Science.gov

Sample records for atlas ddm integration

  1. DDM Workload Emulation

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Rucio is the successor of the current Don Quijote 2 (DQ2) system for the distributed data management (DDM) system of the ATLAS experiment. The reasons for replacing DQ2 are manifold, but besides high maintenance costs and architectural limitations, scalability concerns are on top of the list. Current expectations are that the amount of data will be three to four times as it is today by the end of 2014. Further is the availability of more powerful computing resources pushing additional pressure on the DDM system as it increases the demands on data provisioning. Although DQ2 is capable of handling the current workload, it is already at its limits. To ensure that Rucio will be up to the expected workload, a way to emulate it is needed. To do so, first the current workload, observed in DQ2, must be understood in order to scale it up to future expectations. The paper discusses how selected core concepts are applied to the workload of the experiment and how knowledge about the current workload is derived from various sources (e.g. analysing the central file catalogue logs). Finally a description of the implemented emulation framework, used for stress-testing Rucio, is given.

  2. Lax representations and integrable time discretizations of the DDKdV, DDmKdV, and DDHOKdV

    NASA Astrophysics Data System (ADS)

    Zhu, Zuonong; Huang, Hongci; Xue, Weimin

    1999-02-01

    From a proper 2 × 2 discrete isospectral problem, a new differential-difference integrable equation in Lax sense is proposed by a discrete zero curvature equation. The DDKdV (differential-difference DdV equation) proposed by Ohta and Hirota and DDCDGKS (DD Caudrey-Dodd-Gibbon-Kotera-Sawada equation) are rederived. Some other new discrete KdV equations, discrete mKdV equations and discrete high order KdV equations which converge to the corresponding continuous soliton equations in the continuum limit are obtained. Integrable time discretizations of the DDKdV, DDmKdV (differential-difference mKdV equation) and DDHOKdV (differential-difference high order KdV equations) are given.

  3. Integration of the Eventlndex with other ATLAS systems

    NASA Astrophysics Data System (ADS)

    Barberis, D.; Cárdenas Zárate, S. E.; Gallas, E. J.; Prokoshin, F.

    2015-12-01

    The ATLAS EventIndex System, developed for use in LHC Run 2, is designed to index every processed event in ATLAS, replacing the TAG System used in Run 1. Its storage infrastructure, based on Hadoop open-source software framework, necessitates revamping how information in this system relates to other ATLAS systems. It will store more indexes since the fundamental mechanisms for retrieving these indexes will be better integrated into all stages of data processing, allowing more events from later stages of processing to be indexed than was possible with the previous system. Connections with other systems (conditions database, monitoring) are fundamentally critical to assess dataset completeness, identify data duplication, and check data integrity, and also enhance access to information in EventIndex by user and system interfaces. This paper gives an overview of the ATLAS systems involved, the relevant metadata, and describe the technologies we are deploying to complete these connections.

  4. Hypomethylation and transcriptional reactivation of retrotransposon-like sequences in ddm1 transgenic plants of Brassica rapa.

    PubMed

    Fujimoto, Ryo; Sasaki, Taku; Inoue, Hisashi; Nishio, Takeshi

    2008-03-01

    DNA methylation and histone modification play important roles in regulating gene expression. The DDM1 gene in Arabidopsis thaliana (AtDDM1) is required for the maintenance of DNA methylation level and histone H3 methylation pattern. We isolated DDM1 homologs of Brassica rapa, BrDDM1a and BrDDM1b, which have 84.4% and 84.1% deduced amino acid sequence identities with AtDDM1, respectively. Both the BrDDM1a and BrDDM1b genes were found to be expressed in vegetative and reproductive tissues. B. rapa ddm1-RNAi transgenic plants with reduced levels of BrDDM1a/BrDDM1b expression showed genome-wide and non-tissue-specific demethylation. These results suggest that the BrDDM1a and BrDDM1b genes are orthologs of AtDDM1 and are required for the maintenance of DNA methylation as is AtDDM1. Despite genome-wide demethylation, developmental abnormalities were not found in the ddm1-RNAi transgenic plants. Dominance relationships of SP11/SCR alleles, the determinant of pollen recognition specificity in Brassica self-incompatibility, in S heterozygotes in B. rapa were not influenced by the low level of the BrDDM1 expression. Transcriptional reactivation of retrotransposon-like sequences observed in the ddm1-RNAi transgenic plants indicates that BrDDM1a and BrDDM1b participate in silencing of retrotransposons. Hypomethylation states of the ddm1-RNAi transgenic plants were inherited by plants of the next generation even by plants which had lost the RNAi construct by segregation. Remethylation was observed in a few progenies. Efficiencies of remethylation in the progenies without the RNAi construct were different between 18S rDNA, BoSTF12a/15a, and BrTto1 sequences.

  5. The ATLAS Liquid Argon Calorimeter: Construction, Integration, Commissioning

    SciTech Connect

    Aleksa, Martin

    2006-10-27

    The ATLAS liquid argon (LAr) calorimeter system consists of an electromagnetic barrel calorimeter and two end caps with electromagnetic, hadronic and forward calorimeters. The liquid argon sampling technique, with an accordion geometry was chosen for the barrel electromagnetic calorimeter (EMB) and adapted to the end cap (EMEC). The hadronic end cap calorimeter (HEC) uses a copper-liquid argon sampling technique with flat plate geometry and is subdivided in depth in two wheels per end-cap. Finally, the forward calorimeter (FCAL) is composed of three modules employing cylindrical electrodes with thin liquid argon gaps.The construction of the full calorimeter system is complete since mid-2004. Production modules constructed in the home institutes were integrated into wheels at CERN in 2003-2004, and inserted into the three cryostats. They passed their first complete cold test before the lowering into the ATLAS cavern. Results of quality checks (e.g. electrical, mechanical, ...) performed on all the 190304 read-out channels after cool down will be reported. End 2004 the ATLAS barrel electromagnetic (EM) calorimeter was installed in the ATLAS cavern and since summer 2005 the front-end electronics are being connected and tested. Results of this first commissioning phase will be shown to demonstrate the high standards of quality control for our detectors.

  6. Experience with Intel's Many Integrated Core architecture in ATLAS software

    NASA Astrophysics Data System (ADS)

    Fleischmann, S.; Kama, S.; Lavrijsen, W.; Neumann, M.; Vitillo, R.; Atlas Collaboration

    2014-06-01

    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.

  7. Analysis of target sequences of DDM1s in Brassica rapa by MSAP.

    PubMed

    Sasaki, Taku; Fujimoto, Ryo; Kishitani, Sachie; Nishio, Takeshi

    2011-01-01

    DNA methylation is an important epigenetic modification regulating gene expression and transposon silencing. Although epigenetic regulation is involved in some agricultural traits, there has been relatively little research on epigenetic modifications of genes in Brassica rapa, which includes many important vegetables. In B. rapa, orthologs of DDM1, a chromatin remodeling factor required for maintenance of DNA methylation, have been characterized and DNA hypomethylated knock-down plants by RNAi (ddm1-RNAi plants) have been generated. In this study, we investigated differences of DNA methylation status at the genome-wide level between a wild-type (WT) plant and a ddm1-RNAi plant by methylation-sensitive amplification polymorphism (MSAP) analysis. MSAP analysis detected changes of DNA methylation of many repetitive sequences in the ddm1-RNAi plant. Search for body methylated regions in the WT plant revealed no difference in gene body methylation levels between the WT plant and the ddm1-RNAi plant. These results indicate that repetitive sequences are preferentially methylated by DDM1 genes in B. rapa.

  8. An integrative transcriptomic atlas of organogenesis in human embryos.

    PubMed

    Gerrard, Dave T; Berry, Andrew A; Jennings, Rachel E; Piper Hanley, Karen; Bobola, Nicoletta; Hanley, Neil A

    2016-01-01

    Human organogenesis is when severe developmental abnormalities commonly originate. However, understanding this critical embryonic phase has relied upon inference from patient phenotypes and assumptions from in vitro stem cell models and non-human vertebrates. We report an integrated transcriptomic atlas of human organogenesis. By lineage-guided principal components analysis, we uncover novel relatedness of particular developmental genes across different organs and tissues and identified unique transcriptional codes which correctly predicted the cause of many congenital disorders. By inference, our model pinpoints co-enriched genes as new causes of developmental disorders such as cleft palate and congenital heart disease. The data revealed more than 6000 novel transcripts, over 90% of which fulfil criteria as long non-coding RNAs correlated with the protein-coding genome over megabase distances. Taken together, we have uncovered cryptic transcriptional programs used by the human embryo and established a new resource for the molecular understanding of human organogenesis and its associated disorders. PMID:27557446

  9. The ATLAS integrated structural analysis and design software system

    NASA Technical Reports Server (NTRS)

    Dreisbach, R. L.; Giles, G. L.

    1978-01-01

    The ATLAS system provides an extensive set of integrated technical computer-program modules for the analysis and design of general structural configurations, as well as capabilities that are particularly suited for the aeroelastic design of flight vehicles. The system is based on the stiffness formulation of the finite element structural analysis method and can be executed in batch and interactive computing environments on CDC 6600/CYBER computers. Problem-definition input data are written in an engineering-oriented language using a free field format. Input-data default values, generation options, and data quality checks provided by the preprocessors minimize the amount of data and flowtime for problem definition/verfication. Postprocessors allow selected input and calculated data to be extracted, manipulated, and displayed via on-line and off-line prints or plots for monitoring and verifying problem solutions. The sequence and mode of execution of selected program modules are controlled by a common user-oriented language.

  10. Integration of omic networks in a developmental atlas of maize.

    PubMed

    Walley, Justin W; Sartor, Ryan C; Shen, Zhouxin; Schmitz, Robert J; Wu, Kevin J; Urich, Mark A; Nery, Joseph R; Smith, Laurie G; Schnable, James C; Ecker, Joseph R; Briggs, Steven P

    2016-08-19

    Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide scale. To enable network reconstructions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. Networks in which nodes are genes connected on the basis of highly correlated expression patterns of mRNAs were very different from networks that were based on coexpression of proteins. Roughly 85% of highly interconnected hubs were not conserved in expression between RNA and protein networks. However, networks from either data type were enriched in similar ontological categories and were effective in predicting known regulatory relationships. Integration of mRNA, protein, and phosphoprotein data sets greatly improved the predictive power of GRNs. PMID:27540173

  11. gLExec Integration with the ATLAS PanDA Workload Management System

    NASA Astrophysics Data System (ADS)

    Karavakis, E.; Barreiro, F.; Campana, S.; De, K.; Di Girolamo, A.; Litmaath, M.; Maeno, T.; Medrano, R.; Nilsson, P.; Wenaus, T.

    2015-12-01

    ATLAS user jobs are executed on Worker Nodes (WNs) by pilots sent to sites by pilot factories. This paradigm serves to allow a high job reliability and although it has clear advantages, such as making the working environment homogeneous, the approach presents security and traceability challenges. To address these challenges, gLExec can be used to let the payloads for each user be executed under a different UNIX user id that uniquely identifies the ATLAS user. This paper describes the recent improvements and evolution of the security model within the ATLAS PanDA system, including improvements in the PanDA pilot, in the PanDA server and their integration with MyProxy, a credential caching system that entitles a person or a service to act in the name of the issuer of the credential. Finally, it presents results from ATLAS user jobs running with gLExec and describes the deployment campaign within ATLAS.

  12. ATLAS, an integrated structural analysis and design system. Volume 1: ATLAS user's guide

    NASA Technical Reports Server (NTRS)

    Dreisbach, R. L. (Editor)

    1979-01-01

    Some of the many analytical capabilities provided by the ATLAS Version 4.0 System in the logical sequence are described in which model-definition data are prepared and the subsequent computer job is executed. The example data presented and the fundamental technical considerations that are highlighted can be used as guides during the problem solving process. This guide does not describe the details of the ATLAS capabilities, but provides an introduction to the new user of ATLAS to the level at which the complete array of capabilities described in the ATLAS User's Manual can be exploited fully.

  13. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.

    PubMed

    Sunkin, Susan M; Ng, Lydia; Lau, Chris; Dolbeare, Tim; Gilbert, Terri L; Thompson, Carol L; Hawrylycz, Michael; Dang, Chinh

    2013-01-01

    The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.

  14. Integration of the trigger and data acquisition systems in ATLAS

    NASA Astrophysics Data System (ADS)

    Abolins, M.; Adragna, P.; Aleksandrov, E.; Aleksandrov, I.; Amorim, A.; Anderson, K.; Anduaga, X.; Aracena, I.; Asquith, L.; Avolio, G.; Backlund, S.; Badescu, E.; Baines, J.; Barria, P.; Bartoldus, R.; Batreanu, S.; Beck, H. P.; Bee, C.; Bell, P.; Bell, W. H.; Bellomo, M.; Benslama, K.; Berge, D.; Berger, N.; Berry, T.; Biglietti, M.; Blair, R. E.; Bogaerts, A.; Bold, T.; Bosman, M.; Boyd, J.; Brelier, B.; B-Chromek, D.; Buttar, C.; Campanelli, M.; Caprini, M.; Carlino, G.; Casadei, D.; Casado, P.; Cataldi, G.; Cimino, D.; Ciobotaru, M; . Clements, D.; Coccaro, A.; Muino, P. C.; Conventi, F.; C-Radu, A.; Costa, M. J.; Torres, R. C.; Cranfield, R.; Cranmer, K.; Crone, G.; Dam, M.; Damazio, D.; Dawson, I.; Dawson, J.; Simoes, J. D. A.; Cecco, S. D.; Santo, A. D.; Della Pietra, M.; Delsart, P.-A.; Demers, S.; Demirkoz, B.; Mattia, A. D.; Dionisi, C.; Djilkibaev, R.; Dobinson, R.; Dobson, M.; Dotti, A.; Dova, M.; Drake, G.; Dufour, M.-A.; Eckweiler, S.; Ehrenfeld, W.; Eifert, T.; Ellis, N.; Emeliyanov, D.; Lima, D. E. F. d.; Ermoline, Y.; Eschrich, I.; Facius, K.; Falciano, S.; Farthouat, P.; Feng, E.; Ferland, J.; Ferrari, R.; Ferrer, M. L.; Fischer, G.; F-Martin, T.; Francis, D.; Gadomski, S.; Elejabarrieta, H. G.; Gaudio, G.; Gaumer, O.; George, S.; Giagu, S.; Goncalo, R.; Gorini, B.; Gorini, E.; Gowdy, S.; G-Bold, I.; Grancagnolo, S.; Green, B.; Haas, S.; Haberichter, W.; Hadavand, H.; Haeberli, C.; Haller, J.; Hamilton, A.; Hansen, J. R.; Hauschild, M.; Hauser, R.; Head, S.; Hillier, S.; Hoecker, A.; Hryn'ova, T.; H-Jones, R.; Huston, J.; Idarraga, J.; Igonkina, O.; Inada, M.; Jain, V.; Johns, K.; Joos, M.; Kama, S.; Kanaya, N.; Kazarov, A.; Kehoe, R.; Khoriauli, G.; Kieft, G.; Kilvington, G.; Kirk, J.; Kiyamura, H.; Klous, S.; Kolos, S.; Kono, T.; Konstantinidis, N.; Korcyl, K.; Kordas, K.; Kotov, V.; Krasznahorkay, A.; Kubota, T.; Kugel, A.; Kuhn, D.; Kurasige, H.; Kuwabara, T.; Kwee, R.; Lankford, A.; LeCompte, T.; Leahu, L.; Leahu, M.; Ledroit, F.; Miotto, G. L.; Lei, X.; Lellouch, D.; Leyton, M.; Li, S.; Lim, H.; Lohse, T.; Losada, M.; Luci, C.; Luminari, L.; Mapelli, L.; Martin, B.; Martin, B. T.; Marzano, F.; Masik, J.; McMahon, T.; McPherson, R.; Medinnis, M.; Meessen, C.; Meirosu, C.; Messina, A.; Mincer, A.; Mineev, M.; Misiejuk, A.; Moenig, K.; Monticelli, F.; Moraes, A.; Moreno, D.; Morettini, P.; Garcia, R. M.; Nagano, K.; Nagasaka, Y.; Negri, A.; Nemethy, P.; Neusiedl, A.; Nisati, A.; Nozicka, M.; Omachi, C.; Osculati, B.; Osuna, C.; Padilla, C.; Panikashvili, N.; Parodi, F.; Pasqualucci, E.; Pauly, T.; Perera, V.; Perez, E.; Reale, V. P.; Petersen, J.; Piegaia, R.; Pilcher, J.; Pinzon, G.; Pope, B.; Potter, C.; Primavera, M.; Radescu, V.; Rajagopalan, S.; Renkel, P.; Rescigno, M.; Rieke, S.; Risler, C.; Riu, I.; Robertson, S.; Roda, C.; Rodriguez, D.; Rogriquez, Y.; Ryabov, Y.; Ryan, P.; Salvatore, D.; Santamarina, C.; Rios, C. S.; Scannicchio, D.; Scannicchio, D. A.; Schiavi, C.; Schlereth, J.; Scholtes, I.; Schooltz, D.; Scott, W.; Segura, E.; Shimbo, N.; Sidoti, A.; Siragusa, G.; Sivoklokov, S.; Sloper, J. E.; Smizanska, M.; Soloviev, I.; Soluk, R.; Spagnolo, S.; Spiwoks, R.; Stancu, S.; Steinberg, P.; Stelzer, J.; Stradling, A.; Strom, D.; Strong, J.; Su, D.; Sushkov, S.; Sutton, M.; Szymocha, T.; Tapprogge, S.; Tarem, S.; Tarem, Z.; T-Dias, P.; Tokoshuku, K.; Torrence, E.; Touchard, F.; Tremblet, L.; Tripiana, M.; Usai, G.; Vachon, B.; Vandelli, W.; Ventura, A.; Vercesi, V.; Vermeulen, J.; Schmitt, J. V. D.; Wang, M.; Watson, A.; Wengler, T.; Werner, P.; W-Ellis, S.; Wickens, F.; Wiedenmann, W.; Wielers, M.; Wilkens, H.; Winklmeier, F.; Woehrling, E.-E.; Wu, S.-L.; Wu, X.; Xella, S.; Yamazaki, Y.; Yu, M.; Zema, F.; Zhang, J.; Zhao, L.; Zobernig, H.; dos Anjos, A.; zur Nedden, M.; Özcan, E.; Ünel, G.

    2008-07-01

    During 2006 and the first half of 2007, the installation, integration and commissioning of trigger and data acquisition (TDAQ) equipment in the ATLAS experimental area have progressed. There have been a series of technical runs using the final components of the system already installed in the experimental area. Various tests have been run including ones where level 1 preselected simulated proton-proton events have been processed in a loop mode through the trigger and dataflow chains. The system included the readout buffers containing the events, event building, level 2 and event filter trigger algorithms. The scalability of the system with respect to the number of event building nodes used has been studied and quantities critical for the final system, such as trigger rates and event processing times, have been measured using different trigger algorithms as well as different TDAQ components. This paper presents the TDAQ architecture, the current status of the installation and commissioning and highlights the main test results that validate the system.

  15. An integrative transcriptomic atlas of organogenesis in human embryos

    PubMed Central

    Gerrard, Dave T; Berry, Andrew A; Jennings, Rachel E; Piper Hanley, Karen; Bobola, Nicoletta; Hanley, Neil A

    2016-01-01

    Human organogenesis is when severe developmental abnormalities commonly originate. However, understanding this critical embryonic phase has relied upon inference from patient phenotypes and assumptions from in vitro stem cell models and non-human vertebrates. We report an integrated transcriptomic atlas of human organogenesis. By lineage-guided principal components analysis, we uncover novel relatedness of particular developmental genes across different organs and tissues and identified unique transcriptional codes which correctly predicted the cause of many congenital disorders. By inference, our model pinpoints co-enriched genes as new causes of developmental disorders such as cleft palate and congenital heart disease. The data revealed more than 6000 novel transcripts, over 90% of which fulfil criteria as long non-coding RNAs correlated with the protein-coding genome over megabase distances. Taken together, we have uncovered cryptic transcriptional programs used by the human embryo and established a new resource for the molecular understanding of human organogenesis and its associated disorders. DOI: http://dx.doi.org/10.7554/eLife.15657.001 PMID:27557446

  16. Integration of the Trigger and Data Acquisition Systems in ATLAS

    SciTech Connect

    Abolins, M.; Adragna, P.; Aleksandrov, E.; Aleksandrov, I.; Amorim, A.; Anderson, K.; Anduaga, X.; Aracena, I.; Asquith, L.; Avolio, G.; Backlund, S.; Badescu, E.; Baines, J.; Barria, P.; Bartoldus, R.; Batreanu, S.; Beck, H.P.; Bee, C.; Bell, P.; Bell, W.H.; Bellomo, M.; /more authors..

    2011-11-09

    During 2006 and the first half of 2007, the installation, integration and commissioning of trigger and data acquisition (TDAQ) equipment in the ATLAS experimental area have progressed. There have been a series of technical runs using the final components of the system already installed in the experimental area. Various tests have been run including ones where level 1 preselected simulated proton-proton events have been processed in a loop mode through the trigger and dataflow chains. The system included the readout buffers containing the events, event building, level 2 and event filter trigger algorithms. The scalability of the system with respect to the number of event building nodes used has been studied and quantities critical for the final system, such as trigger rates and event processing times, have been measured using different trigger algorithms as well as different TDAQ components. This paper presents the TDAQ architecture, the current status of the installation and commissioning and highlights the main test results that validate the system.

  17. ATLAS, an integrated structural analysis and design system. Volume 3: User's manual, input and execution data

    NASA Technical Reports Server (NTRS)

    Dreisbach, R. L. (Editor)

    1979-01-01

    The input data and execution control statements for the ATLAS integrated structural analysis and design system are described. It is operational on the Control Data Corporation (CDC) 6600/CYBER computers in a batch mode or in a time-shared mode via interactive graphic or text terminals. ATLAS is a modular system of computer codes with common executive and data base management components. The system provides an extensive set of general-purpose technical programs with analytical capabilities including stiffness, stress, loads, mass, substructuring, strength design, unsteady aerodynamics, vibration, and flutter analyses. The sequence and mode of execution of selected program modules are controlled via a common user-oriented language.

  18. Integrating Retraction Modeling Into an Atlas-Based Framework for Brain Shift Prediction

    PubMed Central

    Chen, Ishita; Ong, Rowena E.; Simpson, Amber L.; Sun, Kay; Thompson, Reid C.

    2015-01-01

    In recent work, an atlas-based statistical model for brain shift prediction, which accounts for uncertainty in the intraoperative environment, has been proposed. Previous work reported in the literature using this technique did not account for local deformation caused by surgical retraction. It is challenging to precisely localize the retractor location prior to surgery and the retractor is often moved in the course of the procedure. This paper proposes a technique that involves computing the retractor-induced brain deformation in the operating room through an active model solve and linearly superposing the solution with the precomputed deformation atlas. As a result, the new method takes advantage of the atlas-based framework’s accounting for uncertainties while also incorporating the effects of retraction with minimal intraoperative computing. This new approach was tested using simulation and phantom experiments. The results showed an improvement in average shift correction from 50% (ranging from 14 to 81%) for gravity atlas alone to 80% using the active solve retraction component (ranging from 73 to 85%). This paper presents a novel yet simple way to integrate retraction into the atlas-based brain shift computation framework. PMID:23864146

  19. Integration of Globus Online with the ATLAS PanDA Workload Management System

    NASA Astrophysics Data System (ADS)

    Contreras, C.; Deng, W.; Maeno, T.; Nilsson, P.; Potekhin, M.

    2012-12-01

    The PanDA Workload Management System is the basis for distributed production and analysis for the ATLAS experiment at the LHC. In this role, it relies on sophisticated dynamic data movement facilities developed in ATLAS. In certain scenarios, such as small research teams in ATLAS Tier-3 sites and non-ATLAS Virtual Organizations, the overhead of installation and operation of these components makes their use not very cost effective. Globus Online is an emerging new tool from the Globus Alliance, which already proved popular within the research community. It provides the users with fast and robust file transfer capabilities that can also be managed from a Web interface, and in addition to grid sites, can have individual workstations and laptops serving as data transmission endpoints. We will describe the integration of the Globus Online functionality into the PanDA suite of software, in order to give more flexibility in choosing the method of data transfer to ATLAS Tier-3 and Open Science Grid (OSG) users.

  20. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism

    PubMed Central

    Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng; Zheng, Zhimin; Yang, Dong-Lei; Zhao, Cheng; Dong, Juan; Gong, Zhizhong; Liu, Renyi; Zhu, Jian-Kang

    2016-01-01

    In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits. PMID:27551435

  1. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism.

    PubMed

    Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng; Zheng, Zhimin; Yang, Dong-Lei; Zhao, Cheng; Dong, Juan; Gong, Zhizhong; Liu, Renyi; Zhu, Jian-Kang

    2016-01-01

    In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits. PMID:27551435

  2. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism.

    PubMed

    Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng; Zheng, Zhimin; Yang, Dong-Lei; Zhao, Cheng; Dong, Juan; Gong, Zhizhong; Liu, Renyi; Zhu, Jian-Kang

    2016-01-01

    In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits.

  3. Integration of the Antennal Lobe Glomeruli and Three Projection Neurons in the Standard Brain Atlas of the Moth Heliothis Virescens

    PubMed Central

    Løfaldli, Bjarte Bye; Kvello, Pål; Mustaparta, Hanna

    2010-01-01

    Digital three dimensional standard brain atlases (SBAs) are valuable tools for integrating neuroimaging data of different preparations. In insects, SBAs of five species are available, including the atlas of the female Heliothis virescens moth brain. Like for the other species, the antennal lobes (ALs) of the moth brain atlas were integrated as one material identity without internal structures. Different from the others, the H. virescens SBA exclusively included the glomerular layer of the AL. This was an advantage in the present study for performing a direct registration of the glomerular layer of individual preparations into the standard brain. We here present the H. virescens female SBA with a new model of the AL glomeruli integrated into the atlas, i.e. with each of the 66 glomeruli identified and labelled with a specific number. The new model differs from the previous H. virescens AL model both in respect to the number of glomeruli and the numbering system; the latter according to the system used for the AL atlases of two other heliothine species. For identifying female specific glomeruli comparison with the male AL was necessary. This required a new male AL atlas, included in this paper. As demonstrated by the integration of three AL projection neurons of different preparations, the new SBA with the integrated glomruli is a helpful tool for determining the glomeruli innervated as well as the relative position of the axonal projections in the protocerebrum. PMID:20179785

  4. Beam tests of an integrated prototype of the ATLAS Forward Proton detector

    NASA Astrophysics Data System (ADS)

    Lange, J.; Adamczyk, L.; Avoni, G.; Banas, E.; Brandt, A.; Bruschi, M.; Buglewicz, P.; Cavallaro, E.; Caforio, D.; Chiodini, G.; Chytka, L.; Cieśla, K.; Davis, P. M.; Dyndal, M.; Grinstein, S.; Janas, K.; Jirakova, K.; Kocian, M.; Korcyl, K.; Lopez Paz, I.; Northacker, D.; Nozka, L.; Rijssenbeek, M.; Seabra, L.; Staszewski, R.; Świerska, P.; Sykora, T.

    2016-09-01

    The ATLAS Forward Proton (AFP) detector is intended to measure protons scattered at small angles from the ATLAS interaction point. To this end, a combination of 3D Silicon pixel tracking modules and Quartz-Cherenkov time-of-flight (ToF) detectors is installed 210 m away from the interaction point at both sides of ATLAS. Beam tests with an AFP prototype detector combining tracking and timing sub-detectors and a common readout have been performed at the CERN-SPS test-beam facility in November 2014 and September 2015 to complete the system integration and to study the detector performance. The successful tracking-timing integration was demonstrated. Good tracker hit efficiencies above 99.9% at a sensor tilt of 14°, as foreseen for AFP, were observed. Spatial resolutions in the short pixel direction with 50 μm pitch of 5.5 ± 0.5 μm per pixel plane and of 2.8 ± 0.5 μm for the full four-plane tracker at 14° were found, largely surpassing the AFP requirement of 10 μm. The timing detector showed also good hit efficiencies above 99%, and a full-system time resolution of 35±6 ps was found for the ToF prototype detector with two Quartz bars in-line (half the final AFP size) without dedicated optimisation, fulfilling the requirements for initial low-luminosity AFP runs.

  5. Off-line commissioning of EBIS and plans for its integration into ATLAS and CARIBU

    NASA Astrophysics Data System (ADS)

    Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.; Mustapha, B.; Perry, A.; Sharamentov, S. I.; Vondrasek, R. C.; Zinkann, G.

    2016-02-01

    An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne to breed radioactive beams from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility at Argonne Tandem Linac Accelerator System (ATLAS). The EBIS-CB will replace the existing ECR charge breeder to increase the intensity and significantly improve the purity of reaccelerated radioactive ion beams. The CARIBU EBIS-CB has been successfully commissioned offline with an external singly charged cesium ion source. The performance of the EBIS fully meets the specifications to breed rare isotope beams delivered from CARIBU. The EBIS is being relocated and integrated into ATLAS and CARIBU. A long electrostatic beam transport system including two 180° bends in the vertical plane has been designed. The commissioning of the EBIS and the beam transport system in their permanent location will start at the end of this year.

  6. Off-line commissioning of EBIS and plans for its integration into ATLAS and CARIBU.

    PubMed

    Ostroumov, P N; Barcikowski, A; Dickerson, C A; Mustapha, B; Perry, A; Sharamentov, S I; Vondrasek, R C; Zinkann, G

    2016-02-01

    An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne to breed radioactive beams from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility at Argonne Tandem Linac Accelerator System (ATLAS). The EBIS-CB will replace the existing ECR charge breeder to increase the intensity and significantly improve the purity of reaccelerated radioactive ion beams. The CARIBU EBIS-CB has been successfully commissioned offline with an external singly charged cesium ion source. The performance of the EBIS fully meets the specifications to breed rare isotope beams delivered from CARIBU. The EBIS is being relocated and integrated into ATLAS and CARIBU. A long electrostatic beam transport system including two 180° bends in the vertical plane has been designed. The commissioning of the EBIS and the beam transport system in their permanent location will start at the end of this year.

  7. Off-line commissioning of EBIS and plans for its integration into ATLAS and CARIBU.

    PubMed

    Ostroumov, P N; Barcikowski, A; Dickerson, C A; Mustapha, B; Perry, A; Sharamentov, S I; Vondrasek, R C; Zinkann, G

    2016-02-01

    An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne to breed radioactive beams from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility at Argonne Tandem Linac Accelerator System (ATLAS). The EBIS-CB will replace the existing ECR charge breeder to increase the intensity and significantly improve the purity of reaccelerated radioactive ion beams. The CARIBU EBIS-CB has been successfully commissioned offline with an external singly charged cesium ion source. The performance of the EBIS fully meets the specifications to breed rare isotope beams delivered from CARIBU. The EBIS is being relocated and integrated into ATLAS and CARIBU. A long electrostatic beam transport system including two 180° bends in the vertical plane has been designed. The commissioning of the EBIS and the beam transport system in their permanent location will start at the end of this year. PMID:26932059

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

    NASA Astrophysics Data System (ADS)

    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.

  9. SPACE code simulation of cold leg small break LOCA in the ATLAS integral test

    SciTech Connect

    Kim, B. J.; Kim, H. T.; Kim, J.; Kim, K. D.

    2012-07-01

    SPACE code is a system analysis code for pressurized water reactors. This code uses a two-fluid and three-field model. For a few years, intensive validations have been performed to secure the prediction accuracy of models and correlations for two-phase flow and heat transfer. Recently, the code version 1.0 was released. This study is to see how well SPACE code predicts thermal hydraulic phenomena of an integral effect test. The target experiment is a cold leg small break LOCA in the ATLAS facility, which has the same two-loop features as APR1400. Predicted parameters were compared with experimental observations. (authors)

  10. Integrated USB based readout interface for silicon strip detectors of the ATLAS SCT module

    NASA Astrophysics Data System (ADS)

    Masek, P.; Linhart, V.; Granja, C.; Pospisil, S.; Husak, M.

    2011-12-01

    An integrated portable USB based readout interface for the ATLAS semiconductor trackers (SCT) has been built. The ATLAS SCT modules are large area silicon strip detectors designed for tracking of high-energy charged particles resulting in collisions on Large Hadron Collider (LHC) in CERN. These modules can be also used on small accelerators for medical or industry applications where a compact and configurable readout interface would be useful. A complete custom made PC-host software tool was written for Windows platform for control and DAQ with build-in online visualization. The new constructed interface provides integrated power, control and DAQ and configurable communication between the detector module and the controlling PC. The interface is based on the Field Programmable Gate Array (FPGA) and the high speed USB 2.0 standard. This design permits to operate the modules under high particle fluence while minimizing the dead time of the whole detection system. Utilization of the programmable device simplifies the operation and permits future expansion of the functionality without any hardware changes. The device includes the high voltage source for detector bias up to 500 V and it is equipped with number of devices for monitoring the operation and conditions of measurement (temperature, humidity, voltage). These features are particularly useful as the strip detector must be operated in a well controlled environment. The operation of the interface will be demonstrated on data measured with different particles from radiation sources.

  11. Source contributions of sulfate aerosol over East Asia estimated by CMAQ-DDM.

    PubMed

    Itahashi, Syuichi; Uno, Itsushi; Kim, Soontae

    2012-06-19

    We applied the decoupled direct method (DDM), a sensitivity analysis technique for computing sensitivities accurately and efficiently, to determine the source-receptor relationships of anthropogenic SO(2) emissions to sulfate aerosol over East Asia. We assessed source contributions from East Asia being transported to Oki Island downwind from China and Korea during two air pollution episodes that occurred in July 2005. The contribution from China, particularly that from central eastern China (CEC), was found to dominate the sulfate aerosols. To study these contributions in more detail, CEC was divided into three regions, and the contributions from each region were examined. Source contributions exhibited both temporal and vertical variability, largely due to transport patterns imposed by the Asian summer monsoon. Our results are consistent with backward trajectory analyses. We found that anthropogenic SO(2) emissions from China produce significant quantities of summertime sulfate aerosols downwind of source areas. We used a parametric scaling method for estimating anthropogenic SO(2) emissions in China. Using column amounts of SO(2) derived from satellite data, and relationships between the column amounts of SO(2) and anthropogenic emissions, 2009 emissions were diagnosed. The results showed that 2009 emissions of SO(2) from China were equivalent to 2004 levels. PMID:22642816

  12. GetDDM: An open framework for testing optimized Schwarz methods for time-harmonic wave problems

    NASA Astrophysics Data System (ADS)

    Thierry, B.; Vion, A.; Tournier, S.; El Bouajaji, M.; Colignon, D.; Marsic, N.; Antoine, X.; Geuzaine, C.

    2016-06-01

    We present an open finite element framework, called GetDDM, for testing optimized Schwarz domain decomposition techniques for time-harmonic wave problems. After a review of Schwarz domain decomposition methods and associated transmission conditions, we discuss the implementation, based on the open source software GetDP and Gmsh. The solver, along with ready-to-use examples for Helmholtz and Maxwell's equations, is freely available online for further testing.

  13. The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource.

    PubMed

    Craig, Thomas; Smelick, Chris; Tacutu, Robi; Wuttke, Daniel; Wood, Shona H; Stanley, Henry; Janssens, Georges; Savitskaya, Ekaterina; Moskalev, Alexey; Arking, Robert; de Magalhães, João Pedro

    2015-01-01

    Multiple studies characterizing the human ageing phenotype have been conducted for decades. However, there is no centralized resource in which data on multiple age-related changes are collated. Currently, researchers must consult several sources, including primary publications, in order to obtain age-related data at various levels. To address this and facilitate integrative, system-level studies of ageing we developed the Digital Ageing Atlas (DAA). The DAA is a one-stop collection of human age-related data covering different biological levels (molecular, cellular, physiological, psychological and pathological) that is freely available online (http://ageing-map.org/). Each of the >3000 age-related changes is associated with a specific tissue and has its own page displaying a variety of information, including at least one reference. Age-related changes can also be linked to each other in hierarchical trees to represent different types of relationships. In addition, we developed an intuitive and user-friendly interface that allows searching, browsing and retrieving information in an integrated and interactive fashion. Overall, the DAA offers a new approach to systemizing ageing resources, providing a manually-curated and readily accessible source of age-related changes.

  14. The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

    PubMed Central

    Craig, Thomas; Smelick, Chris; Tacutu, Robi; Wuttke, Daniel; Wood, Shona H.; Stanley, Henry; Janssens, Georges; Savitskaya, Ekaterina; Moskalev, Alexey; Arking, Robert; de Magalhães, João Pedro

    2015-01-01

    Multiple studies characterizing the human ageing phenotype have been conducted for decades. However, there is no centralized resource in which data on multiple age-related changes are collated. Currently, researchers must consult several sources, including primary publications, in order to obtain age-related data at various levels. To address this and facilitate integrative, system-level studies of ageing we developed the Digital Ageing Atlas (DAA). The DAA is a one-stop collection of human age-related data covering different biological levels (molecular, cellular, physiological, psychological and pathological) that is freely available online (http://ageing-map.org/). Each of the >3000 age-related changes is associated with a specific tissue and has its own page displaying a variety of information, including at least one reference. Age-related changes can also be linked to each other in hierarchical trees to represent different types of relationships. In addition, we developed an intuitive and user-friendly interface that allows searching, browsing and retrieving information in an integrated and interactive fashion. Overall, the DAA offers a new approach to systemizing ageing resources, providing a manually-curated and readily accessible source of age-related changes. PMID:25232097

  15. Digital, Three-dimensional Average Shaped Atlas of the Heliothis Virescens Brain with Integrated Gustatory and Olfactory Neurons

    PubMed Central

    Kvello, Pål; Løfaldli, Bjarte Bye; Rybak, Jürgen; Menzel, Randolf; Mustaparta, Hanna

    2009-01-01

    We use the moth Heliothis virescens as model organism for studying the neural network involved in chemosensory coding and learning. The constituent neurons are characterised by intracellular recordings combined with staining, resulting in a single neuron identified in each brain preparation. In order to spatially relate the neurons of different preparations a common brain framework was required. We here present an average shaped atlas of the moth brain. It is based on 11 female brain preparations, each stained with a fluorescent synaptic marker and scanned in confocal laser-scanning microscope. Brain neuropils of each preparation were manually reconstructed in the computer software Amira, followed by generating the atlas using the Iterative Shape Average Procedure. To demonstrate the application of the atlas we have registered two olfactory and two gustatory interneurons, as well as the axonal projections of gustatory receptor neurons into the atlas, visualising their spatial relationships. The olfactory interneurons, showing the typical morphology of inner-tract antennal lobe projection neurons, projected in the calyces of the mushroom body and laterally in the protocerebral lobe. The two gustatory interneurons, responding to sucrose and quinine respectively, projected in different areas of the brain. The wide projections of the quinine responding neuron included a lateral area adjacent to the projections of the olfactory interneurons. The sucrose responding neuron was confined to the suboesophageal ganglion with dendritic arborisations overlapping the axonal projections of the gustatory receptor neurons on the proboscis. By serving as a tool for the integration of neurons, the atlas offers visual access to the spatial relationship between the neurons in three dimensions, and thus facilitates the study of neuronal networks in the Heliothis virescens brain. The moth standard brain is accessible at http://www.ntnu.no/biolog/english/neuroscience/brain PMID:19949481

  16. ATLAS, an integrated structural analysis and design system. Volume 2: System design document

    NASA Technical Reports Server (NTRS)

    Erickson, W. J. (Editor)

    1979-01-01

    ATLAS is a structural analysis and design system, operational on the Control Data Corporation 6600/CYBER computers. The overall system design, the design of the individual program modules, and the routines in the ATLAS system library are described. The overall design is discussed in terms of system architecture, executive function, data base structure, user program interfaces and operational procedures. The program module sections include detailed code description, common block usage and random access file usage. The description of the ATLAS program library includes all information needed to use these general purpose routines.

  17. ATLAS, an integrated structural analysis and design system. Volume 5: System demonstration problems

    NASA Technical Reports Server (NTRS)

    Samuel, R. A. (Editor)

    1979-01-01

    One of a series of documents describing the ATLAS System for structural analysis and design is presented. A set of problems is described that demonstrate the various analysis and design capabilities of the ATLAS System proper as well as capabilities available by means of interfaces with other computer programs. Input data and results for each demonstration problem are discussed. Results are compared to theoretical solutions or experimental data where possible. Listings of all input data are included.

  18. Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners

    PubMed Central

    Poynton, Clare B; Chen, Kevin T; Chonde, Daniel B; Izquierdo-Garcia, David; Gollub, Randy L; Gerstner, Elizabeth R; Batchelor, Tracy T; Catana, Ciprian

    2014-01-01

    We present a new MRI-based attenuation correction (AC) approach for integrated PET/MRI systems that combines both segmentation- and atlas-based methods by incorporating dual-echo ultra-short echo-time (DUTE) and T1-weighted (T1w) MRI data and a probabilistic atlas. Segmented atlases were constructed from CT training data using a leave-one-out framework and combined with T1w, DUTE, and CT data to train a classifier that computes the probability of air/soft tissue/bone at each voxel. This classifier was applied to segment the MRI of the subject of interest and attenuation maps (μ-maps) were generated by assigning specific linear attenuation coefficients (LACs) to each tissue class. The μ-maps generated with this “Atlas-T1w-DUTE” approach were compared to those obtained from DUTE data using a previously proposed method. For validation of the segmentation results, segmented CT μ-maps were considered to the “silver standard”; the segmentation accuracy was assessed qualitatively and quantitatively through calculation of the Dice similarity coefficient (DSC). Relative change (RC) maps between the CT and MRI-based attenuation corrected PET volumes were also calculated for a global voxel-wise assessment of the reconstruction results. The μ-maps obtained using the Atlas-T1w-DUTE classifier agreed well with those derived from CT; the mean DSCs for the Atlas-T1w-DUTE-based μ-maps across all subjects were higher than those for DUTE-based μ-maps; the atlas-based μ-maps also showed a lower percentage of misclassified voxels across all subjects. RC maps from the atlas-based technique also demonstrated improvement in the PET data compared to the DUTE method, both globally as well as regionally. PMID:24753982

  19. A module concept for the upgrades of the ATLAS pixel system using the novel SLID-ICV vertical integration technology

    NASA Astrophysics Data System (ADS)

    Beimforde, M.; Andricek, L.; Macchiolo, A.; Moser, H.-G.; Nisius, R.; Richter, R. H.; Weigell, P.

    2010-12-01

    The presented R&D activity is focused on the development of a new pixel module concept for the foreseen upgrades of the ATLAS detector towards the Super LHC employing thin n-in-p silicon sensors together with a novel vertical integration technology. A first set of pixel sensors with active thicknesses of 75 μm and 150 μm has been produced using a thinning technique developed at the Max-Planck-Institut für Physik (MPP) and the MPI Semiconductor Laboratory (HLL). Charge Collection Efficiency (CCE) measurements of these sensors irradiated with 26 MeV protons up to a particle fluence of 1016neqcm-2 have been performed, yielding higher values than expected from the present radiation damage models. The novel integration technology, developed by the Fraunhofer Institut EMFT, consists of the Solid-Liquid InterDiffusion (SLID) interconnection, being an alternative to the standard solder bump-bonding, and Inter-Chip Vias (ICVs) for routing signals vertically through electronics. This allows for extracting the digitized signals from the back side of the readout chips, avoiding wire-bonding cantilevers at the edge of the devices and thus increases the active area fraction. First interconnections have been performed with wafers containing daisy chains to investigate the efficiency of SLID at wafer-to-wafer and chip-to-wafer level. In a second interconnection process the present ATLAS FE-I3 readout chips were connected to dummy sensor wafers at chip-to-wafer level. Preparations of ICV within the ATLAS readout chips for back side contacting and the future steps towards a full demonstrator module will be presented.

  20. The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa

    PubMed Central

    Basenko, Evelina Y.; Kamei, Masayuki; Ji, Lexiang; Schmitz, Robert J.; Lewis, Zachary A.

    2016-01-01

    LSH/DDM1 enzymes are required for DNA methylation in higher eukaryotes and have poorly defined roles in genome maintenance in yeast, plants, and animals. The filamentous fungus Neurospora crassa is a tractable system that encodes a single LSH/DDM1 homolog (NCU06306). We report that the Neurospora LSH/DDM1 enzyme is encoded by mutagen sensitive-30 (mus-30), a locus identified in a genetic screen over 25 years ago. We show that MUS-30-deficient cells have normal DNA methylation, but are hypersensitive to DNA damaging agents. MUS-30 is a nuclear protein, consistent with its predicted role as a chromatin remodeling enzyme, and levels of MUS-30 are increased following DNA damage. MUS-30 co-purifies with Neurospora WDR76, a homolog of yeast Changed Mutation Rate-1 and mammalian WD40 repeat domain 76. Deletion of wdr76 rescued DNA damage-hypersensitivity of Δmus-30 strains, demonstrating that the MUS-30-WDR76 interaction is functionally important. DNA damage-sensitivity of Δmus-30 is partially suppressed by deletion of methyl adenine glycosylase-1, a component of the base excision repair machinery (BER); however, the rate of BER is not affected in Δmus-30 strains. We found that MUS-30-deficient cells are not defective for DSB repair, and we observed a negative genetic interaction between Δmus-30 and Δmei-3, the Neurospora RAD51 homolog required for homologous recombination. Together, our findings suggest that MUS-30, an LSH/DDM1 homolog, is required to prevent DNA damage arising from toxic base excision repair intermediates. Overall, our study provides important new information about the functions of the LSH/DDM1 family of enzymes. PMID:26771905

  1. Integration and alignment of ATLAS instrument engineering model components in Optical Development System Lab

    NASA Astrophysics Data System (ADS)

    Evans, Tyler

    2013-09-01

    The ATLAS Instrument for the ICESat-2 mission at NASA's Goddard Space Flight Center required a test-bed to prove out new concepts before the mission launches in 2016. The Optical Development System (ODS) laboratory was created to use breadboard, prototype, and engineering-model levels of hardware and software to model and evaluate the ATLAS alignment system. A one meter parabolic mirror was used to create a collimated light beam to align prototype and engineering model transmitter and receiver optics and test closed-loop alignment algorithms. To achieve an error of less than two micro-radians, an active deformable mirror was used to correct the wave front to subtract out the collimator mount error.

  2. Integrating Individual Differences in Career Assessment: The Atlas Model of Individual Differences and the Strong Ring

    ERIC Educational Resources Information Center

    Armstrong, Patrick Ian; Rounds, James

    2010-01-01

    Career assessment methods often include measures of individual differences constructs, such as interests, personality, abilities, and values. Although many researchers have recently called for the development of integrated models, career counseling professionals have long faced the challenge of integrating this information into their practice. The…

  3. A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana.

    PubMed

    Cho, Eun Ju; Choi, Seung Hee; Kim, Ji Hong; Kim, Ji Eun; Lee, Min Hee; Chung, Byung Yeoup; Woo, Hye Ryun; Kim, Jin-Hong

    2016-01-01

    Leaf senescence is a finely regulated complex process; however, evidence for the involvement of epigenetic processes in the regulation of leaf senescence is still fragmentary. Therefore, we chose to examine the functions of DRD1, a SWI2/SNF2 chromatin remodeling protein, in epigenetic regulation of leaf senescence, particularly because drd1-6 mutants exhibited a delayed leaf senescence phenotype. Photosynthetic parameters such as Fv/Fm and ETRmax were decreased in WT leaves compared to leaves of drd1-6 mutants after dark treatment. The WT leaves remarkably lost more chlorophyll and protein content during dark-induced senescence (DIS) than the drd1-6 leaves did. The induction of senescence-associated genes was noticeably inhibited in the drd1-6 mutant after 5-d of DIS. We compared changes in epigenetic regulation during DIS via quantitative expression analysis of 180-bp centromeric (CEN) and transcriptionally silent information (TSI) repeats. Their expression levels significantly increased in both the WT and the drd1-6 mutant, but did much less in the latter. Moreover, the delayed leaf senescence was observed in ddm1-2 mutants as well as the drd1-6, but not in drd1-p mutants. These data suggest that SWI2/SNF2 chromatin remodeling proteins such as DRD1 and DDM1 may influence leaf senescence possibly via epigenetic regulation.

  4. A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana

    PubMed Central

    Kim, Ji Hong; Kim, Ji Eun; Lee, Min Hee; Chung, Byung Yeoup; Woo, Hye Ryun; Kim, Jin-Hong

    2016-01-01

    Leaf senescence is a finely regulated complex process; however, evidence for the involvement of epigenetic processes in the regulation of leaf senescence is still fragmentary. Therefore, we chose to examine the functions of DRD1, a SWI2/SNF2 chromatin remodeling protein, in epigenetic regulation of leaf senescence, particularly because drd1-6 mutants exhibited a delayed leaf senescence phenotype. Photosynthetic parameters such as Fv/Fm and ETRmax were decreased in WT leaves compared to leaves of drd1-6 mutants after dark treatment. The WT leaves remarkably lost more chlorophyll and protein content during dark-induced senescence (DIS) than the drd1-6 leaves did. The induction of senescence-associated genes was noticeably inhibited in the drd1-6 mutant after 5-d of DIS. We compared changes in epigenetic regulation during DIS via quantitative expression analysis of 180-bp centromeric (CEN) and transcriptionally silent information (TSI) repeats. Their expression levels significantly increased in both the WT and the drd1-6 mutant, but did much less in the latter. Moreover, the delayed leaf senescence was observed in ddm1-2 mutants as well as the drd1-6, but not in drd1-p mutants. These data suggest that SWI2/SNF2 chromatin remodeling proteins such as DRD1 and DDM1 may influence leaf senescence possibly via epigenetic regulation. PMID:26752684

  5. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

    PubMed Central

    Kuperstein, I; Bonnet, E; Nguyen, H-A; Cohen, D; Viara, E; Grieco, L; Fourquet, S; Calzone, L; Russo, C; Kondratova, M; Dutreix, M; Barillot, E; Zinovyev, A

    2015-01-01

    Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless ‘geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses

  6. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.

    PubMed

    Kuperstein, I; Bonnet, E; Nguyen, H-A; Cohen, D; Viara, E; Grieco, L; Fourquet, S; Calzone, L; Russo, C; Kondratova, M; Dutreix, M; Barillot, E; Zinovyev, A

    2015-01-01

    Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless 'geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses

  7. Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

    PubMed Central

    Petryszak, Robert; Keays, Maria; Tang, Y. Amy; Fonseca, Nuno A.; Barrera, Elisabet; Burdett, Tony; Füllgrabe, Anja; Fuentes, Alfonso Muñoz-Pomer; Jupp, Simon; Koskinen, Satu; Mannion, Oliver; Huerta, Laura; Megy, Karine; Snow, Catherine; Williams, Eleanor; Barzine, Mitra; Hastings, Emma; Weisser, Hendrik; Wright, James; Jaiswal, Pankaj; Huber, Wolfgang; Choudhary, Jyoti; Parkinson, Helen E.; Brazma, Alvis

    2016-01-01

    Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons—estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates. PMID:26481351

  8. Lithostratigraphic framework and correlation of the Neoproterozoic northern West African Craton passive margin sequence (Siroua-Zenaga-Bouazzer Elgraara Inliers, Central Anti-Atlas, Morocco): an integrated approach

    NASA Astrophysics Data System (ADS)

    Bouougri, El Hafid; Saquaque, Ali

    2004-06-01

    The Neoproterozoic volcano-sedimentary cover (˜0.8 Ga) deposited on the northern passive margin of the West African craton occurs in the central Anti-Atlas inliers and is a ˜2 km thick succession formally termed the Tizi n-Taghatine Group. The group comprises two sedimentary packages (lower and upper) separated by a middle volcanic unit. An integrated approach of lithostratigraphy, sedimentology, sequence stratigraphy and paleogeographic setting have been combined to provide well constrained correlation and lithostratigraphic organization. The Tizi n-Taghatine Group is formally subdivided into 12 Formations, 10 of which are defined in the lower sedimentary package while the middle volcanic unit and the upper sedimentary package constitute the two uppermost Formations. The lithostratigraphic organization and subdivision of the Tizi n-Taghatine Group constitutes a stratigraphic record of major paleogeographic settings and large cyclic changes in depositional system due to relative sea-level variations. The integrated approach of combination and comparison of various data provides significant information on the nature, origin and time significance of the formal unit boundaries. This leads to proposing a correlative scheme for the Tizi n-Taghatine Group across the Neoproterozoic central Anti-Atlas suture zone.

  9. Health Impact Assessment (HIA) and EnviroAtlas: Integrating Ecosystem Services into the Decision-Making Process-Guide

    EPA Science Inventory

    This document was created to highlight the many ways that the U.S. EPA EnviroAtlas suite of ecosystem services tools can be used to aid in the Health Impact Assessment (HIA) process. Ecosystems provide numerous services and benefits to individuals, communities, businesses, and ot...

  10. MirZ: an integrated microRNA expression atlas and target prediction resource.

    PubMed

    Hausser, Jean; Berninger, Philipp; Rodak, Christoph; Jantscher, Yvonne; Wirth, Stefan; Zavolan, Mihaela

    2009-07-01

    MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens.

  11. MirZ: an integrated microRNA expression atlas and target prediction resource

    PubMed Central

    Hausser, Jean; Berninger, Philipp; Rodak, Christoph; Jantscher, Yvonne; Wirth, Stefan; Zavolan, Mihaela

    2009-01-01

    MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens. PMID:19468042

  12. ATLAS Inner Detector Event Data Model

    SciTech Connect

    ATLAS; Akesson, F.; Costa, M.J.; Dobos, D.; Elsing, M.; Fleischmann, S.; Gaponenko, A.; Gnanvo, K.; Keener, P.T.; Liebig, W.; Moyse, E.; Salzburger, A.; Siebel, M.; Wildauer, A.

    2007-12-12

    The data model for event reconstruction (EDM) in the Inner Detector of the ATLAS experiment is presented. Different data classes represent evolving stages in the reconstruction data flow, and specific derived classes exist for the sub-detectors. The Inner Detector EDM also extends the data model for common tracking in ATLAS and is integrated into the modular design of the ATLAS high-level trigger and off-line software.

  13. Integrated application of gravity and seismic methods for determining the dip angle of a fault plane: Case of Mahjouba fault (Central Tunisian Atlas Province, North Africa)

    NASA Astrophysics Data System (ADS)

    Gabtni, H.; Hajji, O.; Jallouli, C.

