Science.gov

Sample records for atlas ddm integration

  1. The ATLAS DDM Tracer monitoring framework

    NASA Astrophysics Data System (ADS)

    Zang, Dongsong; Garonne, Vincent; Barisits, Martin; Lassnig, Mario; Stewart, Graeme Andrew; Molfetas, Angelos; Beermann, Thomas

    2012-12-01

    The DDM Tracer monitoring framework is aimed to trace and monitor the ATLAS file operations on the Worldwide LHC Computing Grid. The volume of traces has increased significantly since the framework was put in production in 2009. Now there are about 5 million trace messages every day and peaks can be near 250Hz, with peak rates continuing to climb, which gives the current structure a big challenge. Analysis of large datasets based on on-demand queries to the relational database management system (RDBMS), i.e. Oracle, can be problematic, and have a significant effect on the database's performance. Consequently, We have investigated some new high availability technologies like messaging infrastructure, specifically ActiveMQ, and key-value stores. The advantages of key value store technology are that they are distributed and have high scalability; also their write performances are usually much better than RDBMS, all of which are very useful for the Tracer monitoring framework. Indexes and distributed counters have been also tested to improve query performance and provided almost real time results. In this paper, the design principles, architecture and main characteristics of Tracer monitoring framework will be described and examples of its usage will be presented.

  2. 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.

  3. 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.

  4. Atlas - a data warehouse for integrative bioinformatics.

    PubMed

    Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

    2005-02-21

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

  5. 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.

  6. Atlas – a data warehouse for integrative bioinformatics

    PubMed Central

    Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

    2005-01-01

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

  7. Sleep patterns, sleep disorders and mammographic density in spanish women: The DDM-Spain/Var-DDM study.

    PubMed

    Pedraza-Flechas, Ana María; Lope, Virginia; Moreo, Pilar; Ascunce, Nieves; Miranda-García, Josefa; Vidal, Carmen; Sánchez-Contador, Carmen; Santamariña, Carmen; Pedraz-Pingarrón, Carmen; Llobet, Rafael; Aragonés, Nuria; Salas-Trejo, Dolores; Pollán, Marina; Pérez-Gómez, Beatriz

    2017-05-01

    We explored the relationship between sleep patterns and sleep disorders and mammographic density (MD), a marker of breast cancer risk. Participants in the DDM-Spain/var-DDM study, which included 2878 middle-aged Spanish women, were interviewed via telephone and asked questions on sleep characteristics. Two radiologists assessed MD in their left craneo-caudal mammogram, assisted by a validated semiautomatic-computer tool (DM-scan). We used log-transformed percentage MD as the dependent variable and fitted mixed linear regression models, including known confounding variables. Our results showed that neither sleeping patterns nor sleep disorders were associated with MD. However, women with frequent changes in their bedtime due to anxiety or depression had higher MD (e(β):1.53;95%CI:1.04-2.26). Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Performance tests during the ATLAS IBL Stave Integration

    NASA Astrophysics Data System (ADS)

    Jentzsch, J.

    2015-04-01

    In preparation of the ATLAS Pixel Insertable B-Layer integration, detector components, so called staves, were mounted around the Beryllium ATLAS beam pipe and tested using production quality assurance measurements as well as dedicated data taking runs to validate a correct grounding and shielding schema. Each stave consists of 32 new generation readout chips which sum up to over 860k pixels per stave. The integration tests include verification that neither the silicon planar n+-in-n nor the silicon 3D sensors were damaged by mechanical stress, and that their readout chips, including their bump-bond and wire-bond connections, did not suffer from the integration process. Evolution of the detector performance during its integration will be discussed as well as its final performance before installation.

  9. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana.

    PubMed Central

    Kakutani, T; Munakata, K; Richards, E J; Hirochika, H

    1999-01-01

    In contrast to mammalian epigenetic phenomena, where resetting of gene expression generally occurs in each generation, epigenetic states of plant genes are often stably transmitted through generations. The Arabidopsis mutation ddm1 causes a 70% reduction in genomic 5-methylcytosine level. We have previously shown that the ddm1 mutation results in an accumulation of a variety of developmental abnormalities by slowly inducing heritable changes in other loci. Each of the examined ddm1-induced developmental abnormalities is stably transmitted even when segregated from the potentiating ddm1 mutation. Here, the inheritance of DNA hypomethylation induced by ddm1 was examined in outcross progeny by HPLC and Southern analyses. The results indicate that (i) DDM1 gene function is not necessary during the gametophyte stage, (ii) ddm1 mutation is completely recessive, and (iii) remethylation of sequences hypomethylated by the ddm1 mutation is extremely slow or nonexistent even in wild-type DDM1 backgrounds. The stable transmission of DNA methylation status may be related to the meiotic heritability of the ddm1-induced developmental abnormalities. PMID:9927473

  10. Integrator Based Readout in Tile Calorimeter of the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    González Parra, Garoé; ATLAS Collaboration

    TileCal is the Barrel hadronic calorimeter of the ATLAS experiment at LHC/CERN. To equalize the response of individual TileCal cells with a precision better than 1% and to monitor the response of each cell over time, a calibration and monitoring system based on a Cs137 radioactive source driven through the calorimeter volume by liquid flow has been implemented. This calibration system relies on a dedicated readout chain based on slow integrators that read currents from the TileCal photomultipliers integrating over milliseconds during the calibration runs. Moreover, during the LHC collisions the TileCal integrator based readout provides the signal coming from inelastic proton-proton collisions at low momentum transfer. This is used to monitor in ATLAS the instantaneous luminosity as well as the response of all calorimeter cells during data-taking.

  11. 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.

  12. ATLAS, an integrated structural analysis and design system. Volume 4: Random access file catalog

    NASA Technical Reports Server (NTRS)

    Gray, F. P., Jr. (Editor)

    1979-01-01

    A complete catalog is presented for the random access files used by the ATLAS integrated structural analysis and design system. ATLAS consists of several technical computation modules which output data matrices to corresponding random access file. A description of the matrices written on these files is contained herein.

  13. Sequential processing of GNSS-R delay-Doppler maps (DDM's) for ocean wind retrieval

    NASA Astrophysics Data System (ADS)

    Garrison, J. L.; Rodriguez-Alvarez, N.; Hoffman, R.; Annane, B.; Leidner, M.; Kaitie, S.

    2016-12-01

    The delay-Doppler map (DDM) is the fundamental data product from GNSS-Reflectometry (GNSS-R), generated by cross-correlating the scattered signal with a local signal model over a range of delays and Doppler frequencies. Delay and Doppler form a set of coordinates on the ocean surface and the shape of the DDM is related to the distribution of ocean slopes. Wind speed can thus be estimated by fitting a scattering model to the shape of the observed DDM or defining an observable (e.g. average power or leading edge slope) which characterizes the change in DDM shape. For spaceborne measurements, the DDM is composed of signals scattered from a glistening zone, which can extend for up to 100 km or more. Setting a reasonable resolution requirement (25 km or less) will limit the usable portion of the DDM at each observation to only a small region near the specular point. Cyclone-GNSS (CYGNSS) is a NASA mission to study developing tropical cyclones using GNSS-R. CYGNSS science requirements call for wind retrieval with an accuracy of 10 percent above 20 m/s within a 25 km resolution. This requirement can be met using an observable defined for DDM samples between +/- 0.25 chips in delay and +/- 1 kHz in Doppler, with some filtering of the observations using a minimum threshold for range corrected gain (RCG). An improved approach, to be reviewed in this presentation, sequentially processes multiple DDM's, to combine observations generated from different "looks" at the same points on the surface. Applying this sequential process to synthetic data indicates a significant improvement in wind retrieval accuracy over a 10 km grid covering a region around the specular point. The attached figure illustrates this improvement, using simulated CYGNSS DDM's generated using the wind fields from hurricanes Earl and Danielle (left). The middle plots show wind retrievals using only an observable defined within the 25 km resolution cell. The plots on the right side show the retrievals from

  14. 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.

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

    PubMed

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

    2016-01-11

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

  16. Integrated System for Performance Monitoring of the ATLAS TDAQ Network

    NASA Astrophysics Data System (ADS)

    Octavian Savu, Dan; Al-Shabibi, Ali; Martin, Brian; Sjoen, Rune; Batraneanu, Silvia Maria; Stancu, Stefan

    2011-12-01

    The ATLAS TDAQ Network consists of three separate networks spanning four levels of the experimental building. Over 200 edge switches and 5 multi-blade chassis routers are used to interconnect 2000 processors, adding up to more than 7000 high speed interfaces. In order to substantially speed-up ad-hoc and post mortem analysis, a scalable, yet flexible, integrated system for monitoring both network statistics and environmental conditions, processor parameters and data taking characteristics was required. For successful up-to-the-minute monitoring, information from many SNMP compliant devices, independent databases and custom APIs was gathered, stored and displayed in an optimal way. Easy navigation and compact aggregation of multiple data sources were the main requirements; characteristics not found in any of the tested products, either open-source or commercial. This paper describes how performance, scalability and display issues were addressed and what challenges the project faced during development and deployment. A full set of modules, including a fast polling SNMP engine, user interfaces using latest web technologies and caching mechanisms, has been designed and developed from scratch. Over the last year the system proved to be stable and reliable, replacing the previous performance monitoring system and extending its capabilities. Currently it is operated using a precision interval of 25 seconds (the industry standard is 300 seconds). Although it was developed in order to address the needs for integrated performance monitoring of the ATLAS TDAQ network, the package can be used for monitoring any network with rigid demands of precision and scalability, exceeding normal industry standards.

  17. 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.

  18. 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.

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

    PubMed Central

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

    2014-01-01

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

  20. 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.

  1. 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

  2. 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.

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

    PubMed Central

    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. PMID:23193282

  4. Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology.

    PubMed

    Zhu, Ruoqing; Shevchenko, Olga; Ma, Cathleen; Maury, Stéphane; Freitag, Michael; Strauss, Steven H

    2013-06-01

    The Arabidopsis thaliana DDM1 (Decreased DNA Methylation) gene is necessary for the maintenance of DNA methylation and heterochromatin assembly. In Arabidopsis, ddm1 mutants exhibit strong but delayed morphological phenotypes. We used RNA interference (RNAi) to suppress transcripts of two orthologous DDM1 paralogs in Populus trichocarpa and examined effects on whole plant phenotypes during perennial growth and seasonal dormancy. The RNAi-PtDDM1 transgenic poplars showed a wide range of DDM1 transcript suppression; the most strongly suppressed line had 37.5 % of the expression of the non-transgenic control. Genomic cytosine methylation (mC %) was 11.1 % in the non-transgenic control, compared with 9.1 % for the transgenic event with lowest mC %, a reduction of 18.1 %. An evaluation of greenhouse growth directly after acclimation of in vitro grown plants showed no developmental or growth rate abnormalities associated with the decrease in PtDDM1 expression. However, after a dormancy cycle and growth outdoors, a mottled leaf phenotype appeared in some of the transgenic insertion events that had strongly reduced PtDDM1 expression and DNA methylation. The phenotypic consequences of reduced DDM1 activity and DNA methylation appears to increase with cumulative plant propagation and growth.

  5. Direct Deposition of Metal (DDM) as a Repair Process for Metallic Military Parts

    DTIC Science & Technology

    2013-01-20

    welded are low carbon steel , nickel, titanium, and copper. Aluminum and cast iron alloys cannot be easily welded but altering the microstructure... Aluminum There are many possibilities for DDM fabrication with aluminum alloys and perhaps aluminum metal matrix composite materials FSW Tool...15 4340 Steel Deposit Mechanical Tests

  6. Next Generation PanDA Pilot for ATLAS and Other Experiments

    NASA Astrophysics Data System (ADS)

    Nilsson, P.; Barreiro Megino, F.; Caballero Bejar, J.; De, K.; Hover, J.; Love, P.; Maeno, T.; Medrano Llamas, R.; Walker, R.; Wenaus, T.; Atlas Collaboration

    2014-06-01

    The Production and Distributed Analysis system (PanDA) has been in use in the ATLAS Experiment since 2005. It uses a sophisticated pilot system to execute submitted jobs on the worker nodes. While originally designed for ATLAS, the PanDA Pilot has recently been refactored to facilitate use outside of ATLAS. Experiments are now handled as plug-ins such that a new PanDA Pilot user only has to implement a set of prototyped methods in the plug-in classes, and provide a script that configures and runs the experiment-specific payload. We will give an overview of the Next Generation PanDA Pilot system and will present major features and recent improvements including live user payload debugging, data access via the Federated XRootD system, stage-out to alternative storage elements, support for the new ATLAS DDM system (Rucio), and an improved integration with glExec, as well as a description of the experiment-specific plug-in classes. The performance of the pilot system in processing LHC data on the OSG, LCG and Nordugrid infrastructures used by ATLAS will also be presented. We will describe plans for future development on the time scale of the next few years.

  7. DDM at Work. Reply to comments on "Dependency distance: A new perspective on syntactic patterns in natural languages"

    NASA Astrophysics Data System (ADS)

    Xu, Chunshan; Liang, Junying; Liu, Haitao

    2017-07-01

    We provide responses to the commentaries in this volume to evaluate, clarify and extend some of the arguments in Dependency distance: A new perspective on syntactic patterns in natural languages. Evidences show that DDM (dependency distance minimization) is an important linguistic universal, biologically or cognitively motivated, in shaping the language system. As a general tendency, DDM works quite well in theoretical argumentations as well as practical applications. However, this does not mean that DDM is the only linguistic universal that works: it is highly possible that other factors, which might be biologically, physically, socially or culturally motivated, work as well to jointly mold languages.

  8. 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.

  9. TDRS-M: Atlas V 2nd Stage Erection/Off-site Verticle Integration (OVI)

    NASA Image and Video Library

    2017-07-13

    A United Launch Alliance Atlas V Centaur upper stage arrives at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. United Launch Alliance team members monitor the operation progress as the Centaur upper stage is lifted and mated to the Atlas V booster in the vertical position. The rocket is scheduled to help launch the Tracking and Data Relay Satellite, TDRS-M. It will be the latest spacecraft destined for the agency's constellation of communications satellites that allows nearly continuous contact with orbiting spacecraft ranging from the International Space Station and Hubble Space Telescope to the array of scientific observatories. Liftoff atop the ULA Atlas V rocket is scheduled to take place from Cape Canaveral's Space Launch Complex 41 in early August.

  10. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity.

    PubMed

    Vielle-Calzada, J P; Thomas, J; Spillane, C; Coluccio, A; Hoeppner, M A; Grossniklaus, U

    1999-11-15

    In higher plants, seed development requires maternal gene activity in the haploid (gametophytic) as well as diploid (sporophytic) tissues of the developing ovule. The Arabidopsis thaliana gene MEDEA (MEA) encodes a SET-domain protein of the Polycomb group that regulates cell proliferation by exerting a gametophytic maternal control during seed development. Seeds derived from female gametocytes (embryo sacs) carrying a mutant mea allele abort and exhibit cell proliferation defects in both the embryo and the endosperm. In this study we show that the mea mutation affects an imprinted gene expressed maternally in cells of the female gametophyte and after fertilization only from maternally inherited MEA alleles. Paternally inherited MEA alleles are transcriptionally silent in both the young embryo and endosperm. Mutations at the decrease in DNA methylation1 (ddm1) locus are able to rescue mea seeds by functionally reactivating paternally inherited MEA alleles during seed development. Rescued seeds are larger than the wild type and exhibit some of the abnormalities found in aborting mea seeds. Our results indicate that the maintenance of the genomic imprint at the mea locus requires zygotic DDM1 activity. Because DDM1 encodes a putative chromatin remodeling factor, chromatin structure is likely to be interrelated with genomic imprinting in Arabidopsis.

  11. 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.

  12. 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

  13. The ATLAS Distributed Data Management project: Past and Future

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  14. Use of an integrated Atlas of Mental Health Care for evidence informed policy in Catalonia (Spain).

    PubMed

    Fernandez, A; Salinas-Perez, J A; Gutierrez-Colosia, M R; Prat-Pubill, B; Serrano-Blanco, A; Molina, C; Jorda, E; Garcia-Alonso, C R; Salvador-Carulla, L

    2015-12-01

    This paper aims to present the Integrated Atlas of Mental Health of Catalonia (2010) focusing on: (a) the importance of using a taxonomy-based coding and standard system of data collection when assessing health services; and (b) its relevance as a tool for evidence-informed policy. This study maps all the care-related services for people with mental disorders available in Catalonia in 2010, using the 'Description and Evaluation of Services and Directories in Europe for long-term care' (DESDE-LTC). The unit of analysis is the Basic Stable Input of Care (BSIC), which is the minimal organisation unit composed by a set of inputs with temporal stability. We presented data on: (a) availability of BSICs and their capacity; (b) the adequacy of the provision of care, taking into account availability and accessibility; (c) the evolution of BSCIs from 2002 to 2010; and (d) the perceived relevance of Atlas of Mental Health as a tool for evidence-informed policy. We identified a total of 639 BSICs. A lack of Health services was detected in highly rural areas, although there was moderate availability of Social Services. Overall, more than 80% of the small mental health areas in Catalonia had an adequate core mental health service. Since 2002 the availability of mental health services has increased. Decision makers found the Atlas a useful and relevant tool for evidence informed policy. Policy makers can use Atlases to detect gaps and inequities in the provision of care for people with mental health needs.

  15. Mechanical properties and biocompatibility of two polyepoxy matrices: DGEBA-DDM and DGEBA-IPD.

    PubMed

    Berruet, R; Vinard, E; Calle, A; Tighzert, H L; Chabert, B; Magloire, H; Eloy, R

    1987-05-01

    The aim of this paper was to study the biocompatibility and mechanical properties of materials for orthopaedic and odontologic surgical use. The products used were obtained by polycondensation of a diepoxy resin (DGEBA) with two curing agents (DDM or IPD). The materials present a slight swelling in liquid medium and their thermomechanical properties are hardly affected after 12 month implantation. The absence of molecular desorption in isotonic liquid and human serum confirms their hydrolytic stability and thus their inertia. These materials do not give rise to an intolerance reaction by neighbouring tissues during implantation time (1 d to 12 month).

  16. 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.

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

    SciTech Connect

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

    2016-02-15

    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.

  18. 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.

  19. Integrated mental health atlas of the Western Sydney Local Health District: gaps and recommendations.

    PubMed

    Fernandez, Ana; Gillespie, James A; Smith-Merry, Jennifer; Feng, Xiaoqi; Astell-Burt, Thomas; Maas, Cailin; Salvador-Carulla, Luis

    2016-03-24

    Objective Australian mental health care remains hospital centric and fragmented; it is riddled with gaps and does little to promote recovery. Reform must be built on better knowledge of the shape of existing services. Mental health atlases are an essential part of this knowledge base, enabling comparison with other regions and jurisdictions, but must be based on a rigorous classification of services. The main aim of this study is to create an integrated mental health atlas of the Western Sydney LHD in order to help decision makers to better plan informed by local evidence.Methods The standard classification system, namely the Description and Evaluation of Services and Directories in Europe for Long-term Care model, was used to describe and classify adult mental health services in the Western Sydney Local Health District (LHD). This information provided the foundation for accessibility maps and the analysis of the provision of care for people with a lived experience of mental illness in Western Sydney LHD. All this data was used to create the Integrated Mental Health Atlas of Western Sydney LHD.Results The atlas identified four major gaps in mental health care in Western Sydney LHD: (1) a lack of acute and sub-acute community residential care; (2) an absence of services providing acute day care and non-acute day care; (3) low availability of specific employment services for people with a lived experience of mental ill-health; and (4) a lack of comprehensive data on the availability of supported housing.Conclusions The integrated mental health atlas of the Western Sydney LHD provides a tool for evidence-informed planning and critical analysis of the pattern of adult mental health care.What is known about the topic? Several reports have highlighted that the Australian mental health system is hospital based and fragmented. However, this knowledge has had little effect on actually changing the system.What does this paper add? This paper provides a critical analysis of

  20. Integration Of PanDA Workload Management System With Supercomputers for ATLAS and Data Intensive Science

    SciTech Connect

    De, K; Jha, S; Klimentov, A; Maeno, T; Nilsson, P; Oleynik, D; Panitkin, S; Wells, Jack C; Wenaus, T

    2016-01-01

    The Large Hadron Collider (LHC), operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. Experiments at the LHC explore the fundamental nature of matter and the basic forces that shape our universe, and were recently credited for the discovery of a Higgs boson. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 150 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data centers are physically scattered all over the world. While PanDA currently uses more than 250,000 cores with a peak performance of 0.3 petaFLOPS, LHC data taking runs require more resources than Grid computing can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, Europe and Russia (in particular with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF), MIRA supercomputer at Argonne Leadership Computing Facilities (ALCF), Supercomputer at the National Research Center Kurchatov Institute , IT4 in Ostrava and others). Current approach utilizes modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single threaded workloads in parallel on LCFs multi-core worker nodes. This implementation

  1. Integration Of PanDA Workload Management System With Supercomputers for ATLAS and Data Intensive Science

    NASA Astrophysics Data System (ADS)

    Klimentov, A.; De, K.; Jha, S.; Maeno, T.; Nilsson, P.; Oleynik, D.; Panitkin, S.; Wells, J.; Wenaus, T.

    2016-10-01

    The.LHC, operating at CERN, is leading Big Data driven scientific explorations. Experiments at the LHC explore the fundamental nature of matter and the basic forces that shape our universe. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 150 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data centers are physically scattered all over the world. While PanDA currently uses more than 250,000 cores with a peak performance of 0.3 petaFLOPS, LHC data taking runs require more resources than grid can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, in particular with Titan supercomputer at Oak Ridge Leadership Computing Facility. Current approach utilizes modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single threaded workloads in parallel on LCFs multi-core worker nodes. This implementation was tested with a variety of Monte-Carlo workloads on several supercomputing platforms for ALICE and ATLAS experiments and it is in full pro duction for the ATLAS since September 2015. We will present our current accomplishments with running PanDA at supercomputers and demonstrate our ability to use PanDA as a portal independent of the

  2. ATLAS from Data Research Associates: A Fully Integrated Automation System.

    ERIC Educational Resources Information Center

    Mellinger, Michael J.

    1987-01-01

    This detailed description of a fully integrated, turnkey library system includes a complete profile of the system (functions, operational characteristics, hardware, operating system, minimum memory and pricing); history of the technologies involved; and descriptions of customer services and availability. (CLB)

  3. ATLAS from Data Research Associates: A Fully Integrated Automation System.

    ERIC Educational Resources Information Center

    Mellinger, Michael J.

    1987-01-01

    This detailed description of a fully integrated, turnkey library system includes a complete profile of the system (functions, operational characteristics, hardware, operating system, minimum memory and pricing); history of the technologies involved; and descriptions of customer services and availability. (CLB)

  4. 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)

  5. AUTOMATED MULTI-ATLAS LABELING OF THE FORNIX AND ITS INTEGRITY IN ALZHEIMER'S DISEASE.

    PubMed

    Jin, Yan; Shi, Yonggang; Zhan, Liang; Thompson, Paul M

    2015-04-01

    Alzheimer's disease is the most common form of dementia. Diffusion imaging provides information on white matter integrity not available with standard MRI, revealing additional information on how Alzheimer's disease affects the brain. Here we implemented and tested a multi-atlas labeling algorithm to segment the fornix and a point-correspondence tract matching scheme to assess fiber integrity in the fornix in diffusion MRI from 210 participants scanned as part of the Alzheimer's Disease Neuroimaging Initiative. Various diffusion-derived measures were used to relate fornix degeneration to cognitive decline. On 3D parametric tract models, mean diffusivity (MD) was more sen-sitive to group differences than fractional anisotropy (FA). Compared to previous studies, we mapped diffusion information along the fornix, yielding 3-D maps of degenerative changes along the tract in people with different stages of Alzheimer's disease.

  6. Integration of the ATLAS FE-I4 Pixel Chip in the Mini Time Projection Chamber

    NASA Astrophysics Data System (ADS)

    Lopez-Thibodeaux, Mayra; Garcia-Sciveres, Maurice; Kadyk, John; Oliver-Mallory, Kelsey

    2013-04-01

    This project deals with development of readout for a Time Projection Chamber (TPC) prototype. This is a type of detector proposed for direct detection of dark matter (WIMPS) with direction information. The TPC is a gaseous charged particle tracking detector composed of a field cage and a gas avalanche detector. The latter is made of two Gas Electron Multipliers in series, illuminating a pixel readout integrated circuit, which measures the distribution in position and time of the output charge. We are testing the TPC prototype, filled with ArCO2 gas, using a Fe-55 x-ray source and cosmic rays. The present prototype uses an FE-I3 chip for readout. This chip was developed about 10 years ago and is presently in use within the ATLAS pixel detector at the LHC. The aim of this work is to upgrade the TPC prototype to use an FE-I4 chip. The FE-I4 has an active area of 336 mm^2 and 26880 pixels, over nine times the number of pixels in the FE-I3 chip, and an active area about six times as much. The FE-I4 chip represents the state of the art of pixel detector readout, and is presently being used to build an upgrade of the ATLAS pixel detector.

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

    PubMed

    de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir; Arner, Erik; Arner, Peter; Ashoor, Haitham; Åström, Gaby; Babina, Magda; Bertin, Nicolas; Burroughs, A Maxwell; Carlisle, Ailsa J; Daub, Carsten O; Detmar, Michael; Deviatiiarov, Ruslan; Fort, Alexandre; Gebhard, Claudia; Goldowitz, Daniel; Guhl, Sven; Ha, Thomas J; Harshbarger, Jayson; Hasegawa, Akira; Hashimoto, Kosuke; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J; Hon, Chung Chau; Huang, Edward; Ishizu, Yuri; Kai, Chieko; Kasukawa, Takeya; Klinken, Peter; Lassmann, Timo; Lecellier, Charles-Henri; Lee, Weonju; Lizio, Marina; Makeev, Vsevolod; Mathelier, Anthony; Medvedeva, Yulia A; Mejhert, Niklas; Mungall, Christopher J; Noma, Shohei; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Persson, Helena; Rizzu, Patrizia; Roudnicky, Filip; Sætrom, Pål; Sato, Hiroki; Severin, Jessica; Shin, Jay W; Swoboda, Rolf K; Tarui, Hiroshi; Toyoda, Hiroo; Vitting-Seerup, Kristoffer; Winteringham, Louise; Yamaguchi, Yoko; Yasuzawa, Kayoko; Yoneda, Misako; Yumoto, Noriko; Zabierowski, Susan; Zhang, Peter G; Wells, Christine A; Summers, Kim M; Kawaji, Hideya; Sandelin, Albin; Rehli, Michael; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; de Hoon, Michiel J L

    2017-09-01

    MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

  8. SLID-ICV Vertical Integration Technology for the ATLAS Pixel Upgrades

    NASA Astrophysics Data System (ADS)

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

    We present the results of the characterization of pixel modules composed of 75 μm thick n-in-p sensors and ATLAS FE-I3 chips, interconnected with the SLID (Solid Liquid Inter-Diffusion) technology. This technique, developed at Fraunhofer-EMFT, is explored as an alternative to the bump-bonding process. These modules have been designed to demonstrate the feasibility of a very compact detector to be employed in the future ATLAS pixel upgrades, making use of vertical integration technologies. This module concept also envisages Inter-Chip-Vias (ICV) to extract the signals from the backside of the chips, thereby achieving a higher fraction of active area with respect to the present pixel module design. In the case of the demonstrator module, ICVs are etched over the original wire bonding pads of the FE-I3 chip. In the modules with ICVs the FE-I3 chips will be thinned down to 50 um. The status of the ICV preparation is presented.

