of 10^34 cm-2s-1. It has a finely segmented electromagnetic and hadronic calorimeters covering 10 units of rapidity, allowing the study of jets and fragmentation functions in detail in tandem with the inner tracking system. Preliminary studies also indicate that it will be possible to tag b-jets in the heavy ion environment. Upsilon and J/Psi can be reconstructed through the di-muon decay channel. There is also an important "day 1" program planned, that will use the data provided by both p+p and A+A collisions to study bulk features of the collision dynamics. We discuss the current status of simulation studies and plans of the heavy ion physics program with the ATLAS detector during the A+A and p+A runs.

European Wind Atlas and Wind Resource Research in Denmark

DEFF Research Database (Denmark)

Mortensen, Niels Gylling

to estimate the actual wind climate at any specific site and height within this region. The Danish and European Wind Atlases are examples of how the wind atlas methodology can be employed to estimate the wind resource potential for a country or a sub-continent. Recently, the methodology has also been used...... - from wind measurements at prospective sites to wind tunnel simulations and advanced flow modelling. Among these approaches, the wind atlas methodology - developed at Ris0 National Laboratory over the last 25 years - has gained widespread recognition and is presently considered by many as the industry......-standard tool for wind resource assessment and siting of wind turbines. The PC-implementation of the methodology, the Wind Atlas Analysis and Application Program (WAsP), has been applied in more than 70 countries and territories world-wide. The wind atlas methodology is based on physical descriptions and models...

Digital atlas of fetal brain MRI.

Science.gov (United States)

Chapman, Teresa; Matesan, Manuela; Weinberger, Ed; Bulas, Dorothy I

2010-02-01

Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C#, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download from http://radiology.seattlechildrens.org/teaching/fetal_brain . Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development.

PREIMS - AT Atlas | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Targeted Proteins Research Program (TPRP). Data file File name: at_atlas_preims.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...base Database Description Download License Update History of This Database Site Policy | Contact Us PREIMS - AT Atlas | LSDB Archive ...

ATLAS Pixel Detector Operational Experience

CERN Document Server

Di Girolamo, B; The ATLAS collaboration

2011-01-01

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

The new ATLAS Fast Calorimeter Simulation

CERN Document Server

Jacka, Petr; The ATLAS collaboration

2018-01-01

With the huge amount of data collected with ATLAS, there is a need to produce a large number of simulated events. These productions are very CPU and time consuming when using the full GEANT4 simulation. FastCaloSim is a program to quickly simulate the ATLAS calorimeter response, based on a parameterization of the GEANT4 energy deposits of several kinds of particles in a grid of energy and eta. A new version of FastCaloSim is under development and its integration into the ATLAS simulation infrastructure is ongoing. The use of machine learning techniques improves the performance and decreases the memory usage. Dedicated parameterizations for the forward calorimeters are being studied. First results of the new FastCaloSim show substantial improvements of the description of energy and shower shape variables, including the variables for jet substructure.

ATLAS Potential for Beauty Physics Measurements

International Nuclear Information System (INIS)

Smizanska, M.

2001-01-01

The main focus of ATLAS b physics has traditionally been on the standard model. In the last few years also the aspects of new physics in B-decays has been addressed. Another new field of studies started recently is a beauty production. We give an overview of the older as well as more recent results. After an introduction outlining selected trigger and detector performance characteristics, we explain methods and goals of CP violation measurements in decay channels of B d 0 meson, physics of B s 0 system and of rare decays. Finally, the ATLAS program for beauty production measurements is presented. (author)

The ATLAS multi-user upgrade and potential applications

Energy Technology Data Exchange (ETDEWEB)

Mustapha, B.; Nolen, J. A.; Savard, G.; Ostroumov, P. N.

2017-12-01

With the recent integration of the CARIBU-EBIS charge breeder into the ATLAS accelerator system to provide for more pure and efficient charge breeding of radioactive beams, a multi-user upgrade of the ATLAS facility is being proposed to serve multiple users simultaneously. ATLAS was the first superconducting ion linac in the world and is the US DOE low-energy Nuclear Physics National User Facility. The proposed upgrade will take advantage of the continuous-wave nature of ATLAS and the pulsed nature of the EBIS charge breeder in order to simultaneously accelerate two beams with very close mass-to-charge ratios; one stable from the existing ECR ion source and one radioactive from the newly commissioned EBIS charge breeder. In addition to enhancing the nuclear physics program, beam extraction at different points along the linac will open up the opportunity for other potential applications; for instance, material irradiation studies at ~ 1 MeV/u and isotope production at ~ 6 MeV/u or at the full ATLAS energy of ~ 15 MeV/u. The concept and proposed implementation of the ATLAS multi-user upgrade will be presented. Future plans to enhance the flexibility of this upgrade will also be presented.

Object oriented software development in the atlas collaboration

International Nuclear Information System (INIS)

Schaffer, A.

1994-01-01

For more than a year a group within the Atlas Collaboration has been investigating the possibilities of the application of object oriented methodology and program development to the software of Atlas. Recently this group has been joined by members of the CMS Collaboration in the submission of a proposal to the DRDC at CERN to find a common solution for the software development environment for LHC. This talk will discuss the progress achieved so far and the future perspective

Overview of the ATLAS distributed computing system

CERN Document Server

Elmsheuser, Johannes; The ATLAS collaboration

2018-01-01

The CERN ATLAS experiment successfully uses a worldwide computing infrastructure to support the physics program during LHC Run 2. The grid workflow system PanDA routinely manages 250 to 500 thousand concurrently running production and analysis jobs to process simulation and detector data. In total more than 300 PB of data is distributed over more than 150 sites in the WLCG and handled by the ATLAS data management system Rucio. To prepare for the ever growing LHC luminosity in future runs new developments are underway to even more efficiently use opportunistic resources such as HPCs and utilize new technologies. This presentation will review and explain the outline and the performance of the ATLAS distributed computing system and give an outlook to new workflow and data management ideas for the beginning of the LHC Run 3.

The Offshore New European Wind Atlas

Science.gov (United States)

Karagali, I.; Hahmann, A. N.; Badger, M.; Hasager, C.; Mann, J.

2017-12-01

The New European Wind Atlas (NEWA) is a joint effort of research agencies from eight European countries, co-funded under the ERANET Plus Program. The project is structured around two areas of work: development of dynamical downscaling methodologies and measurement campaigns to validate these methodologies, leading to the creation and publication of a European wind atlas in electronic form. This atlas will contain an offshore component extending 100 km from the European coasts. To achieve this, mesoscale models along with various observational datasets are utilised. Scanning lidars located at the coastline were used to compare the coastal wind gradient reproduced by the meso-scale model. Currently, an experimental campaign is occurring in the Baltic Sea, with a lidar located in a commercial ship sailing from Germany to Lithuania, thus covering the entire span of the south Baltic basin. In addition, satellite wind retrievals from scatterometers and Synthetic Aperture Radar (SAR) instruments were used to generate mean wind field maps and validate offshore modelled wind fields and identify the optimal model set-up parameters.The aim of this study is to compare the initial outputs from the offshore wind atlas produced by the Weather & Research Forecasting (WRF) model, still in pre-operational phase, and the METOP-A/B Advanced Scatterometer (ASCAT) wind fields, reprocessed to stress equivalent winds at 10m. Different experiments were set-up to evaluate the model sensitivity for the various domains covered by the NEWA offshore atlas. ASCAT winds were utilised to assess the performance of the WRF offshore atlases. In addition, ASCAT winds were used to create an offshore atlas covering the years 2007 to 2016, capturing the signature of various spatial wind features, such as channelling and lee effects from complex coastal topographical elements.

Performance of the ATLAS muon trigger in run 2

CERN Document Server

Morgenstern, Marcus; The ATLAS collaboration

2017-01-01

Triggering on muons is a crucial ingredient to fulfill the physics program of the ATLAS experiments. The ATLAS trigger system deploys a two stage strategy, a hardware-based Level-1 trigger and a software-based high-level trigger to select events of interest at a suitable recording rate. Both stages underwent upgrades to cope with the challenges in run-II data-taking at centre-of-mass energies of 13 TeV and instantaneous luminosities up to 2x10$^{34} cm^{-2}s^{-1}$. The design of the ATLAS muon triggers and their performance in proton-proton collisions at 13 TeV are presented.

Jet calibration in the ATLAS experiment at LHC

CERN Document Server

The ATLAS collaboration

2009-01-01

Jets produced in the hadronisation of quarks and gluons play a central role in the rich physics program that will be covered by the ATLAS experiment at the LHC, and are central elements of the signature for many physics channels. A well understood energy scale, which for some process demands an uncertainty in the energy scale of order 1%, is a prerequisite. Moreover, in early data we face the challenge of dealing with the unexpected issues of a brand new detector in an unexplored energy domain. The ATLAS collaboration is carrying out a program to revisit the jet calibration strategies used in earlier hadron-collider experiments and develop a strategy which takes account of the new experimental problems and demand for greater measurement precision which will be faced at the LHC. The ATLAS calorimeter is intrinsically non-compensating and we will present the use of different offline approaches based on cell energy density and jet topology to correct for this effect on jet energy resolution and scale. In additio...

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

Science.gov (United States)

Li, Yue; Liang, Minggao; Zhang, Zhaolei

2014-01-01

Gene expression is a combinatorial function of genetic/epigenetic factors such as copy number variation (CNV), DNA methylation (DM), transcription factors (TF) occupancy, and microRNA (miRNA) post-transcriptional regulation. At the maturity of microarray/sequencing technologies, large amounts of data measuring the genome-wide signals of those factors became available from Encyclopedia of DNA Elements (ENCODE) and The Cancer Genome Atlas (TCGA). However, there is a lack of an integrative model to take full advantage of these rich yet heterogeneous data. To this end, we developed RACER (Regression Analysis of Combined Expression Regulation), which fits the mRNA expression as response using as explanatory variables, the TF data from ENCODE, and CNV, DM, miRNA expression signals from TCGA. Briefly, RACER first infers the sample-specific regulatory activities by TFs and miRNAs, which are then used as inputs to infer specific TF/miRNA-gene interactions. Such a two-stage regression framework circumvents a common difficulty in integrating ENCODE data measured in generic cell-line with the sample-specific TCGA measurements. As a case study, we integrated Acute Myeloid Leukemia (AML) data from TCGA and the related TF binding data measured in K562 from ENCODE. As a proof-of-concept, we first verified our model formalism by 10-fold cross-validation on predicting gene expression. We next evaluated RACER on recovering known regulatory interactions, and demonstrated its superior statistical power over existing methods in detecting known miRNA/TF targets. Additionally, we developed a feature selection procedure, which identified 18 regulators, whose activities clustered consistently with cytogenetic risk groups. One of the selected regulators is miR-548p, whose inferred targets were significantly enriched for leukemia-related pathway, implicating its novel role in AML pathogenesis. Moreover, survival analysis using the inferred activities identified C-Fos as a potential AML

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

Science.gov (United States)

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

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

Zheng Ping

2014-01-01

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

Overview of recent results from the ATLAS experiment

CERN Document Server

Grabowska-Bold, Iwona; The ATLAS collaboration

2017-01-01

The heavy-ion program in the ATLAS experiment at the LHC originated as an extensive program to probe and characterize the hot, dense matter created in relativistic lead-lead collisions. In recent years, the program has also broadened to a detailed study of collective behavior in smaller systems. In particular, the techniques used to study larger systems are also applied to proton-proton and proton-lead collisions over a wide range of particle multiplicities, to try and understand the early-time dynamics which lead to similar flow-like features in all of the systems. Another recent development is a program studying ultra-peripheral collisions, which provide gamma-gamma and photonuclear processes over a wide range of CM energy, to probe the nuclear wavefunction. This talk presents the most recent results from the ATLAS experiment based on Run 1 and Run 2 data, including measurements of collectivity over a wide range of collision systems, potential nPDF modifications — using electroweak bosons, inclusive jets,...

Operational status of the uranium beam upgrade of the ATLAS accelerator

International Nuclear Information System (INIS)

Pardo, R.C.; Bollinger, L.M.; Nolen, J.A.

1993-01-01

The Positive-Ion Injector (PII) for ATLAS is complete. First beams from the new injector have been accelerated and used for experiments at ATLAS. The PH consists of an ECR ion source on a 350-kV platform and a low-velocity superconducting linac. The first acceleration of uranium for the experimental program has demonstrated the design goals of the project have been met. Since the summer of 1992, the new injecter has been used for the research program approximately 50% of the time. Longitudinal beam quality from the new injector has been measured to be significantly better than comparable beams from the tandem injecter. Changes to the mix of resonators in the main ATLAS accelerator to match better the velocity profile for heavy beams such as uranium are nearly complete and uranium energies up to 6.45 MeV per nucleon have been achieved. The operating experience of the new ATLAS facility will be discussed with emphasis on the measured beam quality as well as achieved beam energies and currents

Advances in ATLAS@Home towards a major ATLAS computing resource

CERN Document Server

Cameron, David; The ATLAS collaboration

2018-01-01

The volunteer computing project ATLAS@Home has been providing a stable computing resource for the ATLAS experiment since 2013. It has recently undergone some significant developments and as a result has become one of the largest resources contributing to ATLAS computing, by expanding its scope beyond traditional volunteers and into exploitation of idle computing power in ATLAS data centres. Removing the need for virtualization on Linux and instead using container technology has made the entry barrier significantly lower data centre participation and in this paper, we describe the implementation and results of this change. We also present other recent changes and improvements in the project. In early 2017 the ATLAS@Home project was merged into a combined LHC@Home platform, providing a unified gateway to all CERN-related volunteer computing projects. The ATLAS Event Service shifts data processing from file-level to event-level and we describe how ATLAS@Home was incorporated into this new paradigm. The finishing...

ATLAS Distributed Computing: Experience and Evolution

CERN Document Server

Nairz, A; The ATLAS collaboration

2013-01-01

The ATLAS experiment has just concluded its first running period which commenced in 2010. After two years of remarkable performance from the LHC and ATLAS, the experiment has accumulated more than 25 fb-1 of data. The total volume of beam and simulated data products exceeds 100 PB distributed across more than 150 computing centers around the world, managed by the experiment's distributed data management system. These sites have provided up to 150,000 computing cores to ATLAS's global production and analysis processing system, enabling a rich physics program including the discovery of the Higgs-like boson in 2012. The wealth of accumulated experience in global data-intensive computing at this massive scale, and the considerably more challenging requirements of LHC computing from 2014 when the LHC resumes operation, are driving a comprehensive design and development cycle to prepare a revised computing model together with data processing and management systems able to meet the demands of higher trigger rates, e...

ATLAS Future Framework Requirements Group Report

CERN Document Server

The ATLAS collaboration

2016-01-01

The Future Frameworks Requirements Group was constituted in Summer 2013 to consider and summarise the framework requirements from trigger and offline for configuring, scheduling and monitoring the data processing software needed by the ATLAS experiment. The principal motivation for such a re-examination arises from the current and anticipated evolution of CPUs, where multiple cores, hyper-threading and wide vector registers require a shift to a concurrent programming model. Such a model requires extensive changes in the current Gaudi/Athena frameworks and offers the opportunity to consider how HLT and offline processing can be better accommodated within the ATLAS framework. This note contains the report of the Future Frameworks Requirements Group.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

Science.gov (United States)

San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

2014-12-01

Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

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....

Networks in ATLAS

CERN Document Server

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

2017-01-01

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

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.

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...

The ATLAS Trigger algorithms upgrade and performance in Run 2

CERN Document Server

Bernius, Catrin; The ATLAS collaboration

2017-01-01

Title: The ATLAS Trigger algorithms upgrade and performance in Run 2 (TDAQ) The ATLAS trigger has been used very successfully for the online event selection during the first part of the second LHC run (Run-2) in 2015/16 at a center-of-mass energy of 13 TeV. The trigger system is composed of a hardware Level-1 trigger and a software-based high-level trigger; it reduces the event rate from the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. The excellent performance of the ATLAS trigger has been vital for the ATLAS physics program of Run-2, selecting interesting collision events for wide variety of physics signatures with high efficiency. The trigger selection capabilities of ATLAS during Run-2 have been significantly improved compared to Run-1, in order to cope with the higher event rates and pile-up which are the result of the almost doubling of the center-of-mass collision energy and the increase in the instantaneous luminosity of the LHC. At the Level-1 trigger the undertaken impr...

EnviroAtlas - Rare Ecosystems in the Conterminous United States

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset identifies rare ecosystems using base landcover data from the USGS GAP Analysis Program (Version 2, 2011) combined with landscape ecology...