    2016-07-01

    A procedure for a dip angle determination of a fault plane from gravity field data is presented to constrain a seismic profile interpretation. This procedure is applied on Mahjouba normal fault at the western border of Kalaa Khesba graben (Central Tunisian Atlas Province, North Africa). Seismic and detailed gravity data, in this region, were analyzed to provide more constraints on the geometry of the fault dip angle. The Mahjouba fault is mapped as three major parallel lineaments extended for 2 km with a NW-SE to N-S trend. The dip of the Mahjouba fault is estimated from the gravity modeling data to be 45°E. This study reveals that integrating gravity and seismic data provides accurate mapping of faults geometry and such result provides useful information and constraints on the exploration of natural resources.

  14. Integrated application of gravity and seismic methods for determining the dip angle of a fault plane: Case of Mahjouba fault (Central Tunisian Atlas Province, North Africa)

    NASA Astrophysics Data System (ADS)

    Gabtni, H.; Hajji, O.; Jallouli, C.

    2016-07-01

    A procedure for a dip angle determination of a fault plane from gravity field data is presented to constrain a seismic profile interpretation. This procedure is applied on Mahjouba normal fault at the western border of Kalaa Khesba graben (Central Tunisian Atlas Province, North Africa). Seismic and detailed gravity data, in this region, were analyzed to provide more constraints on the geometry of the fault dip angle. The Mahjouba fault is mapped as three major parallel lineaments extended for 2 km with a NW-SE to N-S trend. The dip of the Mahjouba fault is estimated from the gravity modeling data to be 45°E. This study reveals that integrating gravity and seismic data provides accurate mapping of faults geometry and such result provides useful information and constraints on the exploration of natural resources.

  15. ATLAS Cloud R&D

    NASA Astrophysics Data System (ADS)

    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.

  16. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  17. Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy.

    PubMed

    Wang, Haibin; Qi, Xiangyu; Chen, Sumei; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Jiang, Jiafu; Chen, Fadi

    2015-01-01

    Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5'-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation. PMID:26379692

  18. MarsAtlas: A cortical parcellation atlas for functional mapping.

    PubMed

    Auzias, Guillaume; Coulon, Olivier; Brovelli, Andrea

    2016-04-01

    An open question in neuroimaging is how to develop anatomical brain atlases for the analysis of functional data. Here, we present a cortical parcellation model based on macroanatomical information and test its validity on visuomotor-related cortical functional networks. The parcellation model is based on a recently developed cortical parameterization method (Auzias et al., [2013]: IEEE Trans Med Imaging 32:873-887), called HIP-HOP. This method exploits a set of primary and secondary sulci to create an orthogonal coordinate system on the cortical surface. A natural parcellation scheme arises from the axes of the HIP-HOP model running along the fundus of selected sulci. The resulting parcellation scheme, called MarsAtlas, complies with dorsoventral/rostrocaudal direction fields and allows inter-subject matching. To test it for functional mapping, we analyzed a MEG dataset collected from human participants performing an arbitrary visuomotor mapping task. Single-trial high-gamma activity, HGA (60-120 Hz), was estimated using spectral analysis and beamforming techniques at cortical areas arising from a Talairach atlas (i.e., Brodmann areas) and MarsAtlas. Using both atlases, we confirmed that visuomotor associations involve an increase in HGA over the sensorimotor and fronto-parietal network, in addition to medial prefrontal areas. However, MarsAtlas provided: (1) crucial functional information along both the dorsolateral and rostrocaudal direction; (2) an increase in statistical significance. To conclude, our results suggest that the MarsAtlas is a valid anatomical atlas for functional mapping, and represents a potential anatomical framework for integration of functional data arising from multiple techniques such as MEG, intracranial EEG and fMRI. PMID:26813563

  19. Towards multimodal atlases of the human brain

    PubMed Central

    Toga, Arthur W.; Thompson, Paul M.; Mori, Susumu; Amunts, Katrin; Zilles, Karl

    2010-01-01

    Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease. PMID:17115077

  20. Integrative Pathway Analysis of Metabolic Signature in Bladder Cancer: A Linkage to The Cancer Genome Atlas Project and Prediction of Survival

    PubMed Central

    von Rundstedt, Friedrich-Carl; Rajapakshe, Kimal; Ma, Jing; Arnold, James M.; Gohlke, Jie; Putluri, Vasanta; Krishnapuram, Rashmi; Piyarathna, D. Badrajee; Lotan, Yair; Gödde, Daniel; Roth, Stephan; Störkel, Stephan; Levitt, Jonathan M.; Michailidis, George; Sreekumar, Arun; Lerner, Seth P.; Coarfa, Cristian; Putluri, Nagireddy

    2016-01-01

    Purpose We used targeted mass spectrometry to study the metabolic fingerprint of urothelial cancer and determine whether the biochemical pathway analysis gene signature would have a predictive value in independent cohorts of patients with bladder cancer. Materials and Methods Pathologically evaluated, bladder derived tissues, including benign adjacent tissue from 14 patients and bladder cancer from 46, were analyzed by liquid chromatography based targeted mass spectrometry. Differential metabolites associated with tumor samples in comparison to benign tissue were identified by adjusting the p values for multiple testing at a false discovery rate threshold of 15%. Enrichment of pathways and processes associated with the metabolic signature were determined using the GO (Gene Ontology) Database and MSigDB (Molecular Signature Database). Integration of metabolite alterations with transcriptome data from TCGA (The Cancer Genome Atlas) was done to identify the molecular signature of 30 metabolic genes. Available outcome data from TCGA portal were used to determine the association with survival. Results We identified 145 metabolites, of which analysis revealed 31 differential metabolites when comparing benign and tumor tissue samples. Using the KEGG (Kyoto Encyclopedia of Genes and Genomes) Database we identified a total of 174 genes that correlated with the altered metabolic pathways involved. By integrating these genes with the transcriptomic data from the corresponding TCGA data set we identified a metabolic signature consisting of 30 genes. The signature was significant in its prediction of survival in 95 patients with a low signature score vs 282 with a high signature score (p = 0.0458). Conclusions Targeted mass spectrometry of bladder cancer is highly sensitive for detecting metabolic alterations. Applying transcriptome data allows for integration into larger data sets and identification of relevant metabolic pathways in bladder cancer progression. PMID:26802582

  1. Disrupted white matter integrity is associated with cognitive deficits in patients with amnestic mild cognitive impairment: An atlas-based study

    PubMed Central

    Liu, Duan; Wang, Zan; Shu, Hao; Zhang, Zhijun

    2016-01-01

    Objective: This study investigated white matter integrity in patients with amnestic mild cognitive impairment by diffusion tensor imaging. Methods: A total of 83 patients with amnestic mild cognitive impairment and 85 elderly healthy controls underwent neuropsychological testing and a diffusion tensor imaging scan. Whole-brain white matter data were parcellated into 50 regions based on the anatomical ICBM-DTI-81 atlas, and regional diffusion metrics consisting of fractional anisotropy, mean diffusivity, radial diffusivity, and axial diffusivity were calculated for each region. Diffusion tensor imaging indices were compared between groups, and it was determined that between-group differences were significantly correlated with neurocognitive performance. Results: Relative to the healthy controls group, the amnestic mild cognitive impairment group exhibited poorer cognitive performance in all neuropsychological tests except the complex figure test (p = 0.083) and showed decreased mean fractional anisotropy in the fornix, increased mean diffusivity in the fornix and bilateral uncinate fasciculus, elevated axial diffusivity in the fornix and genu of corpus callosum, and elevated radial diffusivity in the fornix and bilateral uncinate fasciculus (p < 0.05). Behaviorally, integrity of the bilateral uncinate fasciculus was correlated positively with episodic memory function, while left uncinate fasciculus integrity was positively associated with language function in the amnestic mild cognitive impairment group (p < 0.05). Conclusion: White matter abnormalities in neural pathways associated with memory were correlated with neurocognitive deficiencies in amnestic mild cognitive impairment. Given that amnestic mild cognitive impairment is putatively a prodromal syndrome for Alzheimer’s disease, this study furthers our understanding of the white matter changes associated with Alzheimer’s disease pathogenesis in the predementia stage. PMID:27354916

  2. Atlas Mountains

    NASA Technical Reports Server (NTRS)

    2002-01-01

    These are the Anti-Atlas Mountains, part of the Atlas Mountain range in southern Morocco, Africa. The region contains some of the world's largest and most diverse mineral resources, most of which are still untouched. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on June 22, 2001. This is a false-color composite image made using shortwave infrared, infrared, and red wavelengths. Image provided by the USGS EROS Data Center Satellite Systems Branch.

  3. Rucio - The next generation of large scale distributed system for ATLAS Data Management

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Rucio is the next-generation Distributed Data Management (DDM) system benefiting from recent advances in cloud and "Big Data" computing to address HEP experiments scaling requirements. Rucio is an evolution of the ATLAS DDM system Don Quijote 2 (DQ2), which has demonstrated very large scale data management capabilities with more than 140 petabytes spread worldwide across 130 sites, and accesses from 1,000 active users. However, DQ2 is reaching its limits in terms of scalability, requiring a large number of support staff to operate and being hard to extend with new technologies. Rucio will deal with these issues by relying on a conceptual data model and new technology to ensure system scalability, address new user requirements and employ new automation framework to reduce operational overheads. We present the key concepts of Rucio, including its data organization/representation and a model of how to manage central group and user activities. The Rucio design, and the technology it employs, is described, specifically looking at its RESTful architecture and the various software components it uses. We show also the performance of the system.

  4. Integration of the Atlas of Natural Hazards and the Ecological Territorial Order Program for Puerto Vallarta using GIS.

    NASA Astrophysics Data System (ADS)

    Trejo-Gómez, E.; Nuñez-Cornu, F.; Suarez-Plascencia, C.; Chavez-Dagostino, R.

    2006-12-01

    The Atlas of Natural Hazards in Puerto Vallarta (ARN) and the Ecological Territorial Order Program (POET), are documents needed to carry out recommendations to the municipal adminitrations for tasks such as the preservation and recoverment of important zones conserning the natural environment in Puerto Vallarta. These tasks can improve the quality level of life and offer security to the financial investors of this tourist destiny. Both documents are generated with the support of HABITAT Program by the Secretary's of Social Development (SEDESOL) and City Council of Puerto Vallarta. The purpose of this work is to recommend the implementation of a Geographical Information System with the ARN and POET, that responds to the necessities of the municipal goverment in areas like State and Municipal Civil Defense, Urban Planning, Tourism and Ecology. The study has a surface of 340.75 square kilometers and the initial information corresponds to a restitution of year 2000; on graphic scale 1:20,000. At the moment, we have alredy included the descriptions of geology, morphology, seismology, hydrology, type of vegetation, flora and fauna with protected and endemic species. By means of field work, we have related 266 sites with geophysical and hydrometereological hazards. The practices performed by the population in these sites increase their own risk. We have also delimited hazard zones by rock fall, flows and floods along the routes. The valuation is obtained like Affectation-Surface including consolidated houses of different surplus values. In the future, it will be necessary to keep updated the ARN and quantify the information of risks caussed by natural hazards in Puerto Vallarta.

  5. Atlas-based identification of cortical sulci

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Raphel, Jose K.; Nguyen, Bonnie T.

    1996-04-01

    The identification of cortical sulci is of great importance. In neurosurgical procedures any target in the cranium can be accessed by following the corridors of the sulci and fissures. The fusion of functional and anatomical data also requires the identification of sulci. Several approaches have been proposed for segmentation of the cortical surface and identification of sulci and fissures. Most of them are bottom-up. They work satisfactorily provided that the sulci are well discernible on MRI images, limiting their use to some major sulci and fissures, such as the central sulcus, interhemispheric fissure, or Sylvian fissure. We propose a sulcal model based approach, overcoming some of the above limitations. The sulcal model is derived from two brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach- Tournoux (TT), and Atlas of Cerebral Sulci by Ono-Kubik-Abernathey (OKA). The OKA atlas contains 403 patterns for 55 sulci along with their incidence rates of interruptions, side branches, and connections. An electronic version of the OKA atlas was constructed, quantitatively enhanced by placing the sulcal patterns in a stereotactic space. The original patterns from the OKA atlas were digitized, converted into geometric representation, placed in the Talairach stereotactic space, preregistered with the TT atlas, and integrated with a multi- atlas, multi-dimensional neuroimaging system developed by our group. The registration of any atlas with the clinical data automatically registers all atlases with this data. This way the sulcal patterns can be superimposed on data, indicating approximate locations of sulci on images. The approach proposed here provides a simple and real-time registration of the sulcal patterns with clinical data, and an interactive identification and labeling of sulci. This approach assists rather the medical professional, instead of providing a complete automated extraction of a few, primary sulci with certain accuracy, where a

  6. WESTCARB Carbon Atlas

    DOE Data Explorer

    The West Coast Regional Carbon Sequestration Partnership (known as WESTCARB) was established in Fall 2003. It is one of seven research partnerships co-funded by DOE to characterize regional carbon sequestration opportunities and conduct pilot-scale validation tests. The California Energy Commission manages WESTCARB and is a major co-funder. WESTCARB is characterizing the extent and capacity of geologic formations capable of storing CO2, known as sinks. Results are entered into a geographic information system (GIS) database, along with the location of major CO2-emitting point sources in each of the six WESTCARB states, enabling researchers and the public to gauge the proximity of candidate CO2 storage sites to emission sources and the feasibility of linking them via pipelines. Specifically, the WESTCARB GIS database (also known as the carbon atlas) stores layers of geologic information about potential underground storage sites, such as porosity and nearby fault-lines and aquifers. Researchers use these data, along with interpreted geophysical data and available oil and gas well logs to estimate the region's potential geologic storage capacity. The database also depicts existing pipeline routes and rights-of-way and lands that could be off-limits, which can aid the development of a regional carbon management strategy. The WESTCARB Carbon Atlas, which is accessible to the public, provides a resource for public discourse on practical solutions for regional CO2 management. A key WESTCARB partner, the Utah Automated Geographic Reference Center, has developed data serving procedures to enable the WESTCARB Carbon Atlas to be integrated with those from other regional partnerships, thereby supporting the U.S. Department of Energy's national carbon atlas, NATCARB

  7. Organization and management of ATLAS offline software releases

    NASA Astrophysics Data System (ADS)

    Obreshkov, E.; Albrand, S.; Collot, J.; Fulachier, J.; Lambert, F.; Adam-Bourdarios, C.; Arnault, C.; Garonne, V.; Rousseau, D.; Schaffer, A.; von der Schmitt, H.; De Salvo, A.; Kabachenko, V.; Ren, Z.; Qing, Di; Nzuobontane, E.; Sherwood, P.; Simmons, B.; George, S.; Rybkine, G.; Lloyd, S.; Undrus, A.; Youssef, S.; Quarrie, D.; Hansl-Kozanecka, T.; Luehring, F.; Moyse, E.; Goldfarb, S.

    2008-01-01

    ATLAS is one of the largest collaborations ever undertaken in the physical sciences. This paper explains how the software infrastructure is organized to manage collaborative code development by around 300 developers with varying degrees of expertise and situated in 30 different countries. ATLAS offline software currently consists of about 2 million source lines of code contained in 6800 C++ classes, organized in more than 1000 packages. We will describe how releases of the offline ATLAS software are built, validated and subsequently deployed to remote sites. Several software management tools have been used, the majority of which are not ATLAS specific; we will show how they have been integrated.

  8. Event selection services in ATLAS

    NASA Astrophysics Data System (ADS)

    Cranshaw, J.; Cuhadar-Donszelmann, T.; Gallas, E.; Hrivnac, J.; Kenyon, M.; McGlone, H.; Malon, D.; Mambelli, M.; Nowak, M.; Viegas, F.; Vinek, E.; Zhang, Q.

    2010-04-01

    ATLAS has developed and deployed event-level selection services based upon event metadata records ("TAGS") and supporting file and database technology. These services allow physicists to extract events that satisfy their selection predicates from any stage of data processing and use them as input to later analyses. One component of these services is a web-based Event-Level Selection Service Interface (ELSSI). ELSSI supports event selection by integrating run-level metadata, luminosity-block-level metadata (e.g., detector status and quality information), and event-by-event information (e.g., triggers passed and physics content). The list of events that survive after some selection criterion is returned in a form that can be used directly as input to local or distributed analysis; indeed, it is possible to submit a skimming job directly from the ELSSI interface using grid proxy credential delegation. ELSSI allows physicists to explore ATLAS event metadata as a means to understand, qualitatively and quantitatively, the distributional characteristics of ATLAS data. In fact, the ELSSI service provides an easy interface to see the highest missing ET events or the events with the most leptons, to count how many events passed a given set of triggers, or to find events that failed a given trigger but nonetheless look relevant to an analysis based upon the results of offline reconstruction, and more. This work provides an overview of ATLAS event-level selection services, with an emphasis upon the interactive Event-Level Selection Service Interface.

  9. MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas

    PubMed Central

    Rizzo, Gaia; Veronese, Mattia; Expert, Paul; Turkheimer, Federico E.; Bertoldo, Alessandra

    2016-01-01

    Introduction Brain-wide mRNA mappings offer a great potential for neuroscience research as they can provide information about system proteomics. In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. This approach is potentially applicable to any imaging modality as long as an efficient procedure of imaging-genomic matching is provided. In the original work we considered mRNA brain maps of the whole human genome derived from the Allen human brain database (ABA) and we performed the analysis with a specific region-based segmentation with a resolution that was limited by the PET data parcellation. There we identified the need for a platform for imaging-genomic integration that should be usable with any imaging modalities and fully exploit the high resolution mapping of ABA dataset. Aim In this work we present MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis), a software platform that allows the investigation of the correlation patterns between neuroimaging data of any sort (both functional and structural) with mRNA gene expression profiles derived from the ABA database at high resolution. Results We applied MENGA to six different imaging datasets from three modalities (PET, single photon emission tomography and magnetic resonance imaging) targeting the dopamine and serotonin receptor systems and the myelin molecular structure. We further investigated imaging-genomic correlations in the case of mismatch between selected proteins and imaging targets. PMID:26882227

  10. Report to users of ATLAS

    SciTech Connect

    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.

  11. ATLAS DBM Module Qualification

    SciTech Connect

    Soha, Aria; Gorisek, Andrej; Zavrtanik, Marko; Sokhranyi, Grygorii; McGoldrick, Garrin; Cerv, Matevz

    2014-06-18

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

  12. Atlas Distributed Analysis Tools

    NASA Astrophysics Data System (ADS)

    de La Hoz, Santiago Gonzalez; Ruiz, Luis March; Liko, Dietrich

    2008-06-01

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

  13. ATLAS F MISSILE FIELDS IN THE UNITED STATES, ATLAS F ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    ATLAS F MISSILE FIELDS IN THE UNITED STATES, ATLAS F- TEXAS RING OF TWELVE - Dyess Air Force Base, Atlas F Missle Site S-8, Approximately 3 miles east of Winters, 500 feet southwest of Highway 177, Winters, Runnels County, TX

  14. ATLAS Live: Collaborative Information Streams

    NASA Astrophysics Data System (ADS)

    Goldfarb, Steven; ATLAS Collaboration

    2011-12-01

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

  15. The Cancer Genome Atlas ovarian cancer analysis

    Cancer.gov

    An analysis of genomic changes in ovarian cancer has provided the most comprehensive and integrated view of cancer genes for any cancer type to date. Ovarian serous adenocarcinoma tumors from 500 patients were examined by The Cancer Genome Atlas (TCGA) Re

  16. SCA controller for the ATLAS calorimeter

    SciTech Connect

    Gingrich, D.M.; Hewlett, J.C.; Holm, L.

    1997-12-31

    The front-end readout of the ATLAS liquid argon calorimeter will store data locally in analog pipeline memories at the LHC beam crossing frequency of 40 MHz. Switched capacitor array chips meeting the ATLAS readout requirements will be used. These new chips axe capable of simultaneous read and write operations, and allow random access to storage locations. To utilize these essential design features requires a substantial amount of fast control and address bookkeeping logic. We have designed a controller capable of operating the pipelines as analog random access memories and that satisfies the ATLAS readout requirements. The pipeline controller manages the data of 144 time samples and can operate at a mean trigger rate of about 75 kHz, when reading out five time samples per event. We are currently prototyping an integrated version of the controller implemented in a FPGA from Xilinx.

  17. Distributed analysis in ATLAS using GANGA

    NASA Astrophysics Data System (ADS)

    Elmsheuser, Johannes; Brochu, Frederic; Cowan, Greig; Egede, Ulrik; Gaidioz, Benjamin; Lee, Hurng-Chun; Maier, Andrew; Móscicki, Jakub; Pajchel, Katarina; Reece, Will; Samset, Bjorn; Slater, Mark; Soroko, Alexander; Vanderster, Daniel; Williams, Michael

    2010-04-01

    Distributed data analysis using Grid resources is one of the fundamental applications in high energy physics to be addressed and realized before the start of LHC data taking. The needs to manage the resources are very high. In every experiment up to a thousand physicists will be submitting analysis jobs to the Grid. Appropriate user interfaces and helper applications have to be made available to assure that all users can use the Grid without expertise in Grid technology. These tools enlarge the number of Grid users from a few production administrators to potentially all participating physicists. The GANGA job management system (http://cern.ch/ganga), developed as a common project between the ATLAS and LHCb experiments, provides and integrates these kind of tools. GANGA provides a simple and consistent way of preparing, organizing and executing analysis tasks within the experiment analysis framework, implemented through a plug-in system. It allows trivial switching between running test jobs on a local batch system and running large-scale analyzes on the Grid, hiding Grid technicalities. We will be reporting on the plug-ins and our experiences of distributed data analysis using GANGA within the ATLAS experiment. Support for all Grids presently used by ATLAS, namely the LCG/EGEE, NDGF/NorduGrid, and OSG/PanDA is provided. The integration and interaction with the ATLAS data management system DQ2 into GANGA is a key functionality. An intelligent job brokering is set up by using the job splitting mechanism together with data-set and file location knowledge. The brokering is aided by an automated system that regularly processes test analysis jobs at all ATLAS DQ2 supported sites. Large numbers of analysis jobs can be sent to the locations of data following the ATLAS computing model. GANGA supports amongst other things tasks of user analysis with reconstructed data and small scale production of Monte Carlo data.

  18. Evolution of the ATLAS Nightly Build System

    NASA Astrophysics Data System (ADS)

    Undrus, A.

    2012-12-01

    The ATLAS Nightly Build System is a major component in the ATLAS collaborative software organization, validation, and code approval scheme. For over 10 years of development it has evolved into a factory for automatic release production and grid distribution. The 50 multi-platform branches of ATLAS releases provide vast opportunities for testing new packages, verification of patches to existing software, and migration to new platforms and compilers for ATLAS code that currently contains 2200 packages with 4 million C++ and 1.4 million python scripting lines written by about 1000 developers. Recent development was focused on the integration of ATLAS Nightly Build and Installation systems. The nightly releases are distributed and validated and some are transformed into stable releases used for data processing worldwide. The ATLAS Nightly System is managed by the NICOS control tool on a computing farm with 50 powerful multiprocessor nodes. NICOS provides the fully automated framework for the release builds, testing, and creation of distribution kits. The ATN testing framework of the Nightly System runs unit and integration tests in parallel suites, fully utilizing the resources of multi-core machines, and provides the first results even before compilations complete. The NICOS error detection system is based on several techniques and classifies the compilation and test errors according to their severity. It is periodically tuned to place greater emphasis on certain software defects by highlighting the problems on NICOS web pages and sending automatic e-mail notifications to responsible developers. These and other recent developments will be presented and future plans will be described.

  19. The commercial Atlas today

    NASA Astrophysics Data System (ADS)

    Patzer, Mike; White, Robert C.

    1990-07-01

    Spanning more than three decades, the General Dynamics Atlas launch vehicle program has contributed greatly to the productive exploitation of space. This paper briefly reviews Atlas history and achievements and then focuses on present Atlas launch vehicle configurations, capabilities, and propulsion systems. The four-vehicle Atlas family is described, inluding manufacturing, performance, and design differences. Vehicle launch options including the fairing and spacecraft adapter are discussed. A mission profile, flight environments, and a nominal sequence of events are described for a standard GTO mission. Details on vehicle enhancements are presented including the addition of solid rocket motors, booster and Centaur engine uprates, and avionics improvements.

  20. Virtual Machine Logbook - Enabling virtualization for ATLAS

    NASA Astrophysics Data System (ADS)

    Yao, Yushu; Calafiura, Paolo; Poffet, Julien; Cavalli, Andrea; Leggett, Charles; Frédéric, Bapst

    2010-04-01

    ATLAS software has been developed mostly on CERN linux cluster lxplus or on similar facilities at the experiment Tier 1 centers. The fast rise of virtualization technology has the potential to change this model, turning every laptop or desktop into an ATLAS analysis platform. In the context of the CernVM project we are developing a suite of tools and CernVM plug-in extensions to promote the use of virtualization for ATLAS analysis and software development. The Virtual Machine Logbook (VML), in particular, is an application to organize work of physicists on multiple projects, logging their progress, and speeding up "context switches" from one project to another. An important feature of VML is the ability to share with a single "click" the status of a given project with other colleagues. VML builds upon the save and restore capabilities of mainstream virtualization software like VMware, and provides a technology-independent client interface to them. A lot of emphasis in the design and implementation has gone into optimizing the save and restore process to makepractical to store many VML entries on a typical laptop disk or to share a VML entry over the network. At the same time, taking advantage of CernVM's plugin capabilities, we are extending the CernVM platform to help increase the usability of ATLAS software. For example, we added the ability to start the ATLAS event display on any computer running CernVM simply by clicking a button in a web browser. We want to integrate seamlessly VML with CernVM unique file system design to distribute efficiently ATLAS software on every physicist computer. The CernVM File System (CVMFS) download files on-demand via HTTP, and cache it locally for future use. This reduces by one order of magnitude the download sizes, making practical for a developer to work with multiple software releases on a virtual machine.

  1. Multilevel Workflow System in the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    Borodin, M.; De, K.; Garcia Navarro, J.; Golubkov, D.; Klimentov, A.; Maeno, T.; Vaniachine, A.; ATLAS Collaboration

    2015-05-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs are executed across more than a hundred distributed computing sites by PanDA - the ATLAS job-level workload management system. On the outer level, the Database Engine for Tasks (DEfT) empowers production managers with templated workflow definitions. On the next level, the Job Execution and Definition Interface (JEDI) is integrated with PanDA to provide dynamic job definition tailored to the sites capabilities. We report on scaling up the production system to accommodate a growing number of requirements from main ATLAS areas: Trigger, Physics and Data Preparation.

  2. BNL ATLAS Grid Computing

    ScienceCinema

    Michael Ernst

    2016-07-12

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  3. BNL ATLAS Grid Computing

    SciTech Connect

    Michael Ernst

    2008-10-02

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  4. ATLAS ACCEPTANCE TEST

    SciTech Connect

    Cochrane, J. C. , Jr.; Parker, J. V.; Hinckley, W. B.; Hosack, K. W.; Mills, D.; Parsons, W. M.; Scudder, D. W.; Stokes, J. L.; Tabaka, L. J.; Thompson, M. C.; Wysocki, Frederick Joseph; Campbell, T. N.; Lancaster, D. L.; Tom, C. Y.

    2001-01-01

    The acceptance test program for Atlas, a 23 MJ pulsed power facility for use in the Los Alamos High Energy Density Hydrodynamics program, has been completed. Completion of this program officially releases Atlas from the construction phase and readies it for experiments. Details of the acceptance test program results and of machine capabilities for experiments will be presented.

  5. Language Industries Atlas.

    ERIC Educational Resources Information Center

    Hearn, P. M., Ed.; Button, D. F., Ed.

    This atlas describes the activities of public and private organizations that create the infrastructure within which languages are able to develop and interact in the European Community (EC). It contains over 1,000 descriptions of activities that play a role in shaping the language industries, from a user or provider perspective. The atlas is…

  6. National Atlas maps

    USGS Publications Warehouse

    ,

    1991-01-01

    The National Atlas of the United States of America was published by the U.S. Geological Survey in 1970. Its 765 maps and charts are on 335 14- by 19-inch pages. Many of the maps span facing pages. It's worth a quick trip to the library just to leaf through all 335 pages of this book. Rapid scanning of its thematic maps yields rich insights to the geography of issues of continuing national interest. On most maps, the geographic patterns are still valid, though the data are not current. The atlas is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. The maps dated after 1970 are either revisions of original atlas maps, or new maps published in atlas format. The titles of the separate maps are listed here.

  7. Diabetes Interactive Atlas.

    PubMed

    Kirtland, Karen A; Burrows, Nilka R; Geiss, Linda S

    2014-02-06

    The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas' maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity.

  8. A Glimpse of Atlas

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Saturn's little moon Atlas orbits Saturn between the outer edge of the A ring and the fascinating, twisted F ring. This image just barely resolves the disk of Atlas, and also shows some of the knotted structure for which the F ring is known. Atlas is 32 kilometers (20 miles) across.

    The bright outer edge of the A ring is overexposed here, but farther down the image several bright ring features can be seen.

    The image was taken in visible light with the Cassini spacecraft narrow-angle camera on April 25, 2005, at a distance of approximately 2.4 million kilometers (1.5 million miles) from Atlas and at a Sun-Atlas-spacecraft, or phase, angle of 60 degrees. Resolution in the original image was 14 kilometers (9 miles) per pixel.

  9. ICESat-2 / ATLAS Flight Science Receiver Algorithms

    NASA Astrophysics Data System (ADS)

    Mcgarry, J.; Carabajal, C. C.; Degnan, J. J.; Mallama, A.; Palm, S. P.; Ricklefs, R.; Saba, J. L.

    2013-12-01

    . This Simulator makes it possible to check all logic paths that could be encountered by the Algorithms on orbit. In addition the NASA airborne instrument MABEL is collecting data with characteristics similar to what ATLAS will see. MABEL data is being used to test the ATLAS Receiver Algorithms. Further verification will be performed during Integration and Testing of the ATLAS instrument and during Environmental Testing on the full ATLAS instrument. Results from testing to date show the Receiver Algorithms have the ability to handle a wide range of signal and noise levels with a very good sensitivity at relatively low signal to noise ratios. In addition, preliminary tests have demonstrated, using the ICESat-2 Science Team's selected land ice and sea ice test cases, the capability of the Algorithms to successfully find and telemeter the surface echoes. In this presentation we will describe the ATLAS Flight Science Receiver Algorithms and the Software Simulator, and will present results of the testing to date. The onboard databases (DEM, DRM and the Surface Reference Mask) are being developed at the University of Texas at Austin as part of the ATLAS Flight Science Receiver Algorithms. Verification of the onboard databases is being performed by ATLAS Receiver Algorithms team members Claudia Carabajal and Jack Saba.

  10. Space-Frequency Detail-Preserving Construction of Neonatal Brain Atlases

    PubMed Central

    Zhang, Yuyao; Shi, Feng; Yap, Pew-Thian; Shen, Dinggang

    2016-01-01

    Brain atlases are an integral component of neuroimaging studies. However, most brain atlases are fuzzy and lack structural details, especially in the cortical regions. In particular, neonatal brain atlases are especially challenging to construct due to the low spatial resolution and low tissue contrast. This is mainly caused by the image averaging process involved in atlas construction, often smoothing out high-frequency contents that indicate fine anatomical details. In this paper, we propose a novel framework for detail-preserving construction of atlases. Our approach combines space and frequency information to better preserve image details. This is achieved by performing reconstruction in the space-frequency domain given by wavelet transform. Sparse patch-based atlas reconstruction is performed in each frequency subband. Combining the results for all these subbands will then result in a refined atlas. Compared with existing atlases, experimental results indicate that our approach has the ability to build an atlas with more structural details, thus leading to better performance when used to normalize a group of testing neonatal images. PMID:27169138

  11. Thin n-in-p pixel sensors and the SLID-ICV vertical integration technology for the ATLAS upgrade at the HL-LHC

    NASA Astrophysics Data System (ADS)

    Macchiolo, A.; Andricek, L.; Ellenburg, M.; Moser, H. G.; Nisius, R.; Richter, R. H.; Terzo, S.; Weigell, P.

    2013-12-01

    This R&D activity is focused on the development of new modules for the upgrade of the ATLAS pixel system at the High Luminosity LHC (HL-LHC). The performance after irradiation of n-in-p pixel sensors of different active thicknesses is studied, together with an investigation of a novel interconnection technique offered by the Fraunhofer Institute EMFT in Munich, the Solid-Liquid-InterDiffusion (SLID), which is an alternative to the standard solder bump-bonding. The pixel modules are based on thin n-in-p sensors, with an active thickness of 75 μm or 150 μm, produced at the MPI Semiconductor Laboratory (MPI HLL) and on 100 μm thick sensors with active edges, fabricated at VTT, Finland. Hit efficiencies are derived from beam test data for thin devices irradiated up to a fluence of 4×1015 neq/cm2. For the active edge devices, the charge collection properties of the edge pixels before irradiation are discussed in detail, with respect to the inner ones, using measurements with radioactive sources. Beyond the active edge sensors, an additional ingredient needed to design four side buttable modules is the possibility of moving the wire bonding area from the chip surface facing the sensor to the backside, avoiding the implementation of the cantilever extruding beyond the sensor area. The feasibility of this process is under investigation with the FE-I3 SLID modules, where Inter Chip Vias are etched, employing an EMFT technology, with a cross section of 3 μm×10 μm, at the positions of the original wire bonding pads.

  12. The Millennium Star Atlas

    NASA Astrophysics Data System (ADS)

    Sinnott, R. W.

    1997-08-01

    Derived from Hipparcos and Tycho observations, the Millennium Star Atlas is a set of 1548 charts covering the entire sky to about magnitude 11. It stands apart from all previous printed atlases in completeness to magnitude 10 and in uniformity around the sky. The generous chart scale has made possible a number of innovations never before seen in a star atlas: arrows on high-proper-motion stars, double-star ticks conveying separation and position angle for a specific modern epoch, distance labels for nearby stars, and variable stars coded by amplitude, period, and type. Among the nonstellar objects plotted, more than 8000 galaxies are shown with aspect ratio and orientation.

  13. Automating ATLAS Computing Operations using the Site Status Board

    NASA Astrophysics Data System (ADS)

    J, Andreeva; Iglesias C, Borrego; S, Campana; Girolamo A, Di; I, Dzhunov; Curull X, Espinal; S, Gayazov; E, Magradze; M, Nowotka M.; L, Rinaldi; P, Saiz; J, Schovancova; A, Stewart G.; M, Wright

    2012-12-01

    The automation of operations is essential to reduce manpower costs and improve the reliability of the system. The Site Status Board (SSB) is a framework which allows Virtual Organizations to monitor their computing activities at distributed sites and to evaluate site performance. The ATLAS experiment intensively uses the SSB for the distributed computing shifts, for estimating data processing and data transfer efficiencies at a particular site, and for implementing automatic exclusion of sites from computing activities, in case of potential problems. The ATLAS SSB provides a real-time aggregated monitoring view and keeps the history of the monitoring metrics. Based on this history, usability of a site from the perspective of ATLAS is calculated. The paper will describe how the SSB is integrated in the ATLAS operations and computing infrastructure and will cover implementation details of the ATLAS SSB sensors and alarm system, based on the information in the SSB. It will demonstrate the positive impact of the use of the SSB on the overall performance of ATLAS computing activities and will overview future plans.

  14. Gulf of Mexico Data Atlas: Digital Data Discovery and Access

    NASA Astrophysics Data System (ADS)

    Rose, K.

    2014-12-01

    The Gulf of Mexico Data Atlas is an online data discovery and access tool that allows users to browse a growing collection of ecosystem-related datasets visualized as map plates. Thematically, the Atlas includes updated long-term assessments of the physical, biological, environmental, economic and living marine resource characteristics that indicate baseline conditions of the Gulf of Mexico ecosystems. These data are crucial components of integrated ecosystem assessments and modeling and support restoration and monitoring efforts in the Gulf. A multi-agency executive steering committee including members from international, federal, state, and non-governmental organizations was established to guide Atlas development and to contribute data and expertise. The Atlas currently contains over 235 maps in 70 subject areas. Each map plate is accompanied by a descriptive summary authored by a subject matter expert and each data set is fully documented by metadata in Federal Geographic Data Committee (FGDC)-compliant standards. Source data are available in native formats and as web mapping services (WMS). Datasets are also searchable through an accompanying Map Catalog and RSS feed. The Gulf of Mexico Data Atlas is an operational example of the philosophy of leveraging resources among agencies and activities involved in geospatial data as outlined in the US Department of Interior and FGDC "Geospatial Platform Modernization Roadmap v4 - March 2011". We continue to update and add datasets through existing and new partnerships to ensure that the Atlas becomes a truly ecosystem-wide resource.

  15. A study of dynamic data placement for ATLAS distributed data management

    NASA Astrophysics Data System (ADS)

    Beermann, T.; Stewart, G. A.; Maettig, P.

    2015-12-01

    This contribution presents a study on the applicability and usefulness of dynamic data placement methods for data-intensive systems, such as ATLAS distributed data management (DDM). In this system the jobs are sent to the data, therefore having a good distribution of data is significant. Ways of forecasting workload patterns are examined which then are used to redistribute data to achieve a better overall utilisation of computing resources and to reduce waiting time for jobs before they can run on the grid. This method is based on a tracer infrastructure that is able to monitor and store historical data accesses and which is used to create popularity reports. These reports provide detailed summaries about data accesses in the past, including information about the accessed files, the involved users and the sites. From this past data it is possible to then make near-term forecasts for data popularity in the future. This study evaluates simple prediction methods as well as more complex methods like neural networks. Based on the outcome of the predictions a redistribution algorithm deletes unused replicas and adds new replicas for potentially popular datasets. Finally, a grid simulator is used to examine the effects of the redistribution. The simulator replays workload on different data distributions while measuring the job waiting time and site usage. The study examines how the average waiting time is affected by the amount of data that is moved, how it differs for the various forecasting methods and how that compares to the optimal data distribution.

  16. Preparation of Northern Mid-Continent Petroleum Atlas

    SciTech Connect

    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

  17. MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection.

    PubMed

    Doshi, Jimit; Erus, Guray; Ou, Yangming; Resnick, Susan M; Gur, Ruben C; Gur, Raquel E; Satterthwaite, Theodore D; Furth, Susan; Davatzikos, Christos

    2016-02-15

    Atlas-based automated anatomical labeling is a fundamental tool in medical image segmentation, as it defines regions of interest for subsequent analysis of structural and functional image data. The extensive investigation of multi-atlas warping and fusion techniques over the past 5 or more years has clearly demonstrated the advantages of consensus-based segmentation. However, the common approach is to use multiple atlases with a single registration method and parameter set, which is not necessarily optimal for every individual scan, anatomical region, and problem/data-type. Different registration criteria and parameter sets yield different solutions, each providing complementary information. Herein, we present a consensus labeling framework that generates a broad ensemble of labeled atlases in target image space via the use of several warping algorithms, regularization parameters, and atlases. The label fusion integrates two complementary sources of information: a local similarity ranking to select locally optimal atlases and a boundary modulation term to refine the segmentation consistently with the target image's intensity profile. The ensemble approach consistently outperforms segmentations using individual warping methods alone, achieving high accuracy on several benchmark datasets. The MUSE methodology has been used for processing thousands of scans from various datasets, producing robust and consistent results. MUSE is publicly available both as a downloadable software package, and as an application that can be run on the CBICA Image Processing Portal (https://ipp.cbica.upenn.edu), a web based platform for remote processing of medical images.

  18. MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection.

    PubMed

    Doshi, Jimit; Erus, Guray; Ou, Yangming; Resnick, Susan M; Gur, Ruben C; Gur, Raquel E; Satterthwaite, Theodore D; Furth, Susan; Davatzikos, Christos

    2016-02-15

    Atlas-based automated anatomical labeling is a fundamental tool in medical image segmentation, as it defines regions of interest for subsequent analysis of structural and functional image data. The extensive investigation of multi-atlas warping and fusion techniques over the past 5 or more years has clearly demonstrated the advantages of consensus-based segmentation. However, the common approach is to use multiple atlases with a single registration method and parameter set, which is not necessarily optimal for every individual scan, anatomical region, and problem/data-type. Different registration criteria and parameter sets yield different solutions, each providing complementary information. Herein, we present a consensus labeling framework that generates a broad ensemble of labeled atlases in target image space via the use of several warping algorithms, regularization parameters, and atlases. The label fusion integrates two complementary sources of information: a local similarity ranking to select locally optimal atlases and a boundary modulation term to refine the segmentation consistently with the target image's intensity profile. The ensemble approach consistently outperforms segmentations using individual warping methods alone, achieving high accuracy on several benchmark datasets. The MUSE methodology has been used for processing thousands of scans from various datasets, producing robust and consistent results. MUSE is publicly available both as a downloadable software package, and as an application that can be run on the CBICA Image Processing Portal (https://ipp.cbica.upenn.edu), a web based platform for remote processing of medical images. PMID:26679328

  19. ATLAS Metadata Task Force

    SciTech Connect

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

    2007-04-04

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

  20. Diabetes Interactive Atlas

    PubMed Central

    Burrows, Nilka R.; Geiss, Linda S.

    2014-01-01

    The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas’ maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity. PMID:24503340

  1. "ATLAS" Advanced Technology Life-cycle Analysis System

    NASA Technical Reports Server (NTRS)

    Lollar, Louis F.; Mankins, John C.; ONeil, Daniel A.

    2004-01-01

    Making good decisions concerning research and development portfolios-and concerning the best systems concepts to pursue - as early as possible in the life cycle of advanced technologies is a key goal of R&D management This goal depends upon the effective integration of information from a wide variety of sources as well as focused, high-level analyses intended to inform such decisions Life-cycle Analysis System (ATLAS) methodology and tool kit. ATLAS encompasses a wide range of methods and tools. A key foundation for ATLAS is the NASA-created Technology Readiness. The toolkit is largely spreadsheet based (as of August 2003). This product is being funded by the Human and Robotics The presentation provides a summary of the Advanced Technology Level (TRL) systems Technology Program Office, Office of Exploration Systems, NASA Headquarters, Washington D.C. and is being integrated by Dan O Neil of the Advanced Projects Office, NASA/MSFC, Huntsville, AL

  2. ATLAS@AWS

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

    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.

  3. Interoperability Between Coastal Web Atlases Using Semantic Mediation: A Case Study of the International Coastal Atlas Network (ICAN)

    NASA Astrophysics Data System (ADS)

    Wright, D. J.; Lassoued, Y.; Dwyer, N.; Haddad, T.; Bermudez, L. E.; Dunne, D.

    2009-12-01

    Coastal mapping plays an important role in informing marine spatial planning, resource management, maritime safety, hazard assessment and even national sovereignty. As such, there is now a plethora of data/metadata catalogs, pre-made maps, tabular and text information on resource availability and exploitation, and decision-making tools. A recent trend has been to encapsulate these in a special class of web-enabled geographic information systems called a coastal web atlas (CWA). While multiple benefits are derived from tailor-made atlases, there is great value added from the integration of disparate CWAs. CWAs linked to one another can query more successfully to optimize planning and decision-making. If a dataset is missing in one atlas, it may be immediately located in another. Similar datasets in two atlases may be combined to enhance study in either region. *But how best to achieve semantic interoperability to mitigate vague data queries, concepts or natural language semantics when retrieving and integrating data and information?* We report on the development of a new prototype seeking to interoperate between two initial CWAs: the Marine Irish Digital Atlas (MIDA) and the Oregon Coastal Atlas (OCA). These two mature atlases are used as a testbed for more regional connections, with the intent for the OCA to use lessons learned to develop a regional network of CWAs along the west coast, and for MIDA to do the same in building and strengthening atlas networks with the UK, Belgium, and other parts of Europe. Our prototype uses semantic interoperability via services harmonization and ontology mediation, allowing local atlases to use their own data structures, and vocabularies (ontologies). We use standard technologies such as OGC Web Map Services (WMS) for delivering maps, and OGC Catalogue Service for the Web (CSW) for delivering and querying ISO-19139 metadata. The metadata records of a given CWA use a given ontology of terms called local ontology. Human or machine

  4. Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

    PubMed

    Kuan, Leonard; Li, Yang; Lau, Chris; Feng, David; Bernard, Amy; Sunkin, Susan M; Zeng, Hongkui; Dang, Chinh; Hawrylycz, Michael; Ng, Lydia

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

  5. Developing a wind atlas for South Africa

    NASA Astrophysics Data System (ADS)

    Lennard, Chris; Hahman, Andrea; Prinsloo, Eric; Mabile, Eugene; Kruger, Andries

    2013-04-01

    The generation of the first verified Wind Atlas for South Africa (WASA) has been a joint undertaking between South African and Danish scientists to provide stakeholders with the best possible information about the wind climate over South Africa. The project is funded by the Royal Danish Embassy, the United Nations Development Programme, the South African Wind Energy Programme and the South African National Energy Development Institute. The project has focused on the western and southern regions of the country and includes a number of activities: 1. An observation campaign during which ten 65 metre masts were erected at selected sites with instruments at 4 levels that have recorded 2 years of data so far, this is ongoing. 2. Mesoscale and micro-scale modelling that consists of two phases. The first phase is complete and used the Karlsruhe Atmospheric Mesoscale Model (KAMM) run at 5 km with the Wind Atlas Analysis and Application Program (WAsP) to generate a wind atlas for the western and southern parts of South Africa. This is a statistical-dynamical method that assumes there is a robust relationship between meteorological situations at the large-scale and meteorological situations at the small-scale. The second phase, to be completed by the end of 2013, will develop a numerical wind atlas using the Weather Research and Forecasting model (WRF) to develop the mesoscale wind climate (4 km resolution) with a continuous 30 year integration from 1980 to 2010. This is a fully dynamical method. The WAsP model will again be used to develop the micro-scale wind climate. 3. An extreme wind climate assessment has identified extreme wind producing synoptic systems, their seasonal and spatial characteristics as well as regions in South Africa particularly prone to extreme wind conditions. 4. New wind climate assessment techniques have been developed in the production of the wind atlas and new techniques to produce the numerical wind atlas will be formulated. 5. Dissemination of

  6. Top quark physics with ATLAS and CMS

    SciTech Connect

    Onofre, A.

    2009-12-17

    The potential of the ATLAS and CMS experiments for studying top quark physics at the LHC is reviewed. The measurements of the tt-bar production cross section and spin correlations, the top quark mass, its electric charge, the structure of the W tb vertex and the measurement of the W boson helicities, the sensitivity to anomalous couplings, top quark rare decays through Flavour Changing Neutral Currents and the single top quark production are discussed. The results shown use the fall Monte Carlo simulation of ATLAS and CMS and assume a center of mass energy of 14 TeV at the LHC. Integrated luminosities in the range between B(10 bp{sup -1}) and B(10 fb{sup -1}) are considered, depending on the physics observables under study.

  7. The ATLAS TRT end-cap detectors

    NASA Astrophysics Data System (ADS)

    ATLAS TRT Collaboration; Abat, E.; Addy, T. N.; Åkesson, T. P. A.; Alison, J.; Anghinolfi, F.; Arik, E.; Arik, M.; Atoian, G.; Auerbach, B.; Baker, O. K.; Banas, E.; Baron, S.; Bault, C.; Becerici, N.; Beddall, A.; Beddall, A. J.; Bendotti, J.; Benjamin, D. P.; Bertelsen, H.; Bingul, A.; Blampey, H.; Bocci, A.; Bochenek, M.; Bondarenko, V. G.; Bychkov, V.; Callahan, J.; Capeáns Garrido, M.; Cardiel Sas, L.; Catinaccio, A.; Cetin, S. A.; Chandler, T.; Chritin, R.; Cwetanski, P.; Dam, M.; Danielsson, H.; Danilevich, E.; David, E.; Degenhardt, J.; Di Girolamo, B.; Dittus, F.; Dixon, N.; Dobos, D.; Dogan, O. B.; Dolgoshein, B. A.; Dressnandt, N.; Driouchi, C.; Ebenstein, W. L.; Eerola, P.; Egede, U.; Egorov, K.; Evans, H.; Farthouat, P.; Fedin, O. L.; Fowler, A. J.; Fratina, S.; Froidevaux, D.; Fry, A.; Gagnon, P.; Gavrilenko, I. L.; Gay, C.; Ghodbane, N.; Godlewski, J.; Goulette, M.; Gousakov, I.; Grigalashvili, N.; Grishkevich, Y.; Grognuz, J.; Hajduk, Z.; Hance, M.; Hansen, F.; Hansen, J. B.; Hansen, J. D.; Hansen, P. H.; Hare, G. A.; Harvey, A., Jr.; Hauviller, C.; High, A.; Hulsbergen, W.; Huta, W.; Issakov, V.; Istin, S.; Jain, V.; Jarlskog, G.; Jeanty, L.; Kantserov, V. A.; Kaplan, B.; Kapliy, A. S.; Katounine, S.; Kayumov, F.; Keener, P. T.; Kekelidze, G. D.; Khabarova, E.; Khristachev, A.; Kisielewski, B.; Kittelmann, T. H.; Kline, C.; Klinkby, E. B.; Klopov, N. V.; Ko, B. R.; Koffas, T.; Kondratieva, N. V.; Konovalov, S. P.; Koperny, S.; Korsmo, H.; Kovalenko, S.; Kowalski, T. Z.; Krüger, K.; Kramarenko, V.; Kudin, L. G.; LeBihan, A.-C.; LeGeyt, B. C.; Levterov, K.; Lichard, P.; Lindahl, A.; Lisan, V.; Lobastov, S.; Loginov, A.; Loh, C. W.; Lokwitz, S.; Long, M. C.; Lucas, S.; Lucotte, A.; Luehring, F.; Lundberg, B.; Mackeprang, R.; Maleev, V. P.; Manara, A.; Mandl, M.; Martin, A. J.; Martin, F. F.; Mashinistov, R.; Mayers, G. M.; McFarlane, K. W.; Mialkovski, V.; Mills, B. M.; Mindur, B.; Mitsou, V. A.; Mjörnmark, J. U.; Morozov, S. V.; Morris, E.; Mouraviev, S. V.; Muir, A. M.; Munar, A.; Nadtochi, A. V.; Nesterov, S. Y.; Newcomer, F. M.; Nikitin, N.; Novgorodova, O.; Novodvorski, E. G.; Ogren, H.; Oh, S. H.; Oleshko, S. B.; Olivito, D.; Olszowska, J.; Ostrowicz, W.; Passmore, M. S.; Patrichev, S.; Penwell, J.; Perez-Gomez, F.; Peshekhonov, V. D.; Petersen, T. C.; Petti, R.; Placci, A.; Poblaguev, A.; Pons, X.; Price, M. J.; hne, O. Rø; Reece, R. D.; Reilly, M. B.; Rembser, C.; Romaniouk, A.; Rousseau, D.; Rust, D.; Ryabov, Y. F.; Ryjov, V.; Söderberg, M.; Savenkov, A.; Saxon, J.; Scandurra, M.; Schegelsky, V. A.; Scherzer, M. I.; Schmidt, M. P.; Schmitt, C.; Sedykh, E.; Seliverstov, D. M.; Shin, T.; Shmeleva, A.; Sivoklokov, S.; Smirnov, S. Yu; Smirnova, L.; Smirnova, O.; Smith, P.; Sosnovtsev, V. V.; Sprachmann, G.; Subramania, S.; Suchkov, S. I.; Sulin, V. V.; Szczygiel, R. R.; Tartarelli, G.; Thomson, E.; Tikhomirov, V. O.; Tipton, P.; Valls Ferrer, J. A.; Van Berg, R.; Vassilakopoulos, V. I.; Vassilieva, L.; Wagner, P.; Wall, R.; Wang, C.; Whittington, D.; Williams, H. H.; Zhelezko, A.; Zhukov, K.

    2008-10-01

    The ATLAS TRT end-cap is a tracking drift chamber using 245,760 individual tubular drift tubes. It is a part of the TRT tracker which consist of the barrel and two end-caps. The TRT end-caps cover the forward and backward pseudo-rapidity region 1.0 < |η| < 2.0, while the TRT barrel central η region |η| < 1.0. The TRT system provides a combination of continuous tracking with many measurements in individual drift tubes (or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. Along with other two sub-system, namely the Pixel detector and Semi Conductor Tracker (SCT), the TRT constitutes the ATLAS Inner Detector. This paper describes the recently completed and installed TRT end-cap detectors, their design, assembly, integration and the acceptance tests applied during the construction.

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

    PubMed

    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.

  9. Distributed analysis in ATLAS

    NASA Astrophysics Data System (ADS)

    Dewhurst, A.; Legger, F.

    2015-12-01

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

  10. Combining multi-atlas segmentation with brain surface estimation

    NASA Astrophysics Data System (ADS)

    Huo, Yuankai; Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-03-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

  11. Combining Multi-atlas Segmentation with Brain Surface Estimation

    PubMed Central

    Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-01-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this “segmentation to surface to parcellation” strategy has shown limitations in various situations. In this work, we propose a novel “multi-atlas segmentation to surface” method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly

  12. Gulf of Mexico Oil and Gas Atlas Series: Play analysis of oligocene and miocene reservoirs from Texas State Offshore Waters

    SciTech Connect

    Seni, S.J.; Finley, R.J.

    1993-12-31

    The objective of the Offshore Northern Gulf of Mexico Oil and Gas Resource Atlas Series is to define hydrocarbon plays by integrating geologic and engineering data for oil and gas reservoirs with large-scale patterns of depositional basin fill and geologic age. The primary product of the program will be an oil and gas atlas set for the offshore northern Gulf of Mexico and a computerized geographical information system of geologic and engineering data linked to reservoir location. The oil and gas atlas for the Gulf of Mexico will provide a critically compiled, comprehensive reference that is needed to more efficiently develop reservoirs, to extend field limits, and to better assess the opportunities for intrafield exploration. The play atlas will provide an organizational framework to aid development in mature areas and to extend exploration paradigms from mature areas into frontier areas deep below the shelf and into deep waters of the continental slope. In addition to serving as a model for exploration and education, the offshore atlas will aid resource assessment efforts of State, Federal, and private agencies by allowing for greater precision in the extrapolation of variables within and between plays. Classification and organization of reservoirs into plays have proved to be effective in previous atlases produced by the Bureau, including the Texas oil and gas atlases, the Midcontinent gas atlas, and Central and Eastern Gulf Coast gas atlas.