  9. High speed dynamic characterization of an E. coli population using advanced optical methods (DDM and DFM)

    NASA Astrophysics Data System (ADS)

    Zhang, Rongjing; Wilson, Laurence

    2012-02-01

    The motility of microbes/bacteria in a complex environment, especially the average motility of the whole group of microorganisms, is directly related to behavior such as virulence, biofilm formation, etc. It is challenging to use traditional tracking methods to quantify the average motility of a large population. It is even more challenging when the environment is constantly changing. Two optical methods were developed to solve the problem: differential dynamic microscopy (DDM) and dark field flickering microscopy (DFM). The key features of bacteria motility were quantified automatically: average swimming speed, motile fraction, diffusion coefficient, cell body rotation speed and flagellar bundle rotation speed. This method is able to measure ˜10^4 cells simultaneously. With the help of a high speed camera, the timescale of the dynamic measurement can be in a wide range from 10-4 s to 10^5 s. Using this tool, temperature effects on E. coli motility were studied. Potential biomedically-relevant applications will also be discussed.

  10. An Integration Framework Tool for ATCA Chassis in the ATLAS Detector Control System

    NASA Astrophysics Data System (ADS)

    Reed, Robert Graham

    2015-10-01

    The Large Hadron Collider at CERN is scheduled to undergo a major upgrade in 2022. The ATLAS collaboration will do major modifications to the detector to account for the increased luminosity. More specifically, a large proportion of the current front-end electronics, on the Tile Calorimeter sub-detector, will be upgraded and relocated to the backend. A Demonstrator program has been established as a proof of principle. A new system will be required to house, manage and connect this new hardware. The proposed solution will be an Advanced Telecommunication Computing Architecture (ATCA) which will not only house but also allow advanced management features and control at a hardware level by integrating the ATCA chassis into the Detector Control System.

  11. 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.

  12. Accurate unrestrained DDM refinement of crystal structures from highly distorted and low-resolution powder diffraction data.

    PubMed

    Solovyov, Leonid A

    2016-10-01

    The structure of benzene:ethane co-crystal at 90 K is refined with anisotropic displacement parameters without geometric restraints from high-resolution synchrotron X-ray powder diffraction (XRPD) data using the derivative difference method (DDM) with properly chosen weighting schemes. The average C-C bond precision achieved is 0.005 Å and the H-atom positions in ethane are refined independently. A new DDM weighting scheme is introduced that compensates for big distortions of experimental data. The results are compared with density functional theory (DFT) calculations reported by Maynard-Casely et al. [(2016). IUCrJ, 3, 192-199] where a rigid-body Rietveld refinement was also applied to the same dataset due to severe distortions of the powder pattern attributable to experimental peculiarities. For the crystal structure of 2-aminopyridinium fumarate-fumaric acid formerly refined applying 77 geometric restraints by Dong et al. [(2013). Acta Cryst. C69, 896-900], an unrestrained DDM refinement using the same XRPD pattern surprisingly gave two times narrower dispersion of interatomic distances.

  13. Electronics design and system integration of the ATLAS New Small Wheels

    NASA Astrophysics Data System (ADS)

    Gkountoumis, P.

    2017-01-01

    The upgrades of the Large Hadron Collider (LHC) at CERN and the experiments in 2019/20 and 2024/26 will allow to increase the instantaneous luminosity to L=2× 1034 cm‑2s‑1 and L=5‑7× 1034 cm‑2s‑1, respectively. For the High Luminosity (HL) HL-LHC phase, the expected mean number of interactions per bunch crossing will be 55 at L=2× 1034 cm‑2s‑1 and 140 at L=5× 1034 cm‑2s‑1. This increase drastically impacts the ATLAS trigger system and trigger rates. For the ATLAS Muon Spectrometer, a replacement of the innermost endcap stations, the so-called ``Small Wheels", which are operating in a magnetic field, is therefore planned for 2019/20 to be able to maintain a low pT threshold for single muons and excellent tracking capability in the HL-LHC regime. The New Small Wheels will feature two new detector technologies: resistive Micromegas and small strip Thin Gap Chambers comprising a system of 2.4 million readout channels. Both detector technologies will provide trigger and tracking primitives fully compliant with the post-2026 HL-LHC operation. To allow for some safety margin, the design studies assume a maximum instantaneous luminosity of L=7× 1034 cm‑2s‑1, 200 pile-up events, trigger rates of 1 MHz at Level-0 and 400 KHz at Level-1. A radiation dose of 1700 Gy (innermost radius) is expected. The on-detector electronics will be implemented on some 8000 boards; four different custom ASICs will be used. The large number of readout channels, high speed output data rate, harsh radiation and magnetic environment, small available space, poor access and low power consumption all impose great challenges for the system design. The overall design and first results from integration of the electronics in a vertical slice test will be presented.

  14. 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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    PubMed

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

    2017-01-03

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

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

    PubMed

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

    2016-01-04

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

  18. An Integrated Geophysical Analysis of the Western High Atlas/Rif Region of Morocco

    NASA Astrophysics Data System (ADS)

    Worthington, C.; Keller, G. R.; Beauchamp, W.

    2009-12-01

    The Atlas Mountains of northern Africa consist of the High Atlas, Middle Atlas, Anti Atlas, Saharan Atlas, and the Tell Atlas. The Tell Atlas along with the Rif and Betic Mountains comprise an arcuate mountain chain that encircles the Alboran Sea and encompasses the westernmost belt of the Alpine Orogeny. Both of these mountain belts underwent deformation that began during the late Mesozoic with the opening of the Atlantic and the western Neo-Tethys Oceans and continued throughout the Cenozoic with the collision between Africa and Europe. The two mountain belts, however, are fundamentally different in their tectonic and geologic structures. Beginning in the Triassic, the Atlas system underwent extensive northwest-southeast extension and rifting that continued through the middle Jurassic. The Atlas rift, which is comparable in shape and size to the similar aged North Sea rift, experienced oblique rifting and was approximately 113 km wide at it greatest extent. The Cenozoic collision between Africa and Europe reactivated the normal faults created during the rifting, making the Atlas Mountains an area of inversion tectonics. The External Rif zone developed during the Oligocene into the Miocene from a combination of the slow but continuous convergence between Africa and Europe. It is characterized by deformed fold and thrust belts that give the domain its distinct arc shape. A variety of data and an evaluation of previous studies were assembled to undertake an extensive look at a section of the External Pre-Rif located between the Internal Rif and the Middle Atlas. In addition to publically available regional gravity and magnetic data, we have analyzed a proprietary 5 km grid of gravity data and six seismic reflection lines. Preliminary modeling shows the crustal thickness ranging from approximately 25 km along the coastline to 40 km beneath the High Atlas. The High Atlas and Rif ranges both exhibit low gravity anomalies that have been explained by a variety of

  19. Evaluation of Atlas-Based Attenuation Correction for Integrated PET/MR in Human Brain: Application of a Head Atlas and Comparison to True CT-Based Attenuation Correction.

    PubMed

    Sekine, Tetsuro; Buck, Alfred; Delso, Gaspar; Ter Voert, Edwin E G W; Huellner, Martin; Veit-Haibach, Patrick; Warnock, Geoffrey

    2016-02-01

    Attenuation correction (AC) for integrated PET/MR imaging in the human brain is still an open problem. In this study, we evaluated a simplified atlas-based AC (Atlas-AC) by comparing (18)F-FDG PET data corrected using either Atlas-AC or true CT data (CT-AC). We enrolled 8 patients (median age, 63 y). All patients underwent clinically indicated whole-body (18)F-FDG PET/CT for staging, restaging, or follow-up of malignant disease. All patients volunteered for an additional PET/MR of the head (additional tracer was not injected). For each patient, 2 AC maps were generated: an Atlas-AC map registered to a patient-specific liver accelerated volume acquisition-Flex MR sequence and using a vendor-provided head atlas generated from multiple CT head images and a CT-based AC map. For comparative AC, the CT-AC map generated from PET/CT was superimposed on the Atlas-AC map. PET images were reconstructed from the list-mode raw data from the PET/MR imaging scanner using each AC map. All PET images were normalized to the SPM5 PET template, and (18)F-FDG accumulation was quantified in 67 volumes of interest (VOIs; automated anatomic labeling atlas). Relative difference (%diff) between images based on Atlas-AC and CT-AC was calculated, and averaged difference images were generated. (18)F-FDG uptake in all VOIs was compared using Bland-Altman analysis. The range of error in all 536 VOIs was -3.0%-7.3%. Whole-brain (18)F-FDG uptake based on Atlas-AC was slightly underestimated (%diff = 2.19% ± 1.40%). The underestimation was most pronounced in the regions below the anterior/posterior commissure line, such as the cerebellum, temporal lobe, and central structures (%diff = 3.69% ± 1.43%, 3.25% ± 1.42%, and 3.05% ± 1.18%), suggesting that Atlas-AC tends to underestimate the attenuation values of the skull base bone. When compared with the gold-standard CT-AC, errors introduced using Atlas-AC did not exceed 8% in any brain region investigated. Underestimation of (18)F-FDG uptake was

  20. 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.

  1. ATLAS, an integrated structural analysis and design system. Volume 6: Design module theory

    NASA Technical Reports Server (NTRS)

    Backman, B. F.

    1979-01-01

    The automated design theory underlying the operation of the ATLAS Design Module is decribed. The methods, applications and limitations associated with the fully stressed design, the thermal fully stressed design and a regional optimization algorithm are presented. A discussion of the convergence characteristics of the fully stressed design is also included. Derivations and concepts specific to the ATLAS design theory are shown, while conventional terminology and established methods are identified by references.

  2. 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.

  3. 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

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

    PubMed

    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.

  5. 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.

  6. Integrated thermal and density modelling of the lithosphere across the Iberia-African plate boundary: the Gulf of Cadiz - Moroccan Atlas Geotransect

    NASA Astrophysics Data System (ADS)

    Zeyen, H.; Ayarza, P.; Fernàndez, M.; Rimi, A.

    2003-04-01

    The thermal and density structure of the lithosphere along a profile from the Gulf of Cadiz through the High Atlas to the Sahara is presented. The model is based on a numerical code that solves simultaneously the geopotential, lithostatic and heat transport equations integrating gravimetric, geoid, topographic and surface heat flow data, taking into account available geological and seismic constraints. Temperatures and densities are coupled by the thermal expansion, and the topography is considered to be in local isostatic equilibrium. The model presents an unusually thin lithosphere underneath the Atlas (60 to no more than 90 km) coinciding with areas of Neogene to Quaternary volcanism and relatively low P-wave velocities in the mantle. In contrast, the lithosphere underneath the Gulf of Cadiz thickens to 140-160 km depth. The relative amplitudes of geoid and gravity anomalies show that the high topography of the Atlas mountains cannot be produced only by crustal thickening. The lithospheric configuration, characterized by mantle thickening beneath the Gulf of Cadiz and thinning beneath the Atlas suggests a strong sub-lithospheric activity. Hence, westward drift of the lithospheric mantle in the Alboran region could be responsible for the observed mantle thickening and trigger sub-lithospheric erosion in the Atlas region.

  7. Learning to Rank Atlases for Multiple-Atlas Segmentation

    PubMed Central

    Sanroma, Gerard; Wu, Guorong; Gao, Yaozong

    2014-01-01

    Recently, multiple-atlas segmentation (MAS) has achieved a great success in the medical imaging area. The key assumption is that multiple atlases have greater chances of correctly labeling a target image than a single atlas. However, the problem of atlas selection still remains unexplored. Traditionally, image similarity is used to select a set of atlases. Unfortunately, this heuristic criterion is not necessarily related to the final segmentation performance. To solve this seemingly simple but critical problem, we propose a learning-based atlas selection method to pick up the best atlases that would lead to a more accurate segmentation. Our main idea is to learn the relationship between the pairwise appearance of observed instances (i.e., a pair of atlas and target images) and their final labeling performance (e.g., using the Dice ratio). In this way, we select the best atlases based on their expected labeling accuracy. Our atlas selection method is general enough to be integrated with any existing MAS method. We show the advantages of our atlas selection method in an extensive experimental evaluation in the ADNI, SATA, IXI, and LONI LPBA40 datasets. As shown in the experiments, our method can boost the performance of three widely used MAS methods, outperforming other learning-based and image-similarity-based atlas selection methods. PMID:24893367

  8. Learning to rank atlases for multiple-atlas segmentation.

    PubMed

    Sanroma, Gerard; Wu, Guorong; Gao, Yaozong; Shen, Dinggang

    2014-10-01

    Recently, multiple-atlas segmentation (MAS) has achieved a great success in the medical imaging area. The key assumption is that multiple atlases have greater chances of correctly labeling a target image than a single atlas. However, the problem of atlas selection still remains unexplored. Traditionally, image similarity is used to select a set of atlases. Unfortunately, this heuristic criterion is not necessarily related to the final segmentation performance. To solve this seemingly simple but critical problem, we propose a learning-based atlas selection method to pick up the best atlases that would lead to a more accurate segmentation. Our main idea is to learn the relationship between the pairwise appearance of observed instances (i.e., a pair of atlas and target images) and their final labeling performance (e.g., using the Dice ratio). In this way, we select the best atlases based on their expected labeling accuracy. Our atlas selection method is general enough to be integrated with any existing MAS method. We show the advantages of our atlas selection method in an extensive experimental evaluation in the ADNI, SATA, IXI, and LONI LPBA40 datasets. As shown in the experiments, our method can boost the performance of three widely used MAS methods, outperforming other learning-based and image-similarity-based atlas selection methods.

  9. The effects of detergents DDM and beta-OG on the singlet excited state lifetime of the chlorophyll a in cytochrome b6f complex from spinach chloroplasts.

    PubMed

    Chen, XiaoBo; Zhao, XiaoHui; Zhang, JianPing; Li, LiangBi; Kuang, TingYun

    2007-08-01

    The singlet excited state lifetime of the chlorophyll a (Chl a) in cytochrome b(6)f (Cyt b(6)f) complex was reported to be shorter than that of free Chl a in methanol, but the value was different for Cyt b(6)f complexes from different sources ( approximately 200 and approximately 600 ps are the two measured results). The present study demonstrated that the singlet excited state lifetime is associated with the detergents n-dodecyl-beta-D-maltoside (DDM) and n-octyl-beta-D-glucopyranoside (beta-OG), but has nothing to do with the different sources of Cyt b(6)f complexes. Compared with the Cyt b(6)f dissolved in beta-OG, the Cyt b(6)f in DDM had a lower fluorescence yield, a lower photodegradation rate of Chl a, and a shorter lifetime of Chl a excited state. In short, the singlet excited state lifetime, approximately 200 ps, of the Chl a in Cyt b(6)f complex in DDM is closer to the true in vivo.

  10. Popularity Prediction Tool for ATLAS Distributed Data Management

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    This paper describes a popularity prediction tool for data-intensive data management systems, such as ATLAS distributed data management (DDM). It is fed by the DDM popularity system, which produces historical reports about ATLAS data usage, providing information about files, datasets, users and sites where data was accessed. The tool described in this contribution uses this historical information to make a prediction about the future popularity of data. It finds trends in the usage of data using a set of neural networks and a set of input parameters and predicts the number of accesses in the near term future. This information can then be used in a second step to improve the distribution of replicas at sites, taking into account the cost of creating new replicas (bandwidth and load on the storage system) compared to gain of having new ones (faster access of data for analysis). To evaluate the benefit of the redistribution a grid simulator is introduced that is able replay real workload on different data distributions. This article describes the popularity prediction method and the simulator that is used to evaluate the redistribution.

  11. Quantitative Evaluation of Atlas-based Attenuation Correction for Brain PET in an Integrated Time-of-Flight PET/MR Imaging System.

    PubMed

    Yang, Jaewon; Jian, Yiqiang; Jenkins, Nathaniel; Behr, Spencer C; Hope, Thomas A; Larson, Peder E Z; Vigneron, Daniel; Seo, Youngho

    2017-02-23

    Purpose To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain positron emission tomography (PET) in an integrated time-of-flight (TOF) PET/magnetic resonance (MR) imaging system. Materials and Methods Thirty recruited patients provided informed consent in this institutional review board-approved study. All patients underwent whole-body fluorodeoxyglucose PET/computed tomography (CT) followed by TOF PET/MR imaging. With use of TOF PET data, PET images were reconstructed with four different attenuation correction (AC) methods: PET with patient CT-based AC (CTAC), PET with ATAC (air and bone from an atlas), PET with ATACpatientBone (air and tissue from the atlas with patient bone), and PET with ATACboneless (air and tissue from the atlas without bone). For quantitative evaluation, PET mean activity concentration values were measured in 14 1-mL volumes of interest (VOIs) distributed throughout the brain and statistical significance was tested with a paired t test. Results The mean overall difference (±standard deviation) of PET with ATAC compared with PET with CTAC was -0.69 kBq/mL ± 0.60 (-4.0% ± 3.2) (P < .001). The results were patient dependent (range, -9.3% to 0.57%) and VOI dependent (range, -5.9 to -2.2). In addition, when bone was not included for AC, the overall difference of PET with ATACboneless (-9.4% ± 3.7) was significantly worse than that of PET with ATAC (-4.0% ± 3.2) (P < .001). Finally, when patient bone was used for AC instead of atlas bone, the overall difference of PET with ATACpatientBone (-1.5% ± 1.5) improved over that of PET with ATAC (-4.0% ± 3.2) (P < .001). Conclusion ATAC in PET/MR imaging achieves similar quantification accuracy to that from CTAC by means of atlas-based bone compensation. However, patient-specific anatomic differences from the atlas causes bone attenuation differences and misclassified sinuses, which result in patient-dependent performance variation of ATAC. (©) RSNA, 2017

  12. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

    PubMed Central

    Yu, Nancy Yiu-Lin; Hallström, Björn M.; Fagerberg, Linn; Ponten, Fredrik; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R. R.; FANTOM Consortium, The; Hayashizaki, Yoshihide; Uhlén, Mathias; Daub, Carsten O.

    2015-01-01

    Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5′-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes. PMID:26117540

  13. Integrative analysis of the connectivity and gene expression atlases in the mouse brain.

    PubMed

    Ji, Shuiwang; Fakhry, Ahmed; Deng, Houtao

    2014-01-01

    Brain function is the result of interneuron signal transmission controlled by the fundamental biochemistry of each neuron. The biochemical content of a neuron is in turn determined by spatiotemporal gene expression and regulation encoded into the genomic regulatory networks. It is thus of particular interest to elucidate the relationship between gene expression patterns and connectivity in the brain. However, systematic studies of this relationship in a single mammalian brain are lacking to date. Here, we investigate this relationship in the mouse brain using the Allen Brain Atlas data. We employ computational models for predicting brain connectivity from gene expression data. In addition to giving competitive predictive performance, these models can rank the genes according to their predictive power. We show that gene expression is predictive of connectivity in the mouse brain when the connectivity signals are discretized. When the expression patterns of 4084 genes are used, we obtain a predictive accuracy of 93%. Our results also show that a small number of genes can almost give the full predictive power of using thousands of genes. We can achieve a prediction accuracy of 91% by using only 25 genes. Gene ontology analysis of the highly ranked genes shows that they are enriched for connectivity related processes.

  14. 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…

  15. 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…

  16. Integrated presentation of 3-D data derived from multisensor imagery and anatomical atlases using a parallel processing system

    NASA Astrophysics Data System (ADS)

    Undrill, Peter E.; Cameron, George G.; Cookson, M. J.; Davies, Chris; Robinson, Neil L.; Hill, Andrew; Cootes, Tim F.; Taylor, Christopher J.; Thornham, Ann; Wysocki, J.; Liddell, Heather M.; Parkinson, Dennis J.

    1992-05-01

    The MIRIAD project (Medical Image Reconstruction, Interpretation, Analysis, and Display) brings together a multidisciplinary team with the objectives of exploring interactive presentation and model-based interpretation of three-dimensional medical images taken from high and low resolution studies respectively. A digitized atlas of normal anatomy can then be used to provide the personal atlas by which the medical image can be appraised and quantified.

  17. 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

  18. 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

    2015-07-20

    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

  19. Anatomy atlases.

    PubMed

    Rosse, C

    1999-01-01

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

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

    PubMed

    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

    2016-01-04

    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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. 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

  2. [Atlas fractures].

    PubMed

    Schären, S; Jeanneret, B

    1999-05-01

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

  3. Body of evidence: integrating Eduard Pernkopf’s Atlas into a librarian-led medical humanities seminar

    PubMed Central

    Mages, Keith C.; Lohr, Linda A.

    2017-01-01

    Background Anatomical subjects depicted in Eduard Pernkopf’s richly illustrated Topographische Anatomie des Menschen may be victims of the Nazi regime. Special collections librarians in the history of medicine can use this primary resource to initiate dialogs about ethics with medical students. Case Presentation Reported here is the authors’ use of Pernkopf’s Atlas in an interactive medical humanities seminar designed for third-year medical students. Topical articles, illustrations, and interviews introduced students to Pernkopf, his Atlas, and the surrounding controversies. We aimed to illustrate how this controversial historical publication can successfully foster student discussion and ethical reflection. Conclusions Pernkopf’s Atlas and our mix of contextual resources facilitated thoughtful discussions about history and ethics amongst the group. Anonymous course evaluations showed student interest in the subject matter, relevance to their studies, and appreciation of our special collection’s space and contents. PMID:28377682

  4. dc3dm: Software to efficiently form and apply a 3D DDM operator for a nonuniformly discretized rectangular planar fault

    NASA Astrophysics Data System (ADS)

    Bradley, A. M.

    2013-12-01

    My poster will describe dc3dm, a free open source software (FOSS) package that efficiently forms and applies the linear operator relating slip and traction components on a nonuniformly discretized rectangular planar fault in a homogeneous elastic (HE) half space. This linear operator implements what is called the displacement discontinuity method (DDM). The key properties of dc3dm are: 1. The mesh can be nonuniform. 2. Work and memory scale roughly linearly in the number of elements (rather than quadratically). 3. The order of accuracy of my method on a nonuniform mesh is the same as that of the standard method on a uniform mesh. Property 2 is achieved using my FOSS package hmmvp [AGU 2012]. A nonuniform mesh (property 1) is natural for some problems. For example, in a rate-state friction simulation, nucleation length, and so required element size, scales reciprocally with effective normal stress. Property 3 assures that if a nonuniform mesh is more efficient than a uniform mesh (in the sense of accuracy per element) at one level of mesh refinement, it will remain so at all further mesh refinements. I use the routine DC3D of Y. Okada, which calculates the stress tensor at a receiver resulting from a rectangular uniform dislocation source in an HE half space. On a uniform mesh, straightforward application of this Green's function (GF) yields a DDM I refer to as DDMu. On a nonuniform mesh, this same procedure leads to artifacts that degrade the order of accuracy of the DDM. I have developed a method I call IGA that implements the DDM using this GF for a nonuniformly discretized mesh having certain properties. Importantly, IGA's order of accuracy on a nonuniform mesh is the same as DDMu's on a uniform one. Boundary conditions can be periodic in the surface-parallel direction (in both directions if the GF is for a whole space), velocity on any side, and free surface. The mesh must have the following main property: each uniquely sized element must tile each element

  5. 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...

  6. 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...

  7. 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.

  8. On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners.

    PubMed

    Chen, Kevin T; Izquierdo-Garcia, David; Poynton, Clare B; Chonde, Daniel B; Catana, Ciprian

    2017-03-01

    To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps ("μ-maps") were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map ("PAC-map") generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach.

  9. Lecturing from the Atlas: An Experiment in Teaching

    ERIC Educational Resources Information Center

    Harris, Lewis D.

    1977-01-01

    Discusses the advantages of lecturing directly from the pages of the school atlas (a compendium of maps) in order to integrate it into introductory world regional geography courses. The approach includes a self-study atlas exercise and classroom lectures based on the school atlas. (Author)

  10. 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.

  11. 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.

  12. 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.

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

    PubMed Central

    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

  14. Measurements of integrated and differential cross sections for isolated photon pair production in p p collisions at √{s }=8 TeV with the ATLAS detector

    NASA Astrophysics Data System (ADS)

    Aaboud, M.; Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; Abouzeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Agatonovic-Jovin, T.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Akerstedt, H.; Åkesson, T. P. A.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amorim, A.; Amoroso, S.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Bagnaia, P.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Becker, K.; Becker, M.; Beckingham, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Beltramello, O.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertolucci, F.; Bertram, I. A.; Bertsche, C.; Bertsche, D.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Betancourt, C.; Bethani, A.; Bethke, S.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Biesuz, N. V.; Biglietti, M.; Bilbao de Mendizabal, J.; Billoud, T. R. V.; Bilokon, H.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, C. W.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blum, W.; Blumenschein, U.; Blunier, S.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boehler, M.; Boerner, D.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bolz, A. E.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossio Sola, J. D.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Breaden Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Briglin, D. L.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Broughton, J. H.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruni, A.; Bruni, G.; Bruni, L. 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F.; Glazov, A.; Goblirsch-Kolb, M.; Godlewski, J.; Goldfarb, S.; Golling, T.; Golubkov, D.; Gomes, A.; Gonçalo, R.; Goncalves Gama, R.; Goncalves Pinto Firmino da Costa, J.; Gonella, G.; Gonella, L.; Gongadze, A.; González de La Hoz, S.; Gonzalez-Sevilla, S.; Goossens, L.; Gorbounov, P. A.; Gordon, H. A.; Gorelov, I.; Gorini, B.; Gorini, E.; Gorišek, A.; Goshaw, A. T.; Gössling, C.; Gostkin, M. I.; Gottardo, C. A.; Goudet, C. R.; Goujdami, D.; Goussiou, A. G.; Govender, N.; Gozani, E.; Graber, L.; Grabowska-Bold, I.; Gradin, P. O. J.; Gramling, J.; Gramstad, E.; Grancagnolo, S.; Gratchev, V.; Gravila, P. M.; Gray, C.; Gray, H. M.; Greenwood, Z. D.; Grefe, C.; Gregersen, K.; Gregor, I. M.; Grenier, P.; Grevtsov, K.; Griffiths, J.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Gris, Ph.; Grivaz, J.-F.; Groh, S.; Gross, E.; Grosse-Knetter, J.; Grossi, G. C.; Grout, Z. 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A.; Jarlskog, G.; Javadov, N.; Javůrek, T.; Javurkova, M.; Jeanneau, F.; Jeanty, L.; Jejelava, J.; Jelinskas, A.; Jenni, P.; Jeske, C.; Jézéquel, S.; Ji, H.; Jia, J.; Jiang, H.; Jiang, Y.; Jiang, Z.; Jiggins, S.; Jimenez Pena, J.; Jin, S.; Jinaru, A.; Jinnouchi, O.; Jivan, H.; Johansson, P.; Johns, K. A.; Johnson, C. A.; Johnson, W. J.; Jon-And, K.; Jones, R. W. L.; Jones, S. D.; Jones, S.; Jones, T. J.; Jongmanns, J.; Jorge, P. M.; Jovicevic, J.; Ju, X.; Juste Rozas, A.; Köhler, M. K.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kahn, S. J.; Kaji, T.; Kajomovitz, E.; Kalderon, C. W.; Kaluza, A.; Kama, S.; Kamenshchikov, A.; Kanaya, N.; Kanjir, L.; Kantserov, V. A.; Kanzaki, J.; Kaplan, B.; Kaplan, L. S.; Kar, D.; Karakostas, K.; Karastathis, N.; Kareem, M. J.; Karentzos, E.; Karpov, S. N.; Karpova, Z. M.; Karthik, K.; Kartvelishvili, V.; Karyukhin, A. N.; Kasahara, K.; Kashif, L.; Kass, R. 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H.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanaka, S.; Tanioka, R.; Tannenwald, B. B.; Tapia Araya, S.; Tapprogge, S.; Tarem, S.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teixeira-Dias, P.; 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, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Tibbetts, M. J.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorova-Nova, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Tornambe, P.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Treado, C. J.; Trefzger, T.; Tresoldi, F.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsang, K. W.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsui, K. M.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tulbure, T. T.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turgeman, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Unverdorben, C.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usui, J.; Vacavant, L.; Vacek, V.; Vachon, B.; Valderanis, C.; Valdes Santurio, E.; Valentinetti, S.; Valero, A.; Valéry, L.; Valkar, S.; Vallier, A.; Valls Ferrer, J. A.; van den Wollenberg, W.; van der Graaf, H.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varni, C.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veeraraghavan, V.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vlasak, M.; Vogel, M.; Vokac, P.; Volpi, G.; von der Schmitt, 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.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. W.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Worm, S. D.; Wosiek, B. K.; Wotschack, J.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Yabsley, B.; Yacoob, S.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamatani, M.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemla, A.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; 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.; Zou, R.; Zur Nedden, M.; Zwalinski, L.; Atlas Collaboration

    2017-06-01

    A measurement of the production cross section for two isolated photons in proton-proton collisions at a center-of-mass energy of √{s }=8 TeV is presented. The results are based on an integrated luminosity of 20.2 fb-1 recorded by the ATLAS detector at the Large Hadron Collider. The measurement considers photons with pseudorapidities satisfying |ηγ|<1.37 or 1.56 <|ηγ|<2.37 and transverse energies of respectively ET,1 γ>40 GeV and ET,2 γ>30 GeV for the two leading photons ordered in transverse energy produced in the interaction. The background due to hadronic jets and electrons is subtracted using data-driven techniques. The fiducial cross sections are corrected for detector effects and measured differentially as a function of six kinematic observables. The measured cross section integrated within the fiducial volume is 16.8 ±0.8 pb . The data are compared to fixed-order QCD calculations at next-to-leading-order and next-to-next-to-leading-order accuracy as well as next-to-leading-order computations including resummation of initial-state gluon radiation at next-to-next-to-leading logarithm or matched to a parton shower, with relative uncertainties varying from 5% to 20%.