Exotics searches in ATLAS

CERN Document Server

Wang, Renjie; The ATLAS collaboration

2017-01-01

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

ATLAS Thesis Award 2017

CERN Multimedia

Anthony, Katarina

2018-01-01

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

ATLAS

CERN Multimedia

Akhnazarov, V; Canepa, A; Bremer, J; Burckhart, H; Cattai, A; Voss, R; Hervas, L; Kaplon, J; Nessi, M; Werner, P; Ten kate, H; Tyrvainen, H; Vandelli, W; Krasznahorkay, A; Gray, H; Alvarez gonzalez, B; Eifert, T F; Rolando, G; Oide, H; Barak, L; Glatzer, J; Backhaus, M; Schaefer, D M; Maciejewski, J P; Milic, A; Jin, S; Von torne, E; Limbach, C; Medinnis, M J; Gregor, I; Levonian, S; Schmitt, S; Waananen, A; Monnier, E; Muanza, S G; Pralavorio, P; Talby, M; Tiouchichine, E; Tocut, V M; Rybkin, G; Wang, S; Lacour, D; Laforge, B; Ocariz, J H; Bertoli, W; Malaescu, B; Sbarra, C; Yamamoto, A; Sasaki, O; Koriki, T; Hara, K; Da silva gomes, A; Carvalho maneira, J; Marcalo da palma, A; Chekulaev, S; Tikhomirov, V; Snesarev, A; Buzykaev, A; Maslennikov, A; Peleganchuk, S; Sukharev, A; Kaplan, B E; Swiatlowski, M J; Nef, P D; Schnoor, U; Oakham, G F; Ueno, R; Orr, R S; Abouzeid, O; Haug, S; Peng, H; Kus, V; Vitek, M; Temming, K K; Dang, N P; Meier, K; Schultz-coulon, H; Geisler, M P; Sander, H; Schaefer, U; Ellinghaus, F; Rieke, S; Nussbaumer, A; Liu, Y; Richter, R; Kortner, S; Fernandez-bosman, M; Ullan comes, M; Espinal curull, J; Chiriotti alvarez, S; Caubet serrabou, M; Valladolid gallego, E; Kaci, M; Carrasco vela, N; Lancon, E C; Besson, N E; Gautard, V; Bracinik, J; Bartsch, V C; Potter, C J; Lester, C G; Moeller, V A; Rosten, J; Crooks, D; Mathieson, K; Houston, S C; Wright, M; Jones, T W; Harris, O B; Byatt, T J; Dobson, E; Hodgson, P; Hodgkinson, M C; Dris, M; Karakostas, K; Ntekas, K; Oren, D; Duchovni, E; Etzion, E; Oren, Y; Ferrer, L M; Testa, M; Doria, A; Merola, L; Sekhniaidze, G; Giordano, R; Ricciardi, S; Milazzo, A; Falciano, S; De pedis, D; Dionisi, C; Veneziano, S; Cardarelli, R; Verzegnassi, C; Soualah, R; Ochi, A; Ohshima, T; Kishiki, S; Linde, F L; Vreeswijk, M; Werneke, P; Muijs, A; Vankov, P H; Jansweijer, P P M; Dale, O; Lund, E; Bruckman de renstrom, P; Dabrowski, W; Adamek, J D; Wolters, H; Micu, L; Pantea, D; Tudorache, V; Mjoernmark, J; Klimek, P J; Ferrari, A; Abdinov, O; Akhoundov, A; Hashimov, R; Shelkov, G; Khubua, J; Ladygin, E; Lazarev, A; Glagolev, V; Dedovich, D; Lykasov, G; Zhemchugov, A; Zolnikov, Y; Ryabenko, M; Sivoklokov, S; Vasilyev, I; Shalimov, A; Lobanov, M; Paramoshkina, E; Mosidze, M; Bingul, A; Nodulman, L J; Guarino, V J; Yoshida, R; Drake, G R; Calafiura, P; Haber, C; Quarrie, D R; Alonso, J R; Anderson, C; Evans, H; Lammers, S W; Baubock, M; Anderson, K; Petti, R; Suhr, C A; Linnemann, J T; Richards, R A; Tollefson, K A; Holzbauer, J L; Stoker, D P; Pier, S; Nelson, A J; Isakov, V; Martin, A J; Adelman, J A; Paganini, M; Gutierrez, P; Snow, J M; Pearson, B L; Cleland, W E; Savinov, V; Wong, W; Goodson, J J; Li, H; Lacey, R A; Gordeev, A; Gordon, H; Lanni, F; Nevski, P; Rescia, S; Kierstead, J A; Liu, Z; Yu, W W H; Bensinger, J; Hashemi, K S; Bogavac, D; Cindro, V; Hoeferkamp, M R; Coelli, S; Iodice, M; Piegaia, R N; Alonso, F; Wahlberg, H P; Barberio, E L; Limosani, A; Rodd, N L; Jennens, D T; Hill, E C; Pospisil, S; Smolek, K; Schaile, D A; Rauscher, F G; Adomeit, S; Mattig, P M; Wahlen, H; Volkmer, F; Calvente lopez, S; Sanchis peris, E J; Pallin, D; Podlyski, F; Says, L; Boumediene, D E; Scott, W; Phillips, P W; Greenall, A; Turner, P; Gwilliam, C B; Kluge, T; Wrona, B; Sellers, G J; Millward, G; Adragna, P; Hartin, A; Alpigiani, C; Piccaro, E; Bret cano, M; Hughes jones, R E; Mercer, D; Oh, A; Chavda, V S; Carminati, L; Cavasinni, V; Fedin, O; Patrichev, S; Ryabov, Y; Nesterov, S; Grebenyuk, O; Sasso, J; Mahmood, H; Polsdofer, E; Dai, T; Ferretti, C; Liu, H; Hegazy, K H; Benjamin, D P; Zobernig, G; Ban, J; Brooijmans, G H; Keener, P; Williams, H H; Le geyt, B C; Hines, E J; Fadeyev, V; Schumm, B A; Law, A T; Kuhl, A D; Neubauer, M S; Shang, R; Gagliardi, G; Calabro, D; Conta, C; Zinna, M; Jones, G; Li, J; Stradling, A R; Hadavand, H K; Mcguigan, P; Chiu, P; Baldelomar, E; Stroynowski, R A; Kehoe, R L; De groot, N; Timmermans, C; Lach-heb, F; Addy, T N; Nakano, I; Moreno lopez, D; Grosse-knetter, J; Tyson, B; Rude, G D; Tafirout, R; Benoit, P; Danielsson, H O; Elsing, M; Fassnacht, P; Froidevaux, D; Ganis, G; Gorini, B; Lasseur, C; Lehmann miotto, G; Kollar, D; Aleksa, M; Sfyrla, A; Duehrssen-debling, K; Fressard-batraneanu, S; Van der ster, D C; Bortolin, C; Schumacher, J; Mentink, M; Geich-gimbel, C; Yau wong, K H; Lafaye, R; Crepe-renaudin, S; Albrand, S; Hoffmann, D; Pangaud, P; Meessen, C; Hrivnac, J; Vernay, E; Perus, A; Henrot versille, S L; Le dortz, O; Derue, F; Piccinini, M; Polini, A; Terada, S; Arai, Y; Ikeno, M; Fujii, H; Nagano, K; Ukegawa, F; Aguilar saavedra, J A; Conde muino, P; Castro, N F; Eremin, V; Kopytine, M; Sulin, V; Tsukerman, I; Korol, A; Nemethy, P; Bartoldus, R; Glatte, A; Chelsky, S; Van nieuwkoop, J; Bellerive, A; Sinervo, J K; Battaglia, A; Barbier, G J; Pohl, M; Rosselet, L; Alexandre, G B; Prokoshin, F; Pezoa rivera, R A; Batkova, L; Kladiva, E; Stastny, J; Kubes, T; Vidlakova, Z; Esch, H; Homann, M; Herten, L G; Zimmermann, S U; Pfeifer, B; Stenzel, H; Andrei, G V; Wessels, M; Buescher, V; Kleinknecht, K; Fiedler, F M; Schroeder, C D; Fernandez, E; Mir martinez, L; Vorwerk, V; Bernabeu verdu, J; Salt, J; Civera navarrete, J V; Bernard, R; Berriaud, C P; Chevalier, L P; Hubbard, R; Schune, P; Nikolopoulos, K; Batley, J R; Brochu, F M; Phillips, A W; Teixeira-dias, P J; Rose, M B D; Buttar, C; Buckley, A G; Nurse, E L; Larner, A B; Boddy, C; Henderson, J; Costanzo, D; Tarem, S; Maccarrone, G; Laurelli, P F; Alviggi, M; Chiaramonte, R; Izzo, V; Palumbo, V; Fraternali, M; Crosetti, G; Marchese, F; Yamaguchi, Y; Hessey, N P; Mechnich, J M; Liebig, W; Kastanas, K A; Sjursen, T B; Zalieckas, J; Cameron, D G; Banka, P; Kowalewska, A B; Dwuznik, M; Mindur, B; Boldea, V; Hedberg, V; Smirnova, O; Sellden, B; Allahverdiyev, T; Gornushkin, Y; Koultchitski, I; Tokmenin, V; Chizhov, M; Gongadze, A; Khramov, E; Sadykov, R; Krasnoslobodtsev, I; Smirnova, L; Kramarenko, V; Minaenko, A; Zenin, O; Beddall, A J; Ozcan, E V; Hou, S; Wang, S; Moyse, E; Willocq, S; Chekanov, S; Le compte, T J; Love, J R; Ciocio, A; Hinchliffe, I; Tsulaia, V; Gomez, A; Luehring, F; Zieminska, D; Huth, J E; Gonski, J L; Oreglia, M; Tang, F; Shochet, M J; Costin, T; Mcleod, A; Uzunyan, S; Martin, S P; Pope, B G; Schwienhorst, R H; Brau, J E; Ptacek, E S; Milburn, R H; Sabancilar, E; Lauer, R; Saleem, M; Mohamed meera lebbai, M R; Lou, X; Reeves, K B; Rijssenbeek, M; Novakova, P N; Rahm, D; Steinberg, P A; Wenaus, T J; Paige, F; Ye, S; Kotcher, J R; Assamagan, K A; Oliveira damazio, D; Maeno, T; Henry, A; Dushkin, A; Costa, G; Meroni, C; Resconi, S; Lari, T; Biglietti, M; Lohse, T; Gonzalez silva, M L; Monticelli, F G; Saavedra, A F; Patel, N D; Ciodaro xavier, T; Asevedo nepomuceno, A; Lefebvre, M; Albert, J E; Kubik, P; Faltova, J; Turecek, D; Solc, J; Schaile, O; Ebke, J; Losel, P J; Zeitnitz, C; Sturm, P D; Barreiro alonso, F; Modesto alapont, P; Soret medel, J; Garzon alama, E J; Gee, C N; Mccubbin, N A; Sankey, D; Emeliyanov, D; Dewhurst, A L; Houlden, M A; Klein, M; Burdin, S; Lehan, A K; Eisenhandler, E; Lloyd, S; Traynor, D P; Ibbotson, M; Marshall, R; Pater, J; Freestone, J; Masik, J; Haughton, I; Manousakis katsikakis, A; Sampsonidis, D; Krepouri, A; Roda, C; Sarri, F; Fukunaga, C; Nadtochiy, A; Kara, S O; Timm, S; Alam, S M; Rashid, T; Goldfarb, S; Espahbodi, S; Marley, D E; Rau, A W; Dos anjos, A R; Haque, S; Grau, N C; Havener, L B; Thomson, E J; Newcomer, F M; Hansl-kozanecki, G; Deberg, H A; Takeshita, T; Goggi, V; Ennis, J S; Olness, F I; Kama, S; Ordonez sanz, G; Koetsveld, F; Elamri, M; Mansoor-ul-islam, S; Lemmer, B; Kawamura, G; Bindi, M; Schulte, S; Kugel, A; Kretz, M P; Kurchaninov, L; Blanchot, G; Chromek-burckhart, D; Di girolamo, B; Francis, D; Gianotti, F; Nordberg, M Y; Pernegger, H; Roe, S; Boyd, J; Wilkens, H G; Pauly, T; Fabre, C; Tricoli, A; Bertet, D; Ruiz martinez, M A; Arnaez, O L; Lenzi, B; Boveia, A J; Gillberg, D I; Davies, J M; Zimmermann, R; Uhlenbrock, M; Kraus, J K; Narayan, R T; John, A; Dam, M; Padilla aranda, C; Bellachia, F; Le flour chollet, F M; Jezequel, S; Dumont dayot, N; Fede, E; Mathieu, M; Gensolen, F D; Alio, L; Arnault, C; Bouchel, M; Ducorps, A; Kado, M M; Lounis, A; Zhang, Z P; De vivie de regie, J; Beau, T; Bruni, A; Bruni, G; Grafstrom, P; Romano, M; Lasagni manghi, F; Massa, L; Shaw, K; Ikegami, Y; Tsuno, S; Kawanishi, Y; Benincasa, G; Blagov, M; Fedorchuk, R; Shatalov, P; Romaniouk, A; Belotskiy, K; Timoshenko, S; Hooft van huysduynen, L; Lewis, G H; Wittgen, M M; Mader, W F; Rudolph, C J; Gumpert, C; Mamuzic, J; Rudolph, G; Schmid, P; Corriveau, F; Belanger-champagne, C; Yarkoni, S; Leroy, C; Koffas, T; Harack, B D; Weber, M S; Beck, H; Leger, A; Gonzalez sevilla, S; Zhu, Y; Gao, J; Zhang, X; Blazek, T; Rames, J; Sicho, P; Kouba, T; Sluka, T; Lysak, R; Ristic, B; Kompatscher, A E; Von radziewski, H; Groll, M; Meyer, C P; Oberlack, H; Stonjek, S M; Cortiana, G; Werthenbach, U; Ibragimov, I; Czirr, H S; Cavalli-sforza, M; Puigdengoles olive, C; Tallada crespi, P; Marti i garcia, S; Gonzalez de la hoz, S; Guyot, C; Meyer, J; Schoeffel, L O; Garvey, J; Hawkes, C; Hillier, S J; Staley, R J; Salvatore, P F; Santoyo castillo, I; Carter, J; Yusuff, I B; Barlow, N R; Berry, T S; Savage, G; Wraight, K G; Steele, G E; Hughes, G; Walder, J W; Love, P A; Crone, G J; Waugh, B M; Boeser, S; Sarkar, A M; Holmes, A; Massey, R; Pinder, A; Nicholson, R; Korolkova, E; Katsoufis, I; Maltezos, S; Tsipolitis, G; Leontsinis, S; Levinson, L J; Shoa, M; Abramowicz, H E; Bella, G; Gershon, A; Urkovsky, E; Taiblum, N; Gatti, C; Della pietra, M; Lanza, A; Negri, A; Flaminio, V; Lacava, F; Petrolo, E; Pontecorvo, L; Rosati, S; Zanello, L; Pasqualucci, E; Di ciaccio, A; Giordani, M; Yamazaki, Y; Jinno, T; Nomachi, M; De jong, P J; Ferrari, P; Homma, J; Van der graaf, H; Igonkina, O B; Stugu, B S; Buanes, T; Pedersen, M; Turala, M; Olszewski, A J; Koperny, S Z; Onofre, A; Castro nunes fiolhais, M; Alexa, C; Cuciuc, C M; Akesson, T P A; Hellman, S L; Milstead, D A; Bondyakov, A; Pushnova, V; Budagov, Y; Minashvili, I; Romanov, V; Sniatkov, V; Tskhadadze, E; Kalinovskaya, L; Shalyugin, A; Tavkhelidze, A; Rumyantsev, L; Karpov, S; Soloshenko, A; Vostrikov, A; Borissov, E; Solodkov, A; Vorob'ev, A; Sidorov, S; Malyaev, V; Lee, S; Grudzinski, J J; Virzi, J S; Vahsen, S E; Lys, J; Penwell, J W; Yan, Z; Bernard, C S; Barreiro guimaraes da costa, J P; Oliver, J N; Merritt, F S; Brubaker, E M; Kapliy, A; Kim, J; Zutshi, V V; Burghgrave, B O; Abolins, M A; Arabidze, G; Caughron, S A; Frey, R E; Radloff, P T; Schernau, M; Murillo garcia, R; Porter, R A; Mccormick, C A; Karn, P J; Sliwa, K J; Demers konezny, S M; Strauss, M G; Mueller, J A; Izen, J M; Klimentov, A; Lynn, D; Polychronakos, V; Radeka, V; Sondericker, J I I I; Bathe, S; Duffin, S; Chen, H; De castro faria salgado, P E; Kersevan, B P; Lacker, H M; Schulz, H; Kubota, T; Tan, K G; Yabsley, B D; Nunes de moura junior, N; Pinfold, J; Soluk, R A; Ouellette, E A; Leitner, R; Sykora, T; Solar, M; Sartisohn, G; Hirschbuehl, D; Huning, D; Fischer, J; Terron cuadrado, J; Glasman kuguel, C B; Lacasta llacer, C; Lopez-amengual, J; Calvet, D; Chevaleyre, J; Daudon, F; Montarou, G; Guicheney, C; Calvet, S P J; Tyndel, M; Dervan, P J; Maxfield, S J; Hayward, H S; Beck, G; Cox, B; Da via, C; Paschalias, P; Manolopoulou, M; Ragusa, F; Cimino, D; Ezzi, M; Fiuza de barros, N F; Yildiz, H; Ciftci, A K; Turkoz, S; Zain, S B; Tegenfeldt, F; Chapman, J W; Panikashvili, N; Bocci, A; Altheimer, A D; Martin, F F; Fratina, S; Jackson, B D; Grillo, A A; Seiden, A; Watts, G T; Mangiameli, S; Johns, K A; O'grady, F T; Errede, D R; Darbo, G; Ferretto parodi, A; Leahu, M C; Farbin, A; Ye, J; Liu, T; Wijnen, T A; Naito, D; Takashima, R; Sandoval usme, C E; Zinonos, Z; Moreno llacer, M; Agricola, J B; Mcgovern, S A; Sakurai, Y; Trigger, I M; Qing, D; De silva, A S; Butin, F; Dell'acqua, A; Hawkings, R J; Lamanna, M; Mapelli, L; Passardi, G; Rembser, C; Tremblet, L; Andreazza, W; Dobos, D A; Koblitz, B; Bianco, M; Dimitrov, G V; Schlenker, S; Armbruster, A J; Rammensee, M C; Romao rodrigues, L F; Peters, K; Pozo astigarraga, M E; Yi, Y; Desch, K K; Huegging, F G; Muller, K K; Stillings, J A; Schaetzel, S; Xella, S; Hansen, J D; Colas, J; Daguin, G; Wingerter, I; Ionescu, G D; Ledroit, F; Lucotte, A; Clement, B E; Stark, J; Clemens, J; Djama, F; Knoops, E; Coadou, Y; Vigeolas-choury, E; Feligioni, L; Iconomidou-fayard, L; Imbert, P; Schaffer, A C; Nikolic, I; Trincaz-duvoid, S; Warin, P; Camard, A F; Ridel, M; Pires, S; Giacobbe, B; Spighi, R; Villa, M; Negrini, M; Sato, K; Gavrilenko, I; Akimov, A; Khovanskiy, V; Talyshev, A; Voronkov, A; Hakobyan, H; Mallik, U; Shibata, A; Konoplich, R; Barklow, T L; Koi, T; Straessner, A; Stelzer, B; Robertson, S H; Vachon, B; Stoebe, M; Keyes, R A; Wang, K; Billoud, T R V; Strickland, V; Batygov, M; Krieger, P; Palacino caviedes, G D; Gay, C W; Jiang, Y; Han, L; Liu, M; Zenis, T; Lokajicek, M; Staroba, P; Tasevsky, M; Popule, J; Svatos, M; Seifert, F; Landgraf, U; Lai, S T; Schmitt, K H; Achenbach, R; Schuh, N; Kiesling, C; Macchiolo, A; Nisius, R; Schacht, P; Von der schmitt, J G; Kortner, O; Atlay, N B; Segura sole, E; Grinstein, S; Neissner, C; Bruckner, D M; Oliver garcia, E; Boonekamp, M; Perrin, P; Gaillot, F M; Wilson, J A; Thomas, J P; Thompson, P D; Palmer, J D; Falk, I E; Chavez barajas, C A; Sutton, M R; Robinson, D; Kaneti, S A; Wu, T; Robson, A; Shaw, C; Buzatu, A; Qin, G; Jones, R; Bouhova-thacker, E V; Viehhauser, G; Weidberg, A R; Gilbert, L; Johansson, P D C; Orphanides, M; Vlachos, S; Behar harpaz, S; Papish, O; Lellouch, D J H; Turgeman, D; Benary, O; La rotonda, L; Vena, R; Tarasio, A; Marzano, F; Gabrielli, A; Di stante, L; Liberti, B; Aielli, G; Oda, S; Nozaki, M; Takeda, H; Hayakawa, T; Miyazaki, K; Maeda, J; Sugimoto, T; Pettersson, N E; Bentvelsen, S; Groenstege, H L; Lipniacka, A; Vahabi, M; Ould-saada, F; Chwastowski, J J; Hajduk, Z; Kaczmarska, A; Olszowska, J B; Trzupek, A; Staszewski, R P; Palka, M; Constantinescu, S; Jarlskog, G; Lundberg, B L A; Pearce, M; Ellert, M F; Bannikov, A; Fechtchenko, A; Iambourenko, V; Kukhtin, V; Pozdniakov, V; Topilin, N; Vorozhtsov, S; Khassanov, A; Fliaguine, V; Kharchenko, D; Nikolaev, K; Kotenov, K; Kozhin, A; Zenin, A; Ivashin, A; Golubkov, D; Beddall, A; Su, D; Dallapiccola, C J; Cranshaw, J M; Price, L; Stanek, R W; Gieraltowski, G; Zhang, J; Gilchriese, M; Shapiro, M; Ahlen, S; Morii, M; Taylor, F E; Miller, R J; Phillips, F H; Torrence, E C; Wheeler, S J; Benedict, B H; Napier, A; Hamilton, S F; Petrescu, T A; Boyd, G R J; Jayasinghe, A L; Smith, J M; Mc carthy, R L; Adams, D L; Le vine, M J; Zhao, X; Patwa, A M; Baker, M; Kirsch, L; Krstic, J; Simic, L; Filipcic, A; Seidel, S C; Cantore-cavalli, D; Baroncelli, A; Kind, O M; Scarcella, M J; Maidantchik, C L L; Seixas, J; Balabram filho, L E; Vorobel, V; Spousta, M; Strachota, P; Vokac, P; Slavicek, T; Bergmann, B L; Biebel, O; Kersten, S; Srinivasan, M; Trefzger, T; Vazeille, F; Insa, C; Kirk, J; Middleton, R; Burke, S; Klein, U; Morris, J D; Ellis, K V; Millward, L R; 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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...

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.

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

Science.gov (United States)

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

2017-09-05

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

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.

ATLAS Offline Software Performance Monitoring and Optimization

CERN Document Server

Chauhan, N; Kittelmann, T; Langenberg, R; Mandrysch , R; Salzburger, A; Seuster, R; Ritsch, E; Stewart, G; van Eldik, N; Vitillo, R

2014-01-01

In a complex multi-developer, multi-package software environment, such as the ATLAS offline Athena framework, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide optimisation. Code can be instrumented firstly using the PAPI tool, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles and instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event gives a good understanding of the whole algorithm level performance of ATLAS code. Further data can be obtained using pin, a dynamic binary instrumentation tool. Pintools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is...

Operational experience with the ATLAS Pixel Detector

CERN Document Server

Ince, T; The ATLAS collaboration

2012-01-01

The ATLAS Pixel Detector is the innermost element of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this paper, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 96.2% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience of the ATLAS Pixel detector

CERN Document Server

Hirschbuehl, D; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience of the ATLAS Pixel Detector

CERN Document Server

Marcisovsky, M; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

ATLAS Offline Software Performance Monitoring and Optimization

CERN Document Server

Chauhan, N; The ATLAS collaboration; Kittelmann, T; Langenberg, R; Mandrysch , R; Salzburger, A; Seuster, R; Ritsch, E; Stewart, G; van Eldik, N; Vitillo, R

2013-01-01

In a complex multi-developer, multi-package software environment, such as the ATLAS offline Athena framework, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide optimisation. Code can be instrumented firstly using the PAPI tool, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles and instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event gives a good understanding of the whole algorithm level performance of ATLAS code. Further data can be obtained using pin, a dynamic binary instrumentation tool. Pintools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is...

Heavy Flavour Production and Properties at CMS and ATLAS

CERN Document Server

Barton, Adam Edward; The ATLAS collaboration

2018-01-01

Measurements of heavy flavour properties and production are an important part of the physics program of the ATLAS and CMS experiments at LHC. They can potentially expose physics beyond the standard model, constrain supersymmetry and advance hadron spectroscopy and test QCD. In the past years, the two collaborations have published results in several different fields, such as rare decays, searches for new states, CP and P violation and quarkonia polarisation. In this note, some of the most recent results from ATLAS and CMS are summarised.

Heavy Flavour Production and Properties at ATLAS and CMS

CERN Document Server

Barton, Adam Edward; The ATLAS collaboration

2017-01-01

Measurements of heavy flavour properties and production are an important part of the physics program of the ATLAS and CMS experiments at LHC. They can potentially expose physics beyond the standard model, constrain supersymmetry and advance hadron spectroscopy and test QCD. In the past years, the two collaborations have published results in several different fields, such as rare decays, searches for new states, CP and P violation and quarkonia polarization. In this note, some of the most recent results from ATLAS and CMS are summarized

Wind Atlas for South Africa (WASA) Observational wind atlas for 10 met. stations in Northern, Western and Eastern Cape provinces

DEFF Research Database (Denmark)

Mortensen, Niels Gylling; Hansen, Jens Carsten; Kelly, Mark C.

As part of the “Wind Atlas for South Africa” project, microscale modelling has been carried out for 10 meteorological stations in Northern, Western and Eastern Cape provinces. Wind speed and direction data from the ten 60-m masts have been analysed using the Wind Atlas Analysis and Application...... Program (WAsP 11). The windclimatological inputs are the observed wind climates derived from the WAsP Climate Analyst. Topographical inputs are elevation maps constructed from SRTM 3 data and rough-ness length maps constructed from SWBD data and Google Earth satellite imagery. Summaries are given...... of the data measured at the 10 masts, mainly for a 3-year reference period from October 2010 to September 2013. The main result of the microscale modelling is observational wind atlas data sets, which can be used for verification of the mesoscale modelling. In addition, the microscale modelling itself has...

Wind Atlas for South Africa (WASA) Observational wind atlas for 10 met. stations in Northern, Western and Eastern Cape provinces

DEFF Research Database (Denmark)

Mortensen, Niels Gylling; Hansen, Jens Carsten; Kelly, Mark C.

As part of the “Wind Atlas for South Africa” project, microscale modelling has been carried out for 10 meteorological stations in Northern, Western and Eastern Cape provinces. Wind speed and direction data from the ten 60-m masts have been analysed using the Wind Atlas Analysis and Application...... Program (WAsP 11). The wind-climatological inputs are the observed wind climates derived from the WAsP Climate Analyst. Topographical inputs are elevation maps constructed from SRTM 3 data and roughness length maps constructed from SWBD data and Google Earth satellite imagery. Summaries are given...... of the data measured at the 10 masts, mainly for a 3-year reference period from October 2010 to September 2013. The main result of the microscale modelling is observational wind atlas data sets, which can be used for verification of the mesoscale modelling. In addition, the microscale modelling itself has...

Constraining Dark Matter with ATLAS

CERN Document Server

Czodrowski, Patrick; The ATLAS collaboration

2017-01-01

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

Heavy Ion Physics Prospects with the ATLAS Detector at the LHC

CERN Document Server

Grau, N

2008-01-01

The next great energy frontier in Relativistic Heavy Ion Collisions is quickly approaching with the completion of the Large Hadron Collider and the ATLAS experiment is poised to make important contributions in understanding QCD matter at extreme conditions. While designed for high-pT measurements in high-energy p+p collisions, the detector is well suited to study many aspects of heavy ion collisions from bulk phenomena to high-pT and heavy flavor physics. With its large and finely segmented electromagnetic and hadronic calorimeters, the ATLAS detector excels in measurements of photons and jets, observables of great interest at the LHC. In this talk, we highlight the performance of the ATLAS detector for Pb+Pb collisions at the LHC with special emphasis on a key feature of the ATLAS physics program: jet and direct photon measurements.

Probabilistic liver atlas construction.

Science.gov (United States)

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

2017-01-13

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

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.

The simulation for the ATLAS experiment Present status and outlook

CERN Document Server

Rimoldi, A; Gallas, M; Nairz, A; Boudreau, J; Tsulaia, V; Costanzo, D

2004-01-01

The simulation program for the ATLAS experiment is presently operational in a full OO environment. This important physics application has been successfully integrated into ATLAS's common analysis framework, ATHENA. In the last year, following a well stated strategy of transition from a GEANT3 to a GEANT4-based simulation, a careful validation programme confirmed the reliability, performance and robustness of this new tool, as well as its consistency with the results of previous simulation. Generation, simulation and digitization steps on different sets of full physics events we retested for performance. The same software used to simulate the full the ATLAS detector is also used with testbeam configurations. Comparisons to real data in the testbeam validate both the detector description and the physics processes within each subcomponent. In this paper we present the current status of ATLAS GEANT4 simulation, describe the functionality tests performed during its validation phase, and the experience with distrib...

Physics potential of ATLAS upgrades at HL-LHC

CERN Document Server

Testa, Marianna; The ATLAS collaboration

2017-01-01

The High Luminosity-Large Hadron Collider (HL-LHC) is expected to start in 2026 and to pro- vide an integrated luminosity of 3000 fb−1 in ten years, a factor 10 more than what will be collected by 2023. This high statistics will allow ATLAS to perform precise measurements in the Higgs sector and improve searches for new physics at the TeV scale. The luminosity needed is L ∼ 7.51034 cm−2 s−1, corresponding to ∼200 additional proton-proton pile- up interactions. To face such harsh environment some sub-detectors of the ATLAS experiment will be upgraded or completely substituted. The performances of the new or upgraded ATLAS sub-detectors are presented, focusing in particular on the new inner tracker and a proposed high granularity time device. The impact of those upgrades on crucial physics measurements for HL-LHC program is also shown.

Event filter monitoring with the ATLAS tile calorimeter

CERN Document Server

Fiorini, L

2008-01-01

The ATLAS Tile Calorimeter detector is presently involved in an intense phase of subsystems integration and commissioning with muons of cosmic origin. Various monitoring programs have been developed at different levels of the data flow to tune the set-up of the detector running conditions and to provide a fast and reliable assessment of the data quality already during data taking. This paper focuses on the monitoring system integrated in the highest level of the ATLAS trigger system, the Event Filter, and its deployment during the Tile Calorimeter commissioning with cosmic ray muons. The key feature of Event Filter monitoring is the capability of performing detector and data quality control on complete physics events at the trigger level, hence before events are stored on disk. In ATLAS' online data flow, this is the only monitoring system capable of giving a comprehensive event quality feedback.

Early operational experience with uranium beams at ATLAS

International Nuclear Information System (INIS)

Pardo, R.C.; Nolen, J.A.; Specht, J.R.

1994-01-01

The first acceleration of a uranium beam using the new ATLAS Positive Ion Injector(PII) took place on July 27, 1992. Since that first run, ATLAS and PII have completely achieved the design goals of the project and now provide high-current heavy-ion beams with energies beyond the Coulomb barrier for the research program. ATLAS routinely and reliably provides low-emittance beams of uranium and other very high-mass ions at energies in excess of 6 MeV/n with available on-target beam intensities exceeding 5 particle nA. The expectation that the beam quality for heavy beams would be significantly better than that of the tandem injector has been fully realized. The longitudinal emittance of beams from the PII is typically one-third that of similar beams from the tandem injector. In the past year ATLAS provided uranium beams for approximately 19% of the total research beam time, while beams with A≥100 were used 33% of the time. The system performance and techniques developed which made for this successful result will be discussed. Improvement projects underway will be presented and future goals described

ATLAS-AWS

International Nuclear Information System (INIS)

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

2010-01-01

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

ATLAS Future Plans: Upgrade and the Physics with High Luminosity

Directory of Open Access Journals (Sweden)

Rajagopalan S.

2013-05-01

Full Text Available The ATLAS experiment is planning a series of detector upgrades to cope with the planned increases in instantaneous luminosity and multiple interactions per crossing to maintain its physics capabilities. During the coming decade, the Large Hadron Collider will collide protons on protons at a center of mass energy up to 14 TeV with luminosities steadily increasing in a phased approach to over 5 × 1034 cm−2s−1. The resulting large data sets will significantly enhance the physics reach of the ATLAS detector building on the recent discovery of the Higgs-like boson. The planned detector upgrades being designed to cope with the increasing luminosity and its impact on the ATLAS physics program will be discussed.

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...

A Roadmap to Continuous Integration for ATLAS Software Development

Science.gov (United States)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Analysis Facility infrastructure (TIER3) for ATLAS High Energy physics experiment

International Nuclear Information System (INIS)

Gonzalez de la Hoz, S.; March, L.; Ros, E.; Sanchez, J.; Amoros, G.; Fassi, F.; Fernandez, A.; Kaci, M.; Lamas, A.; Salt, J.

2007-01-01

ATLAS project has been asked to define the scope and role of Tier-3 resources (facilities or centres) within the existing ATLAS computing model, activities and facilities. This document attempts to address these questions by describing Tier-3 resources generally, and their relationship to the ATLAS Software and Computing Project. Originally the tiered computing model came out of MONARC (see http://monarc.web.cern.ch/MONARC/) work and was predicated upon the network being a scarce resource. In this model the tiered hierarchy ranged from the Tier-0 (CERN) down to the desktop or workstation (Tier 3). The focus on defining the roles of each tiered component has evolved with the initial emphasis on the Tier-0 (CERN) and Tier-1 (National centres) definition and roles. The various LHC projects, including ATLAS, then evolved the tiered hierarchy to include Tier-2s (Regional centers) as part of their projects. Tier-3s, on the other hand, have (implicitly and sometime explicitly) been defined as whatever an institution could construct to support their Physics goals using institutional and otherwise leveraged resources and therefore have not been considered to be part of the official ATLAS Research Program computing resources nor under their control, meaning there is no formal MOU process to designate sites as Tier-3s and no formal control of the program over the Tier-3 resources. Tier-3s are the responsibility of individual institutions to define, fund, deploy and support. However, having noted this, we must also recognize that Tier-3s must exist and will have implications for how our computing model should support ATLAS physicists. Tier-3 users will want to access data and simulations and will want to enable their Tier-3 resources to support their analysis and simulation work. Tiers 3s are an important resource for physicists to analyze LHC (Large Hadron Collider) data. This document will define how Tier-3s should best interact with the ATLAS computing model, detail the

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

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

Science.gov (United States)

Zikic, D; Glocker, B; Criminisi, A

2014-12-01

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

Unifying cancer and normal RNA sequencing data from different sources

Science.gov (United States)

Wang, Qingguo; Armenia, Joshua; Zhang, Chao; Penson, Alexander V.; Reznik, Ed; Zhang, Liguo; Minet, Thais; Ochoa, Angelica; Gross, Benjamin E.; Iacobuzio-Donahue, Christine A.; Betel, Doron; Taylor, Barry S.; Gao, Jianjiong; Schultz, Nikolaus

2018-01-01

Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare. PMID:29664468

Silicon strip detectors for the ATLAS upgrade

CERN Document Server

Gonzalez Sevilla, S; The ATLAS collaboration

2011-01-01

The Large Hadron Collider at CERN will extend its current physics program by increasing the peak luminosity by one order of magnitude. For ATLAS, one of the two general-purpose experiments of the LHC, an upgrade scenario will imply the complete replacement of its internal tracker due to the harsh conditions in terms of particle rates and radiation doses. New radiation-hard prototype n-in-p silicon sensors have been produced for the short-strip region of the future ATLAS tracker. The sensors have been irradiated up to the fluences expected in the high-luminous LHC collider. This paper summarizes recent results on the performance of the irradiated n-in-p detectors.

Myeloid translocation genes differentially regulate colorectal cancer programs

Science.gov (United States)

Parang, Bobak; Bradley, Amber M.; Mittal, Mukul K.; Short, Sarah P.; Thompson, Joshua J.; Barrett, Caitlyn W.; Naik, Rishi D.; Bilotta, Anthony J.; Washington, Mary K.; Revetta, Frank L.; Smith, Jesse J.; Chen, Xi; Wilson, Keith T.; Hiebert, Scott W.; Williams, Christopher S.