  13. Installation, commissioning and operation of the tile hadron calorimeter of ATLAS

    NASA Astrophysics Data System (ADS)

    Blumenschein, Ulla

    2007-03-01

    Within the ATLAS experiment at the pp-collider LHC at CERN, the Tile Hadron Calorimeter is the first subdetector to be assembled, commissioned and operated. The calorimeter has successfully been deployed in the ATLAS cavern. The installation of the services and the routing of connections is in progress. The final certification of the front-end electronics has started, using both a temporary and the final back-end. Cosmic muons are used to test the performance and alignment of the whole calorimeter. In parallel, the integration with other ATLAS systems has started.

  14. Advanced Technology Lifecycle Analysis System (ATLAS)

    NASA Technical Reports Server (NTRS)

    O'Neil, Daniel A.; Mankins, John C.

    2004-01-01

    Developing credible mass and cost estimates for space exploration and development architectures require multidisciplinary analysis based on physics calculations, and parametric estimates derived from historical systems. Within the National Aeronautics and Space Administration (NASA), concurrent engineering environment (CEE) activities integrate discipline oriented analysis tools through a computer network and accumulate the results of a multidisciplinary analysis team via a centralized database or spreadsheet Each minute of a design and analysis study within a concurrent engineering environment is expensive due the size of the team and supporting equipment The Advanced Technology Lifecycle Analysis System (ATLAS) reduces the cost of architecture analysis by capturing the knowledge of discipline experts into system oriented spreadsheet models. A framework with a user interface presents a library of system models to an architecture analyst. The analyst selects models of launchers, in-space transportation systems, and excursion vehicles, as well as space and surface infrastructure such as propellant depots, habitats, and solar power satellites. After assembling the architecture from the selected models, the analyst can create a campaign comprised of missions spanning several years. The ATLAS controller passes analyst specified parameters to the models and data among the models. An integrator workbook calls a history based parametric analysis cost model to determine the costs. Also, the integrator estimates the flight rates, launched masses, and architecture benefits over the years of the campaign. An accumulator workbook presents the analytical results in a series of bar graphs. In no way does ATLAS compete with a CEE; instead, ATLAS complements a CEE by ensuring that the time of the experts is well spent Using ATLAS, an architecture analyst can perform technology sensitivity analysis, study many scenarios, and see the impact of design decisions. When the analyst is

  15. Comprehensive cellular‐resolution atlas of the adult human brain

    PubMed Central

    Royall, Joshua J.; Sunkin, Susan M.; Ng, Lydia; Facer, Benjamin A.C.; Lesnar, Phil; Guillozet‐Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A.; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A.; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L.; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A.; Koch, Christof; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Zielke, H. Ronald; Hohmann, John G.; Jones, Allan R.; Bernard, Amy; Hawrylycz, Michael J.; Hof, Patrick R.; Fischl, Bruce

    2016-01-01

    ABSTRACT Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

  16. Comprehensive cellular-resolution atlas of the adult human brain.

    PubMed

    Ding, Song-Lin; Royall, Joshua J; Sunkin, Susan M; Ng, Lydia; Facer, Benjamin A C; Lesnar, Phil; Guillozet-Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A; Koch, Christof; Phillips, John W; Sestan, Nenad; Wohnoutka, Paul; Zielke, H Ronald; Hohmann, John G; Jones, Allan R; Bernard, Amy; Hawrylycz, Michael J; Hof, Patrick R; Fischl, Bruce; Lein, Ed S

    2016-11-01

    Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

  17. Comprehensive cellular-resolution atlas of the adult human brain.

    PubMed

    Ding, Song-Lin; Royall, Joshua J; Sunkin, Susan M; Ng, Lydia; Facer, Benjamin A C; Lesnar, Phil; Guillozet-Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A; Koch, Christof; Phillips, John W; Sestan, Nenad; Wohnoutka, Paul; Zielke, H Ronald; Hohmann, John G; Jones, Allan R; Bernard, Amy; Hawrylycz, Michael J; Hof, Patrick R; Fischl, Bruce; Lein, Ed S

    2016-11-01

    Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  18. Data federation strategies for ATLAS using XRootD

    NASA Astrophysics Data System (ADS)

    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.

  19. The Evolution of Cloud Computing in ATLAS

    NASA Astrophysics Data System (ADS)

    Taylor, Ryan P.; Berghaus, Frank; Brasolin, Franco; Domingues Cordeiro, Cristovao Jose; Desmarais, Ron; Field, Laurence; Gable, Ian; Giordano, Domenico; Di Girolamo, Alessandro; Hover, John; LeBlanc, Matthew; Love, Peter; Paterson, Michael; Sobie, Randall; Zaytsev, Alexandr

    2015-12-01

    The ATLAS experiment at the LHC has successfully incorporated cloud computing technology and cloud resources into its primarily grid-based model of distributed computing. Cloud R&D activities continue to mature and transition into stable production systems, while ongoing evolutionary changes are still needed to adapt and refine the approaches used, in response to changes in prevailing cloud technology. In addition, completely new developments are needed to handle emerging requirements. This paper describes the overall evolution of cloud computing in ATLAS. The current status of the virtual machine (VM) management systems used for harnessing Infrastructure as a Service resources are discussed. Monitoring and accounting systems tailored for clouds are needed to complete the integration of cloud resources within ATLAS' distributed computing framework. We are developing and deploying new solutions to address the challenge of operation in a geographically distributed multi-cloud scenario, including a system for managing VM images across multiple clouds, a system for dynamic location-based discovery of caching proxy servers, and the usage of a data federation to unify the worldwide grid of storage elements into a single namespace and access point. The usage of the experiment's high level trigger farm for Monte Carlo production, in a specialized cloud environment, is presented. Finally, we evaluate and compare the performance of commercial clouds using several benchmarks.

  20. Analysis Preservation in ATLAS

    NASA Astrophysics Data System (ADS)

    Cranmer, Kyle; Heinrich, Lukas; Jones, Roger; South, David M.

    2015-12-01

    Long before data taking, ATLAS established a policy that all analyses need to be preserved. In the initial data-taking period, this has been achieved by various tools and techniques. ATLAS is now reviewing the analysis preservation with the aim of bringing coherence and robustness to the process and with a clearer view of the level of reproducibility that is reasonably achievable. The secondary aim is to reduce the load on the analysts. Once complete, this will serve for our internal preservation needs but also provide a basis for any subsequent sharing of analysis results with external parties.

  1. The Herschel ATLAS

    NASA Technical Reports Server (NTRS)

    Eales, S.; Dunne, L.; Clements, D.; Cooray, A.; De Zotti, G.; Dye, S.; Ivison, R.; Jarvis, M.; Lagache, G.; Maddox, S.; Negrello, M.; Serjeant, S.; Thompson, M. A.; Van Kampen, E.; Amblard, A.; Andreani, P.; Baes, M.; Beelen, A.; Bendo, G. J.; Bertoldi, F.; Benford, D.; Bock, J.

    2010-01-01

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

  2. Chesapeake Bay Basin Monitoring Program Atlas. Volume 1. Water quality and other physiochemical monitoring programs

    SciTech Connect

    Heasly, P.; Pultz, S.; Batiuk, R.

    1989-08-01

    The Monitoring Program Atlas provides an overview of current long-term environmental monitoring programs in the Chesapeake Bay Basin. The Atlas covers a wide scope of program types, ranging from water quality, living resources, toxics, and physical processes to air quality, acid deposition and climate monitoring programs. The two-volume publication is intended to facilitate coordination and integration of environmental monitoring programs and to encourage the collection of comparable monitoring data basinwide.

  3. Chesapeake Bay Basin Monitoring Program Atlas. Volume 2. Biological and living resource monitoring programs

    SciTech Connect

    Heasly, P.; Pultz, S.; Batiuk, R.

    1989-08-01

    The Monitoring Program Atlas provides an overview of current long-term environmental monitoring programs in the Chesapeake Bay Basin. The Atlas covers a wide scope of program types, ranging from water quality, living resources, toxics, and physical processes to air quality, acid deposition and climate monitoring programs. The two-volume publication is intended to facilitate coordination and integration of environmental monitoring programs and to encourage the collection of comparable monitoring data basinwide.

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

    PubMed Central

    2010-01-01

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

  5. CMOS front end electronics for the ATLAS muon detector

    SciTech Connect

    Huth, J.; Oliver, J.; Hazen, E.; Shank, J.

    1997-12-31

    An all-CMOS design for an integrated ASD (Amplifier-Shaper-Discriminator) chip for readout of the ATLAS Monitored Drift Tubes (MDTs) is presented. Eight channels of charge-sensitive preamp, two-stage pole/zero shaper, Wilkinson ADC and discriminator with programmable hysteresis are integrated on a single IC. Key elements have been prototyped in 1.2 and 0.5 micron CMOS operating at 5V and 3.3V respectively.

  6. Non-local statistical label fusion for multi-atlas segmentation

    PubMed Central

    Asman, Andrew J.; Landman, Bennett A.

    2012-01-01

    Multi-atlas segmentation provides a general purpose, fully-automated approach for transferring spatial information from an existing dataset (“atlases”) to a previously unseen context (“target”) through image registration. The method to resolve voxelwise label conflicts between the registered atlases (“label fusion”) has a substantial impact on segmentation quality. Ideally, statistical fusion algorithms (e.g., STAPLE) would result in accurate segmentations as they provide a framework to elegantly integrate models of rater performance. The accuracy of statistical fusion hinges upon accurately modeling the underlying process of how raters err. Despite success on human raters, current approaches inaccurately model multi-atlas behavior as they fail to seamlessly incorporate exogenous intensity information into the estimation process. As a result, locally weighted voting algorithms represent the de facto standard fusion approach in clinical applications. Moreover, regardless of the approach, fusion algorithms are generally dependent upon large atlas sets and highly accurate registration as they implicitly assume that the registered atlases form a collectively unbiased representation of the target. Herein, we propose a novel statistical fusion algorithm, Non-Local STAPLE (NLS). NLS reformulates the STAPLE framework from a non-local means perspective in order to learn what label an atlas would have observed, given perfect correspondence. Through this reformulation, NLS (1) seamlessly integrates intensity into the estimation process, (2) provides a theoretically consistent model of multi-atlas observation error, and (3) largely diminishes the need for large atlas sets and very high-quality registrations. We assess the sensitivity and optimality of the approach and demonstrate significant improvement in two empirical multi-atlas experiments. PMID:23265798

  7. High-Performance Scalable Information Service for the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    Kolos, S.; Boutsioukis, G.; Hauser, R.

    2012-12-01

    The ATLAS[1] experiment is operated by a highly distributed computing system which is constantly producing a lot of status information which is used to monitor the experiment operational conditions as well as to assess the quality of the physics data being taken. For example the ATLAS High Level Trigger(HLT) algorithms are executed on the online computing farm consisting from about 1500 nodes. Each HLT algorithm is producing few thousands histograms, which have to be integrated over the whole farm and carefully analyzed in order to properly tune the event rejection. In order to handle such non-physics data the Information Service (IS) facility has been developed in the scope of the ATLAS Trigger and Data Acquisition (TDAQ)[2] project. The IS provides a high-performance scalable solution for information exchange in distributed environment. In the course of an ATLAS data taking session the IS handles about a hundred gigabytes of information which is being constantly updated with the update interval varying from a second to a few tens of seconds. IS provides access to any information item on request as well as distributing notification to all the information subscribers. In the latter case IS subscribers receive information within a few milliseconds after it was updated. IS can handle arbitrary types of information, including histograms produced by the HLT applications, and provides C++, Java and Python API. The Information Service is a unique source of information for the majority of the online monitoring analysis and GUI applications used to control and monitor the ATLAS experiment. Information Service provides streaming functionality allowing efficient replication of all or part of the managed information. This functionality is used to duplicate the subset of the ATLAS monitoring data to the CERN public network with a latency of a few milliseconds, allowing efficient real-time monitoring of the data taking from outside the protected ATLAS network. Each information

  8. Interoperable atlases of the human brain.

    PubMed

    Amunts, K; Hawrylycz, M J; Van Essen, D C; Van Horn, J D; Harel, N; Poline, J-B; De Martino, F; Bjaalie, J G; Dehaene-Lambertz, G; Dehaene, S; Valdes-Sosa, P; Thirion, B; Zilles, K; Hill, S L; Abrams, M B; Tass, P A; Vanduffel, W; Evans, A C; Eickhoff, S B

    2014-10-01

    The last two decades have seen an unprecedented development of human brain mapping approaches at various spatial and temporal scales. Together, these have provided a large fundus of information on many different aspects of the human brain including micro- and macrostructural segregation, regional specialization of function, connectivity, and temporal dynamics. Atlases are central in order to integrate such diverse information in a topographically meaningful way. It is noteworthy, that the brain mapping field has been developed along several major lines such as structure vs. function, postmortem vs. in vivo, individual features of the brain vs. population-based aspects, or slow vs. fast dynamics. In order to understand human brain organization, however, it seems inevitable that these different lines are integrated and combined into a multimodal human brain model. To this aim, we held a workshop to determine the constraints of a multi-modal human brain model that are needed to enable (i) an integration of different spatial and temporal scales and data modalities into a common reference system, and (ii) efficient data exchange and analysis. As detailed in this report, to arrive at fully interoperable atlases of the human brain will still require much work at the frontiers of data acquisition, analysis, and representation. Among them, the latter may provide the most challenging task, in particular when it comes to representing features of vastly different scales of space, time and abstraction. The potential benefits of such endeavor, however, clearly outweigh the problems, as only such kind of multi-modal human brain atlas may provide a starting point from which the complex relationships between structure, function, and connectivity may be explored.

  9. Big Sky Carbon Atlas

    DOE Data Explorer

    The Big Sky Carbon Atlas is an online geoportal designed for you to discover, interpret, and access geospatial data and maps relevant to decision support and education on carbon sequestration in the Big Sky Region. In serving as the public face of the Partnership's spatial Data Libraries, the Atlas provides a gateway to geographic information characterizing CO2 sources, potential geologic sinks, terrestrial carbon fluxes, civil and energy infrastructure, energy use, and related themes. In addition to directly serving the BSCSP and its stakeholders, the Atlas feeds regional data to the NatCarb Portal, contributing to a national perspective on carbon sequestration. Established components of the Atlas include a gallery of thematic maps and an interactive map that allows you to: • Navigate and explore regional characterization data through a user-friendly interface • Print your map views or publish them as PDFs • Identify technical references relevant to specific areas of interest • Calculate straight-line or pipeline-constrained distances from point sources of CO2 to potential geologic sink features • Download regional data layers (feature under development) (Acknowledgment to the Big Sky Carbon Sequestration Partnership (BSCSP); see home page at http://www.bigskyco2.org/)

  10. An Icelandic wind atlas

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  11. Atlas of NATO.

    ERIC Educational Resources Information Center

    Young, Harry F.

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

  12. A Volume of Interest (VOI) Atlas for the Analysis of Neurophysiological Image Data

    NASA Astrophysics Data System (ADS)

    Marrett, Sean; Evans, Alan C.; Collins, D. L.; Peters, Terence M.

    1989-05-01

    Accurate and precise neuroanatomical descriptions are essential for the meaningful quantification of Positron Emission Tomographic (PET) images of the human brain. This task is difficult since the radio-tracer distribution imaged by PET does not neccessarily reflect structure. A two-dimensional brain atlas that features the use of a deformable Region-of-Interest (ROI) template has previously been shown to be an effective method for integrating anatomical (Magnetic Resonance Imaging - MRI) images and physiological (PET) data, with an observed reduction in the coefficient of variation amongst observers from 8.1% to 3.4% 1. This method has been adopted for routine MRI image correlation and PET image analysis at our centre. The atlas is most effective when used in studies in which PET and MRI images are acquired in planes parallel to those of the original brain atlas. To allow arbitrary image/atlas orientation, we have implemented a Volume of Interest (VOI) atlas that extends the ROI methodology to three dimensions. The major advantage is that, given adequate axial sampling, arbitrary orientations of PET and MRI scans can be matched to the VOI atlas with no loss in structural recovery. In addition, the VOI atlas can be employed in the quantification of metabolic parameters directly from volumetric PET studies rather than performing the analysis on a slice by slice basis.

  13. Fusion set selection with surrogate metric in multi-atlas based image segmentation

    NASA Astrophysics Data System (ADS)

    Zhao, Tingting; Ruan, Dan

    2016-02-01

    Multi-atlas based image segmentation sees unprecedented opportunities but also demanding challenges in the big data era. Relevant atlas selection before label fusion plays a crucial role in reducing potential performance loss from heterogeneous data quality and high computation cost from extensive data. This paper starts with investigating the image similarity metric (termed ‘surrogate’), an alternative to the inaccessible geometric agreement metric (termed ‘oracle’) in atlas relevance assessment, and probes into the problem of how to select the ‘most-relevant’ atlases and how many such atlases to incorporate. We propose an inference model to relate the surrogates and the oracle geometric agreement metrics. Based on this model, we quantify the behavior of the surrogates in mimicking oracle metrics for atlas relevance ordering. Finally, analytical insights on the choice of fusion set size are presented from a probabilistic perspective, with the integrated goal of including the most relevant atlases and excluding the irrelevant ones. Empirical evidence and performance assessment are provided based on prostate and corpus callosum segmentation.

  14. SUSY Search Strategies at Atlas and CMS

    SciTech Connect

    Autermann, Christian

    2008-11-23

    Supersymmetry is regarded as the most promising candidate for physics beyond the Standard Model. Various search strategies for SUSY are conducted at the Atlas and CMS experiments. In the early data inclusive searches, with different lepton multiplicities, are most sensitive and will be discussed here. The reach of both experiments is interpreted within the mSUGRA model.The LHC has started operation and the experiments are expected to collect of the order of 100 pb{sup -1} integrated luminosity within the first year.

  15. A probabilistic atlas of the cerebellar white matter.

    PubMed

    van Baarsen, K M; Kleinnijenhuis, M; Jbabdi, S; Sotiropoulos, S N; Grotenhuis, J A; van Cappellen van Walsum, A M

    2016-01-01

    Imaging of the cerebellar cortex, deep cerebellar nuclei and their connectivity are gaining attraction, due to the important role the cerebellum plays in cognition and motor control. Atlases of the cerebellar cortex and nuclei are used to locate regions of interest in clinical and neuroscience studies. However, the white matter that connects these relay stations is of at least similar functional importance. Damage to these cerebellar white matter tracts may lead to serious language, cognitive and emotional disturbances, although the pathophysiological mechanism behind it is still debated. Differences in white matter integrity between patients and controls might shed light on structure-function correlations. A probabilistic parcellation atlas of the cerebellar white matter would help these studies by facilitating automatic segmentation of the cerebellar peduncles, the localization of lesions and the comparison of white matter integrity between patients and controls. In this work a digital three-dimensional probabilistic atlas of the cerebellar white matter is presented, based on high quality 3T, 1.25mm resolution diffusion MRI data from 90 subjects participating in the Human Connectome Project. The white matter tracts were estimated using probabilistic tractography. Results over 90 subjects were symmetrical and trajectories of superior, middle and inferior cerebellar peduncles resembled the anatomy as known from anatomical studies. This atlas will contribute to a better understanding of cerebellar white matter architecture. It may eventually aid in defining structure-function correlations in patients with cerebellar disorders.

  16. Development of a numerical wind atlas for South Africa

    NASA Astrophysics Data System (ADS)

    Lennard, Chris; Hahman, Andrea

    2015-04-01

    A Numerical Wind Atlas for South Africa (WASA) is being developed through collaborative efforts between the Climate Systems Analysis Group (UCT), the Council for Scientific and Industrial Research, the South African Weather Service and the Danish Technical University. The method is based on a state-of-the-art approach that includes an observations campaign, both statistical and dynamical mesoscale modelling as well as microscale and extreme wind modelling. One unique feature of the project lies in the application of a dynamical mesoscale model (WRF) for the generation of a dynamical wind atlas in addition to the more conventional statistical-dynamical KAMM-WAsP atlas. We verify the two atlases against an observational wind atlas generated from 10 measurement masts with two years of data observation data and find the KAMM-WAsP method underestimates the generalized mean wind speeds at the sites (mean bias of -8.2% and mean absolute bias of 9.3%). The WRF model was run at 3km over the region of interest in an 8-year integration. In the WRF-based method there is, on average, a difference of 4.7% (either positive or negative) between the WRF-based NWA results and the corresponding observed values. The combined average across all the sites is an over-estimate of 2.5%. The method captures dynamical processes like the land-sea thermal gradient on the west coast of the country and also resolves topographic and topographically enhances flows such as valley breezes that the KAMM-WAsP method cannot. Although within the WRF results there are uncertainties to be considered e.g. the forcing reanalysis, WRF configuration, representativeness of the 8-year period and the generalization method, the results suggest that the dynamical wind atlas presents a more realistic picture of potential wind energy resource.

  17. Atlas Basemaps in Web 2.0 Epoch

    NASA Astrophysics Data System (ADS)

    Chabaniuk, V.; Dyshlyk, O.

    2016-06-01

    The authors have analyzed their experience of the production of various Electronic Atlases (EA) and Atlas Information Systems (AtIS) of so-called "classical type". These EA/AtIS have been implemented in the past decade in the Web 1.0 architecture (e.g., National Atlas of Ukraine, Atlas of radioactive contamination of Ukraine, and others). One of the main distinguishing features of these atlases was their static nature - the end user could not change the content of EA/AtIS. Base maps are very important element of any EA/AtIS. In classical type EA/AtIS they were static datasets, which consisted of two parts: the topographic data of a fixed scale and data of the administrative-territorial division of Ukraine. It is important to note that the technique of topographic data production was based on the use of direct channels of topographic entity observation (such as aerial photography) for the selected scale. Changes in the information technology of the past half-decade are characterized by the advent of the "Web 2.0 epoch". Due to this, in cartography appeared such phenomena as, for example, "neo-cartography" and various mapping platforms like OpenStreetMap. These changes have forced developers of EA/AtIS to use new atlas basemaps. Our approach is described in the article. The phenomenon of neo-cartography and/or Web 2.0 cartography are analysed by authors using previously developed Conceptual framework of EA/AtIS. This framework logically explains the cartographic phenomena relations of three formations: Web 1.0, Web 1.0x1.0 and Web 2.0. Atlas basemaps of the Web 2.0 epoch are integrated information systems. We use several ways to integrate separate atlas basemaps into the information system - by building: weak integrated information system, structured system and meta-system. This integrated information system consists of several basemaps and falls under the definition of "big data". In real projects it is already used the basemaps of three strata: Conceptual

  18. Improving atlas methodology

    USGS Publications Warehouse

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

    1987-01-01

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

  19. A Unified Framework for Cross-modality Multi-atlas Segmentation of Brain MRI

    PubMed Central

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Leemput, Koen Van

    2013-01-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion. PMID:24001931

  20. MARS: a mouse atlas registration system based on a planar x-ray projector and an optical camera

    NASA Astrophysics Data System (ADS)

    Wang, Hongkai; Stout, David B.; Taschereau, Richard; Gu, Zheng; Vu, Nam T.; Prout, David L.; Chatziioannou, Arion F.

    2012-10-01

    This paper introduces a mouse atlas registration system (MARS), composed of a stationary top-view x-ray projector and a side-view optical camera, coupled to a mouse atlas registration algorithm. This system uses the x-ray and optical images to guide a fully automatic co-registration of a mouse atlas with each subject, in order to provide anatomical reference for small animal molecular imaging systems such as positron emission tomography (PET). To facilitate the registration, a statistical atlas that accounts for inter-subject anatomical variations was constructed based on 83 organ-labeled mouse micro-computed tomography (CT) images. The statistical shape model and conditional Gaussian model techniques were used to register the atlas with the x-ray image and optical photo. The accuracy of the atlas registration was evaluated by comparing the registered atlas with the organ-labeled micro-CT images of the test subjects. The results showed excellent registration accuracy of the whole-body region, and good accuracy for the brain, liver, heart, lungs and kidneys. In its implementation, the MARS was integrated with a preclinical PET scanner to deliver combined PET/MARS imaging, and to facilitate atlas-assisted analysis of the preclinical PET images.

  1. Fast and accurate computation of system matrix for area integral model-based algebraic reconstruction technique

    NASA Astrophysics Data System (ADS)

    Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua

    2014-11-01

    Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.

  2. Three-dimensional atlas of iron, copper, and zinc in the mouse cerebrum and brainstem.

    PubMed

    Hare, Dominic J; Lee, Jason K; Beavis, Alison D; van Gramberg, Amanda; George, Jessica; Adlard, Paul A; Finkelstein, David I; Doble, Philip A

    2012-05-01

    Atlases depicting molecular and functional features of the brain are becoming an integral part of modern neuroscience. In this study we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantitatively measure iron (Fe), copper (Cu), and zinc (Zn) levels in a serially sectioned C57BL/6 mouse brain (cerebrum and brainstem). Forty-six sections were analyzed in a single experiment of approximately 158 h in duration. We constructed a 46-plate reference atlas by aligning quantified images of metal distribution with corresponding coronal sections from the Allen Mouse Brain Reference Atlas. The 46 plates were also used to construct three-dimensional models of Fe, Cu, and Zn distribution. This atlas represents the first reconstruction of quantitative trace metal distribution through the brain by LA-ICPMS and will facilitate the study of trace metals in the brain and help to elucidate their role in neurobiology.

  3. Mercury-Atlas Test Launch

    NASA Technical Reports Server (NTRS)

    1961-01-01

    A NASA Project Mercury spacecraft was test launched at 11:15 AM EST on April 25, 1961 from Cape Canaveral, Florida, in a test designed to qualify the Mercury Spacecraft and all systems, which must function during orbit and reentry from orbit. The Mercury-Atlas vehicle was destroyed by Range Safety Officer about 40 seconds after liftoff. The spacecraft was recovered and appeared to be in good condition. Atlas was designed to launch payloads into low Earth orbit, geosynchronous transfer orbit or geosynchronous orbit. NASA first launched Atlas as a space launch vehicle in 1958. Project SCORE, the first communications satellite that transmitted President Eisenhower's pre-recorded Christmas speech around the world, was launched on an Atlas. For all three robotic lunar exploration programs, Atlas was used. Atlas/ Centaur vehicles launched both Mariner and Pioneer planetary probes. The current operational Atlas II family has a 100% mission success rating. For more information about Atlas, please see Chapter 2 in Roger Launius and Dennis Jenkins' book To Reach the High Frontier published by The University Press of Kentucky in 2002.

  4. Assessment Atlas, 1982-83.

    ERIC Educational Resources Information Center

    Yosemite Community Coll. District, Modesto, CA.

    Designed to provide information of value in establishing a base for decisionmaking in the Yosemite Community College District (YCCD), this assessment atlas graphically presents statistical data on the District as a whole, its two campuses, and YCCD Central Services for 1982-83. After an introduction to the use of the assessment atlas and…

  5. Assessment Atlas, 1983-84.

    ERIC Educational Resources Information Center

    Yosemite Community Coll. District, Modesto, CA.

    Designed to provide information of value in establishing a base for decision making in the Yosemite Community College District (YCCD), this assessment atlas graphically presents statistical data for the District as a whole, its two campuses, and YCCD Central Services for 1983-84. After an introduction to the use of the assessment atlas and…

  6. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  7. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  8. ATLAS-1 Logo

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The primary payload for the Space Shuttle mission STS-45, launched March 24, 1992, was the Atmospheric Laboratory for Applications and Science-1 (ATLAS-1)which was mounted on nondeployable Spacelab pallets in the orbiter cargo bay. Eight countries, th U.S., France, Germany, Belgium, United Kingdom, Switzerland, The Netherlands, and Japan, provided 12 instruments designed to perform 14 investigations in four fields. Atmospheric science instruments/investigations: Atmospheric Lyman-Alpha Emissions (ALAE); Atmospheric Trace Molecule Spectroscopy (ATMOS); Grille Spectrometer (GRILLE); Imaging Spectrometric Observatory (ISO); Millimeter-Wave Atmospheric Sounder (MAS). Solar Science: Active Cavity Radiometer Irradiance Monitor (ACRIM); Measurement of the Solar Constant (SOLCON); Solar Spectrum from 180 to 3,200 Nanometers (SOLSPEC); Solar Ultraviolet Spectral Irradiance Monitor (SUSIM). Space Plasma Physics: Atmospheric Emissions Photometric Imaging (AEPI); Space Experiments with Particle Accelerators (SEPAC). Ultraviolet astronomy: Far Ultraviolet Space Telescope (FAUST). This is the logo or emblem that was designed to represent the ATLAS-1 payload.

  9. Preparation of Northern Mid-Continent Petroleum Atlas

    SciTech Connect

    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 data base will be demonstrated as the program covers more geographic territory and the data base 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 data bases 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 free-standing 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

  10. ATLAS V, Launch System for the Next Millenium

    NASA Astrophysics Data System (ADS)

    Sowers, George

    2002-01-01

    The premise behind the Atlas V launch system family is to provide a single system that can accommodate medium-lift to heavy-lift payloads. Lockheed Martin invested significant resources to develop the Atlas V launch vehicle featuring--a Common Core Booster using the RD-180 engine, an advanced solid rocket booster strap-on, advanced fault-tolerant avionics, the Common Element Centaur, and two payload fairings (PLF) sizes--an aluminum 4 meter and a composite 5 meter. With this "mix-and-match" approach, Lockheed Martin can accommodate payloads ranging from 10,900-19,000 lbm to geosynchronous transfer orbit (GTO) and up to 29,000 lbm to low-Earth orbit (LEO) in a single booster configuration. For heavy-lift missions (> 41,000 lbm to geosynchronous orbit), Lockheed Martin has designed a three-body configuration system to place satellites directly into their final orbit. Reliability, producibility, and operability were optimized for this new family while using heritage, flight- proven hardware wherever practical (booster engine, Centaur, payload adapters, payload fairings). With this approach, Lockheed Martin is able to offer a new family of vehicles, with minimum development risk and cost. It is also possible to reduce recurring cost without sacrificing Mission Success accomplishment due to the economies of scale of producing the system and the advanced use of automation during manufacturing and pre-launch processing. Atlas V development, while mainly funded by Lockheed Martin, also received a significant (500M) investment from the USAF under the EELV program. This investment ensures that USAF requirements are an integral part of the Atlas V system, such as standard payload interfaces, and a bracket of USAF and DoD payload performance needs. Lockheed Martin demonstrated the validity of this evolutionary approach on May 24, 2000, when its Atlas III vehicle, AC-201, performed flawlessly placing the EUTELSAT W4 satellite into final orbit. 80% of the Atlas V subsystems were

  11. Preparation of Northern Mid-Continent Petroleum Atlas

    SciTech Connect

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

    1997-12-01

    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 data base will be demonstrated as the program covers more geographic territory and the data base 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 data bases 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 free-standing 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

  12. Chandra Galaxy Atlas

    NASA Astrophysics Data System (ADS)

    Kim, Dong-Woo; Anderson, Craig; Burke, Doug; Fabbiano, Giuseppina; Fruscione, Antonella; Lauer, Jennifer L.; McCollough, Michael L.; Morgan, Doug; Mossman, Amy; O'Sullivan, Ewan; Paggi, Alessandro; Trinchieri, Ginevra

    2016-01-01

    We present the new results from the Chandra Galaxy Atlas prpject. We have systematically analyzed the archival Chandra data of 50 early type galaxies to study their hot ISM. Taking full advantage of the Chandra capabilities, we produced spatially resolved data products with additional spectral information. We will make these products publicly available and use them for our focused science goals, e.g., gas morphology, scaling relation, X-ray based mass profile, circum-nuclear gas.

  13. Topographical atlas sheets

    USGS Publications Warehouse

    Wheeler, George Montague

    1876-01-01

    The following topographical atlas sheets, accompanying Appendix J.J. of the Annual Report of the Chief of Engineers, U.S. Army-being Annual Report upon U. S. Geographical Surveys-have been published during the fiscal year ending June 30, 1876, and are a portion of the series projected to embrace the territory of the United States lying west of the 100th meridian.

  14. ATLAS reliability analysis

    SciTech Connect

    Bartsch, R.R.

    1995-09-01

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

  15. The LUCID detector ATLAS luminosity monitor and its electronic system

    NASA Astrophysics Data System (ADS)

    Manghi, F. Lasagni

    2016-07-01

    In 2015 LHC is starting a new run, at higher center of mass energy (13 TeV) and with 25 ns bunch-spacing. The ATLAS luminosity monitor LUCID has been completely rebuilt, both the detector and the electronics, in order to cope with the new running conditions. The new detector electronics features a new read-out board (LUCROD) for signal acquisition and digitization, PMT-charge integration and single-side luminosity measurements, and a revisited LUMAT board for combination of signals from the two detectors. This note describes the new board design, the firmware and software developments, the implementation of luminosity algorithms, the optical communication between boards and the integration into the ATLAS TDAQ system.

  16. An anatomic gene expression atlas of the adult mouse brain.

    PubMed

    Ng, Lydia; Bernard, Amy; Lau, Chris; Overly, Caroline C; Dong, Hong-Wei; Kuan, Chihchau; Pathak, Sayan; Sunkin, Susan M; Dang, Chinh; Bohland, Jason W; Bokil, Hemant; Mitra, Partha P; Puelles, Luis; Hohmann, John; Anderson, David J; Lein, Ed S; Jones, Allan R; Hawrylycz, Michael

    2009-03-01

    Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three-dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea). PMID:19219037

  17. ATLAS: Forecasting Falling Rocks

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  18. A structural-functional MRI-based disease atlas: application to computer-aided-diagnosis of prostate cancer

    NASA Astrophysics Data System (ADS)

    Xiao, G.; Bloch, B.; Chappelow, J.; Genega, E.; Rofsky, N.; Lenkinski, R.; Madabhushi, A.

    2010-03-01

    Different imaging modalities or protocols of a single patient may convey different types of information regarding a disease for the same anatomical organ/tissue. On the other hand, multi-modal/multi-protocol medical images from several different patients can also provide spatial statistics of the disease occurrence, which in turn can greatly aid in disease diagnosis and aid in improved, accurate biopsy and targeted treatment. It is therefore important to not only integrate medical images from multiple patients into a common coordinate frame (in the form of a population-based atlas), but also find the correlation between these multi-modal/multi-protocol data features and the disease spatial distribution in order to identify different quantitative structural and functional disease signatures. Most previous work on construction of anatomical atlases has focused on deriving a population-based atlas for the purpose of deriving the spatial statistics. Moreover, these models are typically derived from normal or healthy subjects, either explicitly or implicitly, where it is assumed that the inter-patient pathological variation is not large. These methods are not suitable for constructing a disease atlas, where significant differences between patients on account of disease related variations can be expected. In this paper, we present a novel framework for the construction of a multi-parametric MRI-based data-driven disease atlas consisting of multi-modal and multi-protocol data from across multiple patient studies. Our disease atlas contains 3 Tesla structural (T2) and functional (dynamic contrast enhanced (DCE)) prostate in vivo MRI with corresponding whole mount histology specimens obtained via radical prostatectomy. Our atlas construction framework comprises 3 distinct modules: (a) determination of disease spatial extent on the multi-protocol MR imagery for each patient, (b) construction of a multi-protocol MR imaging spatial atlas which captures the geographical

  19. The human brain in 1700 pieces: design and development of a three-dimensional, interactive and reference atlas.

    PubMed

    Nowinski, W L; Chua, B C; Qian, G Y; Nowinska, N G

    2012-02-15

    As the human brain is the most complex living organ, constructing its detailed model with exploration capabilities in a form of an atlas is a challenge. Our overall goal is to construct an advanced, detailed, parcellated, labeled, accurate, interactive, three-dimensional (3D), and scalable whole human brain atlas of structure, vasculature, tracts and systems. The objectives of this work are three-fold; to present: (1) method of atlas design and development including design principles, accuracy requirements, atlas content, architecture, functionality, user interface, and customized tools; (2) creation of an atlas of structure and systems including its modeling method and validation; and (3) integration of this atlas with the cerebrovasculature and tracts created earlier. The atlas is created from multiple in vivo 3/7 T scans. Its design based on "pyramidal principle" enables scalability while preserving design principles and exploits interaction paradigm "from blocks to brain". The atlas contains (1) navigator with modules for system/object/object state management, interaction, user interfacing, and rendering; and (2) brain model with cerebrum, cerebellum, brainstem, spinal cord, white matter, deep structures, systems, ventricles, arteries, veins, sinuses, and tracts. The brain model is parcellated, labeled, consistent, realistic, of high resolution, polygonal/volumetric, dissectible, extendable, and deformable. It has over 1700 3D components. The atlas has sub-voxel accuracy of 0.1mm and the smallest vessels of 80 μm. Brain exploration includes dynamic scene composition, manipulation-independent 3D labeling, interaction combined with animation, meta-labeling, and quantification. This atlas is useful in education, research, and clinical applications. It can potentially be foundation for a multi-level molecular-cellular-anatomical-physiological-behavioral platform. PMID:22062451

  20. SUSY searches at the LHC with the ATLAS experiment

    ScienceCinema

    None

    2016-07-12

    First ATLAS searches for signals of Supersymmetry in proton-proton collisions at the LHC are presented. These searches are performed in various channels containing different lepton and jet multiplicities in the final states; the full data sample recorded in the 2010 LHC run, corresponding to an integrated luminosity of 35 pb-1, has been analysed. Limits on squarks and gluins are the most stringent to date.

  1. Search for the neutral MSSM Higgs bosons with ATLAS

    SciTech Connect

    Schaarschmidt, Jana

    2008-11-23

    The discovery of a neutral Higgs boson with large branching fractions into tau or muon pair final states would be a strong evidence of New Physics beyond the Standard Model. The discovery potential of these processes with the ATLAS detector at the Large Hadron Collider for integrated luminosities of 10 fb{sup -1} and 30 fb{sup -1} is presented. The studies are based on the analysis of fully simulated Monte Carlo samples.

  2. ATLAS 1: Encountering Planet Earth

    NASA Technical Reports Server (NTRS)

    Shea, Charlotte; Mcmahan, Tracy; Accardi, Denise; Tygielski, Michele; Mikatarian, Jeff; Wiginton, Margaret (Editor)

    1984-01-01

    Several NASA science programs examine the dynamic balance of sunlight, atmosphere, water, land, and life that governs Earth's environment. Among these is a series of Space Shuttle-Spacelab missions, named the Atmospheric Laboratory for Applications and Science (ATLAS). During the ATLAS missions, international teams of scientists representing many disciplines combine their expertise to seek answers to complex questions about the atmospheric and solar conditions that sustain life on Earth. The ATLAS program specifically investigates how Earth's middle atmosphere and upper atmospheres and climate are affected by both the Sun and by products of industrial and agricultural activities on Earth.

  3. Automated Loads Analysis System (ATLAS)

    NASA Technical Reports Server (NTRS)

    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.

  4. Methodology of Lithuanian climate atlas mapping

    NASA Astrophysics Data System (ADS)

    Valiukas, Donatas; Galvonaitė, Audronė; Česnulevičius, Algimantas

    2015-06-01

    Climate atlases summarize large sets of quantitative and qualitative data and are results of complex analytical cartographic work. These special geographical publications summarize long term meteorological observations, provide maps and figures which characterise different climate elements. Visual information is supplemented with explanatory texts. A lot of information on short and long term changes of climate elements were provided in published Lithuanian atlases (Atlas of Lithuanian SDR, 1981; Climate Atlas of Lithuania, 2013), as well as in prepared but unpublished Lithuanian Atlas (1989) and in upcoming new national atlas publications (National Atlas of Lithuania. 1st part, 2014). Climate atlases has to be constantly updated to be relevant and to describe current climate conditions. Comprehensive indicators of Lithuanian climate are provided in different cartographic publications. Different time periods, various data sets and diverse cartographic data analysis tools and visualisation methods were used in these different publications.

  5. BioFuels Atlas (Presentation)

    SciTech Connect

    Moriarty, K.

    2011-02-01

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

  6. Ceres' sunlight atlas

    NASA Astrophysics Data System (ADS)

    Molaro, P.; Centurión, M.

    2011-01-01

    Context. Astronomical research dealing with accurate radial velocity measurements need reliable astronomical standards to calibrate the spectrographs and to assess possible systematics. Stellar radial velocity standards offer a reference at the level of a few hundred m s-1 and are not adequate for most present needs. Aims: We aim to show that sunlight reflected by asteroids is a fairly accessible way to record a high-resolution solar spectrum from the whole disk, which can therefore be used as a radial velocity standard and can improve the uncertainties of solar line positions. Methods: We used solar light reflected by the asteroid Ceres observed with HARPS to measure solar lines' wavelengths. Results: We provide a new solar atlas with 491 line wavelengths in the range 540-690 nm and 222 lines in the range 400-410 nm obtained from reflected solar spectrum of Ceres. These measurements are consistent with those of Allende Prieto & Garcia Lopez (1998b) based on FTS solar atlases but with a factor 3 higher precision. Conclusions: This atlas provides a benchmark for wavelength calibration to check radial velocity accuracy down to 44 m s-1 locally and a few m s-1 globally. The asteroid-based technique could provide a new way to track radial velocity shifts with solar activity cycle, as well as to derive convective shifts suitable for comparison with theoretical atmospheric models. It could also be used to study radial velocity deviations in spectrographs such as those recently detected in HIRES and UVES. Dedicated HARPS observations of other asteroids could improve present results substantially and these investigations have been solicited. Full Table 2 is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/525/A74

  7. Application of statistical cancer atlas for 3D biopsy

    NASA Astrophysics Data System (ADS)

    Narayanan, Ramkrishnan; Shen, Dinggang; Davatzikos, Christos; Crawford, E. David; Barqawi, Albaha; Werahera, Priya; Kumar, Dinesh; Suri, Jasjit S.

    2008-02-01

    Prostate cancer is the most commonly diagnosed cancer in males in the United States and the second leading cause of cancer death. While the exact cause is still under investigation, researchers agree on certain risk factors like age, family history, dietary habits, lifestyle and race. It is also widely accepted that cancer distribution within the prostate is inhomogeneous, i.e. certain regions have a higher likelihood of developing cancer. In this regard extensive work has been done to study the distribution of cancer in order to perform biopsy more effectively. Recently a statistical cancer atlas of the prostate was demonstrated along with an optimal biopsy scheme achieving a high detection rate. In this paper we discuss the complete construction and application of such an atlas that can be used in a clinical setting to effectively target high cancer zones during biopsy. The method consists of integrating intensity statistics in the form of cancer probabilities at every voxel in the image with shape statistics of the prostate in order to quickly warp the atlas onto a subject ultrasound image. While the atlas surface can be registered to a pre-segmented subject prostate surface or instead used to perform segmentation of the capsule via optimization of shape parameters to segment the subject image, the strength of our approach lies in the fast mapping of cancer statistics onto the subject using shape statistics. The shape model was trained from over 38 expert segmented prostate surfaces and the atlas registration accuracy was found to be high suggesting the use of this method to perform biopsy in near real time situations with some optimization.

  8. Alaska marine ice atlas

    SciTech Connect

    LaBelle, J.C.; Wise, J.L.; Voelker, R.P.; Schulze, R.H.; Wohl, G.M.

    1982-01-01

    A comprehensive Atlas of Alaska marine ice is presented. It includes information on pack and landfast sea ice and calving tidewater glacier ice. It also gives information on ice and related environmental conditions collected over several years time and indicates the normal and extreme conditions that might be expected in Alaska coastal waters. Much of the information on ice conditions in Alaska coastal waters has emanated from research activities in outer continental shelf regions under assessment for oil and gas exploration and development potential. (DMC)

  9. The ATLAS TRT electronics

    NASA Astrophysics Data System (ADS)

    ATLAS TRT Collaboration; Abat, E.; Addy, T. N.; Åkesson, T. P. A.; Alison, J.; Anghinolfi, F.; Arik, E.; Arik, M.; Atoian, G.; Auerbach, B.; Baker, O. K.; Banas, E.; Baron, S.; Bault, C.; Becerici, N.; Beddall, A.; Beddall, A. J.; Bendotti, J.; Benjamin, D. P.; Bertelsen, H.; Bingul, A.; Blampey, H.; Bocci, A.; Bochenek, M.; Bondarenko, V. G.; Bychkov, V.; Callahan, J.; Capeáns Garrido, M.; Cardiel Sas, L.; Catinaccio, A.; Cetin, S. A.; Chandler, T.; Chritin, R.; Cwetanski, P.; Dam, M.; Danielsson, H.; Danilevich, E.; David, E.; Degenhardt, J.; Di Girolamo, B.; Dittus, F.; Dixon, N.; Dogan, O. B.; Dolgoshein, B. A.; Dressnandt, N.; Driouchi, C.; Ebenstein, W. L.; Eerola, P.; Egede, U.; Egorov, K.; Evans, H.; Farthouat, P.; Fedin, O. L.; Fowler, A. J.; Fratina, S.; Froidevaux, D.; Fry, A.; Gagnon, P.; Gavrilenko, I. L.; Gay, C.; Ghodbane, N.; Godlewski, J.; Goulette, M.; Gousakov, I.; Grigalashvili, N.; Grishkevich, Y.; Grognuz, J.; Hajduk, Z.; Hance, M.; Hansen, F.; Hansen, J. B.; Hansen, P. H.; Hare, G. A.; Harvey, A., Jr.; Hauviller, C.; High, A.; Hulsbergen, W.; Huta, W.; Issakov, V.; Istin, S.; Jain, V.; Jarlskog, G.; Jeanty, L.; Kantserov, V. A.; Kaplan, B.; Kapliy, A. S.; Katounin, S.; Kayumov, F.; Keener, P. T.; Kekelidze, G. D.; Khabarova, E.; Khristachev, A.; Kisielewski, B.; Kittelmann, T. H.; Kline, C.; Klinkby, E. B.; Klopov, N. V.; Ko, B. R.; Koffas, T.; Kondratieva, N. V.; Konovalov, S. P.; Koperny, S.; Korsmo, H.; Kovalenko, S.; Kowalski, T. Z.; Krüger, K.; Kramarenko, V.; Kudin, L. G.; LeBihan, A.-C.; LeGeyt, B. C.; Levterov, K.; Lichard, P.; Lindahl, A.; Lisan, V.; Lobastov, S.; Loginov, A.; Loh, C. W.; Lokwitz, S.; Long, M. C.; Lucas, S.; Lucotte, A.; Luehring, F.; Lundberg, B.; Mackeprang, R.; Maleev, V. P.; Manara, A.; Mandl, M.; Martin, A. J.; Martin, F. F.; Mashinistov, R.; Mayers, G. M.; McFarlane, K. W.; Mialkovski, V.; Mills, B. M.; Mindur, B.; Mitsou, V. A.; Mjörnmark, J. U.; Morozov, S. V.; Morris, E.; Mouraviev, S. V.; Muir, A. M.; Munar, A.; Nadtochi, A. V.; Nesterov, S. Y.; Newcomer, F. M.; Nikitin, N.; Novgorodova, O.; Novodvorski, E. G.; Ogren, H.; Oh, S. H.; Oleshko, S. B.; Olivito, D.; Olszowska, J.; Ostrowicz, W.; Passmore, M. S.; Patrichev, S.; Penwell, J.; Perez-Gomez, F.; Peshekhonov, V. D.; Petersen, T. C.; Petti, R.; Placci, A.; Poblaguev, A.; Pons, X.; Price, M. J.; Røhne, O.; Reece, R. D.; Reilly, M. B.; Rembser, C.; Romaniouk, A.; Rousseau, D.; Rust, D.; Ryabov, Y. F.; Ryjov, V.; Söderberg, M.; Savenkov, A.; Saxon, J.; Scandurra, M.; Schegelsky, V. A.; Scherzer, M. I.; Schmidt, M. P.; Schmitt, C.; Sedykh, E.; Seliverstov, D. M.; Shin, T.; Shmeleva, A.; Sivoklokov, S.; Smirnov, S. Yu; Smirnova, L.; Smirnova, O.; Smith, P.; Sosnovtsev, V. V.; Sprachmann, G.; Subramania, S.; Suchkov, S. I.; Sulin, V. V.; Szczygiel, R. R.; Tartarelli, G.; Thomson, E.; Tikhomirov, V. O.; Tipton, P.; Valls Ferrer, J. A.; Van Berg, R.; Vassilakopoulos, V. I.; Vassilieva, L.; Wagner, P.; Wall, R.; Wang, C.; Whittington, D.; Williams, H. H.; Zhelezko, A.; Zhukov, K.

    2008-06-01

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

  10. Neonatal Atlas Construction Using Sparse Representation

    PubMed Central

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

    2014-01-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases. PMID:24638883

  11. ATLAS Series of Shuttle Missions. Volume 23

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This technical paper contains selected papers from Geophysical Research Letters (Volume 23, Number 17) on ATLAS series of shuttle missions. The ATLAS space shuttle missions were conducted in March 1992, April 1993, and November 1994. This paper discusses solar irradiance, middle atmospheric temperatures, and trace gas concentrations measurements made by the ATLAS payload and companion instruments.

  12. 27 CFR 9.140 - Atlas Peak.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

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

  13. ATLAS discoveries of optical transients

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. ATLAS discoveries of optical transients

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  15. ATLAS discoveries of optical transients

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  16. ATLAS discoveries of optical transients

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  17. Compute farm software for ATLAS IBL calibration

    NASA Astrophysics Data System (ADS)

    Bindi, M.; Flick, T.; Grosse-Knetter, J.; Heim, T.; Hsu, S.-C.; Kretz, M.; Kugel, A.; Marx, M.; Morettini, P.; Potamianos, K.; Takubo, Y.

    2014-06-01

    In 2014 the Insertable B-Layer (IBL) will extend the existing Pixel Detector of the ATLAS experiment at CERN by over 12 million additional pixels. For calibration and monitoring purposes, occupancy and time-over-threshold data are being histogrammed in the read-out hardware. Further processing of the histograms happens on commodity hardware, which not only requires the fast transfer of histogram data from the read-out hardware to the computing farm via Ethernet, but also the integration of the software and hardware into the already existing data-acquisition and calibration framework (TDAQ and PixelDAQ) of the ATLAS experiment and the current Pixel Detector. We implement the software running on the compute cluster with an emphasis on modularity, allowing for flexible adjustment of the infrastructure and a good scalability with respect to the number of network interfaces, available CPU cores, and deployed machines. By using a modular design we are able to not only employ CPU-based fitting algorithms, but also have the possibility to take advantage of the performance offered by a GPU-based approach to fitting.

  18. ATLAS Distributed Computing in LHC Run2

    NASA Astrophysics Data System (ADS)

    Campana, Simone

    2015-12-01

    The ATLAS Distributed Computing infrastructure has evolved after the first period of LHC data taking in order to cope with the challenges of the upcoming LHC Run-2. An increase in both the data rate and the computing demands of the Monte-Carlo simulation, as well as new approaches to ATLAS analysis, dictated a more dynamic workload management system (Prodsys-2) and data management system (Rucio), overcoming the boundaries imposed by the design of the old computing model. In particular, the commissioning of new central computing system components was the core part of the migration toward a flexible computing model. A flexible computing utilization exploring the use of opportunistic resources such as HPC, cloud, and volunteer computing is embedded in the new computing model; the data access mechanisms have been enhanced with the remote access, and the network topology and performance is deeply integrated into the core of the system. Moreover, a new data management strategy, based on a defined lifetime for each dataset, has been defined to better manage the lifecycle of the data. In this note, an overview of an operational experience of the new system and its evolution is presented.

  19. Atlas Multimedia Educational Lab for Interactive Analysis

    2008-04-01

    AMELIA is an application with focus on particle physics processes in ATLAS. This will allow students and othe users to decode the collision events that unfold after the head-on collisions of protons at the Large hadron Collider. AMELIA uses the Irrlicht engine for the 3D graphics and wxWidgets for the interface. It uses the best aspects of technical animation and allows users to control 3D representations of collision events and to manipulate 3D models ofmore » the detector and see how particles are detected as they pass through. It allows the user to rotate, zoom and select virtual pieces of the ATLAS detector and events. The characteristics of the events (momentum etc.) can also be read, and one can select tracks for analysis, activate context-oriented media, etc. This framework intends to integrate different types of media into a single product. This way, videos, animations, sound, interactive visualization and data analysis will be bound together in the same package.-« less

  20. Tampa Bay environmental atlas

    SciTech Connect

    Kunneke, J.T.; Palik, T.F.

    1984-12-01

    Biological and water resource data for Tampa Bay were compiled and mapped at a scale of 1:24,000. This atlas consists of (1) composited information overlain on 18 biological and 20 water resource base maps and (2) an accompanying map narrative. Subjects mapped on the water resource maps are contours of the mean middepth specific conductivity which can be converted to salinity; bathymetry, sediments, tidal currents, the freshwater/saltwater interface, dredge spoil disposal sites; locations of industrial and municipal point source discharges, tide stations, and water quality sampling stations. The point source discharge locations show permitted capacity and the water quality sampling stations show 5-year averages for chlorophyll, conductivity, turbidity, temperature, and total nitrogen. The subjects shown on the biological resource maps are clam and oyster beds, shellfish harvest areas, colonial bird nesting sites, manatee habitat, seagrass beds and artificial reefs. Spawning seasons, nursery habitats, and adult habitats are identified for major fish species. The atlas will provide useful information for coastal planning and management in Tampa Bay.

  1. A Photographic Atlas of Selected Regions of the Milky Way

    NASA Astrophysics Data System (ADS)

    Barnard, Edward Emerson; Orin Dobek, Foreword by Gerald

    2014-08-01

    Foreword Gerald Orin Dobek; Preface from the original Atlas; Introduction from the original Atlas; Bibliography from the original Atlas; Catalogue of 349 dark objects in the sky; Biography of Edward Emerson Barnard.

  2. The silicon microstrip sensors of the ATLAS semiconductor tracker

    SciTech Connect

    ATLAS SCT Collaboration; Spieler, Helmuth G.

    2007-04-13

    This paper describes the AC-coupled, single-sided, p-in-n silicon microstrip sensors used in the Semiconductor Tracker (SCT) of the ATLAS experiment at the CERN Large Hadron Collider (LHC). The sensor requirements, specifications and designs are discussed, together with the qualification and quality assurance procedures adopted for their production. The measured sensor performance is presented, both initially and after irradiation to the fluence anticipated after 10 years of LHC operation. The sensors are now successfully assembled within the detecting modules of the SCT, and the SCT tracker is completed and integrated within the ATLAS Inner Detector. Hamamatsu Photonics Ltd. supplied 92.2percent of the 15,392 installed sensors, with the remainder supplied by CiS.