  15. Measurements of integrated and differential cross sections for isolated photon pair production in pp collisions at s=8TeV with the ATLAS detector

    DOE PAGES

    Aaboud, M.; Aad, G.; Abbott, B.; ...

    2017-06-27

    A measurement of the production cross section for two isolated photons in proton-proton collisions at a center-of-mass energy ofmore » $$\\sqrt{s}$$ = 8 TeV is presented. The results are based on an integrated luminosity of 20.2 fb-1 recorded by the ATLAS detector at the Large Hadron Collider. The measurement considers photons with pseudorapidities satisfying |ηγ| < 1.37 or 1.56 < |ηγ| < 2.37 and transverse energies of respectively E$$γ\\atop{T,1}$$ > 40 GeV and E$$γ\\atop{T,2}$$ > 30 GeV for the two leading photons ordered in transverse energy produced in the interaction. The background due to hadronic jets and electrons is subtracted using data-driven techniques. The fiducial cross sections are corrected for detector effects and measured differentially as a function of six kinematic observables. The measured cross section integrated within the fiducial volume is 16.8 ± 0.8 pb . Lastly, the data are compared to fixed-order QCD calculations at next-to-leading-order and next-to-next-to-leading-order accuracy as well as next-to-leading-order computations including resummation of initial-state gluon radiation at next-to-next-to-leading logarithm or matched to a parton shower, with relative uncertainties varying from 5% to 20%.« less

  16. Experience with 3D integration technologies in the framework of the ATLAS pixel detector upgrade for the HL-LHC

    NASA Astrophysics Data System (ADS)

    Aruntinov, D.; Barbero, M.; Gonella, L.; Hemperek, T.; Hügging, F.; Krüger, H.; Wermes, N.; Breugnon, P.; Chantepie, B.; Clemens, J. C.; Fei, R.; Fougeron, D.; Godiot, S.; Pangaud, P.; Rozanov, A.; Garcia-Sciveres, M.; Mekkaoui, A.

    2013-12-01

    3D technologies are investigated for the upgrade of the ATLAS pixel detector at the HL-LHC. R&D focuses on both, IC design in 3D, as well as on post-processing 3D technologies such as Through Silicon Via (TSV). The first one uses a so-called via first technology, featuring the insertion of small aspect ratio TSV at the pixel level. As discussed in the paper, this technology can still present technical challenges for the industrial partners. The second one consists of etching the TSV via last. This technology is investigated to enable 4-side abuttable module concepts, using today's pixel detector technology. Both approaches are presented in this paper and results from first available prototypes are discussed.

  17. gLExec and MyProxy integration in the ATLAS/OSG PanDA workload management system

    NASA Astrophysics Data System (ADS)

    Caballero, J.; Hover, J.; Litmaath, M.; Maeno, T.; Nilsson, P.; Potekhin, M.; Wenaus, T.; Zhao, X.

    2010-04-01

    Worker nodes on the grid exhibit great diversity, making it difficult to offer uniform processing resources. A pilot job architecture, which probes the environment on the remote worker node before pulling down a payload job, can help. Pilot jobs become smart wrappers, preparing an appropriate environment for job execution and providing logging and monitoring capabilities. PanDA (Production and Distributed Analysis), an ATLAS and OSG workload management system, follows this design. However, in the simplest (and most efficient) pilot submission approach of identical pilots carrying the same identifying grid proxy, end-user accounting by the site can only be done with application-level information (PanDA maintains its own end-user accounting), and end-user jobs run with the identity and privileges of the proxy carried by the pilots, which may be seen as a security risk. To address these issues, we have enabled PanDA to use gLExec, a tool provided by EGEE which runs payload jobs under an end-user's identity. End-user proxies are pre-staged in a credential caching service, MyProxy, and the information needed by the pilots to access them is stored in the PanDA DB. gLExec then extracts from the user's proxy the proper identity under which to run. We describe the deployment, installation, and configuration of gLExec, and how PanDA components have been augmented to use it. We describe how difficulties were overcome, and how security risks have been mitigated. Results are presented from OSG and EGEE Grid environments performing ATLAS analysis using PanDA and gLExec.

  18. ATLAS Detector Upgrade Prospects

    NASA Astrophysics Data System (ADS)

    Dobre, M.; ATLAS Collaboration

    2017-01-01

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

  19. 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.

  20. 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

  1. 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

  2. Planetary atlases

    NASA Technical Reports Server (NTRS)

    Batson, R. M.; Inge, J. L.; Morgan, H. F.

    1991-01-01

    Two kinds of planetary map atlases are in production. Atlases of the first kind contain reduced-scale versions of maps in hard-bound books with dimensions of 11 x 14 inches. These new atlases are intended to: (1) provide concise but comprehensive references to the geography of the planets needed by planetary scientists and others; and (2) allow inexpensive access to the planetary map dataset without requiring acquisition and examination of tens or hundreds of full-size map sheets. Two such atlases have been published and a third is in press. Work was begun of an Atlas of the Satellite of the Outer Planets. The second kind of atlas is a popular or semi-technical version designed for commercial publication and distribution. The first edition, The Atlas of the Solar System, is nearly ready for publication. New funding and contracting constraints now make it unlikely that the atlas can be published in the format originally planned. Currently, the possibility of publishing the maps through the U.S. Geological Survey as a series of folios in the I-map series is being explored. The maps are global views of each solid-surface body of the Solar System. Each map shows airbrushed relief, albedo, and, where available, topography. A set of simplified geologic maps is also included. All of the maps are on equal-area projections. Scales are 1:40,000,000 for the Earth and Venus; 1:2,000,000 for the Saturnian satellites Mimas and Enceladus and the Uranian satellite Miranda; 1:100,000 for the Martian satellites, Phobos and Deimos; and 1:10,000,000 for all other bodies.

  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. Measurement of the centrality and pseudorapidity dependence of the integrated elliptic flow in lead-lead collisions at [Formula: see text] TeV with the ATLAS detector.

    PubMed

    Aad, G; Abbott, B; Abdallah, J; Abdel Khalek, S; Abdinov, O; Aben, R; Abi, B; 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; Agatonovic-Jovin, T; Aguilar-Saavedra, J A; Agustoni, M; Ahlen, S P; Ahmadov, F; Aielli, G; Åkesson, T P A; Akimoto, G; Akimov, A V; Alberghi, G L; Albert, J; Albrand, S; Alconada Verzini, M J; Aleksa, M; Aleksandrov, I N; Alexa, C; Alexander, G; Alexandre, G; Alexopoulos, T; Alhroob, M; Alimonti, G; Alio, L; Alison, J; Allbrooke, B M M; Allison, L J; Allport, P P; Allwood-Spiers, S E; Almond, J; Aloisio, A; Alonso, A; Alonso, F; Alpigiani, C; Altheimer, A; Alvarez Gonzalez, B; Alviggi, M G; 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; Anderson, K J; Andreazza, A; Andrei, V; Anduaga, X S; Angelidakis, S; Angelozzi, I; Anger, P; Angerami, A; Anghinolfi, F; Anisenkov, A V; Anjos, N; Annovi, A; Antonaki, A; Antonelli, M; Antonov, A; Antos, J; Anulli, F; Aoki, M; Aperio Bella, L; Apolle, R; Arabidze, G; Aracena, I; Arai, Y; Araque, J P; Arce, A T H; Arguin, J-F; Argyropoulos, S; Arik, M; Armbruster, A J; Arnaez, O; Arnal, V; Arnold, H; Arslan, O; Artamonov, A; Artoni, G; Asai, S; Asbah, N; Ashkenazi, A; Ask, S; Åsman, B; Asquith, L; Assamagan, K; Astalos, R; Atkinson, M; Atlay, N B; Auerbach, B; Augsten, K; Aurousseau, M; Avolio, G; Azuelos, G; Azuma, Y; Baak, M A; Bacci, C; Bachacou, H; Bachas, K; Backes, M; Backhaus, M; Backus Mayes, J; Badescu, E; Bagiacchi, P; Bagnaia, P; Bai, Y; Bain, T; Baines, J T; Baker, O K; Baker, S; Balek, P; Balli, F; Banas, E; Banerjee, Sw; Bangert, A; Bannoura, A A E; Bansal, V; Bansil, H S; Barak, L; Baranov, S P; Barberio, E L; Barberis, D; Barbero, M; Barillari, T; Barisonzi, M; Barklow, T; Barlow, N; Barnett, B M; Barnett, R M; Barnovska, Z; Baroncelli, A; Barone, G; Barr, A J; 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Vukotic, I; Vykydal, Z; Wagner, W; Wagner, P; Wahrmund, S; Wakabayashi, J; Walder, J; Walker, R; Walkowiak, W; Wall, R; Waller, P; Walsh, B; Wang, C; Wang, C; Wang, F; Wang, H; Wang, H; Wang, J; Wang, J; Wang, K; Wang, R; Wang, S M; Wang, T; Wang, X; Wanotayaroj, C; Warburton, A; Ward, C P; Wardrope, D R; Warsinsky, M; Washbrook, A; Wasicki, C; Watanabe, I; 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; Weigell, P; Weinert, B; Weingarten, J; Weiser, C; Weits, H; Wells, P S; Wenaus, T; Wendland, D; Weng, Z; Wengler, T; Wenig, S; Wermes, N; Werner, M; Werner, P; Wessels, M; Wetter, J; Whalen, K; White, A; White, M J; White, R; White, S; Whiteson, D; Wicke, D; Wickens, F J; Wiedenmann, W; Wielers, M; Wienemann, P; Wiglesworth, C; Wiik-Fuchs, L A M; Wijeratne, P A; Wildauer, A; Wildt, M A; Wilkens, H G; Will, J Z; Williams, H H; Williams, S; Willis, C; Willocq, S; Wilson, J A; Wilson, A; Wingerter-Seez, I; Winklmeier, F; Wittgen, M; Wittig, T; Wittkowski, J; Wollstadt, S J; Wolter, M W; Wolters, H; Wosiek, B K; Wotschack, J; Woudstra, M J; Wozniak, K W; Wright, M; Wu, M; Wu, S L; Wu, X; Wu, Y; Wulf, E; Wyatt, T R; Wynne, B M; Xella, S; Xiao, M; Xu, D; Xu, L; Yabsley, B; Yacoob, S; Yamada, M; Yamaguchi, H; Yamaguchi, Y; Yamamoto, A; Yamamoto, K; Yamamoto, S; Yamamura, T; Yamanaka, T; Yamauchi, K; Yamazaki, Y; Yan, Z; Yang, H; Yang, H; Yang, U K; Yang, Y; Yanush, S; Yao, L; Yao, W-M; Yasu, Y; Yatsenko, E; Yau Wong, K H; Ye, J; Ye, S; Yen, A L; Yildirim, E; Yilmaz, M; Yoosoofmiya, R; 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; Yurkewicz, A; Zabinski, B; Zaidan, R; Zaitsev, A M; Zaman, A; Zambito, S; Zanello, L; Zanzi, D; Zaytsev, A; Zeitnitz, C; Zeman, M; Zemla, A; Zengel, K; Zenin, O; Ženiš, T; Zerwas, D; Zevi Della Porta, G; Zhang, D; Zhang, F; Zhang, H; Zhang, J; Zhang, L; Zhang, X; Zhang, Z; Zhao, Z; Zhemchugov, A; Zhong, J; Zhou, B; Zhou, L; Zhou, N; Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zibell, A; Zieminska, D; Zimine, N I; Zimmermann, C; Zimmermann, R; Zimmermann, S; Zimmermann, S; Zinonos, Z; Ziolkowski, M; Zobernig, G; Zoccoli, A; Zur Nedden, M; Zurzolo, G; Zutshi, V; Zwalinski, L

    The integrated elliptic flow of charged particles produced in Pb+Pb collisions at [Formula: see text] TeV has been measured with the ATLAS detector using data collected at the Large Hadron Collider. The anisotropy parameter, [Formula: see text], was measured in the pseudorapidity range [Formula: see text] with the event-plane method. In order to include tracks with very low transverse momentum [Formula: see text], thus reducing the uncertainty in [Formula: see text] integrated over [Formula: see text], a [Formula: see text] data sample recorded without a magnetic field in the tracking detectors is used. The centrality dependence of the integrated [Formula: see text] is compared to other measurements obtained with higher [Formula: see text] thresholds. The integrated elliptic flow is weakly decreasing with [Formula: see text]. The integrated [Formula: see text] transformed to the rest frame of one of the colliding nuclei is compared to the lower-energy RHIC data.

  5. Integrating atlas and graph cut methods for right ventricle blood-pool segmentation from cardiac cine MRI

    NASA Astrophysics Data System (ADS)

    Dangi, Shusil; Linte, Cristian A.

    2017-03-01

    Segmentation of right ventricle from cardiac MRI images can be used to build pre-operative anatomical heart models to precisely identify regions of interest during minimally invasive therapy. Furthermore, many functional parameters of right heart such as right ventricular volume, ejection fraction, myocardial mass and thickness can also be assessed from the segmented images. To obtain an accurate and computationally efficient segmentation of right ventricle from cardiac cine MRI, we propose a segmentation algorithm formulated as an energy minimization problem in a graph. Shape prior obtained by propagating label from an average atlas using affine registration is incorporated into the graph framework to overcome problems in ill-defined image regions. The optimal segmentation corresponding to the labeling with minimum energy configuration of the graph is obtained via graph-cuts and is iteratively refined to produce the final right ventricle blood pool segmentation. We quantitatively compare the segmentation results obtained from our algorithm to the provided gold-standard expert manual segmentation for 16 cine-MRI datasets available through the MICCAI 2012 Cardiac MR Right Ventricle Segmentation Challenge according to several similarity metrics, including Dice coefficient, Jaccard coefficient, Hausdorff distance, and Mean absolute distance error.

  6. Juno at the Vertical Integration Facility

    NASA Image and Video Library

    2011-08-03

    At Space Launch Complex 41, the Juno spacecraft, enclosed in an Atlas payload fairing, was transferred into the Vertical Integration Facility where it was positioned on top of the Atlas rocket stacked inside.

  7. 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.

  8. A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas

    PubMed Central

    Assou, Said; Lecarrour, Tanguy; Tondeur, Sylvie; Strom, Susanne; Gabelle, Audrey; Marty, Sophie; Nadal, Laure; Pantesco, Véronique; Réme, Thierry; Hugnot, Jean-Philippe; Gasca, Stéphan; Hovatta, Outi; Hamamah, Samir; Klein, Bernard; De Vos, John

    2007-01-01

    Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1076 genes were found overexpressed in hESCs by at least 3 studies when compared to differentiated cell types, thus composing a “consensus hESC gene list”. Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits to purify by flow cytometry hESCs co-cultured on human fibroblasts. The “consensus hESC gene list” also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This “consensus differentiation gene list” included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, (http://amazonia.montp.inserm.fr), to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESC to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15 000 genes. PMID:17204602

  9. A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas.

    PubMed

    Assou, Said; Le Carrour, Tanguy; Tondeur, Sylvie; Ström, Susanne; Gabelle, Audrey; Marty, Sophie; Nadal, Laure; Pantesco, Véronique; Réme, Thierry; Hugnot, Jean-Philippe; Gasca, Stéphan; Hovatta, Outi; Hamamah, Samir; Klein, Bernard; De Vos, John

    2007-04-01

    Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a "consensus hESC gene list." Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This "consensus differentiation gene list" included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, http://amazonia.montp.inserm.fr, to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.

  10. Atlas V OA-7 LVOS Atlas Booster on Stand

    NASA Image and Video Library

    2017-02-22

    The first stage of the United Launch Alliance (ULA) Atlas V rocket is lifted by crane to vertical as it is moved into the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The rocket is being prepared for Orbital ATK's seventh commercial resupply mission, CRS-7, to the International Space Station. Orbital ATK's CYGNUS pressurized cargo module is scheduled to launch atop ULA's Atlas V rocket from Pad 41 on March 19, 2017. CYGNUS will deliver thousands of pounds of supplies, equipment and scientific research materials to the space station

  11. ATLAS computing on CSCS HPC

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. 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

  13. Introduction to the Atlas.

    ERIC Educational Resources Information Center

    Winsor, Roger

    1988-01-01

    Presents an activity designed to introduce middle through high school students to the atlas. To be used specifically with GOODE'S WORLD ATLAS (17th edition), students complete questions that enable them to systematically work their way through the atlas. Includes activity objectives, key terms, and a 52-part atlas exercise. (GEA)

  14. Hypertext atlas of fetal and neonatal pathology.

    PubMed

    Jezová, Marta; Múcková, Katarína; Soucek, Ondrej; Feit, Josef; Vlasín, Pavel

    2008-07-15

    Hypertext atlas of fetal and neonatal pathology is a free resource for pregraduate students of medicine, pathologists and other health professionals dealing with prenatal medicine. The atlas can be found at http://www.muni.cz/atlases. The access is restricted to registered users. Concise texts summarize the gross and microscopic pathology, etiology, and clinical signs of both common and rare fetal and neonatal conditions. The texts are illustrated with over 300 images that are accompanied by short comments. The atlas offers histological pictures of high quality. Virtual microscope interface is used to access the high-resolution histological images. Fetal ultrasound video clips are included. Case studies integrate clinical history, prenatal ultrasonographic examination, gross pathology and histological features. The atlas is available in English (and Czech) and equipped with an active index. The atlas is suitable both for medical students and pathologists as a teaching and reference tool. The atlas is going to be further expanded while keeping the high quality of the images.

  15. "I Have a Love-Hate Relationship with ATLAS.ti"™: Integrating Qualitative Data Analysis Software into a Graduate Research Methods Course

    ERIC Educational Resources Information Center

    Paulus, Trena M.; Bennett, Ann M.

    2017-01-01

    While research on teaching qualitative methods in education has increased, few studies explore teaching qualitative data analysis software within graduate-level methods courses. During 2013, we required students in several such courses to use ATLAS.ti™ as a project management tool for their assignments. By supporting students' early experiences…

  16. "I Have a Love-Hate Relationship with ATLAS.ti"™: Integrating Qualitative Data Analysis Software into a Graduate Research Methods Course

    ERIC Educational Resources Information Center

    Paulus, Trena M.; Bennett, Ann M.

    2017-01-01

    While research on teaching qualitative methods in education has increased, few studies explore teaching qualitative data analysis software within graduate-level methods courses. During 2013, we required students in several such courses to use ATLAS.ti™ as a project management tool for their assignments. By supporting students' early experiences…

  17. Inversed estimation of critical factors for controlling over-prediction of summertime tropospheric O3 over East Asia based of the combination of DDM sensitivity analysis and modeled Green's function method

    NASA Astrophysics Data System (ADS)

    Itahashi, S.; Yumimoto, K.; Uno, I.; Kim, S.

    2012-12-01

    Air quality studies based on the chemical transport model have been provided many important results for promoting our knowledge of air pollution phenomena, however, discrepancies between modeling results and observation data are still important issue to overcome. One of the concerning issue would be an over-prediction of summertime tropospheric ozone in remote area of Japan. This problem has been pointed out in the model comparison study of both regional scale (e.g., MICS-Asia) and global scale model (e.g., TH-FTAP). Several reasons for this issue can be listed as, (i) the modeled reproducibility on the penetration of clean oceanic air mass, (ii) correct estimation of the anthropogenic NOx / VOC emissions over East Asia, (iii) the chemical reaction scheme used in model simulation. In this study, we attempt to inverse estimation of some important chemical reactions based on the combining system of DDM (decoupled direct method) sensitivity analysis and modeled Green's function approach. The decoupled direct method (DDM) is an efficient and accurate way of performing sensitivity analysis to model inputs, calculates sensitivity coefficients representing the responsiveness of atmospheric chemical concentrations to perturbations in a model input or parameter. The inverse solutions with the Green's functions are given by a linear, least-squares method but are still robust against nonlinearities, To construct the response matrix (i.e., Green's functions), we can directly use the results of DDM sensitivity analysis. The solution of chemical reaction constants which have relatively large uncertainties are determined with constraints of observed ozone concentration data over the remote area in Japan. Our inversed estimation demonstrated that the underestimation of reaction constant to produce HNO3 (NO2 + OH + M → HNO3 + M) in SAPRC99 chemical scheme, and the inversed results indicated the +29.0 % increment to this reaction. This estimation has good agreement when compared

  18. 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

  19. 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.

  20. Watching Atlas Waistline

    NASA Image and Video Library

    2006-08-01

    The Cassini spacecraft finds oddly-shaped Atlas gliding along the edge of the A ring. The moon has a prominent equatorial bulge, which is accentuated here by the grazing viewing angle of Cassini, making Atlas appear pointy

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

    PubMed

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

    2012-09-01

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

  2. 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.

  3. Interactive Atlas of Histology

    PubMed Central

    Goubran, Emile Z.; Vinjamury, Sivarama P.

    2007-01-01

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

  4. 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.

  5. ATLAS strip tracker stavelets

    NASA Astrophysics Data System (ADS)

    Phillips, P. W.

    2012-02-01

    The engineering challenges related to the supply of electrical power to future large scale detector systems are well documented. Two options remain under active study in our community, namely serial powering and the use of DC-DC converters. Whilst clearly different in detail, both have the potential to increase the efficiency of the powering system. The ATLAS Upgrade Strip Tracker Community has constructed two demonstrator stavelets using the ABCN-25 ASIC, each comprising four silicon strip detector modules. The first stavelet is serially powered, using shunt transistors integrated into the ABCN-25 chip to maintain the required operating voltage given a constant supply current, and the second stavelet uses STV-10 DC-DC converters provided by the CERN group. Although the detailed test programme shall continue at CERN, results from stavelet tests made at RAL are presented here.

  6. Probabilistic liver atlas construction.

    PubMed

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

    2017-01-13

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

  7. Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience

    PubMed Central

    Heckscher, Ellie S.; Long, Fuhui; Layden, Michael J.; Chuang, Chein-Hui; Manning, Laurina; Richart, Jourdain; Pearson, Joseph C.; Crews, Stephen T.; Peng, Hanchuan; Myers, Eugene; Doe, Chris Q.

    2014-01-01

    A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new ‘atlas-builder’ software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an ‘eNeuro’ atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes – cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters – and linking them to individual neurons. PMID:24917506

  8. Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.

    PubMed

    Heckscher, Ellie S; Long, Fuhui; Layden, Michael J; Chuang, Chein-Hui; Manning, Laurina; Richart, Jourdain; Pearson, Joseph C; Crews, Stephen T; Peng, Hanchuan; Myers, Eugene; Doe, Chris Q

    2014-06-01

    A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new 'atlas-builder' software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an 'eNeuro' atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons. © 2014. Published by The Company of Biologists Ltd.

  9. Readout and trigger for the AFP detector at ATLAS experiment

    NASA Astrophysics Data System (ADS)

    Kocian, M.

    2017-01-01

    AFP, the ATLAS Forward Proton consists of silicon detectors at 205 m and 217 m on each side of ATLAS. In 2016 two detectors in one side were installed. The FEI4 chips are read at 160 Mbps over the optical fibers. The DAQ system uses a FPGA board with Artix chip and a mezzanine card with RCE data processing module based on a Zynq chip with ARM processor running ArchLinux. In this contribution we give an overview of the AFP detector with the commissioning steps taken to integrate with the ATLAS TDAQ. Furthermore first performance results are presented.

  10. Readout and trigger for the AFP detector at ATLAS experiment

    DOE PAGES

    Kocian, M.

    2017-01-25

    AFP, the ATLAS Forward Proton consists of silicon detectors at 205 m and 217 m on each side of ATLAS. In 2016 two detectors in one side were installed. The FEI4 chips are read at 160 Mbps over the optical fibers. The DAQ system uses a FPGA board with Artix chip and a mezzanine card with RCE data processing module based on a Zynq chip with ARM processor running ArchLinux. Finally, in this paper we give an overview of the AFP detector with the commissioning steps taken to integrate with the ATLAS TDAQ. Furthermore first performance results are presented.

  11. 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.

  12. [Integrity].

    PubMed

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  13. 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.

  14. 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.

  15. A Prototype Ontology Tool and Interface for Coastal Atlas Interoperability

    NASA Astrophysics Data System (ADS)

    Wright, D. J.; Bermudez, L.; O'Dea, L.; Haddad, T.; Cummins, V.

    2007-12-01

    While significant capacity has been built in the field of web-based coastal mapping and informatics in the last decade, little has been done to take stock of the implications of these efforts or to identify best practice in terms of taking lessons learned into consideration. This study reports on the second of two transatlantic workshops that bring together key experts from Europe, the United States and Canada to examine state-of-the-art developments in coastal web atlases (CWA), based on web enabled geographic information systems (GIS), along with future needs in mapping and informatics for the coastal practitioner community. While multiple benefits are derived from these tailor-made atlases (e.g. speedy access to multiple sources of coastal data and information; economic use of time by avoiding individual contact with different data holders), the potential exists to derive added value from the integration of disparate CWAs, to optimize decision-making at a variety of levels and across themes. The second workshop focused on the development of a strategy to make coastal web atlases interoperable by way of controlled vocabularies and ontologies. The strategy is based on web service oriented architecture and an implementation of Open Geospatial Consortium (OGC) web services, such as Web Feature Services (WFS) and Web Map Service (WMS). Atlases publishes Catalog Web Services (CSW) using ISO 19115 metadata and controlled vocabularies encoded as Uniform Resource Identifiers (URIs). URIs allows the terminology of each atlas to be uniquely identified and facilitates mapping of terminologies using semantic web technologies. A domain ontology was also created to formally represent coastal erosion terminology as a use case, and with a test linkage of those terms between the Marine Irish Digital Atlas and the Oregon Coastal Atlas. A web interface is being developed to discover coastal hazard themes in distributed coastal atlases as part of a broader International Coastal

  16. Report to users of Atlas

    SciTech Connect

    Ahmad, I.; Glagola, B.

    1996-06-01

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

  17. Integration

    ERIC Educational Resources Information Center

    Kalyn, Brenda

    2006-01-01

    Integrated learning is an exciting adventure for both teachers and students. It is not uncommon to observe the integration of academic subjects such as math, science, and language arts. However, educators need to recognize that movement experiences in physical education also can be linked to academic curricula and, may even lead the…

  18. Activities Using "The State of the World Atlas." Grades 7-12. International Understanding Series.

    ERIC Educational Resources Information Center

    Hursh, Heidi; Prevedel, Michael

    Secondary school teachers in a variety of disciplines will find the teaching activities in this handbook useful in integrating the "State of the World Atlas" into their curricula. Following an activity which introduces students to the atlas, content is divided into three sections focusing on area studies, issues, and research skills.…

  19. 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.