2016-01-01

Myeloid translocation genes (MTGs), originally identified as chromosomal translocations in acute myelogenous leukemia, are transcriptional corepressors that regulate hematopoietic stem cell programs. Analysis of The Cancer Genome Atlas (TCGA) database revealed that MTGs were mutated in epithelial malignancy and suggested that loss of function might promote tumorigenesis. Genetic deletion of MTGR1 and MTG16 in the mouse has revealed unexpected and unique roles within the intestinal epithelium. Mtgr1−/− mice have progressive depletion of all intestinal secretory cells, and Mtg16−/− mice have a decrease in goblet cells. Furthermore, both Mtgr1−/− and Mtg16−/− mice have increased intestinal epithelial cell proliferation. We thus hypothesized that loss of MTGR1 or MTG16 would modify Apc1638/+-dependent intestinal tumorigenesis. Mtgr1−/− mice, but not Mtg16−/− mice, had a 10-fold increase in tumor multiplicity. This was associated with more advanced dysplasia, including progression to invasive adenocarcinoma, and augmented intratumoral proliferation. Analysis of ChIP-seq datasets for MTGR1 and MTG16 targets indicated that MTGR1 can regulate Wnt and Notch signaling. In support of this, immunohistochemistry and gene expression analysis revealed that both Wnt and Notch signaling pathways were hyperactive in Mtgr1−/− tumors. Furthermore, in human colorectal cancer (CRC) samples MTGR1 was downregulated at both the transcript and protein level. Overall our data indicates that MTGR1 has a context dependent effect on intestinal tumorigenesis. PMID:27270437

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.

Concepts and Plans towards fast large scale Monte Carlo production for the ATLAS Experiment

Science.gov (United States)

Ritsch, E.; Atlas Collaboration

2014-06-01

The huge success of the physics program of the ATLAS experiment at the Large Hadron Collider (LHC) during Run 1 relies upon a great number of simulated Monte Carlo events. This Monte Carlo production takes the biggest part of the computing resources being in use by ATLAS as of now. In this document we describe the plans to overcome the computing resource limitations for large scale Monte Carlo production in the ATLAS Experiment for Run 2, and beyond. A number of fast detector simulation, digitization and reconstruction techniques are being discussed, based upon a new flexible detector simulation framework. To optimally benefit from these developments, a redesigned ATLAS MC production chain is presented at the end of this document.

Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

Science.gov (United States)

Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

2017-07-01

Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.

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...

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.

Danish extreme wind atlas: Background and methods for a WAsP engineering option

Energy Technology Data Exchange (ETDEWEB)

Rathmann, O; Kristensen, L; Mann, J [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark); Hansen, S O [Svend Ole Hansen ApS, Copenhagen (Denmark)

1999-03-01

Extreme wind statistics is necessary design information when establishing wind farms and erecting bridges, buildings and other structures in the open air. Normal mean wind statistics in terms of directional and speed distribution may be estimated by wind atlas methods and are used to estimate e.g. annual energy output for wind turbines. It is the purpose of the present work to extend the wind atlas method to also include the local extreme wind statistics so that an extreme value as e.g. the 50-year wind can be estimated at locations of interest. Together with turbulence estimates such information is important regarding the necessary strength of wind turbines or structures to withstand high wind loads. In the `WAsP Engineering` computer program a flow model, which includes a model for the dynamic roughness of water surfaces, is used to realise such an extended wind atlas method. With basis in an extended wind atlas, also containing extreme wind statistics, this allows the program to estimate extreme winds in addition to mean winds and turbulence intensities at specified positions and heights. (au) EFP-97. 15 refs.

New format for ATLAS e-news

CERN Multimedia

Pauline Gagnon

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

Dark Matter Searches at ATLAS

CERN Multimedia

CERN. Geneva

2016-01-01

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

Monitoring radiation damage in the ATLAS pixel detector

CERN Document Server

Schorlemmer, André Lukas; Quadt, Arnulf; Große-Knetter, Jörn; Rembser, Christoph; Di Girolamo, Beniamino

2014-11-05

Radiation hardness is one of the most important features of the ATLAS pixel detector in order to ensure a good performance and a long lifetime. Monitoring of radiation damage is crucial in order to assess and predict the expected performance of the detector. Key values for the assessment of radiation damage in silicon, such as the depletion voltage and depletion depth in the sensors, are measured on a regular basis during operations. This thesis summarises the monitoring program that is conducted in order to assess the impact of radiation damage and compares it to model predictions. In addition, the physics performance of the ATLAS detector highly depends on the amount of disabled modules in the ATLAS pixel detector. A worrying amount of module failures was observed during run I. Thus it was decided to recover repairable modules during the long shutdown (LS1) by extracting the pixel detector. The impact of the module repairs and module failures on the detector performance is analysed in this thesis.

Recent Tests of QCD with the ATLAS Detector

CERN Document Server

Callea, Giuseppe; The ATLAS collaboration

2018-01-01

The ATLAS Collaboration has a large program to study various aspects of Quantum Chromodynamics starting from non-perturbative effects over diffractive physics to high precision perturbative calculations. In this talk, we review the latest results on Bose-Einstein correlations measured with the ATLAS detector along with an analysis of the momentum difference between charged hadrons in high–energy proton–proton collisions. The latter allows the investigation of observables sensitive to the predictions of the quantized string model. Going to higher energy scales, we present first measurements of jet substructure quantities at a hadron collider, calculated at next-to-next-to-leading-logarithm accuracy. In particular, the soft drop mass is measured in dijet events with the ATLAS detector at 13 TeV, unfolded to particle-level and compared to Monte Carlo simulations. Perturbative QCD at highest energies can be precisely tested with the measurement of particle jet production of which we present the latest results...

Data Federation Strategies for ATLAS using XRootD

CERN Document Server

Gardner, R; The ATLAS collaboration; Duckeck, G; Elmsheuser, J; Hanushevski, A; Hönig, F; Iven, J; Legger, F; Vukotic, I; Yang, W

2014-01-01

In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the w...

Data Federation Strategies for ATLAS using XRootD

CERN Document Server

Gardner, R; The ATLAS collaboration; Duckeck, G; Elmsheuser, J; Hanushevski, A; Hönig, F; Iven, J; Legger, F; Vukotic, I; Yang, W

2013-01-01

In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the w...

Heavy flavour production and properties at CMS and ATLAS

CERN Document Server

Barton, Adam Edward; The ATLAS collaboration

2018-01-01

The ATLAS and CMS experiments have carried out a rich heavy flavor physics program since the start of LHC data taking. In the current note some of the most recent results obtained by the two collaborations are shown.

Atlas Pulsed Power System: a Driver for Multi-Megagauss Fields

International Nuclear Information System (INIS)

Cochrane, J.C.; Bartsch, R.R.; Bennett, G.A.; Bowman, D.W.; Davis, H.A.; Ekdahl, C.A.; Gribble, R.F.; Kimerly, H.J.; Nielsen, K.E.; Parsons, W.M.; Paul, J.D.; Scudder, D.W.; Trainor, R.J.; Thompson, M.C.; Watt, R.G.

1998-01-01

Atlas is a pulsed power machine designed for hydrodynamic experiments for the Los Alamos High Energy Density Physics Experimental program. It is presently under construction and should be operational in late 2000. Atlas will store 23 MJ at an erected voltage of 240 kV. This will produce a current of 30 MA into a static load and as much as 32 MA into a dynamic load. The current pulse will have a rise time of approximately5micros and will produce a magnetic field driving the impactor liner of several hundred Tesla at the target radius of one to two centimeters. The collision can produce shock pressures of approximately15 megabars. Design of the pulsed power system will be presented along with data obtained from the Atlas prototype Marx module

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.

Evolution of the ATLAS Distributed Computing during the LHC long shutdown

CERN Document Server

Campana, S; The ATLAS collaboration

2013-01-01

The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the WLCG distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileu...

Concepts and Plans towards fast large scale Monte Carlo production for the ATLAS Experiment

CERN Document Server

Chapman, J; Duehrssen, M; Elsing, M; Froidevaux, D; Harrington, R; Jansky, R; Langenberg, R; Mandrysch, R; Marshall, Z; Ritsch, E; Salzburger, A

2014-01-01

The huge success of the physics program of the ATLAS experiment at the Large Hadron Collider (LHC) during run I relies upon a great number of simulated Monte Carlo events. This Monte Carlo production takes the biggest part of the computing resources being in use by ATLAS as of now. In this document we describe the plans to overcome the computing resource limitations for large scale Monte Carlo production in the ATLAS Experiment for run II, and beyond. A number of fast detector simulation, digitization and reconstruction techniques and are being discussed, based upon a new flexible detector simulation framework. To optimally benefit from these developments, a redesigned ATLAS MC production chain is presented at the end of this document.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

Science.gov (United States)

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Data federation strategies for ATLAS using XRootD

Science.gov (United States)

Gardner, Robert; Campana, Simone; Duckeck, Guenter; Elmsheuser, Johannes; Hanushevsky, Andrew; Hönig, Friedrich G.; Iven, Jan; Legger, Federica; Vukotic, Ilija; Yang, Wei; Atlas Collaboration

2014-06-01

In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the wide area network and staging of remote data files to local disk. To support job-brokering decisions, a time-dependent cost-of-data-access matrix is made taking into account network performance and key site performance factors. The system's response to production-scale physics analysis workloads, either from individual end-users or ATLAS analysis services, is discussed.

The ATLAS Trigger system upgrade and performance in Run 2

CERN Document Server

Shaw, Savanna Marie; The ATLAS collaboration

2017-01-01

The ATLAS trigger has been used very successfully for the online event selection during the first part of the LHC Run-2 in 2015/16 at a centre-of-mass energy of 13 TeV. The trigger system is composed of a hardware Level-1 trigger and a software-based high-level trigger; it reduces the event rate from the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. The excellent performance of the ATLAS trigger has been vital for the ATLAS physics program of Run-2, selecting interesting collision events for wide variety of physics signatures with high efficiency. The trigger selection capabilities of ATLAS during Run-2 have been significantly improved compared to Run-1, in order to cope with the higher event rates and pile-up which are the result of the almost doubling of the center-of-mass collision energy and the increase in the instantaneous luminosity of the LHC. In order to prepare for the anticipated further luminosity increase of the LHC in 2017/18, improving the trigger performance remain...

The ATLAS Trigger Algorithms Upgrade and Performance in Run-2

CERN Document Server

Bernius, Catrin; The ATLAS collaboration

2017-01-01

The ATLAS trigger has been used very successfully for the online event selection during the first part of the second LHC run (Run-2) in 2015/16 at a center-of-mass energy of 13 TeV. The trigger system is composed of a hardware Level-1 trigger and a software-based high-level trigger; it reduces the event rate from the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. The excellent performance of the ATLAS trigger has been vital for the ATLAS physics program of Run-2, selecting interesting collision events for wide variety of physics signatures with high efficiency. The trigger selection capabilities of ATLAS during Run-2 have been significantly improved compared to Run-1, in order to cope with the higher event rates and pile-up which are the result of the almost doubling of the center-of-mass collision energy and the increase in the instantaneous luminosity of the LHC. At the Level-1 trigger the undertaken improvements resulted in more pile-up robust selection efficiencies and event ra...

The ATLAS Trigger system upgrade and performance in Run 2

CERN Document Server

Shaw, Savanna Marie; The ATLAS collaboration

2018-01-01

The ATLAS trigger has been used very successfully for the online event selection during the first part of the second LHC run (Run-2) in 2015/16 at a centre-of-mass energy of 13 TeV. The trigger system is composed of a hardware Level-1 trigger and a software-based high-level trigger; it reduces the event rate from the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. The excellent performance of the ATLAS trigger has been vital for the ATLAS physics program of Run-2, selecting interesting collision events for wide variety of physics signatures with high efficiency. The trigger selection capabilities of ATLAS during Run-2 have been significantly improved compared to Run-1, in order to cope with the higher event rates and pile-up which are the result of the almost doubling of the center-of-mass collision energy and the increase in the instantaneous luminosity of the LHC. At the Level-1 trigger the undertaken improvements resulted in more pile-up robust selection efficiencies and event ra...

Two-stage atlas subset selection in multi-atlas based image segmentation

Energy Technology Data Exchange (ETDEWEB)

Zhao, Tingting, E-mail: tingtingzhao@mednet.ucla.edu; Ruan, Dan, E-mail: druan@mednet.ucla.edu [The Department of Radiation Oncology, University of California, Los Angeles, California 90095 (United States)

2015-06-15

Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

Two-stage atlas subset selection in multi-atlas based image segmentation.

Science.gov (United States)

Zhao, Tingting; Ruan, Dan

2015-06-01

Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. The authors have developed a novel two-stage atlas

Two-stage atlas subset selection in multi-atlas based image segmentation

International Nuclear Information System (INIS)

Zhao, Tingting; Ruan, Dan

2015-01-01

Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

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...

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.

Wind Energy Resource Atlas of Mongolia

Energy Technology Data Exchange (ETDEWEB)

Elliott, D; Schwartz, M; Scott, G.; Haymes, S.; Heimiller, D.; George, R.

2001-08-27

The United States Department of Energy (DOE) and the United States Agency for International Development (USAID) sponsored a project to help accelerate the large-scale use of wind energy technologies in Mongolia through the development of a wind energy resource atlas of Mongolia. DOE's National Renewable Energy Laboratory (NREL) administered and conducted this project in collaboration with USAID and Mongolia. The Mongolian organizations participating in this project were the Scientific, Production, and Trade Corporation for Renewable Energy (REC) and the Institute of Meteorology and Hydrology (IMH). The primary goals of the project were to develop detailed wind resource maps for all regions of Mongolia for a comprehensive wind resource atlas, and to establish a wind-monitoring program to identify prospective sites for wind energy projects and help validate some of the wind resource estimates.

The ATLAS hadronic tau trigger

CERN Document Server

Black, C; The ATLAS collaboration

2012-01-01

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

The ATLAS hadronic tau trigger

CERN Document Server

Black, C; The ATLAS collaboration

2012-01-01

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

ATLAS Distributed Computing

CERN Document Server

Schovancova, J; The ATLAS collaboration

2011-01-01

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

The Error Reporting in the ATLAS TDAQ System

Science.gov (United States)

Kolos, Serguei; Kazarov, Andrei; Papaevgeniou, Lykourgos

2015-05-01

The ATLAS Error Reporting provides a service that allows experts and shift crew to track and address errors relating to the data taking components and applications. This service, called the Error Reporting Service (ERS), gives to software applications the opportunity to collect and send comprehensive data about run-time errors, to a place where it can be intercepted in real-time by any other system component. Other ATLAS online control and monitoring tools use the ERS as one of their main inputs to address system problems in a timely manner and to improve the quality of acquired data. The actual destination of the error messages depends solely on the run-time environment, in which the online applications are operating. When an application sends information to ERS, depending on the configuration, it may end up in a local file, a database, distributed middleware which can transport it to an expert system or display it to users. Thanks to the open framework design of ERS, new information destinations can be added at any moment without touching the reporting and receiving applications. The ERS Application Program Interface (API) is provided in three programming languages used in the ATLAS online environment: C++, Java and Python. All APIs use exceptions for error reporting but each of them exploits advanced features of a given language to simplify the end-user program writing. For example, as C++ lacks language support for exceptions, a number of macros have been designed to generate hierarchies of C++ exception classes at compile time. Using this approach a software developer can write a single line of code to generate a boilerplate code for a fully qualified C++ exception class declaration with arbitrary number of parameters and multiple constructors, which encapsulates all relevant static information about the given type of issues. When a corresponding error occurs at run time, the program just need to create an instance of that class passing relevant values to one

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...

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).

Operational Experience with the ATLAS Pixel Detector at LHC

CERN Document Server

Keil, M

2013-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus crucial for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via front-end chips bump-bonded to 1744 n-on-n silicon substrates. In this paper results from the successful operation of the Pixel Detector at the LHC will be presented, including calibration procedures, detector performance and measurements of radiation damage. The detector performance is excellent: more than 95% of the pixels are operational, noise occupancy and hit efficiency exceed the des...

Atlas - a new pulsed power tool at Los Alamos

CERN Document Server

Scudder, D W; Ballard, E O; Barr, G W; Cochrane, J C; Davis, H A; Griego, J R; Hadden, E S; Hinckley, W B; Hosack, K W; Martínez, J E; Mills, D; Padilla, J N; Parker, J V; Parsons, W M; Reinovsky, R E; Stokes, J L; Thompson, M C; Tom, C Y; Wysocki, F J; Vigil, B N; Elizondo, J; Miller, R B; Anderson, H D; Campbell, T N; Owens, R S

2001-01-01

Summary form only given, as follows. The Atlas pulsed power driver has recently been commissioned at Los Alamos National Laboratory. The paper provides an overview of the Atlas facility, its initial experimental program and plans for the future. The reader desiring more detailed information is referred to papers in this conference by Keinigs et al. on materials studies, Cochrane et al. on machine performance and Ballard et al. on fabrication and assembly. Atlas is a high current generator capable of driving 30 megamps through a low- inductance load. It has been designed to require minimal maintenance, provide excellent diagnostic access, and rapid turnaround. Its capacitor bank stores 23.5 megajoules in a four-stage Marx configuration which erects to 240 kV at maximum charge. It has a quarter-cycle time of 4.5 microseconds. It will typically drive cylindrical aluminum liners in a z-pinch configuration to velocities up to 10 mm/msec while maintaining the inner surface in the solid state. Diagnostic access incl...

Review of the ATLAS experiment at the LHC (CERN)

International Nuclear Information System (INIS)

Taylor, G.

1998-01-01

Full text: This talk gives in overview of the physics program for the next generation high energy physics experiments at CERN's Large Hadron Collider (LHC). Emphasis will be on the ATLAS experiment and in particular on the Australian participation in that experiment. Australian physicists from Melbourne, Sydney and Wollongong are playing a significant role in the development, production, installation and operation of the ambitious Semiconductor Tracker (SCT) in the ATLAS' Inner Detector. The SCT, particularly important for the detection and measurement of high energy electrons, will be essential in the search for the Higgs Boson through electron decay channels (amongst other reactions). The design calls for a total detector surface area an order of magnitude larger than in current silicon detectors, in a harsh radiation environment. Prodigious data rates and high speed electronics add to the complications of this detector. The talk will review progress and describe the schedule for the completion of the SCT and ATLAS

SIGNAL RECONSTRUCTION PERFORMANCE OF THE ATLAS HADRONIC TILE CALORIMETER

CERN Document Server

Do Amaral Coutinho, Y; The ATLAS collaboration

2013-01-01

"The Tile Calorimeter for the ATLAS experiment at the CERN Large Hadron Collider (LHC) is a sampling calorimeter with steel as absorber and scintillators as active medium. The scintillators are readout by wavelength shifting fibers coupled to photomultiplier tubes (PMT). The analogue signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal front-end electronics allows to read out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. The read-out system is responsible for reconstructing the data in real-time fulfilling the tight time constraint imposed by the ATLAS first level trigger rate (100 kHz). The main component of the read-out system is the Digital Signal Processor (DSP) which, using an Optimal Filtering reconstruction algorithm, allows to compute for each channel the signal amplitude, time and quality factor at the required high rate. Currently the ATLAS detector and the LHC are undergoing an upgrade program tha...

Software Validation in ATLAS

International Nuclear Information System (INIS)

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

2012-01-01

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

The 3rd ATLAS Domestic Standard Problem for Improvement of Safety Analysis Technology

International Nuclear Information System (INIS)

Choi, Ki-Yong; Kang, Kyoung-Ho; Park, Yusun; Kim, Jongrok; Bae, Byoung-Uhn; Choi, Nam-Hyun

2014-01-01

The third ATLAS DSP (domestic standard problem exercise) was launched at the end of 2012 in response to the strong need for continuation of the ATLAS DSP. A guillotine break of a main steam line without LOOP at a zero power condition was selected as a target scenario, and it was successfully completed in the beginning of 2014. In the 3 rd ATLAS DSP, comprehensive utilization of the integral effect test data was made by dividing analysis with three topics; 1. scale-up where extrapolation of ATLAS IET data was investigated 2. 3D analysis where how much improvement can be obtained by 3D modeling was studied 3. 1D sensitivity analysis where the key phenomena affecting the SLB simulation were identified and the best modeling guideline was achieved. Through such DSP exercises, it has been possible to effectively utilize high-quality ATLAS experimental data of to enhance thermal-hydraulic understanding and to validate the safety analysis codes. A strong human network and technical expertise sharing among the various nuclear experts are also important outcomes from this program

Evolution of the ATLAS Distributed Computing system during the LHC Long shutdown

CERN Document Server

Campana, S; The ATLAS collaboration

2014-01-01

The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the WLCG distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileu...

AGIS: The ATLAS Grid Information System

CERN Document Server

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

2012-01-01

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

Cartea de Colorat a Experimentului ATLAS - ATLAS Experiment Colouring Book in Romanian

CERN Multimedia

Anthony, Katarina

2018-01-01

Language: Romanian - 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. Limba: Română - Cartea de Colorat a Experimentului ATLAS este o carte educativă gratuită, ideală pentru copiii cu vârsta cuprinsă între 5-9 ani. Scopul său este de a introduce copii în domeniul fizicii de înaltă energie, precum și activitatea desfășurată de colaborarea ATLAS.

Calibrating the CERN ATLAS Experiment with $E/p$

CERN Document Server

Froeschl, R; Aleksa, M

2009-01-01

Inside the ATLAS experiment two proton beams will collide with a center of mass energy of 14 TeV. These proton beams will be delivered with unprecedented high collision rates by the Large Hadron Collider (LHC) at the European Center of Particle Physics, CERN. For important parts of the physics program of ATLAS, e.g. the search for the Higgs boson, the performance of the electromagnetic calorimeter, whose primary task is to measure the energy of electrons and photons, is crucial. The main topic of this thesis is the intercalibration of the energy scale of the electromagnetic calorimeter and the momentum scale of the inner detector. This is an important consistency test for these two detectors. The intercalibration is performed by investigating the ratio E/p for electrons, i.e. the ratio of the energy E measured by the electromagnetic calorimeter and the momentum p measured by the inner detector. The starting point is the Combined Test Beam (CTB) 2004, where a segment of the ATLAS detector was exposed to differ...

Ultimate Performance of the ATLAS Superconducting Solenoid

CERN Document Server

Ruber, R; Kawai, M; Kondo, Y; Doi, Y; Haruyama, T; Haug, F; Kate, H ten; Kondo, T; Pirotte, O; Metselaar, J; Mizumaki, S; Olesen, G; Sbrissa, E; Yamamoto, A

2007-01-01

A 2 tesla, 7730 ampere, 39 MJ, 45 mm thin superconducting solenoid with a 2.3 meters warm bore and 5.3 meters length, is installed in the center of the ATLAS detector and successfully commissioned. The solenoid shares its cryostat with one of the detector's calorimeters and provides the magnetic field required for the inner detectors to accurately track collision products from the LHC at CERN. After several years of a stepwise construction and test program, the solenoid integration 100 meters underground in the ATLAS cavern is completed. Following the on-surface acceptance test, the solenoid is now operated with its final cryogenic, powering and control system. A re-validation of all essential operating parameters is completed. The performance and test results of underground operation are reported and compared to those previously measured.

An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

Science.gov (United States)

Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

2016-01-01

The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

AGIS: The ATLAS Grid Information System

CERN Document Server

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

2012-01-01

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

Computational and mathematical methods in brain atlasing.

Science.gov (United States)

Nowinski, Wieslaw L

2017-12-01

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

Enabling the ATLAS Experiment at the LHC for High Performance Computing

CERN Document Server

AUTHOR|(CDS)2091107; Ereditato, Antonio

In this thesis, I studied the feasibility of running computer data analysis programs from the Worldwide LHC Computing Grid, in particular large-scale simulations of the ATLAS experiment at the CERN LHC, on current general purpose High Performance Computing (HPC) systems. An approach for integrating HPC systems into the Grid is proposed, which has been implemented and tested on the „Todi” HPC machine at the Swiss National Supercomputing Centre (CSCS). Over the course of the test, more than 500000 CPU-hours of processing time have been provided to ATLAS, which is roughly equivalent to the combined computing power of the two ATLAS clusters at the University of Bern. This showed that current HPC systems can be used to efficiently run large-scale simulations of the ATLAS detector and of the detected physics processes. As a first conclusion of my work, one can argue that, in perspective, running large-scale tasks on a few large machines might be more cost-effective than running on relatively small dedicated com...

Data federation strategies for ATLAS using XRootD

International Nuclear Information System (INIS)

Gardner, Robert; Vukotic, Ilija; Campana, Simone; Iven, Jan; Duckeck, Guenter; Elmsheuser, Johannes; Hönig, Friedrich G; Legger, Federica; Hanushevsky, Andrew; Yang, Wei

2014-01-01

In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the wide area network and staging of remote data files to local disk. To support job-brokering decisions, a time-dependent cost-of-data-access matrix is made taking into account network performance and key site performance factors. The system's response to production-scale physics analysis workloads, either from individual end-users or ATLAS analysis services, is discussed.

Research at the fragment mass analyser at ATLAS

International Nuclear Information System (INIS)

Davids, C.N.; Back, B.; Bearden, I.G.

1993-01-01

The experimental program at the Fragment Mass Analyzer (FMA) at the ATLAS heavy ion accelerator of the Argonne National Laboratory is described. The brief description and operational properties of the FMA are presented. The highest mass resolution obtained with the FMA is 525/1. Some experimental results are presented. 5 refs., 7 figs

B-physics with ATLAS

International Nuclear Information System (INIS)

Smizanska, M.

1997-01-01

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

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...

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...

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.

Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

International Nuclear Information System (INIS)

Bouchami, J; Dallaire, F; Gutierrez, A; Idarraga, J; Leroy, C; Picard, S; Scallon, O; Kral, V; PospIsil, S; Solc, J; Suk, M; Turecek, D; Vykydal, Z; Zemlieka, J

2011-01-01

The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6 LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) - based on the ROOT application - allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons ( 252 Cf and 241 AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

SU-E-J-132: Automated Segmentation with Post-Registration Atlas Selection Based On Mutual Information

International Nuclear Information System (INIS)

Ren, X; Gao, H; Sharp, G

2015-01-01

Purpose: The delineation of targets and organs-at-risk is a critical step during image-guided radiation therapy, for which manual contouring is the gold standard. However, it is often time-consuming and may suffer from intra- and inter-rater variability. The purpose of this work is to investigate the automated segmentation. Methods: The automatic segmentation here is based on mutual information (MI), with the atlas from Public Domain Database for Computational Anatomy (PDDCA) with manually drawn contours.Using dice coefficient (DC) as the quantitative measure of segmentation accuracy, we perform leave-one-out cross-validations for all PDDCA images sequentially, during which other images are registered to each chosen image and DC is computed between registered contour and ground truth. Meanwhile, six strategies, including MI, are selected to measure the image similarity, with MI to be the best. Then given a target image to be segmented and an atlas, automatic segmentation consists of: (a) the affine registration step for image positioning; (b) the active demons registration method to register the atlas to the target image; (c) the computation of MI values between the deformed atlas and the target image; (d) the weighted image fusion of three deformed atlas images with highest MI values to form the segmented contour. Results: MI was found to be the best among six studied strategies in the sense that it had the highest positive correlation between similarity measure (e.g., MI values) and DC. For automated segmentation, the weighted image fusion of three deformed atlas images with highest MI values provided the highest DC among four proposed strategies. Conclusion: MI has the highest correlation with DC, and therefore is an appropriate choice for post-registration atlas selection in atlas-based segmentation. Xuhua Ren and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

SU-E-J-132: Automated Segmentation with Post-Registration Atlas Selection Based On Mutual Information

Energy Technology Data Exchange (ETDEWEB)

Ren, X; Gao, H [Shanghai Jiao Tong University, Shanghai, Shanghai (China); Sharp, G [Massachusetts General Hospital, Boston, MA (United States)

2015-06-15

Purpose: The delineation of targets and organs-at-risk is a critical step during image-guided radiation therapy, for which manual contouring is the gold standard. However, it is often time-consuming and may suffer from intra- and inter-rater variability. The purpose of this work is to investigate the automated segmentation. Methods: The automatic segmentation here is based on mutual information (MI), with the atlas from Public Domain Database for Computational Anatomy (PDDCA) with manually drawn contours.Using dice coefficient (DC) as the quantitative measure of segmentation accuracy, we perform leave-one-out cross-validations for all PDDCA images sequentially, during which other images are registered to each chosen image and DC is computed between registered contour and ground truth. Meanwhile, six strategies, including MI, are selected to measure the image similarity, with MI to be the best. Then given a target image to be segmented and an atlas, automatic segmentation consists of: (a) the affine registration step for image positioning; (b) the active demons registration method to register the atlas to the target image; (c) the computation of MI values between the deformed atlas and the target image; (d) the weighted image fusion of three deformed atlas images with highest MI values to form the segmented contour. Results: MI was found to be the best among six studied strategies in the sense that it had the highest positive correlation between similarity measure (e.g., MI values) and DC. For automated segmentation, the weighted image fusion of three deformed atlas images with highest MI values provided the highest DC among four proposed strategies. Conclusion: MI has the highest correlation with DC, and therefore is an appropriate choice for post-registration atlas selection in atlas-based segmentation. Xuhua Ren and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

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

Science.gov (United States)

Van Waes, Carter; Musbahi, Omar

2017-10-01

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

Dark matter searches with the ATLAS detector

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00379232; The ATLAS collaboration

2017-01-01

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

Dark Matter searches with the ATLAS Detector

CERN Document Server

Cortes-Gonzalez, Arely; The ATLAS collaboration

2017-01-01

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

Dark matter searches with the ATLAS detector

CERN Document Server

Whalen, Kathleen; The ATLAS collaboration

2017-01-01

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

EnviroAtlas - Portland, ME - Meter-Scale Urban Land Cover (MULC) Data (2010)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Portland, ME Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green,...

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Directory of Open Access Journals (Sweden)

Christopher J. Ricketts

2018-04-01

Full Text Available Summary: Renal cell carcinoma (RCC is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD ChRCC that associated with extremely poor survival. : Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtype-specific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes. Keywords: clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma, CDKN2A, DNA hypermethylation, immune signature, chromatin remodeling, TCGA, PanCanAtlas

ATLAS@Home looks for CERN volunteers

CERN Multimedia

Rosaria Marraffino

2014-01-01

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

Test Beam Coordination: 2003 ATLAS Combined Test Beam

CERN Multimedia

Di Girolamo, B.

The 2003 Test Beam Period The 2003 Test Beam period has been very fruitful for ATLAS. In spite of several days lost because of the accelerator problems, ATLAS has been able to achieve many results: FCAL has completed the calibration program in H6 Tilecal has completed the calibration program in H8 Pixel has performed extensive studies with normal and high intensity beams (up to 1.4*108 hadrons/spill) SCT has completed a variety of studies with quite a high number of modules operated concurrently TRT has performed several studies at high, low and very low energy (first use of the new H8 beam in the range 1 to 9 GeV) Muons (MDT,RPC and TGC) have been operating a large setup for about 5 months. The almost final MDT ROD (MROD) has been integrated in the readout and the final trigger electronics for TGC and RPC has been tested and certified with normal beam and during dedicated 40 MHz beam periods. The TDAQ has exploited a new generation prototype successfully and the new Event Filter infrastructure f...

Implementation of the ATLAS trigger within the ATLAS Multi­Threaded Software Framework AthenaMT

CERN Document Server

Wynne, Benjamin; The ATLAS collaboration

2016-01-01

We present an implementation of the ATLAS High Level Trigger that provides parallel execution of trigger algorithms within the ATLAS multi­threaded software framework, AthenaMT. This development will enable the ATLAS High Level Trigger to meet future challenges due to the evolution of computing hardware and upgrades of the Large Hadron Collider, LHC, and ATLAS Detector. During the LHC data­taking period starting in 2021, luminosity will reach up to three times the original design value. Luminosity will increase further, to up to 7.5 times the design value, in 2026 following LHC and ATLAS upgrades. This includes an upgrade of the ATLAS trigger architecture that will result in an increase in the High Level Trigger input rate by a factor of 4 to 10 compared to the current maximum rate of 100 kHz. The current ATLAS multiprocess framework, AthenaMP, manages a number of processes that process events independently, executing algorithms sequentially in each process. AthenaMT will provide a fully multi­threaded env...

EnviroAtlas - Tampa, FL - Meter-Scale Urban Land Cover (MULC) Data (2010)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Tampa, FL Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue...

EnviroAtlas - Woodbine, IA - Meter-Scale Urban Land Cover (MULC) Data (2011)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Woodbine, IA Meter-Scale Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red,...

EnviroAtlas - Phoenix, AZ - Meter-Scale Urban Land Cover (MULC) Data (2010)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Phoenix, AZ Meter-Scale Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red,...

EnviroAtlas - Durham, NC - Meter-Scale Urban Land Cover (MULC) Data (2010)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Durham, NC Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue...

Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

Energy Technology Data Exchange (ETDEWEB)

Bouchami, J; Dallaire, F; Gutierrez, A; Idarraga, J; Leroy, C; Picard, S; Scallon, O [Universite de Montreal, Montreal, Quebec H3C 3J7 (Canada); Kral, V; PospIsil, S; Solc, J; Suk, M; Turecek, D; Vykydal, Z; Zemlieka, J, E-mail: scallon@lps.umontreal.ca [Institute of Experimental and Applied Physics of the CTU in Prague, Horska 3a/22, CZ-12800 Praha2 - Albertov (Czech Republic)

2011-01-15

The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of {sup 6}LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) - based on the ROOT application - allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons ({sup 252}Cf and {sup 241}AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

Science.gov (United States)

Bouchami, J.; Dallaire, F.; Gutiérrez, A.; Idarraga, J.; Král, V.; Leroy, C.; Picard, S.; Pospíšil, S.; Scallon, O.; Solc, J.; Suk, M.; Turecek, D.; Vykydal, Z.; Žemlièka, J.

2011-01-01

The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) — based on the ROOT application — allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons (252Cf and 241AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

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.

SU-E-J-128: Two-Stage Atlas Selection in Multi-Atlas-Based Image Segmentation

International Nuclear Information System (INIS)

Zhao, T; Ruan, D

2015-01-01

Purpose: In the new era of big data, multi-atlas-based image segmentation is challenged by heterogeneous atlas quality and high computation burden from extensive atlas collection, demanding efficient identification of the most relevant atlases. This study aims to develop a two-stage atlas selection scheme to achieve computational economy with performance guarantee. Methods: We develop a low-cost fusion set selection scheme by introducing a preliminary selection to trim full atlas collection into an augmented subset, alleviating the need for extensive full-fledged registrations. More specifically, fusion set selection is performed in two successive steps: preliminary selection and refinement. An augmented subset is first roughly selected from the whole atlas collection with a simple registration scheme and the corresponding preliminary relevance metric; the augmented subset is further refined into the desired fusion set size, using full-fledged registration and the associated relevance metric. The main novelty of this work is the introduction of an inference model to relate the preliminary and refined relevance metrics, based on which the augmented subset size is rigorously derived to ensure the desired atlases survive the preliminary selection with high probability. Results: The performance and complexity of the proposed two-stage atlas selection method were assessed using a collection of 30 prostate MR images. It achieved comparable segmentation accuracy as the conventional one-stage method with full-fledged registration, but significantly reduced computation time to 1/3 (from 30.82 to 11.04 min per segmentation). Compared with alternative one-stage cost-saving approach, the proposed scheme yielded superior performance with mean and medium DSC of (0.83, 0.85) compared to (0.74, 0.78). Conclusion: This work has developed a model-guided two-stage atlas selection scheme to achieve significant cost reduction while guaranteeing high segmentation accuracy. The benefit

Searches for new physics at ATLAS

CERN Document Server

Pachal, Katherine; The ATLAS collaboration

2018-01-01

Throughout Run II ATLAS has maintained an extensive, varied program of searches for physics beyond the Standard Model. Searches for supersymmetry cover strong and electroweak production as well as R-parity violating scenarios, while Exotic analyses search for heavy bosons, dark matter mediators, exotic Higgs production, and much more. This talk will show highlights of the Run II search results so far and lay out plans for analyses in the full dataset and beyond.

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...

ATLAS MPGD production status

CERN Document Server

Schioppa, Marco; The ATLAS collaboration

2018-01-01

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

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 ...

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...

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.

Integration of Titan supercomputer at OLCF with ATLAS Production System

CERN Document Server

AUTHOR|(SzGeCERN)643806; The ATLAS collaboration; De, Kaushik; Klimentov, Alexei; Nilsson, Paul; Oleynik, Danila; Padolski, Siarhei; Panitkin, Sergey; Wenaus, Torre

2017-01-01

The PanDA (Production and Distributed Analysis) workload management system was developed to meet the scale and complexity of distributed computing for the ATLAS experiment. PanDA managed resources are distributed worldwide, on hundreds of computing sites, with thousands of physicists accessing hundreds of Petabytes of data and the rate of data processing already exceeds Exabyte per year. While PanDA currently uses more than 200,000 cores at well over 100 Grid sites, future LHC data taking runs will require more resources than Grid computing can possibly provide. Additional computing and storage resources are required. Therefore ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. In this paper we will describe a project aimed at integration of ATLAS Production System with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF). Current approach utilizes modified PanDA Pilot framework for jo...

Report to users of ATLAS [Argonne Tandem-Line Accelerator System

International Nuclear Information System (INIS)

Ahmad, I.; Glagola, B.

1987-03-01

The operation and development of ATLAS are reported, including accelerator improvements. Particularly noted is an upgrade to extend the mass range of projectiles up to uranium and to increase the beam intensity by at least two orders of magnitude for all ions. Meetings are discussed, particularly of the Program Advisory Committee and the User Group Executive Committee. Some basic information is provided for users planning to run experiments at ATLAS, including a table of beams available. The data acquisition system for ATLAS, DAPHNE, is discussed, as are the following experimental facilities: the Argonne-Notre Dame Gamma Ray Facility, a proposal submitted for constructing a large-acceptance Fragment Mass Analyzer. Brief summaries are provided of some recent experiments for which data analysis is complete. Experiments performed during the period from June 1, 1986 to January 31, 1987 are tabulated, providing the experiment number, scientists, institution, experiment name, number of days, beam, and energy

Integration of Titan supercomputer at OLCF with ATLAS production system

CERN Document Server

Panitkin, Sergey; The ATLAS collaboration

2016-01-01

The PanDA (Production and Distributed Analysis) workload management system was developed to meet the scale and complexity of distributed computing for the ATLAS experiment. PanDA managed resources are distributed worldwide, on hundreds of computing sites, with thousands of physicists accessing hundreds of Petabytes of data and the rate of data processing already exceeds Exabyte per year. While PanDA currently uses more than 200,000 cores at well over 100 Grid sites, future LHC data taking runs will require more resources than Grid computing can possibly provide. Additional computing and storage resources are required. Therefore ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. In this talk we will describe a project aimed at integration of ATLAS Production System with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF). Current approach utilizes modified PanDA Pilot framework for job...

Report to users of ATLAS (Argonne Tandem-Line Accelerator System)

Energy Technology Data Exchange (ETDEWEB)

Ahmad, I.; Glagola, B. (eds.)

1987-03-01

The operation and development of ATLAS are reported, including accelerator improvements. Particularly noted is an upgrade to extend the mass range of projectiles up to uranium and to increase the beam intensity by at least two orders of magnitude for all ions. Meetings are discussed, particularly of the Program Advisory Committee and the User Group Executive Committee. Some basic information is provided for users planning to run experiments at ATLAS, including a table of beams available. The data acquisition system for ATLAS, DAPHNE, is discussed, as are the following experimental facilities: the Argonne-Notre Dame Gamma Ray Facility, a proposal submitted for constructing a large-acceptance Fragment Mass Analyzer. Brief summaries are provided of some recent experiments for which data analysis is complete. Experiments performed during the period from June 1, 1986 to January 31, 1987 are tabulated, providing the experiment number, scientists, institution, experiment name, number of days, beam, and energy. (LEW)

Operational Experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Keil, M; The ATLAS collaboration

2012-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC and its status after three years of operation will be presented, including calibration procedures, timing optimization and detector performance. The detector performance is excellent: ~96 % of the pixels are operational, noise occupancy and hit efficiency e...

Operational Experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Keil, M; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Hirschbuehl, D; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this paper results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 96.7% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Lapoire, C; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational Experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Lapoire, C; The ATLAS collaboration

2012-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as B-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this paper, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures and detector performance. The detector performance is excellent: 96.2% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification.

Operational Experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Keil, M

2012-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this paper results from the successful operation of the Pixel Detector at the LHC will be presented, including calibration procedures, timing optimization and detector performance. The detector performance is excellent: approximately 97% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Ince, T; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 96.8% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

Operational experience with the ATLAS Pixel detector at the LHC

CERN Document Server

Deluca, C; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this paper, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5\\% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, ...

Operational Experience with the ATLAS Pixel Detector at the LHC

CERN Document Server

Lange, C; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump- bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, a...

Operational experience with the ATLAS Pixel detector at the LHC

CERN Document Server

Deluca, C; The ATLAS collaboration

2011-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is vital for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. In this talk, results from the successful operation of the Pixel Detector at the LHC will be presented, including monitoring, calibration procedures, timing optimization and detector performance. The detector performance is excellent: 97,5% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, an...

The ATLAS High Level Trigger Steering Framework and the Trigger 
Configuration System.

CERN Document Server

Pérez Cavalcanti, Tiago; The ATLAS collaboration

2011-01-01

The ATLAS High Level Trigger Steering Framework and the Trigger 
Configuration System.
 
The ATLAS detector system installed in the Large Hadron Collider (LHC) 
at CERN is designed to study proton-proton and nucleus-nucleus 
collisions with a maximum center of mass energy of 14 TeV at a bunch 
collision rate of 40MHz.  In March 2010 the four LHC experiments saw 
the first proton-proton collisions at 7 TeV. Still within the year a 
collision rate of nearly 10 MHz is expected. At ATLAS, events of 
potential interest for ATLAS physics are selected by a three-level 
trigger system, with a final recording rate of about 200 Hz. The first 
level (L1) is implemented in custom hardware; the two levels of 
the high level trigger (HLT) are software triggers, running on large 
farms of standard computers and network devices. 

Within the ATLAS physics program more than 500 trigger signatures are 
defined. The HLT tests each signature on each L1-accepted event; the 
test outcome is recor...

Baby brain atlases.

Science.gov (United States)

Oishi, Kenichi; Chang, Linda; Huang, Hao

2018-04-03

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

Glance Information System for ATLAS Management

International Nuclear Information System (INIS)

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

2011-01-01

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

Glance Information System for ATLAS Management

Science.gov (United States)

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

2011-12-01

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

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.

The ATLAS High Level Trigger Steering Framework and the Trigger Configuration System.

CERN Document Server

Perez Cavalcanti, Tiago; The ATLAS collaboration

2011-01-01

The ATLAS detector system installed in the Large Hadron Collider (LHC) at CERN is designed to study proton-proton and nucleus-nucleus collisions with a maximum centre of mass energy of 14 TeV at a bunch collision rate of 40MHz. In March 2010 the four LHC experiments saw the first proton-proton collisions at 7 TeV. Still within the year a collision rate of nearly 10 MHz is expected. At ATLAS, events of potential interest for ATLAS physics are selected by a three-level trigger system, with a final recording rate of about 200 Hz. The first level (L1) is implemented in custom hardware; the two levels of the high level trigger (HLT) are software triggers, running on large farms of standard computers and network devices. Within the ATLAS physics program more than 500 trigger signatures are defined. The HLT tests each signature on each L1-accepted event; the test outcome is recorded for later analysis. The HLT-Steering is responsible for this. It foremost ensures the independent test of each signature, guarantying u...

Input Mezzanine Card for the Fast Tracker at ATLAS

CERN Document Server

Iizawa, Tomoya; The ATLAS collaboration

2016-01-01

The Fast Tracker (FTK) is an integral part of trigger upgrade program for the ATLAS experiment. At LHC Run 2, which started operations in June 2015 at a center-of-mass energy of 13 TeV, the luminosity could reach up to 2*1034 cm-2s-1 and an average of 40-50 simultaneous proton collisions per beam crossing will be expected. The higher luminosity demands a more sophisticated trigger system with increased use of tracking information. The Fast Tracker is a highly-parallel hardware system that rapidly finds and reconstructs tracks in the ATLAS inner-detector at the triggering stage. This paper focuses on the FTK Input Mezzanine Board that is input module of entire system. The functions of this board are to receive the insertable b-layer, pixel and micro-strip data from the ATLAS Silicon read-out drivers, perform clustering, and forward the data to its mother board. Mass production and quality control tests of Mezzanine Boards were completed, and staged installation and commissioning are ongoing. Details of its fun...

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)

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

CERN Multimedia

Anthony, Katarina

2017-01-01

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

Maľovanka Experiment ATLAS - ATLAS Experiment Colouring Book in Slovak

CERN Multimedia

Anthony, Katarina

2017-01-01

Language: Slovak - 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.

ATLAS Deneyi Boyama Kitabı - ATLAS Experiment Colouring Book in Turkish

CERN Multimedia

Anthony, Katarina

2018-01-01

Language: Turkish - 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.

AGIS: The ATLAS Grid Information System

Science.gov (United States)

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

2014-06-01

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

ATLAS beam properties: some implications for target making

International Nuclear Information System (INIS)

Pardo, R.

1984-01-01

The expansion of the tandem-linac booster into the Argonne Tandem-Linac Accelerator System, ATLAS, is approximately 40% complete. When completed, the facility will provide beams of heavy ions from lithium to tin with energies eventually, to 25 MeV/amu. The existing facility continues to provide beams for the experimental program in nuclear and atomic physics during the construction phase. The booster system is capable of accelerating ions as heavy as selenium to energies of 10 MeV/amu for the lighter ions. The good beam quality provided by the linac means that multiple scattering, energy straggling, and target inhomogeneities are major factors in the resolution attainable in experiments. The beam properties that can be expected from ATLAS will be discussed and the present state of high resolution experiments will be reported

The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

Science.gov (United States)

Nowinski, Wieslaw L; Belov, Dmitry

2003-09-01

The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

The Numerical Wind Atlas - the KAMM/WAsP Method

Energy Technology Data Exchange (ETDEWEB)

Frank, H P; Rathmann, O; Mortensen, N G; Landberg, L

2001-06-01

The method of combining the Karlsruhe Atmospheric Mesoscale Model, KAMM, with the Wind Atlas Analysis and Application Program, WAsP, to make local predictions of the wind resource is presented. It combines the advantages of meso-scale modeling - overview over a big region and use of global data bases - with the local prediction capacity of the small-scale model WAsP. Results are presented for Denmark, Ireland, Northern Portugal and Galicia, and the Faroe Islands. Wind atlas files were calculated from wind data simulated with the meso-scale model using model grids with a resolution of 2.5, 5, and 10 km. Using these wind atlas files in WAsP the local prediction of the mean wind does not depend on the grid resolution of the meso-scale model. The local predictions combining KAMM and WAsP are much better than simple interpolation of the wind simulated by KAMM. In addition an investigation was made on the dependence of wind atlas data on the size of WAsP-maps. It is recommended that a topographic map around a site should extend 10 km out from it. If there is a major roughness change like a coast line further away in a frequent wind direction this should be included at even greater distances, perhaps up to 20 km away.

Preparing a new book on ATLAS

CERN Multimedia

Claudia Marcelloni de Oliveira

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

Benchmarking of the simulation of the ATLAS HaLL background

International Nuclear Information System (INIS)

Vincke, H.

2000-01-01

The LHC, mainly to be used as a proton-proton collider, providing collisions at energies of 14 TeV, will be operational in the year 2005. ATLAS, one of the LHC experiments, will provide high accuracy measurements concerning these p-p collisions. In these collisions also a high particle background is produced. This background was already calculated with the Monte Carlo simulation program FLUKA. Unfortunately, the prediction concerning this background rate is only understood within an uncertainty level of five. The main contribution of this factor can be seen as limited knowledge concerning the ability of FLUKA to simulate these kinds of scenarios. In order to reduce the uncertainty, benchmarking simulations of experiments similar to the ATLAS background situation were performed. The comparison of the simulations with the experiments proves to which extent FLUKA is able to provide reliable results concerning the ATLAS background situation. In order to perform this benchmark, an iron construction was irradiated by a hadron beam. The primary particles had ATLAS equivalent energies. Behind the iron structure, the remnants of the shower processes are measured and simulated. The simulation procedure and its encouraging results, including the comparison with the measured numbers, are presented and discussed in this work. (author)

CMOS pixel development for the ATLAS experiment at HL-LHC

CERN Document Server

Risti{c}, Branislav; The ATLAS collaboration

2017-01-01

To cope with the rate and radiation environment expected at the HL-LHC new approaches are being developed on CMOS pixel detectors, providing charge collection in a depleted layer. They are based on: HV enabling technologies that allow to use high depletion voltages (HV-MAPS), high resistivity wafers for large depletion depths (HR-MAPS); radiation hard processed with multiple nested wells to allow CMOS electronics embedded with sufficient shielding into the sensor substrate and backside processing and thinning for material minimization and backside voltage application. Since 2014, members of more than 20 groups in the ATLAS experiment are actively pursuing CMOS pixel R&D in an ATLAS Demonstrator program pursuing sensor design and characterizations. The goal of this program is to demonstrate that depleted CMOS pixels, with monolithic or hybrid designs, are suited for high rate, fast timing and high radiation operation at LHC. For this a number of technologies have been explored and characterized. In this pr...

CMOS pixel development for the ATLAS experiment at HL-LHC

CERN Document Server

Rimoldi, Marco; The ATLAS collaboration

2017-01-01

To cope with the rate and radiation environment expected at the HL-LHC new approaches are being developed on CMOS pixel detectors, providing charge collection in a depleted layer. They are based on: HV enabling technologies that allow to use high depletion voltages, high resistivity wafers for large depletion depths; radiation hard processed with multiple nested wells to allow CMOS electronics embedded with sufficient shielding into the sensor substrate and backside processing and thinning for material minimization and backside voltage application. Since 2014, members of more than 20 groups in the ATLAS experiment are actively pursuing CMOS pixel R$\\&$D in an ATLAS Demonstrator program pursuing sensor design and characterizations. The goal of this program is to demonstrate that depleted CMOS pixels are suited for high rate, fast timing and high radiation operation at LHC. For this a number of technologies have been explored and characterized. In this presentation the challenges for the usage of CMOS pixel...

CMOS Pixel Development for the ATLAS Experiment at HL-LHC

CERN Document Server

Gaudiello, Andrea; The ATLAS collaboration

2017-01-01

To cope with the rate and radiation environment expected at the HL-LHC new approaches are being developed on CMOS pixel detectors, providing charge collection in a depleted layer. They are based on: HV enabling technologies that allow to use high depletion voltages (HV-MAPS), high resistivity wafers for large depletion depths (HR-MAPS); radiation hard processed with multiple nested wells to allow CMOS electronics embedded with sufficient shielding into the sensor substrate and backside processing and thinning for material minimization and backside voltage application. Since 2014, members of more than 20 groups in the ATLAS experiment are actively pursuing CMOS pixel R&D in an ATLAS Demonstrator program pursuing sensor design and characterizations. The goal of this program is to demonstrate that depleted CMOS pixels, with monolithic or hybrid designs, are suited for high rate, fast timing and high radiation operation at LHC. For this a number of technologies have been explored and characterized. In this pr...

Dark Matter Searches with the ATLAS Detector

CERN Document Server

Elliot, Alison; The ATLAS collaboration

2017-01-01

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

Dark Matter Searches with the ATLAS detector

Directory of Open Access Journals (Sweden)

Elliot Alison

2017-01-01

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

EnviroAtlas - Milwaukee, WI - Meter-Scale Urban Land Cover Data (MULC) Data (2010)

Data.gov (United States)

U.S. Environmental Protection Agency — The EnviroAtlas Milwaukee, WI Meter Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green,...

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...

ATLAS Facility Description Report

International Nuclear Information System (INIS)

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

2009-04-01

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

TU-CD-BRA-05: Atlas Selection for Multi-Atlas-Based Image Segmentation Using Surrogate Modeling

International Nuclear Information System (INIS)

Zhao, T; Ruan, D

2015-01-01

Purpose: The growing size and heterogeneity in training atlas necessitates sophisticated schemes to identify only the most relevant atlases for the specific multi-atlas-based image segmentation problem. This study aims to develop a model to infer the inaccessible oracle geometric relevance metric from surrogate image similarity metrics, and based on such model, provide guidance to atlas selection in multi-atlas-based image segmentation. Methods: We relate the oracle geometric relevance metric in label space to the surrogate metric in image space, by a monotonically non-decreasing function with additive random perturbations. Subsequently, a surrogate’s ability to prognosticate the oracle order for atlas subset selection is quantified probabilistically. Finally, important insights and guidance are provided for the design of fusion set size, balancing the competing demands to include the most relevant atlases and to exclude the most irrelevant ones. A systematic solution is derived based on an optimization framework. Model verification and performance assessment is performed based on clinical prostate MR images. Results: The proposed surrogate model was exemplified by a linear map with normally distributed perturbation, and verified with several commonly-used surrogates, including MSD, NCC and (N)MI. The derived behaviors of different surrogates in atlas selection and their corresponding performance in ultimate label estimate were validated. The performance of NCC and (N)MI was similarly superior to MSD, with a 10% higher atlas selection probability and a segmentation performance increase in DSC by 0.10 with the first and third quartiles of (0.83, 0.89), compared to (0.81, 0.89). The derived optimal fusion set size, valued at 7/8/8/7 for MSD/NCC/MI/NMI, agreed well with the appropriate range [4, 9] from empirical observation. Conclusion: This work has developed an efficacious probabilistic model to characterize the image-based surrogate metric on atlas selection

The ATLAS Data Management Software Engineering Process

CERN Document Server

Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A; Molfetas, A

2014-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

The ATLAS Data Management Software Engineering Process

CERN Document Server

Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A

2013-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

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.