  3. Gas gain stabilisation in the ATLAS TRT detector

    NASA Astrophysics Data System (ADS)

    Mindur, B.; Åkesson, T. P. A.; Anghinolfi, F.; Antonov, A.; Arslan, O.; Baker, O. K.; Banas, E.; Bault, C.; Beddall, A. J.; Bendotti, J.; Benjamin, D. P.; Bertelsen, H.; Bingul, A.; Bocci, A.; Boldyrev, A. S.; Brock, I.; Capeáns Garrido, M.; Catinaccio, A.; Celebi, E.; Cetin, S. A.; Choi, K.; Dam, M.; Danielsson, H.; Davis, D.; Degeorge, C.; Derendarz, D.; Desch, K.; Di Girolamo, B.; Dittus, F.; Dixon, N.; Dressnandt, N.; Dubinin, F. A.; Evans, H.; Farthouat, P.; Fedin, O. L.; Froidevaux, D.; Gavrilenko, I. L.; Gay, C.; Gecse, Z.; Godlewski, J.; Grefe, C.; Gurbuz, S.; Hajduk, Z.; Hance, M.; Haney, B.; Hansen, J. B.; Hansen, P. H.; Hawkins, A. D.; Heim, S.; Holway, K.; Kantserov, V. A.; Katounine, S.; Kayumov, F.; Keener, P. T.; Kisielewski, B.; Klopov, N. V.; Konovalov, S. P.; Koperny, S.; Korotkova, N. A.; Kowalski, T. Z.; Kramarenko, V.; Krasnopevtsev, D.; Kruse, M.; Kudin, L. G.; Lichard, P.; Loginov, A.; Martinez, N. Lorenzo; Lucotte, A.; Luehring, F.; Lytken, E.; Maleev, V. P.; Maevskiy, A. S.; Manjarres Ramos, J.; Mashinistov, R. Y.; Meyer, C.; Mialkovski, V.; Mistry, K.; Mitsou, V. A.; Nadtochi, A. V.; Newcomer, F. M.; Novodvorski, E. G.; Ogren, H.; Oh, S. H.; Oleshko, S. B.; Olszowska, J.; Ostrowicz, W.; Palacino, G.; Patrichev, S.; Penwell, J.; Perez-Gomez, F.; Peshekhonov, V. D.; RØhne, O.; Reilly, M. B.; Rembser, C.; Ricken, O.; Romaniouk, A.; Rousseau, D.; Ryjov, V.; Sasmaz, U.; Schaepe, S.; Schegelsky, V. A.; Shmeleva, A. P.; Shulga, E.; Sivoklokov, S.; Smirnov, S.; Smirnov, Yu.; Smirnova, L. N.; Soldatov, E.; Sulin, V. V.; Tartarelli, G.; Taylor, W.; Thomson, E.; Tikhomirov, V. O.; Tipton, P.; Valls Ferrer, J. A.; Van Berg, R.; Vasquez, J.; Vasilyeva, L. F.; Vlazlo, O.; Weinert, B.; Williams, H. H.; Wong, V.; Zhukov, K. I.; Zieminska, D.

    2016-04-01

    The ATLAS (one of two general purpose detectors at the LHC) Transition Radiation Tracker (TRT) is the outermost of the three tracking subsystems of the ATLAS Inner Detector. It is a large straw-based detector and contains about 350,000 electronics channels. The performance of the TRT as tracking and particularly particle identification detector strongly depends on stability of the operation parameters with most important parameter being the gas gain which must be kept constant across the detector volume. The gas gain in the straws can vary significantly with atmospheric pressure, temperature, and gas mixture composition changes. This paper presents a concept of the gas gain stabilisation in the TRT and describes in detail the Gas Gain Stabilisation System (GGSS) integrated into the Detector Control System (DCS). Operation stability of the GGSS during Run-1 is demonstrated.

  4. Measurement of the properties of the Higgs boson at ATLAS

    SciTech Connect

    Bristow, Timothy; Collaboration: ATLAS Collaboration

    2014-03-05

    An update on the Higgs boson search in the decay channels H→γγ, H→ZZ{sup (*)}→4l, H→WW{sup (*)}→lvlv, H→τ{sup +}τ{sup −} and H→bb{sup ¯} at the ATLAS detector is presented. Proton-proton collision data recorded by the ATLAS experiment corresponding to an integrated luminosity of up to 25/fb at centre-of-mass energies of 7 and 8 TeV are used for these results. The latest combined and individual channel measurements of the mass, signal strength, spin and parity, coupling constants and Higgs boson production are reported. Results on the measurements of the properties of the Higgs boson are all consistent with the Standard Model.

  5. National Atlas of the United States Maps

    USGS Publications Warehouse

    ,

    2001-01-01

    The 'National Atlas of the United States of America?', published by the U.S. Geological Survey (USGS) in 1970, is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. Maps dated after 1970 and before 1997 are either revisions of original atlas maps or new maps published in the original atlas format. The USGS and its partners in government and industry began work on a new 'National Atlas' in 1997. Though most new atlas products are designed for the World Wide Web, we are continuing our tradition of printing high-quality maps of America. In 1998, the first completely redesigned maps of the 'National Atlas of the United States?' were published.

  6. Anti-Atlas Mountains, Morocco

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Anti-Atlas Mountains of northern Africa and the nearby Atlas mountains were created by the prolonged collision of the African and Eurasian tectonic plates, beginning about 80 million years ago. Massive sandstone and limestone layers have been crumpled and uplifted more than 4,000 meters in the High Atlas and to lower elevations in the Anti-Atlas. Between more continuous major fold structures, such as the Jbel Ouarkziz in the southwestern Anti-Atlas, tighter secondary folds (arrow) have developed. Earlier, the supercontinent of Pangea rifted apart to form precursors to the Mediterranean and the Atlantic Ocean (Beauchamp and others, 1996). In those seas sands, clays, limey sediments, and evaporite layers (gypsum, rock salt) were deposited. Later, during the mountain-building plate collision, the gypsum layers flowed under the pressure and provided a slippery surface on which overlying rigid rocks could glide (Burkhard, 2001). The broad, open style of folds seen in this view is common where evaporites are involved in the deformation. Other examples can be found in the Southern Zagros of Iran and the Sierra Madre Oriental of Mexico. Information Sources: Beauchamp, W., Barazangi, M., Demnati, A., and El Alji, M., 1996, Intracontinental rifting and inversion: Missour Basin and Atlas Mountains, Morocco: Tulsa, American Association of Petroleum Geologists Bulletin, v. 80, No. 9, p. 1459-1482. Burkhard, Martin, 2001, Tectonics of the Anti-Atlas of Morocco -- Thin-skin/thick-skin relationships in an atypical foreland fold belt. University of Neuchatel, Switzerland: http://www-geol.unine.ch/Structural/Antiatlas.html (accessed 1/29/02). STS108-711-25 was taken in December, 2001 by the crew of Space Shuttle mission 108 using a Hasselblad camera with 250-mm lens. The image is provided by the Earth Sciences and Image Analysis Laboratory at Johnson Space Center. Additional images taken by astronauts and cosmonauts can be viewed at the NASA-JSC Gateway to Astronaut Photography

  7. Activities Using the New State of the World Atlas. Grades 7-12.

    ERIC Educational Resources Information Center

    Hursh, Heidi; Prevedel, Michael

    Teachers of social studies, foreign language, science, and journalism will find these learning activities useful in integrating "The New State of the World Atlas" (Simon and Schuster, 1984) into their curriculum. The book is organized into three sections. The first section uses an area studies approach. Activities focus on geopolitical and…

  8. Cassini Tour Atlas Automated Generation

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  9. It's On: Early Interpretations of ATLAS Results in Jets and Missing Energy

    SciTech Connect

    Alves, Daniele S.M.; Izaguirre, Eder; Wacker, Jay G.; /SLAC

    2011-08-12

    The first search for supersymmetry from ATLAS with 70 nb{sup -1} of integrated luminosity extends the Tevatron's reach for colored particles that decay into jets plus missing transverse energy. For gluinos that decay directly or through a one step cascade into the LSP and two jets, the mass range m{sub {bar g}} {le} 205 GeV is disfavored by the ATLAS searches, regardless of the mass of the LSP. In some cases the coverage extends up to m{sub {bar g}} {approx_equal} 295 GeV, already surpassing the Tevatron's reach for compressed supersymmetry spectra.

  10. Chandra Galaxy Atlas

    NASA Astrophysics Data System (ADS)

    Kim, Dong-Woo; Mossman, Amy; Fruscione, Antonella; Anderson, Craig; Morgan, Doug; Burke, Douglas J.; O'Sullivan, E. J; Fabbiano, Giuseppina; Lauer, Jennifer; McCollough, Mike

    2014-06-01

    The hot ISM in early type galaxies plays a crucial role for understanding their formation and evolution. Structural features of the hot ISM identified by Chandra (including jets, cavities, cold fronts, filaments and tails) point to key evolutionary mechanisms, e.g., AGN feedback, merging history, accretion/stripping and star formation and its quenching. In our new project, Chandra Galaxy Atlas, we will systematically analyze the archival Chandra data of 137 ETGs to study the hot ISM. Taking full advantage of the Chandra capabilities, we will derive uniform data products of spatially resolved dataset with additional spectral information. We will make these products publicly available and use them for our focused science goals.

  11. Atlas of Nuclear Isomers

    SciTech Connect

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

    2015-09-15

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

  12. Consumer Energy Atlas

    SciTech Connect

    Not Available

    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.

  13. Development of a read out driver for ATLAS micromegas based on the Scalable Readout System

    NASA Astrophysics Data System (ADS)

    Zibell, A.

    2014-01-01

    With future LHC luminosity upgrades, part of the ATLAS muon spectrometer has to be changed, to cope with the increased flux of uncorrelated neutron and gamma particles. Micromegas detectors were chosen as precision tracker for the New Small Wheels, that will replace the current Small Wheel muon detector stations during the LHC shutdown foreseen for 2018. To read out these detectors together with all other ATLAS subsystems, a readout driver was developed to integrate these micromegas detectors into the ATLAS data acquisition infrastructure. The readout driver is based on the Scalable Readout System, and its tasks include trigger handling, slow control, event building and data transmission to the high-level readout systems. This article describes the layout and functionalities of this readout driver and its components, as well as a test of its functionalities in the cosmic ray facility of Ludwig-Maximilians University Munich.

  14. Status of the ATLAS Liquid Argon calorimeter and its performance after two years of LHC operation

    NASA Astrophysics Data System (ADS)

    Aperio Bella, L.

    2013-08-01

    The ATLAS detector is designed to study proton-proton collisions produced at the Large Hadron Collider (LHC) at CERN. Its calorimeter system, for the electromagnetic and forward part and for a fraction of the hadronic part, is made of liquid argon sampling calorimeters. During the 2011 data taking period, ATLAS operated with an excellent efficiency and recorded more than 5fb-1 integrated luminosity of 7 TeV center of mass energy proton-proton collisions. The ATLAS Liquid Argon calorimeters played a significant role in this achievement. Its main features are first described. Then, some of its performances over the past two years are given. Highlights are put on its operation, calibration, stability and data taking efficiency, as well as on the related physics performances.

  15. Automated segmentation of CBCT image using spiral CT atlases and convex optimization.

    PubMed

    Wang, Li; Chen, Ken Chung; Shi, Feng; Liao, Shu; Li, Gang; Gao, Yaozong; Shen, Steve G F; Yan, Jin; Lee, Philip K M; Chow, Ben; Liu, Nancy X; Xia, James J; Shen, Dinggang

    2013-01-01

    Cone-beam computed tomography (CBCT) is an increasingly utilized imaging modality for the diagnosis and treatment planning of the patients with craniomaxillofacial (CMF) deformities. CBCT scans have relatively low cost and low radiation dose in comparison to conventional spiral CT scans. However, a major limitation of CBCT scans is the widespread image artifacts such as noise, beam hardening and inhomogeneity, causing great difficulties for accurate segmentation of bony structures from soft tissues, as well as separating mandible from maxilla. In this paper, we presented a novel fully automated method for CBCT image segmentation. In this method, we first estimated a patient-specific atlas using a sparse label fusion strategy from predefined spiral CT atlases. This patient-specific atlas was then integrated into a convex segmentation framework based on maximum a posteriori probability for accurate segmentation. Finally, the performance of our method was validated via comparisons with manual ground-truth segmentations. PMID:24505768

  16. The ATLAS Positron Experiment -- APEX

    SciTech Connect

    Ahmad, I.; Back, B.B.; Betts, R.R.; Dunford, R.; Kutschera, W.; Rhein, M.D.; Schiffer, J.P.; Wilt, P.; Wuosmaa, A.; Austin, S.M.; Kashy, E.; Winfield, J.S.; Yurkon, J.E.; Bazin, D.; Calaprice, F.P.; Young, A.; Chan, K.C.; Chisti, A.; Chowhury, P.; Greenberg, J.S.; Kaloskamis, N.; Lister, C.J.; Fox, J.D.; Roa, E.; Freedman, S.; Maier, M.R.; Freer, M.; Gazes, S.; Hallin, A.L.; Liu, M.; Happ, T.; Perera, A.; Wolfs, F.L.H.; Trainor, T.; Wolanski, M. |

    1994-03-01

    APEX -- the ATLAS Positron Experiment -- is designed to measure electrons and positrons emitted in heavy-ion collisions. Its scientific goal is to gain insight into the puzzling positron-line phenomena observed at the GSI Darmstadt. It is in operation at the ATLAS accelerator at Argonne National Lab. The assembly of the apparatus is finished and beginning 1993 the first positrons produced in heavy-ion collisions were observed. The first full scale experiment was carried out in December 1993, and the data are currently being analyzed. In this paper, the principles of operation are explained and a status report on the experiment is given.

  17. Liquid Argon Calorimetry for ATLAS

    NASA Astrophysics Data System (ADS)

    Robinson, Alan

    2008-05-01

    This summer, the largest collaborative physics project since the Manhattan project will go online. One of four experiments for the Large Hadron Collider at CERN in Geneva, ATLAS, employs over 2000 people. Canadians have helped design, construct, and calibrate the liquid argon calorimeters for ATLAS to capture the products of the high energy collisions produced by the LHC. From an undergraduate's perspective, explore how these calorimeters are made to handle their harsh requirement. From nearly a billion proton-proton collisions a second, physicists hope to discover the Higgs boson and other new fundamental particles.

  18. Efficient multi-atlas abdominal segmentation on clinically acquired CT with SIMPLE context learning.

    PubMed

    Xu, Zhoubing; Burke, Ryan P; Lee, Christopher P; Baucom, Rebeccah B; Poulose, Benjamin K; Abramson, Richard G; Landman, Bennett A

    2015-08-01

    Abdominal segmentation on clinically acquired computed tomography (CT) has been a challenging problem given the inter-subject variance of human abdomens and complex 3-D relationships among organs. Multi-atlas segmentation (MAS) provides a potentially robust solution by leveraging label atlases via image registration and statistical fusion. We posit that the efficiency of atlas selection requires further exploration in the context of substantial registration errors. The selective and iterative method for performance level estimation (SIMPLE) method is a MAS technique integrating atlas selection and label fusion that has proven effective for prostate radiotherapy planning. Herein, we revisit atlas selection and fusion techniques for segmenting 12 abdominal structures using clinically acquired CT. Using a re-derived SIMPLE algorithm, we show that performance on multi-organ classification can be improved by accounting for exogenous information through Bayesian priors (so called context learning). These innovations are integrated with the joint label fusion (JLF) approach to reduce the impact of correlated errors among selected atlases for each organ, and a graph cut technique is used to regularize the combined segmentation. In a study of 100 subjects, the proposed method outperformed other comparable MAS approaches, including majority vote, SIMPLE, JLF, and the Wolz locally weighted vote technique. The proposed technique provides consistent improvement over state-of-the-art approaches (median improvement of 7.0% and 16.2% in DSC over JLF and Wolz, respectively) and moves toward efficient segmentation of large-scale clinically acquired CT data for biomarker screening, surgical navigation, and data mining. PMID:26046403

  19. Efficient multi-atlas abdominal segmentation on clinically acquired CT with SIMPLE context learning.

    PubMed

    Xu, Zhoubing; Burke, Ryan P; Lee, Christopher P; Baucom, Rebeccah B; Poulose, Benjamin K; Abramson, Richard G; Landman, Bennett A

    2015-08-01

    Abdominal segmentation on clinically acquired computed tomography (CT) has been a challenging problem given the inter-subject variance of human abdomens and complex 3-D relationships among organs. Multi-atlas segmentation (MAS) provides a potentially robust solution by leveraging label atlases via image registration and statistical fusion. We posit that the efficiency of atlas selection requires further exploration in the context of substantial registration errors. The selective and iterative method for performance level estimation (SIMPLE) method is a MAS technique integrating atlas selection and label fusion that has proven effective for prostate radiotherapy planning. Herein, we revisit atlas selection and fusion techniques for segmenting 12 abdominal structures using clinically acquired CT. Using a re-derived SIMPLE algorithm, we show that performance on multi-organ classification can be improved by accounting for exogenous information through Bayesian priors (so called context learning). These innovations are integrated with the joint label fusion (JLF) approach to reduce the impact of correlated errors among selected atlases for each organ, and a graph cut technique is used to regularize the combined segmentation. In a study of 100 subjects, the proposed method outperformed other comparable MAS approaches, including majority vote, SIMPLE, JLF, and the Wolz locally weighted vote technique. The proposed technique provides consistent improvement over state-of-the-art approaches (median improvement of 7.0% and 16.2% in DSC over JLF and Wolz, respectively) and moves toward efficient segmentation of large-scale clinically acquired CT data for biomarker screening, surgical navigation, and data mining.

  20. Three-dimensional stereotactic atlas of the extracranial vasculature correlated with the intracranial vasculature, cranial nerves, skull and muscles.

    PubMed

    Nowinski, Wieslaw L; Shoon Let Thaung, Thant; Choon Chua, Beng; Hnin Wut Yi, Su; Yang, Yili; Urbanik, Andrzej

    2015-04-01

    Our objective was to construct a 3D, interactive, and reference atlas of the extracranial vasculature spatially correlated with the intracranial blood vessels, cranial nerves, skull, glands, and head muscles.The atlas has been constructed from multiple 3T and 7T magnetic resonance angiogram (MRA) brain scans, and 3T phase contrast and inflow MRA neck scans of the same specimen in the following steps: vessel extraction from the scans, building 3D tubular models of the vessels, spatial registration of the extra- and intracranial vessels, vessel editing, vessel naming and color-coding, vessel simplification, and atlas validation.This new atlas contains 48 names of the extracranial vessels (25 arterial and 23 venous) and it has been integrated with the existing brain atlas.The atlas is valuable for medical students and residents to easily get familiarized with the extracranial vasculature with a few clicks; is useful for educators to prepare teaching materials; and potentially can serve as a reference in the diagnosis of vascular disease and treatment, including craniomaxillofacial surgeries and radiologic interventions of the face and neck. PMID:25923683

  1. Bringing ATLAS production to HPC resources - A use case with the Hydra supercomputer of the Max Planck Society

    NASA Astrophysics Data System (ADS)

    Kennedy, J. A.; Kluth, S.; Mazzaferro, L.; Walker, Rodney

    2015-12-01

    The possible usage of HPC resources by ATLAS is now becoming viable due to the changing nature of these systems and it is also very attractive due to the need for increasing amounts of simulated data. In recent years the architecture of HPC systems has evolved, moving away from specialized monolithic systems, to a more generic linux type platform. This change means that the deployment of non HPC specific codes has become much easier. The timing of this evolution perfectly suits the needs of ATLAS and opens a new window of opportunity. The ATLAS experiment at CERN will begin a period of high luminosity data taking in 2015. This high luminosity phase will be accompanied by a need for increasing amounts of simulated data which is expected to exceed the capabilities of the current Grid infrastructure. ATLAS aims to address this need by opportunistically accessing resources such as cloud and HPC systems. This paper presents the results of a pilot project undertaken by ATLAS and the MPP/RZG to provide access to the HYDRA supercomputer facility. Hydra is the supercomputer of the Max Planck Society, it is a linux based supercomputer with over 80000 cores and 4000 physical nodes located at the RZG near Munich. This paper describes the work undertaken to integrate Hydra into the ATLAS production system by using the Nordugrid ARC-CE and other standard Grid components. The customization of these components and the strategies for HPC usage are discussed as well as possibilities for future directions.

  2. Three-dimensional stereotactic atlas of the extracranial vasculature correlated with the intracranial vasculature, cranial nerves, skull and muscles.

    PubMed

    Nowinski, Wieslaw L; Shoon Let Thaung, Thant; Choon Chua, Beng; Hnin Wut Yi, Su; Yang, Yili; Urbanik, Andrzej

    2015-04-01

    Our objective was to construct a 3D, interactive, and reference atlas of the extracranial vasculature spatially correlated with the intracranial blood vessels, cranial nerves, skull, glands, and head muscles.The atlas has been constructed from multiple 3T and 7T magnetic resonance angiogram (MRA) brain scans, and 3T phase contrast and inflow MRA neck scans of the same specimen in the following steps: vessel extraction from the scans, building 3D tubular models of the vessels, spatial registration of the extra- and intracranial vessels, vessel editing, vessel naming and color-coding, vessel simplification, and atlas validation.This new atlas contains 48 names of the extracranial vessels (25 arterial and 23 venous) and it has been integrated with the existing brain atlas.The atlas is valuable for medical students and residents to easily get familiarized with the extracranial vasculature with a few clicks; is useful for educators to prepare teaching materials; and potentially can serve as a reference in the diagnosis of vascular disease and treatment, including craniomaxillofacial surgeries and radiologic interventions of the face and neck.

  3. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  4. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  5. Atlas-based system for functional neurosurgery

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Yeo, Tseng T.; Yang, Guo L.; Dow, Douglas E.

    1997-05-01

    This paper addresses the development of an atlas-based system for preoperative functional neurosurgery planning and training, intraoperative support and postoperative analysis. The system is based on Atlas of Stereotaxy of the Human Brain by Schaltenbrand and Wahren used for interactive segmentation and labeling of clinical data in 2D/3D, and for assisting stereotactic targeting. The atlas microseries are digitized, enhanced, segmented, labeled, aligned and organized into mutually preregistered atlas volumes 3D models of the structures are also constructed. The atlas may be interactively registered with the actual patient's data. Several other features are also provided including data reformatting, visualization, navigation, mensuration, and stereotactic path display and editing in 2D/3D. The system increases the accuracy of target definition, reduces the time of planning and time of the procedure itself. It also constitutes a research platform for the construction of more advanced neurosurgery supporting tools and brain atlases.

  6. Anatomical Variant of Atlas : Arcuate Foramen, Occpitalization of Atlas, and Defect of Posterior Arch of Atlas

    PubMed Central

    2015-01-01

    Objective We sought to examine anatomic variations of the atlas and the clinical significance of these variations. Methods We retrospectively reviewed 1029 cervical 3-dimensional (3D) CT images. Cervical 3D CT was performed between November 2011 and August 2014. Arcuate foramina were classified as partial or complete and left and/or right. Occipitalization of the atlas was classified in accordance with criteria specified by Mudaliar et al. Posterior arch defects of the atlas were classified in accordance with criteria specified by Currarino et al. Results One hundred and eight vertebrae (108/1029, 10.5%) showed an arcuate foramen. Bilateral arcuate foramina were present in 41 of these vertebrae and the remaining 67 arcuate foramina were unilateral (right 31, left 36). Right-side arcuate foramina were partial on 18 sides and complete on 54 sides. Left-side arcuate foramina were partial on 24 sides and complete on 53 sides. One case of atlas assimilation was found. Twelve patients (12/1029, 1.17%) had a defect of the atlantal posterior arch. Nine of these patients (9/1029, 0.87%) had a type A posterior arch defect. We also identified one type B, one type D, and one type E defect. Conclusion Preoperative diagnosis of occipitalization of the atlas and arcuate foramina using 3D CT is of paramount importance in avoiding neurovascular injury during surgery. It is important to be aware of posterior arch defects of the atlas because they may be misdiagnosed as a fracture. PMID:26819687

  7. The ATLAS Facility at Argonne National Laboratory

    SciTech Connect

    1997-07-01

    The Argonne Tandem Linac Accelerator System (ATLAS) is a superconducting low-energy heavy ion accelerator. Its primary purpose is to provide beams for research in nuclear structure physics. This report begins with a brief history of ATLAS and then describes the current design of the facility. Also summarized are the experimental equipment and research programs. It concludes with a proposal for turning ATLAS into a radioactive beam facility.

  8. Report to users of ATLAS, December 1995

    SciTech Connect

    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 {sup 12}C(g.s.) + {sup 12}C(3{minus},9.64MeV) inelastic scattering; and the AYE-ball (Argonne-Yale-European gamma spectrometer) used to study the structure of nuclei far from stability.

  9. Image database for digital hand atlas

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  10. Global GIS database; digital atlas of Africa

    USGS Publications Warehouse

    Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

    2001-01-01

    This CD-ROM contains a digital atlas of the countries of Africa. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make this atlas easier to use, are also included.

  11. Book review: Oklahoma Breeding Bird Atlas

    USGS Publications Warehouse

    Peterjohn, Bruce G.

    2004-01-01

    The first North American breeding bird atlases were initiated during the 1970s. With atlases completed or ongoing in more than 40 U.S. states and most Canadian provinces, these projects are now familiar to professional ornithologists and amateur birders. This book provides the results of the Oklahoma Breeding Bird Atlas, the data for which were collected during 1997–2001. Its appearance less than 3 years after completing fieldwork is remarkable and everyone associated with its timely publication should be congratulated for their efforts.Review info: Oklahoma Breeding Bird Atlas. By Dan L. Reinking, 2004. ISBN: 0806136146, 528 pp.

  12. Commissioning of the ATLAS pixel detector

    SciTech Connect

    ATLAS Collaboration; Golling, Tobias

    2008-09-01

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

  13. Learning with the ATLAS experiment at CERN

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    With the start of the LHC, the new particle collider at CERN, the ATLAS experiment is also providing high-energy particle collisions for educational purposes. Several education projects—education scenarios—have been developed and tested on students and teachers in several European countries within the Learning with ATLAS@CERN project. These highly appreciated projects could become a new component in many teachers' classrooms. The Learning with ATLAS portal and the information on the ATLAS public website make it possible for teachers to design educational material for their own situations. To be able to work with real data adds a new dimension to particle physics explorations at school.

  14. Digital atlas for spinal x rays

    NASA Astrophysics Data System (ADS)

    Long, L. Rodney; Pillemer, Stanley R.; Goh, Gin-Hua; Berman, Lewis E.; Neve, Leif; Thoma, George R.; Premkumar, Ahalya; Ostchega, Yechiam; Lawrence, Reva C.; Altman, Roy D.; Lane, Nancy E.; Scott, William W., Jr.

    1997-05-01

    At the National Library of Medicine we are developing a digital atlas to serve as a reference tool for the interpretation of cervical and lumbar spine x-rays. The atlas contains representative images for four grades of severity for cervical/lumbar spondylolisthesis. A prototype version of the atlas has been built using images for which expert rheumatologist readers reached exact agreement in grading. The atlas functionality includes the ability to display cervical and lumbar anatomy, display of single images or multiple simultaneous images, image processing functions, and capability to ad user-defined images to the atlas. Images are selected for display by the user specifying feature and grade. Currently, the atlas runs on a Sun SPARC workstation under the Solaris operating system. THe initial use of the atlas is to aid in reading a collection of 17,000 NHANES II digitized x-rays. The atlas may also be used as a general digital reference tool for the standardized interpretation of digital x-rays for osteoarthritis. We are investigating further development of the atlas to accommodate a wider set of images, to operate on multiple platforms, and to be accessible via the WWW.

  15. Pictorial Atlas of the Netherlands.

    ERIC Educational Resources Information Center

    Information and Documentation Centre for the Geography of the Netherlands, Utrecht.

    The atlas contains almost 40 photographs and 40 maps of geographical aspects of the Netherlands: the coast, dikes, canals, towns, and farmland. Each page contains a photograph, a section of a map showing the area in which the photograph was taken, and a discussion of several paragraphs about the geographical problems of the area and how they have…

  16. Atlas of fetal skeletal radiology

    SciTech Connect

    Ornov, A.; Borochowitz, Z.; Lachman, R.; Rimoin, D.L.

    1987-01-01

    This atlas presents anterior, posterior and lateral views of normal but spontaneously aborted fetuses from 10 weeks through 27 weeks of gestation. The series of radiographs exhibits a wide array of skeletal dysplasia, and a chapter on the normal chondroosseous development - the formation of cartilage and bone and ossification of individual bones is included for further clarification.

  17. Atlas of the Soviet Union.

    ERIC Educational Resources Information Center

    Young, Harry F.

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

  18. Atlas of the African Child.

    ERIC Educational Resources Information Center

    Patel, Mahesh, Ed.

    Using data primarily from United Nations Statistical Yearbooks, but from other sources as well, this Atlas provides an overview, in graphical form, of issues affecting children in Africa. Some of the issues covered, such as immunization, affect children directly. Others, such as economic progress, are included because they form part of the…

  19. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.

    PubMed

    Bakker, Rembrandt; Tiesinga, Paul; Kötter, Rolf

    2015-07-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays.

  20. The Molecular Atlas Project

    NASA Astrophysics Data System (ADS)

    Silverberg, Jesse; Yin, Peng

    The promise of super-resolution microscopy is a technology to discover new biological mechanisms that occur at smaller length scales then previously observable. However, with higher-resolution, we generally lose the larger spatial context of the image itself. The Molecular Atlas Project (MAP) directly asks how these competing interests between super-resolution imaging and broader spatially contextualized information can be reconciled. MAP enables us to acquire, visualize, explore, and annotate proteomic image data representing 7 orders of magnitude in length ranging from molecular (nm) to tissue (cm) scales. This multi-scale understanding is made possible by combining multiplexed DNA-PAINT, a DNA nanotechnology approach to super-resolution imaging, with ``big-data'' strategies for information management and image visualization. With these innovations combined, MAP enables us to explore cell-specific heterogeneity in ductal carcinoma for every cellin a cm-sized tissue section, analyze organoid growth for advances in high-throughput tissue-on-a-chip technology, and examine individual synapses for connectome mapping over extremely wide areas. Ultimately, MAP is a fundamentally new way to interact with multiscale biophysical data.

  1. The Cancer Genome Atlas Pan-Cancer analysis project.

    PubMed

    Weinstein, John N; Collisson, Eric A; Mills, Gordon B; Shaw, Kenna R Mills; Ozenberger, Brad A; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M

    2013-10-01

    The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

  2. Beam tests of ATLAS SCT silicon strip detector modules

    SciTech Connect

    Campabadal, F.; Fleta, C.; Key, M.; Lozano, M.; Martinez, C.; Pellegrini, G.; Rafi, J.M.; Ullan, M.; Johansen, L.; Pommeresche, B.; Stugu, B.; Ciocio, A.; Fadeyev, V.; Gilchriese, M.; Haber, C.; Siegrist,J.; Spieler, H.; Vu, C.; Bell, P.J.; Charlton, D.G.; Dowell, J.D.; Gallop, B.J.; Homer, R.J.; Jovanovic, P.; Mahout, G.; McMahon, T.J.; Wilson, J.A.; Barr, A.J.; Carter, J.R.; Fromant, B.P.; Goodrick, M.J.; Hill, J.C.; Lester, C.G.; Palmer, M.J.; Parker, M.A.; Robinson, D.; Sabetfakhri, A.; Shaw, R.J.; Anghinolfi, F.; Chesi, E.; Chouridou, S.; Fortin, R.; Grosse-Knetter, M.; Gruwe, M.; Ferrari, P.; Jarron, P.; Kaplon, J.; Macpherson, A.; Niinikoski, T.; Pernegger, H.; Roe, S.; Rudge, A.; Ruggiero, G.; Wallny, R.; Weilhammer, P.; Bialas, W.; Dabrowski, W.; Grybos, P.; Koperny, S.; Blocki, J.; Bruckman, P.; Gadomski, S.; Godlewski, J.; Gornicki, E.; Malecki, P.; Moszczynski, A.; Stanecka, E.; Stodulski, M.; Szczygiel, R.; Turala, M.; Wolter, M.; Ahmad, A.; Benes, J.; Carpentieri, C.; Feld, L.; Ketterer, C.; Ludwig,J.; Meinhardt, J.; Runge, K.; Mikulec, B.; Mangin-Brinet, M.; D'Onofrio,M.; Donega, M.; Moed, S.; Sfyrla, A.; Ferrere, D.; Clark, A.G.; Perrin,E.; Weber, M.; Bates, R.L.; Cheplakov, A.; Saxon, D.H.; O'Shea, V.; Smith, K.M.; Iwata, Y.; Ohsugi, T.; Kohriki, T.; Kondo, T.; Terada, S.; Ujiie, N.; Ikegami, Y.; Unno, Y.; Takashima, R.; Brodbeck, T.; Chilingarov, A.; Hughes, G.; Ratoff, P.; Sloan, T.; Allport, P.P.; Casse,G.-L.; Greenall, A.; Jackson, J.N.; Jones, T.J.; King, B.T.; Maxfield,S.J.; Smith, N.A.; Sutcliffe, P.; Vossebeld, J.; Beck, G.A.; Carter,A.A.; Lloyd, S.L.; Martin, A.J.; Morris, J.; Morin, J.; Nagai, K.; Pritchard, T.W.; Anderson, B.E.; Butterworth, J.M.; Fraser, T.J.; Jones,T.W.; Lane, J.B.; Postranecky, M.; Warren, M.R.M.; Cindro, V.; Kramberger, G.; Mandic, I.; Mikuz, M.; Duerdoth, I.P.; Freestone, J.; Foster, J.M.; Ibbotson, M.; Loebinger, F.K.; Pater, J.; Snow, S.W.; Thompson, R.J.; Atkinson, T.M.; et al.

    2004-08-18

    The design and technology of the silicon strip detector modules for the Semiconductor Tracker (SCT) of the ATLAS experiment have been finalized in the last several years. Integral to this process has been the measurement and verification of the tracking performance of the different module types in test beams at the CERN SPS and the KEK PS. Tests have been performed to explore the module performance under various operating conditions including detector bias voltage, magnetic field, incidence angle, and state of irradiation up to 3 1014 protons per square centimeter. A particular emphasis has been the understanding of the operational consequences of the binary readout scheme.

  3. The Cancer Genome Atlas Pan-Cancer analysis project.

    PubMed

    Weinstein, John N; Collisson, Eric A; Mills, Gordon B; Shaw, Kenna R Mills; Ozenberger, Brad A; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M

    2013-10-01

    The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. PMID:24071849

  4. Vincenzo Quercioli (1876-1939), researcher and pioneer of the atlas fracture.

    PubMed

    Domenicucci, Maurizio; Dugoni, Demo Eugenio; Mancarella, Cristina; D'Elia, Alessandro; Missori, Paolo

    2015-03-01

    A review of early 20th century literature regarding fractures of the atlas led the authors to discover a paper written in Italian by Professor Vincenzo Quercioli in 1908, at that time an assistant surgeon at the University of Siena. The work was published in the journal Il Policlinico, which at that time was directed by Professor Francesco Durante. The paper described the first case of a quadripartite fracture of the atlas, and it accurately reported the mechanism of injury, symptoms, neurological examination, treatment, complications, and cause of death of the patient. Quercioli performed an autopsy on the patient and gave a detailed description of anatomopathological features. In particular, he identified the 4 symmetrical fracture lines related to the arches of the atlas and the substantial integrity of the atlantoaxial ligaments, particularly the transverse ligament. Based on those findings, Quercioli concluded that the mechanism of trauma was an axial force. This force passed through the center of the vertebral ring and caused symmetrical displacement and compression of the articular masses. These concepts of dynamic physics led Quercioli to conclude that, because the atlas is wedge shaped, the masses of the atlas reacted to stress by moving away from the center. This reaction resulted in stretching the front and rear arches, which then fractured at their 4 points of weakness. The integrity of the spinal cord was intact, based on a negative neurological examination for CNS lesions. Thus, he concluded that these injuries were not fatal and could be cured by appropriate treatment with a Minerva cast and, in the presence of swallowing disorders, with a nasogastric tube. The case described by Quercioli was later mentioned in two classic works on atlas fractures by Sir Geoffrey Jefferson, published in 1920 and 1927. In those works, Jefferson proposed his classification of 5 different anatomopathological classes; this work is widely cited in the literature and

  5. Vincenzo Quercioli (1876-1939), researcher and pioneer of the atlas fracture.

    PubMed

    Domenicucci, Maurizio; Dugoni, Demo Eugenio; Mancarella, Cristina; D'Elia, Alessandro; Missori, Paolo

    2015-03-01

    A review of early 20th century literature regarding fractures of the atlas led the authors to discover a paper written in Italian by Professor Vincenzo Quercioli in 1908, at that time an assistant surgeon at the University of Siena. The work was published in the journal Il Policlinico, which at that time was directed by Professor Francesco Durante. The paper described the first case of a quadripartite fracture of the atlas, and it accurately reported the mechanism of injury, symptoms, neurological examination, treatment, complications, and cause of death of the patient. Quercioli performed an autopsy on the patient and gave a detailed description of anatomopathological features. In particular, he identified the 4 symmetrical fracture lines related to the arches of the atlas and the substantial integrity of the atlantoaxial ligaments, particularly the transverse ligament. Based on those findings, Quercioli concluded that the mechanism of trauma was an axial force. This force passed through the center of the vertebral ring and caused symmetrical displacement and compression of the articular masses. These concepts of dynamic physics led Quercioli to conclude that, because the atlas is wedge shaped, the masses of the atlas reacted to stress by moving away from the center. This reaction resulted in stretching the front and rear arches, which then fractured at their 4 points of weakness. The integrity of the spinal cord was intact, based on a negative neurological examination for CNS lesions. Thus, he concluded that these injuries were not fatal and could be cured by appropriate treatment with a Minerva cast and, in the presence of swallowing disorders, with a nasogastric tube. The case described by Quercioli was later mentioned in two classic works on atlas fractures by Sir Geoffrey Jefferson, published in 1920 and 1927. In those works, Jefferson proposed his classification of 5 different anatomopathological classes; this work is widely cited in the literature and

  6. Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

    PubMed

    Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

    2016-01-15

    Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation. PMID:26499813

  7. Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

    PubMed

    Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

    2016-01-15

    Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation.

  8. Electron identification with a prototype of the Transition Radiation Tracker for the ATLAS experiment. ATLAS TRT collaboration

    NASA Astrophysics Data System (ADS)

    Akesson, T.; Antonov, A.; Bondarenko, V.; Bytchkov, V.; Carling, H.; Commichau, K.; Danielsson, H.; Dittus, F.; Dolgoshein, B.; Dressnandt, N.; Dulny, B.; Ebenstein, W. L.; Egede, U.; Farthouat, P.; Fent, J.; Froidevaux, D.; Gavrilenko, I.; Hanson, G.; Holder, M.; Ivochkin, V. G.; Jagielski, S.; Jaroslawski, S.; Keener, P. T.; Kisielewski, B.; Konovalov, S.; Konstantinov, A.; Kramarenko, V. A.; Lichard, P.; Lundberg, B.; Luehring, F.; Lutsch, Y.; Malecki, P.; Muraviev, S.; Nadtochy, A.; Nevski, P.; Newcomer, F. M.; Norton, P.; Nuennerich, R.; Ogren, H.; Oh, S. H.; Olszowska, J.; Pavlenko, S.; Peshekhonov, V.; Richter, R.; Romaniouk, A.; Rust, D. R.; Ryjov, V.; Saxon, D. H.; Schegelsky, V.; Schulte, R.; Semenov, S.; Shmeleva, A.; Smirnov, S.; Smirnova, L. N.; Soderberg, M.; Sosnovtsev, V.; Spiridenkov, E.; Stavrianakou, M.; Thulesius, M.; Tikhomirov, V.; Van Berg, R.; Wang, C.; White, D. J.; Williams, H. H.

    A prototype of the Transition Radiation Tracker (TRT) for the ATLAS detector at the LHC has been built and tested. The TRT is an array of straw tubes which integrate tracking and electron identification by transition radiation into one device. Results of experimental measurements and of comparisons with Monte-Carlo simulations are presented for the electron identification performance as a function of various detector parameters. Under optimal operating conditions, a rejection against pions of a factor 100 was achieved with 90% electron efficiency.

  9. Distributed usability evaluation of the Pennsylvania Cancer Atlas

    PubMed Central

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

    2008-01-01

    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 assessment strategy, we find

  10. Philippines Wind Energy Resource Atlas Development

    SciTech Connect

    Elliott, D.

    2000-11-29

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

  11. World Bank Atlas. [Twenty-Fourth Edition.

    ERIC Educational Resources Information Center

    World Bank, Washington, DC.

    This edition of the World Bank Atlas presents curent economic and social data for 185 countries and territories in the world. A number of maps, tables, and graphs highlight key relationships and trends in the development of the countries. The atlas includes data on population, gross national product (GNP), share of agriculture in gross domestic…

  12. The Copernicus ultraviolet spectral atlas of Sirius

    NASA Technical Reports Server (NTRS)

    Rogerson, John B., Jr.

    1987-01-01

    A near-ultraviolet spectral atlas for the A1 V star Alpha CMa (Sirius) has been prepared from data taken by the Princeton spectrometer aboard the Copernicus satellite. The spectral region from 1649 to 3170 A has been scanned with a resolution of 0.1 A. The atlas is presented in graphs, and line identifications for the absorption features have been tabulated.

  13. Learning with the ATLAS Experiment at CERN

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  14. Detailed transcriptome atlas of the pancreatic beta cell

    PubMed Central

    Kutlu, Burak; Burdick, David; Baxter, David; Rasschaert, Joanne; Flamez, Daisy; Eizirik, Decio L; Welsh, Nils; Goodman, Nathan; Hood, Leroy

    2009-01-01

    Background Gene expression patterns provide a detailed view of cellular functions. Comparison of profiles in disease vs normal conditions provides insights into the processes underlying disease progression. However, availability and integration of public gene expression datasets remains a major challenge. The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing beta cell gene expression, the Beta Cell Gene Atlas (BCGA). Methods We performed Massively Parallel Signature Sequencing (MPSS) analysis of human pancreatic islet samples and microarray analyses of purified rat beta cells, alpha cells and INS-1 cells, and compared the information with available array data in the literature. Results MPSS analysis detected around 7600 mRNA transcripts, of which around a third were of low abundance. We identified 2000 and 1400 transcripts that are enriched/depleted in beta cells compared to alpha cells and INS-1 cells, respectively. Microarray analysis identified around 200 transcription factors that are differentially expressed in either beta or alpha cells. We reanalyzed publicly available gene expression data and integrated these results with the new data from this study to build the BCGA. The BCGA contains basal (untreated conditions) gene expression level estimates in beta cells as well as in different cell types in human, rat and mouse pancreas. Hierarchical clustering of expression profile estimates classify cell types based on species while beta cells were clustered together. Conclusion Our gene atlas is a valuable source for detailed information on the gene expression distribution in beta cells and pancreatic islets along with insulin producing cell lines. The BCGA tool, as well as the data and code used to generate the Atlas are available at the T1Dbase website (T1DBase.org). PMID:19146692

  15. The ATLAS All-Sky Survey

    NASA Astrophysics Data System (ADS)

    Denneau, L.

    The Asteroid Terrestrial-impact Last Alert System (ATLAS) is a small project with an ambitious goal: early warning of asteroid impacts on Earth. We aim to provide one day warning for the smallest "town-killer" 30-kiloton asteroids up to three weeks for a 100-megaton impactor. ATLAS will execute a wide-field all-sky survey with four visits per footprint per night down to a sensitivity limit of V=20, suitable for detection dangerous asteroids and enabling other exciting time-domain astronomy. ATLAS is currently under construction and expects to be fully operational in late 2015. We provide an overview of the ATLAS system and discuss how ATLAS can participate in the emerging community of time-domain astronomy.

  16. Renewable Energy Atlas of the United States

    SciTech Connect

    Kuiper, J.; Hlava, K.; Greenwood, H.; Carr, A.

    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.

  17. Prostatome: A combined anatomical and disease based MRI atlas of the prostate

    SciTech Connect

    Rusu, Mirabela; Madabhushi, Anant; Bloch, B. Nicolas; Jaffe, Carl C.; Genega, Elizabeth M.; Lenkinski, Robert E.; Rofsky, Neil M.; Feleppa, Ernest

    2014-07-15

    Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides “ground truth” mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework

  18. Prostatome: A combined anatomical and disease based MRI atlas of the prostate

    PubMed Central

    Rusu, Mirabela; Bloch, B. Nicolas; Jaffe, Carl C.; Genega, Elizabeth M.; Lenkinski, Robert E.; Rofsky, Neil M.; Feleppa, Ernest; Madabhushi, Anant

    2014-01-01

    Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides “ground truth” mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework

  19. The ATLAS Detector Control System

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  20. The ATLAS TRT Barrel Detector

    NASA Astrophysics Data System (ADS)

    ATLAS TRT Collaboration; Abat, E.; Addy, T. N.; Åkesson, T. P. A.; Alison, J.; Anghinolfi, F.; Arik, E.; Arik, M.; Atoian, G.; Auerbach, B.; Baker, O. K.; Banas, E.; Baron, S.; Bault, C.; Becerici, N.; Beddall, A.; Beddall, A. J.; Bendotti, J.; Benjamin, D. P.; Bertelsen, H.; Bingul, A.; Blampey, H.; Bocci, A.; Bochenek, M.; Bondarenko, V. G.; Bychkov, V.; Callahan, J.; Capeáns Garrido, M.; Cardiel Sas, L.; Catinaccio, A.; Cetin, S. A.; Chandler, T.; Chritin, R.; Cwetanski, P.; Dam, M.; Danielsson, H.; Danilevich, E.; David, E.; Degenhardt, J.; Di Girolamo, B.; Dittus, F.; Dixon, N.; Dogan, O. B.; Dolgoshein, B. A.; Dressnandt, N.; Driouchi, C.; Ebenstein, W. L.; Eerola, P.; Egede, U.; Egorov, K.; Evans, H.; Farthouat, P.; Fedin, O. L.; Fowler, A. J.; Fratina, S.; Froidevaux, D.; Fry, A.; Gagnon, P.; Gavrilenko, I. L.; Gay, C.; Ghodbane, N.; Godlewski, J.; Goulette, M.; Gousakov, I.; Grigalashvili, N.; Grishkevich, Y.; Grognuz, J.; Hajduk, Z.; Hance, M.; Hansen, F.; Hansen, J. B.; Hansen, P. H.; Hanson, G.; Hare, G. A.; Harvey, A., Jr.; Hauviller, C.; High, A.; Hulsbergen, W.; Huta, W.; Issakov, V.; Istin, S.; Jain, V.; Jarlskog, G.; Jeanty, L.; Kantserov, V. A.; Kaplan, B.; Kapliy, A. S.; Katounine, S.; Kayumov, F.; Keener, P. T.; Kekelidze, G. D.; Khabarova, E.; Khristachev, A.; Kisielewski, B.; Kittelmann, T. H.; Kline, C.; Klinkby, E. B.; Klopov, N. V.; Ko, B. R.; Koffas, T.; Kondratieva, N. V.; Konovalov, S. P.; Koperny, S.; Korsmo, H.; Kovalenko, S.; Kowalski, T. Z.; Krüger, K.; Kramarenko, V.; Kudin, L. G.; LeBihan, A.-C.; LeGeyt, B. C.; Levterov, K.; Lichard, P.; Lindahl, A.; Lisan, V.; Lobastov, S.; Loginov, A.; Loh, C. W.; Lokwitz, S.; Long, M. C.; Lucas, S.; Lucotte, A.; Luehring, F.; Lundberg, B.; Mackeprang, R.; Maleev, V. P.; Manara, A.; Mandl, M.; Martin, A. J.; Martin, F. F.; Mashinistov, R.; Mayers, G. M.; McFarlane, K. W.; Mialkovski, V.; Mills, B. M.; Mindur, B.; Mitsou, V. A.; Mjörnmark, J. U.; Morozov, S. V.; Morris, E.; Mouraviev, S. V.; Muir, A. M.; Munar, A.; Nadtochi, A. V.; Nesterov, S. Y.; Newcomer, F. M.; Nikitin, N.; Novgorodova, O.; Novodvorski, E. G.; Ogren, H.; Oh, S. H.; Oleshko, S. B.; Olivito, D.; Olszowska, J.; Ostrowicz, W.; Passmore, M. S.; Patrichev, S.; Penwell, J.; Perez-Gomez, F.; Peshekhonov, V. D.; Petersen, T. C.; Petti, R.; Placci, A.; Poblaguev, A.; Pons, X.; Price, M. J.; hne, O. Rø; Reece, R. D.; Reilly, M. B.; Rembser, C.; Romaniouk, A.; Rousseau, D.; Rust, D.; Ryabov, Y. F.; Ryjov, V.; Söderberg, M.; Savenkov, A.; Saxon, J.; Scandurra, M.; Schegelsky, V. A.; Scherzer, M. I.; Schmidt, M. P.; Schmitt, C.; Sedykh, E.; Seliverstov, D. M.; Shin, T.; Shmeleva, A.; Sivoklokov, S.; Smirnov, S. Yu; Smirnova, L.; Smirnova, O.; Smith, P.; Sosnovtsev, V. V.; Sprachmann, G.; Subramania, S.; Suchkov, S. I.; Sulin, V. V.; Szczygiel, R. R.; Tartarelli, G.; Thomson, E.; Tikhomirov, V. O.; Tipton, P.; Valls Ferrer, J. A.; Van Berg, R.; Vassilakopoulos, V. I.; Vassilieva, L.; Wagner, P.; Wall, R.; Wang, C.; Whittington, D.; Williams, H. H.; Zhelezko, A.; Zhukov, K.

    2008-02-01

    The ATLAS TRT barrel is a tracking drift chamber using 52,544 individual tubular drift tubes. It is one part of the ATLAS Inner Detector, which consists of three sub-systems: the pixel detector spanning the radius range 4 to 20 cm, the semiconductor tracker (SCT) from 30 to 52 cm, and the transition radiation tracker (TRT) from 56 to 108 cm. The TRT barrel covers the central pseudo-rapidity region |η|< 1, and the TRT while endcaps cover the forward and backward eta regions. These TRT systems provide a combination of continuous tracking with many measurements in individual drift tubes (or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. This paper describes the recently-completed construction of the TRT Barrel detector, including the quality control procedures used in the fabrication of the detector.

  1. The New European Wind Atlas

    NASA Astrophysics Data System (ADS)

    Lundtang Petersen, Erik

    2013-04-01

    The New European Wind Atlas 1. European wind resource assessment through a ERA-NET Plus project 1.1 The new EU Atlas The Commission decided earlier this year to issue an ERA-NET Plus call for the creation and publication of a new EU wind atlas. The atlas will cover Member states as well as Member states' exclusive economic zones, both onshore and offshore. It involved the launch of a single joint call for proposals by promoters of national and/or regional programmes, thereby allowing a more efficient use of existing financial resources. Therefore the funding scheme is that of ERA-NET Plus which implies that at least 5 MS shall commit at least 1 million Euros each and the Commission tops up with on third of the MS contribution. Basically it is the MS research programmes that will execute the project but an important part of the project is to create "open project development platforms" with associated protocols allowing a wider range of scientists worldwide to contribute. The project has a duration of 5 years. The decision on the new wind atlas was taken after several years of work by the European Wind Energy Technology Platform and the European Energy Research Alliances' Joint programme for Wind Energy. 2. Structure of the project The project will be structured around three areas of work, to be implemented in parallel: 2.1 Creation and publication of a European wind atlas in electronic form, which will include the underlying data and a new EU wind climate database. The database will at a minimum include: Wind resources and their associated uncertainty; Extreme wind; Turbulence characteristics; Adverse weather conditions; Predictability for short term prediction; Guidelines. 2.2 Development of dynamical downscaling methodologies and open-source models. The developed downscaling methodologies and models will be fully documented and made public available and will be used to produce overview maps of wind resources and relevant data at several heights and a horizontal

  2. Overview of the Atlas project

    SciTech Connect

    Trainor, R.J.; Ballard, E.O.; Bartsch, R.R.

    1997-09-01

    Atlas is a high energy pulsed power facility under development at Los Alamos National Laboratory to perform high energy-density experiments in support of the Department of Energy`s stockpile stewardship responsibility. Its design is optimized for materials properties and hydrodynamics experiments under extreme conditions. Atlas will be operational in late-1999 and is designed to provide 100 shots per year. The Atlas capacitor bank design consists of a 36-MJ array of 240-kV Marx modules. The system is designed to deliver a peak current of 45--50 MA with a 4--5 {micro}s risetime. The Marx modules are designed to be reconfigured to a 480-kV configuration, if needed, for opening switch development. The bank is resistively damped to limit fault currents and capacitor voltage reversal. The system is configured for very low-inductance operation (total inductance {approximately} 10 nH) to rapidly implode heavy liner loads. An experimental program for testing and certifying prototype components is currently underway. For many applications the Atlas liner will be nominal 70g aluminum cylinder. Using composite inner layers and a variety of interior target designs, a wide variety of experiments in {approximately}cm{sup 3} volumes may be performed. These include shock compression experiments up to {approximately} 3 TPa (30 Mbar), quasi-adiabatic compressions up to 6-fold compression and pressures above 10 TPa, hydrodynamic instability studies in nonlinear and turbulent regimes over multi-cm propagation lengths, experiments with dense plasmas in the so-called high-gamma regime, studies of materials response at very high strains and strain rates, and materials studies in ultrahigh magnetic fields (above 10{sup 3} T).

  3. Stuart R. Stidolph diatom atlas

    USGS Publications Warehouse

    Stidolph, S.R.; Sterrenburg, F.A.S.; Smith, K.E.L.; Kraberg, A.

    2012-01-01

    The "Stuart R. Stidolph Diatom Atlas" is a comprehensive volume of diatom taxa identified and micrographed by Stuart R. Stidoph during the 1980s and 1990s. The samples were collected from marine coasts of various geographic regions within tropical and subtropical climates. The plates included within this report have never been published and are being published by the USGS as an online reference so that others may have access to this incredible collection.