  20. 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.

  1. Atlas in the Distance

    NASA Image and Video Library

    2012-08-13

    NASA Cassini spacecraft looks past Saturn main rings to spy the tiny moon Atlas, which orbits between the main rings and the thin F ring. The main rings are closer to the spacecraft than Atlas is, and the moon appears as only a small, white dot.

  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. An Everyday Atlas.

    ERIC Educational Resources Information Center

    Austin, Robert F.

    1984-01-01

    Having students make an everyday atlas, a collection of maps, generally of a small area, that illustrates features of particular local interest, is a good way to introduce them to the methods and materials of geography. How to make an atlas is discussed. Two examples are described. (RM)

  4. 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,

  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. 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.

  7. 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.

  8. [Computerized atlas for image-guided stereotactic functional neurosurgery].

    PubMed

    Carballo-Barreda, M; RodríGuez-Rojas, R; Torres-Montoya, A; LóPez-Flores, G

    2007-12-01

    A computerized version of the Schaltenbrand and Wahren's stereotactic brain atlas for image-guided functional neurosurgery planning has been developed and integrated into our PC-based planning system. The SW atlas plates were digitized, contoured and labeled for both hemispheres. The computerized atlas may be interactively registered with patient's data using linear and non-linear transformation. The implemented computational tools and applications are presented. Our computer system permits navigation through original or reconstructed slices, multiple-views synchronization and zoom to improve the localization of the commisures and the surgical targets, likewise the optimum path selection. Atlas position in the target's region can be interactively actualized and lesion's position and volume may be simulated. Its benefits of this approach include increased accuracy of target definition, decreased the number of electrode tracts and for instance the time of the surgery, and reduced surgical complications.

  9. [Research on Atlas of Viscera].

    PubMed

    Jin, S

    1994-01-01

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

  10. 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.

  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. Developing a stereotypical Drosophila brain atlas.

    PubMed

    Shao, Hao-Chiang; Wu, Cheng-Chi; Chen, Guan-Yu; Chang, Hsiu-Ming; Chiang, Ann-Shyn; Chen, Yung-Chang

    2014-12-01

    Brain research requires a standardized brain atlas to describe both the variance and invariance in brain anatomy and neuron connectivity. In this study, we propose a system to construct a standardized 3D Drosophila brain atlas by integrating labeled images from different preparations. The 3D fly brain atlas consists of standardized anatomical global and local reference models, e.g., the inner and external brain surfaces and the mushroom body. The averaged global and local reference models are generated by the model averaging procedure, and then the standard Drosophila brain atlas can be compiled by transferring the averaged neuropil models into the averaged brain surface models. The main contribution and novelty of our study is to determine the average 3D brain shape based on the isosurface suggested by the zero-crossings of a 3D accumulative signed distance map. Consequently, in contrast with previous approaches that also aim to construct a stereotypical brain model based on the probability map and a user-specified probability threshold, our method is more robust and thus capable to yield more objective and accurate results. Moreover, the obtained 3D average shape is useful for defining brain coordinate systems and will be able to provide boundary conditions for volume registration methods in the future. This method is distinguishable from those focusing on 2D + Z image volumes because its pipeline is designed to process 3D mesh surface models of Drosophila brains.

  13. The ATLAS IBL CO2 cooling system

    NASA Astrophysics Data System (ADS)

    Verlaat, B.; Ostrega, M.; Zwalinski, L.; Bortolin, C.; Vogt, S.; Godlewski, J.; Crespo-Lopez, O.; Van Overbeek, M.; Blaszcyk, T.

    2017-02-01

    The ATLAS Pixel detector has been equipped with an extra pixel layer in the space obtained by a smaller radius beam pipe. This new pixel layer called the Insertable B-Layer (IBL) was installed in 2014 and is operational in the current ATLAS data taking. The IBL detector is cooled with evaporative CO2 and is the first of its kind in ATLAS. The ATLAS IBL CO2 cooling system is designed for lower temperature operation (< ‑35oC) than the previous developed CO2 cooling systems in High Energy Physics experiments. The cold temperatures are required to protect the pixel sensors for the expected high radiation dose received at an integrated luminosity of 550 fb1. This paper describes the design, development, construction and commissioning of the IBL CO2 cooling system. It describes the challenges overcome and the important lessons learned for the development of future systems which are now under design for the Phase-II upgrade detectors.

  14. The ATLAS Liquid Argon Electromagnetic Calorimeter

    SciTech Connect

    Carminati, L.

    2005-10-12

    The construction of the ATLAS Liquid Argon Electromagnetic calorimeter has been completed and commissioning is in progress. After a brief description of the detector layout, readout electronics and calibration, a review of the present status of the integration and the detector qualification is reported. Finally a selection of performance results obtained during several test beams will be presented with particular attention to linearity, uniformity, position reconstruction and {gamma}/{pi}0 separation.

  15. 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.

  16. EnviroAtlas - New York, NY - Atlas Area Boundary

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the boundary of the New York, NY EnviroAtlas Community. It represents the outside edge of all the block groups included in the EnviroAtlas community. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets)

  17. 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.

  18. Atlas Skills for Learning Rather than Learning Atlas Skills.

    ERIC Educational Resources Information Center

    Carswell, R. J. B.

    1986-01-01

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

  19. 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.

  20. 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.

  1. 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

  2. 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).

  3. General Dynamics Atlas family

    NASA Astrophysics Data System (ADS)

    Oates, James

    Developments concerning the Atlas family of launch vehicles over the last three or four years are summarized. Attention is given to the center of gravity, load factors, acoustics, pyroshock, low-frequency sinusoidal vibration, and high-frequency random vibration.

  4. The Dione Atlas

    NASA Image and Video Library

    2011-09-28

    The latest version of a complete set of cartographic map sheets from a high-resolution Dione atlas was released today by the Cassini Imaging Team. Full photomosaic maps are available at the Photojournal.

  5. 'Whose atlas I use, his song I sing?' - The impact of anatomical atlases on fiber tract contributions to cognitive deficits after stroke.

    PubMed

    de Haan, Bianca; Karnath, Hans-Otto

    2017-09-25

    Nowadays, different anatomical atlases exist for the anatomical interpretation of the results from neuroimaging and lesion analysis studies that investigate the contribution of white matter fiber tract integrity to cognitive (dys)function. A major problem with the use of different atlases in different studies, however, is that the anatomical interpretation of neuroimaging and lesion analysis results might vary as a function of the atlas used. This issue might be particularly prominent in studies that investigate the contribution of white matter fiber tract integrity to cognitive (dys)function. We used a single large-sample dataset of right brain damaged stroke patients with and without cognitive deficit (here: spatial neglect) to systematically compare the influence of three different, widely-used white matter fiber tract atlases (1 histology-based atlas and 2 DTI tractography-based atlases) on conclusions concerning the involvement of white matter fiber tracts in the pathogenesis of cognitive dysfunction. We both calculated the overlap between the statistical lesion analysis results and each long association fiber tract (topological analyses) and performed logistic regressions on the extent of fiber tract damage in each individual for each long association white matter fiber tract (hodological analyses). For the topological analyses, our results suggest that studies that use tractography-based atlases are more likely to conclude that white matter integrity is critical for a cognitive (dys)function than studies that use a histology-based atlas. The DTI tractography-based atlases classified approximately 10 times as many voxels of the statistical map as being located in a long association white matter fiber tract than the histology-based atlas. For hodological analyses on the other hand, we observed that the conclusions concerning the overall importance of long association fiber tract integrity to cognitive function do not necessarily depend on the white matter

  6. 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

  7. TAG Based Skimming In ATLAS

    NASA Astrophysics Data System (ADS)

    Doherty, T.; Cranshaw, J.; Hrivnac, J.; Slater, M.; Nowak, M.; Quilty, D.; Zhang, Q.

    2012-12-01

    The ATLAS detector at the LHC takes data at 200-500 Hz for several months per year accumulating billions of events for hundreds of physics analyses. TAGs are event-level metadata allowing a quick search for interesting events based on selection criteria defined by the user. They are stored in a file-based format as well as in relational databases. The overall TAG system architecture encompasses a range of interconnected services that provide functionality for the required use cases such as event selection, display, extraction and skimming. Skimming can be used to navigate to any of the pre-TAG data products. The services described in this paper address use cases that range in scale from selecting a handful of interesting events for an analysis specific study to creating physics working group samples on the ATLAS production system. This paper will focus on the workflow aspects involved in creating pre and post TAG data products from a TAG selection using the Grid in the context of the overall TAG system architecture. The emphasis will be on the range of demands that the implemented use cases place on these workflows and on the infrastructure. The tradeoffs of various workflow strategies will be discussed including scalability issues and other concerns that occur when integrating with data management and production systems.

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

    PubMed Central

    Ou, Yangming; Resnick, Susan M.; Gur, Ruben C.; Gur, Raquel E.; Satterthwaite, Theodore D.; Furth, Susan; Davatzikos, Christos

    2016-01-01

    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

  9. 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.

  10. 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.

  11. "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

  12. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. 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

  14. Hydrological Atlas of Austria

    NASA Astrophysics Data System (ADS)

    Lins, Harry

    2004-11-01

    At a time when we routinely search for dynamically updated maps on the Internet, the publication of a large-format, coffee-table-style atlas may seem anachronistic. Yet Austria's Federal Ministry of Agriculture, Forestry, Environment and Water Management has attempted to reconcile past and present publishing practices in its Hydrological Atlas of Austria, with an eye toward meeting the needs of both hard-copy traditionalists and soft-copy devotees. In the process, they have provided a reference document that contains a lot more than just maps. The Hydrological Atlas of Austria depicts the hydrology of Austria in a series of national-scale thematic maps and related text organized around the components of the hydrological cycle, with sections on mass balance and themes such as water management and water and the environment. The atlas is published as a two-in-one product: a conventional printed, loose-leaf-style atlas that facilitates easy update and expansion, and a digital, GIS-based version on CD-ROM. Both forms are derived from GIS datasets.

  15. 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.

  16. 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.

  17. OA-7 Atlas V Centaur mate to Booster

    NASA Image and Video Library

    2017-02-23

    The Centaur upper stage of the United Launch Alliance (ULA) Atlas V rocket arrives at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Centaur stage is lifted and mated to the first stage booster. The rocket is being prepared for Orbital ATK's seventh commercial resupply mission, CRS-7, to the International Space Station. Orbital ATK's CYGNUS pressurized cargo module is scheduled to launch atop ULA's Atlas V rocket from Pad 41 on March 19, 2017. CYGNUS will deliver 7,600 of pounds of supplies, equipment and scientific research materials to the space station

  18. 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

  19. 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

  20. Calorimetry Triggering in ATLAS

    SciTech Connect

    Igonkina, O.; Achenbach, R.; Adragna, P.; Aharrouche, M.; Alexandre, G.; Andrei, V.; Anduaga, X.; Aracena, I.; Backlund, S.; Baines, J.; Barnett, B.M.; Bauss, B.; Bee, C.; Behera, P.; Bell, P.; Bendel, M.; Benslama, K.; Berry, T.; Bogaerts, A.; Bohm, C.; Bold, T.; /UC, Irvine /AGH-UST, Cracow /Birmingham U. /Barcelona, IFAE /CERN /Birmingham U. /Rutherford /Montreal U. /Santa Maria U., Valparaiso /DESY /DESY, Zeuthen /Geneva U. /City Coll., N.Y. /Barcelona, IFAE /CERN /Birmingham U. /Kirchhoff Inst. Phys. /Birmingham U. /Lisbon, LIFEP /Rio de Janeiro Federal U. /City Coll., N.Y. /Birmingham U. /Copenhagen U. /Copenhagen U. /Brookhaven /Rutherford /Royal Holloway, U. of London /Pennsylvania U. /Montreal U. /SLAC /CERN /Michigan State U. /Chile U., Catolica /City Coll., N.Y. /Oxford U. /La Plata U. /McGill U. /Mainz U., Inst. Phys. /Hamburg U. /DESY /DESY, Zeuthen /Geneva U. /Queen Mary, U. of London /CERN /Rutherford /Rio de Janeiro Federal U. /Birmingham U. /Montreal U. /CERN /Kirchhoff Inst. Phys. /Liverpool U. /Royal Holloway, U. of London /Pennsylvania U. /Kirchhoff Inst. Phys. /Geneva U. /Birmingham U. /NIKHEF, Amsterdam /Rutherford /Royal Holloway, U. of London /Rutherford /Royal Holloway, U. of London /AGH-UST, Cracow /Mainz U., Inst. Phys. /Mainz U., Inst. Phys. /Birmingham U. /Hamburg U. /DESY /DESY, Zeuthen /Geneva U. /Kirchhoff Inst. Phys. /Michigan State U. /Stockholm U. /Stockholm U. /Birmingham U. /CERN /Montreal U. /Stockholm U. /Arizona U. /Regina U. /Regina U. /Rutherford /NIKHEF, Amsterdam /Kirchhoff Inst. Phys. /DESY /DESY, Zeuthen /City Coll., N.Y. /University Coll. London /Humboldt U., Berlin /Queen Mary, U. of London /Argonne /LPSC, Grenoble /Arizona U. /Kirchhoff Inst. Phys. /Birmingham U. /Antonio Narino U. /Hamburg U. /DESY /DESY, Zeuthen /Kirchhoff Inst. Phys. /Birmingham U. /Chile U., Catolica /Indiana U. /Manchester U. /Kirchhoff Inst. Phys. /Rutherford /City Coll., N.Y. /Stockholm U. /La Plata U. /Antonio Narino U. /Queen Mary, U. of London /Kirchhoff Inst. Phys. /Antonio Narino U. /Pavia U. /City Coll., N.Y. /Mainz U., Inst. Phys. /Mainz U., Inst. Phys. /Pennsylvania U. /Barcelona, IFAE /Barcelona, IFAE /Chile U., Catolica /Genoa U. /INFN, Genoa /Rutherford /Barcelona, IFAE /Nevis Labs, Columbia U. /CERN /Antonio Narino U. /McGill U. /Rutherford /Santa Maria U., Valparaiso /Rutherford /Chile U., Catolica /Brookhaven /Oregon U. /Mainz U., Inst. Phys. /Barcelona, IFAE /McGill U. /Antonio Narino U. /Antonio Narino U. /Kirchhoff Inst. Phys. /Sydney U. /Rutherford /McGill U. /McGill U. /Pavia U. /Genoa U. /INFN, Genoa /Kirchhoff Inst. Phys. /Kirchhoff Inst. Phys. /Mainz U., Inst. Phys. /Barcelona, IFAE /SLAC /Stockholm U. /Moscow State U. /Stockholm U. /Birmingham U. /Kirchhoff Inst. Phys. /DESY /DESY, Zeuthen /Birmingham U. /Geneva U. /Oregon U. /Barcelona, IFAE /University Coll. London /Royal Holloway, U. of London /Birmingham U. /Mainz U., Inst. Phys. /Birmingham U. /Birmingham U. /Oregon U. /La Plata U. /Geneva U. /Chile U., Catolica /McGill U. /Pavia U. /Barcelona, IFAE /Regina U. /Birmingham U. /Birmingham U. /Kirchhoff Inst. Phys. /Oxford U. /CERN /Kirchhoff Inst. Phys. /UC, Irvine /UC, Irvine /Wisconsin U., Madison /Rutherford /Mainz U., Inst. Phys. /CERN /Geneva U. /Copenhagen U. /City Coll., N.Y. /Wisconsin U., Madison /Rio de Janeiro Federal U. /Wisconsin U., Madison /Stockholm U. /University Coll. London

    2011-12-08

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

  1. The Tomato Expression Atlas.

    PubMed

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

    2017-08-01

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

  2. Atlas Regeneration, Inc.

    PubMed

    Makarev, Eugene; Isayev, Olexandr; Atala, Anthony

    2016-03-01

    Atlas Regeneration is dedicated to the development of novel data-driven solutions for regenerative medicine, adapting proven technologies, and analysis strategies to take a multiomics-wide view of stem cell quality and cell fate design. Our core offering is a global comprehensive map of stem cell differentiation, Universal Signalome Atlas for Regenerative Medicine, reflecting the pathway activation states across all characterized stem cells and their differentiated products. Key applications of Universal Signalome Atlas for Regenerative Medicine will include quality assurance for engineered cell products, and directed regeneration pharmacology, where we will screen and identify compounds that can efficiently convert pluripotent cells into desired subtypes. Another marketable piece of IP is development of specialized signaling pathway analysis systems Regeneration Intelligence which supposed to target the unmet needs of determination and prediction of stem cell signaling pathway activation to govern cell differentiation in specific directions.

  3. 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.

  4. 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

  5. Combining Multi-atlas Segmentation with Brain Surface Estimation.

    PubMed

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

    2016-02-27

    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 population.

  6. Atlas of temporal variations - interdisciplinary scientific work

    NASA Astrophysics Data System (ADS)

    Gamburtsev, A. G.; Oleinik, O. V.

    2003-04-01

    The year 2002 will culminate in the publication of the third volume of the fundamental interdisciplinary work "Atlas of Temporal Variations in Natural, Anthropogenic and Social Processes", which now will comprise three volumes (1994, 1998, 2002). The Atlas has pooled the information on the main peculiarities of processes' behaviour in various natural and humanitarian spheres over the widest temporal and spatial range. The main scientific goal of the work consists in discovering the behaviour pattern of natural, anthropogenic and social processes and the cause and effect links between them. Thus, the Atlas contains extensive comparative generalisation from the vastly different data. For one thing, it is a fundamental work on the law-governed nature of evolution in natural and social spheres; for another, it can be used as a reference book and valuable source of information for research in different directions. The authors seek to treat every piece of information as part of an integrated whole. When analysing the data, we operate on the premise that surrounding nature, society and their elements are open dynamic systems. Systems of this kind exhibit non-linear characteristics and a tendency towards ordered and chaotic behaviour. These features are revealed in the course of the analysis of time series. The data processing procedures applied are unified, all processes being generally expressed in terms of their time series and time-spectral diagrams. The technique is aimed at determination of investigated parameters' rhythms and the analysis of their evolution. This approach enables us to show the dynamics of processes occurring in absolutely dissimilar objects and performs their comparative analysis, with particular emphasis placed on rhythms and trends. As a result successions of illustrations are obtained and formed the basis of the Atlas. The Atlas covers processes that occur in objects belonging to the lithosphere, atmosphere, hydrosphere and social sphere as well

  7. 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.

  8. Micromegas detectors for the upgrade of the ATLAS muon spectrometer

    NASA Astrophysics Data System (ADS)

    Zibell, A.

    2014-08-01

    The upcoming luminosity upgrades of the LHC accelerator up to an ultimate value of 5 × 1034 cm-2s-1 require a replacement of the innermost forward muon tracking stations (Small Wheels) of the ATLAS detector in 2018 and 2019. These New Small Wheels (NSW) will contain resistive strip micromegas and small-strip Thin Gap Chamber detectors. The resistive strip micromegas detector concept is presented, together with the μTPC (micro Time Projection Chamber) track reconstruction technique for a single plane track angle measurement. The mechanical layout of the NSW micromegas chambers is discussed as well, as the features of the specially designed front-end electronics. A pre-series micromegas chamber will be installed within ATLAS already in 2014. It will be integrated into the ATLAS data acquisition system with help of a custom micromegas Read Out Driver (ROD), based on the Scalable Readout System (SRS).

  9. 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.

  10. 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.

  11. 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.

  12. 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. Copyright © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  13. 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

  14. ATLAS database application enhancements using Oracle 11g

    NASA Astrophysics Data System (ADS)

    Dimitrov, G.; Canali, L.; Blaszczyk, M.; Sorokoletov, R.

    2012-12-01

    The ATLAS experiment at LHC relies on databases for detector online data-taking, storage and retrieval of configurations, calibrations and alignments, post data-taking analysis, file management over the grid, job submission and management, condition data replication to remote sites. Oracle Relational Database Management System (RDBMS) has been addressing the ATLAS database requirements to a great extent for many years. Ten database clusters are currently deployed for the needs of the different applications, divided in production, integration and standby databases. The data volume, complexity and demands from the users are increasing steadily with time. Nowadays more than 20 TB of data are stored in the ATLAS production Oracle databases at CERN (not including the index overhead), but the most impressive number is the hosted 260 database schemes (for the most common case each schema is related to a dedicated client application with its own requirements). At the beginning of 2012 all ATLAS databases at CERN have been upgraded to the newest Oracle version at the time: Oracle 11g Release 2. Oracle 11g come with several key improvements compared to previous database engine versions. In this work we present our evaluation of the most relevant new features of Oracle 11g of interest for ATLAS applications and use cases. Notably we report on the performance and scalability enhancements obtained in production since the Oracle 11g deployment during Q1 2012 and we outline plans for future work in this area.

  15. Developing an educational curriculum for EnviroAtlas ...

    EPA Pesticide Factsheets

    EnviroAtlas is a web-based tool developed by the EPA and its partners, which provides interactive tools and resources for users to explore the benefits that people receive from nature, often referred to as ecosystem goods and services.Ecosystem goods and services are important to human health and well-being. Using EnviroAtlas, users can access, view, and analyze diverse information to better understand the potential impacts of decisions. EnviroAtlas provides two primary tools, the Interactive Map and the Eco-Health Relationship Browser. EnviroAtlas integrates geospatial data from a variety of sources so that users can visualize the impacts of decision-making on ecosystems. The Interactive Map allows users to investigate various ecosystem elements (i.e. land cover, pollution, and community development) and compare them across localities in the United States. The best part of the Interactive Map is that it does not require specialized software for map application; rather, it requires only a computer and an internet connection. As such, it can be used as a powerful educational tool. The Eco-Health Relationship Browser is also a web-based, highly interactive tool that uses existing scientific literature to visually demonstrate the connections between the environment and human health.As an ASPPH/EPA Fellow with a background in environmental science and secondary science education, I am currently developing an educational curriculum to support the EnviroAtlas to

  16. 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.

  17. 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

  18. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    Technicians with United Launch Alliance (ULA) monitor the progress as the solid rocket motor is mated to the ULA Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  19. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    Preparations are underway to lift the solid rocket motor up from its transporter for mating to the United Launch Alliance Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  20. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    The solid rocket motor is lifted on its transporter for mating to the United Launch Alliance Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  1. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    Inside the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida, the solid rocket motor is mated to the United Launch Alliance Atlas V rocket for its upcoming launch. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  2. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    The solid rocket motor has been lifted to the vertical position for mating to the United Launch Alliance Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  3. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    Technicians with United Launch Alliance (ULA) assist as the solid rocket motor is mated to the ULA Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  4. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    Inside the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida, the solid rocket motor is being mated to the United Launch Alliance Atlas V rocket for its upcoming launch. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  5. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    The solid rocket motor has been lifted to the vertical position on its transporter for mating to the United Launch Alliance Atlas V rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  6. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    The solid rocket motor has been lifted to the vertical position and moved into the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida for mating to the United Launch Alliance Atlas V rocket. NOAA's Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  7. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage is in the vertical position in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  8. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage has been lifted to the vertical position in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  9. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage has been lifted to the vertical position inside the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  10. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    United Launch Alliance team members monitor the progress as the operation begins to lift the Atlas V first stage to the vertical position at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  11. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage is lifted to the vertical position in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  12. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage is lifted to the vertical position at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  13. GOES-R Atlas V Transport from ASOC to VIF; Lift to Vertical on S

    NASA Image and Video Library

    2016-10-24

    The United Launch Alliance Atlas V first stage has arrived at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. A crane has been attached to the first stage to begin the lift to the vertical position. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R will be the first satellite in a series of next-generation NOAA GOES Satellites.

  14. GOES-R Atlas V Centaur Transport from DOCC to VIF at Pad 41

    NASA Image and Video Library

    2016-10-31

    A colorful sunrise fills the early morning sky as the United Launch Alliance Atlas V Centaur second stage is transported along the beach road to the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Geostationary Operational Environmental Satellite (GOES-R) will launch aboard the Atlas V rocket in November. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  15. 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.

  16. 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.

  17. 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…

  18. 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.

  19. Ceres Survey Atlas

    NASA Image and Video Library

    2015-12-01

    This atlas of Ceres was created using images taken by NASA Dawn spacecraft in June 2015. Researchers used 12,000 points on Ceres to construct a terrain model, which served as the basis for other maps. http://photojournal.jpl.nasa.gov/catalog/PIA20014

  20. 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/)

  1. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Connecting Imaging Mass Spectrometry and Magnetic Resonance Imaging-based Anatomical Atlases for Automated Anatomical Interpretation and Differential Analysis.

    PubMed

    Verbeeck, Nico; Spraggins, Jeffrey M; Murphy, Monika J M; Wang, Hui-Dong; Deutch, Ariel Y; Caprioli, Richard M; de Plas, Raf Van

    2017-02-27

    Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model, which are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities.

  3. 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.

  4. FATRAS - the ATLAS Fast Track Simulation project

    NASA Astrophysics Data System (ADS)

    Mechnich, Jörg; ATLAS Collaboration

    2011-12-01

    The Monte Carlo simulation of the detector response is an integral component of any analysis performed with data from the LHC experiments. As these simulated data sets must be both large and precise, their production is a CPU-intensive task. ATLAS has developed full and fast detector simulation techniques to achieve this goal within the computing limits of the collaboration. At the current early stages of data-taking, it is necessary to reprocess the Monte Carlo event samples continuously, while integrating adaptations to the simulation modules in order to improve the agreement with data taken by means of the detector itself. FATRAS is a fast track simulation engine which produces a Monte Carlo simulation based on modules and the geometry of the standard ATLAS track reconstruction algorithm. It can be combined with a fast parametrized-response simulation of the calorimeters. This approach shows a high level of agreement with the full simulation, while achieving a relative timing gain of two orders of magnitude. FATRAS was designed to provide a fast feedback cycle for tuning the MC simulation with real data: this includes the material distribution inside the detector, the integration of misalignment and current conditions, as well as calibration at the hit level. We present the updated and calibrated version of FATRAS based on the first LHC data. Extensive comparisons of the fast track simulation with the full simulation and data at 900 GeV are shown.

  5. 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.

  6. A population-average MRI-based atlas collection of the rhesus macaque.

    PubMed

    McLaren, Donald G; Kosmatka, Kristopher J; Oakes, Terrance R; Kroenke, Christopher D; Kohama, Steven G; Matochik, John A; Ingram, Don K; Johnson, Sterling C

    2009-03-01

    Magnetic resonance imaging (MRI) studies of non-human primates are becoming increasingly common; however, the well-developed voxel-based methodologies used in human studies are not readily applied to non-human primates. In the present study, we create a population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to creating a publicly available T1-weighted atlas (http://www.brainmap.wisc.edu/monkey.html), probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem, K.S. and Logothetis, N.K. (2006) atlas providing an explicit link to histological sections. Additionally, we have created a transform to integrate these atlases with the F99 surface-based atlas in CARET. It is anticipated that these tools will help facilitate voxel-based imaging methodologies in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.

  7. 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.

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

    PubMed

    Zhao, Tingting; Ruan, Dan

    2016-02-07

    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.

  9. A Population-Average MRI-Based Atlas Collection of the Rhesus Macaque

    PubMed Central

    McLaren, Donald G.; Kosmatka, Kristopher J.; Oakes, Terrance R.; Kroenke, Christopher D.; Kohama, Steven G.; Matochik, John A.; Ingram, Don K.; Johnson, Sterling C.