Atlas Pulsed Power Facility for High Energy Density Physics Experiments

International Nuclear Information System (INIS)

Miller, R.B.; Ballard, E.O.; Barr, G.W.; Bowman, D.W.; Chochrane, J.C.; Davis, H.A.; Elizondo, J.M.; Gribble, R.F.; Griego, J.R.; Hicks, R.D.; Hinckley, W.B.; Hosack, K.W.; Nielsen, K.E.; Parker, J.V.; Parsons, M.O.; Rickets, R.L.; Salazar, H.R.; Sanchez, P.G.; Scudder, D.W.; Shapiro, C.; Thompson, M.C.; Trainor, R.J.; Valdez, G.A.; Vigil, B.N.; Watt, R.G.; Wysock, F.J.

1999-01-01

The Atlas facility, now under construction at Los Alamos National Laboratory (LANL), will provide a unique capability for performing high-energy-density experiments in support of weapon-physics and basic-research programs. It is intended to be an international user facility, providing opportunities for researchers from national laboratories and academic institutions around the world. Emphasizing institutions around the world. Emphasizing hydrodynamic experiments, Atlas will provide the capability for achieving steady shock pressures exceeding 10-Mbar in a volume of several cubic centimeters. In addition, the kinetic energy associated with solid liner implosion velocities exceeding 12 km/s is sufficient to drive dense, hydrodynamic targets into the ionized regime, permitting the study of complex issues associated with strongly-coupled plasmas. The primary element of Atlas is a 23-MJ capacitor bank, comprised of 96 separate Marx generators housed in 12 separate oil-filled tanks, surrounding a central target chamber. Each tank will house two, independently-removable maintenance units, with each maintenance unit consisting of four Marx modules. Each Marx module has four capacitors that can each be charged to a maximum of 60 kilovolts. When railgap switches are triggered, the marx modules erect to a maximum of 240 kV. The parallel discharge of these 96 Marx modules will deliver a 30-MA current pulse with a 4-5-micros risetime to a cylindrical, imploding liner via 24 vertical, tri-plate, oil-insulated transmission lines. An experimental program for testing and certifying all Marx and transmission line components has been completed. A complete maintenance module and its associated transmission line (the First Article) are now under construction and testing. The current Atlas schedule calls for construction of the machine to be complete by August, 2000. Acceptance testing is scheduled to begin in November, 2000, leading to initial operations in January, 2001

Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

Directory of Open Access Journals (Sweden)

Kishan Andre Liyanage

Full Text Available Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap to 1 (complete overlap. For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma.

Science.gov (United States)

Creighton, Chad J; Hernandez-Herrera, Anadulce; Jacobsen, Anders; Levine, Douglas A; Mankoo, Parminder; Schultz, Nikolaus; Du, Ying; Zhang, Yiqun; Larsson, Erik; Sheridan, Robert; Xiao, Weimin; Spellman, Paul T; Getz, Gad; Wheeler, David A; Perou, Charles M; Gibbs, Richard A; Sander, Chris; Hayes, D Neil; Gunaratne, Preethi H

2012-01-01

The Cancer Genome Atlas (TCGA) Network recently comprehensively catalogued the molecular aberrations in 487 high-grade serous ovarian cancers, with much remaining to be elucidated regarding the microRNAs (miRNAs). Here, using TCGA ovarian data, we surveyed the miRNAs, in the context of their predicted gene targets. Integration of miRNA and gene patterns yielded evidence that proximal pairs of miRNAs are processed from polycistronic primary transcripts, and that intronic miRNAs and their host gene mRNAs derive from common transcripts. Patterns of miRNA expression revealed multiple tumor subtypes and a set of 34 miRNAs predictive of overall patient survival. In a global analysis, miRNA:mRNA pairs anti-correlated in expression across tumors showed a higher frequency of in silico predicted target sites in the mRNA 3'-untranslated region (with less frequency observed for coding sequence and 5'-untranslated regions). The miR-29 family and predicted target genes were among the most strongly anti-correlated miRNA:mRNA pairs; over-expression of miR-29a in vitro repressed several anti-correlated genes (including DNMT3A and DNMT3B) and substantially decreased ovarian cancer cell viability. This study establishes miRNAs as having a widespread impact on gene expression programs in ovarian cancer, further strengthening our understanding of miRNA biology as it applies to human cancer. As with gene transcripts, miRNAs exhibit high diversity reflecting the genomic heterogeneity within a clinically homogeneous disease population. Putative miRNA:mRNA interactions, as identified using integrative analysis, can be validated. TCGA data are a valuable resource for the identification of novel tumor suppressive miRNAs in ovarian as well as other cancers.

Taking ATLAS to new heights

CERN Document Server

Abha Eli Phoboo, ATLAS experiment

2013-01-01

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

ATLAS DataFlow Infrastructure: Recent results from ATLAS cosmic and first-beam data-taking

Energy Technology Data Exchange (ETDEWEB)

Vandelli, Wainer, E-mail: wainer.vandelli@cern.c

2010-04-01

The ATLAS DataFlow infrastructure is responsible for the collection and conveyance of event data from the detector front-end electronics to the mass storage. Several optimized and multi-threaded applications fulfill this purpose operating over a multi-stage Gigabit Ethernet network which is the backbone of the ATLAS Trigger and Data Acquisition System. The system must be able to efficiently transport event-data with high reliability, while providing aggregated bandwidths larger than 5 GByte/s and coping with many thousands network connections. Nevertheless, routing and streaming capabilities and monitoring and data accounting functionalities are also fundamental requirements. During 2008, a few months of ATLAS cosmic data-taking and the first experience with the LHC beams provided an unprecedented test-bed for the evaluation of the performance of the ATLAS DataFlow, in terms of functionality, robustness and stability. Besides, operating the system far from its design specifications helped in exercising its flexibility and contributed in understanding its limitations. Moreover, the integration with the detector and the interfacing with the off-line data processing and management have been able to take advantage of this extended data taking-period as well. In this paper we report on the usage of the DataFlow infrastructure during the ATLAS data-taking. These results, backed-up by complementary performance tests, validate the architecture of the ATLAS DataFlow and prove that the system is robust, flexible and scalable enough to cope with the final requirements of the ATLAS experiment.

ATLAS DataFlow Infrastructure: Recent results from ATLAS cosmic and first-beam data-taking

International Nuclear Information System (INIS)

Vandelli, Wainer

2010-01-01

The ATLAS DataFlow infrastructure is responsible for the collection and conveyance of event data from the detector front-end electronics to the mass storage. Several optimized and multi-threaded applications fulfill this purpose operating over a multi-stage Gigabit Ethernet network which is the backbone of the ATLAS Trigger and Data Acquisition System. The system must be able to efficiently transport event-data with high reliability, while providing aggregated bandwidths larger than 5 GByte/s and coping with many thousands network connections. Nevertheless, routing and streaming capabilities and monitoring and data accounting functionalities are also fundamental requirements. During 2008, a few months of ATLAS cosmic data-taking and the first experience with the LHC beams provided an unprecedented test-bed for the evaluation of the performance of the ATLAS DataFlow, in terms of functionality, robustness and stability. Besides, operating the system far from its design specifications helped in exercising its flexibility and contributed in understanding its limitations. Moreover, the integration with the detector and the interfacing with the off-line data processing and management have been able to take advantage of this extended data taking-period as well. In this paper we report on the usage of the DataFlow infrastructure during the ATLAS data-taking. These results, backed-up by complementary performance tests, validate the architecture of the ATLAS DataFlow and prove that the system is robust, flexible and scalable enough to cope with the final requirements of the ATLAS experiment.

EnviroAtlas - Big Game Hunting Recreation Demand by 12-Digit HUC in the Conterminous United States

Science.gov (United States)

This EnviroAtlas dataset includes the total number of recreational days per year demanded by people ages 18 and over for big game hunting by location in the contiguous United States. Big game includes deer, elk, bear, and wild turkey. These values are based on 2010 population distribution, 2011 U.S. Fish and Wildlife Service (FWS) Fish, Hunting, and Wildlife-Associated Recreation (FHWAR) survey data, and 2011 U.S. Department of Agriculture (USDA) Forest Service National Visitor Use Monitoring program data, and have been summarized by 12-digit hydrologic unit code (HUC). This dataset was produced by the US EPA to support research and online mapping activities related to the EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Brief retrospection on Hungarian school atlases

Science.gov (United States)

Klinghammer, István; Jesús Reyes Nuñez, José

2018-05-01

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

ATLAS Virtual Visits: Bringing the World into the ATLAS Control Room

International Nuclear Information System (INIS)

Goldfarb, S

2012-01-01

The newfound ability of Social Media to transform public communication back to a conversational nature provides HEP with a powerful tool for Outreach and Communication. By far, the most effective component of nearly any visit or public event is that fact that the students, teachers, media, and members of the public have a chance to meet and converse with real scientists. While more than 30,000 visitors passed through the ATLAS Visitor Centre in 2011, nearly 7 billion did not have a chance to make the trip. Clearly this is not for lack of interest. Rather, the costs of travel, in terms of time and money, and limited parking, put that number somewhat out of reach. On the other hand, during the LHC “First Physics” event of 2010, more than 2 million visitors joined the experiment control rooms via webcast for the celebration. This document presents a project developed for the ATLAS Experiment's Outreach and Education program that complements the webcast infrastructure with video conferencing and wireless sound systems, allowing the public to interact with hosts in the control room with minimal disturbance to the shifters. These “Virtual Visits” have included high school classes, LHC Masterclasses, conferences, expositions and other events in Europe, USA, Japan and Australia, to name a few. We discuss the technology used, potential pitfalls (and ways to avoid them), and our plans for the future.

ATLAS Maintenance and Operation management system

CERN Document Server

Copy, B

2007-01-01

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

Soft QCD at CMS and ATLAS

CERN Document Server

Starovoitov, Pavel; The ATLAS collaboration

2018-01-01

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

AGIS: The ATLAS Grid Information System

OpenAIRE

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

2012-01-01

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

Status of the physics validation studies using Geant4 in ATLAS

CERN Document Server

AUTHOR|(CDS)2108477

2003-01-01

The new simulation for the ATLAS detector at LHC is performed using Geant4 in a complete OO/C++ environment. In this framework the simulation of the various test beams for the different ATLAS subdetectors offers an excellent opportunity to perform physics validation studies over a wide range of physics domains: the electromagnetic processes, the individual hadronic interactions, the electromagnetic and hadronic signals in calorimeters. The simulation is implemented by paying special attention to all details of the experimental layout and by testing all possible physics processes which may be of relevance to the specific detector under test: the resulting simulation programs are often more detailed than the corresponding Geant3-based simulation suites. In this paper we present relevant features of muon, electron and pion signals in various ATLAS detectors. All remaining discrepancies between Geant4 and test-beam data are currently being addressed and progress is continuous. This work shows that Geant4 is becom...

EnviroAtlas - Ecosystem Rarity Metrics by 12-digit HUC for the Conterminous United States

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset identifies rare ecosystems using base landcover data from the USGS GAP Analysis Program (Version 2, 2011) combined with landscape ecology...

Explicit state representation and the ATLAS event data model: theory and practice

International Nuclear Information System (INIS)

Nowak, M; Snyder, S; Cranmer, K; Malon, D; Gemmeren, P v; Schaffer, A; Binet, S

2008-01-01

In anticipation of data taking, ATLAS has undertaken a program of work to develop an explicit state representation of the experiment's complex transient event data model. This effort has provided both an opportunity to consider explicitly the structure, organization, and content of the ATLAS persistent event store before writing tens of petabytes of data (replacing simple streaming, which uses the persistent store as a core dump of transient memory), and a locus for support of event data model evolution, including significant refactoring, beyond the automatic schema evolution capabilities of underlying persistence technologies. ATLAS has encountered the need for such non-trivial schema evolution on several occasions already. This paper describes the state representation strategy (transient/persistent separation) and its implementation, including both the payoffs that ATLAS has seen (significant and sometimes surprising space and performance improvements, the extra layer notwithstanding, and extremely general schema evolution support) and the costs (additional and relatively pervasive additional infrastructure development and maintenance). The paper further discusses how these costs are mitigated, and how ATLAS is able to implement this strategy without losing the ability to take advantage of the (improving!) automatic schema evolution capabilities of underlying technology layers when appropriate. Implications of state representations for direct ROOT browsability, and current strategies for associating physics analysis views with such state representations, are also described

ATLAS. LHC experiments

International Nuclear Information System (INIS)

Anon.

1995-01-01

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

Metadata aided run selection at ATLAS

International Nuclear Information System (INIS)

Buckingham, R M; Gallas, E J; Tseng, J C-L; Viegas, F; Vinek, E

2011-01-01

Management of the large volume of data collected by any large scale scientific experiment requires the collection of coherent metadata quantities, which can be used by reconstruction or analysis programs and/or user interfaces, to pinpoint collections of data needed for specific purposes. In the ATLAS experiment at the LHC, we have collected metadata from systems storing non-event-wise data (Conditions) into a relational database. The Conditions metadata (COMA) database tables not only contain conditions known at the time of event recording, but also allow for the addition of conditions data collected as a result of later analysis of the data (such as improved measurements of beam conditions or assessments of data quality). A new web based interface called 'runBrowser' makes these Conditions Metadata available as a Run based selection service. runBrowser, based on PHP and JavaScript, uses jQuery to present selection criteria and report results. It not only facilitates data selection by conditions attributes, but also gives the user information at each stage about the relationship between the conditions chosen and the remaining conditions criteria available. When a set of COMA selections are complete, runBrowser produces a human readable report as well as an XML file in a standardized ATLAS format. This XML can be saved for later use or refinement in a future runBrowser session, shared with physics/detector groups, or used as input to ELSSI (event level Metadata browser) or other ATLAS run or event processing services.

De novo pathway-based biomarker identification

DEFF Research Database (Denmark)

Alcaraz, Nicolas; List, Markus; Batra, Richa

2017-01-01

in a large cohort of breast cancer samples from The Cancer Genome Atlas (TCGA) revealed that MGs are considerably more stable than SG models, while also providing valuable insight into the cancer hallmarks that drive them. In addition, when tested on an independent benchmark non-TCGA dataset, MG features......Gene expression profiles have been extensively discussed as an aid to guide the therapy by predicting disease outcome for the patients suffering from complex diseases, such as cancer. However, prediction models built upon single-gene (SG) features show poor stability and performance on independent...... on their molecular subtypes can provide a detailed view of the disease and lead to more personalized therapies. We propose and discuss a novel MG approach based on de novo pathways, which for the first time have been used as features in a multi-class setting to predict cancer subtypes. Comprehensive evaluation...

Proteogenomic characterization of human colon and rectal cancer

Energy Technology Data Exchange (ETDEWEB)

Zhang, Bing; Wang, Jing; Wang, Xiaojing; Zhu, Jing; Liu, Qi; Shi, Zhiao; Chambers, Matthew C.; Zimmerman, Lisa J.; Shaddox, Kent F.; Kim, Sangtae; Davies, Sherri; Wang, Sean; Wang, Pei; Kinsinger, Christopher; Rivers, Robert; Rodriguez, Henry; Townsend, Reid; Ellis, Matthew; Carr, Steven A.; Tabb, David L.; Coffey, Robert J.; Slebos, Robbert; Liebler, Daniel

2014-09-18

We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic analyses. Protein sequence variants encoded by somatic genomic variations displayed reduced expression compared to protein variants encoded by germline variations. mRNA transcript abundance did not reliably predict protein expression differences between tumors. Proteomics identified five protein expression subtypes, two of which were associated with the TCGA "MSI/CIMP" transcriptional subtype, but had distinct mutation and methylation patterns and associated with different clinical outcomes. Although CNAs showed strong cis- and trans-effects on mRNA expression, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. Our analyses identified HNF4A, a novel candidate driver gene in tumors with chromosome 20q amplifications. Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords novel insights into cancer biology.

ATLAS Grid Workflow Performance Optimization

CERN Document Server

Elmsheuser, Johannes; The ATLAS collaboration

2018-01-01

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

Increasing Drought Sensitivity and Decline of Atlas Cedar (Cedrus atlantica in the Moroccan Middle Atlas Forests

Directory of Open Access Journals (Sweden)

Jesús Julio Camarero

2011-09-01

Full Text Available An understanding of the interactions between climate change and forest structure on tree growth are needed for decision making in forest conservation and management. In this paper, we investigated the relative contribution of tree features and stand structure on Atlas cedar (Cedrus atlantica radial growth in forests that have experienced heavy grazing and logging in the past. Dendrochronological methods were applied to quantify patterns in basal-area increment and drought sensitivity of Atlas cedar in the Middle Atlas, northern Morocco. We estimated the tree-to-tree competition intensity and quantified the structure in Atlas cedar stands with contrasting tree density, age, and decline symptoms. The relative contribution of tree age and size and stand structure to Atlas cedar growth decline was estimated by variance partitioning using partial-redundancy analyses. Recurrent drought events and temperature increases have been identified from local climate records since the 1970s. We detected consistent growth declines and increased drought sensitivity in Atlas cedar across all sites since the early 1980s. Specifically, we determined that previous growth rates and tree age were the strongest tree features, while Quercus rotundifolia basal area was the strongest stand structure measure related to Atlas cedar decline. As a result, we suggest that Atlas cedar forests that have experienced severe drought in combination with grazing and logging may be in the process of shifting dominance toward more drought-tolerant species such as Q. rotundifolia.

Integrating Networking into ATLAS

CERN Document Server

Mc Kee, Shawn Patrick; The ATLAS collaboration

2018-01-01

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

ATLAS End-cap Part II

CERN Multimedia

2007-01-01

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

An overview of the mechanical design of the Atlas pulsed power machine

CERN Document Server

Bowman, D W; Barr, G W; Bennett, G A; Cochrane, J C; Davis, H A; Davis, T O; Dorr, G; Gribble, R F; Griego, J R; Hood, M; Kimerly, H J; Martínez, A; McCuistian, B T; Miller, R B; Ney, S A; Nielsen, K; Pankuch, P; Parsons, W M; Potter, C; Ricketts, R L; Salazar, H R; Scudder, D W; Shapiro, C; Thompson, M C; Trainor, R J; Valdez, G A; Yonemoto, W; Kirbie, H C

1999-01-01

Atlas is a pulsed-power facility being designed at Los Alamos National Laboratory to perform high-energy density experiments in support of Science-Based Stockpile Stewardship and basic research programs. Atlas will consist of 24 individual maintenance units, each consisting of 4 240-kV Marx units. Maintenance units are contained in large oil tanks arrayed in a circle about a central target chamber. Total stored energy of the capacitor bank will be 23 MJ. Maintenance units will discharge through an output shorting switch into a vertical tri-plate transmission line, and from there into a transition area/collector inside a large vacuum chamber. An overview of mechanical design aspects of the Atlas machine is presented. These include maintenance unit design and design of the tri-plate transmission line and transition region. Findings from fabrication and testing of prototype systems are discussed. (2 refs).

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.

Major Achievements and Prospect of the ATLAS Integral Effect Tests

International Nuclear Information System (INIS)

Choi, K.; Kim, Y.; Song, C.; Baek, W.

2012-01-01

A large-scale thermal-hydraulic integral effect test facility, ATLAS (Advanced Thermal-hydraulic Test Loop for Accident Simulation), has been operated by KAERI. The reference plant of ATLAS is the APR1400 (Advanced Power Reactor, 1400 MWe). Since 2007, an extensive series of experimental works were successfully carried out, including large break loss of coolant accident tests, small break loss of coolant accident tests at various break locations, steam generator tube rupture tests, feed line break tests, and steam line break tests. These tests contributed toward an understanding of the unique thermal-hydraulic behavior, resolving the safety-related concerns and providing validation data for evaluation of the safety analysis codes and methodology for the advanced pressurized water reactor, APR1400. Major discoveries and lessons found in the past integral effect tests are summarized in this paper. As the demand for integral effect tests is on the rise due to the active national nuclear R and D program in Korea, the future prospects of the application of the ATLAS facility are also discussed.

22 March 2012 - Canada Foundation for Innovation Senior Programs Officer H.-C. Bandulet with spouse in the ATLAS visitor centre guided by Former Spokesperson P. Jenni.

CERN Multimedia

Maximilien Brice

2012-01-01

CERN-HI-1203073 16: Senior Canadian Scientist, ATLAS Collaboration, University of Toronto/IPP R. Teuscher; L. Andrzejewski(Spouse); H.-C. Bandulet; R.Voss (behind);ATLAS Collaboration, University of Toronto N.Ilic; ;ATLAS Collaboration, University of Toronto, R. Rezvani; ATLAS Collaboration Former Spokesperson P. Jenni.

Mindboggle: Automated brain labeling with multiple atlases

International Nuclear Information System (INIS)

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

2005-01-01

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

The ATLAS Level-2 Trigger Pilot Project

CERN Document Server

Blair, R; Haberichter, W N; Schlereth, J L; Bock, R; Bogaerts, A; Boosten, M; Dobinson, Robert W; Dobson, M; Ellis, Nick; Elsing, M; Giacomini, F; Knezo, E; Martin, B; Shears, T G; Tapprogge, Stefan; Werner, P; Hansen, J R; Wäänänen, A; Korcyl, K; Lokier, J; George, S; Green, B; Strong, J; Clarke, P; Cranfield, R; Crone, G J; Sherwood, P; Wheeler, S; Hughes-Jones, R E; Kolya, S; Mercer, D; Hinkelbein, C; Kornmesser, K; Kugel, A; Männer, R; Müller, M; Sessler, M; Simmler, H; Singpiel, H; Abolins, M; Ermoline, Y; González-Pineiro, B; Hauser, R; Pope, B; Sivoklokov, S Yu; Boterenbrood, H; Jansweijer, P; Kieft, G; Scholte, R; Slopsema, R; Vermeulen, J C; Baines, J T M; Belias, A; Botterill, David R; Middleton, R; Wickens, F J; Falciano, S; Bystrický, J; Calvet, D; Gachelin, O; Huet, M; Le Dû, P; Mandjavidze, I D; Levinson, L; González, S; Wiedenmann, W; Zobernig, H

2002-01-01

The Level-2 Trigger Pilot Project of ATLAS, one of the two general purpose LHC experiments, is part of the on-going program to develop the ATLAS high-level triggers (HLT). The Level-2 Trigger will receive events at up to 100 kHz, which has to be reduced to a rate suitable for full event-building of the order of 1 kHz. To reduce the data collection bandwidth and processing power required for the challenging Level-2 task it is planned to use Region of Interest guidance (from Level-1) and sequential processing. The Pilot Project included the construction and use of testbeds of up to 48 processing nodes, development of optimized components and computer simulations of a full system. It has shown how the required performance can be achieved, using largely commodity components and operating systems, and validated an architecture for the Level-2 system. This paper describes the principal achievements and conclusions of this project. (28 refs).

The ATLAS data management software engineering process

International Nuclear Information System (INIS)

Lassnig, M; Garonne, V; Stewart, G A; Barisits, M; Serfon, C; Goossens, L; Nairz, A; Beermann, T; Vigne, R; Molfetas, A

2014-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

The ATLAS data management software engineering process

Science.gov (United States)

Lassnig, M.; Garonne, V.; Stewart, G. A.; Barisits, M.; Beermann, T.; Vigne, R.; Serfon, C.; Goossens, L.; Nairz, A.; Molfetas, A.; Atlas Collaboration

2014-06-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

Recently Published Lectures and Tutorials for ATLAS

CERN Multimedia

Herr, J.

2006-01-01

As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project, WLAP, a collaboration between the University of Michigan and CERN, has developed a synchronized system for recording and publishing educational multimedia presentations, using the Web as medium. This year, the University of Michigan team has been asked to record and publish all ATLAS Plenary sessions, as well as a large number of Physics and Computing tutorials. A significant amount of this material has already been published and can be accessed via the links below. The WLAP model is spreading. This summer, the CERN's High School Teachers program has used WLAP's system to record several physics lectures directed toward a broad audience. And a new project called MScribe, which is essentially the WLAP system coupled with an infrared tracking camera, is being used by the University of Michigan to record several University courses this academic year. All lectures can be viewed on any major platform with any common internet browser...

Pixel-Cluster Counting Luminosity Measurement in ATLAS

CERN Document Server

McCormack, William Patrick; The ATLAS collaboration

2016-01-01

A precision measurement of the delivered luminosity is a key component of the ATLAS physics program at the Large Hadron Collider (LHC). A fundamental ingredient of the strategy to control the systematic uncertainties affecting the absolute luminosity has been to compare the measurements of several luminometers, most of which use more than one counting technique. The level of consistency across the various methods provides valuable cross-checks as well as an estimate of the detector-related systematic uncertainties. This poster describes the development of a luminosity algorithm based on pixel-cluster counting in the recently installed ATLAS inner b-layer (IBL), using data recorded during the 2015 pp run at the LHC. The noise and background contamination of the luminosity-associated cluster count is minimized by a multi-component fit to the measured cluster-size distribution in the forward pixel modules of the IBL. The linearity, long-term stability and statistical precision of the cluster-counting method are ...

Pixel-Cluster Counting Luminosity Measurement In ATLAS

CERN Document Server

AUTHOR|(SzGeCERN)782710; The ATLAS collaboration

2017-01-01

A precision measurement of the delivered luminosity is a key component of the ATLAS physics program at the Large Hadron Collider (LHC). A fundamental ingredient of the strategy to control the systematic uncertainties affecting the absolute luminosity has been to compare the measure- ments of several luminometers, most of which use more than one counting technique. The level of consistency across the various methods provides valuable cross-checks as well as an estimate of the detector-related systematic uncertainties. This poster describes the development of a luminosity algorithm based on pixel-cluster counting in the recently installed ATLAS inner b-layer (IBL), using data recorded during the 2015 pp run at the LHC. The noise and background contamination of the luminosity-associated cluster count is minimized by a multi-component fit to the measured cluster-size distribution in the forward pixel modules of the IBL. The linearity, long-term stability and statistical precision of the cluster- counting method a...

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.

ATLAS rewards industry

CERN Document Server

Maximilien Brice

2006-01-01

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

Physics Capabilities of the ATLAS Experiment in Pb+Pb Collisions at the LHC

CERN Document Server

Derendarz, D; The ATLAS collaboration

2010-01-01

Relativistic heavy ion collisions at the LHC will uncover properties of hot and dense medium formed at collision energy thirty times larger than energy presently available at RHIC. ATLAS is one of three experiments participating in the heavy ion program at the LHC. A brief overview of variety of observables which will be measured by ATLAS to study soft and hard QCD phenomena in heavy ion environment is presented. In particular the detector will measure global observables like charged particle multiplicity, azimuthal anisotropy and energy flow. The detector provides also an excellent capability to probe the quark gluon plasma by measurement of high energy jets and photons as well as quarkonia states. Performance of a high granularity calorimeter, silicon tracking detector and muon spectrometer in heavy ion collisions is reported. A unique ATLAS potential to study Pb+Pb interactions is discussed.