  4. Atlas-based diffusion tensor imaging correlates of executive function

    PubMed Central

    Nowrangi, Milap A.; Okonkwo, Ozioma; Lyketsos, Constantine; Oishi, Kenichi; Mori, Susumu; Albert, Marilyn; Mielke, Michelle M.

    2015-01-01

    Impairment in executive function (EF) is commonly found in Alzheimer’s Dementia (AD) and Mild Cognitive Impairment (MCI). Atlas-based Diffusion Tensor Imaging (DTI) methods may be useful in relating regional integrity to EF measures in MCI and AD. 66 participants (25 NC, 22 MCI, and 19 AD) received DTI scans and clinical evaluation. DTI scans were applied to a pre-segmented atlas and fractional anisotropy (FA) and mean diffusivity (MD) were calculated. ANOVA was used to assess group differences in frontal, parietal, and cerebellar regions. For regions differing between groups (p<0.01), linear regression examined the relationship between EF scores and regional FA and MD. Anisotropy and diffusivity in frontal and parietal lobe white matter (WM) structures were associated with EF scores in MCI and only frontal lobe structures in AD. EF was more strongly associated with FA than MD. The relationship between EF and anisotropy and diffusivity was strongest in MCI. These results suggest that regional WM integrity is compromised in MCI and AD and that FA may be a better correlate of EF than MD. PMID:25318544

  5. Recent faulting and active shortening of the Middle Atlas Mountains, Morocco, within the diffuse African-Eurasian plate boundary

    NASA Astrophysics Data System (ADS)

    Rigby, M.; Gomez, F.; Zakir, A.; Hahou, Y.; Jabour, N.

    2007-12-01

    The NE-SW trending Middle Atlas Mountains are an active intracontinental mountain belt within the diffuse African - Eurasian plate boundary. The mountain belt is obliquely oriented to the NNW-SSE direction of Late Cenozoic plate convergence. Both shear and compressional features are exhibited with apparent slip partitioning: Folding and thrusting is concentrated in the Folded Middle Atlas, whereas strike-slip dominates in the Tabular Middle Atlas. In the central part of the Folded Middle Atlas, fault scarps of Quaternary alluvium, including a 4.5 meter (probably composite) scarp and a 1 meter (possibly single event) scarp, attest to recent faulting along the mountain front. Detailed topographic mapping of the scarps provides a basis for geomorphic analysis and degradation modeling. Furthermore, the reconstruction of longitudinal stream terrace profiles helps constrain a long term deformation history. Radiocarbon and pending cosmogenic dates provide age constraints on the faulted surfaces and the multiple stream terraces in the area. To place these active tectonic observations in a larger context, the fault and fold geometry has been assessed by completing a 10 km structural transect across the frontal thrust, providing basis for the construction of a balanced cross-section. By combining the structural geometry with the uplift rate, a minimum estimate of the rate of horizontal shortening in the Middle Atlas can be evaluated. Preliminary results suggest the Middle Atlas may accommodate 5 - 10 percent of the total 4.5 mm/yr convergence between the African and Eurasian plates. These results demonstrate that the Middle Atlas Mountains are a integral part of the diffuse plate boundary, as well as suggesting a modest level of earthquake hazard in the region.

  6. Geomorphology and geomorphological heritage of the Ifrane-Azrou region (Middle Atlas, Morocco)

    NASA Astrophysics Data System (ADS)

    de Waele, Jo; Melis, Maria Teresa

    2009-08-01

    Geomorphological heritage is a widely used term in European and North-American countries, but is still scarcely mentioned in Africa. Nevertheless, the attractiveness of the African countries is often intimately connected to its breathtaking and endless geological landscapes. Morocco is one of those countries that has the widest diversity in landscapes and landforms, ranging from the Mediterranean and Atlantic coasts over the Rif, Middle Atlas, High Atlas and Anti-Atlas mountain chains to the great rocky and sandy deserts in the South. A wide variety of geological units hosting different types of important economic mineral deposits cover a temporal range from Late Precambrian to Quaternary. A detailed geomorphological study has been carried out in the region of Ifrane and Azrou (Middle Atlas, Central Morocco) using a combination of high resolution satellite data and direct field observations integrated by geological maps and scientific literature. In order to describe and evaluate the geomorphological heritage of this area, 40 geomorphosites have been selected comprising springs, karst landforms (polje, dolines, caves, sinkholes, stone forests, cryptokarstic dolines), carbonate depositional landforms (travertines and waterfalls), fluvial landforms (meanders, canyons, palaeo-valleys, etc.), structural landforms (triangular facets, hogbacks, cuestas, residual outcrops, etc.) and volcanic landforms (volcanoes, caldeira, pyroclastic cones, lava tube). The results of this research have been summarised in a thematic map, representing the geomorphosites related to various landscape units.

  7. Detector control system for the ATLAS Transition Radiation Tracker: architecture and development techniques

    NASA Astrophysics Data System (ADS)

    Banaś, ElŻbieta; Hajduk, Zbigniew; Olszowska, Jolanta

    2012-05-01

    The ATLAS Transition Radiation Tracker (TRT) is the outermost of the three sub-systems of the ATLAS Inner Detector at the Large Hadron Collider at CERN. With ~300000 drift tube proportional counters (straws) filled with stable gas mixture and high voltage biased it provides precise quasi-continuous tracking and particles identification. Safe, coherent and efficient operation of the TRT is fulfilled with the help of the Detector Control System (DCS) running on 11 computers as PVSS (industrial SCADA) projects. Standard industrial and custom developed server applications and protocols are used for reading hardware parameters. Higher level control system layers based on the CERN JCOP framework allow for automatic control procedures, efficient error recognition and handling and provide a synchronization mechanism with the ATLAS data acquisition system. Different data bases are used to store the detector online parameters, the configuration parameters and replicate a subset of them used to flag data quality for physics reconstruction. The TRT DCS is fully integrated with the ATLAS Detector Control System.

  8. Space qualification of the optical filter assemblies for the ICESat-2/ATLAS instrument

    NASA Astrophysics Data System (ADS)

    Troupaki, E.; Denny, Z. H.; Wu, S.; Bradshaw, H. N.; Smith, K. A.; Hults, J. A.; Ramos-Izquierdo, L. A.; Cook, W. B.

    2015-02-01

    The Advanced Topographic Laser Altimeter System (ATLAS) will be the only instrument on the Ice, Cloud, and Land Elevation Satellite -2 (ICESat-2). ICESat-2 is the 2nd-generation of the orbiting laser altimeter ICESat, which will continue polar ice topography measurements with improved precision laser-ranging techniques. In contrast to the original ICESat design, ICESat-2 will use a micro-pulse, multi-beam approach that provides dense cross-track sampling to help scientists determine a surface's slope with each pass of the satellite. The ATLAS laser will emit visible, green laser pulses at a wavelength of 532 nm and a rate of 10 kHz and will be split into 6 beams. A set of six identical, thermally tuned optical filter assemblies (OFA) will be used to remove background solar radiation from the collected signal while transmitting the laser light to the detectors. A seventh assembly will be used to monitor the laser center wavelength during the mission. In this paper, we present the design and optical performance measurements of the ATLAS OFA in air and in vacuum prior to their integration on the ATLAS instrument.

  9. Space Qualification of the Optical Filter Assemblies for the ICESat-2/ATLAS Instrument

    NASA Technical Reports Server (NTRS)

    Troupaki, E.; Denny, Z. H.; Wu, S.; Bradshaw, H. N.; Smith, K. A.; Hults, J. A.; Ramos-Izquierdo, L. A.; Cook, W. B.

    2015-01-01

    The Advanced Topographic Laser Altimeter System (ATLAS) will be the only instrument on the Ice, Cloud, and Land Elevation Satellite -2 (ICESat-2). ICESat-2 is the 2nd-generation of the orbiting laser altimeter ICESat, which will continue polar ice topography measurements with improved precision laser-ranging techniques. In contrast to the original ICESat design, ICESat-2 will use a micro-pulse, multi-beam approach that provides dense cross-track sampling to help scientists determine a surface's slope with each pass of the satellite. The ATLAS laser will emit visible, green laser pulses at a wavelength of 532 nm and a rate of 10 kHz and will be split into 6 beams. A set of six identical, thermally tuned optical filter assemblies (OFA) will be used to remove background solar radiation from the collected signal while transmitting the laser light to the detectors. A seventh assembly will be used to monitor the laser center wavelength during the mission. In this paper, we present the design and optical performance measurements of the ATLAS OFA in air and in vacuum prior to their integration on the ATLAS instrument.

  10. Space Qualification of the Optical Filter Assemblies for the ICESat-2/ATLAS Instrument

    NASA Technical Reports Server (NTRS)

    Troupaki, Elisavet; Denny, Zachary; Wu, Stewart; Bradshaw, Heather; Smith, Kevin; Hults, Judy; Ramos-Izquierdo, Luis; Cook, William

    2015-01-01

    The Advanced Topographic Laser Altimeter System (ATLAS) will be the only instrument on the Ice, Cloud, and Land Elevation Satellite -2 (ICESat-2). ICESat-2 is the 2nd-generation of the orbiting laser altimeter ICESat, which will continue polar ice topography measurements with improved precision laser-ranging techniques. In contrast to the original ICESat design, ICESat-2 will use a micro-pulse, multi-beam approach that provides dense cross-track sampling to help scientists determine a surface's slope with each pass of the satellite. The ATLAS laser will emit visible, green laser pulses at a wavelength of 532 nm and a rate of 10 kHz and will be split into 6 beams. A set of six identical, thermally-tuned etalon filter assemblies will be used to remove background solar radiation from the collected signal while transmitting the laser light to the detectors. A seventh etalon assembly will be used to monitor the laser center wavelength during the mission. In this paper, we present the design and optical performance measurements of the ATLAS optical filter assemblies (OFA) in air and in vacuum before integration on the ATLAS instrument.

  11. STS-56 ATLAS-2 pallet is lowered into OV-103's payload bay at KSC's OPF HB-3

    NASA Technical Reports Server (NTRS)

    1993-01-01

    STS-56 Atmospheric Laboratory for Applications and Science 2 (ATLAS-2) unpressurized spacelab pallet and the mission peculiar support structure (MPESS)-mounted Shuttle Pointed Autonomous Research Tool for Astronomy 201 (SPARTAN-201) are lowered into the payload bay (PLB) of Discovery, Orbiter Vehicle (OV) 103, at the Kennedy Space Center's (KSC's) Orbiter Processing Facility (OPF) High Bay 3 (HB-3) during preflight integration. Clean-suited technicians monitor the progress and operation of the overhead crane from which the ATLAS-2 pallet/SPARTAN MPESS are suspended. ATLAS-2 equipment and instruments include: the igloo (cylindrical tank - front and center); the inverters and pump package (far right); port conical scan sensor (next to pump package at far right); the millimeter-wave atmospheric sounder (MAS) antenna (pallet center, just above igloo); the starboard conical scan sensor (small cylinder at far left); and the atmospheric trace module spectroscopy (ATMOS) (box behind conical se

  12. ATLAS: Big Data in a Small Package

    NASA Astrophysics Data System (ADS)

    Denneau, Larry; Tonry, John

    2015-08-01

    For even small telescope projects, the petabyte scale is now upon us. The Asteroid Terrestrial-impact Last Alert System (ATLAS; Tonry 2011) will robotically survey the entire visible sky from Hawaii multiple times per night to search for near-Earth asteroids (NEAs) on impact trajectories. While the ATLAS optical system is modest by modern astronomical standards -- two 0.5 m F/2.0 telescopes -- each year the ATLAS system will obtain ~103 measurements of 109 astronomical sources to a photometric accuracy of <5%. This ever-growing dataset must be searched in real-time for moving objects then archived for further analysis, and alerts for newly discovered near-Earth NEAs disseminated within tens of minutes from detection. ATLAS's all-sky coverage ensures it will discover many ``rifle shot'' near-misses moving rapidly on the sky as they shoot past the Earth, so the system will need software to automatically detect highly-trailed sources and discriminate them from the thousands of satellites and pieces of space junk that ATLAS will see each night. Additional interrogation will identify interesting phenomena from beyond the solar system occurring over millions of transient sources per night. The data processing and storage requirements for ATLAS demand a ``big data'' approach typical of commercial Internet enterprises. We describe our approach to deploying a nimble, scalable and reliable data processing infrastructure, and promote ATLAS as steppingstone to eventual processing scales in the era of LSST.

  13. Atlas capabilities for non-geosynchronous orbits

    NASA Astrophysics Data System (ADS)

    Henley, M.; Huynh, C.

    1992-03-01

    Atlas, with the Centaur upper stage, is well known for launching geosynchronous communications satellites. Atlas, however, also has excellent capabilities for launches to other, nongeosynchronous orbits which can be useful for communications. In 1958, an Atlas launched Score, the first spacecraft to be used for communications, into a nongeosynchronous orbit. In the 1990s, single launches of Atlas vehicles will be able to deliver many small spacecraft at a time to deploy constellations of communications satellites in low earth orbits. Atlas vehicles are also well suited to launch specialized spacecraft into escape trajectories for communication between earth and the moon, Mars, and other planetary bodies. Payload weight capabilities of the Atlas family cover the range necessary for the wide variety of nongeosynchronous communications satellite systems being considered. This robust range of capabilities provides enough margin to accommodate potential spacecraft weight growth during development. Atlas capabilities, developed through 33 years of communications satellite launch experience, are readily adaptable to meet the needs of the new market for communications satellites in nongeosynchronous orbits.

  14. Experimental and code simulation of a station blackout scenario for APR1400 with test facility ATLAS and MARS code

    SciTech Connect

    Yu, X. G.; Kim, Y. S.; Choi, K. Y.; Park, H. S.; Cho, S.; Kang, K. H.; Choi, N. H.

    2012-07-01

    A SBO (station blackout) experiment named SBO-01 was performed at full-pressure IET (Integral Effect Test) facility ATLAS (Advanced Test Loop for Accident Simulation) which is scaled down from the APR1400 (Advanced Power Reactor 1400 MWe). In this study, the transient of SBO-01 is discussed and is subdivided into three phases: the SG fluid loss phase, the RCS fluid loss phase, and the core coolant depletion and core heatup phase. In addition, the typical phenomena in SBO-01 test - SG dryout, natural circulation, core coolant boiling, the PRZ full, core heat-up - are identified. Furthermore, the SBO-01 test is reproduced by the MARS code calculation with the ATLAS model which represents the ATLAS test facility. The experimental and calculated transients are then compared and discussed. The comparison reveals there was malfunction of equipments: the SG leakage through SG MSSV and the measurement error of loop flow meter. As the ATLAS model is validated against the experimental results, it can be further employed to investigate the other possible SBO scenarios and to study the scaling distortions in the ATLAS. (authors)

  15. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.

    PubMed

    Omberg, Larsson; Ellrott, Kyle; Yuan, Yuan; Kandoth, Cyriac; Wong, Chris; Kellen, Michael R; Friend, Stephen H; Stuart, Josh; Liang, Han; Margolin, Adam A

    2013-10-01

    The Cancer Genome Atlas Pan-Cancer Analysis Working Group collaborated on the Synapse software platform to share and evolve data, results and methodologies while performing integrative analysis of molecular profiling data from 12 tumor types. The group's work serves as a pilot case study that provides (i) a template for future large collaborative studies; (ii) a system to support collaborative projects; and (iii) a public resource of highly curated data, results and automated systems for the evaluation of community-developed models.

  16. Evaluation of Atlas-Based White Matter Segmentation with Eve

    PubMed Central

    Plassard, Andrew J.; Hinton, Kendra E.; Venkatraman, Vijay; Gonzalez, Christopher; Resnick, Susan M.; Landman, Bennett A.

    2015-01-01

    Multi-atlas labeling has come in wide spread use for whole brain labeling on magnetic resonance imaging. Recent challenges have shown that leading techniques are near (or at) human expert reproducibility for cortical gray matter labels. However, these approaches tend to treat white matter as essentially homogeneous (as white matter exhibits isointense signal on structural MRI). The state-of-the-art for white matter atlas is the single-subject Johns Hopkins Eve atlas. Numerous approaches have attempted to use tractography and/or orientation information to identify homologous white matter structures across subjects. Despite success with large tracts, these approaches have been plagued by difficulties in with subtle differences in course, low signal to noise, and complex structural relationships for smaller tracts. Here, we investigate use of atlas-based labeling to propagate the Eve atlas to unlabeled datasets. We evaluate single atlas labeling and multi-atlas labeling using synthetic atlases derived from the single manually labeled atlas. On 5 representative tracts for 10 subjects, we demonstrate that (1) single atlas labeling generally provides segmentations within 2mm mean surface distance, (2) morphologically constraining DTI labels within structural MRI white matter reduces variability, and (3) multi-atlas labeling did not improve accuracy. These efforts present a preliminary indication that single atlas labels with correction is reasonable, but caution should be applied. To purse multi-atlas labeling and more fully characterize overall performance, more labeled datasets would be necessary. PMID:25914503

  17. An Atlas of Submarine Glacial Landforms: Modern, Quaternary and Ancient

    NASA Astrophysics Data System (ADS)

    Jakobsson, M.; Dowdeswell, J. A.; Canals, M.; Todd, B. J.; Dowdeswell, E. K.; Hogan, K. A.

    2014-12-01

    In the past two decades there have been several advances that make the production of an atlas of submarine glacial landforms timely. First is the development of high-resolution imaging technologies; multi-beam echo-sounding or swath bathymetry that allows the detailed mapping of the sea floor at water depths of tens to thousands of metres across continental margins, and 3-D seismic methods that enable the visualisation of palaeo-continental shelves in Quaternary sediments and ancient palaeo-glacial rocks (e.g. Late Ordovician of Northern Africa). A second technological development is that of ice-breaking or ice-strengthened ships that can penetrate deep into the ice-infested waters of the Arctic and Antarctic, to deploy the multibeam systems. A third component is that of relevance - through both the recognition that the polar regions, and especially the Arctic, are particularly sensitive parts of the global environmental system and that these high-latitude margins (both modern and ancient) are likely to contain significant hydrocarbon resources. An enhanced understanding of the sediments and landforms of these fjord-shelf-slope systems is, therefore, of increasing importance to both academics and industry. We are editing an Atlas of Submarine Glacial Landforms that presents a series of individual contributions that describe, discuss and illustrate features on the high-latitude, glacier-influenced sea floor. Contributions are organised in two ways: first, by position on a continental margin - from fjords, through continental shelves to the continental slope and rise; secondly, by scale - as individual landforms and assemblages of landforms. A final section provides discussion of integrated fjord-shelf-slope systems. Over 100 contributions by scientists from many countries contain descriptions and interpretation of swath-bathymetric data from both Arctic and Antarctic margins and use 3D seismic data to investigate ancient glacial landforms. The Atlas will be

  18. ATLAS diboson excess from Stueckelberg mechanism

    NASA Astrophysics Data System (ADS)

    Feng, Wan-Zhe; Liu, Zuowei; Nath, Pran

    2016-04-01

    We discuss the diboson excess seen by the ATLAS collaboration around 2 TeV in the LHC run I at √{s}=8 TeV. We explore the possibility that such an excess can arise from a Z' boson which acquires mass through a U(1) X Stueckelberg extension. The corresponding Z' gauge boson is leptophobic with a mass of around 2 TeV and has interactions with SU(2) L Yang-Mills fields and gauge fields of the hypercharge. The analysis predicts Z' decays into WW and ZZ as well as into Zγ. Further three-body as well as four-body decays of the Z' such as WWZ, WWγ, WWZZ etc are predicted. In the analysis we use the helicity formalism which allows us to exhibit the helicity structure of the Z' decay processes in an transparent manner. In particular, we are able to show the set of vanishing helicity amplitudes in the decay of the massive Z' into two vector bosons due to angular momentum conservation with a special choice of the reference momenta. The residual set of non-vanishing helicity amplitudes are identified. The parameter space of the model compatible with the diboson excess seen by the ATLAS experiment at √{s}=8 TeV is exhibited. Estimate of the diboson excess expected at √{s}=13 TeV with 20 fb-1 of integrated luminosity at LHC run II is also given. It is shown that the WW, ZZ and Zγ modes are predicted to be in the approximate ratio 1 : cos2 θ W (1 + α tan2 θ W )2 /2 : (1 - α)2 sin2 θ W /2 where α is the strength of the coupling of Z' with the hypercharge gauge field relative to the coupling with the Yang-Mills gauge fields. Thus observation of the Zγ mode as well as three-body and four-body decay modes of the Z' will provide a definite test of the model and of a possible new source of interaction beyond the standard model.

  19. Full supersymmetry simulation for ATLAS in DC1

    SciTech Connect

    Biglietti, Michela; Brochu, Frederic; Costanzo, Davide; De, Kaushik; Duchovni, Ehud; Gupta, Ambreesh; Hinchliffe, Ian; Lester, Chris; Lipniacka, Anna; Loch, Peter; Lytken, Else; Ma, Hong; Nielsen, Jakob L.; Paige, Frank; Polesello, Giacomo; Rajagopalan, Srini; Schrager, Dan; Stavropoulos, Georgios; Tovey, Dan; Wielers, Monika

    2004-01-26

    This note reports results from a simulation of 100k events for one example of a minimal SUGRA supersymmetry case at the LHC using full simulation of the ATLAS detector. It was carried out as part ATLAS Data Challenge 1.

  20. Atlases in the Collection of Moellering Memorial Library, Valparaiso University. A Selected and Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hess, Elmer B., Comp.

    Following a brief discussion of the evolution of the atlas and its importance as a library reference tool, an annotated description is provided of each atlas found in this university library collection. Items in the bibliography are arranged in the following categories: (1) world atlases; (2) regional atlases; (3) national atlases; (4) state…

  1. ATLAS job monitoring in the Dashboard Framework

    NASA Astrophysics Data System (ADS)

    Andreeva, J.; Campana, S.; Karavakis, E.; Kokoszkiewicz, L.; Saiz, P.; Sargsyan, L.; Schovancova, J.; Tuckett, D.

    2012-12-01

    Monitoring of the large-scale data processing of the ATLAS experiment includes monitoring of production and user analysis jobs. The Experiment Dashboard provides a common job monitoring solution, which is shared by ATLAS and CMS experiments. This includes an accounting portal as well as real-time monitoring. Dashboard job monitoring for ATLAS combines information from the PanDA job processing database, Production system database and monitoring information from jobs submitted through GANGA to Workload Management System (WMS) or local batch systems. Usage of Dashboard-based job monitoring applications will decrease load on the PanDA database and overcome scale limitations in PanDA monitoring caused by the short job rotation cycle in the PanDA database. Aggregation of the task/job metrics from different sources provides complete view of job processing activity in ATLAS scope.

  2. Pocket atlas of cranial magnetic resonance imaging

    SciTech Connect

    Haughton, V.M.; Daniels, D.L.

    1986-01-01

    This atlas illustrates normal cerebral anatomy in magnetic resonance images. From their studies in cerebral anatomy utilizing cryomicrotome and other techniques, the authors selected more than 100 high-resolution images that represent the most clinically useful scans.

  3. HEAVY ION PHYSICS WITH THE ATLAS DETECTOR.

    SciTech Connect

    WHITE, S.

    2005-02-05

    Soon after the LHC is commissioned with proton beams the ATLAS experiment will begin studies of Pb-Pb collisions with a center of mass energy of {radical}s{sub NN} = 5.5 TeV. The ATLAS program is a natural extension of measurements at RHIC in a direction that exploits the higher LHC energies and the superb ATLAS calorimeter and tracking coverage. At LHC energies, collisions will be produced with even higher energy density than observed at RHIC. The properties of the resulting hot medium can be studied with higher energy probes, which are more directly interpreted through modification of jet properties emerging from these collisions, for example. Other topics which are enabled by the 30-fold increase in center of mass energy include probing the partonic structure of nuclei with hard photoproduction (in UltraPeripheral collisions) and in p-Pb collisions. Here we report on evaluation of ATLAS capabilities for Heavy Ion Physics.

  4. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.

    PubMed

    Henry, Alex M; Hohmann, John G

    2012-10-01

    Knowledge of the structure, genetics, circuits, and physiological properties of the mammalian brain in both normal and pathological states is ever increasing as research labs worldwide probe the various aspects of brain function. Until recently, however, comprehensive cataloging of gene expression across the central nervous system has been lacking. The Allen Institute for Brain Science, as part of its mission to propel neuroscience research, has completed several large gene-mapping projects in mouse, nonhuman primate, and human brain, producing informative online public resources and tools. Here we present the Allen Mouse Brain Atlas, covering ~20,000 genes throughout the adult mouse brain; the Allen Developing Mouse Brain Atlas, detailing expression of approximately 2,000 important developmental genes across seven embryonic and postnatal stages of brain growth; and the Allen Spinal Cord Atlas, revealing expression for ~20,000 genes in the adult and neonatal mouse spinal cords. Integrated data-mining tools, including reference atlases, informatics analyses, and 3-D viewers, are described. For these massive-scale projects, high-throughput industrial techniques were developed to standardize and reliably repeat experimental goals. To verify consistency and accuracy, a detailed analysis of the 1,000 most viewed genes for the adult mouse brain (according to website page views) was performed by comparing our data with peer-reviewed literature and other databases. We show that our data are highly consistent with independent sources and provide a comprehensive compendium of information and tools used by thousands of researchers each month. All data and tools are freely available via the Allen Brain Atlas portal (www.brain-map.org).

  5. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.

    PubMed

    Henry, Alex M; Hohmann, John G

    2012-10-01

    Knowledge of the structure, genetics, circuits, and physiological properties of the mammalian brain in both normal and pathological states is ever increasing as research labs worldwide probe the various aspects of brain function. Until recently, however, comprehensive cataloging of gene expression across the central nervous system has been lacking. The Allen Institute for Brain Science, as part of its mission to propel neuroscience research, has completed several large gene-mapping projects in mouse, nonhuman primate, and human brain, producing informative online public resources and tools. Here we present the Allen Mouse Brain Atlas, covering ~20,000 genes throughout the adult mouse brain; the Allen Developing Mouse Brain Atlas, detailing expression of approximately 2,000 important developmental genes across seven embryonic and postnatal stages of brain growth; and the Allen Spinal Cord Atlas, revealing expression for ~20,000 genes in the adult and neonatal mouse spinal cords. Integrated data-mining tools, including reference atlases, informatics analyses, and 3-D viewers, are described. For these massive-scale projects, high-throughput industrial techniques were developed to standardize and reliably repeat experimental goals. To verify consistency and accuracy, a detailed analysis of the 1,000 most viewed genes for the adult mouse brain (according to website page views) was performed by comparing our data with peer-reviewed literature and other databases. We show that our data are highly consistent with independent sources and provide a comprehensive compendium of information and tools used by thousands of researchers each month. All data and tools are freely available via the Allen Brain Atlas portal (www.brain-map.org). PMID:22832508

  6. EnviroAtlas: Two Use Cases in the EnviroAtlas

    EPA Science Inventory

    EnviroAtlas is an online spatial decision support tool for viewing and analyzing the supply, demand, and drivers of change related to natural and built infrastructure at multiple scales for the nation. To maximize usefulness to a broad range of users, EnviroAtlas contains trainin...

  7. EnviroAtlas: Incorporation of EnviroAtlas as a Major Component of EcoInforma

    EPA Science Inventory

    EnviroAtlas is a collection of interactive tools and resources that help inform decision-making and allow users to explore the many benefits people receive from nature, often referred to as ecosystem services. EnviroAtlas was publicly released in May 2014. Ecoinformatics-based O...

  8. Atlas F entry aerothermic study

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The feasibility of obtaining heat transfer data on an expended Atlas F booster launch vehicle was investigated in the altitude range of 300,000 to 200,000 feet during entry conditions, with a velocity in the range of 20,000 to 25,000 feet per second, and through a range of vehicle attitudes of plus or minus 90 degrees. These data are desired for correlation with turbulent heat transfer and boundary layer transition data obtained from wind tunnel test facilities. The data would also be valuable in assessing rarified gas and surface catalicity effects in a real gas environment.

  9. The ATLAS Series of Shuttle Missions

    NASA Technical Reports Server (NTRS)

    Kaye, Jack A.; Miller, Timothy L.

    1996-01-01

    The ATLAS space shuttle missions were conducted in March 1992, April 1993, and November 1994. The ATLAS payload and companion instruments made measurements of solar irradiance and middle atmospheric temperatures and trace gas concentrations. The solar irradiance measurements included total and spectrally resolved solar irradiance. The atmospheric measurements included microwave, infrared, and ultraviolet limb sounding, nadir ultraviolet backscatter, and solar occultation techniques. This paper introduces a special section in this issue of Geophysical Research Letters.

  10. ATLAS discovery of an optical transient

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  11. Optimal atlas construction through hierarchical image registration

    NASA Astrophysics Data System (ADS)

    Grevera, George J.; Udupa, Jayaram K.; Odhner, Dewey; Torigian, Drew A.

    2016-03-01

    Atlases (digital or otherwise) are common in medicine. However, there is no standard framework for creating them from medical images. One traditional approach is to pick a representative subject and then proceed to label structures/regions of interest in this image. Another is to create a "mean" or average subject. Atlases may also contain more than a single representative (e.g., the Visible Human contains both a male and a female data set). Other criteria besides gender may be used as well, and the atlas may contain many examples for a given criterion. In this work, we propose that atlases be created in an optimal manner using a well-established graph theoretic approach using a min spanning tree (or more generally, a collection of them). The resulting atlases may contain many examples for a given criterion. In fact, our framework allows for the addition of new subjects to the atlas to allow it to evolve over time. Furthermore, one can apply segmentation methods to the graph (e.g., graph-cut, fuzzy connectedness, or cluster analysis) which allow it to be separated into "sub-atlases" as it evolves. We demonstrate our method by applying it to 50 3D CT data sets of the chest region, and by comparing it to a number of traditional methods using measures such as Mean Squared Difference, Mattes Mutual Information, and Correlation, and for rigid registration. Our results demonstrate that optimal atlases can be constructed in this manner and outperform other methods of construction using freely available software.

  12. The Copernicus ultraviolet spectral atlas Tau Scorpii

    NASA Technical Reports Server (NTRS)

    Rogerson, J. B., Jr.; Upson, W. L., II

    1977-01-01

    An ultraviolet spectral atlas was presented for the B0 V star, Tau Scorpii. It was scanned from 949 to 1560 A by the Princeton spectrometer aboard the Copernicus satellite. From 949 to 1420 A the observations have a nominal resolution of 0.05 A. At the longer wavelengths, the resolution was 0.1 A. The atlas was presented in both tables and graphs.

  13. The Copernicus ultraviolet spectral atlas of Vega

    NASA Technical Reports Server (NTRS)

    Rogerson, John B., Jr.

    1989-01-01

    A near-ultraviolet spectral atlas for the A0 V star Alpha Lyr (Vega) has been prepared from data taken by the Princeton spectrometer aboard the Copernicus satellite. The spectral region from 2000 to 3187 A has been scanned with a resolution of 0.1 A. The atlas is presented in graphs with a normalized continuum, and an identification table for the absorption features has been prepared.

  14. Statistical 3D prostate imaging atlas construction via anatomically constrained registration

    NASA Astrophysics Data System (ADS)

    Rusu, Mirabela; Bloch, B. Nicolas; Jaffe, Carl C.; Rofsky, Neil M.; Genega, Elizabeth M.; Feleppa, Ernest; Lenkinski, Robert E.; Madabhushi, Anant

    2013-03-01

    Statistical imaging atlases allow for integration of information from multiple patient studies collected across different image scales and modalities, such as multi-parametric (MP) MRI and histology, providing population statistics regarding a specific pathology within a single canonical representation. Such atlases are particularly valuable in the identification and validation of meaningful imaging signatures for disease characterization in vivo within a population. Despite the high incidence of prostate cancer, an imaging atlas focused on different anatomic structures of the prostate, i.e. an anatomic atlas, has yet to be constructed. In this work we introduce a novel framework for MRI atlas construction that uses an iterative, anatomically constrained registration (AnCoR) scheme to enable the proper alignment of the prostate (Pr) and central gland (CG) boundaries. Our current implementation uses endorectal, 1.5T or 3T, T2-weighted MRI from 51 patients with biopsy confirmed cancer; however, the prostate atlas is seamlessly extensible to include additional MRI parameters. In our cohort, radical prostatectomy is performed following MP-MR image acquisition; thus ground truth annotations for prostate cancer are available from the histological specimens. Once mapped onto MP-MRI through elastic registration of histological slices to corresponding T2-w MRI slices, the annotations are utilized by the AnCoR framework to characterize the 3D statistical distribution of cancer per anatomic structure. Such distributions are useful for guiding biopsies toward regions of higher cancer likelihood and understanding imaging profiles for disease extent in vivo. We evaluate our approach via the Dice similarity coefficient (DSC) for different anatomic structures (delineated by expert radiologists): Pr, CG and peripheral zone (PZ). The AnCoR-based atlas had a CG DSC of 90.36%, and Pr DSC of 89.37%. Moreover, we evaluated the deviation of anatomic landmarks, the urethra and

  15. The Read Out Controller for the ATLAS New Small Wheel

    NASA Astrophysics Data System (ADS)

    Coliban, R.-M.; Popa, S.; Tulbure, T.; Nicula, D.; Ivanovici, M.; Martoiu, S.; Levinson, L.; Vermeulen, J.

    2016-02-01

    In the upgrade process of the ATLAS detector, the innermost stations of the endcaps (Small Wheels) will be replaced. The New Small Wheel will have two chamber technologies, small-strip Thin Gap Chambers and Micromegas, each providing triggering and precision track measurement. Custom front-end Application Specific Integrated Circuits will be used to read and filter information from both types of detectors. In the context of the New Small Wheel data path, the Read Out Controller ASIC is used for handling, preprocessing and formatting the data generated by the VMM upstream chips. The Read Out Controller will concentrate the data streams from 8 VMMs, filter data based on the ATLAS Level-1 trigger which identifies bunch crossings of interest and transmit the data to FELIX via the L1DDC. The Read Out Controller is composed of 8 VMM Capture modules, a cross-bar and 4 sROC modules. The output data is sent via up to 4 serial links with a configurable speed of 80, 160 or 320 Mbps per link.

  16. Disease-Specific Probabilistic Brain Atlases

    PubMed Central

    Thompson, Paul; Mega, Michael S.; Toga, Arthur W.

    2009-01-01

    Atlases of the human brain, in health and disease, provide a comprehensive framework for understanding brain structure and function. The complexity and variability of brain structure, especially in the gyral patterns of the human cortex, present challenges in creating standardized brain atlases that reflect the anatomy of a population. This paper introduces the concept of a population-based, disease-specific brain atlas that can reflect the unique anatomy and physiology of a particular clinical subpopulation. Based on well-characterized patient groups, disease-specific atlases contain thousands of structure models, composite maps, average templates, and visualizations of structural variability, asymmetry and group-specific differences. They correlate the structural, metabolic, molecular and histologic hallmarks of the disease. Rather than simply fusing information from multiple subjects and sources, new mathematical strategies are introduced to resolve group-specific features not apparent in individual scans. High-dimensional elastic mappings, based on covariant partial differential equations, are developed to encode patterns of cortical variation. In the resulting brain atlas, disease-specific features and regional asymmetries emerge that are not apparent in individual anatomies. The resulting probabilistic atlas can identify patterns of altered structure and function, and can guide algorithms for knowledge-based image analysis, automated image labeling, tissue classification, data mining and functional image analysis. PMID:19424457

  17. A Digital Atlas of the Dog Brain

    PubMed Central

    Datta, Ritobrato; Lee, Jongho; Duda, Jeffrey; Avants, Brian B.; Vite, Charles H.; Tseng, Ben; Gee, James C.; Aguirre, Gustavo D.; Aguirre, Geoffrey K.

    2012-01-01

    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). PMID:23284904

  18. Statistical Atlas Construction via Weighted Functional Boxplots

    PubMed Central

    Hong, Yi; Davis, Brad; Marron, J.S.; Kwitt, Roland; Singh, Nikhil; Kimbell, Julia S.; Pitkin, Elizabeth; Superfine, Richard; Davis, Stephanie D.; Zdanski, Carlton J.; Niethammer, Marc

    2014-01-01

    Atlas-building from population data is widely used in medical imaging. However, the emphasis of atlas-building approaches is typically to estimate a spatial alignment to compute a mean / median shape or image based on population data. In this work, we focus on the statistical characterization of the population data, once spatial alignment has been achieved. We introduce and propose the use of the weighted functional boxplot. This allows the generalization of concepts such as the median, percentiles, or outliers to spaces where the data objects are functions, shapes, or images, and allows spatio-temporal atlas-building based on kernel regression. In our experiments, we demonstrate the utility of the approach to construct statistical atlases for pediatric upper airways and corpora callosa revealing their growth patterns. We also define a score system based on the pediatric airway atlas to quantitatively measure the severity of subglottic stenosis (SGS) in the airway. This scoring allows the classification of pre- and post-surgery SGS subjects and radiographically normal controls. Experimental results show the utility of atlas information to assess the effect of airway surgery in children. PMID:24747271

  19. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  20. The New World: A Librarian's Guide to CD-ROM & Print Atlases.

    ERIC Educational Resources Information Center

    Del Vecchio, Stephen

    1998-01-01

    Provides an annotated bibliography of print atlases for pre-K through 12, general atlases for under and over $50, Facts on File loose-leaf map collections, and CD-ROM atlases. Lists the top atlases' best bets of print and CD-ROM, provides guidelines for selection, and argues that although print atlases are superior, a good CD-ROM atlas is useful…

  1. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture

    PubMed Central

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.; Yu, Chunshui; Jiang, Tianzi

    2016-01-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  2. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  3. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states.

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

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    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. PMID:27285947

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

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    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.

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

    PubMed Central

    Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O’Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    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. PMID:27285947

  7. The Atlas Mountains: why there? Why now?

    NASA Astrophysics Data System (ADS)

    Ruiz, G.; Negro, F.; Foeken, J.; Stuart, F.; Babault, J.; Frizon de Lamotte, D.; Stockli, D.

    2009-04-01

    In Morocco, the High and Middle Atlas of Morocco are intra-continental fold-thrust belts situated in the southern foreland of the Rif orogen. The High Atlas and its eastern continuation in Algeria and Tunisia is an ENE-WSW to E-W trending belt about 2000kms long and 100kms wide. It is a key natural laboratory because it 1) is the southern and westernmost expression of Alpine-Himalayan orogeny, and 2) encompasses Pre-Cambrian to recent evolution of the region. Phases of shortening and exhumation of this orogen remain however ill constrained and the few available quantitative, data do not allow the present-day high topography (over 4000m) to be explained. In order to put constrains on the recent orogenic growth of the Atlas system, we investigated the temperature-time history of rocks combining extensive low-temperature thermochronological analysis (Fission tracks and (U-Th)/He on zircon and apatite) and peak temperature estimation by Raman spectroscopy of carbonaceous material. The target area is a NE-SW oriented transect between Marrakech and Igherm crossing the different structural segments of the western Atlas away from present-day fault systems. Results are much contrasted from one domain to the other: Pre-Cambrian bedrocks from the Anti-Atlas domain yield old Fission-Track ages on zircon (380-300 Ma), apatite (180-120 Ma) but also U-Th/He (150-110 Ma) still on apatite that are discussed in another contribution. U-Th/He ages on apatite are many from the High-Atlas (#>20) and much younger ranging between ~35 and 5 Ma. Maximum peak temperatures have also been calculated from carbon-rich lithologies of Paleozoic ages. Results indicate that these schists underwent maximum temperatures from 550-500°C in the axial zone of the High-Atlas to less than 250-200°C in the southern Sub-Atlas zone and Souss plain. The latter temperature window corresponds to the temperature range of the Partial Annealing/Retention Zone for Fission-Track (270-210°C) and (U-Th)/He (200-180

  8. Exploiting Virtualization and Cloud Computing in ATLAS

    NASA Astrophysics Data System (ADS)

    Harald Barreiro Megino, Fernando; Benjamin, Doug; De, Kaushik; Gable, Ian; Hendrix, Val; Panitkin, Sergey; Paterson, Michael; De Silva, Asoka; van der Ster, Daniel; Taylor, Ryan; Vitillo, Roberto A.; Walker, Rod

    2012-12-01

    The ATLAS Computing Model was designed around the concept of grid computing; since the start of data-taking, this model has proven very successful in the federated operation of more than one hundred Worldwide LHC Computing Grid (WLCG) sites for offline data distribution, storage, processing and analysis. However, new paradigms in computing, namely virtualization and cloud computing, present improved strategies for managing and provisioning IT resources that could allow ATLAS to more flexibly adapt and scale its storage and processing workloads on varied underlying resources. In particular, ATLAS is developing a “grid-of-clouds” infrastructure in order to utilize WLCG sites that make resources available via a cloud API. This work will present the current status of the Virtualization and Cloud Computing R&D project in ATLAS Distributed Computing. First, strategies for deploying PanDA queues on cloud sites will be discussed, including the introduction of a “cloud factory” for managing cloud VM instances. Next, performance results when running on virtualized/cloud resources at CERN LxCloud, StratusLab, and elsewhere will be presented. Finally, we will present the ATLAS strategies for exploiting cloud-based storage, including remote XROOTD access to input data, management of EC2-based files, and the deployment of cloud-resident LCG storage elements.

  9. Developing the eHistology Atlas

    PubMed Central

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

    2015-01-01

    The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook ‘The Atlas of Mouse Development’ by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php PMID:26500249

  10. Renewable energy atlas of the United States.

    SciTech Connect

    Kuiper, J.A.; Hlava, K.Greenwood, H.; Carr, A.

    2012-05-01

    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. It is designed for the U.S. Department of Agriculture Forest Service (USFS) and other federal land management agencies to evaluate existing and proposed renewable energy projects. Much of the content of the Atlas was compiled at Argonne National Laboratory (Argonne) to support recent and current energy-related Environmental Impact Statements and studies, including the following projects: (1) West-wide Energy Corridor Programmatic Environmental Impact Statement (PEIS) (BLM 2008); (2) Draft PEIS for Solar Energy Development in Six Southwestern States (DOE/BLM 2010); (3) Supplement to the Draft PEIS for Solar Energy Development in Six Southwestern States (DOE/BLM 2011); (4) Upper Great Plains Wind Energy PEIS (WAPA/USFWS 2012, in progress); and (5) Energy Transport Corridors: The Potential Role of Federal Lands in States Identified by the Energy Policy Act of 2005, Section 368(b) (in progress). This report explains how to add the Atlas to your computer and install the associated software; describes each of the components of the Atlas; lists the Geographic Information System (GIS) database content and sources; and provides a brief introduction to the major renewable energy technologies.

  11. Engineering the ATLAS TAG Browser

    NASA Astrophysics Data System (ADS)

    Zhang, Qizhi; ATLAS Collaboration

    2011-12-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

  12. Radiologic atlas of rheumatic diseases

    SciTech Connect

    Dihlmann, W.

    1986-01-01

    This book is an ''atlas of rheumatic joint disease'' selected from 20 years of personal experience by the author. The author sets a goal of demonstrating the value of soft-tissue imaging in the diagnosis of early joint disease. This goal is achieved with high quality reproductions, many of which are presented in duplicate to illustrate bone and soft-tissue changes. The contents include an introductory overview of the ''Mosaic of Arthritis'' followed by sections on adult rheumatoid arthritis, seronegative spondyloarthropathies, classic collagen disease, enthesiopathies, and lastly a section on gout and psuedogout. The subject index is specific and indexes figures with boldface type. Each section is introduced by a brief outline or overview of the radiographic spectrum of the joint disorder to be illustrated.

  13. Local hadron calibration with ATLAS

    NASA Astrophysics Data System (ADS)

    Giovannini, Paola; ATLAS Liquid Argon Calorimeter Group

    2011-04-01

    The method of Local Hadron Calibration is used in ATLAS as one of the two major calibration schemes for the reconstruction of jets and missing transverse energy. The method starts from noise suppressed clusters and corrects them for non-compensation effects and for losses due to noise threshold and dead material. Jets are reconstructed using the calibrated clusters and are then corrected for out of cone effects. The performance of the corrections applied to the calorimeter clusters is tested with detailed GEANT4 information. Results obtained with this procedure are discussed both for single pion simulations and for di-jet simulations. The calibration scheme is validated on data, by comparing the calibrated cluster energy in data with Mote Carlo simulations. Preliminary results obtained with GeV collision data are presented. The agreement between data and Monte Carlo is within 5% for the final cluster scale.

  14. Multi-Atlas Segmentation with Joint Label Fusion

    PubMed Central

    Wang, Hongzhi; Suh, Jung W.; Das, Sandhitsu R.; Pluta, John; Craige, Caryne; Yushkevich, Paul A.

    2013-01-01

    Multi-atlas segmentation is an effective approach for automatically labeling objects of interest in biomedical images. In this approach, multiple expert-segmented example images, called atlases, are registered to a target image, and deformed atlas segmentations are combined using label fusion. Among the proposed label fusion strategies, weighted voting with spatially varying weight distributions derived from atlas-target intensity similarity have been particularly successful. However, one limitation of these strategies is that the weights are computed independently for each atlas, without taking into account the fact that different atlases may produce similar label errors. To address this limitation, we propose a new solution for the label fusion problem, in which weighted voting is formulated in terms of minimizing the total expectation of labeling error, and in which pairwise dependency between atlases is explicitly modeled as the joint probability of two atlases making a segmentation error at a voxel. This probability is approximated using intensity similarity between a pair of atlases and the target image in the neighborhood of each voxel. We validate our method in two medical image segmentation problems: hippocampus segmentation and hippocampus subfield segmentation in magnetic resonance (MR) images. For both problems, we show consistent and significant improvement over label fusion strategies that assign atlas weights independently. PMID:22732662

  15. Implementing planetary protection on the Atlas V fairing and ground systems used to launch the Mars Science Laboratory.

    PubMed

    Benardini, James N; La Duc, Myron T; Ballou, David; Koukol, Robert

    2014-01-01

    On November 26, 2011, the Mars Science Laboratory (MSL) launched from Florida's Cape Canaveral Air Force Station aboard an Atlas V 541 rocket, taking its first step toward exploring the past habitability of Mars' Gale Crater. Because microbial contamination could profoundly impact the integrity of the mission, and compliance with international treaty was a necessity, planetary protection measures were implemented on all MSL hardware to verify that bioburden levels complied with NASA regulations. The cleanliness of the Atlas V payload fairing (PLF) and associated ground support systems used to launch MSL were also evaluated. By applying proper recontamination countermeasures early and often in the encapsulation process, the PLF was kept extremely clean and was shown to pose little threat of recontaminating the enclosed MSL flight system upon launch. Contrary to prelaunch estimates that assumed that the interior PLF spore burden ranged from 500 to 1000 spores/m², the interior surfaces of the Atlas V PLF were extremely clean, housing a mere 4.65 spores/m². Reported here are the practices and results of the campaign to implement and verify planetary protection measures on the Atlas V launch vehicle and associated ground support systems used to launch MSL. All these facilities and systems were very well kept and exceeded the levels of cleanliness and rigor required in launching the MSL payload.

  16. Implementing planetary protection on the Atlas V fairing and ground systems used to launch the Mars Science Laboratory.

    PubMed

    Benardini, James N; La Duc, Myron T; Ballou, David; Koukol, Robert

    2014-01-01

    On November 26, 2011, the Mars Science Laboratory (MSL) launched from Florida's Cape Canaveral Air Force Station aboard an Atlas V 541 rocket, taking its first step toward exploring the past habitability of Mars' Gale Crater. Because microbial contamination could profoundly impact the integrity of the mission, and compliance with international treaty was a necessity, planetary protection measures were implemented on all MSL hardware to verify that bioburden levels complied with NASA regulations. The cleanliness of the Atlas V payload fairing (PLF) and associated ground support systems used to launch MSL were also evaluated. By applying proper recontamination countermeasures early and often in the encapsulation process, the PLF was kept extremely clean and was shown to pose little threat of recontaminating the enclosed MSL flight system upon launch. Contrary to prelaunch estimates that assumed that the interior PLF spore burden ranged from 500 to 1000 spores/m², the interior surfaces of the Atlas V PLF were extremely clean, housing a mere 4.65 spores/m². Reported here are the practices and results of the campaign to implement and verify planetary protection measures on the Atlas V launch vehicle and associated ground support systems used to launch MSL. All these facilities and systems were very well kept and exceeded the levels of cleanliness and rigor required in launching the MSL payload. PMID:24432777

  17. Atlas performance and imploding liner parameter space

    SciTech Connect

    Reinovsky, R.; Lindemuth, I. R.; Atchison, W. L.; Cochrane, J. C. , Jr.; Faehl, R. J.

    2002-01-01

    Ultra-high magnetic fields have many applications in the confining and controlling plasmas and in exploring electron physics as manifested in the magnetic properties of materials. Another application of high fields is the acceleration of metal conductors to velocities higher than that achievable with conventional high explosive drive or gas guns. The Atlas pulse power system is the world's first pulse power system specifically designed to implode solid and near-solid density metal liners for use in pulse power hydrodynamic experiments. This paper describes the Atlas system during the first year of its operational life at Los Alamos, (comprising 10-15 implosion experiments); describes circuit models that adequately predicted the bulk kinematic behavior of liner implosions; and shows how those (now validated) models can be used to describe the range of parameters accessible through Atlas implosions.

  18. Development of a Gene-Centered SSR Atlas as a Resource for Papaya (Carica papaya) Marker-Assisted Selection and Population Genetic Studies

    PubMed Central

    Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

    2014-01-01

    Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community. PMID:25393538

  19. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

    PubMed

    Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

    2014-01-01

    Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  20. ATLAS: Big Data in a Small Package?

    NASA Astrophysics Data System (ADS)

    Denneau, Larry

    2016-01-01

    For even small astronomy projects, the petabyte scale is now upon us. The Asteroid Terrestrial-impact Last Alert System (Tonry 2011) will survey the entire visible sky from Hawaii multiple times per night to search for near-Earth asteroids on impact trajectories. While the ATLAS optical system is modest by modern astronomical standards - two 0.5 m F/2.0 telescopes - each night the ATLAS system will measure nearly 109 astronomical sources to a photometric accuracy of <5%, totaling 1012 individual observations over its initial 3-year mission. This ever-growing dataset must be searched in real-time for moving objects and transients then archived for further analysis, and alerts for newly discovered near-Earth asteroids (NEAs) disseminated within tens of minutes from detection. ATLAS's all-sky coverage ensures it will discover many `rifle shot' near-misses moving rapidly on the sky as they shoot past the Earth, so the system will need software to automatically detect highly-trailed sources and discriminate them from the thousands of low-Earth orbit (LEO) and geosynchronous orbit (GEO) satellites ATLAS will see each night. Additional interrogation will identify interesting phenomena from millions of transient sources per night beyond the solar system. The data processing and storage requirements for ATLAS demand a `big data' approach typical of commercial internet enterprises. We describe our experience in deploying a nimble, scalable and reliable data processing infrastructure, and suggest ATLAS as steppingstone to data processing capability needed as we enter the era of LSST.

  1. Congenital anomaly of combined atlas-odontoid process fusion and bipartite atlas.

    PubMed

    Gil, Jea Ryoung; Kim, Wan Tae; Seo, Min Jeong

    2015-12-01

    Congenital fusion of the atlas with the odontoid process of the axis is a very rare condition caused by a segmental defect of the first cervical somite. Only 9 such cases have been reported in the literature to date. The bipartite atlas, another well-documented rare anomaly, has been observed in only 0.1% of the general population. We describe the first case of a 70-year-old male with both of these complex congenital anomalies.

  2. Implementation of nonlinear registration of brain atlas based on piecewise grid system

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Gu, Lixu; Xu, Jianrong

    2007-12-01

    In this paper, a multi-step registration method of brain atlas and clinical Magnetic Resonance Imaging (MRI) data based on Thin-Plate Splines (TPS) and Piecewise Grid System (PGS) is presented. The method can help doctors to determine the corresponding anatomical structure between patient image and the brain atlas by piecewise nonlinear registration. Since doctors mostly pay attention to particular Region of Interest (ROI), and a global nonlinear registration is quite time-consuming which is not suitable for real-time clinical application, we propose a novel method to conduct linear registration in global area before nonlinear registration is performed in selected ROI. The homogenous feature points are defined to calculate the transform matrix between patient data and the brain atlas to conclude the mapping function. Finally, we integrate the proposed approach into an application of neurosurgical planning and guidance system which lends great efficiency in both neuro-anatomical education and guiding of neurosurgical operations. The experimental results reveal that the proposed approach can keep an average registration error of 0.25mm in near real-time manner.

  3. ATLAS user analysis on private cloud resources at GoeGrid

    NASA Astrophysics Data System (ADS)

    Glaser, F.; Nadal Serrano, J.; Grabowski, J.; Quadt, A.

    2015-12-01

    User analysis job demands can exceed available computing resources, especially before major conferences. ATLAS physics results can potentially be slowed down due to the lack of resources. For these reasons, cloud research and development activities are now included in the skeleton of the ATLAS computing model, which has been extended by using resources from commercial and private cloud providers to satisfy the demands. However, most of these activities are focused on Monte-Carlo production jobs, extending the resources at Tier-2. To evaluate the suitability of the cloud-computing model for user analysis jobs, we developed a framework to launch an ATLAS user analysis cluster in a cloud infrastructure on demand and evaluated two solutions. The first solution is entirely integrated in the Grid infrastructure by using the same mechanism, which is already in use at Tier-2: A designated Panda-Queue is monitored and additional worker nodes are launched in a cloud environment and assigned to a corresponding HTCondor queue according to the demand. Thereby, the use of cloud resources is completely transparent to the user. However, using this approach, submitted user analysis jobs can still suffer from a certain delay introduced by waiting time in the queue and the deployed infrastructure lacks customizability. Therefore, our second solution offers the possibility to easily deploy a totally private, customizable analysis cluster on private cloud resources belonging to the university.

  4. The Plio-Pleistocene evolution of the Southern Middle Atlas Fault Zone (SMAFZ) front of Morocco

    NASA Astrophysics Data System (ADS)

    Laville, E.; Delcaillau, B.; Charroud, M.; Dugué, O.; Ait Brahim, L.; Cattaneo, G.; Deluca, P.; Bouazza, A.