    2008-01-01

    Magnetic resonance imaging (MRI) studies of non-human primates are becoming increasingly common; however, the well-developed voxel-based methodologies used in human studies are not readily applied to non-human primates. In the present study, we create a population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to creating a publicly available T1-weighted atlas (http://www.brainmap.wisc.edu/monkey.html), probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem-Logothetis (2006) atlas providing an explicit link to histological sections. Additionally, we have created a transform to integrate these atlases with the F99 surface-based atlas in CARET. It is anticipated that these tools will help facilitate voxel-based imaging methodologies in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution. PMID:19059346

  10. Construction of An Unbiased Spatio-Temporal Atlas of the Tongue During Speech.

    PubMed

    Woo, Jonghye; Xing, Fangxu; Lee, Junghoon; Stone, Maureen; Prince, Jerry L

    2015-01-01

    Quantitative characterization and comparison of tongue motion during speech and swallowing present fundamental challenges because of striking variations in tongue structure and motion across subjects. A reliable and objective description of the dynamics tongue motion requires the consistent integration of inter-subject variability to detect the subtle changes in populations. To this end, in this work, we present an approach to constructing an unbiased spatio-temporal atlas of the tongue during speech for the first time, based on cine-MRI from twenty two normal subjects. First, we create a common spatial space using images from the reference time frame, a neutral position, in which the unbiased spatio-temporal atlas can be created. Second, we transport images from all time frames of all subjects into this common space via the single transformation. Third, we construct atlases for each time frame via groupwise diffeomorphic registration, which serves as the initial spatio-temporal atlas. Fourth, we update the spatio-temporal atlas by realigning each time sequence based on the Lipschitz norm on diffeomorphisms between each subject and the initial atlas. We evaluate and compare different configurations such as similarity measures to build the atlas. Our proposed method permits to accurately and objectively explain the main pattern of tongue surface motion.

  11. 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.

  12. Mesure des champs de radiation dans le detecteur ATLAS et sa caverne avec les detecteurs au silicium a pixels ATLAS-MPX

    NASA Astrophysics Data System (ADS)

    Bouchami, Jihene

    -MPX devices response and the luminosity are correlated, the results of measuring radiation levels are expressed in terms of particle fluences per unit integrated luminosity. A significant deviation has been obtained when comparing these fluences with those predicted by GCALOR, which is one of the ATLAS detector simulations. In addition, radiation measurements performed at the end of proton-proton collisions have demonstrated that the decay of radionuclides produced during collisions can be observed with the ATLAS-MPX devices. The residual activation of ATLAS components can be measured with these devices by means of ambient dose equivalent calibration. Keywords: pattern recognition, charge sharing effect, neutron detection efficiency, luminosity, van der Meer method, particle fluences, GCALOR simulation, residual activation, ambient dose equivalent.

  13. 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

  14. 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

  15. 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

  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.

    2016-03-01

    We report the following transients found by the ATLAS survey (Tonry et al. ATel #8680). ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is robotically operational on Haleakala (see http://www.fallingstar.com).

  17. 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…

  18. 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…

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

    PubMed

    Lee, Byron H

    2017-09-01

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

  20. Lighting technology atlas

    SciTech Connect

    1994-12-31

    This Atlas is a comprehensive guide to energy efficient lighting, covering both design and technology fundamentals. It presents a ``systems approach`` to lighting design, and characterizes the existing stock of lighting technology, with descriptions of available and emerging energy efficient alternatives. Technologies covered include incandescent, fluorescent, and HID lighting systems, along with daylighting, controls, reflectors, and specialty products such as exit signs and traffic signals. Market trends and the energy impact of lighting are detailed, as well as implementation issues such as economics, maintenance, and the environmental impacts of lamp and ballast recycling. The Atlas also offers practical tips for lighting installers and facility personnel, as well as a resource section with extensive product lists, a guide to available software, and a glossary.

  1. A unified framework for cross-modality multi-atlas segmentation of brain MRI.

    PubMed

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

    2013-12-01

    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.

  2. 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

  3. A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.

    PubMed

    Ullmann, Jeremy F P; Watson, Charles; Janke, Andrew L; Kurniawan, Nyoman D; Reutens, David C

    2013-09-01

    The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders.

  4. 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.

  5. Topographical atlas sheets

    USGS Publications Warehouse

    Wheeler, George Montague

    1877-01-01

    The following topographical atlas maps, published during the year, accompany the copies of Appendix N.N. of the Annual Report of the Chief of Engineers for 1877, beinig Annual Report of Lieut. Geo. M. Wheeler, Corps of Engineers, in charge of U. S. Geographical Surveys, are in continuation of the series ninety-five in number, on a scale of 1 inch to 8 miles, embracing the territory of the United States lying west of the 100th meridian.

  6. MAVEN Atlas V Launch

    NASA Image and Video Library

    2013-11-18

    The United Launch Alliance Atlas V rocket with NASA’s Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft launches from the Cape Canaveral Air Force Station Space Launch Complex 41, Monday, Nov. 18, 2013, Cape Canaveral, Florida. NASA’s Mars-bound spacecraft, the Mars Atmosphere and Volatile EvolutionN, or MAVEN, is the first spacecraft devoted to exploring and understanding the Martian upper atmosphere. Photo Credit: (NASA/Bill Ingalls)

  7. MAVEN Atlas V Launch

    NASA Image and Video Library

    2013-11-18

    The United Launch Alliance Atlas V rocket with NASA’s Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft launches from the Cape Canaveral Air Force Station Space Launch Complex 41, Monday, Nov. 18, 2013, Cape Canaveral, Florida. NASA’s Mars-bound spacecraft, the Mars Atmosphere and Volatile EvolutioN, or MAVEN, is the first spacecraft devoted to exploring and understanding the Martian upper atmosphere. Photo Credit: (NASA/Bill Ingalls)

  8. 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.

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

    PubMed

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

    2012-10-07

    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.

  10. JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

    PubMed Central

    Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

    2005-01-01

    Background Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. Results We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. Conclusion We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily. PMID:15757508

  11. JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

    PubMed

    Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

    2005-03-09

    Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

  12. 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

  13. 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

  14. 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

  15. 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

  16. The ATLAS ITk strip detector. Status of R&D

    NASA Astrophysics Data System (ADS)

    García Argos, Carlos

    2017-02-01

    While the LHC at CERN is ramping up luminosity after the discovery of the Higgs Boson in the ATLAS and CMS experiments in 2012, upgrades to the LHC and experiments are planned. The major upgrade is foreseen for 2024, with a roughly tenfold increase in luminosity, resulting in corresponding increases in particle rates and radiation doses. In ATLAS the entire Inner Detector will be replaced for Phase-II running with an all-silicon system. This paper concentrates on the strip part. Its layout foresees low-mass and modular yet highly integrated double-sided structures for the barrel and forward region. The design features conceptually simple modules made from electronic hybrids glued directly onto the silicon. Modules will then be assembled on both sides of large carbon-core structures with integrated cooling and electrical services.

  17. 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.

  18. Search for a heavy boson in WW γγ channel at the Large Hadron Collider in pp at \\sqrt{s}=13\\,{\\rm{TeV}} and integrated luminosity of 36.5 fb‑1 with the ATLAS detector

    NASA Astrophysics Data System (ADS)

    Fadol, A.; Mellado, B.; Ruan, X.

    2017-09-01

    In this study, a search for heavy boson H, decaying into the Standard Model Higgs h, and scalar boson S using 36.5 fb‑1 of proton-proton collision data recorded at \\sqrt{s}=13 {{TeV}} by the ATLAS detector at the Large Hadron Collider is presented in this note. The investigation is carried out with h decaying into two photons and the semileptonic decays of two W’s from S. The analysis procedures are described and the sensitivity of the analysis is presented.

  19. Three-dimensional event visualization for the ATLAS calorimeter

    NASA Astrophysics Data System (ADS)

    de Andrade Filho, Luciano M.; de Seixas, José Manoel; Vitillo, Roberto Agostino; Martin, Brian Thomas

    2012-02-01

    The ATLAS detector was commissioned with cosmic rays. For such commissioning, a number of software tools has been developed to support data analysis. Among ATLAS sub-detectors, commissioning the calorimeter system demanded a considerable effort due to its segmentation into seven detection layers, which produce more than a hundred thousand readout channels. Tasks like performance evaluation of the calorimeter, calibration and handling noisy or dead channels benefit a lot from cosmic muon track visualization, which facilitates the identification of the activated cells in the calorimeter. The coherence of the reconstructed data can be visually checked and potential problems can be detected in a easier way. This work presents a 3D visualization tool for the ATLAS calorimeter system, the CaloGeoView. The tool was built using ROOT Framework, which provides a smooth integration with analyses currently performed by the ATLAS community. The CaloGeoView structure and some applications with reconstructed data are presented. Due to its 3D graphical interface, the CaloGeoView has been providing a simple and intuitive way to analyze results of event reconstruction.

  20. Waxholm Space atlas of the Sprague Dawley rat brain

    PubMed Central

    Papp, Eszter A.; Leergaard, Trygve B.; Calabrese, Evan; Johnson, G. Allan; Bjaalie, Jan G.

    2014-01-01

    Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 µm isotropic voxels for the MRI volume and 78 µm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multilevel data integration and analysis across reference spaces. PMID:24726336

  1. Teaching science with technology: Using EPA's EnviroAtlas in ...

    EPA Pesticide Factsheets

    Background/Question/Methods U.S. EPA’s EnviroAtlas provides a collection of web-based, interactive tools and resources for exploring ecosystem goods and services. EnviroAtlas contains two primary tools: An Interactive Map, which provides access to 300+ maps at multiple extents for the U.S., and an Eco-Health Relationship Browser, which displays evidence from hundreds of scientific publications on the linkages between ecosystems, the services they provide, and human health. EnviroAtlas is readily available, only requires an internet browser to use, and can be used by anyone with some introduction, which this session will provide. This session introduces an educational curriculum that has been designed for use with the tools in EnviroAtlas. The curriculum contains three lesson plan packages for varying grade levels: Exploring Your Watershed for 4th and 5th grades, Making Connections Between Ecosystems and Human Health for 7th-12th grades, and a lesson that encourages students to be collaborative decision-makers in a role-playing exercise that integrates ecology, public health, and city-planning in Building a Greenway Case Study for high school and undergraduate classes. All lesson plans are free and available for download. Results/Conclusions These educational activities encourage critical thinking and engage students and community users in a variety of ways, including physical engagement and technological exploration of their local environment and communities.

  2. Waxholm Space atlas of the Sprague Dawley rat brain.

    PubMed

    Papp, Eszter A; Leergaard, Trygve B; Calabrese, Evan; Johnson, G Allan; Bjaalie, Jan G

    2014-08-15

    Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. The PeptideAtlas Project.

    PubMed

    Deutsch, Eric W

    2010-01-01

    PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw data is returned to the community via several web-based data exploration tools. The PeptideAtlas resource is useful for experiment planning, improving genome annotation, and other data mining projects. PeptideAtlas has become especially useful for planning targeted proteomics experiments.

  8. [Interactive mortality atlas in Andalusia, Spain (AIMA)].

    PubMed

    Ocaña-Riola, Ricardo; Mayoral-Cortés, José María; Sánchez-Cantalejo, Carmen; Toro-Cárdenas, Silvia; Fernández-Ajuria, Alberto; Méndez-Martínez, Camila

    2008-01-01

    Until now, mortality atlases have been static. Most of them describe the geographical distribution of mortality using count data aggregated over time and standardized mortality rates. However, this methodology has several limitations. Count data aggregated over time produce a bias in the estimation of death rates. Moreover, this practice difficult the study of temporal changes in geographical distribution of mortality. On the other hand, using standardized mortality hamper to check differences in mortality among groups. The Interactive Mortality Atlas in Andalusia (AIMA) is an alternative to conventional static atlases. It is a dynamic Geographical Information System that allows visualizing in web-site more than 12.000 maps and 338.00 graphics related to the spatio-temporal distribution of the main death causes in Andalusia by age and sex groups from 1981. The objective of this paper is to describe the methods used for AIMA development, to show technical specifications and to present their interactivity. The system is available from the link products in www.demap.es. AIMA is the first interactive GIS that have been developed in Spain with these characteristics. Spatio-temporal Hierarchical Bayesian Models were used for statistical data analysis. The results were integrated into web-site using a PHP environment and a dynamic cartography in Flash. Thematic maps in AIMA demonstrate that the geographical distribution of mortality is dynamic, with differences among year, age and sex groups. The information nowadays provided by AIMA and the future updating will contribute to reflect on the past, the present and the future of population health in Andalusia.

  9. Silicon strip staves and petals for the ATLAS Upgrade tracker of the HL-LHC

    NASA Astrophysics Data System (ADS)

    Díez, Sergio; Atlas Collaboration

    2013-01-01

    This paper describes the baseline integration structures for the silicon strip sensors to be used in the ATLAS detector for the Phase-II upgrade of the Large Hadron Collider (LHC) machine, the so-called High Luminosity LHC (HL-LHC). Highly modular structures have been developed for the integration of the silicon strips sensors, readout electronics, cooling, and support structures, called 'staves' for the barrel region and 'petals' for the end-caps of the ATLAS strips tracker. This work describes the status of the current prototypes, the building procedure, designed for mass production even at a prototyping stage, and their electrical performances.

  10. 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

  11. 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.

  12. Computerized Anatomy Atlas Of The Human Brain

    NASA Astrophysics Data System (ADS)

    Adair, Taylor; Bajcsy, Ruzena; Karp, Peter; Stein, Alan

    1981-10-01

    A software for developing, editing and displaying a 3-D computerized anatomic atlas of a human brain is described. The objective of this atlas is to serve as a reference in identifying various structures in CT scans.

  13. QCD Measurements at ATLAS

    NASA Astrophysics Data System (ADS)

    Hubacek, Z.; Atlas Collaboration

    2017-07-01

    This paper presents recent QCD related measurements from the ATLAS Experiment at the LHC at CERN. The results on the total inelastic cross-section, charged particle production, jet production, photon production, and W -, Z -bosons productions are briefly summarized. The measurments are performed at different center-of-mass energies √{s}=7, 8, and 13 TeV . The measured cross-sections are generally found to be in agreement with the expectations from the Standard Model within the estimated uncertainties.

  14. 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)

  15. 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.

  16. Report to users of ATLAS, January 1998

    SciTech Connect

    Ahmad, I.; Hofman, D.

    1998-01-01

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

  17. Multi-atlas segmentation enables robust multi-contrast MRI spleen segmentation for splenomegaly

    NASA Astrophysics Data System (ADS)

    Huo, Yuankai; Liu, Jiaqi; Xu, Zhoubing; Harrigan, Robert L.; Assad, Albert; Abramson, Richard G.; Landman, Bennett A.

    2017-02-01

    Non-invasive spleen volume estimation is essential in detecting splenomegaly. Magnetic resonance imaging (MRI) has been used to facilitate splenomegaly diagnosis in vivo. However, achieving accurate spleen volume estimation from MR images is challenging given the great inter-subject variance of human abdomens and wide variety of clinical images/modalities. Multi-atlas segmentation has been shown to be a promising approach to handle heterogeneous data and difficult anatomical scenarios. In this paper, we propose to use multi-atlas segmentation frameworks for MRI spleen segmentation for splenomegaly. To the best of our knowledge, this is the first work that integrates multi-atlas segmentation for splenomegaly as seen on MRI. To address the particular concerns of spleen MRI, automated and novel semi-automated atlas selection approaches are introduced. The automated approach interactively selects a subset of atlases using selective and iterative method for performance level estimation (SIMPLE) approach. To further control the outliers, semi-automated craniocaudal length based SIMPLE atlas selection (L-SIMPLE) is proposed to introduce a spatial prior in a fashion to guide the iterative atlas selection. A dataset from a clinical trial containing 55 MRI volumes (28 T1 weighted and 27 T2 weighted) was used to evaluate different methods. Both automated and semi-automated methods achieved median DSC > 0.9. The outliers were alleviated by the L-SIMPLE (≍1 min manual efforts per scan), which achieved 0.9713 Pearson correlation compared with the manual segmentation. The results demonstrated that the multi-atlas segmentation is able to achieve accurate spleen segmentation from the multi-contrast splenomegaly MRI scans.

  18. Multi-atlas Segmentation Enables Robust Multi-contrast MRI Spleen Segmentation for Splenomegaly.

    PubMed

    Huo, Yuankai; Liu, Jiaqi; Xu, Zhoubing; Harrigan, Robert L; Assad, Albert; Abramson, Richard G; Landman, Bennett A

    2017-02-11

    Non-invasive spleen volume estimation is essential in detecting splenomegaly. Magnetic resonance imaging (MRI) has been used to facilitate splenomegaly diagnosis in vivo. However, achieving accurate spleen volume estimation from MR images is challenging given the great inter-subject variance of human abdomens and wide variety of clinical images/modalities. Multi-atlas segmentation has been shown to be a promising approach to handle heterogeneous data and difficult anatomical scenarios. In this paper, we propose to use multi-atlas segmentation frameworks for MRI spleen segmentation for splenomegaly. To the best of our knowledge, this is the first work that integrates multi-atlas segmentation for splenomegaly as seen on MRI. To address the particular concerns of spleen MRI, automated and novel semi-automated atlas selection approaches are introduced. The automated approach interactively selects a subset of atlases using selective and iterative method for performance level estimation (SIMPLE) approach. To further control the outliers, semi-automated craniocaudal length based SIMPLE atlas selection (L-SIMPLE) is proposed to introduce a spatial prior in a fashion to guide the iterative atlas selection. A dataset from a clinical trial containing 55 MRI volumes (28 T1 weighted and 27 T2 weighted) was used to evaluate different methods. Both automated and semi-automated methods achieved median DSC > 0.9. The outliers were alleviated by the L-SIMPLE (≈1 min manual efforts per scan), which achieved 0.9713 Pearson correlation compared with the manual segmentation. The results demonstrated that the multi-atlas segmentation is able to achieve accurate spleen segmentation from the multi-contrast splenomegaly MRI scans.

  19. Multi-atlas Segmentation Enables Robust Multi-contrast MRI Spleen Segmentation for Splenomegaly

    PubMed Central

    Liu, Jiaqi; Xu, Zhoubing; Harrigan, Robert L.; Assad, Albert; Abramson, Richard G.; Landman, Bennett A.

    2016-01-01

    Non-invasive spleen volume estimation is essential in detecting splenomegaly. Magnetic resonance imaging (MRI) has been used to facilitate splenomegaly diagnosis in vivo. However, achieving accurate spleen volume estimation from MR images is challenging given the great inter-subject variance of human abdomens and wide variety of clinical images/modalities. Multi-atlas segmentation has been shown to be a promising approach to handle heterogeneous data and difficult anatomical scenarios. In this paper, we propose to use multi-atlas segmentation frameworks for MRI spleen segmentation for splenomegaly. To the best of our knowledge, this is the first work that integrates multi-atlas segmentation for splenomegaly as seen on MRI. To address the particular concerns of spleen MRI, automated and novel semi-automated atlas selection approaches are introduced. The automated approach interactively selects a subset of atlases using selective and iterative method for performance level estimation (SIMPLE) approach. To further control the outliers, semi-automated craniocaudal length based SIMPLE atlas selection (L-SIMPLE) is proposed to introduce a spatial prior in a fashion to guide the iterative atlas selection. A dataset from a clinical trial containing 55 MRI volumes (28 T1 weighted and 27 T2 weighted) was used to evaluate different methods. Both automated and semi-automated methods achieved median DSC > 0.9. The outliers were alleviated by the L-SIMPLE (≈1 min manual efforts per scan), which achieved 0.9713 Pearson correlation compared with the manual segmentation. The results demonstrated that the multi-atlas segmentation is able to achieve accurate spleen segmentation from the multi-contrast splenomegaly MRI scans. PMID:28649156

  20. A deformable digital brain atlas system according to Talairach and Tournoux.

    PubMed

    Ganser, Klaus A; Dickhaus, Hartmut; Metzner, Roland; Wirtz, Christian R

    2004-03-01

    Brain atlases are valuable tools which assist neurosurgeons during the planning of an intervention. Since a printed atlas book has several disadvantages-among them the difficulty to map the information onto a patient's individual anatomy-we have developed a digital version of the well-established stereotaxic brain atlas of Talairach and Tournoux. Our atlas system is mainly dedicated to assist neurosurgical planning, and its benefits are: (i) a three-dimensional (3D) representation of most brain structures contained in the Talairach atlas; (ii) a nonrigid matching capability which warps the standard atlas anatomy to an individual brain magnetic resonance imaging (MRI) dataset in a few minutes and which is able to take deformations due to tumors into account; (iii) the integration of several sources of neuroanatomical knowledge; (iv) an interface to a navigation system which allows utilization of atlas information intraoperatively. In this paper we outline the algorithm we have developed to achieve 3D surface models of the brain structures. Moreover, we describe the nonrigid matching method which consists of two tasks: firstly, point correspondences between the atlas and the patient are established in an automatic fashion, and secondly these displacement vectors are interpolated using a radial basis function approach to form a continuous transformation function. To generate appropriate target structures for the first of these tasks, we implemented a quick segmentation tool which is capable to segment the cortex and ventricles in less than 5 min. An evaluation shows that our nonrigid approach is more precise than the conventional piecewise linear matching, though it should be further improved for the region around the deep grey nuclei. Summarizing, we developed a Win32 program which permits the convenient and fast application of standardized anatomy to individual brains which potentially contain tumors.

  1. Three-dimensional atlas of lymph node topography based on the visible human data set.

    PubMed

    Qatarneh, Sharif M; Kiricuta, Ion-Christian; Brahme, Anders; Tiede, Ulf; Lind, Bengt K

    2006-05-01

    Comprehensive atlases of lymph node topography are necessary tools to provide a detailed description of the lymphatic distribution in relation to other organs and structures. Despite the recent developments of atlases and guidelines focusing on definitions of lymphatic regions, a comprehensive and detailed description of the three-dimensional (3D) nodal distribution is lacking. This article describes a new 3D atlas of lymph node topography based on the digital images of the Visible Human Male Anatomical (VHMA) data set. About 1,200 lymph nodes were localized in the data set and their distribution was compared with data from current cross-sectional lymphatic atlases. The identified nodes were delineated and then labeled with different colors that corresponded to their anatomical locations. A series of 2D illustrations, showing discrete locations, description, and distribution of major lymph nodes, was compiled to form a cross-sectional atlas. The resultant contours of all localized nodes in the VHMA data set were superimposed to develop a volumetric model. A 3D reconstruction was generated for the lymph nodes and surrounding structures. The volumetric lymph node topography was also integrated into the existing VOXEL-MAN digital atlas to obtain an interactive and photo-realistic visualization of the lymph nodes showing their proximity to blood vessels and surrounding organs. The lymph node topography forms part of our whole body atlas database, which includes organs, definitions, and parameters that are related to radiation therapy. The lymph node topography atlas could be utilized for visualization and exploration of the 3D lymphatic distribution to assist in defining the target volume for treatment based on the lymphatic spread surrounding the primary tumor.

  2. 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.

  3. 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.

  4. 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.

    2016-03-01

    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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. The ATLAS-1 Shuttle mission

    NASA Technical Reports Server (NTRS)

    Torr, Marsha R.; Sullivan, Kathryn D.

    1992-01-01

    The Atmospheric Laboratory for Applications and Science (ATLAS-1) encompasses instruments which will be useful in determining long-term solar variability as well as in forging links to the measurements obtained by other spacecraft for the perturbed middle and upper atmosphere. The simultaneous measurements that will be conducted by ATLAS-1 of stratospheric concentrations of ozone, chlorine monoxide and water vapor, at relatively high latitudes during the northern spring, will be especially timely.

  10. An atlas of human kinase regulation.

    PubMed

    Ochoa, David; Jonikas, Mindaugas; Lawrence, Robert T; El Debs, Bachir; Selkrig, Joel; Typas, Athanasios; Villén, Judit; Santos, Silvia Dm; Beltrao, Pedro

    2016-12-01

    The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision-making has been limited by the small number of simultaneously monitored phospho-regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co-regulation along the conditions predicts kinase-complex and kinase-substrate associations. Additionally, the kinase regulation profile acts as a molecular fingerprint to identify related and opposing signaling states. Using this atlas, we identified essential mediators of stem cell differentiation, modulators of Salmonella infection, and new targets of AKT1. This provides a global view of human phosphorylation-based signaling and the necessary context to better understand kinase-driven decision-making. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  11. Atlas Multimedia Educational Lab for Interactive Analysis

    SciTech Connect

    Pequenao, Joao

    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 of 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.-

  12. Distributed analysis with PROOF in ATLAS collaboration

    NASA Astrophysics Data System (ADS)

    Panitkin, S. Y.; Benjamin, D.; Carillo Montoya, G.; Cranmer, K.; Ernst, M.; Guan, W.; Ito, H.; Maeno, T.; Majewski, S.; Mellado, B.; Rind, O.; Shibata, A.; Tarrade, F.; Wenaus, T.; Xu, N.; Ye, S.

    2010-04-01

    The Parallel ROOT Facility - PROOF is a distributed analysis system which allows to exploit inherent event level parallelism of high energy physics data. PROOF can be configured to work with centralized storage systems, but it is especially effective together with distributed local storage systems - like Xrootd, when data are distributed over computing nodes. It works efficiently on different types of hardware and scales well from a multi-core laptop to large computing farms. From that point of view it is well suited for both large central analysis facilities and Tier 3 type analysis farms. PROOF can be used in interactive or batch like regimes. The interactive regime allows the user to work with typically distributed data from the ROOT command prompt and get a real time feedback on analysis progress and intermediate results. We will discuss our experience with PROOF in the context of ATLAS Collaboration distributed analysis. In particular we will discuss PROOF performance in various analysis scenarios and in multi-user, multi-session environments. We will also describe PROOF integration with the ATLAS distributed data management system and prospects of running PROOF on geographically distributed analysis farms.

  13. 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.

  14. Spatiotemporal-atlas-based dynamic speech imaging

    NASA Astrophysics Data System (ADS)

    Fu, Maojing; Woo, Jonghye; Liang, Zhi-Pei; Sutton, Bradley P.

    2016-03-01

    Dynamic magnetic resonance imaging (DS-MRI) has been recognized as a promising method for visualizing articulatory motion of speech in scientific research and clinical applications. However, characterization of the gestural and acoustical properties of the vocal tract remains a challenging task for DS-MRI because it requires: 1) reconstructing high-quality spatiotemporal images by incorporating stronger prior knowledge; and 2) quantitatively interpreting the reconstructed images that contain great motion variability. This work presents a novel imaging method that simultaneously meets both requirements by integrating a spatiotemporal atlas into a Partial Separability (PS) model-based imaging framework. Through the use of an atlas-driven sparsity constraint, this method is capable of capturing high-quality articulatory dynamics at an imaging speed of 102 frames per second and a spatial resolution of 2.2 × 2.2 mm2. Moreover, the proposed method enables quantitative characterization of variability of speech motion, compared to the generic motion pattern across all subjects, through the spatial residual components.

  15. 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.

  16. 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.