The Atlas pulsed power facility for high energy density physics experiments

CERN Document Server

Miller, R B; Barr, G W; Bowman, D W; Cochrane, J C; Davis, H A; Elizondo, J M; Gribble, R F; Griego, J R; Hicks, R D; Hinckley, W B; Hosack, K W; Nielsen, K E; Parker, J V; Parsons, M O; Rickets, R L; Salazar, H R; Sánchez, P G; Scudder, D W; Shapiro, C; Thompson, M C; Trainor, R J; Valdez, G A; Vigil, B N; Watt, R G; Wysocki, F J; Kirbie, H C

1999-01-01

The Atlas facility, now under construction at Los Alamos National Laboratory (LANL), will provide a unique capability for performing high-energy-density experiments in support of weapon-physics and basic-research programs. Here, the authors describe how the primary element of Atlas is a 23-MJ capacitor bank, comprised of 96 separate Marx generators housed in 12 separate oil-filled tanks, surrounding a central target chamber. Each tank will house two, independently- removable maintenance units, with each maintenance unit consisting of four Marx modules. Each Marx module has four capacitors that can each be charged to a maximum of 60 kilovolts. When railgap switches are triggered, the Marx modules erect to a maximum of 240 kV. The parallel discharge of these 96 Marx modules will deliver a 30-MA current pulse with a 4-5-ys risetime to a cylindrical, imploding liner via 24 vertical, tri-plate, oil-insulated transmission lines. An experimental program for testing and certifying all Marx and transmission line compo...

The ATLAS Experiment Laboratory - Overview

International Nuclear Information System (INIS)

Malecki, P.

1999-01-01

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

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 ...

ATLAS & Google - The Data Ocean Project

CERN Document Server

Lassnig, Mario; The ATLAS collaboration

2018-01-01

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

ATLAS OF EUROPEAN VALUES

NARCIS (Netherlands)

M Ed Uwe Krause

2008-01-01

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

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.

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.

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.

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.

The Hatfield SCT lunar atlas photographic atlas for Meade, Celestron, and other SCT telescopes

CERN Document Server

2014-01-01

In a major publishing event for lunar observers, the justly famous Hatfield atlas is updated in even more usable form. This version of Hatfield’s classic atlas solves the problem of mirror images, making identification of left-right reversed imaged lunar features both quick and easy. SCT and Maksutov telescopes – which of course include the best-selling models from Meade and Celestron – reverse the visual image left to right. Thus it is extremely difficult to identify lunar features at the eyepiece of one of the instruments using a conventional Moon atlas, as the human brain does not cope well when trying to compare the real thing with a map that is a mirror image of it. Now this issue has at last been solved.   In this atlas the Moon’s surface is shown at various sun angles, and inset keys show the effects of optical librations. Smaller non-mirrored reference images are also included to make it simple to compare the mirrored SCT plates and maps with those that appear in other atlases. This edition s...

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.

Top quark studies with Atlas at the LHC. Electromagnetic calorimeter commissioning; Etude du quark top avec Atlas au LHC. Mise en route du calorimetre electromagnetique

Energy Technology Data Exchange (ETDEWEB)

Resende Vaz de Melo Xavier, B

2007-05-15

The first proton-proton collisions in the Large Hadron Collider at CERN will take place on 2007. It aims at understanding the origins of mass. and it will also look for new physics. The ATLAS experiment will exploit all those physics potentialities. using a multilayer generalist detector. Quark top studies will be an important step in ATLAS physics program: its properties may reveal hints of new phenomena. One way to look for new physics is through quark top and W boson polarizations. which are studied here. This detailed simulation study has confirmed previous fast simulation results including extensive systematics estimation. ATLAS should thus yield a precision of a few percents with 10 fb{sup -1} of data. that is a year of LHC working. This precision is sufficient to select among several new physics models. Among ATLAS subsystems, the electromagnetic calorimeter plays a crucial role in the characterisation of electrons and photons. which are used in particular for the Higgs boson search. This document deals with the calorimeter commissioning as the time of the first collisions approaches. The detector itself and its electronics will be described, as well as its installation and calibration. Cosmic muons observation will then be presented. as the first overall test of the reading and reconstruction electronics chain in actual working conditions. (author)

NATIONAL ATLAS OF THE ARCTIC

Directory of Open Access Journals (Sweden)

Nikolay S. Kasimov

2018-01-01

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

EnviroAtlas - Ecosystem Service Market and Project Locations, U.S., 2015, Forest Trends' Ecosystem Marketplace

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset contains points depicting the location of market-based programs, referred to herein as markets, and projects addressing ecosystem services...

EnviroAtlas - Ecosystem Service Market and Project Areas, U.S., 2015, Forest Trends' Ecosystem Marketplace

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting the geographic areas of market-based programs, referred to herein as markets, and projects addressing ecosystem...

World atlas of nuclear industry: civil and military; Atlas mondial du nucleaire: Civil et militaire

Energy Technology Data Exchange (ETDEWEB)

Alexandre, Nicolas

2011-07-01

Todays, with the energy supplies and global warming concerns, nuclear energy in making a come-back, witness the numerous nuclear programs launched or re-launched in the US, in Europe, China and India. In parallel, on the military side, the deterrence strategy remains in the center of security politics of big powers. This atlas takes stock of the overall issues linked with the nuclear technology: production, civil applications (power generation, medicine etc..), military usages (naval propulsion, weapons). It answers the main questions of this complex world, often dominated by secrecy: who does what in the nuclear domain in France? Is an accident, like the Chernobyl's one, possible today in Europe? What solutions for radioactive wastes? Do we take risks when we export our reactor technologies to Middle-East countries? Are we at the dawn of a new arms rush? What do international agreements foresee in this domain? Taking into account the costs, the hazards and the advantages of nuclear industry, the atlas shows that it is possible to establish solid technical and legal barriers between its civil and military sides. (J.S.)

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...

Development, deployment and operations of ATLAS databases

International Nuclear Information System (INIS)

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

2008-01-01

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

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...

The Cerefy registered clinical brain atlas on CD-ROM. Based on the classic Talairach-Tournoux and Schaltenbrand-Wahren brain atlases. 2. ed.

International Nuclear Information System (INIS)

Nowinski, W.L.; Thirunavuukarasuu, A.

2001-01-01

This remarkable CD-ROM provides enhanced and extended versions of three world-famous Thieme atlases, (Schaltenbrand and Wahren's Atlas for Stereotaxy of the Human Brain, Talairach and Tournoux's Co-Planar Stereotaxis Atlas of the Human Brain and Referentially Oriented Cerebral MRI Anatomy). It contains the electronic atlases as well as an easy navigation system to facilitate searching for and displaying more than 525 anatomical structures. Revolutionizing the field of brain anatomy, the authors have segmented, labeled, and cross referenced all the information contained in the books, and created contours for all three atlases. The Cerefy registered Clinical Brain Atlas now allows you to electronically navigate these atlases simultaneously on axial, coronal, and sagittal planes, and enjoy the ability to: 1. Access 210 high-quality, fully segmented, and labeled atlas images with corresponding contours, 2. Display and manipulate spatially co-registered atlases, 3. Dynamically label images with structure names and descriptions, and then highlight selected structures in the atlas image, 4. Image zoom in five different levels, mensurate, search, set triplanar, get coordinates, save, and print, 5. Access on-line help, glossary, and supportive atlas materials. (orig.)

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

A Slice of ATLAS

CERN Document Server

2004-01-01

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

Evolution of the ATLAS distributed computing system during the LHC long shutdown

Science.gov (United States)

Campana, S.; Atlas Collaboration

2014-06-01

The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the Worldwide LHC Computing Grid (WLCG) distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1 PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileup. We will describe the evolution of the ADC software foreseen during this period. This includes consolidating the existing Production and Distributed Analysis framework (PanDA) and ATLAS Grid Information System (AGIS), together with the development and commissioning of next generation systems for distributed data management (DDM/Rucio) and production (Prodsys-2). We will explain how new technologies such as Cloud Computing and NoSQL databases, which ATLAS investigated as R&D projects in past years, will be integrated in production. Finally, we will describe more fundamental developments such as breaking job-to-data locality by exploiting storage federations and caches, and event level (rather than file or dataset level) workload engines.

Evolution of the ATLAS distributed computing system during the LHC long shutdown

International Nuclear Information System (INIS)

Campana, S

2014-01-01

The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the Worldwide LHC Computing Grid (WLCG) distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1 PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileup. We will describe the evolution of the ADC software foreseen during this period. This includes consolidating the existing Production and Distributed Analysis framework (PanDA) and ATLAS Grid Information System (AGIS), together with the development and commissioning of next generation systems for distributed data management (DDM/Rucio) and production (Prodsys-2). We will explain how new technologies such as Cloud Computing and NoSQL databases, which ATLAS investigated as R and D projects in past years, will be integrated in production. Finally, we will describe more fundamental developments such as breaking job-to-data locality by exploiting storage federations and caches, and event level (rather than file or dataset level) workload engines.

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 ...

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....

Letter of Intent for the Phase-I Upgrade of the ATLAS Experiment

CERN Document Server

ATLAS Collaboration

2011-01-01

After the first successful years of running at the LHC, the ATLAS Collaboration is preparing to fully exploit the unprecedented physics opportunities offered by exploration of a completely new energy domain. This program builds on the excellent LHC accelerator complex performance demonstrated to date. A plan to consolidate and improve the physics capabilities of the current detector over the next decade, targeting the 2018 LHC shutdown as installation milestone, is presented in this Letter of Intent. The document primarily addresses the proposed enhancements to the ATLAS trigger system to cope with luminosities beyond the LHC nominal design value, while retaining the same physics performance. The Phase-I upgrades will allow ATLAS to maintain low pT trigger thresholds for isolated leptons by increasing the granularity of the calorimeters involved in the Level-1 trigger and by introducing new muon trigger and tracking detectors in the forward direction. Precision measurements of the couplings of the Higgs boson...

The High-Resolution IRAS Galaxy Atlas

Science.gov (United States)

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

1997-01-01

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

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

CERN Multimedia

ATLAS Outreach

2010-01-01

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

EnviroAtlas - Ecosystem Service Market and Project Enabling Conditions, U.S., 2016, Forest Trends' Ecosystem Marketplace

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting conditions enabling market-based programs, referred to herein as markets, and projects addressing ecosystem...

The geosystems of complex geographical atlases

Directory of Open Access Journals (Sweden)

Jovanović Jasmina

2012-01-01

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

The ATLAS distributed analysis system

OpenAIRE

Legger, F.

2014-01-01

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

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.

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.

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.

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.

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.

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.

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.

TU-AB-202-10: How Effective Are Current Atlas Selection Methods for Atlas-Based Auto-Contouring in Radiotherapy Planning?

Energy Technology Data Exchange (ETDEWEB)

Peressutti, D; Schipaanboord, B; Kadir, T; Gooding, M [Mirada Medical Limited, Science and Medical Technology, Oxford (United Kingdom); Soest, J van; Lustberg, T; Elmpt, W van; Dekker, A [Maastricht University Medical Centre, Department of Radiation Oncology MAASTRO - GROW School for Oncology Developmental Biology, Maastricht (Netherlands)

2016-06-15

Purpose: To investigate the effectiveness of atlas selection methods for improving atlas-based auto-contouring in radiotherapy planning. Methods: 275 H&N clinically delineated cases were employed as an atlas database from which atlases would be selected. A further 40 previously contoured cases were used as test patients against which atlas selection could be performed and evaluated. 26 variations of selection methods proposed in the literature and used in commercial systems were investigated. Atlas selection methods comprised either global or local image similarity measures, computed after rigid or deformable registration, combined with direct atlas search or with an intermediate template image. Workflow Box (Mirada-Medical, Oxford, UK) was used for all auto-contouring. Results on brain, brainstem, parotids and spinal cord were compared to random selection, a fixed set of 10 “good” atlases, and optimal selection by an “oracle” with knowledge of the ground truth. The Dice score and the average ranking with respect to the “oracle” were employed to assess the performance of the top 10 atlases selected by each method. Results: The fixed set of “good” atlases outperformed all of the atlas-patient image similarity-based selection methods (mean Dice 0.715 c.f. 0.603 to 0.677). In general, methods based on exhaustive comparison of local similarity measures showed better average Dice scores (0.658 to 0.677) compared to the use of either template image (0.655 to 0.672) or global similarity measures (0.603 to 0.666). The performance of image-based selection methods was found to be only slightly better than a random (0.645). Dice scores given relate to the left parotid, but similar results patterns were observed for all organs. Conclusion: Intuitively, atlas selection based on the patient CT is expected to improve auto-contouring performance. However, it was found that published approaches performed marginally better than random and use of a fixed set of

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...

ATLAS construction status

International Nuclear Information System (INIS)

Jenni, P.

2006-01-01

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

ATLAS cloud R and D

International Nuclear Information System (INIS)

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

2014-01-01

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

The ATLAS Pixel Detector

CERN Document Server

Huegging, Fabian

2006-06-26

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

The Next Generation ATLAS Production System

CERN Document Server

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

2015-01-01

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

Status of the ATLAS Pixel Detector and its performance after three years of operation

CERN Document Server

Favareto, A; The ATLAS collaboration

2012-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is very important for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. The detector performance is excellent: ~96 % of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, and a good alignment allows high quality track resolution

Status of the ATLAS Pixel Detector and its performance after three years of operation

CERN Document Server

Favareto, A; The ATLAS collaboration

2012-01-01

The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high radiation environment close to the collision region. This capability is very important for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers and three layers of forward and backward pixel detectors. It consists of approximately 80 million pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. The detector performance is excellent: ~96% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, and a good alignment allows high quality track resolution.

4th ATLAS Physics Workshop (Athens) - Report from the Physics Sessions

CERN Multimedia

Kersevan, B P

The 4th ATLAS Physics Workshop provided a showcase for studies of some of the most exciting aspects of LHC physics, both within the Standard Model and beyond. It was clear from the wide range of topics covered, from QCD studies to TeV-scale Black Hole production, that preparations are well in hand for understanding whatever Nature, and the LHC, may throw at us. The Standard Model session concentrated on QCD and Electroweak physics, which will form the core of the ATLAS physics program during the first years of LHC operation. Convenor Matt Dobbs began by summarising recent and ongoing studies and pointed out that the first ATLAS papers will aim to prove that we understand LHC physics in the regime where the Standard Model is reliable. Only then will we be able to make convincing claims for the existence of New Physics. Subsequent talks discussed our understanding of this 'bread-and-butter' physics, including minimum bias processes and underlying events (Arthur Moraes), Parton Distribution Functions (Jon Butte...

Hidden Valley Search at ATLAS

CERN Document Server

Verducci, M

2011-01-01

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

ATLAS end-cap detector

CERN Multimedia

Maximilien Brice

2003-01-01

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

Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival.

Science.gov (United States)

Phan, John H; Hoffman, Ryan; Kothari, Sonal; Wu, Po-Yen; Wang, May D

2016-02-01

The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization. Results indicate that integration of multiple data modalities improves prediction of cancer grade and outcome. Specifically, stacked generalization, a method that integrates multiple data modalities to produce a single prediction result, outperforms both single-data-modality prediction and majority vote. Moreover, stacked generalization reveals the contribution of each data modality (and specific features within each data modality) to the final prediction result and may provide biological insights to explain prediction performance.

R-Hadron Search at ATLAS

DEFF Research Database (Denmark)

Heisterkamp, Simon Johann Franz

In this thesis I motivate and present a search for long lived massive R-hadrons using the data collected by the ATLAS detector in 2011. Both ionisation- and time-of-ight-based methods are described. Since no signal was found, a lower limit on the mass of such particles is set. The analysis was also...... published by the ATLAS collboration in Phys.Lett.B. titled `Searches for heavy long-lived sleptons and R-Hadrons with the ATLAS detector in pp collisions at sqrt(s) = 7 TeV'....

The ATLAS Women's Network: one year of activities

CERN Multimedia

Paula Eerola

The idea for an ATLAS Women's Network was born during the ATLAS overview week in October 2005, when a few of us discussed our experiences and were pondering about what we could do. We felt that it was important to increase the visibility of women working in ATLAS in order to make a better and more effective use of the ATLAS human resources, that is, make sure that women are duly included at all levels. Furthermore, it is our belief that making ATLAS a better working environment for female collaborators and other female co-workers will benefit both us and the collaboration as a whole. On the individual level, all of us thought that we could benefit from peer support and experience sharing, and an ATLAS Women's Network could facilitate this by developing contacts between the ATLAS Women in ATLAS Institutes worldwide. Finally, we thought that it was important to increase the number of women studying physics and working in the field of physics research by identifying gender barriers in the career paths of women i...

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).

Renewable Energy Atlas of the United States

Energy Technology Data Exchange (ETDEWEB)

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

2013-12-13

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

The ATLAS IBL CO2 Cooling System

CERN Document Server

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

2017-01-01

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

Innovating science communication: the structure supporting ATLAS Education & Outreach

Science.gov (United States)

Goldfarb, Steven; Marcelloni, Claudia; Shaw, Kate; ATLAS Experiment

2016-04-01

The ATLAS Education & Outreach project has, over the years, developed a strong reputation for supporting innovation. Animated event displays, musical CDs, 3d movies, 3-storey murals, photo books, data sonifications, multi-media art installations, pub slams, masterclasses, documentaries, pop-up books, LEGO® models, and virtual visits are among the many diverse methods being exploited to communicate to the world the goals and accomplishments of the ATLAS Experiment at CERN. This variety of creativity and innovation does not pop out of a vacuum. It requires underlying motivation by the collaboration to communicate with the public; freedom and encouragement to do so in a creative manner; and a support structure for developing, implementing and promoting these activities. The ATLAS Outreach project has built this support structure on a well-defined communication plan, high-quality content, and effective delivery platforms. Most importantly, implementation of the program has been based on the effective engagement of the participating institutes and other key partners, not only to leverage modest human resources and funding, but also to take advantage of the rich imagination and inspiration of a diverse, global human collaboration. We present our current plan, on-going activities, and a few more fun innovations for the future.

Commissioning of the ATLAS pixel detector

International Nuclear Information System (INIS)

Golling, Tobias

2008-01-01

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

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...

ATLAS solenoid operates underground

CERN Multimedia

2006-01-01

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

Evolution of the ATLAS Software Framework towards Concurrency

CERN Document Server

Jones, Roger; The ATLAS collaboration; Leggett, Charles; Wynne, Benjamin

2015-01-01

The ATLAS experiment has successfully used its Gaudi/Athena software framework for data taking and analysis during the first LHC run, with billions of events successfully processed. However, the design of Gaudi/Athena dates from early 2000 and the software and the physics code has been written using a single threaded, serial design. This programming model has increasing difficulty in exploiting the potential of current CPUs, which offer their best performance only through taking full advantage of multiple cores and wide vector registers. Future CPU evolution will intensify this trend, with core counts increasing and memory per core falling. Maximising performance per watt will be a key metric, so all of these cores must be used as efficiently as possible. In order to address the deficiencies of the current framework, ATLAS has embarked upon two projects: first, a practical demonstration of the use of multi-threading in our reconstruction software, using the GaudiHive framework; second, an exercise to gather r...

Extending ATLAS Computing to Commercial Clouds and Supercomputers

CERN Document Server

Nilsson, P; The ATLAS collaboration; Filipcic, A; Klimentov, A; Maeno, T; Oleynik, D; Panitkin, S; Wenaus, T; Wu, W

2014-01-01

The Large Hadron Collider will resume data collection in 2015 with substantially increased computing requirements relative to its first 2009-2013 run. A near doubling of the energy and the data rate, high level of event pile-up, and detector upgrades will mean the number and complexity of events to be analyzed will increase dramatically. A naive extrapolation of the Run 1 experience would suggest that a 5-6 fold increase in computing resources are needed - impossible within the anticipated flat computing budgets in the near future. Consequently ATLAS is engaged in an ambitious program to expand its computing to all available resources, notably including opportunistic use of commercial clouds and supercomputers. Such resources present new challenges in managing heterogeneity, supporting data flows, parallelizing workflows, provisioning software, and other aspects of distributed computing, all while minimizing operational load. We will present the ATLAS experience to date with clouds and supercomputers, and des...

A Fast hardware tracker for the ATLAS Trigger

CERN Document Server

Pandini, Carlo Enrico; The ATLAS collaboration

2015-01-01

The trigger system at the ATLAS experiment is designed to lower the event rate occurring from the nominal bunch crossing at 40 MHz to about 1 kHz for a designed LHC luminosity of 10$^{34}$ cm$^{-2}$ s$^{-1}$. To achieve high background rejection while maintaining good efficiency for interesting physics signals, sophisticated algorithms are needed which require extensive use of tracking information. The Fast TracKer (FTK) trigger system, part of the ATLAS trigger upgrade program, is a highly parallel hardware device designed to perform track-finding at 100 kHz and based on a mixture of advanced technologies. Modern, powerful Field Programmable Gate Arrays (FPGA) form an important part of the system architecture, and the combinatorial problem of pattern recognition is solved by ~8000 standard-cell ASICs named Associative Memories. The availability of the tracking and subsequent vertex information within a short latency ensures robust selections and allows improved trigger performance for the most difficult sign...

EnviroAtlas - Reptile Biodiversity Ecosystem Services Metrics by 12-digit HUC for the Conterminous United States

Science.gov (United States)

This EnviroAtlas dataset contains biodiversity metrics reflecting ecosystem services or other aspects of biodiversity for reptile species, based on the number of reptile species as measured by predicted habitat present within a pixel. These metrics were created from grouping national level single species habitat models created by the USGS Gap Analysis Program into smaller ecologically based, phylogeny based, or stakeholder suggested composites. The dataset includes reptile species richness metrics for all reptile species, lizards, snakes, turtles, poisonous reptiles, Natureserve-listed G1,G2, and G3 reptile species, and reptile species listed by IUCN (International Union for Conservation of Nature), PARC (Partners in Amphibian and Reptile Conservation) and SWPARC (Southwest Partners in Amphibian and Reptile Conservation). This dataset was produced by a joint effort of New Mexico State University, US EPA, and USGS to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa

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...

Validating atlas-guided DOT: a comparison of diffuse optical tomography informed by atlas and subject-specific anatomies.

Science.gov (United States)

Cooper, Robert J; Caffini, Matteo; Dubb, Jay; Fang, Qianqian; Custo, Anna; Tsuzuki, Daisuke; Fischl, Bruce; Wells, William; Dan, Ippeita; Boas, David A

2012-09-01

We describe the validation of an anatomical brain atlas approach to the analysis of diffuse optical tomography (DOT). Using MRI data from 32 subjects, we compare the diffuse optical images of simulated cortical activation reconstructed using a registered atlas with those obtained using a subject's true anatomy. The error in localization of the simulated cortical activations when using a registered atlas is due to a combination of imperfect registration, anatomical differences between atlas and subject anatomies and the localization error associated with diffuse optical image reconstruction. When using a subject-specific MRI, any localization error is due to diffuse optical image reconstruction only. In this study we determine that using a registered anatomical brain atlas results in an average localization error of approximately 18 mm in Euclidean space. The corresponding error when the subject's own MRI is employed is 9.1 mm. In general, the cost of using atlas-guided DOT in place of subject-specific MRI-guided DOT is a doubling of the localization error. Our results show that despite this increase in error, reasonable anatomical localization is achievable even in cases where the subject-specific anatomy is unavailable. Copyright © 2012 Elsevier Inc. All rights reserved.

Hidden Valley Searches at ATLAS

CERN Document Server

Ventura, D; The ATLAS collaboration

2011-01-01

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

Physics of ridge and hard processes in proton-lead and lead-lead collisions with ATLAS

CERN Document Server

Spousta, Martin; The ATLAS collaboration

2018-01-01

In this short report, we provide an overview of selected new results from the heavy-ion physics program of the ATLAS experiment with the emphasis on jet quenching, quarkonia suppression and long range azimuthal correlations.

ATLAS Plans for the High-Luminosity LHC

CERN Document Server

Walkowiak, Wolfgang; The ATLAS collaboration

2018-01-01

Despite the excellent performance of the Large Hadron Collider (LHC) at CERN an upgrade to a High-Luminosity LHC (HL-LHC) with a peak instantaneous luminosity of up to $7.5\\times 10^{34}$ fb$^{-1}$ will be required after collecting a total dataset of approximately 300 fb$^{-1}$ by the end of Run 3 (in 2023). The upgrade will substantially increase the statistics available to the experiments for addressing the remaining open puzzles of particle physics. The HL-LHC is expected to start operating in 2026 and to deliver up to 4000 fb$^{-1}$ within twelve years. The corresponding upgrades of the ATLAS detector and the ATLAS beauty physics program at the HL-LHC are being discussed. As examples, preliminary results on the expected sensitivities for the search for CP-violation in the decay channel $B^0_s \\to J/\\psi \\,\\phi$ using the parameters $\\Delta\\Gamma_s$ and $\\phi_s$ as well as projections for the branching fractions of the rare decays $B^0_s \\to \\mu^+\\mu^-$ and $B^0\\to\\mu^+\\mu^-$ are provided.

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...

Electroweak and BSM Searches in B Physics with ATLAS

CERN Document Server

Cerri, Alessandro; The ATLAS collaboration

2017-01-01

A wide program of studies is performed by ATLAS in the B0 and B0s systems.  The talk will discuss the measurement of the width difference in the B0 system (currently, the most precise single measurement) and the recent study of the angular correlations in the B0 to K* mu+mu- decays.  
The ongoing programs on the rare decays of B0(s) to muon pairs and on the B0s width difference and CP violating phase phi_s in the decay B0s to J/psi phi will also be discussed.

28 May 2010 - Representatives of the Netherlands School of Public Administration guided in the ATLAS visitor centre by ATLAS Collaboration Member and NIKHEF G. Bobbink and ATLAS Magnet Project Leader H.ten Kate.

CERN Document Server

Maximilien Brice

2010-01-01

28 May 2010 - Representatives of the Netherlands School of Public Administration guided in the ATLAS visitor centre by ATLAS Collaboration Member and NIKHEF G. Bobbink and ATLAS Magnet Project Leader H.ten Kate.