    2007-06-01

    The South Middle Atlas front constitutes a northeast-trending shear zone, located north of the Neogene Missour basin and east of the Taza Guercif basin. This paper analyses the Southern Middle Atlas Fault Zone (SMAFZ) deformation since the Pliocene. The set of structures observed suggests that reverse and thrust faulting along the central part of the SMAFZ are combined with left-lateral slip along N S striking faults of its south-western termination and right-lateral faulting along E NE striking faults of the east northeast termination. Thrusts and oblique thrust-related anticlines of the two lateral ramps partly accommodate north-west directed motion of the African plate. The Thrusts probably resulted from rejuvenation of Jurassic normal faults; they were active during the Upper Miocene Pliocene and the Pleistocene. The geometries of positive inversion structures and buttressing effects are clearly dependent on the geometry and sedimentology of the original basin-controlling fault system and on the presence of a décollement level. Field mapping is integrated with Landsat imagery and a digital elevation model to investigate the morphotectonic evolution of the south-eastern range front of the Middle Atlas. Geomorphological features provide significant information on the processes that govern lateral propagation of active anticlines. Both suggest that the deformation front may have been active since Pliocene.

  5. PanDA: Exascale Federation of Resources for the ATLAS Experiment at the LHC

    NASA Astrophysics Data System (ADS)

    Barreiro Megino, Fernando; Caballero Bejar, Jose; De, Kaushik; Hover, John; Klimentov, Alexei; Maeno, Tadashi; Nilsson, Paul; Oleynik, Danila; Padolski, Siarhei; Panitkin, Sergey; Petrosyan, Artem; Wenaus, Torre

    2016-02-01

    After a scheduled maintenance and upgrade period, the world's largest and most powerful machine - the Large Hadron Collider(LHC) - is about to enter its second run at unprecedented energies. In order to exploit the scientific potential of the machine, the experiments at the LHC face computational challenges with enormous data volumes that need to be analysed by thousand of physics users and compared to simulated data. Given diverse funding constraints, the computational resources for the LHC have been deployed in a worldwide mesh of data centres, connected to each other through Grid technologies. The PanDA (Production and Distributed Analysis) system was developed in 2005 for the ATLAS experiment on top of this heterogeneous infrastructure to seamlessly integrate the computational resources and give the users the feeling of a unique system. Since its origins, PanDA has evolved together with upcoming computing paradigms in and outside HEP, such as changes in the networking model, Cloud Computing and HPC. It is currently running steadily up to 200 thousand simultaneous cores (limited by the available resources for ATLAS), up to two million aggregated jobs per day and processes over an exabyte of data per year. The success of PanDA in ATLAS is triggering the widespread adoption and testing by other experiments. In this contribution we will give an overview of the PanDA components and focus on the new features and upcoming challenges that are relevant to the next decade of distributed computing workload management using PanDA.

  6. Fine grained event processing on HPCs with the ATLAS Yoda system

    NASA Astrophysics Data System (ADS)

    Calafiura, Paolo; De, Kaushik; Guan, Wen; Maeno, Tadashi; Nilsson, Paul; Oleynik, Danila; Panitkin, Sergey; Tsulaia, Vakhtang; Van Gemmeren, Peter; Wenaus, Torre

    2015-12-01

    High performance computing facilities present unique challenges and opportunities for HEP event processing. The massive scale of many HPC systems means that fractionally small utilization can yield large returns in processing throughput. Parallel applications which can dynamically and efficiently fill any scheduling opportunities the resource presents benefit both the facility (maximal utilization) and the (compute-limited) science. The ATLAS Yoda system provides this capability to HEP-like event processing applications by implementing event-level processing in an MPI-based master-client model that integrates seamlessly with the more broadly scoped ATLAS Event Service. Fine grained, event level work assignments are intelligently dispatched to parallel workers to sustain full utilization on all cores, with outputs streamed off to destination object stores in near real time with similarly fine granularity, such that processing can proceed until termination with full utilization. The system offers the efficiency and scheduling flexibility of preemption without requiring the application actually support or employ check-pointing. We will present the new Yoda system, its motivations, architecture, implementation, and applications in ATLAS data processing at several US HPC centers.

  7. A flexible demonstrator system for the ATLAS level-1 calorimeter trigger

    SciTech Connect

    Brawn, I.; Carney, R.; Connors, A.

    1996-12-31

    The proposed level-1 calorimeter trigger system for ATLAS relies upon several key technologies which we have been testing in a demonstrator programme. We describe here the final phase of this programme, which concentrates on crucial aspects of high-speed data transmission inherent in the trigger architecture while operating with signals from prototype ATLAS calorimeters. The 36-channel trigger demonstrator system has been designed to provide a flexible infrastructure for the study of alternative techniques of communication between the calorimeters and the trigger processor, including both analogue links and high-speed digital optical and electrical links operating at up to 1.6 Gbaud. Data fan-out at 160 Mbit/s between trigger processor modules using serializing Application Specific Integrated Circuits (ASICs) driving transmission-line backplanes is also evaluated. A programmable timing system re-synchronizes all channels before pipeline processing by ASICs executing an electromagnetic cluster-finding algorithm. Some preliminary results are presented from the operation of this demonstrator system installed in the ATLAS test-beam at CERN.

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

    PubMed

    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.

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

    PubMed

    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%. PMID:27536233

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

    PubMed Central

    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%. PMID:27536233

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

    PubMed

    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%.

  12. Estimating species diversity from bird atlas data

    SciTech Connect

    Campbell, K.

    1992-12-01

    Observations for a breeding bird atlas for Los Alamos (NM) county were collected over a six-year period by a number of different observers and with variable number and duration of visits to different parts of the county. The resulting data set, while thorough by the standards of such atlases, poses many problems for statistical analyses proposed after data gathering was complete. This paper examines some statistical models that might usefully supplement the data and make possible inferences about such questions as the impact of land use -- residential, Laboratory, wilderness -- on the use of local habitats by approximately 100 species known to breed in the county.

  13. Estimating species diversity from bird atlas data

    SciTech Connect

    Campbell, K.

    1992-01-01

    Observations for a breeding bird atlas for Los Alamos (NM) county were collected over a six-year period by a number of different observers and with variable number and duration of visits to different parts of the county. The resulting data set, while thorough by the standards of such atlases, poses many problems for statistical analyses proposed after data gathering was complete. This paper examines some statistical models that might usefully supplement the data and make possible inferences about such questions as the impact of land use -- residential, Laboratory, wilderness -- on the use of local habitats by approximately 100 species known to breed in the county.

  14. The ATLAS ARC backend to HPC

    NASA Astrophysics Data System (ADS)

    Haug, S.; Hostettler, M.; Sciacca, F. G.; Weber, M.

    2015-12-01

    The current distributed computing resources used for simulating and processing collision data collected by ATLAS and the other LHC experiments are largely based on dedicated x86 Linux clusters. Access to resources, job control and software provisioning mechanisms are quite different from the common concept of self-contained HPC applications run by particular users on specific HPC systems. We report on the development and the usage in ATLAS of a SSH backend to the Advanced Resource Connector (ARC) middleware to enable HPC compliant access and on the corresponding software provisioning mechanisms.

  15. The ATLAS level 2 trigger supervisor.

    SciTech Connect

    Abolins, M.; Blair, R. E.; Dawson, J. W.; Owen, D.; Pope, B. G.; Schlereth, J. L.; Weber dos Santos, R.

    1997-04-03

    This paper presents an overview of the hardware and software proposed for the ATLAS level 2 Trigger ROI Builder/Supervisor. The essential requirements of this system are that it operate at the design Level 1 Trigger rate of 100kHz and that it support the technical requirements of the architectures suggested for the ATLAS Level 2 Trigger. Commercial equipment and software support are used to the maximum extent possible, with support from dedicated hardware. Timing requirements and latencies are discussed and simulation results are presented.

  16. Atlas of major Appalachian basin gas plays

    SciTech Connect

    Aminian, K.; Avary, K.L.; Baranoski, M.T.; Flaherty, K.; Humphreys, M.; Smosna, R.A.

    1995-06-01

    This regional study of gas reservoirs in the Appalachian basin has four main objectives: to organize all of the -as reservoirs in the Appalachian basin into unique plays based on common age, lithology, trap type and other geologic similarities; to write, illustrate and publish an atlas of major gas plays; to prepare and submit a digital data base of geologic, engineering and reservoir parameters for each gas field; and technology transfer to the oil and gas industry during the preparation of the atlas and data base.

  17. Top quark property measurements with ATLAS

    NASA Astrophysics Data System (ADS)

    Rudolph, M.; Atlas Collaboration

    2016-07-01

    This contribution covers recent results on the properties of the top quark as measured with the ATLAS detector at the Large Hadron Collider, using data collected at center-of-mass energies of 7 and 8TeV during 2011 and 2012. Results on the t bar{{t}} charge asymmetry and spin correlation, and on the mass of the top quark are discussed. The most recent results expand on the first ATLAS measurements with complementary analysis channels, new observables, and direct comparisons to new physics models. No significant deviations from Standard Model predictions have been found.

  18. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

    PubMed

    Subramanian, Sai Lakshmi; Kitchen, Robert R; Alexander, Roger; Carter, Bob S; Cheung, Kei-Hoi; Laurent, Louise C; Pico, Alexander; Roberts, Lewis R; Roth, Matthew E; Rozowsky, Joel S; Su, Andrew I; Gerstein, Mark B; Milosavljevic, Aleksandar

    2015-01-01

    The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data. PMID:26320941

  19. Automated anatomical interpretation of ion distributions in tissue: linking imaging mass spectrometry to curated atlases.

    PubMed

    Verbeeck, Nico; Yang, Junhai; De Moor, Bart; Caprioli, Richard M; Waelkens, Etienne; Van de Plas, Raf

    2014-09-16

    Imaging mass spectrometry (IMS) has become a prime tool for studying the distribution of biomolecules in tissue. Although IMS data sets can become very large, computational methods have made it practically feasible to search these experiments for relevant findings. However, these methods lack access to an important source of information that many human interpretations rely upon: anatomical insight. In this work, we address this need by (1) integrating a curated anatomical data source with an empirically acquired IMS data source, establishing an algorithm-accessible link between them and (2) demonstrating the potential of such an IMS-anatomical atlas link by applying it toward automated anatomical interpretation of ion distributions in tissue. The concept is demonstrated in mouse brain tissue, using the Allen Mouse Brain Atlas as the curated anatomical data source that is linked to MALDI-based IMS experiments. We first develop a method to spatially map the anatomical atlas to the IMS data sets using nonrigid registration techniques. Once a mapping is established, a second computational method, called correlation-based querying, gives an elementary demonstration of the link by delivering basic insight into relationships between ion images and anatomical structures. Finally, a third algorithm moves further beyond both registration and correlation by providing automated anatomical interpretation of ion images. This task is approached as an optimization problem that deconstructs ion distributions as combinations of known anatomical structures. We demonstrate that establishing a link between an IMS experiment and an anatomical atlas enables automated anatomical annotation, which can serve as an important accelerator both for human and machine-guided exploration of IMS experiments.

  20. Pancreas segmentation from 3D abdominal CT images using patient-specific weighted subspatial probabilistic atlases

    NASA Astrophysics Data System (ADS)

    Karasawa, Kenichi; Oda, Masahiro; Hayashi, Yuichiro; Nimura, Yukitaka; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Rueckert, Daniel; Mori, Kensaku

    2015-03-01

    Abdominal organ segmentations from CT volumes are now widely used in the computer-aided diagnosis and surgery assistance systems. Among abdominal organs, the pancreas is especially difficult to segment because of its large individual differences of the shape and position. In this paper, we propose a new pancreas segmentation method from 3D abdominal CT volumes using patient-specific weighted-subspatial probabilistic atlases. First of all, we perform normalization of organ shapes in training volumes and an input volume. We extract the Volume Of Interest (VOI) of the pancreas from the training volumes and an input volume. We divide each training VOI and input VOI into some cubic regions. We use a nonrigid registration method to register these cubic regions of the training VOI to corresponding regions of the input VOI. Based on the registration results, we calculate similarities between each cubic region of the training VOI and corresponding region of the input VOI. We select cubic regions of training volumes having the top N similarities in each cubic region. We subspatially construct probabilistic atlases weighted by the similarities in each cubic region. After integrating these probabilistic atlases in cubic regions into one, we perform a rough-to-precise segmentation of the pancreas using the atlas. The results of the experiments showed that utilization of the training volumes having the top N similarities in each cubic region led good results of the pancreas segmentation. The Jaccard Index and the average surface distance of the result were 58.9% and 2.04mm on average, respectively.

  1. Radiation tests of ATLAS full-sized n-in-n prototype detectors

    NASA Astrophysics Data System (ADS)

    Allport, P. P.; Apsimon, R. J.; Becker, C.; Bizzell, J.; Bonino, R.; Booth, P. S. L.; Boulter, B.; Carter, A. A.; Carter, J. R.; Clark, A. G.; Couyoumtzelis, C.; Goodrick, M. J.; Green, C.; Greenall, A.; Hanlon, M.; Hill, J. C.; Jackson, J. N.; Jones, T. J.; Kowalewski, R.; Macina, D.; García, S. Martí i.; Munday, D. J.; Newman-Coburn, D.; Orme, E.; O'Shea, V.; Perrin, E.; Richardson, J. D.; Riedler, P.; Robinson, D.; Roe, S.; Smith, N. A.; Thüne, R.; Turner, P. R.; Tyndel, M.; Vuaridel, B.; Wormald, M. P.; Wunstorf, R.; Wüstenfeld, J.; Wyllie, K. H.

    1998-11-01

    ATLAS Technical Proposal, CERN/LHCC/94-43 has adopted n-side read out single-sided detectors as the baseline technology for the silicon microstrips due to the anticipated radiation tolerance of such a design ATLAS Inner Detector Technical Design Report, CERN/LHCC/97-17. This results from the reasonable efficiencies anticipated for charge collection, even when the detectors are run well below the final depletion voltage. Full-sized prototypes 64×63.6 mm 2 detectors have been produced with a range of manufacturers to a common specification and shown to work well in test-beam with ATLAS electronics. A selection of detectors was also scanned in the CERN PS beam for runs of two weeks giving an integrated dose over the full surface of 2×10 14 p/cm 2. This dose corresponds to the highest charged hadron fluence expected in 10 yr of operation in ATLAS. Results are presented on these detectors both from parametric measurements and from studies using analogue LHC speed electronics. The detectors are shown to remain fully operational after these doses and to yield high signal/noise for read-out of 12 cm strip length. The performance partially depleted is also shown to match expectations and operation at down to half the final depletion voltage gives adequate efficiencies. Uncertainties in the anticipated dose and damage effects argue strongly for this additional robustness in detectors which must operate with very limited access in the hostile environment of the LHC for 10 yr.

  2. Measurement of the top quark pair production cross section with ATLAS detector

    NASA Astrophysics Data System (ADS)

    Abi, Babak

    This thesis describes two measurement of the tt¯ production cross-section, the inclusive sigmatt¯j and sigmatt¯j in association with at least one jet in lepton + jets channel with ATLAS detector. The measurements employ multivariate technique with a binned maximum likelihood template fit. Several kinematic variables of the reconstructed collision events are selected to discriminate tt¯ signal events from the various background sources. The inclusive sigmatt¯ measurement uses approximately 35.3 pb-1 of ATLAS data collected in 2010 and selecting events with one isolated high-pT electron or muon, large missing transverse energy and two jet bins of 3 or at least 4 high-pT jets. The measured tt¯ cross section assuming the top quark mass of 172.5 GeV yields: stt¯=173+/- 17stat.+20 -17syst.+/- 6lumi.pb The measured value is in a good agreement with the Standard Model prediction. The second measurement is performed on ATLAS data collected in 2011 corresponding to an integrated luminosity of 4.7 fb-1. The same analysis technique and event selection employed as the first measurement but in 4th and 5th jet bins. The cross-section for sigmatt¯ with at least one additional jet is found to be: stt¯j=102+/- 2stat.+/-6 ISR/FSR+22-25 syst.pb Finally the results of study on PiN diodes radiation hardness are presented. Results were performed with several irradiation beams to investigate the proper optical components for ATLAS Pixel upgrade.

  3. A framework for probabilistic atlas-based organ segmentation

    NASA Astrophysics Data System (ADS)

    Dong, Chunhua; Chen, Yen-Wei; Foruzan, Amir Hossein; Han, Xian-Hua; Tateyama, Tomoko; Wu, Xing

    2016-03-01

    Probabilistic atlas based on human anatomical structure has been widely used for organ segmentation. The challenge is how to register the probabilistic atlas to the patient volume. Additionally, there is the disadvantage that the conventional probabilistic atlas may cause a bias toward the specific patient study due to a single reference. Hence, we propose a template matching framework based on an iterative probabilistic atlas for organ segmentation. Firstly, we find a bounding box for the organ based on human anatomical localization. Then, the probabilistic atlas is used as a template to find the organ in this bounding box by using template matching technology. Comparing our method with conventional and recently developed atlas-based methods, our results show an improvement in the segmentation accuracy for multiple organs (p < 0:00001).

  4. Anti-Atlas Mountains, Morocco

    NASA Technical Reports Server (NTRS)

    2003-01-01

    The Anti-Atlas Mountains of Morocco formed as a result of the collision of the African and Eurasian tectonic plates about 80 million years ago. This collision destroyed the Tethys Ocean; the limestone, sandstone, claystone, and gypsum layers that formed the ocean bed were folded and crumpled to create the Atlas and Anti-Atlas Mountains. In this ASTER image, short wavelength infrared bands are combined to dramatically highlight the different rock types, and illustrate the complex folding. The yellowish, orange and green areas are limestones, sandstones and gypsum; the dark blue and green areas are underlying granitic rocks. The ability to map geology using ASTER data is enhanced by the multiple short wavelength infrared bands, that are sensitive to differences in rock mineralogy. This image was acquired on June 13, 2001 by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils

  5. Difficulties in distinguishing between an atlas fracture and a congenital posterior atlas arch defect in postmortem analysis.

    PubMed

    Sanchis-Gimeno, Juan A; Blanco-Perez, Esther; Aparicio, Luis; Martinez-Soriano, Francisco; Martinez-Sanjuan, Vicente

    2014-09-01

    We found one atlas from a sample of 148 skeletons (0.67%) that presented different anatomical variations which made it difficult to determine whether the vertebra had an atlas fracture, an unusual Type B posterior atlas arch defect, or a combination of both. We carried out a stereomicroscopy, radiographic, and computerized tomography scan study that revealed that the dry atlas we found presented a very uncommon congenital Type B posterior atlas arch defect, simulating a fracture. In short, the present paper has revealed that differentiating Type B posterior atlas arch defects from fractures in post-mortem dry vertebrae is more difficult than expected. Thus we believe that it can be easier than expected to mistake Type B posterior arch defects for fractures and vice versa in postmortem studies. PMID:25037687

  6. Global GIS database; digital atlas of South Asia

    USGS Publications Warehouse

    Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

    2001-01-01

    This CD-ROM contains a digital atlas of the countries of South Asia. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included.

  7. Global GIS database; digital atlas of South Pacific

    USGS Publications Warehouse

    Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

    2001-01-01

    This CD-ROM contains a digital atlas of the countries of the South Pacific. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included.

  8. The SRI24 multichannel brain atlas: construction and applications

    NASA Astrophysics Data System (ADS)

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2008-03-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T I-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain.

  9. Australasian Gastrointestinal Trials Group (AGITG) Contouring Atlas and Planning Guidelines for Intensity-Modulated Radiotherapy in Anal Cancer

    SciTech Connect

    Ng, Michael; Leong, Trevor; Chander, Sarat; Chu, Julie; Kneebone, Andrew; Carroll, Susan; Wiltshire, Kirsty; Ngan, Samuel; Kachnic, Lisa

    2012-08-01

    Purpose: To develop a high-resolution target volume atlas with intensity-modulated radiotherapy (IMRT) planning guidelines for the conformal treatment of anal cancer. Methods and Materials: A draft contouring atlas and planning guidelines for anal cancer IMRT were prepared at the Australasian Gastrointestinal Trials Group (AGITG) annual meeting in September 2010. An expert panel of radiation oncologists contoured an anal cancer case to generate discussion on recommendations regarding target definition for gross disease, elective nodal volumes, and organs at risk (OARs). Clinical target volume (CTV) and planning target volume (PTV) margins, dose fractionation, and other IMRT-specific issues were also addressed. A steering committee produced the final consensus guidelines. Results: Detailed contouring and planning guidelines and a high-resolution atlas are provided. Gross tumor and elective target volumes are described and pictorially depicted. All elective regions should be routinely contoured for all disease stages, with the possible exception of the inguinal and high pelvic nodes for select, early-stage T1N0. A 20-mm CTV margin for the primary, 10- to 20-mm CTV margin for involved nodes and a 7-mm CTV margin for the elective pelvic nodal groups are recommended, while respecting anatomical boundaries. A 5- to 10-mm PTV margin is suggested. When using a simultaneous integrated boost technique, a dose of 54 Gy in 30 fractions to gross disease and 45 Gy to elective nodes with chemotherapy is appropriate. Guidelines are provided for OAR delineation. Conclusion: These consensus planning guidelines and high-resolution atlas complement the existing Radiation Therapy Oncology Group (RTOG) elective nodal ano-rectal atlas and provide additional anatomic, clinical, and technical instructions to guide radiation oncologists in the planning and delivery of IMRT for anal cancer.

  10. ATLAS distributed computing: experience and evolution

    NASA Astrophysics Data System (ADS)

    Nairz, A.; Atlas Collaboration

    2014-06-01

    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 centres 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 programme 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 2015 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, energies and event complexities. An essential requirement will be the efficient utilisation of current and future processor technologies as well as a broad range of computing platforms, including supercomputing and cloud resources. We will report on experience gained thus far and our progress in preparing ATLAS computing for the future.

  11. Augmentation of the IUE Ultraviolet Spectral Atlas

    NASA Technical Reports Server (NTRS)

    Wu, Chi-Chao

    1996-01-01

    The IUE Ultraviolet Spectral Atlas and the first addendum were published by Wu et al. in printed and machine readable versions. This atlas and addendum contain UV spectra of 315 stars with spectral types ranging from O3 to M5 and many spectral type-luminosity class combinations. There were three criteria for selecting these stars: (1) they were not spectroscopic binaries or variables with significant changes in magnitude or color, (2) they must have well-determined spectral types (many are MK standards), and (3) the stars should not be heavily reddened. Further augmentation of the atlas is desirable to provide a more complete coverage of the spectral type-luminosity class combinations and more than one star per combination. The extra spectral type-luminosity class combinations reduce the need for interpolation. The extra stars within a given combination guard against variability and peculiarity, and allow for a finite range of temperature, metallicity and gravity. The previous atlas and addendum presented data that were obtained through the eleventh episode under IUE programs with C.-C. Wu and D. Burstein as principal investigators. In this second addendum, we present the spectra obtained by Wu's programs during the twelfth through seventeenth episodes: SALCW, SAMCW, SANCW, SAOCW, SAPCW and SAQCW. During the period between July 1989 and September 1994, Wu observed 183 stars under these programs. Most of these observations are high quality trails or pseudo-trails (multiple exposures in the large aperture).

  12. United States Atlas of Renewable Resources

    DOE Data Explorer

    The Atlas is an interactive application of the renewable energy resources in the contiguous United States, Alaska and Hawaii. It illustrates the geographic distribution of wind, solar, geothermal, and biomass resources, as well as other pertinent information such as transportation network and administrative boundaries.[Copied from http://www.nrel.gov/gis/maps.html

  13. ATLAS Large Scale Thin Gap Chambers

    SciTech Connect

    Soha, Aria

    2014-04-29

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of the ATLAS sTGC New Small Wheel collaboration who have committed to participate in beam tests to be carried out during the FY2014 Fermilab Test Beam Facility program.

  14. The new ATLAS track reconstruction (NEWT)

    NASA Astrophysics Data System (ADS)

    Cornelissen, T.; Elsing, M.; Gavrilenko, I.; Liebig, W.; Moyse, E.; Salzburger, A.

    2008-07-01

    The track reconstruction of modern high energy physics experiments is a very complex task that puts stringent requirements onto the software realisation. The ATLAS track reconstruction software has been in the past dominated by a collection of individual packages, each of which incorporating a different intrinsic event data model, different data flow sequences and calibration data. Recently, the ATLAS track reconstruction has undergone a major design revolution to ensure maintainability during the long lifetime of the ATLAS experiment and the flexibility needed for the startup phase. The entire software chain has been re-organised in modular components and a common event data model has been deployed. A complete new track reconstruction that concentrates on common tools aimed to be used by both ATLAS tracking devices, the Inner Detector and the Muon System, has been established. It has been already used during many large scale tests with data from Monte Carlo simulation and from detector commissioning projects such as the combined test beam 2004 and cosmic ray events. This document concentrates on the technical and conceptual details of the newly developed track reconstruction.

  15. World atlas of large optical telescopes

    NASA Technical Reports Server (NTRS)

    Meszaros, S. P.

    1979-01-01

    By 1980 there will be approximately 100 large optical telescopes in the world with mirror or lens diameters of one meter (39 inches) and larger. This atlas gives information on these telescopes and shows their locations on continent-sized maps. Observatory locations considered suitable for the construction of future large telescopes are also shown.

  16. DISTRIBUTED CONTROL AND DA FOR ATLAS

    SciTech Connect

    D. SCUDDER; ET AL

    1999-05-01

    The control system for the Atlas pulsed power generator being built at Los Alamos National Laboratory will utilize a significant level of distributed control. Other principal design characteristics include noise immunity, modularity and use of commercial products wherever possible. The data acquisition system is tightly coordinated with the control system. Both share a common database server and a fiber-optic ethernet communications backbone.

  17. Inclusive Standard Model Higgs searches with ATLAS

    SciTech Connect

    Polci, Francesco

    2008-11-23

    The update of the discovery potential for a Standard Model Higgs boson through the inclusive searches H{yields}{gamma}{gamma}, H{yields}ZZ* and H{yields}WW with the ATLAS detector is reported. The analysis are based on the most recent available simulations of signal, backgrounds as well as the detector response.

  18. Chesapeake Bay Program: Point-Source Atlas

    SciTech Connect

    Macknis, J.

    1988-08-01

    The atlas contains pollutant loadings from Chesapeake Bay watershed municipal and industrial point sources drawn from the Chesapeake Bay Program computerized data base. Nutrient and toxic discharges are included. Effluent data are averaged for the calendar year 1985. Detailed information is presented in 23 tables and 14 figures.

  19. The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart

    PubMed Central

    Fonseca, Carissa G.; Backhaus, Michael; Bluemke, David A.; Britten, Randall D.; Chung, Jae Do; Cowan, Brett R.; Dinov, Ivo D.; Finn, J. Paul; Hunter, Peter J.; Kadish, Alan H.; Lee, Daniel C.; Lima, Joao A. C.; Medrano−Gracia, Pau; Shivkumar, Kalyanam; Suinesiaputra, Avan; Tao, Wenchao; Young, Alistair A.

    2011-01-01

    Motivation: Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups. Results: Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt). Availability: http://www.cardiacatlas.org Contact: a.young@auckland.ac.nz Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21737439

  20. Subcortical structure segmentation using probabilistic atlas priors

    NASA Astrophysics Data System (ADS)

    Gouttard, Sylvain; Styner, Martin; Joshi, Sarang; Smith, Rachel G.; Cody Hazlett, Heather; Gerig, Guido

    2007-03-01

    The segmentation of the subcortical structures of the brain is required for many forms of quantitative neuroanatomic analysis. The volumetric and shape parameters of structures such as lateral ventricles, putamen, caudate, hippocampus, pallidus and amygdala are employed to characterize a disease or its evolution. This paper presents a fully automatic segmentation of these structures via a non-rigid registration of a probabilistic atlas prior and alongside a comprehensive validation. Our approach is based on an unbiased diffeomorphic atlas with probabilistic spatial priors built from a training set of MR images with corresponding manual segmentations. The atlas building computes an average image along with transformation fields mapping each training case to the average image. These transformation fields are applied to the manually segmented structures of each case in order to obtain a probabilistic map on the atlas. When applying the atlas for automatic structural segmentation, an MR image is first intensity inhomogeneity corrected, skull stripped and intensity calibrated to the atlas. Then the atlas image is registered to the image using an affine followed by a deformable registration matching the gray level intensity. Finally, the registration transformation is applied to the probabilistic maps of each structures, which are then thresholded at 0.5 probability. Using manual segmentations for comparison, measures of volumetric differences show high correlation with our results. Furthermore, the dice coefficient, which quantifies the volumetric overlap, is higher than 62% for all structures and is close to 80% for basal ganglia. The intraclass correlation coefficient computed on these same datasets shows a good inter-method correlation of the volumetric measurements. Using a dataset of a single patient scanned 10 times on 5 different scanners, reliability is shown with a coefficient of variance of less than 2 percents over the whole dataset. Overall, these validation

  1. Augmentation of IUE Ultraviolet Spectral Atlas

    NASA Astrophysics Data System (ADS)

    Wu, Chi-Chao

    The first edition of the IUE Ultraviolet Spectral Atlas was published in 1983 by Wu et al in printed and magnetic tape versions and it has been widely used by the astronomical community for research and teaching purposes. It was recognized then that numerous spectral type-luminosity class combinations were not available in the Atlas, but the authors decided that it was important to provide the Atlas to the community early. Now we are proposing a 3-year program to augment the Atlas (1) to provide as complete a coverage of the spectral type-luminosity class as possible and (2) to provide more than one star per spectral type-luminosity class combination to guard against variability and pecularity and to allow a finite range of temperature, gravity and metallicity in a given combination. Almost all the data in the 1983 Atlas are the high quality, high SIN trailed spectra, we propose to obtain trailed spectra or images with multiple exposures in the large aperture such that the data for the augmentation effort will have the same quality and SIN as the 1983 Atlas. Our primary goal is to collect the data and make them available to the community immediately (without claiming the 6-month proprietary right) and at the end of each year we will provide National Space Science Data Center (NSSDC) an annual incremental delivery of the data at an earliest possible date, so the data can be distributed to the general astronomical community. At the end of the 3rd year, our delivery to the NSSDC will contain all the data collected by this program combined with those from the 1983 Atlas and 50 stars from the archive. These data can be used by other astronomers for stellar population synthesis of galaxies, to study the nature of distant galaxies, to attempt establishing a UV spectral classification system, as comparison stars for interstellar extinction studies and for peculiar objects or binary systems, for the study of the effects of temperature, gravity and metallicity on stellar UV

  2. Higgs Boson Physics at Atlas

    NASA Astrophysics Data System (ADS)

    Denis, Richard St.

    2015-03-01

    The discovery of a new boson with the ATLAS detector at the LHC proton-proton collider is confirmed using the full data set collected at centre-of-mass energies of 7 and 8 TeV. The spin and parity properties of the boson are consistent with that of a scalar particle with positive parity. Comparison of the JP = 0+ hypothesis to alternatives JP = 0-, 1+, 1-, 2+ result in exclusion of these other choices at 97.8%, 99.97%, 99.7%, and 99.3% CL. The Higgs boson mass is m_H = 125.5 pm 0.2l( {stat. right)_{ - 0.5}^{ + 0.5} l( {syst.} right)GeV. Evidence for production of the Higgs boson by vector boson fusion is obtained in a model-independent approach by comparing the signal strengths μ of vector boson fusion and production associated with a vector boson to that for gluon fusion including associated production of top quark pairs: μ _{VBF + VH /μ _{gg F + ttH = 1.4_{ - 0.3}^{ + 0.4} l( {stat.} right)_{ - 0.4}^{ + 0.6} l( {syst.} right) which is 3.3 Gaussian standard deviations from zero.

  3. Machine-inudced backgrounds: their origin and loads on ATLAS/CMS

    SciTech Connect

    Mokhov, N.V.; Weiler, T.; /CERN

    2008-05-01

    A detailed analysis of machine-induced backgrounds (MIB) in the LHC collider detectors is performed with focus on origin and rates for three sources: tertiary beam halo, beam-gas interactions and kicker prefire. Particle fluxes originating from these operational and accidental beam losses are carefully calculated with the MARS15 code and presented at the entrance to the ATLAS and CMS experimental halls. It is shown that background rates in detector subsystems strongly depend on the origin of MIB, particle energy and type. Using this source term, instantaneous and integrated loads on the detectors and impact on the detector performance can be derived.

  4. Medical workstation design: enhancing graphical interface with 3D anatomical atlas

    NASA Astrophysics Data System (ADS)

    Soo Hoo, Kent; Wong, Stephen T.; Grant, Ellen

    1997-05-01

    The huge data archive of the UCSF Hospital Integrated Picture Archiving and Communication System gives healthcare providers access to diverse kinds of images and text for diagnosis and patient management. Given the mass of information accessible, however, conventional graphical user interface (GUI) approach overwhelms the user with forms, menus, fields, lists, and other widgets and causes 'information overloading.' This article describes a new approach that complements the conventional GUI with 3D anatomical atlases and presents the usefulness of this approach with a clinical neuroimaging application.

  5. Search for Higgs and Z Boson Decays to ϕγ with the ATLAS Detector.

    PubMed

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    2016-09-01

    A search for the decays of the Higgs and Z bosons to a ϕ meson and a photon is performed with a pp collision data sample corresponding to an integrated luminosity of 2.7  fb^{-1} collected at sqrt[s]=13  TeV with the ATLAS detector at the LHC. No significant excess of events is observed above the background, and 95% confidence level upper limits on the branching fractions of the Higgs and Z boson decays to ϕγ of 1.4×10^{-3} and 8.3×10^{-6}, respectively, are obtained. PMID:27661680

  6. Search for Higgs and Z Boson Decays to ϕγ with the ATLAS Detector.

    PubMed

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Zhou, M; Zhou, N; Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zhukov, K; Zibell, A; Zieminska, D; Zimine, N I; Zimmermann, C; Zimmermann, S; Zinonos, Z; Zinser, M; Ziolkowski, M; Živković, L; Zobernig, G; Zoccoli, A; Zur Nedden, M; Zwalinski, L

    2016-09-01

    A search for the decays of the Higgs and Z bosons to a ϕ meson and a photon is performed with a pp collision data sample corresponding to an integrated luminosity of 2.7  fb^{-1} collected at sqrt[s]=13  TeV with the ATLAS detector at the LHC. No significant excess of events is observed above the background, and 95% confidence level upper limits on the branching fractions of the Higgs and Z boson decays to ϕγ of 1.4×10^{-3} and 8.3×10^{-6}, respectively, are obtained.

  7. Radiation hardness tests of GaAs amplifiers operated in liquid argon in the ATLAS calorimeter

    NASA Astrophysics Data System (ADS)

    Ban, J.; Brettel, H.; Cheplakov, A.; Cwienk, W.; Fent, J.; Golikov, V.; Golubyh, S.; Jakobs, K.; Kukhtin, V.; Kulagin, E.; Kurchaninov, L.; Ladygin, E.; Luschikov, V.; Oberlack, H.; Obudovsky, V.; Schacht, P.; Shalyugin, A.; Stiegler, U.; Zweimüller, T.

    2008-09-01

    Highly integrated Gallium Arsenide (GaAs) chips of preamplifiers and summing amplifiers have been exposed to high fluence of fast neutrons and γ-dose at the IBR-2 reactor in Dubna. A stable performance of the electronics has been demonstrated up to a fluence of 5×1014 n cm-2 and a γ-dose of 55 kGy. The radiation hardness tests confirm the applicability of the preamplifiers for more than 10 years operation in the ATLAS hadronic end-cap calorimeter at LHC.

  8. Search for new, long-lived, charged particles using ionization in the ATLAS Pixel Detector

    NASA Astrophysics Data System (ADS)

    Axen, Bradley; Atlas Collaboration

    2016-03-01

    Several extensions of the Standard Model predict the existence of charged, very massive, and long-lived particles. Because of their high masses these particles would propagate non-relativistically through the ATLAS pixel detector and are therefore be identifiable through a measurement of large specific energy loss. Measuring heavy, long-lived particles through their track parameters in the pixel detector allows sensitivity to particles with lifetimes in the nanosecond range and above. This search presents an inner detector driven method for identifying such particles in proton-proton collisions at 13 TeV with the 2015 dataset corresponding to an integrated luminosity of 3.5 pb-1.

  9. Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

    PubMed Central

    Grocott, Timothy; Thomas, Paul; Münsterberg, Andrea E.

    2016-01-01

    Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states. PMID:26864723

  10. A digital rat atlas of sectional anatomy

    NASA Astrophysics Data System (ADS)

    Yu, Li; Liu, Qian; Bai, Xueling; Liao, Yinping; Luo, Qingming; Gong, Hui

    2006-09-01

    This paper describes a digital rat alias of sectional anatomy made by milling. Two healthy Sprague-Dawley (SD) rat weighing 160-180 g were used for the generation of this atlas. The rats were depilated completely, then euthanized by Co II. One was via vascular perfusion, the other was directly frozen at -85 °C over 24 hour. After that, the frozen specimens were transferred into iron molds for embedding. A 3% gelatin solution colored blue was used to fill the molds and then frozen at -85 °C for one or two days. The frozen specimen-blocks were subsequently sectioned on the cryosection-milling machine in a plane oriented approximately transverse to the long axis of the body. The surface of specimen-blocks were imaged by a scanner and digitalized into 4,600 x2,580 x 24 bit array through a computer. Finally 9,475 sectional images (arterial vessel were not perfused) and 1,646 sectional images (arterial vessel were perfused) were captured, which made the volume of the digital atlas up to 369.35 Gbyte. This digital rat atlas is aimed at the whole rat and the rat arterial vessels are also presented. We have reconstructed this atlas. The information from the two-dimensional (2-D) images of serial sections and three-dimensional (3-D) surface model all shows that the digital rat atlas we constructed is high quality. This work lays the foundation for a deeper study of digital rat.

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

    SciTech Connect

    Zhao, Tingting Ruan, Dan

    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

  12. The ATLAS Fast Monte Carlo Production Chain Project

    NASA Astrophysics Data System (ADS)

    Jansky, Roland

    2015-12-01

    During the last years ATLAS has successfully deployed a new integrated simulation framework (ISF) which allows a flexible mixture of full and fast detector simulation techniques within the processing of one event. The thereby achieved possible speed-up in detector simulation of up to a factor 100 makes subsequent digitization and reconstruction the dominant contributions to the Monte Carlo (MC) production CPU cost. The slowest components of both digitization and reconstruction are inside the Inner Detector due to the complex signal modeling needed in the emulation of the detector readout and in reconstruction due to the combinatorial nature of the problem to solve, respectively. Alternative fast approaches have been developed for these components: for the silicon based detectors a simpler geometrical clustering approach has been deployed replacing the charge drift emulation in the standard digitization modules, which achieves a very high accuracy in describing the standard output. For the Inner Detector track reconstruction, a Monte Carlo generator information based trajectory building has been deployed with the aim of bypassing the CPU intensive pattern recognition. Together with the ISF all components have been integrated into a new fast MC production chain, aiming to produce fast MC simulated data with sufficient agreement with fully simulated and reconstructed data at a processing time of seconds per event, compared to several minutes for full simulation.

  13. Search for lepton-flavour-violating H → μτ decays of the Higgs boson with the ATLAS detector

    DOE PAGES

    Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Aben, R.; Abolins, M.; AbouZeid, O. S.; Abramowicz, H.; Abreu, H.; Abreu, R.; et al

    2015-11-30

    A direct search for lepton-flavour-violating H → μτ decays of the recently discovered Higgs boson with the ATLAS detector at the LHC is presented. The analysis is performed in the H → μτ had channel, where τ had is a hadronically decaying τ -lepton. The search is based on the data sample of proton-proton collisions collected by the ATLAS experiment corresponding to an integrated luminosity of 20.3 fb–1 at a centre-of-mass energy of √s = 8 TeV. No statistically significant excess of data over the predicted background is observed. As a result, the observed (expected) 95% confidence-level upper limit onmore » the branching fraction, Br( H → μτ ), is 1.85% (1.24%).« less

  14. Search for lepton-flavour-violating H → μτ decays of the Higgs boson with the ATLAS detector

    SciTech Connect

    Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Aben, R.; Abolins, M.; AbouZeid, O. S.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adamczyk, L.; Adams, D. L.; Adelman, J.; Adomeit, S.; Adye, T.; Affolder, A. A.; Agatonovic-Jovin, T.; Agricola, J.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akerstedt, H.; Åkesson, T. P. A.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albrand, S.; Alconada Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Alimonti, G.; Alio, L.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Altheimer, A.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amako, K.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amorim, A.; Amoroso, S.; Amram, N.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, G.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Anger, P.; Angerami, A.; Anghinolfi, F.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antonelli, M.; Antonov, A.; Antos, J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Arce, A. T. H.; Arduh, F. A.; Arguin, J-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnal, V.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Asai, S.; Asbah, N.; Ashkenazi, A.; Åsman, B.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Aurousseau, M.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baak, M. A.; Baas, A. E.; Baca, M. J.; Bacci, C.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Bagiacchi, P.; Bagnaia, P.; Bai, Y.; Bain, T.; Baines, J. T.; Baker, O. K.; Baldin, E. M.; Balek, P.; Balestri, T.; Balli, F.; Balunas, W. K.; Banas, E.; Banerjee, Sw.; Bannoura, A. A. E.; Bansil, H. S.; Barak, L.; Barberio, E. 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F.; Catastini, P.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Ceradini, F.; Cerio, B. C.; Cerny, K.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cerv, M.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chalupkova, I.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, K.; Chen, L.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, Y.; Cheplakov, A.; Cheremushkina, E.; Cherkaoui El Moursli, R.; Chernyatin, V.; Cheu, E.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chislett, R. T.; Chitan, A.; Chizhov, M. V.; Choi, K.; Chouridou, S.; Chow, B. K. B.; Christodoulou, V.; Chromek-Burckhart, D.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Ciapetti, G.; Ciftci, A. K.; Cinca, D.; Cindro, V.; Cioara, I. A.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Ciubancan, M.; Clark, A.; Clark, B. L.; Clark, P. J.; Clarke, R. N.; Cleland, W.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coffey, L.; Cogan, J. G.; Colasurdo, L.; Cole, B.; Cole, S.; Colijn, A. P.; Collot, J.; Colombo, T.; Compostella, G.; Conde Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Consorti, V.; Constantinescu, S.; Conta, C.; Conti, G.; Conventi, F.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Corso-Radu, A.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Côté, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Cribbs, W. A.; Crispin Ortuzar, M.; Cristinziani, M.; Croft, V.; Crosetti, G.; Cuhadar Donszelmann, T.; Cummings, J.; Curatolo, M.; Cúth, J.; Cuthbert, C.; Czirr, H.; Czodrowski, P.; D’Auria, S.; D’Onofrio, M.; Da Cunha Sargedas De Sousa, M. J.; Da Via, C.; Dabrowski, W.; Dafinca, A.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Dandoy, J. R.; Dang, N. P.; Daniells, A. C.; Danninger, M.; Dano Hoffmann, M.; Dao, V.; Darbo, G.; Darmora, S.; Dassoulas, J.; Dattagupta, A.; Davey, W.; David, C.; Davidek, T.; Davies, E.; Davies, M.; Davison, P.; Davygora, Y.; Dawe, E.; Dawson, I.; Daya-Ishmukhametova, R. K.; De, K.; de Asmundis, R.; De Benedetti, A.; De Castro, S.; De Cecco, S.; De Groot, N.; de Jong, P.; De la Torre, H.; De Lorenzi, F.; De Pedis, D.; De Salvo, A.; De Sanctis, U.; De Santo, A.; De Vivie De Regie, J. B.; Dearnaley, W. J.; Debbe, R.; Debenedetti, C.; Dedovich, D. V.; Deigaard, I.; Del Peso, J.; Del Prete, T.; Delgove, D.; Deliot, F.; Delitzsch, C. M.; Deliyergiyev, M.; Dell’Acqua, A.; Dell’Asta, L.; Dell’Orso, M.; Della Pietra, M.; della Volpe, D.; Delmastro, M.; Delsart, P. A.; Deluca, C.; DeMarco, D. A.; Demers, S.; Demichev, M.; Demilly, A.; Denisov, S. P.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; Di Ciaccio, A.; Di Ciaccio, L.; Di Domenico, A.; Di Donato, C.; Di Girolamo, A.; Di Girolamo, B.; Di Mattia, A.; Di Micco, B.; Di Nardo, R.; Di Simone, A.; Di Sipio, R.; Di Valentino, D.; Diaconu, C.; Diamond, M.; Dias, F. A.; Diaz, M. A.; Diehl, E. B.; Dietrich, J.; Diglio, S.; Dimitrievska, A.; Dingfelder, J.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Djuvsland, J. I.; do Vale, M. A. B.; Dobos, D.; Dobre, M.; Doglioni, C.; Dohmae, T.; Dolejsi, J.; Dolezal, Z.; Dolgoshein, B. A.; Donadelli, M.; Donati, S.; Dondero, P.; Donini, J.; Dopke, J.; Doria, A.; Dova, M. T.; Doyle, A. 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X.; Graber, L.; Grabowska-Bold, I.; Gradin, P. O. J.; Grafström, P.; Grahn, K-J.; Gramling, J.; Gramstad, E.; Grancagnolo, S.; Gratchev, V.; Gray, H. M.; Graziani, E.; Greenwood, Z. D.; Grefe, C.; Gregersen, K.; Gregor, I. M.; Grenier, P.; Griffiths, J.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Gris, Ph.; Grivaz, J. -F.; Grohs, J. P.; Grohsjean, A.; Gross, E.; Grosse-Knetter, J.; Grossi, G. C.; Grout, Z. J.; Guan, L.; Guenther, J.; Guescini, F.; Guest, D.; Gueta, O.; Guido, E.; Guillemin, T.; Guindon, S.; Gul, U.; Gumpert, C.; Guo, J.; Guo, Y.; Gupta, S.; Gustavino, G.; Gutierrez, P.; Gutierrez Ortiz, N. G.; Gutschow, C.; Guyot, C.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haber, C.; Hadavand, H. K.; Haddad, N.; Haefner, P.; Hageböck, S.; Hajduk, Z.; Hakobyan, H.; Haleem, M.; Haley, J.; Hall, D.; Halladjian, G.; Hallewell, G. D.; Hamacher, K.; Hamal, P.; Hamano, K.; Hamilton, A.; Hamity, G. N.; Hamnett, P. 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C.; Hiller, K. H.; Hillier, S. J.; Hinchliffe, I.; Hines, E.; Hinman, R. R.; Hirose, M.; Hirschbuehl, D.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M. R.; Hoenig, F.; Hohlfeld, M.; Hohn, D.; Holmes, T. R.; Homann, M.; Hong, T. M.; Hopkins, W. H.; Horii, Y.; Horton, A. J.; Hostachy, J-Y.; Hou, S.; Hoummada, A.; Howard, J.; Howarth, J.; Hrabovsky, M.; Hristova, I.; Hrivnac, J.; Hryn’ova, T.; Hrynevich, A.; Hsu, C.; Hsu, P. J.; Hsu, S. -C.; Hu, D.; Hu, Q.; Hu, X.; Huang, Y.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Huffman, T. B.; Hughes, E. W.; Hughes, G.; Huhtinen, M.; Hülsing, T. 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F-W.; Sadykov, R.; Safai Tehrani, F.; Sahinsoy, M.; Saimpert, M.; Saito, T.; Sakamoto, H.; Sakurai, Y.; Salamanna, G.; Salamon, A.; Salazar Loyola, J. E.; Saleem, M.; Salek, D.; Sales De Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sammel, D.; Sampsonidis, D.; Sanchez, A.; Sánchez, J.; Sanchez Martinez, V.; Sandaker, H.; Sandbach, R. L.; Sander, H. G.; Sanders, M. P.; Sandhoff, M.; Sandoval, C.; Sandstroem, R.; Sankey, D. P. C.; Sannino, M.; Sansoni, A.; Santoni, C.; Santonico, R.; Santos, H.; Santoyo Castillo, I.; Sapp, K.; Sapronov, A.; Saraiva, J. G.; Sarrazin, B.; Sasaki, O.; Sasaki, Y.; Sato, K.; Sauvage, G.; Sauvan, E.; Savage, G.; Savard, P.; Sawyer, C.; Sawyer, L.; Saxon, J.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Scarcella, M.; Scarfone, V.; Schaarschmidt, J.; Schacht, P.; Schaefer, D.; Schaefer, R.; Schaeffer, J.; Schaepe, S.; Schaetzel, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Schiavi, C.; Schillo, C.; Schioppa, M.; Schlenker, S.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitt, S.; Schneider, B.; Schnellbach, Y. J.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schoenrock, B. D.; Schopf, E.; Schorlemmer, A. L. S.; Schott, M.; Schouten, D.; Schovancova, J.; Schramm, S.; Schreyer, M.; Schroeder, C.; Schuh, N.; Schultens, M. J.; Schultz-Coulon, H. -C.; Schulz, H.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schwarz, T. A.; Schwegler, Ph.; Schweiger, H.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Schwindt, T.; Sciacca, F. G.; Scifo, E.; Sciolla, G.; Scuri, F.; Scutti, F.; Searcy, J.; Sedov, G.; Sedykh, E.; Seema, P.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Sekhon, K.; Sekula, S. J.; Seliverstov, D. M.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Serkin, L.; Serre, T.; Sessa, M.; Seuster, R.; Severini, H.; Sfiligoj, T.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L. Y.; Shang, R.; Shank, J. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Shaw, S. M.; Shcherbakova, A.; Shehu, C. Y.; Sherwood, P.; Shi, L.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shiyakova, M.; Shmeleva, A.; Shoaleh Saadi, D.; Shochet, M. J.; Shojaii, S.; Shrestha, S.; Shulga, E.; Shupe, M. A.; Shushkevich, S.; Sicho, P.; Sidebo, P. E.; Sidiropoulou, O.; Sidorov, D.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silva, J.; Silver, Y.; Silverstein, S. B.; Simak, V.; Simard, O.; Simic, Lj.; Simion, S.; Simioni, E.; Simmons, B.; Simon, D.; Sinervo, P.; Sinev, N. B.; Sioli, M.; Siragusa, G.; Sisakyan, A. N.; Sivoklokov, S. Yu.; Sjölin, J.; Sjursen, T. B.; Skinner, M. B.; Skottowe, H. P.; Skubic, P.; Slater, M.; Slavicek, T.; Slawinska, M.; Sliwa, K.; Smakhtin, V.; Smart, B. H.; Smestad, L.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, M. N. K.; Smith, R. W.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snidero, G.; Snyder, S.; Sobie, R.; Socher, F.; Soffer, A.; Soh, D. A.; Sokhrannyi, G.; Solans, C. A.; Solar, M.; Solc, J.; Soldatov, E. Yu.; Soldevila, U.; Solodkov, A. A.; Soloshenko, A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Song, H. Y.; Soni, N.; Sood, A.; Sopczak, A.; Sopko, B.; Sopko, V.; Sorin, V.; Sosa, D.; Sosebee, M.; Sotiropoulou, C. L.; Soualah, R.; Soukharev, A. M.; South, D.; Sowden, B. C.; Spagnolo, S.; Spalla, M.; Spangenberg, M.; Spanò, F.; Spearman, W. R.; Sperlich, D.; Spettel, F.; Spighi, R.; Spigo, G.; Spiller, L. A.; Spousta, M.; Spreitzer, T.; Denis, R. D. St.; Stabile, A.; Staerz, S.; Stahlman, J.; Stamen, R.; Stamm, S.; Stanecka, E.; Stanescu, C.; Stanescu-Bellu, M.; Stanitzki, M. M.; Stapnes, S.; Starchenko, E. A.; Stark, J.; Staroba, P.; Starovoitov, P.; Staszewski, R.; Steinberg, P.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stewart, G. A.; Stillings, J. A.; Stockton, M. C.; Stoebe, M.; Stoicea, G.; Stolte, P.; Stonjek, S.; Stradling, A. R.; Straessner, A.; Stramaglia, M. E.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strauss, E.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Subramaniam, R.; Succurro, A.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Sundermann, J. E.; Suruliz, K.; Susinno, G.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Sykora, I.; Sykora, T.; Ta, D.; Taccini, C.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Taiblum, N.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tam, J. Y. C.; Tan, K. G.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tannenwald, B. B.; Tannoury, N.; Tapprogge, S.; Tarem, S.; Tarrade, F.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, F. E.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teischinger, F. A.; Teixeira Dias Castanheira, M.; Teixeira-Dias, P.; Temming, K. K.; Temple, D.; Ten Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Theveneaux-Pelzer, T.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, E. N.; Thompson, P. D.; Thompson, R. J.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Thomson, M.; Thun, R. P.; Tibbetts, M. J.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tiouchichine, E.; Tipton, P.; Tisserant, S.; Todome, K.; Todorov, T.; Todorova-Nova, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tollefson, K.; Tolley, E.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C-L.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tudorache, A.; Tudorache, V.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turecek, D.; Turra, R.; Turvey, A. J.; Tuts, P. M.; Tykhonov, A.; Tylmad, M.; Tyndel, M.; Ueda, I.; Ueno, R.; Ughetto, M.; Ugland, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Unverdorben, C.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usanova, A.; Vacavant, L.; Vacek, V.; Vachon, B.; Valderanis, C.; Valencic, N.; Valentinetti, S.; Valero, A.; Valery, L.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; Van Den Wollenberg, W.; Van Der Deijl, P. C.; van der Geer, R.; van der Graaf, H.; van Eldik, N.; van Gemmeren, P.; Van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vanguri, R.; Vaniachine, A.; Vannucci, F.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veloce, L. M.; Veloso, F.; Velz, T.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vest, A.; Vetterli, M. C.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigne, R.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vladoiu, D.; Vlasak, M.; Vogel, M.; Vokac, P.; Volpi, G.; Volpi, M.; von der Schmitt, H.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Vykydal, Z.; Wagner, P.; Wagner, W.; Wahlberg, H.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, K.; Wang, R.; Wang, S. M.; Wang, T.; Wang, T.; Wang, X.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Wasicki, C.; Watkins, P. M.; Watson, A. T.; Watson, I. J.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, S.; Weber, M. S.; Weber, S. W.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Wessels, M.; Wetter, J.; Whalen, K.; Wharton, A. M.; White, A.; White, M. J.; White, R.; White, S.; Whiteson, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, A.; Wilson, J. A.; Wingerter-Seez, I.; Winklmeier, F.; Winter, B. T.; Wittgen, M.; Wittkowski, J.; Wollstadt, S. J.; Wolter, M. W.; Wolters, H.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wozniak, K. W.; Wu, M.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xu, D.; Xu, L.; Yabsley, B.; Yacoob, S.; Yakabe, R.; Yamada, M.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yao, W-M.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yen, A. L.; Yildirim, E.; Yorita, K.; Yoshida, R.; Yoshihara, K.; Young, C.; Young, C. J. S.; Youssef, S.; Yu, D. R.; Yu, J.; Yu, J. M.; Yu, J.; Yuan, L.; Yuen, S. P. Y.; Yurkewicz, A.; Yusuff, I.; Zabinski, B.; Zaidan, R.; Zaitsev, A. M.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanello, L.; Zanzi, D.; Zeitnitz, C.; Zeman, M.; Zemla, A.; Zeng, Q.; Zengel, K.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, F.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, R.; Zhang, X.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, L.; Zhou, M.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; zur Nedden, M.; Zurzolo, G.; Zwalinski, L.