  17. ATLAS liquid argon calorimeter front end electronics

    NASA Astrophysics Data System (ADS)

    Buchanan, N. J.; Chen, L.; Gingrich, D. M.; Liu, S.; Chen, H.; Damazio, D.; Densing, F.; Duffin, S.; Farrell, J.; Kandasamy, S.; Kierstead, J.; Lanni, F.; Lissauer, D.; Ma, H.; Makowiecki, D.; Muller, T.; Radeka, V.; Rescia, S.; Ruggiero, R.; Takai, H.; Wolniewicz, K.; Ghazlane, H.; Hoummada, A.; Hervas, L.; Hott, T.; Wilkens, H. G.; Ban, J.; Boettcher, S.; Brooijmans, G.; Chi, C.-Y.; Caughron, S.; Cooke, M.; Copic, K.; Dannheim, D.; Gara, A.; Haas, A.; Katsanos, I.; Parsons, J. A.; Simion, S.; Sippach, W.; Zhang, L.; Zhou, N.; Eckstein, P.; Kobel, M.; Ladygin, E.; Auge, E.; Bernier, R.; Bouchel, M.; Bozzone, A.; Breton, D.; de la Taille, C.; Falleau, I.; Fournier, D.; Imbert, P.; Martin-Chassard, G.; Perus, A.; Richer, J. P.; Seguin Moreau, N.; Serin, L.; Tocut, V.; Veillet, J.-J.; Zerwas, D.; Colas, J.; Dumont-Dayot, N.; Massol, N.; Perrodo, P.; Perrot, G.; Wingerter-Seez, I.; Escalier, M.; Hubaut, F.; Laforge, B.; LeDortz, O.; Schwemling, Ph; Collot, J.; Dzahini, D.; Gallin-Martel, M.-L.; Martin, P.; Cwienk, W. D.; Fent, J.; Kurchaninov, L.; Citterio, M.; Mazzanti, M.; Tartarelli, F.; Bansal, V.; Boulahouache, C.; Cleland, W.; Liu, B.; McDonald, J.; Paolone, V.; Rabel, J.; Savinov, V.; Zuk, G.; Benslama, K.; Borgeaud, P.; de la Broïse, X.; Delagnes, E.; LeCoguie, A.; Mansoulié, B.; Pascual, J.; Teiger, J.; Dinkespiler, B.; Liu, T.; Stroynowski, R.; Ye, J.; Zarzhitsky, P.; Grahn, K.-J.; Hansson, P.; Lund-Jensen, B.; Chu, M. L.; Lee, S.-C.; Su, D. S.; Teng, P. K.; Braun, H. M.

    2008-09-01

    The ATLAS detector has been designed for operation at CERN's Large Hadron Collider. ATLAS includes a complex system of liquid argon calorimeters. This paper describes the architecture and implementation of the system of custom front end electronics developed for the readout of the ATLAS liquid argon calorimeters.

  18. Neonatal atlas construction using sparse representation.

    PubMed

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

    2014-09-01

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

  19. Thermal Testing and Model Correlation for Advanced Topographic Laser Altimeter Instrument (ATLAS)

    NASA Technical Reports Server (NTRS)

    Patel, Deepak

    2016-01-01

    The Advanced Topographic Laser Altimeter System (ATLAS) part of the Ice Cloud and Land Elevation Satellite 2 (ICESat-2) is an upcoming Earth Science mission focusing on the effects of climate change. The flight instrument passed all environmental testing at GSFC (Goddard Space Flight Center) and is now ready to be shipped to the spacecraft vendor for integration and testing. This topic covers the analysis leading up to the test setup for ATLAS thermal testing as well as model correlation to flight predictions. Test setup analysis section will include areas where ATLAS could not meet flight like conditions and what were the limitations. Model correlation section will walk through changes that had to be made to the thermal model in order to match test results. The correlated model will then be integrated with spacecraft model for on-orbit predictions.

  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. Jet measurements in ATLAS

    NASA Astrophysics Data System (ADS)

    Loch, Peter; ATLAS Collaboration

    2011-11-01

    The reconstruction of jets generated in the proton-proton collisions at the Large Hadron Collider (LHC) at a center of mass energy of TeV with the ATLAS detector is discussed. Beginning with a brief review of the calorimeter signal definitions relevant for jet finding, and the use of reconstructed charged particle tracks, the jet reconstruction strategy is described in some detail. Emphasis is put on the jet energy scale (JES) calibration strategy applied for first data, which is based on a short sequence of data driven and simulation based calibrations and corrections to restore the measured jet energy to particle level. The level of understanding of the signal patterns entering the JES corrections is shown for selected variables in comparisons to simulations. The present systematic uncertainties on the JES, which can be as low as 2% for central jets, are presented and analyzed with respect to the individual fractional contributions entering their determination. Some characteristic jet reconstruction performance and selected results from the first year of jet physics with ATLAS in a newly accessible kinematic domain are shown in conclusion.

  2. A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth.

    PubMed

    Gholipour, Ali; Rollins, Caitlin K; Velasco-Annis, Clemente; Ouaalam, Abdelhakim; Akhondi-Asl, Alireza; Afacan, Onur; Ortinau, Cynthia M; Clancy, Sean; Limperopoulos, Catherine; Yang, Edward; Estroff, Judy A; Warfield, Simon K

    2017-03-28

    Longitudinal characterization of early brain growth in-utero has been limited by a number of challenges in fetal imaging, the rapid change in size, shape and volume of the developing brain, and the consequent lack of suitable algorithms for fetal brain image analysis. There is a need for an improved digital brain atlas of the spatiotemporal maturation of the fetal brain extending over the key developmental periods. We have developed an algorithm for construction of an unbiased four-dimensional atlas of the developing fetal brain by integrating symmetric diffeomorphic deformable registration in space with kernel regression in age. We applied this new algorithm to construct a spatiotemporal atlas from MRI of 81 normal fetuses scanned between 19 and 39 weeks of gestation and labeled the structures of the developing brain. We evaluated the use of this atlas and additional individual fetal brain MRI atlases for completely automatic multi-atlas segmentation of fetal brain MRI. The atlas is available online as a reference for anatomy and for registration and segmentation, to aid in connectivity analysis, and for groupwise and longitudinal analysis of early brain growth.

  3. Cortical sulcal atlas construction using a diffeomorphic mapping approach.

    PubMed

    Joshi, Shantanu H; Cabeen, Ryan P; Sun, Bo; Joshi, Anand A; Gutman, Boris; Zamanyan, Alen; Chakrapani, Shruthi; Dinov, Ivo; Woods, Roger P; Toga, Arthur W

    2010-01-01

    We present a geometric approach for constructing shape atlases of sulcal curves on the human cortex. Sulci and gyri are represented as continuous open curves in R3, and their shapes are studied as elements of an infinite-dimensional sphere. This shape manifold has some nice properties--it is equipped with a Riemannian L2 metric on the tangent space and facilitates computational analyses and correspondences between sulcal shapes. Sulcal mapping is achieved by computing geodesics in the quotient space of shapes modulo rigid rotations and reparameterizations. The resulting sulcal shape atlas is shown to preserve important local geometry inherently present in the sample population. This is demonstrated in our experimental results for deep brain sulci, where we integrate the elastic shape model into surface registration framework for a population of 69 healthy young adult subjects.

  4. Top Quark Properties Measurements with the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    Murillo Quijada, J. A.

    2016-10-01

    Results on recent measurements of top quark properties with the ATLAS experiment at the European Laboratory, CERN, are shown. The measurements are performed using the full data set recorded during the LHC Run-I. The full data set consists of a collected integrated luminosities ∫Tdt of 4.6 fb-1 recorded at a proton-proton collision energy of √s = 7 TeV and 20.3 fb-1 collected at 8 TeV. The mentioned top quark properties include: spin correlation, charge asymmetry, W-boson polarization, color flow, top mass and top width in events with a top and anti-top quark pair (tt). An introduction to the LHC and the ATLAS detector is included and latest main results from this experiment. The contents include the current world benchmark results for the different properties and plans for future measurements during the ongoing LHC Run-II.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. Design of the ATLAS IBL Readout System

    NASA Astrophysics Data System (ADS)

    Polini, Alessandro; Bruni, Graziano; Bruschi, Marco; D'Antone, Ignazio; Dopke, Jens; Falchieri, Davide; Flick, Tobias; Gabrielli, Alessandro; Grosse-Knetter, Joern; Joseph, John; Krieger, Nina; Kugel, Andreas; Morettini, Paolo; Rizzi, Matteo; Schroer, Nicolai; Travaglini, Riccardo; Zannoli, Samuele; Zoccoli, Antonio

    An Insertable B-Layer is planned for the upgrade of the ATLAS detector and will add a fourth and innermost pixel layer to the existing Pixel Detector. 12 million pixels attached to new FE-I4 readout ASICs will require new off-detector electronics which is currently realized with two VME-based boards: a Back Of Crate module implementing optical I/O functionality and a Readout Driver module for data processing. This paper illustrates the new readout chain, focusing on the design of the new Readout Driver Card, which, with a fourfold integration with respect to the previous design, builds up the detector data, controls the calibration procedures and interacts via Gigabit links with a novel calibration farm. Future prospects and back compatibility to the existing system are also addressed.

  11. Large-scale ATLAS production on EGEE

    NASA Astrophysics Data System (ADS)

    Espinal, X.; Campana, S.; Walker, R.

    2008-07-01

    In preparation for first data at the LHC, a series of Data Challenges, of increasing scale and complexity, have been performed. Large quantities of simulated data have been produced on three different Grids, integrated into the ATLAS production system. During 2006, the emphasis moved towards providing stable continuous production, as is required in the immediate run-up to first data, and thereafter. Here, we discuss the experience of the production done on EGEE resources, using submission based on the gLite WMS, CondorG and a system using Condor Glide-ins. The overall wall time efficiency of around 90% is largely independent of the submission method, and the dominant source of wasted cpu comes from data handling issues. The efficiency of grid job submission is significantly worse than this, and the glide-in method benefits greatly from factorising this out.

  12. 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.

  13. Three-dimensional stereotactic atlas of the adult human skull correlated with the brain, cranial nerves, and intracranial vasculature.

    PubMed

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

    2015-05-15

    Although the adult human skull is a complex and multifunctional structure, its 3D, complete, realistic, and stereotactic atlas has not yet been created. This work addresses the construction of a 3D interactive atlas of the adult human skull spatially correlated with the brain, cranial nerves, and intracranial vasculature. The process of atlas construction included computed tomography (CT) high-resolution scan acquisition, skull extraction, skull parcellation, 3D disarticulated bone surface modeling, 3D model simplification, brain-skull registration, 3D surface editing, 3D surface naming and color-coding, integration of the CT-derived 3D bony models with the existing brain atlas, and validation. The virtual skull model created is complete with all 29 bones, including the auditory ossicles (being among the smallest bones). It contains all typical bony features and landmarks. The created skull model is superior to the existing skull models in terms of completeness, realism, and integration with the brain along with blood vessels and cranial nerves. This skull atlas is valuable for medical students and residents to easily get familiarized with the skull and surrounding anatomy with a few clicks. The atlas is also useful for educators to prepare teaching materials. It may potentially serve as a reference aid in the reading and operating rooms. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. 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.

  15. Atlas of fatigue curves

    SciTech Connect

    Boyer, H.E.

    1986-01-01

    This Atlas was developed to serve engineers who are looking for fatigue data on a particular metal or alloy. Having these curves compiled in a single book will also facilitate the computerization of the involved data. It is pointed out that plans are under way to make the data in this book available in ASCII files for analysis by computer programs. S-N curves which typify effects of major variables are considered along with low-carbon steels, medium-carbon steels, alloy steels, HSLA steels, high-strength alloy steels, heat-resisting steels, stainless steels, maraging steels, cast irons, and heat-resisting alloys. Attention is also given to aluminum alloys, copper alloys, magnesium alloys, molybdenum, tin alloys, titanium and titanium alloys, zirconium, steel castings, closed-die forgings, powder metallurgy parts, composites, effects of surface treatments, and test results for component parts.

  16. ATLAS IBL Pixel Upgrade

    NASA Astrophysics Data System (ADS)

    La Rosa, A.; Atlas Ibl Collaboration

    2011-06-01

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

  17. The ATLAS Tile Calorimeter

    SciTech Connect

    Henriques, A.

    2015-07-01

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

  18. 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.

  19. 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…

  20. Activities Using the "State of the World Atlas, 5th Edition."

    ERIC Educational Resources Information Center

    Hursh, Heidi

    This activity book highlights recent changes in international political and economic systems of the world. Teachers of geography, history, economics, political science, current issues, foreign languages, and journalism will find these activities useful in integrating the "State of the World Atlas" into their curriculum. Two introductory activities…

  1. 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.

  2. 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.

  3. GPU-Based Tracking Algorithms for the ATLAS High-Level Trigger

    NASA Astrophysics Data System (ADS)

    Emeliyanov, D.; Howard, J.

    2012-12-01

    Results on the performance and viability of data-parallel algorithms on Graphics Processing Units (GPUs) in the ATLAS Level 2 trigger system are presented. We describe the existing trigger data preparation and track reconstruction algorithms, motivation for their optimization, GPU-parallelized versions of these algorithms, and a “client-server” solution for hybrid CPU/GPU event processing used for integration of the GPU-oriented algorithms into existing ATLAS trigger software. The resulting speed-up of event processing times obtained with high-luminosity simulated data is presented and discussed.

  4. TDRS-M Atlas V 1st Stage Erection Launch Vehicle on Stand

    NASA Image and Video Library

    2017-07-12

    A United Launch Alliance Atlas V first stage is lifted at the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The rocket is scheduled to launch the Tracking and Data Relay Satellite, TDRS-M. It will be the latest spacecraft destined for the agency's constellation of communications satellites that allows nearly continuous contact with orbiting spacecraft ranging from the International Space Station and Hubble Space Telescope to the array of scientific observatories. Liftoff atop the ULA Atlas V rocket is scheduled to take place from Cape Canaveral's Space Launch Complex 41 on Aug. 3, 2017 at 9:02 a.m. EDT.

  5. ATLAS pixel IBL modules construction experience and developments for future upgrade

    NASA Astrophysics Data System (ADS)

    Gaudiello, A.

    2015-10-01

    The first upgrade of the ATLAS Pixel Detector is the Insertable B-Layer (IBL), installed in May 2014 in the core of ATLAS. Two different silicon sensor technologies, planar n-in-n and 3D, are used. Sensors are connected with the new generation 130 nm IBM CMOS FE-I4 read-out chip via solder bump-bonds. Production quality control tests were set up to verify and rate the performance of the modules before integration into staves. An overview of module design and construction, the quality control results and production yield will be discussed, as well as future developments foreseen for future detector upgrades.

  6. Sleep atlas and multimedia database.

    PubMed

    Penzel, T; Kesper, K; Mayer, G; Zulley, J; Peter, J H

    2000-01-01

    The ENN sleep atlas and database was set up on a dedicated server connected to the internet thus providing all services such as WWW, ftp and telnet access. The database serves as a platform to promote the goals of the European Neurological Network, to exchange patient cases for second opinion between experts and to create a case-oriented multimedia sleep atlas with descriptive text, images and video-clips of all known sleep disorders. The sleep atlas consists of a small public and a large private part for members of the consortium. 20 patient cases were collected and presented with educational information similar to published case reports. Case reports are complemented with images, video-clips and biosignal recordings. A Java based viewer for biosignals provided in EDF format was installed in order to move free within the sleep recordings without the need to download the full recording on the client.

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

    PubMed

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

    2015-12-23

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

  8. 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.

  9. Argonne's atlas control system upgrade.

    SciTech Connect

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

    1999-09-27

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

  10. SEGMENTATION OF SERIAL MRI OF TBI PATIENTS USING PERSONALIZED ATLAS CONSTRUCTION AND TOPOLOGICAL CHANGE ESTIMATION.

    PubMed

    Wang, Bo; Prastawa, Marcel; Awate, Suyash P; Irimia, Andrei; Chambers, Micah C; Vespa, Paul M; van Horn, John D; Gerig, Guido

    2012-01-01

    Traumatic brain injury (TBI) due to falls, car accidents, and warfare affects millions of people annually. Determining personalized therapy and assessment of treatment efficacy can substantially benefit from longitudinal (4D) magnetic resonance imaging (MRI). In this paper, we propose a method for segmenting longitudinal brain MR images with TBI using personalized atlas construction. Longitudinal images with TBI typically present topological changes over time due to the effect of the impact force on tissue, skull, and blood vessels and the recovery process. We address this issue by defining a novel atlas construction scheme that explicitly models the effect of topological changes. Our method automatically estimates the probability of topological changes jointly with the personalized atlas. We demonstrate the effectiveness of this approach on MR images with TBI that also have been segmented by human raters, where our method that integrates 4D information yields improved validation measures compared to temporally independent segmentations.

  11. The Auto-Tuned Land Data Assimilation System (ATLAS)

    NASA Astrophysics Data System (ADS)

    Crow, W. T.; Yilmaz, M. Tugrul

    2014-01-01

    Land data assimilation systems are commonly tasked with merging remotely sensed surface soil moisture retrievals with information derived from a soil water balance model driven by observed rainfall. The performance of such systems can be degraded by the incorrect specification of parameters describing modeling and observation errors. Here the Auto-Tuned Land Data Assimilation System (ATLAS) is introduced to simultaneously solve for all parameters required for the application of a simple land data assimilation system to integrate satellite-based rainfall and soil moisture retrievals for drought monitoring applications. The approach is based on combining a triple collocation (TC) strategy with the statistical analysis of filtering innovations and designed to leverage the simultaneous availability of satellite-based soil moisture products acquired from both active and passive microwave remote sensing. A number of variants of the ATLAS approach—each based on a different strategy for leveraging TC and innovation analysis within an adaptive filtering framework—are derived and evaluated through a synthetic twin experiment. In addition, a preliminary real data analysis is conducted using actual satellite-based products and evaluated against independent ground-based observations. Results illustrate the potential of ATLAS to improve the analysis of soil moisture anomalies using data products derived from the Global Precipitation Measurement (GPM) and the NASA Soil Moisture Active/Passive missions.

  12. EPA's EnviroAtlas: Identifying Nature's benefits, deficits, and ...

    EPA Pesticide Factsheets

    Cities, towns, and Tribes rely on clean air, water and other natural resources for public health and well-being. Yet natural infrastructure and its benefits are not always fully understood or considered in local decisions. EnviroAtlas is a free, online, easy-to-use mapping toolkit designed for citizens, analysts, and decision-makers to assess the status of local and regional “green” assets, their relevance to society, current threats, and future opportunities. Research-based maps, analysis tools, and descriptive information address seven environmental benefit categories: - Clean air - Clean and plentiful water - Natural hazard mitigation - Climate stabilization - Recreation, culture, and aesthetics - Food, fuel, and materials - Biodiversity conservation More than 300 datasets for the coterminous U.S. summarize ecosystem processes, stressors, and end users at the spatial scale of sub-watersheds (n = ~90,000). A fine-scale component for selected communities features one-meter resolution landcover data and ~100 “green infrastructure” maps summarized by census block-group. Demographic data and built environment metrics are integrated into some of these maps, and are also provided by block group for overlays and other analyses. Numerous pixel-level maps are available as well. Map layers are consistent across EnviroAtlas communities; 18 of these are currently online, with six communities added annually. EnviroAtlas community maps and information addr

  13. Bone Age Assessment of Children using a Digital Hand Atlas

    PubMed Central

    Gertych, Arkadiusz; Zhang, Aifeng; Sayre, James; Pospiech-Kurkowska, Sylwia; Huang, H.K

    2007-01-01

    We have developed an automated method to assess bone age of children using a digital hand atlas. The hand Atlas consists of two components. The first component is a database which is comprised of a collection of 1,400 digitized left hand radiographs from evenly distributed normally developed children of Caucasian (CA), Asian (AS), African-American (AA) and Hispanic (HI) origin, male (M) and female (F), ranged from 1 to 18 year old; and relevant patient demographic data along with pediatric radiologists' readings of each radiograph. This data is separate into eight categories: CAM, CAF, AAM, AAF, HIM, HIF, ASM, and ASF. In addition, CAM, AAM, HIM, and ASM are combined as one male category; and CAF, AAF, HIF, and ASF are combined as one female category. The male and female are further combined as the F & M category. The second component is a computer-assisted diagnosis (CAD) module to assess a child bone age based on the collected data. The CAD method is derived from features extracted from seven regions of interest (ROIs): the carpal bone ROI, and six phanlangeal PROIs. The PROIs are six areas including the distal and middle regions of three middle fingers. These features were used to train the eleven category fuzzy classifiers: one for each race and gender, one for the female, one male, and one F & M, to assess the bone age of a child. The digital hand atlas is being integrated with a PACS for validation of clinical use. PMID:17387000

  14. Grid Operation at Tokyo Tier-2 Centre for ATLAS

    NASA Astrophysics Data System (ADS)

    Matsunaga, Hiroyuki; Isobe, Tadaaki; Mashimo, Tetsuro; Sakamoto, Hiroshi; Ueda, Ikuo

    International Centre for Elementary Particle Physics, the University of Tokyo, has been involved in the Worldwide LHC Computing Grid since 2003. After extensive R&D experience of the PC computing farm, disk and tape storage systems, network technology and the integration of these components, it is now operating a regional centre for the ATLAS data analysis. The regional centre includes an ATLAS Tier-2 site which is running the gLite middleware developed by the Enabling Grids for E-sciencE (EGEE) project. One of the biggest challenges at the regional centre is efficient data transfer between the Tier-2 site in Tokyo and other sites, in particular the associated Tier-1 site in France, because the large round trip time due to the long distance makes it difficult to transfer data at a high rate. We have been studying to achieve a good performance of the data transfer, and some results of network tests and ATLAS data transfer are described. Hardware and software components and the operational experience are also reported in this article.

  15. Shape-constrained multi-atlas segmentation of spleen in CT

    NASA Astrophysics Data System (ADS)

    Xu, Zhoubing; Li, Bo; Panda, Swetasudha; Asman, Andrew J.; Merkle, Kristen L.; Shanahan, Peter L.; Abramson, Richard G.; Landman, Bennett A.

    2014-03-01

    Spleen segmentation on clinically acquired CT data is a challenging problem given the complicity and variability of abdominal anatomy. Multi-atlas segmentation is a potential method for robust estimation of spleen segmentations, but can be negatively impacted by registration errors. Although labeled atlases explicitly capture information related to feasible organ shapes, multi-atlas methods have largely used this information implicitly through registration. We propose to integrate a level set shape model into the traditional label fusion framework to create a shape-constrained multi-atlas segmentation framework. Briefly, we (1) adapt two alternative atlas-to-target registrations to obtain the loose bounds on the inner and outer boundaries of the spleen shape, (2) project the fusion estimate to registered shape models, and (3) convert the projected shape into shape priors. With the constraint of the shape prior, our proposed method offers a statistically significant improvement in spleen labeling accuracy with an increase in DSC by 0.06, a decrease in symmetric mean surface distance by 4.01 mm, and a decrease in symmetric Hausdorff surface distance by 23.21 mm when compared to a locally weighted vote (LWV) method.

  16. Automated 3-Dimensional Brain Atlas Fitting to Microelectrode Recordings from Deep Brain Stimulation Surgeries

    PubMed Central

    Luján, J. Luis; Noecker, Angela M.; Butson, Christopher R.; Cooper, Scott E.; Walter, Benjamin L.; Vitek, Jerrold L.; McIntyre, Cameron C.

    2009-01-01

    Objective Deep brain stimulation (DBS) surgeries commonly rely on brain atlases and microelectrode recordings (MER) to help identify the target location for electrode implantation. We present an automated method for optimally fitting a 3-dimensional brain atlas to intraoperative MER and predicting a target DBS electrode location in stereotactic coordinates for the patient. Methods We retrospectively fit a 3-dimensional brain atlas to MER points from 10 DBS surgeries targeting the subthalamic nucleus (STN). We used a constrained optimization algorithm to maximize the MER points correctly fitted (i.e., contained) within the appropriate atlas nuclei. We compared our optimization approach to conventional anterior commissure-posterior commissure (AC/PC) scaling, and to manual fits performed by four experts. A theoretical DBS electrode target location in the dorsal STN was customized to each patient as part of the fitting process and compared to the location of the clinically defined therapeutic stimulation contact. Results The human expert and computer optimization fits achieved significantly better fits than the AC/PC scaling (80, 81, and 41% of correctly fitted MER, respectively). However, the optimization fits were performed in less time than the expert fits and converged to a single solution for each patient, eliminating interexpert variance. Conclusions and Significance DBS therapeutic outcomes are directly related to electrode implantation accuracy. Our automated fitting techniques may aid in the surgical decision-making process by optimally integrating brain atlas and intraoperative neurophysiological data to provide a visual guide for target identification. PMID:19556832

  17. 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

  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.

  19. 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

  20. 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.

  1. 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.

  2. Hubble's Cosmic Atlas

    NASA Image and Video Library

    2017-09-27

    Morphologies, masses, and structures - oh, my! This beautiful clump of glowing gas, dark dust and glittering stars is the spiral galaxy NGC 4248, located about 24 million light-years away in the constellation of Canes Venatici (The Hunting Dogs). This image was produced by the NASA/ESA Hubble Space Telescope as it embarked upon compiling the first Hubble ultraviolet “atlas,” for which the telescope targeted 50 nearby star-forming galaxies. The collection spans all kinds of different morphologies, masses, and structures. Studying this sample can help us to piece together the star-formation history of the Universe. By exploring how massive stars form and evolve within such galaxies, astronomers can learn more about how, when, and where star formation occurs, how star clusters change over time, and how the process of forming new stars is related to the properties of both the host galaxy and the surrounding interstellar medium (the gas and dust that fills the space between individual stars). This galaxy was imaged with observations from Hubble’s Wide Field Camera 3. Image credit: ESA/Hubble & NASA

  3. 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.

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

    PubMed Central

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

    2015-01-01

    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

  5. 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. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  6. The VLT Survey Telescope ATLAS

    NASA Astrophysics Data System (ADS)

    Shanks, T.; Metcalfe, N.; Chehade, B.; Findlay, J. R.; Irwin, M. J.; Gonzalez-Solares, E.; Lewis, J. R.; Yoldas, A. Kupcu; Mann, R. G.; Read, M. A.; Sutorius, E. T. W.; Voutsinas, S.

    2015-08-01

    The VLT Survey Telescope ATLAS survey is an optical ugriz survey aiming to cover ≈4700 deg2 of the southern sky to similar depths as the Sloan Digital Sky Survey (SDSS). From reduced images and object catalogues provided by the Cambridge Astronomical Surveys Unit, we first find that the median seeing ranges from 0.8 arcsec FWHM (full width at half-maximum) in i to 1.0 arcsec in u, significantly better than the 1.2-1.5 arcsec seeing for SDSS. The 5σ mag limit for stellar sources is rAB = 22.7 and in all bands these limits are at least as faint as SDSS. SDSS and ATLAS are more equivalent for galaxy photometry except in the z band where ATLAS has significantly higher throughput. We have improved the original ESO magnitude zero-points by comparing m < 16 star magnitudes with the AAVSO Photometric All-Sky Survey in gri, also extrapolating into u and z, resulting in zero-points accurate to ≈ ± 0.02 mag. We finally compare star and galaxy number counts in a 250 deg2 area with SDSS and other count data and find good agreement. ATLAS data products can be retrieved from the ESO Science Archive, while support for survey science analyses is provided by the OmegaCAM Science Archive, operated by the Wide-Field Astronomy Unit in Edinburgh.

  7. Atlas Transmission Line Breakdown Analysis

    DTIC Science & Technology

    1999-06-01

    The Atlas facility will use 24 radially converging, vertically oriented and tapered, oil insulated, triplate transmission lines between the Marx ...taper from a height of 1.75 m at the Marx end to 0.32 m at the output end. The aluminum conductors, held together by 20 insulating spacers, are

  8. 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…

  9. 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…

  10. 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…

  11. 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…

  12. MERCURY ASTRONAUTS - ATLAS - AUTOGRAPHED PICTURE

    NASA Image and Video Library

    1963-10-01

    S62-02704 (1959) --- The original Mercury astronauts are pictured around a table admiring an Atlas model. Standing, left to right, are Alan B. Shepard Jr., Walter M. Schirra Jr., and John H. Glenn Jr.; sitting, left to right are Virgil I. Grissom, M. Scott Carpenter, Donald Slayton, and L. Gordon Cooper Jr. Photo credit: NASA

  13. 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…

  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. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Glance Information System for ATLAS Management

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    PubMed

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

    2015-01-01

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

  3. Contextual Atlas Regression Forests: Multiple-Atlas-Based Automated Dose Prediction in Radiation Therapy.

    PubMed

    McIntosh, Chris; Purdie, Thomas G

    2016-04-01

    Radiation therapy is an integral part of cancer treatment, but to date it remains highly manual. Plans are created through optimization of dose volume objectives that specify intent to minimize, maximize, or achieve a prescribed dose level to clinical targets and organs. Optimization is NP-hard, requiring highly iterative and manual initialization procedures. We present a proof-of-concept for a method to automatically infer the radiation dose directly from the patient's treatment planning image based on a database of previous patients with corresponding clinical treatment plans. Our method uses regression forests augmented with density estimation over the most informative features to learn an automatic atlas-selection metric that is tailored to dose prediction. We validate our approach on 276 patients from 3 clinical treatment plan sites (whole breast, breast cavity, and prostate), with an overall dose prediction accuracies of 78.68%, 64.76%, 86.83% under the Gamma metric.