ATLAS DataFlow Infrastructure recent results from ATLAS cosmic and first-beam data-taking

CERN Document Server

Vandelli, W

2010-01-01

The ATLAS DataFlow infrastructure is responsible for the collection and conveyance of event data from the detector front-end electronics to the mass storage. Several optimized and multi-threaded applications fulfill this purpose operating over a multi-stage Gigabit Ethernet network which is the backbone of the ATLAS Trigger and Data Acquisition System. The system must be able to efficiently transport event-data with high reliability, while providing aggregated bandwidths larger than 5 GByte/s and coping with many thousands network connections. Nevertheless, routing and streaming capabilities and monitoring and data accounting functionalities are also fundamental requirements. During 2008, a few months of ATLAS cosmic data-taking and the first experience with the LHC beams provided an unprecedented testbed for the evaluation of the performance of the ATLAS DataFlow, in terms of functionality, robustness and stability. Besides, operating the system far from its design specifications helped in exercising its fle...

Analytics Platform for ATLAS Computing Services

CERN Document Server

Vukotic, Ilija; The ATLAS collaboration; Bryant, Lincoln

2016-01-01

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

ATLAS Cloud Computing R&D project

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; Ohman, H; Paterson, M; Sobie, R; Taylor, R; Walker, R; Zaytsev, A

2013-01-01

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...

ATLAS: last few metresfor the Calorimeter

CERN Multimedia

2005-01-01

On Friday 4th November, the ATLAS Barrel Calorimeter was moved from its assembly point at the side of the ATLAS cavern to the centre of the toroidal magnet system. The detector was finally aligned, to the precision of within a millimetre, on Wednesday 9th November. The ATLAS installation team, led by Tommi Nyman, after having positioned the Barrel Calorimeter in its final location in the ATLAS experimental cavern UX15. The Barrel Calorimeter which will absorb and measure the energy of photons, electrons and hadrons at the core of the ATLAS detector is 8.6 meters in diameter, 6.8 meters long, and weighs over 1600 Tonnes. It consists of two concentric cylindrical detector elements. The innermost comprises aluminium pressure vessels containing the liquid argon electromagnetic calorimeter and the solenoid magnet. The outermost is an assembly of 64 hadron tile calorimeter sectors. Assembled 18 meters away from its final position, the Barrel Calorimeter was relocated with the help of a railway, which allows the ...

The ATLAS Level-1 Calorimeter Trigger

International Nuclear Information System (INIS)

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

2008-01-01

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

The ATLAS Level-1 Calorimeter Trigger

Energy Technology Data Exchange (ETDEWEB)

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

2008-03-15

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

Prospects of diffractive physics with the ATLAS forward detectors

CERN Document Server

Lopez Paz, Ivan; The ATLAS collaboration

2017-01-01

The ATLAS Forward Proton (AFP) detector provides measurements of the momentum and emission angle of very forward protons. This enables the observation and measurement of a range of processes where one or both protons remain intact. Such processes are associated with elastic and diffractive scattering. In this talk, we give on overview of the technical details of the AFP, its current status as well as its associated physics program.

Atlas of Yellowstone

Science.gov (United States)

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

2012-01-01

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

ATLAS Facility and Instrumentation Description Report

International Nuclear Information System (INIS)

Kang, Kyoung Ho; Moon, Sang Ki; Park, Hyun Sik

2009-06-01

A thermal-hydraulic integral effect test facility, ATLAS (Advanced Thermal-hydraulic Test Loop for Accident Simulation), has been constructed at KAERI (Korea Atomic Energy Research Institute). The ATLAS is a half-height and 1/288-volume scaled test facility with respect to the APR1400. The fluid system of the ATLAS consists of a primary system, a secondary system, a safety injection system, a break simulating system, a containment simulating system, and auxiliary systems. The primary system includes a reactor vessel, two hot legs, four cold legs, a pressurizer, four reactor coolant pumps, and two steam generators. The secondary system of the ATLAS is simplified to be of a circulating looptype. Most of the safety injection features of the APR1400 and the OPR1000 are incorporated into the safety injection system of the ATLAS. In the ATLAS test facility, about 1300 instrumentations are installed to precisely investigate the thermal-hydraulic behavior in simulation of the various test scenarios. This report describes the scaling methodology, the geometric data of the individual component, and the specification and the location of the instrumentations which are specific to the simulation of 50% DVI line break accident of the APR1400 for supporting the 50 th OECD/NEA International Standard Problem Exercise (ISP-50)

Trigger Menu-aware Monitoring for the ATLAS experiment

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00441925; The ATLAS collaboration

2017-01-01

Changes in the trigger menu, the online algorithmic event-selection of the ATLAS experiment at the LHC, are followed by adjustments to the ATLAS trigger monitoring systems. During Run 1, and so far in Run 2, ATLAS has deployed monitoring updates with the installation of new software releases at Tier-0, the first level of the ATLAS computing grid. Having to wait for a new software release to be installed at Tier-0, in order to update ATLAS offline trigger monitoring configurations, results in a lag with respect to the modification of the trigger menu. We present the design and implementation of a `trigger menu-aware' monitoring system that aims to simplify the ATLAS operational workflows by allowing monitoring configuration changes to be made at the Tier-0 site by utilising an Oracle SQL database.

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...

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...

The next generation PanDA Pilot for and beyond the ATLAS experiment

CERN Document Server

Nilsson, Paul; The ATLAS collaboration

2018-01-01

The Production and Distributed Analysis system (PanDA) is a pilot-based workload management system that was originally designed for the ATLAS Experiment at the LHC to operate on grid sites. Since the coming LHC data taking runs will require more resources than grid computing alone can provide, the various LHC experiments are engaged in an ambitious program to extend the computing model to include opportunistically used resources such as High Performance Computers (HPCs), clouds and volunteer computers. To this end, PanDA is being extended beyond grids and ATLAS to be used on the new types of resources as well as by other experiments. A new key component is being developed, the next generation PanDA Pilot (Pilot 2). Pilot 2 is a complete rewrite of the original PanDA Pilot which has been used in the ATLAS Experiment for over a decade. The new Pilot architecture follows a component-based approach which improves system flexibility, enables a clear workflow control, evolves the system according to modern function...

Das Ausmalbuch zum ATLAS-Experiment

CERN Multimedia

Anthony, Katarina

2017-01-01

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

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.

The ATLAS Distributed Data Management project: Past and Future

CERN Document Server

Garonne, V; The ATLAS collaboration; Lassnig, M; Molfetas, A; Barisits, M; Beermann, T; Nairz, A; Goossens, L; Barreiro Megino, F; Serfon, C; Oleynik, D; Petrosyan, A

2012-01-01

ATLAS has recorded almost 8PB of RAW data since the LHC started running at the end of 2009. Many more derived data products and complimentary simulation data have also been produced by the collaboration and, in total, 90PB is currently stored in the Worldwide LHC Computing Grid by ATLAS. All this data is managed by the ATLAS Distributed Data Management system, called Don Quijote 2 (DQ2). DQ2 has evolved rapidly to help ATLAS Computing operations manage these large quantities of data across the many grid sites at which ATLAS runs, and to help ATLAS physicists get access to this data. In this paper, we describe new and improved DQ2 services, and the experience of data management operation in ATLAS computing, showing how these services enable the management of petabyte scale computing operations. We also present the concepts of the new version of the ATLAS Distributed Data Management (DDM) system, Rucio.

The ATLAS Distributed Data Management project: Past and Future

International Nuclear Information System (INIS)

Garonne, Vincent; Stewart, Graeme A; Lassnig, Mario; Molfetas, Angelos; Barisits, Martin; Beermann, Thomas; Nairz, Armin; Goossens, Luc; Barreiro Megino, Fernando; Serfon, Cedric; Oleynik, Danila; Petrosyan, Artem

2012-01-01

ATLAS has recorded more than 8 petabyte(PB) of RAW data since the LHC started running at the end of 2009. Many more derived data products and complimentary simulation data have also been produced by the collaboration and, in total, 90PB are currently stored in the Worldwide LHC Computing Grid by ATLAS. All these data are managed by the ATLAS Distributed Data Management system, called Don Quijote 2 (DQ2). DQ2 has evolved rapidly to help ATLAS Computing operations manage these large quantities of data across the many grid sites at which ATLAS runs, and to help ATLAS physicists get access to these data. In this paper, we describe new and improved DQ2 services, and the experience of data management operation in ATLAS computing, showing how these services enable the management of PB scale computing operations. We also present the concepts of the new version of the ATLAS Distributed Data Management (DDM) system, Rucio.

The ATLAS Distributed Data Management project: Past and Future

Science.gov (United States)

Garonne, Vincent; Stewart, Graeme A.; Lassnig, Mario; Molfetas, Angelos; Barisits, Martin; Beermann, Thomas; Nairz, Armin; Goossens, Luc; Barreiro Megino, Fernando; Serfon, Cedric; Oleynik, Danila; Petrosyan, Artem

2012-12-01

ATLAS has recorded more than 8 petabyte(PB) of RAW data since the LHC started running at the end of 2009. Many more derived data products and complimentary simulation data have also been produced by the collaboration and, in total, 90PB are currently stored in the Worldwide LHC Computing Grid by ATLAS. All these data are managed by the ATLAS Distributed Data Management system, called Don Quijote 2 (DQ2). DQ2 has evolved rapidly to help ATLAS Computing operations manage these large quantities of data across the many grid sites at which ATLAS runs, and to help ATLAS physicists get access to these data. In this paper, we describe new and improved DQ2 services, and the experience of data management operation in ATLAS computing, showing how these services enable the management of PB scale computing operations. We also present the concepts of the new version of the ATLAS Distributed Data Management (DDM) system, Rucio.

Dedication of the massive ATLAS art mural painted by Josef Kristofoletti directly above the cavern of the ATLAS Experiment at CERN

CERN Multimedia

Claudia Marcelloni, Michael Barnett

2010-01-01

Ceremony to celebrate the massive mural of the ATLAS detector at CERN painted by artist Josef Kristofoletti. The mural is located at the ATLAS Experiment site, and it shows on two perpendicular walls the detector with a collision event superimposed. The event on the large wall shows a simulation of an event that would be recorded in ATLAS if a Higgs boson was produced. The cavern of the ATLAS Experiment with the detector is 100 meters directly below the mural. The height of the mural is about 12 meters (40 feet). The actual ATLAS detector is more than twice as big.

ProstAtlas: A digital morphologic atlas of the prostate

International Nuclear Information System (INIS)

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

2012-01-01

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

ATLAS Distributed Computing: Its Central Services core

CERN Document Server

Lee, Christopher Jon; The ATLAS collaboration

2018-01-01

The ATLAS Distributed Computing (ADC) Project is responsible for the off-line processing of data produced by the ATLAS experiment at the Large Hadron Collider (LHC) at CERN. It facilitates data and workload management for ATLAS computing on the Worldwide LHC Computing Grid (WLCG). ADC Central Services operations (CSops)is a vital part of ADC, responsible for the deployment and configuration of services needed by ATLAS computing and operation of those services on CERN IT infrastructure, providing knowledge of CERN IT services to ATLAS service managers and developers, and supporting them in case of issues. Currently this entails the management of thirty seven different OpenStack projects, with more than five thousand cores allocated for these virtual machines, as well as overseeing the distribution of twenty nine petabytes of storage space in EOS for ATLAS. As the LHC begins to get ready for the next long shut-down, which will bring in many new upgrades to allow for more data to be captured by the on-line syste...

Distributed usability evaluation of the Pennsylvania Cancer Atlas.

Science.gov (United States)

Bhowmick, Tanuka; Robinson, Anthony C; Gruver, Adrienne; MacEachren, Alan M; Lengerich, Eugene J

2008-07-11

The Pennsylvania Cancer Atlas (PA-CA) is an interactive online atlas to help policy-makers, program managers, and epidemiologists with tasks related to cancer prevention and control. The PA-CA includes maps, graphs, tables, that are dynamically linked to support data exploration and decision-making with spatio-temporal cancer data. Our Atlas development process follows a user-centered design approach. To assess the usability of the initial versions of the PA-CA, we developed and applied a novel strategy for soliciting user feedback through multiple distributed focus groups and surveys. Our process of acquiring user feedback leverages an online web application (e-Delphi). In this paper we describe the PA-CA, detail how we have adapted e-Delphi web application to support usability and utility evaluation of the PA-CA, and present the results of our evaluation. We report results from four sets of users. Each group provided structured individual and group assessments of the PA-CA as well as input on the kinds of users and applications for which it is best suited. Overall reactions to the PA-CA are quite positive. Participants did, however, provide a range of useful suggestions. Key suggestions focused on improving interaction functions, enhancing methods of temporal analysis, addressing data issues, and providing additional data displays and help functions. These suggestions were incorporated in each design and implementation iteration for the PA-CA and used to inform a set of web-atlas design principles. For the Atlas, we find that a design that utilizes linked map, graph, and table views is understandable to and perceived to be useful by the target audience of cancer prevention and control professionals. However, it is clear that considerable variation in experience using maps and graphics exists and for those with less experience, integrated tutorials and help features are needed. In relation to our usability assessment strategy, we find that our distributed, web

Distributed usability evaluation of the Pennsylvania Cancer Atlas

Directory of Open Access Journals (Sweden)

MacEachren Alan M

2008-07-01

Full Text Available Abstract Background The Pennsylvania Cancer Atlas (PA-CA is an interactive online atlas to help policy-makers, program managers, and epidemiologists with tasks related to cancer prevention and control. The PA-CA includes maps, graphs, tables, that are dynamically linked to support data exploration and decision-making with spatio-temporal cancer data. Our Atlas development process follows a user-centered design approach. To assess the usability of the initial versions of the PA-CA, we developed and applied a novel strategy for soliciting user feedback through multiple distributed focus groups and surveys. Our process of acquiring user feedback leverages an online web application (e-Delphi. In this paper we describe the PA-CA, detail how we have adapted e-Delphi web application to support usability and utility evaluation of the PA-CA, and present the results of our evaluation. Results We report results from four sets of users. Each group provided structured individual and group assessments of the PA-CA as well as input on the kinds of users and applications for which it is best suited. Overall reactions to the PA-CA are quite positive. Participants did, however, provide a range of useful suggestions. Key suggestions focused on improving interaction functions, enhancing methods of temporal analysis, addressing data issues, and providing additional data displays and help functions. These suggestions were incorporated in each design and implementation iteration for the PA-CA and used to inform a set of web-atlas design principles. Conclusion For the Atlas, we find that a design that utilizes linked map, graph, and table views is understandable to and perceived to be useful by the target audience of cancer prevention and control professionals. However, it is clear that considerable variation in experience using maps and graphics exists and for those with less experience, integrated tutorials and help features are needed. In relation to our usability

Validations of SCT Methylation as a Hallmark Biomarker for Lung Cancers

Science.gov (United States)

Fujimoto, Junya; Wistuba, Ignacio; Lam, Stephen; Yatabe, Yasushi; Wang, Yi-Wei; Stastny, Victor; Gao, Boning; Larsen, Jill E; Girard, Luc; Liu, Xiaoyun; Song, Kai; Behrens, Carmen; Kalhor, Neda; Xie, Yang; Zhang, Michael Q; Minna, John D; Gazdar, Adi F

2016-01-01

Background The human secretin (SCT) gene encodes secretin, a hormone with limited tissue distribution. Analysis of The Cancer Genome Atlas (TCGA) 450K methylation array data indicated that the SCT promoter region is differentially hypermethylated in lung cancer. Our purpose was to validate SCT methylation as a potential cancer biomarker for lung cancer. Methods We analyzed TCGA data, and developed and applied SCT-specific bisulfite DNA sequencing and quantitative methylation specific PCR (qMSP) assays. Results The analyses of TCGA 450K data of 801 samples showed that SCT hypermethylation has an area under curve (AUC) value >0.98 to distinguish lung adenocarcinomas or squamous cell carcinomas from non-malignant lung. We confirmed the highly discriminative SCT methylation by bisulfite sequencing of lung cancer cell lines and normal blood cells. By applying qMSP, we found that SCT hypermethylation was frequently detected in all major subtypes of malignant NSCLC (AUC=0.92, n=108) and SCLC cancers (AUC=0.93, n=40) but less frequently present in lung carcinoids (AUC=0.54, n=20). SCT hypermethylation appeared in lung carcinoma in situ samples during multistage pathogenesis and increased in invasive samples. Further analyses of TCGA 450K data showed that SCT hypermethylation is highly discriminative in most types of other malignant tumors but less frequently present in low-grade malignant tumors. The only normal tissue with high methylation was the placenta. Conclusions Our findings demonstrated that SCT methylation is a highly discriminative biomarker for lung and other malignant tumors, and less frequently present in low-grade malignant tumors including lung carcinoids, and appears at the carcinoma in situ stage. PMID:26725182

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...

Searches for the Higgs Boson with the ATLAS detector at the LHC

International Nuclear Information System (INIS)

Mazini, Rachid

2007-01-01

Searching for the Higgs boson lies at the heart of the physics program of the Large Hadron Collider (LHC). The prospects for Higgs searches with the ATLAS detector at the LHC are reviewed. The discovery potential of most prominent Higgs final states predicted by the Standard Model and the MSSM are reviewed. (Author)

Bone age assessment in Hispanic children: digital hand atlas compared with the Greulich and Pyle (G&P) atlas

Science.gov (United States)

Fernandez, James Reza; Zhang, Aifeng; Vachon, Linda; Tsao, Sinchai

2008-03-01

Bone age assessment is most commonly performed with the use of the Greulich and Pyle (G&P) book atlas, which was developed in the 1950s. The population of theUnited States is not as homogenous as the Caucasian population in the Greulich and Pyle in the 1950s, especially in the Los Angeles, California area. A digital hand atlas (DHA) based on 1,390 hand images of children of different racial backgrounds (Caucasian, African American, Hispanic, and Asian) aged 0-18 years was collected from Children's Hospital Los Angeles. Statistical analysis discovered significant discrepancies exist between Hispanic and the G&P atlas standard. To validate the usage of DHA as a clinical standard, diagnostic radiologists performed reads on Hispanic pediatric hand and wrist computed radiography images using either the G&P pediatric radiographic atlas or the Children's Hospital Los Angeles Digital Hand Atlas (DHA) as reference. The order in which the atlas is used (G&P followed by DHA or vice versa) for each image was prepared before actual reading begins. Statistical analysis of the results was then performed to determine if a discrepancy exists between the two readings.

Advances in service and operations for ATLAS data management

International Nuclear Information System (INIS)

Stewart, Graeme A; Garonne, Vincent; Lassnig, Mario; Molfetas, Angelos; Barisits, Martin; Calvet, Ivan; Beermann, Thomas; Megino, Fernando Barreiro; Campana, Simone; Zhang, Donal; Tykhonov, Andrii; Serfon, Cedric; Oleynik, Danila; Petrosyan, Artem

2012-01-01

ATLAS has recorded almost 5PB of RAW data since the LHC started running at the end of 2009. Many more derived data products and complimentary simulation data have also been produced by the collaboration and, in total, 70PB is currently stored in the Worldwide LHC Computing Grid by ATLAS. All of this data is managed by the ATLAS Distributed Data Management system, called Don Quixote 2 (DQ2). DQ2 has evolved rapidly to help ATLAS Computing operations manage these large quantities of data across the many grid sites at which ATLAS runs and to help ATLAS physicists get access to this data. In this paper we describe new and improved DQ2 services: popularity; space monitoring and accounting; exclusion service; cleaning agents; deletion agents. We describe the experience of data management operation in ATLAS computing, showing how these services enable management of petabyte scale computing operations. We illustrate the coupling of data management services to other parts of the ATLAS computing infrastructure, in particular showing how feedback from the distributed analysis system in ATLAS has enabled dynamic placement of the most popular data, helping users and groups to analyse the increasing data volumes on the grid.

Advances in service and operations for ATLAS data management

Science.gov (United States)

Stewart, Graeme A.; Garonne, Vincent; Lassnig, Mario; Molfetas, Angelos; Barisits, Martin; Zhang, Donal; Calvet, Ivan; Beermann, Thomas; Barreiro Megino, Fernando; Tykhonov, Andrii; Campana, Simone; Serfon, Cedric; Oleynik, Danila; Petrosyan, Artem; ATLAS Collaboration

2012-06-01

ATLAS has recorded almost 5PB of RAW data since the LHC started running at the end of 2009. Many more derived data products and complimentary simulation data have also been produced by the collaboration and, in total, 70PB is currently stored in the Worldwide LHC Computing Grid by ATLAS. All of this data is managed by the ATLAS Distributed Data Management system, called Don Quixote 2 (DQ2). DQ2 has evolved rapidly to help ATLAS Computing operations manage these large quantities of data across the many grid sites at which ATLAS runs and to help ATLAS physicists get access to this data. In this paper we describe new and improved DQ2 services: popularity; space monitoring and accounting; exclusion service; cleaning agents; deletion agents. We describe the experience of data management operation in ATLAS computing, showing how these services enable management of petabyte scale computing operations. We illustrate the coupling of data management services to other parts of the ATLAS computing infrastructure, in particular showing how feedback from the distributed analysis system in ATLAS has enabled dynamic placement of the most popular data, helping users and groups to analyse the increasing data volumes on the grid.

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.

Custom-made power for ATLAS

CERN Multimedia

2005-01-01

A small team of engineers and technicians has recently finished the design of power supplies specially tailored to working in the demanding environment of the ATLAS Tile Calorimeter. Mass production of the units has now begun. The ATLAS Tile Calorimeter power supply development team (left to right): Ivan Hruska (holding brick), Francisca Calheiros, Bohuslav Palan, Jiri Palacky and Zdenek Kotek. Power supplies are an important component of any particle detector. In ATLAS, as in the other experiments at the Large Hadron Collider, it is not easy to use standard, 'off the shelf' power supplies; they must survive radiation, tolerate magnetic fields, and satisfy limited space and water-cooling constraints. For the ATLAS Tile Calorimeter, these constraints all proved challenging for the engineers designing the power supplies. The aim was to produce a universal power module in terms of input/output voltage, delivered power and cooling, for general use in a radiation environment. The result is a distributed low-vo...

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...

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 ...

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 ...

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 ...

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...

ATLAS Software Installation on Supercomputers

CERN Document Server

Undrus, Alexander; The ATLAS collaboration

2018-01-01

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

Non-collision backgrounds in ATLAS

CERN Document Server

Gibson, S M; The ATLAS collaboration

2012-01-01

The proton-proton collision events recorded by the ATLAS experiment are on top of a background that is due to both collision debris and non-collision components. The latter comprises of three types: beam-induced backgrounds, cosmic particles and detector noise. We present studies that focus on the first two of these. We give a detailed description of beam-related and cosmic backgrounds based on the full 2011 ATLAS data set, and present their rates throughout the whole data-taking period. Studies of correlations between tertiary proton halo and muon backgrounds, as well as, residual pressure and resulting beam-gas events seen in beam-condition monitors will be presented. Results of simulations based on the LHC geometry and its parameters will be presented. They help to better understand the features of beam-induced backgrounds in each ATLAS sub-detector. The studies of beam-induced backgrounds in ATLAS reveal their characteristics and serve as a basis for designing rejection tools that can be applied in physic...

Fabiola Gianotti, the newly elected Spokesperson of ATLAS

CERN Multimedia

2008-01-01

On 11 July Fabiola Gianotti was elected by the ATLAS Collaboration as its future Spokesperson. Her term of office will start on 1 March 2009 and will last for two years. She will take over from Peter Jenni who has been ATLAS Spokesperson since its formalization in 1992. Three distinguished physicists stood as candidates for this election: Fabiola Gianotti (CERN), Marzio Nessi (CERN), and Leonardo Rossi (INFN Genova, Italy). The nomination process started on 30 October 2007, with a general email sent to the ATLAS collaboration calling for nominations, and closed on 25 January 2008. Any ATLAS physicist could nominate a candidate, and 24 nominees were proposed before the ATLAS search committee narrowed them to the final three. After the voting process, which concluded the ATLAS general meeting in Bern, the Collaboration Board greeted the result with warm applause.

Identification of b-jets with a low pΤ muon using ATLAS Tile Calorimeter simulation data and artificial neural networks technique

International Nuclear Information System (INIS)

Astvatsaturov, A.; Budagov, Yu.; Shigaev, V.; Nessi, M.; Pantea, D.

1996-01-01

The possibility to enhance the capability of ATLAS Tile Calorimeter to identify low p Τ muons (2 Τ Τ =20 and 40 GeV/c in the central region 0 b g is 4-10 times higher in NND case compared to LTD. The results obtained are based on 2000 jets simulated with the use of ATLAS simulation programs. 8 refs., 13 figs., 2 tabs

Special people visit the ATLAS cavern

CERN Multimedia

Muriel

ATLAS has been host to many important visitors lately. Here are a selected few: Professor Stephen Hawking visits the ATLAS cavern On Tuesday 26 September 2006 the ATLAS Collaboration was honoured by a very special visit to the detector in the underground cavern. We were pleased to guide Professor Stephen Hawking, the famous cosmologist holding the post of Lucasian Professor of Mathematics at Cambridge University (position held by Isaac Newton in the 17th century), on a tour of the ATLAS pit and the LHC tunnel. The visit was accompanied by a few colleagues from the CERN Theory group, and was only possible thanks to the professional assistance of Olga Beltramello and Bernard Lebegue, who had also taken care of all the necessary preparatory work in the cavern. Professor Hawking was very keen to check for himself the status of the detector installation, and he admired, in particular, the spectacular TGC big wheel on side C. (left) Stephen Hawking in the ATLAS cavern side-C (right) and in the LHC tunnel...

The Pig PeptideAtlas

DEFF Research Database (Denmark)

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

2016-01-01

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

Luminosity Monitoring in ATLAS with MPX Detectors

CERN Document Server

AUTHOR|(CDS)2086061

2013-01-01

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

Searches for Exotic New Physics with ATLAS and CMS

CERN Document Server

Hance, Michael; The ATLAS collaboration

2018-01-01

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

Status and Prospects of measurements of exclusive and diffractive processes with the ATLAS detector

CERN Document Server

Foster, Andrew Geoffrey; The ATLAS collaboration

2018-01-01

In the absence of forward proton tagging, exclusive processes can be distinguished in the central part of the ATLAS detector exploiting the large rapidity gap in the central region and the absence of charged particles reconstructed in the inner tracking detector. This strategy has been exploited to study the exclusive production of dilepton pairs in the data taken at centre-of-mass energies of 7 TeV and the exclusive production of W pairs in the 8 TeV data. We also present the latest results on exclusive dimuon production at 13 TeV. Moreover, the ATLAS collaboration has carried out a study of diffractive dijet production. The data distributions are compared with Monte Carlo models and the rapidity gap survival probability has been estimated in the kinematic region with high diffractive contribution. The talk will conclude with prospects of the upcoming physics program with the Atlas Forward Proton detector. Recent results demonstrate its capabilities to distinguish single diffractive events via forward proton...