    2015-11-30

    A direct search for lepton-flavour-violating H → μτ decays of the recently discovered Higgs boson with the ATLAS detector at the LHC is presented. The analysis is performed in the H → μτ had channel, where τ had is a hadronically decaying τ -lepton. The search is based on the data sample of proton-proton collisions collected by the ATLAS experiment corresponding to an integrated luminosity of 20.3 fb–1 at a centre-of-mass energy of √s = 8 TeV. No statistically significant excess of data over the predicted background is observed. As a result, the observed (expected) 95% confidence-level upper limit on the branching fraction, Br( H → μτ ), is 1.85% (1.24%).

  15. Search for decays of stopped, long-lived particles from 7 TeV pp collisions with the ATLAS detector

    SciTech Connect

    Aad G.; Abbott, B; Abdallah, J; Abdelalim, AA; Abdesselam, A; Abdinov, O; Abi, B; Abolins, M; Abramowicz, H; Abreu, H; Acerbia, E; Acharya, BS; Adams, DL; Addy, TN; Adelman, J; Aderholz, M; Adomeit, S; Adragna, P; Adye, T; Aefsky, S; Aguilar-Saavedra, JA; et al.

    2012-04-01

    New metastable massive particles with electric and color charge are features of many theories beyond the Standard Model. A search is performed for long-lived gluino-based R-hadrons with the ATLAS detector at the LHC using a data sample corresponding to an integrated luminosity of 31 pb{sup -1}. We search for evidence of particles that have come to rest in the ATLAS detector and decay at some later time during the periods in the LHC bunch structure without proton-proton collisions. No significant deviations from the expected backgrounds are observed, and a cross-section limit is set. It can be interpreted as excluding gluino-based R-hadrons with masses less than 341 GeV at the 95 % C.L., for lifetimes from 10{sup -5} to 10{sup 3} seconds and a neutralino mass of 100 GeV.

  16. Research and development for a free-running readout system for the ATLAS LAr Calorimeters at the high luminosity LHC

    NASA Astrophysics Data System (ADS)

    Hils, Maximilian

    2016-07-01

    The ATLAS Liquid Argon (LAr) Calorimeters were designed and built to measure electromagnetic and hadronic energy in proton-proton collisions produced at the Large Hadron Collider (LHC) at centre-of-mass energies up to 14 TeV and instantaneous luminosities up to 1034 cm-2 s-1. The High Luminosity LHC (HL-LHC) programme is now developed for up to 5-7 times the design luminosity, with the goal of accumulating an integrated luminosity of 3000 fb-1. In the HL-LHC phase, the increased radiation levels and an improved ATLAS trigger system require a replacement of the Front-end (FE) and Back-end (BE) electronics of the LAr Calorimeters. Results from research and development of individual components and their radiation qualification as well as the overall system design will be presented.

  17. DIGITAL ATLAS OF LAKE TEXOMA (CD-ROM)

    EPA Science Inventory

    The U.S. Environmental Protection Agency, U.S. Geological Survey, and U.S. Army Corps of Engineers worked together to create a Digital Atlas of Lake Texoma. The Digital Atlas of Lake Texoma contains 29 digital map data sets covering Cooke and Grayson Counties in Texas, and Bryan,...

  18. World Bank Atlas: Population, Per Capita Product and Growth Rates.

    ERIC Educational Resources Information Center

    World Bank, Washington, DC.

    The ninth edition of the World Bank Atlas shows estimates of population, gross national product, and per capita production of 189 countries and territories for 1972. The data presented in the atlas are the result of the work of the World Bank Group whose major purpose is to provide both financial and technical assistance and to improve the living…

  19. Prospects for SUSY searches in CMS and ATLAS

    SciTech Connect

    Jong, Paul de

    2008-11-23

    We discuss how the CMS and ATLAS experiments are preparing for the analysis of first LHC data with emphasis on the search for supersymmetry. We will show the importance of the understanding of detector, trigger, reconstruction and backgrounds, and we will present realistic estimates of the reach of CMS and ATLAS.

  20. ATLAS-3 correlative measurement opportunities with UARS and surface observations

    NASA Technical Reports Server (NTRS)

    Harrison, Edwin F.; Denn, Fred M.; Gibson, Gary G.

    1995-01-01

    The third ATmospheric Laboratory for Applications and Science (ATLAS-3) mission was flown aboard the Space Shuttle launched on November 3, 1994. The mission length was approximately 10 days and 22 hours. The ATLAS-3 Earth-viewing instruments provided a large number of measurements which were nearly coincident with observations from experiments on the Upper Atmosphere Research Satellite (UARS). Based on ATLAS-3 instrument operating schedules, simulations were performed to determine when and where correlative measurements occurred between ATLAS and UARS instruments, and between ATLAS and surface observations. Results of these orbital and instrument simulations provide valuable information for scientists to compare measurements between various instruments on the two satellites and at selected surface sites.

  1. Global GIS database; digital atlas of Central and South America

    USGS Publications Warehouse

    Hearn,, Paul P.; Hare, T.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

    2000-01-01

    This CD-ROM contains a digital atlas of the countries of Central and South America. This atlas is part of a global database compiled from USGS and other data sources at the nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may also be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included. The atlas contains the following datasets: country political boundaries, digital shaded relief map, elevation, slope, hydrology, locations of cities and towns, airfields, roads, railroads, utility lines, population density, geology, ecological regions, historical seismicity, volcanoes, ore deposits, oil and gas fields, climate data, landcover, vegetation index, and lights at night.

  2. Alignment of the ATLAS inner detector tracking system

    NASA Astrophysics Data System (ADS)

    Kollár, Daniel; ATLAS Collaboration

    2010-04-01

    The Large Hadron Collider (LHC) at CERN is the world's largest particle accelerator. ATLAS is one of the two general purpose experiments. The inner tracking system of ATLAS, the Inner Detector, is built on two technologies: silicon detectors and drift tube based detectors. The required precision for the alignment of the most sensitive coordinates of the Silicon sensors is just a few microns. Therefore the alignment of the ATLAS Inner Detector is performed using complex algorithms requiring extensive CPU and memory usage. The proposed alignment algorithms were exercised on several applications. This proceedings present the outline of the alignment approach and results from Cosmic Ray runs and large scale computing simulation of physics samples mimicking the ATLAS operation during real data-taking. The full alignment chain was tested using these samples and alignment constants were produced and validated within 24 hours. Early alignment of the ATLAS Inner Detector is provided even before the LHC start up by analysing Cosmic Ray data.

  3. The Atlas High-Energy Density Physics Project

    NASA Astrophysics Data System (ADS)

    Davis, Harold A.; Keinigs, Rhon K.; Anderson, Wallace E.; Atchison, Walter L.; Bartsch, R. Richard; Benage, John F.; Ballard, Evan O.; Bowman, David W.; Cochrane, James C.; Ekdahl, Carl A.; Elizondo, Juan M.; Faehl, Rickey J.; Fulton, Robert D.; Gribble, Robert F.; Guzik, Joyce A.; Kyrala, George A.; Miller, R. Bruce; Nielsen, Kurt E.; Parker, Jerald V.; Parsons, W. Mark; Munson, Carter P.; Oro, David M.; Rodriguez, George E.; Rogers, Harold H.; Scudder, David W.; Shlachter, Jack S.; Stokes, John L.; Taylor, Antoinette J.; Trainor, R. James; Turchi, Peter J.; Wood, Blake P.

    2001-02-01

    Atlas is a pulsed-power facility under development at Los Alamos National Laboratory to drive high-energy density experiments. Atlas will be operational in the summer of 2000 and is optimized for the study of dynamic material properties, hydrodynamics, and dense plasmas under extreme conditions. Atlas is designed to implode heavy-liner loads in a z-pinch configuration. The peak current of 30 MA is delivered in 4 μs. A typical Atlas liner is a 47-gram-aluminum cylinder with ˜4-cm radius and 4-cm length. Three to five MJ of kinetic energy will be delivered to the load. Using composite layers and a variety of interior target designs, a wide variety of experiments in ˜cm3 volumes will be performed. Atlas applications, machine design, and the status of the project are reviewed.

  4. Atlas-guided prostate intensity modulated radiation therapy (IMRT) planning.

    PubMed

    Sheng, Yang; Li, Taoran; Zhang, You; Lee, W Robert; Yin, Fang-Fang; Ge, Yaorong; Wu, Q Jackie

    2015-09-21

    An atlas-based IMRT planning technique for prostate cancer was developed and evaluated. A multi-dose atlas was built based on the anatomy patterns of the patients, more specifically, the percent distance to the prostate and the concaveness angle formed by the seminal vesicles relative to the anterior-posterior axis. A 70-case dataset was classified using a k-medoids clustering analysis to recognize anatomy pattern variations in the dataset. The best classification, defined by the number of classes or medoids, was determined by the largest value of the average silhouette width. Reference plans from each class formed a multi-dose atlas. The atlas-guided planning (AGP) technique started with matching the new case anatomy pattern to one of the reference cases in the atlas; then a deformable registration between the atlas and new case anatomies transferred the dose from the atlas to the new case to guide inverse planning with full automation. 20 additional clinical cases were re-planned to evaluate the AGP technique. Dosimetric properties between AGP and clinical plans were evaluated. The classification analysis determined that the 5-case atlas would best represent anatomy patterns for the patient cohort. AGP took approximately 1 min on average (corresponding to 70 iterations of optimization) for all cases. When dosimetric parameters were compared, the differences between AGP and clinical plans were less than 3.5%, albeit some statistical significances observed: homogeneity index (p  >  0.05), conformity index (p  <  0.01), bladder gEUD (p  <  0.01), and rectum gEUD (p  =  0.02). Atlas-guided treatment planning is feasible and efficient. Atlas predicted dose can effectively guide the optimizer to achieve plan quality comparable to that of clinical plans.

  5. A Complete UV Atlas of Standard Stars

    NASA Technical Reports Server (NTRS)

    Wu, Chi-Chao

    2000-01-01

    The general objective of this project is to provide a comprehensive ultraviolet spectral atlas of stars based on the data in the IUE Final Archive. The data have been uniformly processed by the IUE NEWSIPS pipeline system. The NEWSIPS gives an improved signal to noise ratio for the data that will be especially beneficial to low signal portions of the spectra; and it also gives more accurate fluxes for stars by adopting the latest absolute calibration and measured instrument parameters. Our new atlas, therefore, provides more uniform and accurate data than the version previously published. In addition, considerable efforts were devoted to obtain reliable spectral types, V,B-V, and E(B-V). Our goal is to provide the information which can be used with reasonable confidence by scientists.

  6. X-ray atlas of rheumatic diseases

    SciTech Connect

    Dihlmann, W.

    1986-01-01

    This atlas comprises instructive X-rays of the various inflammatory rheumatic joint diseases in all stages at the extremities and the spinal column. In addition, the complex pattern of the wide range of arthroses, also known as degenerative rheumatic disease is included. Besides the instructive pointers to X-ray diagnosis, the book is also a guide to differential diagnosis. Hence, this book is actually an X-ray atlas of joint diseases in general. Selected Contents: Introduction: What Does ''Rheumatism'' Actually Mean./Radiographic Methodology in Rheumatic Diseases of the Locomotor System/The Mosaic of Arthritis/Adult Rheumatoid Arthritis/Seronegative Spondylarthritis/Classic Collagen Diseases/Enthesiopathies/Gout-Pseudogout

  7. A Candida albicans PeptideAtlas

    PubMed Central

    Vialas, Vital; Sun, Zhi; Penha, Carla Verónica Loureiro y; Carrascal, Montserrat; Abian, Joaquin; Monteoliva, Lucía; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Gil, Concha

    2013-01-01

    Candida albicans public proteomic data sets, though growing steadily in the last few years, still have a very limited presence in online repositories. We report here the creation of a C. albicans PeptideAtlas comprising near 22000 distinct peptides at a 0.24 % False Discovery Rate (FDR) that account for over 2500 canonical proteins at a 1.2% FDR. Based on data from 16 experiments, we attained coverage of 41% of the C.albicans open reading frame sequences (ORFs) in the database used for the searches. This PeptideAtlas provides several useful features, including comprehensive protein and peptide-centered search capabilities and visualization tools that establish a solid basis for the study of basic biological mechanisms key to virulence and pathogenesis such as dimorphism, adherence, and apoptosis. Further, it is a valuable resource for the selection of candidate proteotypic peptides for targeted proteomic experiments via selected reaction monitoring (SRM) or SWATH-MS. PMID:23811049

  8. Atlas of monochromatic images of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Weidmann, W. A.; Schmidt, E. O.; Vena Valdarenas, R. R.; Ahumada, J. A.; Volpe, M. G.; Mudrik, A.

    2016-08-01

    We present an atlas of more than one hundred original images of planetary nebulae (PNe). These images were taken in a narrow-band filter centred on the nebular emission of the [N ii] during several observing campaigns using two moderate-aperture telescopes, at the Complejo Astronómico El Leoncito (CASLEO), and the Estación Astrofísica de Bosque Alegre (EABA), both in Argentina. The data provided by this atlas represent one of the most extensive image surveys of PNe in [N ii]. We compare the new images with those available in the literature, and briefly describe all cases in which our [N ii] images reveal new and interesting structures. The reduced images as FITS files are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/592/A103

  9. Characterization of the ATLAS Micromegas quadruplet prototype

    NASA Astrophysics Data System (ADS)

    Sidiropoulou, O.; Bianco, M.; Danielsson, H.; Degrange, J.; Farina, E. M.; Gomez, F. P.; Iengo, P.; Kuger, F.; Lin, T. H.; Schott, M.; Sekhniaidze, G.; Valderanis, C.; Vergain, M.; Wotschack, J.

    2016-07-01

    A Micromegas [1] detector with four active layers, serving as prototype for the upgrade of the ATLAS muon spectrometer [2], was designed and constructed in 2014 at CERN and represents the first example of a Micromegas quadruplet ever built. The detector has been realized using the resistive-strip technology and decoupling the amplification mesh from the readout structure. The four readout layers host overall 4096 strips with a pitch of 415 μm; two layers have strips running parallel (η in the ATLAS reference system, for measuring the muon bending coordinate) and two layers have inclined strips by ±1.5° angle with respect to the η coordinate in order to provide measurement of the second coordinate. A detector characterization carried out with cosmic muons and under X-ray irradiation is presented with the obtained results.

  10. Constructing a WISE High Resolution Galaxy Atlas

    NASA Astrophysics Data System (ADS)

    Jarrett, T. H.; Masci, F.; Tsai, C. W.; Petty, S.; Cluver, M.; Assef, Roberto J.; Benford, D.; Blain, A.; Bridge, C.; Donoso, E.; Eisenhardt, P.; Fowler, J.; Koribalski, B.; Lake, S.; Neill, James D.; Seibert, M.; Sheth, K.; Stanford, S.; Wright, E.

    2012-08-01

    After eight months of continuous observations, the Wide-field Infrared Survey Explorer (WISE) mapped the entire sky at 3.4 μm, 4.6 μm, 12 μm, and 22 μm. We have begun a dedicated WISE High Resolution Galaxy Atlas project to fully characterize large, nearby galaxies and produce a legacy image atlas and source catalog. Here we summarize the deconvolution techniques used to significantly improve the spatial resolution of WISE imaging, specifically designed to study the internal anatomy of nearby galaxies. As a case study, we present results for the galaxy NGC 1566, comparing the WISE enhanced-resolution image processing to that of Spitzer, Galaxy Evolution Explorer, and ground-based imaging. This is the first paper in a two-part series; results for a larger sample of nearby galaxies are presented in the second paper.

  11. Constructing a WISE High Resolution Galaxy Atlas

    NASA Technical Reports Server (NTRS)

    Jarrett, T. H.; Masci, F.; Tsai, C. W.; Petty, S.; Cluver, M.; Assef, Roberto J.; Benford, D.; Blain, A.; Bridge, C.; Donoso, E.; Eisenhardt, P.; Fowler, J.; Koribalski, B.; Lake, S.; Neill, James D.; Seibert, M.; Stanford, S.; Wright, E.

    2012-01-01

    After eight months of continuous observations, the Wide-field Infrared Survey Explorer (WISE) mapped the entire sky at 3.4 micron, 4.6 micron, 12 micron, and 22 micron. We have begun a dedicated WISE High Resolution Galaxy Atlas project to fully characterize large, nearby galaxies and produce a legacy image atlas and source catalog. Here we summarize the deconvolution techniques used to significantly improve the spatial resolution of WISE imaging, specifically designed to study the internal anatomy of nearby galaxies. As a case study, we present results for the galaxy NGC 1566, comparing the WISE enhanced-resolution image processing to that of Spitzer, Galaxy Evolution Explorer, and ground-based imaging. This is the first paper in a two-part series; results for a larger sample of nearby galaxies are presented in the second paper.

  12. ATLAS Beam Steering Mechanism Lessons Learned

    NASA Technical Reports Server (NTRS)

    Blumenstock, Kenneth A.; Cramer, Alexander K.; Gostin, Alan B.; Hakun, Claef F.; Haney, Paul G.; Hinkle, Matthew R.; Lee, Kenneth Y.; Lugo, Carlos F.; Matuszeski, Adam J.; Morrell, Armando; Armani, Nerses V.; Bonafede, Joseph; Jackson, Molly I.; Steigner, Peter J.; Stromsdorfer, Juan J.

    2016-01-01

    This paper describes the design, testing, and lessons learned during the development of the Advanced Topographic Laser Altimeter System (ATLAS) Beam Steering Mechanism (BSM). The BSM is a 2 degree-of-freedom tip-tilt mechanism for the purpose of pointing a flat mirror to tightly control the co-alignment of the transmitted laser and the receiver telescope of the ATLAS instrument. The high resolution needs of the mission resulted in sub-arcsecond pointing and knowledge requirements, which have been met. Development of the methodology to verify performance required significant effort. The BSM will fly as part of the Ice, Cloud, and Elevation Satellite II Mission (ICESat II), which is scheduled to be launched in 2017. The ICESat II primary mission is to map the earth's surface topography for the determination of seasonal changes of ice sheet thickness and vegetation canopy thickness to establish long-term trends.

  13. ATLAS Beam Steering Mechanism (BSM) Lessons Learned

    NASA Technical Reports Server (NTRS)

    Blumenstock, Kenneth A.; Cramer, Alexander K.; Gosten, Alan B.; Hakun, Claef F.; Haney, Paul G.; Hinkle, Matthew R.; Lee, Kenneth Y.; Lugo, Carlos F.; Matuszeski, Adam J.; Morell, Armando; Armani, Nerses V.; Bonafede, Joseph; Jackson, Molly I.; Steigner, Peter J.; Stromsdorfer, Juan J.

    2016-01-01

    This paper describes the design, testing, and lessons learned during the development of the Advanced Topographic Laser Altimeter System (ATLAS) Beam Steering Mechanism (BSM). The BSM is a 2 degree-of-freedom tip-tilt mechanism for the purpose of pointing a flat mirror to tightly control the co-alignment of the transmitted laser and the receiver telescope of the ATLAS instrument. The high resolution needs of the mission resulted in sub-arcsecond pointing and knowledge requirements, which have been met. Development of the methodology to verify performance required significant effort. The BSM will fly as part of the Ice, Cloud, and Elevation Satellite II Mission (ICESat II), which is scheduled to be launched in 2017. The ICESat II primary mission is to map the Earth's surface topography for the determination of seasonal changes of ice sheet thickness and vegetation canopy thickness to establish long-term trends.

  14. Virtual planets atlas 1.0 freeware

    NASA Astrophysics Data System (ADS)

    Legrand, C.; Chevalley, P.

    2015-10-01

    Since 2002, we develop the "Virtual Moon Atlas -http://www.ap-i.net/avl/en/start" a freeware to help Moon observing and to improve interest for Moon in general public. VMA freeware has been downloaded near 900000 times all over the world and is or has been used by several professional organizations such as Kitt Peak Observatory, National Japan Observatory, Birkbeck College / University College London (K. Joy), BBC Sky at night, several French astronomy magazines and astronomy writers (P. Harrington, S. French...) . Recommended by ESA, registered as educational software by French ministry for education, it has also yet been presented at 2006 & 2007 LPSC and PCC2 in 2011 We have declined this freeware in a new tool with the same goals, but for the telluric planets and satellites, the "Virtual Planets Atlas (VPA / http://www.ap-i.net/avp/en/start") now in version 1.0.

  15. Interpretations of the ATLAS diboson anomaly

    NASA Astrophysics Data System (ADS)

    Cheung, Kingman; Keung, Wai-Yee; Tseng, Po-Yan; Yuan, Tzu-Chiang

    2015-12-01

    Recently, the ATLAS Collaboration recorded an interesting anomaly in diboson production with excesses at the diboson invariant mass around 2 TeV in boosted jets of all the WZ, W+W-, and ZZ channels. We offer a theoretical interpretation of the anomaly using a phenomenological right-handed model with extra W‧ and Z‧ bosons. Constraints from narrow total decay widths, dijet cross sections, and W / Z + H production are taken into account. We also comment on a few other possibilities.

  16. Statistical atlas based extrapolation of CT data

    NASA Astrophysics Data System (ADS)

    Chintalapani, Gouthami; Murphy, Ryan; Armiger, Robert S.; Lepisto, Jyri; Otake, Yoshito; Sugano, Nobuhiko; Taylor, Russell H.; Armand, Mehran

    2010-02-01

    We present a framework to estimate the missing anatomical details from a partial CT scan with the help of statistical shape models. The motivating application is periacetabular osteotomy (PAO), a technique for treating developmental hip dysplasia, an abnormal condition of the hip socket that, if untreated, may lead to osteoarthritis. The common goals of PAO are to reduce pain, joint subluxation and improve contact pressure distribution by increasing the coverage of the femoral head by the hip socket. While current diagnosis and planning is based on radiological measurements, because of significant structural variations in dysplastic hips, a computer-assisted geometrical and biomechanical planning based on CT data is desirable to help the surgeon achieve optimal joint realignments. Most of the patients undergoing PAO are young females, hence it is usually desirable to minimize the radiation dose by scanning only the joint portion of the hip anatomy. These partial scans, however, do not provide enough information for biomechanical analysis due to missing iliac region. A statistical shape model of full pelvis anatomy is constructed from a database of CT scans. The partial volume is first aligned with the statistical atlas using an iterative affine registration, followed by a deformable registration step and the missing information is inferred from the atlas. The atlas inferences are further enhanced by the use of X-ray images of the patient, which are very common in an osteotomy procedure. The proposed method is validated with a leave-one-out analysis method. Osteotomy cuts are simulated and the effect of atlas predicted models on the actual procedure is evaluated.

  17. Recent Higgs results from the ATLAS experiment

    SciTech Connect

    Brendlinger, Kurt; Collaboration: ATLAS Collaboration

    2014-06-24

    This paper presents recent results on the Higgs boson from the ATLAS experiment at the Large Hadron Collider. The Collaboration reports on measurements of the signal strength, couplings, and spin of the Higgs in several decay channels. We find all measurements to be consistent with Standard Model predictions. The Higgs branching fraction to invisible particles is constrained and no evidence of physics beyond the Standard Model is found.

  18. Progress with the single-sided module prototypes for the ATLAS tracker upgrade stave

    NASA Astrophysics Data System (ADS)

    Allport, P. P.; Affolder, A. A.; Anghinolfi, F.; Bates, R.; Betancourt, C.; Buttar, C.; Carter, J. R.; Casse, G.; Chen, H.; Chilingarov, A.; Civera, J. V.; Clark, A.; Colijn, A. P.; Dabrowski, W.; Dawson, N.; Dewilde, B.; Dhawan, S.; Dressnandt, N.; Dwužnik, M.; Eklund, L.; Fadeyev, V.; Farthouat, P.; Ferrère, D.; Fox, H.; French, R.; Gallop, B.; García, C.; Gerling, M.; Gibson, M.; Gilchriese, M.; Gonzalez Sevilla, S.; Goodrick, M.; Greenall, A.; Grillo, A. A.; Haber, C. H.; Hessey, N. P.; Holt, R.; Hommels, L. B. A.; Jakobs, K.; Jones, T. J.; Kaplon, J.; Kierstead, J.; Koffeman, E.; Köhler, M.; Lacasta, C.; La Marra, D.; Li, Z.; Lindgren, S.; Lynn, D.; Maddock, P.; Mahboubi, K.; Martinez-McKinney, F.; Matheson, J.; Maunu, R.; McCarthy, R.; Newcomer, M.; Nickerson, R.; O'Shea, V.; Paganis, S.; Parzefall, U.; Pernecker, S.; Phillips, P.; Poltorak, K.; Puldon, D.; Robinson, D.; Sadrozinski, H. F.-W.; Santoyo, D.; Sattari, S.; Schamberger, D.; Seiden, A.; Sutcliffe, P.; Swientek, K.; Tsionou, D.; Tyndel, M.; Unno, Y.; Viehhauser, G.; Villani, E. G.; von Wilpert, J.; Wastie, R.; Weber, M.; Weidberg, A.; Wiik, L.; Wilmut, I.; Wormald, M.; Wright, J.; Xu, D.

    2011-04-01

    The ATLAS experiment is preparing for the planned luminosity upgrade of the LHC (the super-luminous LHC or sLHC) with a programme of development for tracking able to withstand an order of greater magnitude radiation fluence and much greater hit occupancy rates than the current detector. This has led to the concept of an all-silicon tracker with an enhanced performance pixel-based inner region and short-strips for much of the higher radii. Both sub-systems employ many common technologies, including the proposed “stave” concept for integrated cooling and support. For the short-strip region, use of this integrated stave concept requires single-sided modules mounted on either side of a thin central lightweight support.Each sensor is divided into four rows of 23.82 mm length strips; within each row, there are 1280 strips of 74.5μm pitch. Well over a hundred prototype sensors are being delivered by Hamamatsu Photonics (HPK) to Japan, Europe and the US.We present results of the first 20 chip ABCN25 ASIC hybrids for these sensors, results of the first prototype 5120 strip module built with 40 ABCN25 read-out ASICs, and the status of the hybrids and modules being developed for the ATLAS tracker upgrade stave programme.

  19. The Resistive Plate Chambers of the ATLAS experiment:. performance studies on Calibration Stream

    NASA Astrophysics Data System (ADS)

    Mazzaferro, Luca

    2012-08-01

    ATLAS (A Toroidal LHC ApparatuS) is one of the four experiments installed on the hadron-hadron collider LHC at CERN. It is a general purpose experiment, with a physics program which spans from the search for the Higgs Boson to the search of physics Beyond the Standard Model (BSM). An integrated luminosity of about 5 fb-1 is expected to be reached by the end of 2011. The Resistive Plate Chambers, installed in the barrel region, are used to provide the first muon level trigger, and cover an area of 16000 m2, readout by about 350000 electronic channels. To ensure optimal trigger performance, the RPC operational parameters like cluster size, efficiency and spatial resolution are constantly monitored. In order to achieve the desired precision, the data used for the analysis are extracted directly from the second level of the trigger, hence assuring very high statistics. This dedicated event stream, called Calibration Stream, is sent automatically to the RPC Calibration Center in Naples. Here the analysis is performed using an automatic tool tightly integrated in the ATLAS GRID environment, the Local Calibration Data Splitter (LCDS), which configures and manages all the operations required by the analysis (e.g. software environment initialization, grid jobs configuration and submission, data saving and retrieval, etc). The monitored RPC operational parameters, the performance analysis and the LCDS will be presented.

  20. A framework for incorporating DTI Atlas Builder registration into tract-based spatial statistics and a simulated comparison to standard TBSS

    NASA Astrophysics Data System (ADS)

    Leming, Matthew; Steiner, Rachel; Styner, Martin

    2016-03-01

    Tract-based spatial statistics (TBSS)6 is a software pipeline widely employed in comparative analysis of the white matter integrity from diffusion tensor imaging (DTI) datasets. In this study, we seek to evaluate the relationship between different methods of atlas registration for use with TBSS and different measurements of DTI (fractional anisotropy, FA, axial diffusivity, AD, radial diffusivity, RD, and medial diffusivity, MD). To do so, we have developed a novel tool that builds on existing diffusion atlas building software, integrating it into an adapted version of TBSS called DAB-TBSS (DTI Atlas Builder-Tract-Based Spatial Statistics) by using the advanced registration offered in DTI Atlas Builder7. To compare the effectiveness of these two versions of TBSS, we also propose a framework for simulating population differences for diffusion tensor imaging data, providing a more substantive means of empirically comparing DTI group analysis programs such as TBSS. In this study, we used 33 diffusion tensor imaging datasets and simulated group-wise changes in this data by increasing, in three different simulations, the principal eigenvalue (directly altering AD), the second and third eigenvalues (RD), and all three eigenvalues (MD) in the genu, the right uncinate fasciculus, and the left IFO. Additionally, we assessed the benefits of comparing the tensors directly using a functional analysis of diffusion tensor tract statistics (FADTTS10). Our results indicate comparable levels of FA-based detection between DAB-TBSS and TBSS, with standard TBSS registration reporting a higher rate of false positives in other measurements of DTI. Within the simulated changes investigated here, this study suggests that the use of DTI Atlas Builder's registration enhances TBSS group-based studies.

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

    SciTech Connect

    Zhao, T; Ruan, D

    2015-06-15

    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

  2. PREPARATION OF NORTHERN MID-CONTINENT PETROLEUM ATLAS

    SciTech Connect

    Lee C. Gerhard; Timothy R. Carr

    2005-03-28

    Report covers the fifth year of the Digital Petroleum Atlas (DPA) Project. To the present day, the DPA remains a long-term effort to develop new methodologies for efficient and timely access to the latest petroleum data and technology for the domestic oil and gas industry, research organizations and local governmental units. The DPA is an evolving approach to generating and publishing petroleum reservoir, field, play and basin studies. Atlas products are integrated with the Kansas Geological Survey web site and are available for every field in Kansas (6,395 fields in Kansas), anywhere in the world using a standard point-and-click world-wide-web interface (http://www.kgs.ku.edu/PRS/petroIndex.html). In order to provide efficient transfer of the technology for client-defined solutions, all information and technology in the DPA can be accessed, manipulated and downloaded. The DPA increases and improves online access from data through to ''final publication''. Until recently the petroleum atlas circulated like all scholarly information, through personal exchanges, subscriptions, and libraries. Today, digital scientific information is becoming the norm. The result--a dramatic increase in the international and disciplinary scope of information exchange in the petroleum industry. Digital communication has made traditional collaborative activity more informal, intimate, instantaneous, and continuous. At the present the DPA provides worldwide access to constantly increasing data and interpreted information. For example, data from each of over 300,000 oil and gas wells in Kansas are being accessed online for projects in locations from Chanute, Kansas, to Houston, Texas, to Berlin, Germany. Programs developed through the DPA provide oil and gas operators and the public tools to make exploration and development decisions using production data, interpreted well logs, and real-time mapped petroleum information. The DPA provides online access to digital versions of published

  3. Organization and management of ATLAS nightly builds

    NASA Astrophysics Data System (ADS)

    Luehring, F.; Obreshkov, E.; Quarrie, D.; Rybkine, G.; Undrus, A.

    2010-04-01

    The automated multi-platform software nightly build system is a major component in the ATLAS collaborative software organization, validation and code approval schemes. Code developers from ATLAS participating Institutes spread all around the world use about 30 branches of nightly releases for testing new packages, verification of patches to existing software, and migration to new platforms and compilers. The nightly releases lead up to, and are the basis of, stable software releases used for data processing worldwide. The ATLAS nightly builds are managed by the fully automated NICOS framework on the computing farm with 44 powerful multiprocessor nodes. The ATN test tool is embedded within the nightly system and provides results shortly after full compilations complete. Other test frameworks are synchronized with NICOS jobs and run larger scale validation jobs using the nightly releases. NICOS web pages dynamically provide information about the progress and results of the builds. For faster feedback, e-mail notifications about nightly releases problems are automatically distributed to the developers responsible.

  4. Metadata aided run selection at ATLAS

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    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.

  5. Alignment of the ATLAS silicon tracker

    NASA Astrophysics Data System (ADS)

    Morley, Anthony

    2008-10-01

    ATLAS is one of the four experiments currently under preparation at Large Hadron Collider. Charged particle track reconstruction in the ATLAS Inner Detector is performed both with silicon and drift-tube-based detectors. The alignment of the ATLAS tracking system is one of the challenges that the experiment must overcome in order to achieve its physics goals. This requires the determination of almost 35 000 degrees of freedom. The precision required for the most sensitive coordinate of the silicon devices is of the order of few microns. This precision will be attained with a combination of two techniques: a hardware system with Frequency Scan Interferometers, and track-based alignment. The latter requires the application of complex alignment algorithms that can be both CPU and memory intensive due to the possible requirement of large matrix inversion or many iterations. The alignment algorithms have been already exercised on several challenges such as a Combined Test Beam, cosmic ray runs and large scale computing simulation of physics samples. This note reports on the methods, their computing requirements and preliminary results.

  6. Evolution of Atlasic basins in Tunisia

    SciTech Connect

    Burollet, P.F. )

    1990-05-01

    Below the Atlasic Tunisia and the Pelagian Sea, there is no information about the nature, the age, and the depth of the basement. The Triassic series includes large thicknesses of evaporites. Therefore, the Atlasic Tunisia including its offshore, is disconnected from the basement and is folded as plis de couverture. The main structural and tectonic features are north-south discontinuities in the basement, as the north-south axis, from Tunis to Gabes; east-west distension features, corresponding to large steps of the southern margin of the Tethys, underlined by thick Jurassic and Cretaceous deposits; extreme youth of tectonics, sketched during preliminary phases: Late Cretaceous, middle Eocene, Oligocene, and early Miocene (folding actually began with the middle Miocene during the first arrival of the Tellian nappes in the north; however, the most active tectonics occurred at the end of the Miocene and after the Pliocene. New tectonic motions are known during the Pleistocene and even during historic times.); many extrusions of Triassic mixed shale, evaporite, and dolomite; outcrops of mainly insoluble caprocks; and the rare wells, drilled through diapirs, that encountered massive salt below 200-300 m of gypsum. Recent discoveries and important oil shows have proven the existence of oil and gas in newly identified depocenters and reservoirs. In general, except for some areas around producing fields, Atlasic Tunisia is largely underdrilled.

  7. Tau Trigger at the ATLAS Experiment

    SciTech Connect

    Benslama, K.; Kalinowski, A.; Belanger-Champange, C.; Brenner, R.; Bosman, M.; Casado, P.; Osuna, C.; Perez, E.; Vorwerk, V.; Czyczula, Z.; Dam, M.; Xella, S.; Demers, S.; Farrington, S.; Igonkina, O.; Kanaya, N.; Tsuno, S.; Ptacek, E.; Reinsch, A.; Strom, David M.; Torrence, E.; /Oregon U. /Sydney U. /Lancaster U. /Birmingham U.

    2011-11-09

    Many theoretical models, like the Standard Model or SUSY at large tan({beta}), predict Higgs bosons or new particles which decay more abundantly to final states including tau leptons than to other leptons. At the energy scale of the LHC, the identification of tau leptons, in particular in the hadronic decay mode, will be a challenging task due to an overwhelming QCD background which gives rise to jets of particles that can be hard to distinguish from hadronic tau decays. Equipped with excellent tracking and calorimetry, the ATLAS experiment has developed tau identification tools capable of working at the trigger level. This contribution presents tau trigger algorithms which exploit the main features of hadronic tau decays and describes the current tau trigger commissioning activities. Many of the SM processes being investigated at ATLAS, as well as numerous BSM searches, contain tau leptons in their final states. Being able to trigger effectively on the tau leptons in these events will contribute to the success of the ATLAS experiment. The tau trigger algorithms and monitoring infrastructure are ready for the first data, and are being tested with the data collected with cosmic muons. The development of efficiency measurements methods using QCD and Z {yields} {tau}{tau} events is well advanced.

  8. Integrated Means Integrity

    ERIC Educational Resources Information Center

    Odegard, John D.

    1978-01-01

    Describes the operation of the Cessna Pilot Center (CPC) flight training systems. The program is based on a series of integrated activities involving stimulus, response, reinforcement and association components. Results show that the program can significantly reduce in-flight training time. (CP)

  9. Pseudospread of the atlas: false sign of Jefferson fracture in young children

    SciTech Connect

    Suss, R.A.; Zimmerman, R.D.; Leeds, N.E.

    1983-06-01

    Jefferson fractures are rare prior to teen-age. Three young children examined after trauma exhibited the characteristic spread appearance of the atlas, but fractures were excluded radiographically and clinically. A retrospective study demonstrated a similar appearance, termed pseudospread, in most children aged 3 months to 4 years, including over 90% during the second year. Pseudospread results from a discrepancy between the neural growth pattern of the atlas and the somatic pattern of the axis. An atlas spread index is defined and a normal range presented. When an atlas fracture is suggested by apparent lateral spread of the lateral atlas masses, computed tomography is useful to demonstrate an intact atlas ring.

  10. On the Efficiency of NHS Ester Cross-Linkers for Stabilizing Integral Membrane Protein Complexes

    NASA Astrophysics Data System (ADS)

    Chen, Fan; Gerber, Sabina; Korkhov, Volodymyr M.; Mireku, Samantha; Bucher, Monika; Locher, Kaspar P.; Zenobi, Renato

    2015-03-01

    We have previously presented a straightforward approach based on high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) to study membrane proteins. In addition, the stoichiometry of integral membrane protein complexes could be determined by MALDI-MS, following chemical cross-linking via glutaraldehyde. However, glutaraldehyde polymerizes in solution and reacts nonspecifically with various functional groups of proteins, limiting its usefulness for structural studies of protein complexes. Here, we investigated the capability of N-hydroxysuccinimide (NHS) esters, which react much more specifically, to cross-link membrane protein complexes such as PglK and BtuC2D2. We present clear evidence that NHS esters are capable of stabilizing membrane protein complexes in situ, in the presence of detergents such as DDM, C12E8, and LDAO. The stabilization efficiency strongly depends on the membrane protein structure (i.e, the number of primary amine groups and the distances between primary amines). A minimum number of primary amine groups is required, and the distances between primary amines govern whether a cross-linker with a specific spacer arm length is able to bridge two amine groups.

  11. Integrating Art.

    ERIC Educational Resources Information Center

    BCATA Journal for Art Teachers, 1991

    1991-01-01

    These articles focus on art as a component of interdisciplinary integration. (1) "Integrated Curriculum and the Visual Arts" (Anna Kindler) considers various aspects of integration and implications for art education. (2) "Integration: The New Literacy" (Tim Varro) illustrates how the use of technology can facilitate cross-curricular integration.…

  12. Waxholm Space atlas of the rat brain hippocampal region: three-dimensional delineations based on magnetic resonance and diffusion tensor imaging.

    PubMed

    Kjonigsen, Lisa J; Lillehaug, Sveinung; Bjaalie, Jan G; Witter, Menno P; Leergaard, Trygve B

    2015-03-01

    Atlases of the rat brain are widely used as reference for orientation, planning of experiments, and as tools for assigning location to experimental data. Improved quality and use of magnetic resonance imaging (MRI) and other tomographical imaging techniques in rats have allowed the development of new three-dimensional (3-D) volumetric brain atlas templates. The rat hippocampal region is a commonly used model for basic research on memory and learning, and for preclinical investigations of brain disease. The region features a complex anatomical organization with multiple subdivisions that can be identified on the basis of specific cytoarchitectonic or chemoarchitectonic criteria. We here investigate the extent to which it is possible to identify boundaries of divisions of the hippocampal region on the basis of high-resolution MRI contrast. We present the boundaries of 13 divisions, identified and delineated based on multiple types of image contrast observed in the recently published Waxholm Space MRI/DTI template for the Sprague Dawley rat brain (Papp et al., Neuroimage 97:374-386, 2014). The new detailed delineations of the hippocampal formation and parahippocampal region (Waxholm Space atlas of the Sprague Dawley rat brain, v2.0) are shared via the INCF Software Center (http://software.incf.org/), where also the MRI/DTI reference template is available. The present update of the Waxholm Space atlas of the rat brain is intended to facilitate interpretation, analysis, and integration of experimental data from this anatomically complex region.

  13. Three-dimensional interactive and stereotactic atlas of the cranial nerves and their nuclei correlated with surface neuroanatomy, vasculature and magnetic resonance imaging.

    PubMed

    Nowinski, Wieslaw L; Johnson, Aleksandra; Chua, Beng Choon; Nowinska, Natalia G

    2012-01-01

    Knowledge of the cranial nerves and their nuclei is critical in clinical practice, medical research and education. However to our best knowledge, a comprehensive source capturing full three-dimensional (3D) relationships of the cranial nerves along with surrounding neuroanatomy is not yet available. This work addresses the construction and validation of an atlas of the cranial nerves with their nuclei, correlated with surface neuroanatomy, vasculature, and magnetic resonance imaging. The atlas is interactive, stereotactic, 3D, detailed, fully parcellated, completely labeled, consistent in 3D, electronically dissectible, and scalable. A 3D geometrical model of the 12 pairs of cranial nerves with nuclei was created from an in vivo magnetic resonance scan exploiting in-house developed tools and methods, including tubular and iso-surface modeling, interactive editing, and mesh compression. This virtual model contains 439 objects with 121 different names, labeled based on Terminologia Anatomica. The model was integrated with a 3D atlas of structure, vasculature and tracts developed earlier, and correlated with sectional magnetic resonance anatomy. The whole model or its components can be interactively rotated, zoomed, panned, and add or removed with a simple few clicks. The studied material can be adaptively selected in an in-depth manner by using controls available in the user interface. This atlas is potentially useful for anatomy browsing, user self-testing, automatic student assessment, preparing materials, and localization in clinical neurology.

  14. Analysis facility infrastructure (Tier-3) for ATLAS experiment

    NASA Astrophysics Data System (ADS)

    González de La Hoz, S.; March, L.; Ros, E.; Sánchez, J.; Amorós, G.; Fassi, F.; Fernández, A.; Kaci, M.; Lamas, A.; Salt, J.

    2008-04-01

    In the ATLAS computing model the tiered hierarchy ranged from the Tier-0 (CERN) down to desktops or workstations (Tier-3). The focus on defining the roles of each tiered component has evolved with the initial emphasis on the Tier-0 and Tier-1 definition and roles. The various LHC (Large Hadron Collider) projects, including ATLAS, then evolved the tiered hierarchy to include Tier-2’s (Regional centers) as part of their projects. Tier-3 centres, on the other hand, have 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 computing resources. However, Tier-3 centres are going to exist and will have implications on how the computing model should support ATLAS physicists. Tier-3 users will want to access LHC data and simulations and will want to enable their resources to support their analysis and simulation work. This document will define how IFIC (Instituto de Física Corpuscular de Valencia), after discussing with the ATLAS Tier-3 task force, should interact with the ATLAS computing model, detail the conditions under which Tier-3 centres can expect some level of support and set reasonable expectations for the scope and support of ATLAS Tier-3 sites.

  15. ATLAS discovery of bright nuclear transient flux in NGC4708 : ATLAS16bdg

    NASA Astrophysics Data System (ADS)

    Tonry, J.; Denneau, L.; Stalder, B.; Heinze, A.; Sherstyuk, A.; Rest, A.; Smith, K. W.; Smartt, S. J.; Wright, D.; Young, D. R.; Huber, M.; Chambers, K. C.; Flewelling, H.; Willman, M.; Primak, N.; Schultz, A.; Gibson, B.; Magnier, E.; Waters, C.; Tonry, J.; Wainscoat, R. J.

    2016-06-01

    ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is operational on Haleakala and is robotically surveying the sky. Two filters are used, cyan and orange (denoted c and o, all mags in AB system), more information is on http://www.fallingstar.com.

  16. ATLAS discovery of a probable SN in 2MASX J17093078+2136344 (ATLAS16bcb)

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is operational on Haleakala and is robotically surveying the sky. Two filters are used, cyan and orange (denoted c and o, all mags in AB system), more information is on http://www.fallingstar.com.

  17. View-centralized multi-atlas classification for Alzheimer's disease diagnosis.

    PubMed

    Liu, Mingxia; Zhang, Daoqiang; Shen, Dinggang

    2015-05-01

    Multi-atlas based methods have been recently used for classification of Alzheimer's disease (AD) and its prodromal stage, that is, mild cognitive impairment (MCI). Compared with traditional single-atlas based methods, multiatlas based methods adopt multiple predefined atlases and thus are less biased by a certain atlas. However, most existing multiatlas based methods simply average or concatenate the features from multiple atlases, which may ignore the potentially important diagnosis information related to the anatomical differences among different atlases. In this paper, we propose a novel view (i.e., atlas) centralized multi-atlas classification method, which can better exploit useful information in multiple feature representations from different atlases. Specifically, all brain images are registered onto multiple atlases individually, to extract feature representations in each atlas space. Then, the proposed view-centralized multi-atlas feature selection method is used to select the most discriminative features from each atlas with extra guidance from other atlases. Next, we design a support vector machine (SVM) classifier using the selected features in each atlas space. Finally, we combine multiple SVM classifiers for multiple atlases through a classifier ensemble strategy for making a final decision. We have evaluated our method on 459 subjects [including 97 AD, 117 progressive MCI (p-MCI), 117 stable MCI (s-MCI), and 128 normal controls (NC)] from the Alzheimer's Disease Neuroimaging Initiative database, and achieved an accuracy of 92.51% for AD versus NC classification and an accuracy of 78.88% for p-MCI versus s-MCI classification. These results demonstrate that the proposed method can significantly outperform the previous multi-atlas based classification methods.

  18. Morphometric Atlas Selection for Automatic Brachial Plexus Segmentation

    SciTech Connect

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

    2015-07-01

    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.

  19. Construction and application of human neonatal DTI atlases

    PubMed Central

    Deshpande, Rajiv; Chang, Linda; Oishi, Kenichi

    2015-01-01

    Atlas-based MRI analysis is one of many analytical methods and is used to investigate typical as well as abnormal neurodevelopment. It has been widely applied to the adult and pediatric populations. Successful applications of atlas-based analysis (ABA) in those cohorts have motivated the creation of a neonatal atlas and parcellation map (PM). The purpose of this review is to discuss the various neonatal diffusion tensor imaging (DTI) atlases that are available for use in ABA, examine how such atlases are constructed, review their applications, and discuss future directions in DTI. Neonatal DTI atlases are created from a template, which can be study-specific or standardized, and merged with the corresponding PM. Study-specific templates can retain higher image registration accuracy, but are usually not applicable across different studies. However, standardized templates can be used to make comparisons among various studies, but may not accurately reflect the anatomies of the study population. Methods such as volume-based template estimation are being developed to overcome these limitations. The applications for ABA, including atlas-based image quantification and atlas-based connectivity analysis, vary from quantifying neurodevelopmental progress to analyzing population differences in groups of neonates. ABA can also be applied to detect pathology related to prematurity at birth or exposure to toxic substances. Future directions for this method include research designed to increase the accuracy of the image parcellation. Methods such as multi-atlas label fusion and multi-modal analysis applied to neonatal DTI currently comprise an active field of research. Moreover, ABA can be used in high-throughput analysis to efficiently process medical images and to assess longitudinal brain changes. The overarching goal of neonatal ABA is application to the clinical setting, to assist with diagnoses, monitor disease progression and, ultimately, outcome prediction. PMID:26578899

  20. Enhancing atlas based segmentation with multiclass linear classifiers

    SciTech Connect

    Sdika, Michaël

    2015-12-15

    Purpose: To present a method to enrich atlases for atlas based segmentation. Such enriched atlases can then be used as a single atlas or within a multiatlas framework. Methods: In this paper, machine learning techniques have been used to enhance the atlas based segmentation approach. The enhanced atlas defined in this work is a pair composed of a gray level image alongside an image of multiclass classifiers with one classifier per voxel. Each classifier embeds local information from the whole training dataset that allows for the correction of some systematic errors in the segmentation and accounts for the possible local registration errors. The authors also propose to use these images of classifiers within a multiatlas framework: results produced by a set of such local classifier atlases can be combined using a label fusion method. Results: Experiments have been made on the in vivo images of the IBSR dataset and a comparison has been made with several state-of-the-art methods such as FreeSurfer and the multiatlas nonlocal patch based method of Coupé or Rousseau. These experiments show that their method is competitive with state-of-the-art methods while having a low computational cost. Further enhancement has also been obtained with a multiatlas version of their method. It is also shown that, in this case, nonlocal fusion is unnecessary. The multiatlas fusion can therefore be done efficiently. Conclusions: The single atlas version has similar quality as state-of-the-arts multiatlas methods but with the computational cost of a naive single atlas segmentation. The multiatlas version offers a improvement in quality and can be done efficiently without a nonlocal strategy.

  1. Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas.

    PubMed

    McKenna, Neil J; Cooney, Austin J; DeMayo, Francesco J; Downes, Michael; Glass, Christopher K; Lanz, Rainer B; Lazar, Mitchell A; Mangelsdorf, David J; Moore, David D; Qin, Jun; Steffen, David L; Tsai, Ming-Jer; Tsai, Sophia Y; Yu, Ruth; Margolis, Ronald N; Evans, Ronald M; O'Malley, Bert W

    2009-06-01

    Nuclear receptors and coregulators are multifaceted players in normal metabolic and homeostatic processes in addition to a variety of disease states including cancer, inflammation, diabetes, obesity, and atherosclerosis. Over the past 7 yr, the Nuclear Receptor Signaling Atlas (NURSA) research consortium has worked toward establishing a discovery-driven platform designed to address key questions concerning the expression, organization, and function of these molecules in a variety of experimental model systems. By applying powerful technologies such as quantitative PCR, high-throughput mass spectrometry, and embryonic stem cell manipulation, we are pursuing these questions in a series of transcriptomics-, proteomics-, and metabolomics-based research projects and resources. The consortium's web site (www.nursa.org) integrates NURSA datasets and existing public datasets with the ultimate goal of furnishing the bench scientist with a comprehensive framework for hypothesis generation, modeling, and testing. We place a strong emphasis on community input into the development of this resource and to this end have published datasets from academic and industrial laboratories, established strategic alliances with Endocrine Society journals, and are developing tools to allow web site users to act as data curators. With the ongoing support of the nuclear receptor and coregulator signaling communities, we believe that NURSA can make a lasting contribution to research in this dynamic field. PMID:19423650

  2. A Mass Spectrometric-Derived Cell Surface Protein Atlas

    PubMed Central

    Bausch-Fluck, Damaris; Hofmann, Andreas; Bock, Thomas; Frei, Andreas P.; Cerciello, Ferdinando; Jacobs, Andrea; Moest, Hansjoerg; Omasits, Ulrich; Gundry, Rebekah L.; Yoon, Charles; Schiess, Ralph; Schmidt, Alexander; Mirkowska, Paulina; Härtlová, Anetta; Van Eyk, Jennifer E.; Bourquin, Jean-Pierre; Aebersold, Ruedi; Boheler, Kenneth R.; Zandstra, Peter; Wollscheid, Bernd

    2015-01-01

    Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments. PMID:25894527

  3. A mass spectrometric-derived cell surface protein atlas.

    PubMed

    Bausch-Fluck, Damaris; Hofmann, Andreas; Bock, Thomas; Frei, Andreas P; Cerciello, Ferdinando; Jacobs, Andrea; Moest, Hansjoerg; Omasits, Ulrich; Gundry, Rebekah L; Yoon, Charles; Schiess, Ralph; Schmidt, Alexander; Mirkowska, Paulina; Härtlová, Anetta; Van Eyk, Jennifer E; Bourquin, Jean-Pierre; Aebersold, Ruedi; Boheler, Kenneth R; Zandstra, Peter; Wollscheid, Bernd

    2015-01-01

    Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments. PMID:25894527

  4. Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas.

    PubMed

    McKenna, Neil J; Cooney, Austin J; DeMayo, Francesco J; Downes, Michael; Glass, Christopher K; Lanz, Rainer B; Lazar, Mitchell A; Mangelsdorf, David J; Moore, David D; Qin, Jun; Steffen, David L; Tsai, Ming-Jer; Tsai, Sophia Y; Yu, Ruth; Margolis, Ronald N; Evans, Ronald M; O'Malley, Bert W

    2009-06-01

    Nuclear receptors and coregulators are multifaceted players in normal metabolic and homeostatic processes in addition to a variety of disease states including cancer, inflammation, diabetes, obesity, and atherosclerosis. Over the past 7 yr, the Nuclear Receptor Signaling Atlas (NURSA) research consortium has worked toward establishing a discovery-driven platform designed to address key questions concerning the expression, organization, and function of these molecules in a variety of experimental model systems. By applying powerful technologies such as quantitative PCR, high-throughput mass spectrometry, and embryonic stem cell manipulation, we are pursuing these questions in a series of transcriptomics-, proteomics-, and metabolomics-based research projects and resources. The consortium's web site (www.nursa.org) integrates NURSA datasets and existing public datasets with the ultimate goal of furnishing the bench scientist with a comprehensive framework for hypothesis generation, modeling, and testing. We place a strong emphasis on community input into the development of this resource and to this end have published datasets from academic and industrial laboratories, established strategic alliances with Endocrine Society journals, and are developing tools to allow web site users to act as data curators. With the ongoing support of the nuclear receptor and coregulator signaling communities, we believe that NURSA can make a lasting contribution to research in this dynamic field.