  4. Search for heavy resonances with the ATLAS detector

    NASA Astrophysics Data System (ADS)

    Schuh, Natascha

    2015-05-01

    The ATLAS detector at the Large Hadron Collider (LHC) is used to search for heavy resonances in various final states. Recent results from different analyses of the proton-proton (pp) collisions recorded in 2012 at a center-of-mass energy of √s =8 TeV corresponding to an integrated luminosity of Lint ≈ 20 fb-1 are presented. Various models are considered such as W' and Z' bosons, chiral bosons, excited quarks and technicolor, as well as a Randall-Sundrum graviton, the ADD large extra dimension scenario, (quantum) black holes and contact interactions.

  5. Atlas_V_OA-7_Payload_Mate_to_Booster

    NASA Image and Video Library

    2017-03-17

    The payload fairing containing the Orbital ATK Cygnus pressurized cargo module is lifted and mated onto the Centaur upper stage, or second stage, of the United Launch Alliance (ULA) rocket in the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The Orbital ATK CRS-7 commercial resupply services mission to the International Space Station is scheduled to launch atop the Atlas V from pad 41. Cygnus will deliver 7,600 pounds of supplies, equipment and scientific research materials to the space station.

  6. 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.

  7. 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.

  8. Design and implementation of the ATLAS TRT front end electronics

    NASA Astrophysics Data System (ADS)

    Newcomer, Mitch; Atlas TRT Collaboration

    2006-07-01

    The ATLAS TRT subsystem is comprised of 380,000 4 mm straw tube sensors ranging in length from 30 to 80 cm. Polypropelene plastic layers between straws and a xenon-based gas mixture in the straws allow the straws to be used for both tracking and transition radiation detection. Detector-mounted electronics with data sparsification was chosen to minimize the cable plant inside the super-conducting solenoid of the ATLAS inner tracker. The "on detector" environment required a small footprint, low noise, low power and radiation-tolerant readout capable of triggering at rates up to 20 MHz with an analog signal dynamic range of >300 times the discriminator setting. For tracking, a position resolution better than 150 μm requires leading edge trigger timing with ˜1 ns precision and for transition radiation detection, a charge collection time long enough to integrate the direct and reflected signal from the unterminated straw tube is needed for position-independent energy measurement. These goals have been achieved employing two custom Application-specific integrated circuits (ASICS) and board design techniques that successfully separate analog and digital functionality while providing an integral part of the straw tube shielding.

  9. 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

  10. Resource Atlases for Multi-Atlas Brain Segmentations with Multiple Ontology Levels Based on T1-Weighted MRI

    PubMed Central

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

    2015-01-01

    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 – 82 years 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, are expected to support the further development of multi-atlas image segmentation. PMID:26499813

  11. 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.

  12. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.

    PubMed

    Clarkson, Melissa D

    2016-05-21

    A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.

  13. Lymphatic atlas-based target volume definition for intensity-modulated radiation therapy planning

    NASA Astrophysics Data System (ADS)

    Qatarneh, S. M.; Kiricuta, I. C.; Brahme, A.; Noz, M. E.; Ferreira, B.; Kim, W. C.; Lind, B. K.

    2007-10-01

    Despite the improvements in current imaging modalities such as CT and MRI, the detection of normal or malignant lymph nodes remains a challenge due to the large variability in lymph node characteristics and the variation in imaging quality and the limited imaging resolution. A computerized lymph node atlas could be the ideal tool for target volume definition based on the distribution of normal lymph nodes surrounding the verified malignant nodes to improve the accuracy of intensity-modulated radiation therapy planning. The standard lymph node topography in the newly constructed 3D lymph node atlas offers a detailed topographical distribution of discrete nodal locations in relation to surrounding organs at risk. In the present paper, the recently developed lymph node atlas is used for selection and delineation of target volumes in the head and neck, thorax and pelvic region. Image registration techniques were implemented to integrate the topography of the lymph node atlas into the patient's data set. By combining the knowledge-based lymph node distribution with the patient's data set, more detailed definitions of the target volumes were obtained to facilitate biologically based treatment plan optimization. The response values of the biologically optimized treatment plans were used to derive the probability of tumor control and the probability of complications in organs at risk. The treatment outcome of the lung reference plan showed a lower probability of recurrence in comparison to planning without the lymph node atlas. The lymph node atlas can improve and standardize the target volume definition by including more accurate anatomical knowledge for target volume definition and biologically optimized radiation therapy planning.

  14. 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

  15. The Latest Results from the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    Tsuno, S.; ATLAS Collaboration

    Recent results from the ATLAS experiment at the CERN LargeHadron Collider are presented. The experiment operates with high data taking efficiency since the first collision. The results show an excellent detector performance and rapid achievement of the ATLAS physics program. This paper provides a breif overview of the highlights of phyiscs results.

  16. A Water "Atlas" Exercise with Conservation Students.

    ERIC Educational Resources Information Center

    Wije, Chand

    1992-01-01

    Describes how a water atlas can be used as a tool in conservation courses. Presents a three stage approach to a classroom exercise. Includes textbook study of a significance of water as a resource, student preparation of a list of local and state of Ohio environmental issues, and collection or creation of maps to create an atlas. (DK)

  17. 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.

  18. Development, deployment and operations of ATLAS databases.

    SciTech Connect

    Vaniachine, A. V.; von der Schmitt, J. G.; High Energy Physics; Mac-Planck-Inst.

    2008-01-01

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

  19. Onboard Photo : STS-45 Atlas-1

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Space Shuttle Atlantis (STS-45) onboard photo of Mission Specialist Kathryn Sullivan working in the Atmospheric Laboratory for Applications and Science (Atlas-1) module. Atlas-1 flew in a series of Spacelab flights that measured long term variability in the total energy radiated by the Sun and determined the variability in the solar spectrum.

  20. Onboard photo: STS-56 ATLAS-2

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Space Shuttle Discovery (STS-56) onboard photo of Mission Specialist Michael Foale working in the Atmospheric Laboratory for Applications and Science (ATLAS-2). The ATLAS program was designed to measure the long term variability in the total energy radiated by the sun and determine the variability in the solar spectrum.

  1. 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…

  2. 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…

  3. 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…

  4. 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.

  5. Diffraction and central exclusive production at ATLAS

    SciTech Connect

    Tasevsky, Marek

    2011-07-15

    The diffractive physics program for the ATLAS experiment with an emphasis on the central exclusive production is discussed. The key point in this discussion is the need for an unambiguous experimental definition of diffractive signature which would be acceptable and reproducible by theorists. Recent ATLAS results from samples enhanced in diffraction contribution underline this need.

  6. Detailed transcriptome atlas of the pancreatic beta cell.

    PubMed

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

    2009-01-15

    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). 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. 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. 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).

  7. 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.

  8. 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.

  9. 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

  10. Computerized atlas for functional stereotaxis

    NASA Astrophysics Data System (ADS)

    Hardy, Tyrone L.; Brynildson, L. R. D.

    1993-09-01

    Our original brain mapping techniques have been expanded so that MR and CT images can be displayed in a three-dimensionally simulated localization environment. Various combinations of MR images as well as CT images (or combinations of both and angiography) can be selectively displayed and viewed in three-dimensional stereotactic space. Data from the Talairach anatomical library, the architectonics of the atlases of Van Buren and Borke, Schaltenbrand and Bailey, Schaltenbrand and Wahren, and Brodmann's cortico-architectonics have been used to develop a detailed anatomical atlas library and brain mapping system based on brain reference structures common to each of these databases. The data in this mapping and imaging environment can be interrogated to create computerized anatomical displays showing any given functional anatomical region in two-dimensional displays or three-dimensional relief. This composite mapping system allows the interrogation and cross referencing of data from virtually any other brain mapping or localization system.

  11. 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.

  12. 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).

  13. 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.

  14. The Atlas Genome Assembly System

    PubMed Central

    Havlak, Paul; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xing-Zhi; Weinstock, George M.; Gibbs, Richard A.

    2004-01-01

    Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This “sequence-based” growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects. PMID:15060016

  15. Anti-Atlas Mountains, Morocco

    NASA Image and Video Library

    2003-01-08

    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. http://photojournal.jpl.nasa.gov/catalog/PIA03893

  16. 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

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

    PubMed

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

    2014-07-01

    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. 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. AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework yielded a central gland Dice

  18. 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

  19. Congenital Anomaly of the Atlas Misdiagnosed as Posterior Arch Fracture of the Atlas and Atlantoaxial Subluxation

    PubMed Central

    Park, Yung; Kim, Seong Min; Lee, Yun Tae; Yoo, Ju Hyung; Oh, Hyun Chul; Sung, Seung Yong; Yoon, Han Kook; Chang, Jee-Hoon; Jung, Jeung-Yeul

    2014-01-01

    Partial or complete absence of the posterior arch of the atlas is a well-documented anomaly but a relatively rare condition. This condition is usually asymptomatic so most are diagnosed incidentally. There have been a few documented cases of congenital defects of the posterior arch of the atlas combined with atlantoaxial subluxation. We report a very rare case of congenital anomaly of the atlas combined with atlantoaxial subluxation, that can be misdiagnosed as posterior arch fracture. PMID:24605195

  20. In vivo DTI tractography of the rat brain: an atlas of the main tracts in Paxinos space with histological comparison.

    PubMed

    Figini, Matteo; Zucca, Ileana; Aquino, Domenico; Pennacchio, Paolo; Nava, Simone; Di Marzio, Alessandro; Preti, Maria Giulia; Baselli, Guseppe; Spreafico, Roberto; Frassoni, Carolina

    2015-04-01

    Diffusion tensor imaging (DTI) is a magnetic resonance modality that permits to characterize the orientation and integrity of white matter (WM). DTI-based tractography techniques, allowing the virtual reconstruction of WM tract pathways, have found wide application in preclinical neurological research. Recently, anatomically detailed rat brain atlases including DTI data were constructed from ex vivo DTI images, but tractographic atlases of normal rats in vivo are still lacking. We propose here a probabilistic tractographic atlas of the main WM tracts in the healthy rat brain based on in vivo DTI acquisition. Our study was carried out on 10 adult female Sprague-Dawley rats using a 7T preclinical scanner. The MRI protocol permitted a reliable reconstruction of the main rat brain bundles: corpus callosum, cingulum, external capsule, internal capsule, anterior commissure, optic tract. The reconstructed fibers were compared with histological data, proving the viability of in vivo DTI tractography in the rat brain with the proposed acquisition and processing protocol. All the data were registered to a rat brain template in the coordinate system of the commonly used atlas by Paxinos and Watson; then the individual tracts were binarized and averaged, obtaining a probabilistic atlas in Paxinos-Watson space of the main rat brain WM bundles. With respect to the recent high-resolution MRI atlases, the resulting tractographic atlas, available online, provides complementary information about the average anatomical position of the considered WM tracts and their variability between normal animals. Furthermore, reference values for the main DTI-derived parameters, mean diffusivity and fractional anisotropy, were provided. Both these results can be used as references in preclinical studies on pathological rat models involving potential alterations of WM. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. The cerefy brain atlases: continuous enhancement of the electronic talairach-tournoux brain atlas.

    PubMed

    Nowinski, Wieslaw L

    2005-01-01

    The Talairach-Tournoux (TT) atlas is probably the most often used brain atlas. We overview briefly the activities in developments of electronic versions of the TT atlas and focus on our more than 10-yr efforts in its continuous enhancement resulting in three main versions: TT-1997, TT-2000, and TT-2004. The recent TT-2004 version is substantially improved over the digitized print original with a higher structure parcellation, better quality and resolution of individual structures, and improved three-dimensional (3D) spatial consistency. It is also much more suitable for developing atlas-based applications owing to pure color-coding (for automatic structure labeling), contour representation (to avoid scan blocking by the overlaid atlas), and color cross-atlas consistency (for the simultaneous use of multiple atlases). We also provide a procedure for 3D spatial consistency improvement and illustrate its use. Finally, we present some of our latest atlas-assisted applications for fast and automatic interpretation of morphological, stroke, and molecular images, and discuss the future steps in TT atlas enhancement.

  2. 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.

  3. Onboard Photo: ATLAS Payload in Cargo Bay

    NASA Technical Reports Server (NTRS)

    1994-01-01

    This is an STS-66 mission onboard photo showing the Remote Manipulator System (RMS) moving toward one of the solar science instruments for the third Atmospheric Laboratory for Applications and Science (ATLAS-3) mission in the cargo bay of the Orbiter Atlantis. During the ATLAS missions, international teams of scientists representing many disciplines combined their expertise to seek answers to complex questions about the atmospheric and solar conditions that sustain life on Earth. The ATLAS program specifically investigated how Earth's middle and upper atmospheres and climate are affected by by the sun and by products of industrial and agricultural activities on Earth. Thirteen ATLAS instruments supported experiments in atmospheric sciences, solar physics, space plasma physics, and astronomy. The instruments were mounted on two Spacelab pallets in the Space Shuttle payload bay. The ATLAS-3 mission continued a variety of atmospheric and solar studies, to improve understanding of the Earth's atmosphere and its energy input from the sun. A key scientific objective was to refine existing data on variations in the fragile ozone layer of the atmosphere. The Shuttle Orbiter Atlantis was launched on November 3, 1994 for the ATLAS-3 mission (STS-66). The ATLAS program was managed by the Marshall Space Flight Center.

  4. An MRI Von Economo - Koskinas atlas.

    PubMed

    Scholtens, Lianne H; de Reus, Marcel A; de Lange, Siemon C; Schmidt, Ruben; van den Heuvel, Martijn P

    2016-12-28

    The cerebral cortex displays substantial variation in cellular architecture, a regional patterning that has been of great interest to anatomists for centuries. In 1925, Constantin von Economo and George Koskinas published a detailed atlas of the human cerebral cortex, describing a cytoarchitectonic division of the cortical mantle into over 40 distinct areas. Von Economo and Koskinas accompanied their seminal work with large photomicrographic plates of their histological slides, together with tables containing for each described region detailed morphological layer-specific information on neuronal count, neuron size and thickness of the cortical mantle. Here, we aimed to make this legacy data accessible and relatable to in vivo neuroimaging data by constructing a digital Von Economo - Koskinas atlas compatible with the widely used FreeSurfer software suite. In this technical note we describe the procedures used for manual segmentation of the Von Economo - Koskinas atlas onto individual T1 scans and the subsequent construction of the digital atlas. We provide the files needed to run the atlas on new FreeSurfer data, together with some simple code of how to apply the atlas to T1 scans within the FreeSurfer software suite. The digital Von Economo - Koskinas atlas is easily applicable to modern day anatomical MRI data and is made publicly available online.

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

    PubMed

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

    2017-01-15

    Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. The FoldAtlas website can be accessed at www.foldatlas.com Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  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. 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.

  8. 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.

  9. An extensible infrastructure for querying and mining event-level metadata in ATLAS

    NASA Astrophysics Data System (ADS)

    Malon, D.; Cranshaw, J.; Zhang, Q.

    2012-12-01

    The ATLAS event-level metadata infrastructure supports applications that range from data quality monitoring, anomaly detection, and fast physics monitoring to event-level selection and navigation to file-resident event data at any processing stage, from raw through analysis object data, in globally distributed analysis. A central component of the infrastructure is a distributed TAG database, which contains event-level metadata records for all ATLAS events, real and simulated. This resource offers a unique global view of ATLAS data, and provides an opportunity, not only for stream-style mining of event data, but also for an examination of data across streams, across runs, and across (re)processings. The TAG database serves as a natural locus for run-level and processing-level integrity checks, for investigations of event duplication and other issues in the trigger and offline systems, for questions about stream overlap, for queries about interesting but out-of-stream events, for statistics, and more. In early ATLAS running, such database queries were largely ad hoc, and were handled manually. In this paper, we describe an extensible infrastructure for addressing these and other use cases during upload and post-upload processing, and discuss some of the uses to which this infrastructure has been applied.

  10. 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.

  11. GOES-R Atlas V Solid Rocket Motor (SRM) Lift and Mate

    NASA Image and Video Library

    2016-10-27

    A United Launch Alliance (ULA) technician inspects the solid rocket motor for the ULA Atlas V rocket on its transporter near the Vertical Integration Facility at Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida. The solid rocket motor will be lifted and mated to the rocket in preparation for the launch of NOAA's Geostationary Operational Environmental Satellite (GOES-R) this month. GOES-R is the first satellite in a series of next-generation NOAA GOES Satellites.

  12. 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

  13. Bronchopulmonary segments approximation using anatomical atlas

    NASA Astrophysics Data System (ADS)

    Busayarat, Sata; Zrimec, Tatjana

    2007-03-01

    Bronchopulmonary segments are valuable as they give more accurate localization than lung lobes. Traditionally, determining the segments requires segmentation and identification of segmental bronchi, which, in turn, require volumetric imaging data. In this paper, we present a method for approximating the bronchopulmonary segments for sparse data by effectively using an anatomical atlas. The atlas is constructed from a volumetric data and contains accurate information about bronchopulmonary segments. A new ray-tracing based image registration is used for transferring the information from the atlas to a query image. Results show that the method is able to approximate the segments on sparse HRCT data with slice gap up to 25 millimeters.

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

    PubMed

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

    2015-03-20

    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.

  15. 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

  16. Phylogeography of North African Atlas cedar (Cedrus atlantica, Pinaceae): Combined molecular and fossil data reveal a complex Quaternary history.

    PubMed

    Terrab, Anass; Hampe, Arndt; Lepais, Olivier; Talavera, Salvador; Vela, Errol; Stuessy, Tod F

    2008-10-01

    Northwest Africa is a major hotspot of plant biodiversity, but very little is known about the Quaternary range dynamics of plant species in this region. Here we investigate the range-wide population structure and phylogeography of Atlas cedar (Cedrus atlantica), an emblematic forest tree endemic to Morocco and Algeria. We genotyped 261 individuals from 11 populations using AFLP markers. Data were analyzed using both conventional F(ST)-based techniques and Bayesian clustering. Overall population differentiation was high (F(ST) = 0.25). Two major groups of populations were identified, one distributed through the Rif and Middle Atlas mountains in Morocco and the other through the Algerian Tell Atlas and Aurès mountains as well as the Middle Atlas. Combined molecular and fossil data indicate that C. atlantica survived the Last Glacial Maximum in at least three disjunct refugia along the coast of the Mediterranean Sea, whereas the Middle Atlas, today the core of the species range, has been colonized relatively recently (<10000 yr BP). The colonization history of individual populations has left clear imprints in their present-day diversity, which may vary greatly even between nearby stands. Our study illustrates how integrating different data sources and analytical approaches can help elucidate complex range dynamics that would otherwise remain undeciphered.

  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. Optical development system lab alignment solutions for the ICESat-2 ATLAS instrument

    NASA Astrophysics Data System (ADS)

    Evans, T.

    The ATLAS Instrument for the ICESat-2 mission at NASA's Goddard Space Flight Center requires an alignment test-bed to prove out new concepts. The Optical Development System (ODS) lab was created to test prototype models of individual instrument components to simulate how they will act as a system. The main ICESat-2 instrument is the Advanced Topographic Laser Altimeter System (ATLAS). It measures ice elevation by transmitting laser pulses, and collecting the reflection in a telescope. Because the round trip time is used to calculate distance, alignment between the outgoing transmitter beam and the incoming receiver beams are critical. An automated closed loop monitoring control system is currently being tested at the prototype level to prove out implementation for the final spacecraft. To achieve an error of less than 2 micro-radians, an active deformable mirror was used to correct the lab wave front from the collimated “ ground reflection” beam. The lab includes a focal plane assembly set up, a one meter diameter collimator optic, and a 0.8 meter flight spare telescope for alignment. ATLAS prototypes and engineering models of transmitter and receiver optics and sub-systems are brought in to develop and integrate systems as well as write procedures to be used in integration and testing. By having a fully integrated system with prototypes and engineering units, lessons can be learned before flight designs are finalized.

  19. Multi-atlas based segmentation of brain images: atlas selection and its effect on accuracy.

    PubMed

    Aljabar, P; Heckemann, R A; Hammers, A; Hajnal, J V; Rueckert, D

    2009-07-01

    Quantitative research in neuroimaging often relies on anatomical segmentation of human brain MR images. Recent multi-atlas based approaches provide highly accurate structural segmentations of the brain by propagating manual delineations from multiple atlases in a database to a query subject and combining them. The atlas databases which can be used for these purposes are growing steadily. We present a framework to address the consequent problems of scale in multi-atlas segmentation. We show that selecting a custom subset of atlases for each query subject provides more accurate subcortical segmentations than those given by non-selective combination of random atlas subsets. Using a database of 275 atlases, we tested an image-based similarity criterion as well as a demographic criterion (age) in a leave-one-out cross-validation study. Using a custom ranking of the database for each subject, we combined a varying number n of atlases from the top of the ranked list. The resulting segmentations were compared with manual reference segmentations using Dice overlap. Image-based selection provided better segmentations than random subsets (mean Dice overlap 0.854 vs. 0.811 for the estimated optimal subset size, n=20). Age-based selection resulted in a similar marked improvement. We conclude that selecting atlases from large databases for atlas-based brain image segmentation improves the accuracy of the segmentations achieved. We show that image similarity is a suitable selection criterion and give results based on selecting atlases by age that demonstrate the value of meta-information for selection.

  20. Distributed data analysis in ATLAS

    NASA Astrophysics Data System (ADS)

    Nilsson, Paul; Atlas Collaboration

    2012-12-01

    Data analysis using grid resources is one of the fundamental challenges to be addressed before the start of LHC data taking. The ATLAS detector will produce petabytes of data per year, and roughly one thousand users will need to run physics analyses on this data. Appropriate user interfaces and helper applications have been made available to ensure that the grid resources can be used without requiring expertise in grid technology. These tools enlarge the number of grid users from a few production administrators to potentially all participating physicists. ATLAS makes use of three grid infrastructures for the distributed analysis: the EGEE sites, the Open Science Grid, and Nordu Grid. These grids are managed by the gLite workload management system, the PanDA workload management system, and ARC middleware; many sites can be accessed via both the gLite WMS and PanDA. Users can choose between two front-end tools to access the distributed resources. Ganga is a tool co-developed with LHCb to provide a common interface to the multitude of execution backends (local, batch, and grid). The PanDA workload management system provides a set of utilities called PanDA Client; with these tools users can easily submit Athena analysis jobs to the PanDA-managed resources. Distributed data is managed by Don Quixote 2, a system developed by ATLAS; DQ2 is used to replicate datasets according to the data distribution policies and maintains a central catalog of file locations. The operation of the grid resources is continually monitored by the Ganga Robot functional testing system, and infrequent site stress tests are performed using the Hammer Cloud system. In addition, the DAST shift team is a group of power users who take shifts to provide distributed analysis user support; this team has effectively relieved the burden of support from the developers.

  1. EnviroAtlas - New York, NY - Block Groups

    EPA Pesticide Factsheets

    This EnviroAtlas dataset is the base layer for the New York, NY EnviroAtlas community. The block groups are from the US Census Bureau and are included/excluded based on EnviroAtlas criteria described in the procedure log. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  2. Electroweak diboson production at ATLAS

    NASA Astrophysics Data System (ADS)

    Solodkov, A.; Atlas Collaboration

    2017-07-01

    This paper is giving an overview of recent ATLAS results on the production cross sections of gauge boson pairs decaying leptonically using data from pp collisions at √{s} = 13{ TeV} for ZZ and at √{s} = 8{ TeV} for W^{±}Z and W^{±}W^{±} at the LHC at CERN. The cross sections are found to be in agreement with the expectations from the Standard Model within the estimated uncertainties. The production cross section measurements also allow for studies of anomalous triple and quartic gauge couplings for which 95% confidence level limits are set.

  3. The IRAS Galaxy Atlas (IGA)

    NASA Technical Reports Server (NTRS)

    Prince, Thomas A.; Oliversen, R. (Technical Monitor)

    1999-01-01

    In 1993 we proposed a project to NASA having the goal of producing a new infrared map of our Galaxy. In particular, we proposed to reprocess the IRAS data taken in the early 1980's using modern image processing algorithms and the large Intel parallel computers of the Center for Advanced Computing Research, (at that time called the Caltech Concurrent Supercomputing Facilities - CCSF). The rationale was simple: what took approximately 100 days on a typical workstation would take less than a day on the multi-processor parallel computers, thus making a high-resolution infrared atlas of the Galaxy feasible.

  4. The ATLAS IBL BOC prototype

    NASA Astrophysics Data System (ADS)

    Schroer, N.

    2011-12-01

    The Pixel Detector of the ATLAS experiment at CERN will be upgraded with an Insertable B-Layer (IBL) in 2013. To handle the data readout the currently used VME card pairs consisting of a back of crate card (BOC) and a read out driver (ROD) are being redesigned. This paper presents details of the hardware design of the new BOC prototype, which takes advantage from modern FPGA technology and commercial optical modules and abandons the need for a variety of custom components used on the old card. Also the throughput is four times higher and additional features are implemented.

  5. Electroweak diboson production at ATLAS

    NASA Astrophysics Data System (ADS)

    Solodkov, A. A.

    2017-09-01

    This paper is giving an overview of recent ATLAS results on the production cross sections of gauge boson pairs decaying leptonically using data from pp collisions at √ s = 13 TeV for ZZ and at √ s = 8 TeV for W ± Z and W ± W ± at the LHC at CERN. The cross sections are found to be in agreement with the expectations from the Standard Model within the estimated uncertainties. The production cross section measurements also allow for studies of anomalous triple and quartic gauge couplings for which 95% confidence level limits are set.

  6. 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.

  7. Probabilistic brain atlas encoding using Bayesian inference.

    PubMed

    Van Leemput, Koen

    2006-01-01

    This paper addresses the problem of creating probabilistic brain atlases from manually labeled training data. We propose a general mesh-based atlas representation, and compare different atlas models by evaluating their posterior probabilities and the posterior probabilities of their parameters. Using such a Baysian framework, we show that the widely used "average" brain atlases constitute relatively poor priors, partly because they tend to overfit the training data, and partly because they do not allow to align corresponding anatomical features across datasets. We also demonstrate that much more powerful representations can be built using content-adaptive meshes that incorporate non-rigid deformation field models. We believe extracting optimal prior probability distributions from training data is crucial in light of the central role priors play in many automated brain MRI analysis techniques.

  8. 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.

  9. 27 CFR 9.140 - Atlas Peak.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...). (c) Boundaries. The Atlas Peak viticultural area is located in Napa County, California. It lies entirely within the Napa Valley viticultural area. The beginning point is Haystack (peak) found in...

  10. Upgrading the ATLAS fast calorimeter simulation

    NASA Astrophysics Data System (ADS)

    Hubacek, Z.; ATLAS Collaboration

    2016-10-01

    Many physics and performance studies with the ATLAS detector at the Large Hadron Collider require very large samples of simulated events, and producing these using the full Geant4 detector simulation is highly CPU intensive. Often, a very detailed detector simulation is not needed, and in these cases fast simulation tools can be used to reduce the calorimeter simulation time. In ATLAS, a fast simulation of the calorimeter systems was developed, called Fast Calorimeter Simulation (FastCaloSim). It provides a parametrized simulation of the particle energy response at the calorimeter read-out cell level. It is interfaced to the standard ATLAS digitization and reconstruction software and can be tuned to data more easily than Geant4. An improved parametrization is being developed, to eventually address shortcomings of the original version. It makes use of statistical techniques such as principal component analysis and a neural network parametrization to optimise the amount of information to store in the ATLAS simulation infrastructure.