The radiation environment in the ATLAS inner detector

CERN Document Server

Dawson, I

2000-01-01

The radiation environment in the inner detector has been simulated using the particle transport program FLUKA with a recent description of the ATLAS experiment. Given in this paper are particle fluences and doses at positions relevant to the three inner detector subsystems; the Pixel, SCT and TRT detectors. In addition, studies are reported on in which (1) information concerning the optimization of the inner detector neutron-moderators is obtained and (2) the impact of including additional vacuum-equipment material is assessed. (19 refs).

EnviroAtlas - Number of Water Markets per HUC8 Watershed, U.S., 2015, Forest Trends' Ecosystem Marketplace

Data.gov (United States)

U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting the number of watershed-level market-based programs, referred to herein as markets, in operation per 8-digit HUC...

A practical workflow for making anatomical atlases for biological research.

Science.gov (United States)

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

2012-01-01

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

Atlas : A library for numerical weather prediction and climate modelling

Science.gov (United States)

Deconinck, Willem; Bauer, Peter; Diamantakis, Michail; Hamrud, Mats; Kühnlein, Christian; Maciel, Pedro; Mengaldo, Gianmarco; Quintino, Tiago; Raoult, Baudouin; Smolarkiewicz, Piotr K.; Wedi, Nils P.

2017-11-01

The algorithms underlying numerical weather prediction (NWP) and climate models that have been developed in the past few decades face an increasing challenge caused by the paradigm shift imposed by hardware vendors towards more energy-efficient devices. In order to provide a sustainable path to exascale High Performance Computing (HPC), applications become increasingly restricted by energy consumption. As a result, the emerging diverse and complex hardware solutions have a large impact on the programming models traditionally used in NWP software, triggering a rethink of design choices for future massively parallel software frameworks. In this paper, we present Atlas, a new software library that is currently being developed at the European Centre for Medium-Range Weather Forecasts (ECMWF), with the scope of handling data structures required for NWP applications in a flexible and massively parallel way. Atlas provides a versatile framework for the future development of efficient NWP and climate applications on emerging HPC architectures. The applications range from full Earth system models, to specific tools required for post-processing weather forecast products. The Atlas library thus constitutes a step towards affordable exascale high-performance simulations by providing the necessary abstractions that facilitate the application in heterogeneous HPC environments by promoting the co-design of NWP algorithms with the underlying hardware.

Report from the ATLAS Architecture TaskForce

CERN Document Server

Haywood, S

1999-01-01

In this report, the activities and conclusions of the ATLAS Architecture TaskForce (ATF) are summarised. A key part of the ATF's work has been the first attempt at a design of the global architecture for the ATLAS Offline Software. This is contained in this document and an auxillary report and should lead to a realisation of the ATLAS Framework.

ATLAS Silicon Microstrip Tracker Operation and Performance

CERN Document Server

Rosendahl, P L; The ATLAS collaboration

2012-01-01

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

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...

ATLAS DAQ/HLT rack DCS

International Nuclear Information System (INIS)

Ermoline, Yuri; Burckhart, Helfried; Francis, David; Wickens, Frederick J.

2007-01-01

The ATLAS Detector Control System (DCS) group provides a set of standard tools, used by subsystems to implement their local control systems. The ATLAS Data Acquisition and High Level Trigger (DAQ/HLT) rack DCS provides monitoring of the environmental parameters (air temperatures, humidity, etc.). The DAQ/HLT racks are located in the underground counting room (20 racks) and in the surface building (100 racks). The rack DCS is based on standard ATLAS tools and integrated into overall operation of the experiment. The implementation is based on the commercial control package and additional components, developed by CERN Joint Controls Project Framework. The prototype implementation and measurements are presented

Volunteer computing experience with ATLAS@Home

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00068610; The ATLAS collaboration; Bianchi, Riccardo-Maria; Cameron, David; Filipčič, Andrej; Lançon, Eric; Wu, Wenjing

2016-01-01

ATLAS@Home is a volunteer computing project which allows the public to contribute to computing for the ATLAS experiment through their home or office computers. The project has grown continuously since its creation in mid-2014 and now counts almost 100,000 volunteers. The combined volunteers’ resources make up a sizeable fraction of overall resources for ATLAS simulation. This paper takes stock of the experience gained so far and describes the next steps in the evolution of the project. These improvements include running natively on Linux to ease the deployment on for example university clusters, using multiple cores inside one task to reduce the memory requirements and running different types of workload such as event generation. In addition to technical details the success of ATLAS@Home as an outreach tool is evaluated.

Volunteer Computing Experience with ATLAS@Home

CERN Document Server

Cameron, David; The ATLAS collaboration; Bourdarios, Claire; Lan\\c con, Eric

2016-01-01

ATLAS@Home is a volunteer computing project which allows the public to contribute to computing for the ATLAS experiment through their home or office computers. The project has grown continuously since its creation in mid-2014 and now counts almost 100,000 volunteers. The combined volunteers' resources make up a sizable fraction of overall resources for ATLAS simulation. This paper takes stock of the experience gained so far and describes the next steps in the evolution of the project. These improvements include running natively on Linux to ease the deployment on for example university clusters, using multiple cores inside one job to reduce the memory requirements and running different types of workload such as event generation. In addition to technical details the success of ATLAS@Home as an outreach tool is evaluated.

Volunteer Computing Experience with ATLAS@Home

Science.gov (United States)

Adam-Bourdarios, C.; Bianchi, R.; Cameron, D.; Filipčič, A.; Isacchini, G.; Lançon, E.; Wu, W.; ATLAS Collaboration

2017-10-01

ATLAS@Home is a volunteer computing project which allows the public to contribute to computing for the ATLAS experiment through their home or office computers. The project has grown continuously since its creation in mid-2014 and now counts almost 100,000 volunteers. The combined volunteers’ resources make up a sizeable fraction of overall resources for ATLAS simulation. This paper takes stock of the experience gained so far and describes the next steps in the evolution of the project. These improvements include running natively on Linux to ease the deployment on for example university clusters, using multiple cores inside one task to reduce the memory requirements and running different types of workload such as event generation. In addition to technical details the success of ATLAS@Home as an outreach tool is evaluated.

ATLAS DDM integration in ARC

DEFF Research Database (Denmark)

Behrmann, Gerd; Cameron, David; Ellert, Mattias

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

The ATLAS hadronic tile calorimeter from construction toward physics

CERN Document Server

Adragna, P; Anderson, K; Antonaki, A; Batusov, V; Bednar, P; Binet, S; Biscarat, C; Blanchot, G; Bogush, A A; Bohm, C; Boldea, V; Bosman, M; Bromberg, C; Budagov, Yu A; Caloba, L; Calvet, D; Carvalho, J; Castelo, J; Castillo, M V; Sforza, M C; Cavasinni, V; Cerqueira, A S; Chadelas, R; Costanzo, D; Cogswell, F; Constantinescu, S; Crouau, M; Cuenca, C; Damazio, D O; Daudon, F; David, M; Davidek, T; De, K; Del Prete, T; Di Girolamo, B; Dita, S; Dolejsi, J; Dolezal, Z; Dotti, A; Downing, R; Efthymiopoulos, I; Errede, D; Errede, S; Farbin, A; Fassouliotis, D; Fedorko, I; Fenyuk, A; Ferdi, C; Ferrer, A; Flaminio, V; Fullana, E; Garde, V; Giakoumopoulou, V; Gildemeister, O; Gilewsky, V; Giangiobbe, V; Giokaris, N; Gomes, A; González, V; Grabskii, V; Grenier, P; Gris, P; Guarino, V; Guicheney, C; Sen-Gupta, A; Hakobyan, H; Haney, M; Henriques, A; Higón, E; Holmgren, S O; Hurwitz, M; Huston, J; Iglesias, C; And, K J; Junk, T; Karyukhin, A N; Khubua, J; Klereborn, J; Korolkov, I Ya; Krivkova, P; Kulchitskii, Yu A; Kurochkin, Yu; Kuzhir, P; Lambert, D; Le Compte, T; Lefèvre, R; Leitner, R; Lembesi, M; Li, J; Liablin, M; Lokajícek, M; Lomakin, Y; Amengual, J M L; Lupi, A; Maidantchik, C; Maio, A; Maliukov, S; Manousakis, A; Marques, C; Marroquim, F; Martin, F; Mazzoni, E; Montarou, G; Merritt, F S; Myagkov, A; Miller, R; Minashvili, I A; Miralles, L; Némécek, S; Nessi, M; Nodulman, L; Norniella, O; Onofre, A; Oreglia, M J; Pantea, D; Pallin, D; Pilcher, J E; Pina, J; Pinhão, J; Podlyski, F; Portell, X; Poveda, J; Price, L E; Pribyl, L; Proudfoot, J; Ramstedt, M; Reinmuth, G; Richards, R; Roda, C; Romanov, V; Rosnet, P; Roy, P; Rumiantsau, V; Russakovich, N; Salto, O; Salvachúa, B; Sanchis, E; Sanders, H; Santoni, C; Santos, J; Saraiva, J G; Sarri, F; Satsunkevich, I S; Says, L P; Schlager, G; Schlereth, J L; Seixas, J M; Selldén, B; Shevtsov, P; Shochet, M; Da Silva, P; Silva, J; Simaitis, V; Sissakian, A N; Solodkov, A; Solovyanov, O; Sosebee, M; Spanó, F; Stanek, R; Starchenko, E A; Starovoitov, P; Suk, M; Sykora, I; Tang, F; Tas, P; Teuscher, R; Tokar, S; Topilin, N; Torres, J; Tsulaia, V; Underwood, D; Usai, G; Valkár, S; Valls, J A; Vartapetian, A H; Vazeille, F; Vichou, I; Vinogradov, V; Vivarelli, I; Volpi, M; White, A; Zaitsev, A; Zenine, A; Zenis, T

2006-01-01

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. The construction phase of the calorimeter is nearly complete, and most of the effort now is directed toward the final assembly and commissioning in the underground experimental hall. The layout of the calorimeter and the tasks carried out during construction are described, first with a brief reminder of the requirements that drove the calorimeter design. During the last few years a comprehensive test-beam program has been followed in order to establish the calorimeter electromagnetic energy scale, to study its uniformity, and to compare real data to Monte Carlo simulation. The test-beam setup and first results from the data are described. During the test-beam period in 2004, lasting several months, data have been acquired with a complete slice of the central ATLAS calorimeter. The data collected in the test-beam are crucial in order to study...

Experience with Intel's many integrated core architecture in ATLAS software

International Nuclear Information System (INIS)

Fleischmann, S; Neumann, M; Kama, S; Lavrijsen, W; Vitillo, R

2014-01-01

Intel recently released the first commercial boards of its Many Integrated Core (MIC) Architecture. MIC is Intel's solution for the domain of throughput computing, currently dominated by general purpose programming on graphics processors (GPGPU). MIC allows the use of the more familiar x86 programming model and supports standard technologies such as OpenMP, MPI, and Intel's Threading Building Blocks (TBB). This should make it possible to develop for both throughput and latency devices using a single code base. In ATLAS Software, track reconstruction has been shown to be a good candidate for throughput computing on GPGPU devices. In addition, the newly proposed offline parallel event-processing framework, GaudiHive, uses TBB for task scheduling. The MIC is thus, in principle, a good fit for this domain. In this paper, we report our experiences of porting to and optimizing ATLAS tracking algorithms for the MIC, comparing the programmability and relative cost/performance of the MIC against those of current GPGPUs and latency-optimized CPUs.

Control Logic for the Interlock system of the ATLAS Insertable B-Layer

CERN Document Server

Riegel, Christian

Part of the first upgrade program of the ATLAS detector is the installation of the Insertable B-Layer (IBL) as a fourth and innermost detector layer of the ATLAS pixel detector to prepare the tracking system for the expected increase of pile-up events. As with every sub-detector, the IBL and its components have to be monitored and controlled via a Detector Control System (DCS). A hardware-based interlock system is installed on-site to prevent detector and people working at the detector from serious harm and damage. For the IBL, the logical processing of interlock signals is realised in Interlock Matrix Crates (IMCs) using Complex Programmable Logic Devices (CPLD). One part of this master thesis is the automatic implementation of the logical assignments from database information. A script was developed to generate the needed file to program the CPLD. The second part of this thesis is the design of a test setup to verify the functionality of the electrical components of each IMC and to confirm the correct proce...

Morphometric Atlas Selection for Automatic Brachial Plexus Segmentation

International Nuclear Information System (INIS)

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

2015-01-01

Purpose: The purpose of this study was to determine the effects of atlas selection based on different morphometric parameters, on the accuracy of automatic brachial plexus (BP) segmentation for radiation therapy planning. The segmentation accuracy was measured by comparing all of the generated automatic segmentations with anatomically validated gold standard atlases developed using cadavers. Methods and Materials: Twelve cadaver computed tomography (CT) atlases (3 males, 9 females; mean age: 73 years) were included in the study. One atlas was selected to serve as a patient, and the other 11 atlases were registered separately onto this “patient” using deformable image registration. This procedure was repeated for every atlas as a patient. Next, the Dice and Jaccard similarity indices and inclusion index were calculated for every registered BP with the original gold standard BP. In parallel, differences in several morphometric parameters that may influence the BP segmentation accuracy were measured for the different atlases. Specific brachial plexus-related CT-visible bony points were used to define the morphometric parameters. Subsequently, correlations between the similarity indices and morphometric parameters were calculated. Results: A clear negative correlation between difference in protraction-retraction distance and the similarity indices was observed (mean Pearson correlation coefficient = −0.546). All of the other investigated Pearson correlation coefficients were weak. Conclusions: Differences in the shoulder protraction-retraction position between the atlas and the patient during planning CT influence the BP autosegmentation accuracy. A greater difference in the protraction-retraction distance between the atlas and the patient reduces the accuracy of the BP automatic segmentation result

The ATLAS distributed analysis system

International Nuclear Information System (INIS)

Legger, F

2014-01-01

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

The ATLAS distributed analysis system

Science.gov (United States)

Legger, F.; Atlas Collaboration

2014-06-01

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

The social atlas of women from ethnic minorities

NARCIS (Netherlands)

Saskia Keuzenkamp; Ans Merens

2006-01-01

Original title: Sociale atlas van vrouwen uit etnische minderheden. The Social atlas of women from ethnic minorities (Sociale atlas van vrouwen uit etnische minderheden) offers a look in breadth and depth at the social position and participation of these women. The themes covered

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.

A digital atlas of the dog brain.

Directory of Open Access Journals (Sweden)

Ritobrato Datta

Full Text Available There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1 A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head; 2 A co-registered, high-resolution (0.33 mm isotropic template created from imaging of ex-vivo brains at 7 Tesla; 3 A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features. The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta.

Stellar Atmospheric Modelling for the ACCESS Program

Science.gov (United States)

Morris, Matthew; Kaiser, Mary Elizabeth; Bohlin, Ralph; Kurucz, Robert; ACCESS Team

2018-01-01

A goal of the ACCESS program (Absolute Color Calibration Experiment for Standard Stars) is to enable greater discrimination between theoretical astrophysical models and observations, where the comparison is limited by systematic errors associated with the relative flux calibration of the targets. To achieve these goals, ACCESS has been designed as a sub-orbital rocket borne payload and ground calibration program, to establish absolute flux calibration of stellar targets at flight candidates, as well as a selection of A and G stars from the CALSPEC database. Stellar atmosphere models were generated using Atlas 9 and Atlas 12 Kurucz stellar atmosphere software. The effective temperature, log(g), metallicity, and redenning were varied and the chi-squared statistic was minimized to obtain a best-fit model. A comparison of these models and the results from interpolation between grids of existing models will be presented. The impact of the flexibility of the Atlas 12 input parameters (e.g. solar metallicity fraction, abundances, microturbulent velocity) is being explored.

Comparaison of Atlas Tilecal module

CERN Document Server

Batusov1, V; Gayde, J C; Khubua, J I; Lasseur, C; Lyablin, M V; Miralles-Verge, L; Nessi, Marzio; Rusakovitch, N A; Sissakian, A N; Topilin, N D

2002-01-01

The high precision assembly of a large experimental set-ups is of a principal necessity for the successful execution of the forthcoming LHC research program in the TeV-beams. The creation of an adequate Survey&Control METROLOGY METHODs are an essential part of the detector construction scenario. This work contains the dimension measurement data for ATLAS hadron calorimeter MODULE#8 (6m long, 22tons) which were obtained by LASER and by PHOTOGRAMMETRY methods. The comparative data analysis demonstrates the measurements agreement within ±70mm. It means these two clearly independent methods can be combined and lead to the rise of a new generation engineering culture: high precision metrology when precision assembly of large scale massive objects.

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...

AGIS: The ATLAS Grid Information System

CERN Document Server

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

2014-01-01

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

AGIS: The ATLAS Grid Information System

OpenAIRE

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

2013-01-01

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

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...

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...

Wind Energy Resource Atlas of Oaxaca

Energy Technology Data Exchange (ETDEWEB)

Elliott, D.; Schwartz, M.; Scott, G.; Haymes, S.; Heimiller, D.; George, R.

2003-08-01

The Oaxaca Wind Resource Atlas, produced by the National Renewable Energy Laboratory's (NREL's) wind resource group, is the result of an extensive mapping study for the Mexican State of Oaxaca. This atlas identifies the wind characteristics and distribution of the wind resource in Oaxaca. The detailed wind resource maps and other information contained in the atlas facilitate the identification of prospective areas for use of wind energy technologies, both for utility-scale power generation and off-grid wind energy applications.

Picturing diversity in the ATLAS collaboration

CERN Document Server

Biondi, Silvia; The ATLAS collaboration

2017-01-01

With over 3000 members from 178 institutes, the ATLAS Collaboration is naturally diverse. However, capturing this diversity through pictures can be a challenge. Photography is a powerful tool, allowing us to reveal the faces behind a story and give the public the unique opportunity to understand and appreciate the human aspects of ATLAS's scientific research. The role of photographs in portraying the diversity of the ATLAS Collaboration and on various communication platforms will be described. Their impact will be examined, with focus on engagement of new audiences.

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.

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...

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...

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...

An important step for the ATLAS toroid magnet

CERN Multimedia

2000-01-01

The ATLAS experiment's prototype toroid coil arrives at CERN from the CEA laboratory in Saclay on 6 October. The world's largest superconducting toroid magnet is under construction for the ATLAS experiment. A nine-metre long fully functional prototype coil was delivered to CERN at the beginning of October and has since been undergoing tests in the West Area. Built mainly by companies in France and Italy under the supervision of engineers from the CEA-Saclay laboratory near Paris and Italy's INFN-LASA, the magnet is a crucial step forward in the construction of the ATLAS superconducting magnet system. Unlike any particle detector that has gone before, the ATLAS detector's magnet system consists of a large toroidal system enclosing a small central solenoid. The barrel part of the toroidal system will use eight toroid coils, each a massive 25 metres in length. These will dwarf the largest toroids in the world when ATLAS was designed, which measure about six metres. So the ATLAS collaboration decided to build a...

Alignment of the ATLAS Inner Detector Tracking System

CERN Document Server

Moles-Valls, R

2008-01-01

The ATLAS experiment is equipped with a tracking system for c harged particles built on two technologies: silicon and drift tube base detectors. These kind of detectors compose the ATLAS Inner Detector (ID). The Alignment of the ATLAS ID tracking s ystem requires the determination of almost 36000 degrees of freedom. From the tracking point o f view, the alignment parameters should be know to a few microns precision. This permits to att ain optimal measurements of the parameters of the charged particles trajectories, thus ena bling ATLAS to achieve its physics goals. The implementation of the alignment software, its framewor k and the data flow will be discussed. Special attention will be paid to the recent challenges wher e large scale computing simulation of the ATLAS detector has been performed, mimicking the ATLAS o peration, which is going to be very important for the LHC startup scenario. The alignment r esult for several challenges (real cosmic ray data taking and computing system commissioning) will be...

Robustness studies of the photomultipliers reading out TileCal, the central hadron calorimeter of the ATLAS experiment

CERN Document Server

Di Gregorio, Giulia; The ATLAS collaboration

2018-01-01

TileCal, the hadron calorimeter of the ATLAS experiment in LHC, is a 10000 channel detector readout by photomultipliers (PMTs). A challenging goal is to understand whether the full sample of PMTs installed at the beginning of the ATLAS detector operation can be used until completion of the High-Luminosity Large Hadron Collider (HL-LHC) program or not. For this reason, a reliable study of the PMT robustness against ageing is required. Detailed studies modelling the PMT response variation as a function of the integrated anode charge were done.

A detailed and verified wind resource atlas for Denmark

Energy Technology Data Exchange (ETDEWEB)

Mortensen, N G; Landberg, L; Rathmann, O; Nielsen, M N [Risoe National Lab., Roskilde (Denmark); Nielsen, P [Energy and Environmental Data, Aalberg (Denmark)

1999-03-01

A detailed and reliable wind resource atlas covering the entire land area of Denmark has been established. Key words of the methodology are wind atlas analysis, interpolation of wind atlas data sets, automated generation of digital terrain descriptions and modelling of local wind climates. The atlas contains wind speed and direction distributions, as well as mean energy densities of the wind, for 12 sectors and four heights above ground level: 25, 45, 70 and 100 m. The spatial resolution is 200 meters in the horizontal. The atlas has been verified by comparison with actual wind turbine power productions from over 1200 turbines. More than 80% of these turbines were predicted to within 10%. The atlas will become available on CD-ROM and on the Internet. (au)

World atlas of nuclear industry: civil and military

International Nuclear Information System (INIS)

Alexandre, Nicolas

2011-01-01

Todays, with the energy supplies and global warming concerns, nuclear energy in making a come-back, witness the numerous nuclear programs launched or re-launched in the US, in Europe, China and India. In parallel, on the military side, the deterrence strategy remains in the center of security politics of big powers. This atlas takes stock of the overall issues linked with the nuclear technology: production, civil applications (power generation, medicine etc..), military usages (naval propulsion, weapons). It answers the main questions of this complex world, often dominated by secrecy: who does what in the nuclear domain in France? Is an accident, like the Chernobyl's one, possible today in Europe? What solutions for radioactive wastes? Do we take risks when we export our reactor technologies to Middle-East countries? Are we at the dawn of a new arms rush? What do international agreements foresee in this domain? Taking into account the costs, the hazards and the advantages of nuclear industry, the atlas shows that it is possible to establish solid technical and legal barriers between its civil and military sides. (J.S.)

Alignment of the ATLAS Silicon Tracker and measurement of the top quark mass

CERN Document Server

Escobar, C; Marti i García, S

2010-01-01

The Large Hadron Collider (LHC) era started with its first proton-proton collisions produced in November 2009 at the CERN laboratory. In the coming decade, the high energy physics program will be dominated by the LHC and its experiments. Discoveries such as the Higgs or supersymmetric particles are some of the dreams that hopefully the LHC will bring us. This thesis is framed within the ATLAS experiment, which is one of the four large detectors located at the LHC. The work presented in this thesis is divided in two parts. The first part is dedicated to the alignment of the ATLAS silicon tracking detector using the GlobalChi2 algorithm, which is the actual baseline algorithm. It covers performance studies with Monte Carlo samples with a realistic detector description, with real cosmic rays as well as with first LHC collisions at 900 GeV. The main achievement was the production of a set of alignment constants for the real ATLAS detector. Those constants were obtained from the alignment of real cosmic ray data, ...

Integration of Titan supercomputer at OLCF with ATLAS Production System

Science.gov (United States)

Barreiro Megino, F.; De, K.; Jha, S.; Klimentov, A.; Maeno, T.; Nilsson, P.; Oleynik, D.; Padolski, S.; Panitkin, S.; Wells, J.; Wenaus, T.; ATLAS Collaboration

2017-10-01

The PanDA (Production and Distributed Analysis) workload management system was developed to meet the scale and complexity of distributed computing for the ATLAS experiment. PanDA managed resources are distributed worldwide, on hundreds of computing sites, with thousands of physicists accessing hundreds of Petabytes of data and the rate of data processing already exceeds Exabyte per year. While PanDA currently uses more than 200,000 cores at well over 100 Grid sites, future LHC data taking runs will require more resources than Grid computing can possibly provide. Additional computing and storage resources are required. Therefore ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. In this paper we will describe a project aimed at integration of ATLAS Production System with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF). Current approach utilizes modified PanDA Pilot framework for job submission to Titan’s batch queues and local data management, with lightweight MPI wrappers to run single node workloads in parallel on Titan’s multi-core worker nodes. It provides for running of standard ATLAS production jobs on unused resources (backfill) on Titan. The system already allowed ATLAS to collect on Titan millions of core-hours per month, execute hundreds of thousands jobs, while simultaneously improving Titans utilization efficiency. We will discuss the details of the implementation, current experience with running the system, as well as future plans aimed at improvements in scalability and efficiency. Notice: This manuscript has been authored, by employees of Brookhaven Science Associates, LLC under Contract No. DE-AC02-98CH10886 with the U.S. Department of Energy. The publisher by accepting the manuscript for publication acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to

A Lego version of ATLAS

CERN Multimedia

Laëtitia Pedroso

2010-01-01

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

The ATLAS semiconductor tracker (SCT)

International Nuclear Information System (INIS)

Jackson, J.N.

2005-01-01

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

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...

ATLAS virtual visit features Birzeit University, first university in Palestine and a member of the International Association of Universities since 1977.

CERN Multimedia

claudia marcelloni

2012-01-01

This ATLAS virtual visit features Birzeit University, first university in Palestine and a member of the International Association of Universities since 1977. As part of the "Physics Without Frontiers" project, funded by the International Centre for Theoretical Physics (ICTP), Birzeit is hosting a one day particle physics masterclass. During the day the physics major students are given an introduction to experimental particle physics, the LHC and the ATLAS Experiment, before having the chance to analyze real LHC data. This virtual visit comprises of a live tour around the ATLAS control room and the opportunity to ask questions to the ATLAS physicists. The Department of Physics at Birzeit University provides an exciting environment for the training of both graduate and undergraduate students. Some of the Physics department graduates participated in the CERN Summer Program over the past few years.

16 December 2011 - Israeli Minister of Industry, Trade and Labour S.Simhon visiting ATLAS undeground area, ATLAS visitor centre and LHC tunnel with Senior Physicist G. Mikenberg. ATLAS Collaboration Former Spokesperson is also present.

CERN Multimedia

Maximilien Brice

2011-01-01

Israeli minister of industry, trade and labour, Shalom Simhon, was welcomed in the ATLAS visitor centre before he toured the ATLAS underground experimental area, where he could see the ATLAS detector. He also had a chance to see the LHC tunnel and the CERN Control Centre.

Hidden Valley Search at ATLAS

CERN Document Server

Verducci, M; The ATLAS collaboration

2011-01-01

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

The ATLAS IBL CO2 Cooling System

CERN Document Server

Verlaat, Bartholomeus; The ATLAS collaboration

2016-01-01

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