  5. Geosites inventory of the northwestern Tabular Middle Atlas of Morocco

    NASA Astrophysics Data System (ADS)

    El Wartiti, Mohamed; Malaki, Amina; Zahraoui, Mohamed; El Ghannouchi, Abdelilah; di Gregorio, Felice

    2008-07-01

    Across the northwestern Tabular Middle Atlas of Morocco there are many examples of landscapes, rocks and fossils that provide key evidence of a particular moment or period in Earth history. Such Earth heritage sites are important for educating the general public in environmental matters. They also serve as tools for demonstrating sustainable development and for illustrating methods of site conservation as well as remembering that rocks, minerals, fossils, soils, landforms form an integral part of the natural world. The significance of certain sites for aesthetic or tourism reasons is obvious. There are numerous geosites, which could contribute to effective exploitation of geotourism, often in conjunction with ecotourism. The strategy employed to such sites involves close consultation with all communities in the vicinity of the respective geosite and is not only aimed at tourism and education, but also at sustainable improvement of the infrastructure of the people of this area. Geological heritage sites, properly managed, can generate employment and new economic activities, especially in regions in need of new or additional sources of income.

  6. MARS-KS code validation activity through the atlas domestic standard problem

    SciTech Connect

    Choi, K. Y.; Kim, Y. S.; Kang, K. H.; Park, H. S.; Cho, S.

    2012-07-01

    The 2 nd Domestic Standard Problem (DSP-02) exercise using the ATLAS integral effect test data was executed to transfer the integral effect test data to domestic nuclear industries and to contribute to improving the safety analysis methodology for PWRs. A small break loss of coolant accident of a 6-inch break at the cold leg was determined as a target scenario by considering its technical importance and by incorporating interests from participants. Ten calculation results using MARS-KS code were collected, major prediction results were described qualitatively and code prediction accuracy was assessed quantitatively using the FFTBM. In addition, special code assessment activities were carried out to find out the area where the model improvement is required in the MARS-KS code. The lessons from this DSP-02 and recommendations to code developers are described in this paper. (authors)

  7. Atlasing the frontal lobe connections and their variability due to age and education: a spherical deconvolution tractography study.

    PubMed

    Rojkova, K; Volle, E; Urbanski, M; Humbert, F; Dell'Acqua, F; Thiebaut de Schotten, M

    2016-04-01

    In neuroscience, there is a growing consensus that higher cognitive functions may be supported by distributed networks involving different cerebral regions, rather than by single brain areas. Communication within these networks is mediated by white matter tracts and is particularly prominent in the frontal lobes for the control and integration of information. However, the detailed mapping of frontal connections remains incomplete, albeit crucial to an increased understanding of these cognitive functions. Based on 47 high-resolution diffusion-weighted imaging datasets (age range 22-71 years), we built a statistical normative atlas of the frontal lobe connections in stereotaxic space, using state-of-the-art spherical deconvolution tractography. We dissected 55 tracts including U-shaped fibers. We further characterized these tracts by measuring their correlation with age and education level. We reported age-related differences in the microstructural organization of several, specific frontal fiber tracts, but found no correlation with education level. Future voxel-based analyses, such as voxel-based morphometry or tract-based spatial statistics studies, may benefit from our atlas by identifying the tracts and networks involved in frontal functions. Our atlas will also build the capacity of clinicians to further understand the mechanisms involved in brain recovery and plasticity, as well as assist clinicians in the diagnosis of disconnection or abnormality within specific tracts of individual patients with various brain diseases.

  8. SU-E-J-129: Atlas Development for Cardiac Automatic Contouring Using Multi-Atlas Segmentation

    SciTech Connect

    Zhou, R; Yang, J; Pan, T; Milgrom, S; Pinnix, C; Shi, A; Yang, J; Liu, Y; Nguyen, Q; Gomez, D; Dabaja, B; Balter, P; Court, L; Liao, Z

    2015-06-15

    Purpose: To develop a set of atlases for automatic contouring of cardiac structures to determine heart radiation dose and the associated toxicity. Methods: Six thoracic cancer patients with both contrast and non-contrast CT images were acquired for this study. Eight radiation oncologists manually and independently delineated cardiac contours on the non-contrast CT by referring to the fused contrast CT and following the RTOG 1106 atlas contouring guideline. Fifteen regions of interest (ROIs) were delineated, including heart, four chambers, four coronary arteries, pulmonary artery and vein, inferior and superior vena cava, and ascending and descending aorta. Individual expert contours were fused using the simultaneous truth and performance level estimation (STAPLE) algorithm for each ROI and each patient. The fused contours became atlases for an in-house multi-atlas segmentation. Using leave-one-out test, we generated auto-segmented contours for each ROI and each patient. The auto-segmented contours were compared with the fused contours using the Dice similarity coefficient (DSC) and the mean surface distance (MSD). Results: Inter-observer variability was not obvious for heart, chambers, and aorta but was large for other structures that were not clearly distinguishable on CT image. The average DSC between individual expert contours and the fused contours were less than 50% for coronary arteries and pulmonary vein, and the average MSD were greater than 4.0 mm. The largest MSD of expert contours deviating from the fused contours was 2.5 cm. The mean DSC and MSD of auto-segmented contours were within one standard deviation of expert contouring variability except the right coronary artery. The coronary arteries, vena cava, and pulmonary vein had DSC<70% and MSD>3.0 mm. Conclusion: A set of cardiac atlases was created for cardiac automatic contouring, the accuracy of which was comparable to the variability in expert contouring. However, substantial modification may need

  9. Out-of-atlas likelihood estimation using multi-atlas segmentation

    PubMed Central

    Asman, Andrew J.; Chambless, Lola B.; Thompson, Reid C.; Landman, Bennett A.

    2013-01-01

    Purpose: Multi-atlas segmentation has been shown to be highly robust and accurate across an extraordinary range of potential applications. However, it is limited to the segmentation of structures that are anatomically consistent across a large population of potential target subjects (i.e., multi-atlas segmentation is limited to “in-atlas” applications). Herein, the authors propose a technique to determine the likelihood that a multi-atlas segmentation estimate is representative of the problem at hand, and, therefore, identify anomalous regions that are not well represented within the atlases. Methods: The authors derive a technique to estimate the out-of-atlas (OOA) likelihood for every voxel in the target image. These estimated likelihoods can be used to determine and localize the probability of an abnormality being present on the target image. Results: Using a collection of manually labeled whole-brain datasets, the authors demonstrate the efficacy of the proposed framework on two distinct applications. First, the authors demonstrate the ability to accurately and robustly detect malignant gliomas in the human brain—an aggressive class of central nervous system neoplasms. Second, the authors demonstrate how this OOA likelihood estimation process can be used within a quality control context for diffusion tensor imaging datasets to detect large-scale imaging artifacts (e.g., aliasing and image shading). Conclusions: The proposed OOA likelihood estimation framework shows great promise for robust and rapid identification of brain abnormalities and imaging artifacts using only weak dependencies on anomaly morphometry and appearance. The authors envision that this approach would allow for application-specific algorithms to focus directly on regions of high OOA likelihood, which would (1) reduce the need for human intervention, and (2) reduce the propensity for false positives. Using the dual perspective, this technique would allow for algorithms to focus on

  10. Common Accounting System for Monitoring the ATLAS Distributed Computing Resources

    NASA Astrophysics Data System (ADS)

    Karavakis, E.; Andreeva, J.; Campana, S.; Gayazov, S.; Jezequel, S.; Saiz, P.; Sargsyan, L.; Schovancova, J.; Ueda, I.; Atlas Collaboration

    2014-06-01

    This paper covers in detail a variety of accounting tools used to monitor the utilisation of the available computational and storage resources within the ATLAS Distributed Computing during the first three years of Large Hadron Collider data taking. The Experiment Dashboard provides a set of common accounting tools that combine monitoring information originating from many different information sources; either generic or ATLAS specific. This set of tools provides quality and scalable solutions that are flexible enough to support the constantly evolving requirements of the ATLAS user community.

  11. Performance of the ATLAS detector using first collision data

    NASA Astrophysics Data System (ADS)

    Aad, G.; Abat, E.; Abbott, B.; Abdallah, J.; Abdelalim, A. A.; Abdesselam, A.; Abdinov, O.; Abi, B.; Abolins, M.; Abramowicz, H.; Abreu, H.; Acerbi, E.; Acharya, B. S.; Ackers, M.; Adams, D. L.; Addy, T. N.; Adelman, J.; Aderholz, M.; Adomeit, S.; Adorisio, C.; Adragna, P.; Adye, T.; Aefsky, S.; Aguilar-Saavedra, J. A.; Aharrouche, M.; Ahlen, S. P.; Ahles, F.; Ahmad, A.; Ahmed, H.; Ahsan, M.; Aielli, G.; Akdogan, T.; Åkesson, P. F.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Aktas, Å.; Alam, M. S.; Alam, M. A.; Albrand, S.; Aleksa, M.; Aleksandrov, I. N.; Aleppo, M.; Alessandria, F.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Aliev, M.; Alimonti, G.; Alison, J.; Aliyev, M.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alonso, J.; Alviggi, M. G.; Amako, K.; Amaral, P.; Ambrosini, G.; Ambrosio, G.; Amelung, C.; Ammosov, V. V.; Ammosov, V. V.; Amorim, A.; Amorós, G.; Amram, N.; Anastopoulos, C.; Andeen, T.; Anders, C. F.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Andrieux, M.-L.; Anduaga, X. S.; Angerami, A.; Anghinolfi, F.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonelli, S.; Antos, J.; Antunovic, B.; Anulli, F.; Aoun, S.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A. T. H.; Archambault, J. P.; Arfaoui, S.; Arguin, J.-F.; Argyropoulos, T.; Arik, E.; Arik, M.; Armbruster, A. J.; Arms, K. E.; Armstrong, S. R.; Arnaez, O.; Arnault, C.; Artamonov, A.; Arutinov, D.; Asai, M.; Asai, S.; Asfandiyarov, R.; Ask, S.; Åsman, B.; Asner, D.; Asquith, L.; Assamagan, K.; Astbury, A.; Astvatsatourov, A.; Atoian, G.; Aubert, B.; Auerbach, B.; Auge, E.; Augsten, K.; Aurousseau, M.; Austin, N.; Avolio, G.; Avramidou, R.; Axen, D.; Ay, C.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Baccaglioni, G.; Bacci, C.; Bach, A. M.; Bachacou, H.; Bachas, K.; Bachy, G.; Backes, M.; Badescu, E.; Bagnaia, P.; Bai, Y.; Bailey, D. C.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, M. D.; Baker, S.; Baltasar Dos Santos Pedrosa, F.; Banas, E.; Banerjee, P.; Banerjee, S.; Banfi, D.; Bangert, A.; Bansal, V.; Baranov, S. P.; Baranov, S.; Barashkou, A.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Bardin, D. Y.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Baroncelli, A.; Barone, M.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Barrillon, P.; Bartoldus, R.; Bartsch, D.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battaglia, A.; Battistin, M.; Battistoni, G.; Bauer, F.; Bawa, H. S.; Bazalova, M.; Beare, B.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Becerici, N.; Bechtle, P.; Beck, G. A.; Beck, H. P.; Beckingham, M.; Becks, K. H.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bee, C.; Begel, M.; Behar Harpaz, S.; Behera, P. K.; Beimforde, M.; Belanger, G. A. N.; Belanger-Champagne, C.; Belhorma, B.; Bell, P. J.; Bell, W. 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G.; Roda, C.; Roda Dos Santos, D.; Rodier, S.; Rodriguez, D.; Rodriguez Garcia, Y.; Roe, S.; Røhne, O.; Rojo, V.; Rolli, S.; Romaniouk, A.; Romanov, V. M.; Romeo, G.; Romero Maltrana, D.; Roos, L.; Ros, E.; Rosati, S.; Rosenbaum, F.; Rosenbaum, G. A.; Rosenberg, E. I.; Rosselet, L.; Rossetti, V.; Rossi, L. P.; Rossi, L.; Rotaru, M.; Rothberg, J.; Rottländer, I.; Rousseau, D.; Royon, C. R.; Rozanov, A.; Rozen, Y.; Ruan, X.; Ruckert, B.; Ruckstuhl, N.; Rud, V. I.; Rudolph, G.; Rühr, F.; Ruggieri, F.; Ruiz-Martinez, A.; Rulikowska-Zarebska, E.; Rumiantsev, V.; Rumyantsev, L.; Runge, K.; Runolfsson, O.; Rurikova, Z.; Rusakovich, N. A.; Rust, D. R.; Rutherfoord, J. P.; Ruwiedel, C.; Ruzicka, P.; Ryabov, Y. F.; Ryadovikov, V.; Ryan, P.; Rybkin, G.; Rzaeva, S.; Saavedra, A. F.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Sakamoto, H.; Sala, P.; Salamanna, G.; Salamon, A.; Saleem, M. S.; Salihagic, D.; Salnikov, A.; Salt, J.; Saltó Bauza, O.; Salvachua Ferrando, B. M.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sampsonidis, D.; Samset, B. H.; Sánchez Sánchez, C. A.; Sandaker, H.; Sander, H. G.; Sanders, M. P.; Sandhoff, M.; Sandhu, P.; Sandstroem, R.; Sandvoss, S.; Sankey, D. P. C.; Sanny, B.; Sansoni, A.; Santamarina Rios, C.; Santoni, C.; Santonico, R.; Saraiva, J. G.; Sarangi, T.; Sarkisyan-Grinbaum, E.; Sarri, F.; Sasaki, O.; Sasaki, T.; Sasao, N.; Satsounkevitch, I.; Sauvage, G.; Savard, P.; Savine, A. Y.; Savinov, V.; Savoy-Navarro, A.; Savva, P.; Sawyer, L.; Saxon, D. H.; Says, L. P.; Sbarra, C.; Sbrizzi, A.; Scannicchio, D. A.; Schaarschmidt, J.; Schacht, P.; Schäfer, U.; Schaetzel, S.; Schaffer, A. C.; Schaile, D.; Schaller, M.; Schamberger, R. D.; Schamov, A. G.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Scherzer, M. I.; Schiavi, C.; Schieck, J.; Schioppa, M.; Schlager, G.; Schlenker, S.; Schlereth, J. L.; Schmidt, E.; Schmidt, M. P.; Schmieden, K.; Schmitt, C.; Schmitz, M.; Scholte, R. C.; Schönig, A.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schreiner, A.; Schricker, A.; Schroeder, C.; Schroer, N.; Schroers, M.; Schroff, D.; Schuh, S.; Schuler, G.; Schultes, J.; Schultz-Coulon, H.-C.; Schumacher, J. W.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schweiger, D.; Schwemling, Ph.; Schwienhorst, R.; Schwierz, R.; Schwindling, J.; Scott, W. G.; Searcy, J.; Sedykh, E.; Segura, E.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Seliverstov, D. M.; Sellden, B.; Seman, M.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Seuster, R.; Severini, H.; Sevior, M. E.; Sfyrla, A.; Shabalina, E.; Shah, T. P.; Shamim, M.; Shan, L. Y.; Shank, J. T.; Shao, Q. T.; Shapiro, M.; Shatalov, P. B.; Shaver, L.; Shaw, C.; Shaw, K.; Sherman, D.; Sherwood, P.; Shibata, A.; Shield, P.; Shimojima, M.; Shin, T.; Shmeleva, A.; Shochet, M. J.; Shupe, M. A.; Sicho, P.; Sidoti, A.; Siebel, A.; Siebel, M.; Siegert, F.; Siegrist, J.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S. B.; Simak, V.; Simic, Lj.; Simion, S.; Simmons, B.; Simonyan, M.; Sinervo, P.; Sinev, N. B.; Sipica, V.; Siragusa, G.; Sisakyan, A. N.; Sivoklokov, S. Yu.; Sjoelin, J.; Sjursen, T. B.; Skovpen, K.; Skubic, P.; Skvorodnev, N.; Slater, M.; Slattery, P.; Slavicek, T.; Sliwa, K.; Sloan, T. J.; Sloper, J.; Sluka, T.; Smakhtin, V.; Small, A.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, B. C.; Smith, D.; Smith, K. M.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snow, S. W.; Snow, J.; Snuverink, J.; Snyder, S.; Soares, M.; Sobie, R.; Sodomka, J.; Soffer, A.; Solans, C. A.; Solar, M.; Solc, J.; Solfaroli Camillocci, E.; Solodkov, A. A.; Solovyanov, O. V.; Soluk, R.; Sondericker, J.; Sopko, V.; Sopko, B.; Sorbi, M.; Sosebee, M.; Soukharev, A.; Spagnolo, S.; Spanò, F.; Speckmayer, P.; Spencer, E.; Spighi, R.; Spigo, G.; Spila, F.; Spiriti, E.; Spiwoks, R.; Spogli, L.; Spousta, M.; Spreitzer, T.; Spurlock, B.; Denis, R. D. St.; Stahl, T.; Stahlman, J.; Stamen, R.; Stancu, S. N.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stapnes, S.; Starchenko, E. A.; Stark, J.; Staroba, P.; Starovoitov, P.; Stastny, J.; Staude, A.; Stavina, P.; Stavropoulos, G.; Steele, G.; Stefanidis, E.; Steinbach, P.; Steinberg, P.; Stekl, I.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stevenson, K.; Stewart, G. A.; Stewart, T. D.; Stiller, W.; Stockmanns, T.; Stockton, M. C.; Stodulski, M.; Stoerig, K.; Stoicea, G.; Stonjek, S.; Strachota, P.; Stradling, A. R.; Straessner, A.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strang, M.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Strong, J. A.; Stroynowski, R.; Strube, J.; Stugu, B.; Stumer, I.; Sturm, P.; Soh, D. A.; Su, D.; Subramania, S.; Sugaya, Y.; Sugimoto, T.; Suhr, C.; Suita, K.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, X. H.; Sundermann, J. E.; Suruliz, K.; Sushkov, S.; Susinno, G.; Sutton, M. R.; Suzuki, T.; Suzuki, Y.; Sviridov, Yu. M.; Sykora, I.; Sykora, T.; Szczygiel, R. R.; Szeless, B.; Szymocha, T.; Sánchez, J.; Ta, D.; Taboada Gameiro, S.; Tackmann, K.; Taffard, A.; Tafirout, R.; Taga, A.; Takahashi, Y.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Talby, M.; Talyshev, A.; Tamsett, M. C.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tanaka, Y.; Tani, K.; Tappern, G. P.; Tapprogge, S.; Tardif, D.; Tarem, S.; Tarrade, F.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tassi, E.; Tatarkhanov, M.; Tayalati, Y.; Taylor, C.; Taylor, F. E.; Taylor, G.; Taylor, G. N.; Taylor, R. P.; Taylor, W.; Teixeira Dias Castanheira, M.; Teixeira-Dias, P.; Ten Kate, H.; Teng, P. K.; Tennenbaum-Katan, Y. D.; Terada, S.; Terashi, K.; Terron, J.; Terwort, M.; Testa, M.; Teuscher, R. J.; Tevlin, C. M.; Thadome, J.; Therhaag, J.; Thioye, M.; Thoma, S.; Thomas, J. P.; Thompson, E. N.; Thompson, P. D.; Thompson, P. D.; Thompson, R. J.; Thompson, A. S.; Thomson, E.; Thun, R. P.; Tic, T.; Tikhomirov, V. O.; Tikhonov, Y. A.; Timmermans, C. J. W. P.; Tipton, P.; Tique Aires Viegas, F. J.; Tisserant, S.; Tobias, J.; Toczek, B.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokár, S.; Tokunaga, K.; Tokushuku, K.; Tollefson, K.; Tomasek, L.; Tomasek, M.; Tomoto, M.; Tompkins, D.; Tompkins, L.; Toms, K.; Tonazzo, A.; Tong, G.; Tonoyan, A.; Topfel, C.; Topilin, N. D.; Torchiani, I.; Torrence, E.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Trefzger, T.; Treis, J.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trilling, G.; Trincaz-Duvoid, S.; Trinh, T. N.; Tripiana, M. F.; Triplett, N.; Trischuk, W.; Trivedi, A.; Trocmé, B.; Troncon, C.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C.-L.; Tsiakiris, M.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsung, J.-W.; Tsuno, S.; Tsybychev, D.; Tuggle, J. M.; Turala, M.; Turecek, D.; Turk Cakir, I.; Turlay, E.; Tuts, P. M.; Twomey, M. S.; Tylmad, M.; Tyndel, M.; Typaldos, D.; Tyrvainen, H.; Tzamarioudaki, E.; Tzanakos, G.; Uchida, K.; Ueda, I.; Ueno, R.; Ugland, M.; Uhlenbrock, M.; Uhrmacher, M.; Ukegawa, F.; Unal, G.; Underwood, D. G.; Undrus, A.; Unel, G.; Unno, Y.; Urbaniec, D.; Urkovsky, E.; Urquijo, P.; Urrejola, P.; Usai, G.; Uslenghi, M.; Vacavant, L.; Vacek, V.; Vachon, B.; Vahsen, S.; Valderanis, C.; Valenta, J.; Valente, P.; Valentinetti, S.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; van Berg, R.; van der Graaf, H.; van der Kraaij, E.; van der Poel, E.; van der Ster, D.; van Eijk, B.; van Eldik, N.; van Gemmeren, P.; van Kesteren, Z.; van Vulpen, I.; Vandelli, W.; Vandoni, G.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Varela Rodriguez, F.; Vari, R.; Varnes, E. W.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasilyeva, L.; Vassilakopoulos, V. I.; Vazeille, F.; Vegni, G.; Veillet, J. J.; Vellidis, C.; Veloso, F.; Veness, R.; Veneziano, S.; Ventura, A.; Ventura, D.; Ventura, S.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vertogardov, L.; Vetterli, M. C.; Vichou, I.; Vickey, T.; Viehhauser, G. H. A.; Villa, M.; Villani, E. G.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinek, E.; Vinogradov, V. B.; Virchaux, M.; Viret, S.; Virzi, J.; Vitale, A.; Vitells, O.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vlasak, M.; Vlasov, N.; Vogel, A.; Vogt, H.; Vokac, P.; Vollmer, C. F.; Volpi, M.; Volpini, G.; von der Schmitt, H.; von Loeben, J.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorobiev, A. P.; Vorwerk, V.; Vos, M.; Voss, K. C.; Voss, R.; Voss, T. T.; Vossebeld, J. H.; Vovenko, A. S.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vu Anh, T.; Vuaridel, B.; Vudragovic, D.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wahlen, H.; Walbersloh, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Walsh, S.; Wang, C.; Wang, H.; Wang, J.; Wang, J. C.; Wang, S. M.; Warburton, A.; Ward, C. P.; Warsinsky, M.; Wastie, R.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, A. T.; Waugh, B. M.; Webel, M.; Weber, G.; Weber, J.; Weber, M. D.; Weber, M.; Weber, M. S.; Weber, P.; Weidberg, A. R.; Weingarten, J.; Weiser, C.; Wellenstein, H.; Wellisch, H. P.; Wells, P. S.; Wen, M.; Wenaus, T.; Wendler, S.; Weng, Z.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Werth, M.; Werthenbach, U.; Wessels, M.; Whalen, K.; Wheeler-Ellis, S. J.; Whitaker, S. P.; White, A.; White, M. J.; White, S.; Whitehead, S. R.; Whiteson, D.; Whittington, D.; Wicek, F.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiesmann, M.; Wiglesworth, C.; Wiik, L. A. M.; Wildauer, A.; Wildt, M. A.; Wilhelm, I.; Wilkens, H. G.; Williams, E.; Williams, H. H.; Willis, W.; Willocq, S.; Wilson, J. A.; Wilson, M. G.; Wilson, A.; Wingerter-Seez, I.; Winklmeier, F.; Wittgen, M.; Woehrling, E.; Wolter, M. W.; Wolters, H.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wraight, K.; Wright, C.; Wright, D.; Wrona, B.; Wu, S. L.; Wu, X.; Wuestenfeld, J.; Wulf, E.; Wunstorf, R.; Wynne, B. M.; Xaplanteris, L.; Xella, S.; Xie, S.; Xie, Y.; Xu, D.; Xu, G.; Xu, N.; Yamada, M.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamaoka, J.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, S.; Yang, U. K.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yao, Y.; Yasu, Y.; Ye, J.; Ye, S.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Young, C.; Youssef, S. P.; Yu, D.; Yu, J.; Yuan, J.; Yuan, L.; Yurkewicz, A.; Zaets, V. G.; Zaidan, R.; Zaitsev, A. M.; Zajacova, Z.; Zalite, Yo. K.; Zambrano, V.; Zanello, L.; Zarzhitsky, P.; Zaytsev, A.; Zdrazil, M.; Zeitnitz, C.; Zeller, M.; Zema, P. F.; Zemla, A.; Zendler, C.; Zenin, A. V.; Zenin, O.; Zenis, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; Zevi Della Porta, G.; Zhan, Z.; Zhang, H.; Zhang, J.; Zhang, Q.; Zhang, X.; Zhao, L.; Zhao, T.; Zhao, Z.; Zhemchugov, A.; Zheng, S.; Zhong, J.; Zhou, B.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, Y.; Zhuang, X.; Zhuravlov, V.; Zilka, B.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Ziolkowski, M.; Zitoun, R.; Živković, L.; Zmouchko, V. V.; Zobernig, G.; Zoccoli, A.; Zolnierowski, Y.; Zsenei, A.; Zur Nedden, M.; Zutshi, V.; ATLAS Collaboration

    2010-09-01

    More than half a million minimum-bias events of LHC collision data were collected by the ATLAS experiment in December 2009 at centre-of-mass energies of 0.9 TeV and 2.36 TeV. This paper reports on studies of the initial performance of the ATLAS detector from these data. Comparisons between data and Monte Carlo predictions are shown for distributions of several track-and calorimeter-based quantities. The good performance of the ATLAS detector in these first data gives confidence for successful running at higher energies.

  12. Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box (TTB)

    NASA Technical Reports Server (NTRS)

    Doyle, Monica; ONeil, Daniel A.; Christensen, Carissa B.

    2005-01-01

    The Advanced Technology Lifecycle Analysis System (ATLAS) is a decision support tool designed to aid program managers and strategic planners in determining how to invest technology research and development dollars. It is an Excel-based modeling package that allows a user to build complex space architectures and evaluate the impact of various technology choices. ATLAS contains system models, cost and operations models, a campaign timeline and a centralized technology database. Technology data for all system models is drawn from a common database, the ATLAS Technology Tool Box (TTB). The TTB provides a comprehensive, architecture-independent technology database that is keyed to current and future timeframes.

  13. The feasibility of atlas-based automatic segmentation of MRI for H&N radiotherapy planning.

    PubMed

    Wardman, Kieran; Prestwich, Robin J D; Gooding, Mark J; Speight, Richard J

    2016-01-01

    Atlas-based autosegmentation is an established tool for segmenting structures for CT-planned head and neck radiotherapy. MRI is being increasingly integrated into the planning process. The aim of this study is to assess the feasibility of MRI-based, atlas-based autosegmentation for organs at risk (OAR) and lymph node levels, and to compare the segmentation accuracy with CT-based autosegmentation. Fourteen patients with locally advanced head and neck cancer in a prospective imaging study underwent a T1-weighted MRI and a PET-CT (with dedicated contrast-enhanced CT) in an immobilization mask. Organs at risk (orbits, parotids, brainstem, and spinal cord) and the left level II lymph node region were manually delineated on the CT and MRI separately. A 'leave one out' approach was used to automatically segment structures onto the remaining images separately for CT and MRI. Contour comparison was performed using multiple positional metrics: Dice index, mean distance to conformity (MDC), sensitivity index (Se Idx), and inclusion index (Incl Idx). Automatic segmentation using MRI of orbits, parotids, brainstem, and lymph node level was acceptable with a DICE coefficient of 0.73-0.91, MDC 2.0-5.1mm, Se Idx 0.64-0.93, Incl Idx 0.76-0.93. Segmentation of the spinal cord was poor (Dice coefficient 0.37). The process of automatic segmentation was significantly better on MRI compared to CT for orbits, parotid glands, brainstem, and left lymph node level II by multiple positional metrics; spinal cord segmentation based on MRI was inferior compared with CT. Accurate atlas-based automatic segmentation of OAR and lymph node levels is feasible using T1-MRI; segmentation of the spinal cord was found to be poor. Comparison with CT-based automatic segmentation suggests that the process is equally as, or more accurate, using MRI. These results support further translation of MRI-based segmentation methodology into clinicalpractice. PMID:27455480

  14. The Las Vegas Sustainability Atlas: Modeling Place-based Interactions and Implications in the Las Vegas Valley Bioregion

    NASA Astrophysics Data System (ADS)

    Ego, H.; McCown, K.; Saghafi, N.; Gross, E.; Hunter, W.; Zawarus, P.; Gann, A.; Piechota, T. C.

    2014-12-01

    Las Vegas, Nevada, with 2 million residents and 40 million annual visitors, is one of the driest metropolitan environments of its size in the world. The metro imports nearly all of its resources, including energy, water and food. Rapid population increases, drought, and temperature increases due to climate change create challenges for planning resilient systems in the Las Vegas Valley. Because of its growth rate, aridity, Las Vegas, Nevada is a significant and relevant region for the study of the water, energy, food and climate nexus. Cities in the United States and the world are seeing increasing trends in urbanization and water scarcity. How does the water-energy-climate-food nexus affect each metropolitan area? How can this complex information be used for resiliency planning? How can it be related to the public, so they can understand the issues in a way that makes them meaningful participants in the planning process? The topic of our presentation is a 'resiliency atlas.' The atlas is a place-based model tested in Las Vegas to explore bioregional distinctiveness of the water-energy-climate-food nexus, including regional transportation systems. The atlas integrates the systems within a utilitarian organization of information. Systems in this place-based model demonstrate how infrastructure services are efficiently provided for the Las Vegas Valley population. This resiliency atlas can clarify how the nexus applies to place; and how it can be used to spur geographically germane adaption strategies. In the Las Vegas Valley, climate change (drought and high sustained temperatures) and population affect water, energy, and food systems. This clarity of a place based model can help educate the public about the resilience of their place, and facilitate and organize the planning process in the face of uncertainty.

  15. The ATLAS Experiment at the CERN Large Hadron Collider

    NASA Astrophysics Data System (ADS)

    ATLAS Collaboration; Aad, G.; Abat, E.; Abdallah, J.; Abdelalim, A. A.; Abdesselam, A.; Abdinov, O.; Abi, B. A.; Abolins, M.; Abramowicz, H.; Acerbi, E.; Acharya, B. S.; Achenbach, R.; Ackers, M.; Adams, D. L.; Adamyan, F.; Addy, T. N.; Aderholz, M.; Adorisio, C.; Adragna, P.; Aharrouche, M.; Ahlen, S. P.; Ahles, F.; Ahmad, A.; Ahmed, H.; Aielli, G.; Åkesson, P. F.; Åkesson, T. P. A.; Akimov, A. V.; Alam, S. M.; Albert, J.; Albrand, S.; Aleksa, M.; Aleksandrov, I. N.; Aleppo, M.; Alessandria, F.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alimonti, G.; Aliyev, M.; Allport, P. P.; Allwood-Spiers, S. E.; Aloisio, A.; Alonso, J.; Alves, R.; Alviggi, M. G.; Amako, K.; Amaral, P.; Amaral, S. P.; Ambrosini, G.; Ambrosio, G.; Amelung, C.; Ammosov, V. V.; Amorim, A.; Amram, N.; Anastopoulos, C.; Anderson, B.; Anderson, K. J.; Anderssen, E. C.; Andreazza, A.; Andrei, V.; Andricek, L.; Andrieux, M.-L.; Anduaga, X. S.; Anghinolfi, F.; Antonaki, A.; Antonelli, M.; Antonelli, S.; Apsimon, R.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A. T. H.; Archambault, J. P.; Arguin, J.-F.; Arik, E.; Arik, M.; Arms, K. E.; Armstrong, S. R.; Arnaud, M.; Arnault, C.; Artamonov, A.; Asai, S.; Ask, S.; Åsman, B.; Asner, D.; Asquith, L.; Assamagan, K.; Astbury, A.; Athar, B.; Atkinson, T.; Aubert, B.; Auerbach, B.; Auge, E.; Augsten, K.; Aulchenko, V. M.; Austin, N.; Avolio, G.; Avramidou, R.; Axen, A.; Ay, C.; Azuelos, G.; Baccaglioni, G.; Bacci, C.; Bachacou, H.; Bachas, K.; Bachy, G.; Badescu, E.; Bagnaia, P.; Bailey, D. C.; Baines, J. T.; Baker, O. K.; Ballester, F.; Baltasar Dos Santos Pedrosa, F.; Banas, E.; Banfi, D.; Bangert, A.; Bansal, V.; Baranov, S. P.; Baranov, S.; Barashkou, A.; Barberio, E. L.; Barberis, D.; Barbier, G.; Barclay, P.; Bardin, D. Y.; Bargassa, P.; Barillari, T.; Barisonzi, M.; Barnett, B. M.; Barnett, R. M.; Baron, S.; Baroncelli, A.; Barone, M.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Barrillon, P.; Barriuso Poy, A.; Barros, N.; Bartheld, V.; Bartko, H.; Bartoldus, R.; Basiladze, S.; Bastos, J.; Batchelor, L. E.; Bates, R. L.; Batley, J. R.; Batraneanu, S.; Battistin, M.; Battistoni, G.; Batusov, V.; Bauer, F.; Bauss, B.; Baynham, D. E.; Bazalova, M.; Bazan, A.; Beauchemin, P. H.; Beaugiraud, B.; Beccherle, R. B.; Beck, G. A.; Beck, H. P.; Becks, K. H.; Bedajanek, I.; Beddall, A. J.; Beddall, A.; Bednár, P.; Bednyakov, V. A.; Bee, C.; Behar Harpaz, S.; Belanger, G. A. N.; Belanger-Champagne, C.; Belhorma, B.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellachia, F.; Bellagamba, L.; Bellina, F.; Bellomo, G.; Bellomo, M.; Beltramello, O.; Belymam, A.; Ben Ami, S.; Ben Moshe, M.; Benary, O.; Benchekroun, D.; Benchouk, C.; Bendel, M.; Benedict, B. H.; Benekos, N.; Benes, J.; Benhammou, Y.; Benincasa, G. P.; Benjamin, D. P.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Beretta, M.; Berge, D.; Bergeaas, E.; Berger, N.; Berghaus, F.; Berglund, S.; Bergsma, F.; Beringer, J.; Bernabéu, J.; Bernardet, K.; Berriaud, C.; Berry, T.; Bertelsen, H.; Bertin, A.; Bertinelli, F.; Bertolucci, S.; Besson, N.; Beteille, A.; Bethke, S.; Bialas, W.; Bianchi, R. M.; Bianco, M.; Biebel, O.; Bieri, M.; Biglietti, M.; Bilokon, H.; Binder, M.; Binet, S.; Bingefors, N.; Bingul, A.; Bini, C.; Biscarat, C.; Bischof, R.; Bischofberger, M.; Bitadze, A.; Bizzell, J. P.; Black, K. M.; Blair, R. E.; Blaising, J. J.; Blanch, O.; Blanchot, G.; Blocker, C.; Blocki, J.; Blondel, A.; Blum, W.; Blumenschein, U.; Boaretto, C.; Bobbink, G. J.; Bocci, A.; Bocian, D.; Bock, R.; Boehm, M.; Boek, J.; Bogaerts, J. A.; Bogouch, A.; Bohm, C.; Bohm, J.; Boisvert, V.; Bold, T.; Boldea, V.; Bondarenko, V. G.; Bonino, R.; Bonis, J.; Bonivento, W.; Bonneau, P.; Boonekamp, M.; Boorman, G.; Boosten, M.; Booth, C. N.; Booth, P. S. L.; Booth, P.; Booth, J. R. 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N.; Sivoklokov, S.; Sjölin, J.; Skubic, P.; Skvorodnev, N.; Slattery, P.; Slavicek, T.; Sliwa, K.; Sloan, T. J.; Sloper, J.; Smakhtin, V.; Small, A.; Smirnov, S. Yu; Smirnov, Y.; Smirnova, L.; Smirnova, O.; Smith, N. A.; Smith, B. C.; Smith, D. S.; Smith, J.; Smith, K. M.; Smith, B.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snow, S. W.; Snow, J.; Snuverink, J.; Snyder, S.; Soares, M.; Soares, S.; Sobie, R.; Sodomka, J.; Söderberg, M.; Soffer, A.; Solans, C. A.; Solar, M.; Sole, D.; Solfaroli Camillocci, E.; Solodkov, A. A.; Solov'yanov, O. V.; Soloviev, I.; Soluk, R.; Sondericker, J.; Sopko, V.; Sopko, B.; Sorbi, M.; Soret Medel, J.; Sosebee, M.; Sosnovtsev, V. V.; Sospedra Suay, L.; Soukharev, A.; Soukup, J.; Spagnolo, S.; Spano, F.; Speckmayer, P.; Spegel, M.; Spencer, E.; Spighi, R.; Spigo, G.; Spila, F.; Spiriti, E.; Spiwoks, R.; Spogli, L.; Spousta, M.; Sprachmann, G.; Spurlock, B.; St. Denis, R. D.; Stahl, T.; Staley, R. J.; Stamen, R.; Stancu, S. N.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stapnes, S.; Starchenko, E. A.; Staroba, P.; Stastny, J.; Staude, A.; Stavina, P.; Stavrianakou, M.; Stavropoulos, G.; Stefanidis, E.; Steffens, J. L.; Stekl, I.; Stelzer, H. J.; Stenzel, H.; Stewart, G.; Stewart, T. D.; Stiller, W.; Stockmanns, T.; Stodulski, M.; Stonjek, S.; Stradling, A.; Straessner, A.; Strandberg, J.; Strandlie, A.; Strauss, M.; Strickland, V.; Striegel, D.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Strong, J. A.; Stroynowski, R.; Stugu, B.; Stumer, I.; Su, D.; Subramania, S.; Suchkov, S. I.; Sugaya, Y.; Sugimoto, T.; Suk, M.; Sulin, V. V.; Sultanov, S.; Sun, Z.; Sundal, B.; Sushkov, S.; Susinno, G.; Sutcliffe, P.; Sutton, M. R.; Sviridov, Yu M.; Sykora, I.; Szczygiel, R. R.; Szeless, B.; Szymocha, T.; Sánchez, J.; Ta, D.; Taboada Gameiro, S.; Tadel, M.; Tafirout, R.; Taga, A.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Talby, M.; Talyshev, A.; Tamsett, M. C.; Tanaka, J.; Tanaka, K.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tanaka, Y.; Tappern, G. P.; Tapprogge, S.; Tarem, S.; Tarrade, F.; Tarrant, J.; Tartarelli, G.; Tas, P.; Tasevsky, M.; Tayalati, Y.; Taylor, F. E.; Taylor, G.; Taylor, G. N.; Taylor, R. P.; Tcherniatine, V.; Tegenfeldt, F.; Teixeira-Dias, P.; Ten Kate, H.; Teng, P. K.; Ter-Antonyan, R.; Terada, S.; Terron, J.; Terwort, M.; Teuscher, R. J.; Tevlin, C. M.; Thadome, J.; Thion, J.; Thioye, M.; Thomas, A.; Thomas, J. P.; Thomas, T. L.; Thomas, E.; Thompson, R. J.; Thompson, A. S.; Thun, R. P.; Tic, T.; Tikhomirov, V. O.; Tikhonov, Y. A.; Timm, S.; Timmermans, C. J. W. P.; Tipton, P.; Tique Aires Viegas, F. J.; Tisserant, S.; Titov, M.; Tobias, J.; Tocut, V. M.; Toczek, B.; Todorova-Nova, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tomasek, L.; Tomasek, M.; Tomasz, F.; Tomoto, M.; Tompkins, D.; Tompkins, L.; Toms, K.; Tonazzo, A.; Tong, G.; Tonoyan, A.; Topfel, C.; Topilin, N. D.; Torrence, E.; Torres Pais, J. G.; Toth, J.; Touchard, F.; Tovey, D. R.; Tovey, S. N.; Towndrow, E. F.; Trefzger, T.; Treichel, M.; Treis, J.; Tremblet, L.; Tribanek, W.; Tricoli, A.; Trigger, I. M.; Trilling, G.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trka, Z.; Trocmé, B.; Troncon, C.; C-L Tseng, J.; Tsiafis, I.; Tsiareshka, P. V.; Tsipolitis, G.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Turala, M.; Turk Cakir, I.; Turlay, E.; Tuts, P. M.; Twomey, M. S.; Tyndel, M.; Typaldos, D.; Tyrvainen, H.; Tzamarioudaki, E.; Tzanakos, G.; Ueda, I.; Uhrmacher, M.; Ukegawa, F.; Ullán Comes, M.; Unal, G.; Underwood, D. G.; Undrus, A.; Unel, G.; Unno, Y.; Urkovsky, E.; Usai, G.; Usov, Y.; Vacavant, L.; Vacek, V.; Vachon, B.; Vahsen, S.; Valderanis, C.; Valenta, J.; Valente, P.; Valero, A.; Valkar, S.; Valls Ferrer, J. A.; Van der Bij, H.; van der Graaf, H.; van der Kraaij, E.; Van Eijk, B.; van Eldik, N.; van Gemmeren, P.; van Kesteren, Z.; van Vulpen, I.; Van Berg, R.; Vandelli, W.; Vandoni, G.; Vaniachine, A.; Vannucci, F.; Varanda, M.; Varela Rodriguez, F.; Vari, R.; Varnes, E. W.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vassilakopoulos, V. I.; Vassilieva, L.; Vataga, E.; Vaz, L.; Vazeille, F.; Vedrine, P.; Vegni, G.; Veillet, J. J.; Vellidis, C.; Veloso, F.; Veness, R.; Veneziano, S.; Ventura, A.; Ventura, S.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vertogardov, L.; Vetterli, M. C.; Vichou, I.; Vickey, T.; Viehhauser, G. H. A.; Vigeolas, E.; Villa, M.; Villani, E. G.; Villate, J.; Villella, I.; Vilucchi, E.; Vincent, P.; Vincke, H.; Vincter, M. G.; Vinogradov, V. B.; Virchaux, M.; Viret, S.; Virzi, J.; Vitale, A.; Vivarelli, I.; Vives, R.; Vives Vaques, F.; Vlachos, S.; Vogt, H.; Vokac, P.; Vollmer, C. F.; Volpi, M.; Volpini, G.; von Boehn-Buchholz, R.; von der Schmitt, H.; von Toerne, E.; Vorobel, V.; Vorobiev, A. P.; Vorozhtsov, A. S.; Vorozhtsov, S. B.; Vos, M.; Voss, K. C.; Voss, R.; Vossebeld, J. H.; Vovenko, A. S.; Vranjes, N.; Vrba, V.; Vreeswijk, M.; Anh, T. Vu; Vuaridel, B.; Vudragovic, M.; Vuillemin, V.; Vuillermet, R.; Wänanen, A.; Wahlen, H.; Walbersloh, J.; Walker, R.; Walkowiak, W.; Wall, R.; Wallny, R. S.; Walsh, S.; Wang, C.; Wang, J. C.; Wappler, F.; Warburton, A.; Ward, C. P.; Warner, G. P.; Warren, M.; Warsinsky, M.; Wastie, R.; Watkins, P. M.; Watson, A. T.; Watts, G.; Waugh, A. T.; Waugh, B. M.; Weaverdyck, C.; Webel, M.; Weber, G.; Weber, J.; Weber, M.; Weber, P.; Weidberg, A. R.; Weilhammer, P. M.; Weingarten, J.; Weiser, C.; Wellenstein, H.; Wellisch, H. P.; Wells, P. S.; Wemans, A.; Wen, M.; Wenaus, T.; Wendler, S.; Wengler, T.; Wenig, S.; Wermes, N.; Werneke, P.; Werner, P.; Werthenbach, U.; Wheeler-Ellis, S. J.; Whitaker, S. P.; White, A.; White, M. J.; White, S.; Whittington, D.; Wicek, F.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiesmann, M.; Wiesmann, M.; Wijnen, T.; Wildauer, A.; Wilhelm, I.; Wilkens, H. G.; Williams, H. H.; Willis, W.; Willocq, S.; Wilmut, I.; Wilson, J. A.; Wilson, A.; Wingerter-Seez, I.; Winton, L.; Witzeling, W.; Wlodek, T.; Woehrling, E.; Wolter, M. W.; Wolters, H.; Wosiek, B.; Wotschack, J.; Woudstra, M. J.; Wright, C.; Wu, S. L.; Wu, X.; Wuestenfeld, J.; Wunstorf, R.; Xella-Hansen, S.; Xiang, A.; Xie, S.; Xie, Y.; Xu, G.; Xu, N.; Yamamoto, A.; Yamamoto, S.; Yamaoka, H.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, J. C.; Yang, S.; Yang, U. K.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yao, Y.; Yarradoddi, K.; Yasu, Y.; Ye, J.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, H.; Yoshida, R.; Young, C.; Youssef, S. P.; Yu, D.; Yu, J.; Yu, M.; Yu, X.; Yuan, J.; Yurkewicz, A.; Zaets, V. G.; Zaidan, R.; Zaitsev, A. M.; Zajac, J.; Zajacova, Z.; Zalite, A. Yu; Zalite, Yo K.; Zanello, L.; Zarzhitsky, P.; Zaytsev, A.; Zdrazil, M.; Zeitnitz, C.; Zeller, M.; Zema, P. F.; Zendler, C.; Zenin, A. V.; Zenis, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; Zhang, H.; Zhang, J.; Zheng, W.; Zhang, X.; Zhao, L.; Zhao, T.; Zhao, X.; Zhao, Z.; Zhelezko, A.; Zhemchugov, A.; Zheng, S.; Zhichao, L.; Zhou, B.; Zhou, N.; Zhou, S.; Zhou, Y.; Zhu, C. G.; Zhu, H. Z.; Zhuang, X. A.; Zhuravlov, V.; Zilka, B.; Zimin, N. I.; Zimmermann, S.; Ziolkowski, M.; Zitoun, R.; Zivkovic, L.; Zmouchko, V. V.; Zobernig, G.; Zoccoli, A.; Zoeller, M. M.; Zolnierowski, Y.; Zsenei, A.; zur Nedden, M.; Zychacek, V.

    2008-08-01

    The ATLAS detector as installed in its experimental cavern at point 1 at CERN is described in this paper. A brief overview of the expected performance of the detector when the Large Hadron Collider begins operation is also presented.

  16. Remote control of ATLAS-MPX Network and Data Visualization

    NASA Astrophysics Data System (ADS)

    Turecek, D.; Holy, T.; Pospisil, S.; Vykydal, Z.

    2011-05-01

    The ATLAS-MPX Network is a network of 15 Medipix2-based detector devices, installed in various positions in the ATLAS detector at CERN, Geneva. The aim of the network is to perform a real-time measurement of the spectral characteristics and the composition of radiation inside the ATLAS detector during its operation. The remote control system of ATLAS-MPX controls and configures all the devices from one place, via a web interface, accessible from different operating systems. The Data Visualization application, also with a web interface, has been developed in order to present measured data to the scientific community. It allows to browse through recorded frames from all devices and to search for specific frames by date and time. Charts containing the number of different types of tracks in each frame as a function of time may be rendered from the database.

  17. Automating the Generation of the Cassini Tour Atlas Database

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

    The Tour Atlas is a large database of geometrical tables, plots, and graphics used by Cassini science planning engineers and scientists primarily for science observation planning. Over time, as the contents of the Tour Atlas grew, the amount of time it took to recreate the Tour Atlas similarly grew--to the point that it took one person a week of effort. When Cassini tour designers estimated that they were going to create approximately 30 candidate Extended Mission trajectories--which needed to be analyzed for science return in a short amount of time--it became a necessity to automate. We report on the automation methodology that reduced the amount of time it took one person to (re)generate a Tour Atlas from a week to, literally, one UNIX command.

  18. ATLAS@Home: Harnessing Volunteer Computing for HEP

    NASA Astrophysics Data System (ADS)

    Adam-Bourdarios, C.; Cameron, D.; Filipčič, A.; Lancon, E.; Wu, W.; ATLAS Collaboration

    2015-12-01

    A recent common theme among HEP computing is exploitation of opportunistic resources in order to provide the maximum statistics possible for Monte Carlo simulation. Volunteer computing has been used over the last few years in many other scientific fields and by CERN itself to run simulations of the LHC beams. The ATLAS@Home project was started to allow volunteers to run simulations of collisions in the ATLAS detector. So far many thousands of members of the public have signed up to contribute their spare CPU cycles for ATLAS, and there is potential for volunteer computing to provide a significant fraction of ATLAS computing resources. Here we describe the design of the project, the lessons learned so far and the future plans.

  19. Atlas of computed body tomography: normal and abnormal anatomy

    SciTech Connect

    Chiu, L.C.; Schapiro, R.L.

    1980-01-01

    This atlas contains comparative sections on normal and abnormal computed tomography of the neck, chest, abdomen, pelvis, upper and lower limbs, fascia, and peritoneum. Also included is a subject index to aid in the identification of abnormal scans. (DLS)

  20. 15. VIEW OF ATLAS CONTROL CONSOLE NEAR WEST WALL OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    15. VIEW OF ATLAS CONTROL CONSOLE NEAR WEST WALL OF SLC-3W CONTROL ROOM - Vandenberg Air Force Base, Space Launch Complex 3, Launch Operations Building, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

  1. DETAIL VIEW OF BATCH CAR, BUILT BY ATLAS CAR & ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    DETAIL VIEW OF BATCH CAR, BUILT BY ATLAS CAR & MANUFACTURING COMPANY. BATCH STORAGE SILOS IN BACKGROUND - Chambers Window Glass Company, Batch Plant, North of Drey (Nineteenth) Street, West of Constitution Boulevard, Arnold, Westmoreland County, PA

  2. Assimilation of the atlas and occiput: a case report

    PubMed Central

    Grilliot, James R; Oswald, Christopher A

    1988-01-01

    Assimilation of the atlas is an osseous abnormality which occurs at the base of the skull in the region of the foramen magnum. It is demonstrated by the union of the atlas with the occipital bone. This may be a partial or complete union. Assimilation of the atlas is the most common anomaly found at the cranio-cervical junction. Other terms describing this abnormality are atlanto-occipital fusion and/or occipitalization of the atlas. Of importance, is not that the diagnostician be aware of the varied terms given to this osseous anomaly - but that such anomaly may exist without any typical symptom presentation, and thus, serious consequences of upper cervical spinal manipulative therapy may arise without a complete and adequate clinical assessment. ImagesFigure 1Figure 2Figure 3

  3. Mechanical construction and installation of the ATLAS tile calorimeter

    NASA Astrophysics Data System (ADS)

    Abdallah, J.; Adragna, P.; Alexa, C.; Alves, R.; Amaral, P.; Ananiev, A.; Anderson, K.; Andresen, X.; Antonaki, A.; Batusov, V.; Bednar, P.; Behrens, A.; Bergeaas, E.; Biscarat, C.; Blanch, O.; Blanchot, G.; Blocki, J.; Bohm, C.; Boldea, V.; Bosi, F.; Bosman, M.; Bromberg, C.; Brunel, B.; Budagov, J.; Calderón, D.; Calvet, D.; Cardeira, C.; Carli, T.; Carvalho, J.; Cascella, M.; Castillo, M. V.; Costello, J.; Cavalli-Sforza, M.; Cavasinni, V.; Cerqueira, A. S.; Clement, C.; Cobal, M.; Cogswell, F.; Constantinescu, S.; Costanzo, D.; Da Silva, P.; David, M.; Davidek, T.; Dawson, J.; De, K.; Del Prete, T.; Di Girolamo, B.; Dita, S.; Dolejsi, J.; Dolezal, Z.; Dotti, A.; Downing, R.; Drake, G.; Efthymiopoulos, I.; Errede, D.; Errede, S.; Farbin, A.; Fassouliotis, D.; Feng, E.; Fenyuk, A.; Ferdi, C.; Ferreira, B. C.; Ferrer, A.; Ferrer, J.; Flaminio, V.; Flix, J.; Francavilla, P.; Fullana, E.; Garde, V.; Gayde, J. C.; Gellerstedt, K.; Giakoumopoulou, V.; Giangiobbe, V.; Gildemeister, O.; Gilewsky, V.; Giokaris, N.; Gollub, N.; Gomes, A.; Gonzalez, V.; Gouveia, J.; Grenier, P.; Gris, P.; Grudzinski, J.; Guarino, V.; Guicheney, C.; Gupta, A.; Hakobyan, H.; Haney, M.; Hellman, S.; Henriques, A.; Higon, E.; Hill, N.; Holmgren, S.; Hruska, I.; Hurwitz, M.; Huston, J.; Jen-La Plante, I.; Jon-And, K.; Junk, T.; Karyukhin, A.; Khubua, J.; Klereborn, J.; Kopikov, S.; Korolkov, I.; Krivkova, P.; Kulchitsky, Y.; Kurochkin, Y.; Kuzhir, P.; Lapin, V.; Lasseur, C.; LeCompte, T.; Lefevre, R.; Leitner, R.; Li, J.; Lyablin, M.; Lim, H.; Lokajicek, M.; Lomakin, Y.; Lourtie, P.; Lovas, L.; Lupi, A.; Maidantchik, C.; Maio, A.; Maliukov, S.; Manousakis, A.; Marques, C.; Marroquim, F.; Martin, F.; Mazzoni, E.; Mergelkuhl, D.; Merritt, F.; Miagkov, A.; Miller, R.; Minashvili, I.; Miralles, L.; Montarou, G.; Nemecek, S.; Nessi, M.; Nikitine, I.; Nodulman, L.; Norniella, O.; Nyman, T.; Onofre, A.; Oreglia, M.; Palan, B.; Pallin, D.; Pantea, D.; Pereira, A.; Pilcher, J.; Pina, J.; Pinhão, J.; Pod, E.; Podlyski, F.; Portell, X.; Poveda, J.; Pribyl, L.; Price, L. E.; Proudfoot, J.; Ramalho, M.; Ramstedt, M.; Raposeiro, L.; Reis, J.; Richards, R.; Roda, C.; Romanov, V.; Rose-Dulcina, L.; Rosnet, P.; Roy, P.; Ruiz, A.; Rumiantsau, V.; Russakovich, N.; da Costa, J. Sa; Salto, O.; Salvachua, B.; Sanchis, E.; Sanders, H.; Santoni, C.; Santos, J.; Saraiva, J. G.; Sarri, F.; Says, L.-P.; Schlager, G.; Schlereth, J.; Seixas, J. M.; Selldèn, B.; Shalanda, N.; Shchelchkov, A.; Shevtsov, P.; Shochet, M.; Silva, J.; Simaitis, V.; Simonyan, M.; Sissakian, A.; Sjoelin, J.; Skrzecz, F.; Solans, C.; Solodkov, A.; Solovianov, O.; Soro