  11. Kingdom of Saudi Arabia Solar Radiation Atlas

    SciTech Connect

    NREL

    1998-12-16

    This atlas provides a record of monthly mean solar radiation generated by a Climatological Solar Radiation model, using quasi-climatological inputs of cloud cover, aerosol optical depth, precipitable water vapor, ozone, surface albedo, and atmospheric pressure.

  12. Mini-atlas of the marmoset brain.

    PubMed

    Senoo, Aya; Tokuno, Hironobu; Watson, Charles

    2015-04-01

    A mini-atlas of the brain is designed to help students and young researchers who are not familiar with neuroanatomy. In the mini-atlas, a limited number of important nuclei and fiber tracts are shown on a small number of brain sections from posterior end to the anterior end of the brain. The first mini-atlas was introduced for the rat brain (Watson et al., 2010). Here we present a mini-atlas of the common marmoset (Callithrix jaccus), which is one of representative experimental primates for modern neuroscience. We further discuss the differences of brain structures between rodents and primates. Copyright © 2015 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. Observations of ATLAS17gzd/AT2017esf with GREAT (GRond-Epessto-ATlas)

    NASA Astrophysics Data System (ADS)

    Chen, T.-W.; Schady, P.; Kruehler, T.; Wiseman, P.; Schweyer, T.; Yates, R. M.; Bolmer, J.; Smartt, S. J.; Smith, K. W.; Young, D.; Inserra, C.; Maguire, K.; Kankare, E.; Sullivan, M.; Valenti, S.; Tonry, O. Yaron J.; Stalder, B.; Denneau, L.; Heinze, A.; Weiland, H.; Rest, A.

    2017-06-01

    The ''GREAT'' (GRond-Epessto-ATlas) survey of early superluminous supernova bumps project is a broad collaboration mainly coordinated by members of the GROND (Greiner et al. 2008, PASP 120, 405), ePESSTO (Smartt et al. 2015 A & A, 579, 40; www.pessto.org) and ATLAS team (Tonry et al. 2011, PASP, 123, 58; Tonry et al. ATel #8680).

  18. Supervised method to build an atlas database for multi-atlas segmentation-propagation

    NASA Astrophysics Data System (ADS)

    Shen, Kaikai; Bourgeat, Pierrick; Fripp, Jurgen; Mériaudeau, Fabrice; Ames, David; Ellis, Kathryn A.; Masters, Colin L.; Villemagne, Victor L.; Rowe, Christopher C.; Salvado, Olivier

    2010-03-01

    Multiatlas based segmentation-propagation approaches have been shown to obtain accurate parcelation of brain structures. However, this approach requires a large number of manually delineated atlases, which are often not available. We propose a supervised method to build a population specific atlas database, using the publicly available Internet Brain Segmentation Repository (IBSR). The set of atlases grows iteratively as new atlases are added, so that its segmentation capability may be enhanced in the multiatlas based approach. Using a dataset of 210 MR images of elderly subjects (170 elderly control, 40 Alzheimer's disease) from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study, 40 MR images were segmented to build a population specific atlas database for the purpose of multiatlas segmentation-propagation. The population specific atlases were used to segment the elderly population of 210 MR images, and were evaluated in terms of the agreement among the propagated labels. The agreement was measured by using the entropy H of the probability image produced when fused by voting rule and the partial moment μ2 of the histogram. Compared with using IBSR atlases, the population specific atlases obtained a higher agreement when dealing with images of elderly subjects.

  19. 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.

  20. 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.

  1. 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.

  2. A high-resolution anatomical rat atlas

    PubMed Central

    Bai, Xueling; Yu, Li; Liu, Qian; Zhang, Jie; Li, Anan; Han, Dao; Luo, Qingming; Gong, Hui

    2006-01-01

    This paper reports the availability of a high-resolution atlas of the adult rat. The atlas is composed of 9475 cryosectional images captured in 4600 × 2580 × 24-bit TIFF format, constructed using serial cryosection-milling techniques. Cryosection images were segmented, labelled and reconstructed into three-dimensional (3D) computerized models. These images, 3D models, technical details, relevant software and further information are available at our website, http://vchibp.vicp.net/vch/mice/. PMID:17062027

  3. MERCURY-ATLAS (MA)-2 - LIFTOFF - CAPE

    NASA Image and Video Library

    1961-02-21

    S61-01226 (21 Feb. 1961) --- Launch of the unmanned Mercury-Atlas 2 (MA-2) vehicle for a suborbital test flight of the Mercury capsule. The upper part of Atlas is stengthened by an eight-inch wide stainless steel band. The capsule was recovered less than one hour after launch. The altitude was 108 miles. Speed was 13,000 mph. Recovered 1,425 miles downrange. Photo credit: NASA

  4. 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.

  5. 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.

  6. The calibration of the resistive plate chambers of ATLAS

    NASA Astrophysics Data System (ADS)

    Di Simone, Andrea

    2010-04-01

    Resistive Plate Chambers (RPC) are used in ATLAS to provide the first level muon trigger in the barrel region. The total size of the system is about 16000 m2 readout by about 350000 electronic channels. To reach the needed trigger performance, a precise knowledge of the detector working point (from the point of view of both high and low voltage settings) is necessary and the high number of readout channels calls for severe requirements on the analysis tools. First of all, high-statistics data samples will have to be used as input. Second, the results would me unmanageable without a proper interface to some database technology. Moreover, the CPU power needed for the analysis makes it necessary to use distributed computing resources. A set of analysis tools will be presented, coping with all the critical aspects of this task, ranging from the use of a dedicated data stream (the so-called muon calibration stream), to the automatic job submission on the GRID, to the implementation of an interface to the conditions database of ATLAS. The integration with Detector Control System information and the impact of the calibration on the performance of the reconstruction algorithms will be discussed as well.

  7. ATLAS Liquid Argon Endcap Calorimeter R&D for sLHC

    NASA Astrophysics Data System (ADS)

    Schacht, P.

    2010-04-01

    The performance of the ATLAS liquid argon endcap has been studied for luminosities as expected for the operation at sLHC. The increase of integrated luminosity by a factor of ten has serious consequences for the signal reconstruction, radiation hardness requirements and operations of the forward liquid argon calorimeters. The response has been studied with small modules of the type as built for ATLAS in a very high intensity beam at IHEP/Protvino. The highest intensity obtained was well above the level of energy impact expected for ATLAS at sLHC. The signal processing of the ATLAS Hadronic Endcap Calorimeter employs the concept of 'active pads' which keep the detector capacities at the input of the amplifiers small and thereby achieves a fast rise time of the signal. This concept is realized using highly integrated amplifier and summing chips in GaAs technology. With an increase of luminosity by a factor of ten the safety factor for the radiation hardness is essentially eliminated. Therefore new, more radiation hard technologies have been studied: SiGe bipolar, Si CMOS FET and GaAs FET transistors have been irradiated with neutrons up to an integrated fluence of 2.2 × 1016n/cm2. All technologies exceed the limit required for the radiation hardness for the operation at sLHC of 2 × 1015n/cm2. The temperature dependence of the gain has been studied as well. Here the bipolar technologies - in contrast to CMOS - need an adjustment of the operation point when going from room temperature to liquid nitrogen temperature.

  8. The fiber optic system for the Advanced Topographic Laser Altimeter System (ATLAS) instrument

    PubMed Central

    Ott, Melanie N.; Thomes, Joe; Onuma, Eleanya; Switzer, Robert; Chuska, Richard; Blair, Diana; Frese, Erich; Matyseck, Marc

    2017-01-01

    The Advanced Topographic Laser Altimeter System (ATLAS) Instrument has been in integration and testing over the past 18 months in preparation for the Ice, Cloud and Land Elevation Satellite – 2 (ICESat-2) Mission, scheduled to launch in 2017. ICESat-2 is the follow on to ICESat which launched in 2003 and operated until 2009. ATLAS will measure the elevation of ice sheets, glaciers and sea ice or the “cryosphere” (as well as terrain) to provide data for assessing the earth’s global climate changes. Where ICESat’s instrument, the Geo-Science Laser Altimeter (GLAS) used a single beam measured with a 70 m spot on the ground and a distance between spots of 170 m, ATLAS will measure a spot size of 10 m with a spacing of 70 cm using six beams to measure terrain height changes as small as 4 mm.[1] The ATLAS pulsed transmission system consists of two lasers operating at 532 nm with transmitter optics for beam steering, a diffractive optical element that splits the signal into 6 separate beams, receivers for start pulse detection and a wavelength tracking system. The optical receiver telescope system consists of optics that focus all six beams into optical fibers that feed a filter system that transmits the signal via fiber assemblies to the detectors. Also included on the instrument is a system that calibrates the alignment of the transmitted pulses to the receiver optics for precise signal capture. The larger electro optical subsystems for transmission, calibration, and signal receive, stay aligned and transmitting sufficiently due to the optical fiber system that links them together. The robust design of the fiber optic system, consisting of a variety of multi fiber arrays and simplex assemblies with multiple fiber core sizes and types, will enable the system to maintain consistent critical alignments for the entire life of the mission. Some of the development approaches used to meet the challenging optical system requirements for ATLAS are discussed here. PMID

  9. High-precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization.

    PubMed

    Marquart, Gregory D; Tabor, Kathryn M; Horstick, Eric J; Brown, Mary; Geoca, Alexandra K; Polys, Nicholas F; Nogare, Damian Dalle; Burgess, Harold A

    2017-08-01

    Atlases provide a framework for spatially mapping information from diverse sources into a common reference space. Specifically, brain atlases allow annotation of gene expression, cell morphology, connectivity, and activity. In larval zebrafish, advances in genetics, imaging, and computational methods now allow the collection of such information brain-wide. However, due to technical considerations, disparate datasets may use different references and may not be aligned to the same coordinate space. Two recent larval zebrafish atlases exemplify this problem: Z-Brain, containing gene expression, neural activity, and neuroanatomical segmentations, was acquired using immunohistochemical stains, while the Zebrafish Brain Browser (ZBB) was constructed from live scans of fluorescent reporters in transgenic larvae. Although different references were used, the atlases included several common transgenic patterns that provide potential "bridges" for transforming each into the other's coordinate space. We tested multiple bridging channels and registration algorithms and found that the symmetric diffeomorphic normalization algorithm improved live brain registration precision while better preserving cell morphology than B-spline-based registrations. Symmetric diffeomorphic normalization also corrected for tissue distortion introduced during fixation. Multi-reference channel optimization provided a transformation that enabled Z-Brain and ZBB to be co-aligned with precision of approximately a single cell diameter and minimal perturbation of cell and tissue morphology. Finally, we developed software to visualize brain regions in 3 dimensions, including a virtual reality neuroanatomy explorer. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate reference templates and acquisition protocols, when sufficient information is present for bridging. Increased accuracy and interoperability of zebrafish digital brain atlases will facilitate

  10. The Fiber Optic System for the Advanced Topographic Laser Altimeter System (ATLAS) Instrument

    NASA Technical Reports Server (NTRS)

    Ott, Melanie N.; Thomes, Joe; Onuma, Eleanya; Switzer, Robert; Chuska, Richard; Blair, Diana; Frese, Erich; Matyseck, Marc

    2016-01-01

    The Advanced Topographic Laser Altimeter System (ATLAS) Instrument has been in integration and testing over the past 18 months in preparation for the Ice, Cloud and Land Elevation Satellite - 2 (ICESat-2) Mission, scheduled to launch in 2017. ICESat-2 is the follow on to ICESat which launched in 2003 and operated until 2009. ATLAS will measure the elevation of ice sheets, glaciers and sea ice or the "cryosphere" (as well as terrain) to provide data for assessing the earth's global climate changes. Where ICESat's instrument, the Geo-Science Laser Altimeter (GLAS) used a single beam measured with a 70 m spot on the ground and a distance between spots of 170 m, ATLAS will measure a spot size of 10 m with a spacing of 70 cm using six beams to measure terrain height changes as small as 4 mm. The ATLAS pulsed transmission system consists of two lasers operating at 532 nm with transmitter optics for beam steering, a diffractive optical element that splits the signal into 6 separate beams, receivers for start pulse detection and a wavelength tracking system. The optical receiver telescope system consists of optics that focus all six beams into optical fibers that feed a filter system that transmits the signal via fiber assemblies to the detectors. Also included on the instrument is a system that calibrates the alignment of the transmitted pulses to the receiver optics for precise signal capture. The larger electro optical subsystems for transmission, calibration, and signal receive, stay aligned and transmitting sufficiently due to the optical fiber system that links them together. The robust design of the fiber optic system, consisting of a variety of multi fiber arrays and simplex assemblies with multiple fiber core sizes and types, will enable the system to maintain consistent critical alignments for the entire life of the mission. Some of the development approaches used to meet the challenging optical system requirements for ATLAS are discussed here.

  11. The fiber optic system for the Advanced Topographic Laser Altimeter System (ATLAS) instrument.

    PubMed

    Ott, Melanie N; Thomes, Joe; Onuma, Eleanya; Switzer, Robert; Chuska, Richard; Blair, Diana; Frese, Erich; Matyseck, Marc

    2016-08-28

    The Advanced Topographic Laser Altimeter System (ATLAS) Instrument has been in integration and testing over the past 18 months in preparation for the Ice, Cloud and Land Elevation Satellite - 2 (ICESat-2) Mission, scheduled to launch in 2017. ICESat-2 is the follow on to ICESat which launched in 2003 and operated until 2009. ATLAS will measure the elevation of ice sheets, glaciers and sea ice or the "cryosphere" (as well as terrain) to provide data for assessing the earth's global climate changes. Where ICESat's instrument, the Geo-Science Laser Altimeter (GLAS) used a single beam measured with a 70 m spot on the ground and a distance between spots of 170 m, ATLAS will measure a spot size of 10 m with a spacing of 70 cm using six beams to measure terrain height changes as small as 4 mm.[1] The ATLAS pulsed transmission system consists of two lasers operating at 532 nm with transmitter optics for beam steering, a diffractive optical element that splits the signal into 6 separate beams, receivers for start pulse detection and a wavelength tracking system. The optical receiver telescope system consists of optics that focus all six beams into optical fibers that feed a filter system that transmits the signal via fiber assemblies to the detectors. Also included on the instrument is a system that calibrates the alignment of the transmitted pulses to the receiver optics for precise signal capture. The larger electro optical subsystems for transmission, calibration, and signal receive, stay aligned and transmitting sufficiently due to the optical fiber system that links them together. The robust design of the fiber optic system, consisting of a variety of multi fiber arrays and simplex assemblies with multiple fiber core sizes and types, will enable the system to maintain consistent critical alignments for the entire life of the mission. Some of the development approaches used to meet the challenging optical system requirements for ATLAS are discussed here.

  12. 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).

  13. The fiber optic system for the advanced topographic laser altimeter system instrument (ATLAS)

    NASA Astrophysics Data System (ADS)

    Ott, Melanie N.; Thomes, W. Joe; Onuma, Eleanya; Switzer, Robert; Chuska, Richard; Blair, Diana; Frese, Erich; Matyseck, Marc

    2016-09-01

    The Advanced Topographic Laser Altimeter System (ATLAS) Instrument has been in integration and testing over the past 18 months in preparation for the Ice, Cloud and Land Elevation Satellite - 2 (ICESat-2) Mission, scheduled to launch in 2017. ICESat-2 is the follow on to ICESat which launched in 2003 and operated until 2009. ATLAS will measure the elevation of ice sheets, glaciers and sea ice or the "cryosphere" (as well as terrain) to provide data for assessing the earth's global climate changes. Where ICESat's instrument, the Geo-Science Laser Altimeter (GLAS) used a single beam measured with a 70 m spot on the ground and a distance between spots of 170 m, ATLAS will measure a spot size of 10 m with a spacing of 70 cm using six beams to measure terrain height changes as small as 4 mm.[1] The ATLAS pulsed transmission system consists of two lasers operating at 532 nm with transmitter optics for beam steering, a diffractive optical element that splits the signal into 6 separate beams, receivers for start pulse detection and a wavelength tracking system. The optical receiver telescope system consists of optics that focus all six beams into optical fibers that feed a filter system that transmits the signal via fiber assemblies to the detectors. Also included on the instrument is a system that calibrates the alignment of the transmitted pulses to the receiver optics for precise signal capture. The larger electro optical subsystems for transmission, calibration, and signal receive, stay aligned and transmitting sufficiently due to the optical fiber system that links them together. The robust design of the fiber optic system, consisting of a variety of multi fiber arrays and simplex assemblies with multiple fiber core sizes and types, will enable the system to maintain consistent critical alignments for the entire life of the mission. Some of the development approaches used to meet the challenging optical system requirements for ATLAS are discussed here.

  14. Developing a Digital Atlas of Environmental Risks and Hazards.

    ERIC Educational Resources Information Center

    Thomas, Deborah S. K.; Mitchell, Jerry T.; Scott, Michael S.; Cutter, Susan L.

    1999-01-01

    Describes the development of "The South Carolina Atlas of Environmental Risks and Hazards," a digital atlas that provides people with information on environmental hazards in South Carolina. Discusses the content and navigation of the atlas and considers its utility for classroom instruction and public resource. (CMK)

  15. Onboard photo: STS-45 forward portion of Atlas-1

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Space Shuttle Atlantis (STS-45) onboard photo of Atmospheric Laboratory for Applications and Science (Atlas-1) module in open cargo bay. Atlas-1 pallets are back dropped against the Atlas Mountains. Taken over Mali in the western Sahara, shows dunes in the Iguidi Dune Sea.

  16. Planning the Next Generation of Regional Atlases: Input from Educators.

    ERIC Educational Resources Information Center

    Keller, C. Peter; And Others

    1995-01-01

    Maintains that regional atlases are an important educational tool that must be updated to remain current and valuable. Reports on a user survey among 123 Canadian geography teachers about content and design of atlases. Finds that teachers value simplicity and up-to-date information and not CD-ROM atlases. (CFR)

  17. Statistical atlas construction via weighted functional boxplots.

    PubMed

    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

    2014-05-01

    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.

  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. 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

  20. A digital atlas of the dog brain.

    PubMed

    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).

  1. The Associative Memory System Infrastructures for the ATLAS Fast Tracker

    NASA Astrophysics Data System (ADS)

    Sotiropoulou, C.-L.; Maznas, I.; Citraro, S.; Annovi, A.; Ancu, L. S.; Beccherle, R.; Bertolucci, F.; Biesuz, N.; Calabrò, D.; Crescioli, F.; Dimas, D.; Dell'Orso, M.; Donati, S.; Gentsos, C.; Giannetti, P.; Gkaitatzis, S.; Gramling, J.; Greco, V.; Kalaitzidis, P.; Kordas, K.; Kimura, N.; Kubota, T.; Iovene, A.; Lanza, A.; Luciano, P.; Magnin, B.; Mermikli, K.; Nasimi, H.; Negri, A.; Nikolaidis, S.; Piendibene, M.; Sakellariou, A.; Sampsonidis, D.; Volpi, G.

    2017-06-01

    The associative memory (AM) system of fast tracker (FTK) processor has been designed for the tracking trigger upgrade to the ATLAS detector at the Conseil Europeen Pour La Recherche Nucleaire large hadron collider. The system performs pattern matching (PM) using the detector hits of particles in the ATLAS silicon tracker. The AM system is the main processing element of FTK and is mainly based on the use of application-specified integrated circuits (ASICs) (AM chips) designed to execute PM with a high degree of parallelism. It finds track candidates at low resolution which become seeds for a full resolution track fitting. The AM system implementation is based on a collection of large 9U Versa Module Europa (VME) boards, named “serial link processors” (AMBSLPs). On these boards, a huge traffic of data is implemented on a network of 900 2-Gb/s serial links. The complete AM-based processor consumes much less power ( 50 kW) than its CPU equivalent and its size is much smaller. The AMBSLP has a power consumption of 250 W and there will be 16 of them in a crate. This results in unusually large power consumption for a VME crate and the need for complex custom infrastructure in order to have sufficient cooling. This paper reports on the design and testing of the infrastructures needed to run and cool the system which will include 16 AMBSLPs in the same crate, the integration of the AMBSLP inside a first FTK slice, the performance of the produced prototypes (both hardware and firmware), as well as their tests in the global FTK integration. This is an important milestone to be satisfied before the FTK production.

  2. ATLAS Virtual Visits: bringing the world into the ATLAS control room

    NASA Astrophysics Data System (ADS)

    Goldfarb, Steven; Yacoob, Sahal; ATLAS Experiment

    2016-04-01

    ATLAS Virtual Visits is a project initiated in 2011 for the Education & Outreach program of the ATLAS Experiment at CERN [1]. Its goal is to promote public appreciation of the LHC physics program and particle physics, in general, through direct dialogue between ATLAS physicists and remote audiences. A Virtual Visit is an IP-based videoconference, coupled with a public webcast and video recording, between ATLAS physicists and remote locations around the world, that typically include high school or university classrooms, Masterclasses, science fairs, or other special events, usually hosted by collaboration members. Over the past two years, more than 10,000 people, from all of the world's continents, have actively participated in ATLAS Virtual Visits, with many more enjoying the experience from the publicly available webcasts and recordings. We present an overview of our experience and discuss potential development for the future.

  3. 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…

  4. 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…

  5. 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

  6. ATLAS Versus NextGen Model Atmospheres: A Combined Analysis of Synthetic Spectral Energy Distributions

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.; Chávez, M.; Rodríguez-Merino, L. H.

    2004-08-01

    We carried out a critical appraisal of the two theoretical models, Kurucz' ATLAS9 and PHOENIX/NextGen, for stellar atmosphere synthesis. Our tests relied on the theoretical fit of spectral energy distributions (SEDs) for a sample of 334 target stars along the whole spectral-type sequence, from the classical optical catalogs of Gunn & Stryker and Jacoby et al. The best-fitting physical parameters (Teff, logg) of stars allowed an independent calibration of the temperature and bolometric scale versus empirical classification parameters (i.e., spectral type and MK luminosity class); in addition, the comparison of the synthetic templates from the ATLAS and NextGen grids allowed us to probe the capability of the models to match spectrophotometric properties of real stars and assess the impact of the different input physics. We can sketch the following main conclusions of our analysis: (1) Fitting accuracy of both theoretical libraries drastically degrades at low Teff at which both ATLAS and NextGen models still fail to properly account for the contribution of molecular features in the observed SED of K-M stars. (2) Compared with empirical calibrations, both ATLAS and NextGen fits tend, on average, to predict slightly warmer (by 4%-8%) Teff for both giant and dwarf stars of fixed spectral type, but ATLAS provides, in general, a sensibly better fit (a factor of 2 lower σ of flux residuals) than NextGen. (3) There is a striking tendency of NextGen to label target stars with an effective temperature and surface gravity higher than that of ATLAS. The effect is especially evident for MK I-III objects for which about one in four stars is clearly misclassified by NextGen in logg. This is a consequence of some ``degeneracy'' in the solution space, partly induced by the different input physics and geometry constraints in the computation of the integrated emerging flux (ATLAS model atmospheres assume standard plane-parallel layers, while NextGen adopts, for low-gravity stars, a

  7. 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.

  8. Beagle-2 landing site atlas

    NASA Astrophysics Data System (ADS)

    Michael, G.; Chicarro, A.; Rodionova, J.; Shevchenko, V.; Ilukhina, J.; Kozlova, K.

    2003-04-01

    The Beagle-2 lander of the Mars Express mission will come to rest on the surface of Isidis Planitia in late December 2003 to carry out a range of geochemistry and exobiology experi-ments. We are compiling an atlas of the presently available data products pertinent to the landing site at 11.6N 90.75E, which is intended for distribution both as a printed and an electronic resource. The atlas will include Viking and MOC-WA image mosaics, and a catalogue of high-resolution im-ages from MOC and THEMIS with location maps. There will be various MOLA topography-based products: colour-scaled, contoured, and shaded maps, slope, and detrended relief. Simulated camera panoramas from various potential landing locations may assist in determining the spacecraft’s position. Other maps, both raw, and in composites with image mosa-ics, will cover TES thermal inertia and spectroscopy, and Odyssey gamma and neutron spectroscopy. Maps at the scale of the Isidis context will additionally cover geology, tem-perature cycles, and atmospheric circulation. Sample are shown below.

  9. Experience with the gLite workload management system in ATLAS Monte Carlo production on LCG

    NASA Astrophysics Data System (ADS)

    Campana, S.; Rebatto, D.; Sciaba', A.

    2008-07-01

    The ATLAS experiment has been running continuous simulated events production since more than two years. A considerable fraction of the jobs is daily submitted and handled via the gLite Workload Management System, which overcomes several limitations of the previous LCG Resource Broker. The gLite WMS has been tested very intensively for the LHC experiments use cases for more than six months, both in terms of performance and reliability. The tests were carried out by the LCG Experiment Integration Support team (in close contact with the experiments) together with the EGEE integration and certification team and the gLite middleware developers. A pragmatic iterative and interactive approach allowed a very quick rollout of fixes and their rapid deployment, together with new functionalities, for the ATLAS production activities. The same approach is being adopted for other middleware components like the gLite and CREAM Computing Elements. In this contribution we will summarize the learning from the gLite WMS testing activity, pointing out the most important achievements and the open issues. In addition, we will present the current situation of the ATLAS simulated event production activity on the EGEE infrastructure based on the gLite WMS, showing the main improvements and benefits from the new middleware. Finally, the gLite WMS is being used by many other VOs, including the LHC experiments. In particular, some statistics will be shown on the CMS experience running WMS user analysis via the WMS

  10. The GALEX Ultraviolet Atlas of Nearby Galaxies

    NASA Astrophysics Data System (ADS)

    Gil de Paz, Armando; Boissier, Samuel; Madore, Barry F.; Seibert, Mark; Joe, Young H.; Boselli, Alessandro; Wyder, Ted K.; Thilker, David; Bianchi, Luciana; Rey, Soo-Chang; Rich, R. Michael; Barlow, Tom A.; Conrow, Tim; Forster, Karl; Friedman, Peter G.; Martin, D. Christopher; Morrissey, Patrick; Neff, Susan G.; Schiminovich, David; Small, Todd; Donas, José; Heckman, Timothy M.; Lee, Young-Wook; Milliard, Bruno; Szalay, Alex S.; Yi, Sukyoung

    2007-12-01

    We present images, integrated photometry, and surface-brightness and color profiles for a total of 1034 nearby galaxies recently observed by the Galaxy Evolution Explorer (GALEX) satellite in its far-ultraviolet (FUV; λeff=1516 Å) and near-ultraviolet (NUV; λeff=2267 Å) bands. Our catalog of objects is derived primarily from the GALEX Nearby Galaxies Survey (NGS) supplemented by galaxies larger than 1' in diameter serendipitously found in these fields and in other GALEX exposures of similar of greater depth. The sample analyzed here adequately describes the distribution and full range of properties (luminosity, color, star formation rate [SFR]) of galaxies in the local universe. From the surface brightness profiles obtained we have computed asymptotic magnitudes, colors, and luminosities, along with the concentration indices C31 and C42. We have also morphologically classified the UV surface brightness profiles according to their shape. This data set has been complemented with archival optical, near-infrared, and far-infrared fluxes and colors. We find that the integrated (FUV-K) color provides robust discrimination between elliptical and spiral/irregular galaxies and also among spiral galaxies of different subtypes. Elliptical galaxies with brighter K-band luminosities (i.e., more massive) are redder in (NUV-K) color but bluer in (FUV-NUV) (a color sensitive to the presence of a strong UV upturn) than less massive ellipticals. In the case of the spiral/irregular galaxies our analysis shows the presence of a relatively tight correlation between the (FUV-NUV) color (or, equivalently, the slope of the UV spectrum, β) and the total infrared-to-UV ratio. The correlation found between (FUV-NUV) color and K-band luminosity (with lower luminosity objects being bluer than more luminous ones) can be explained as due to an increase in the dust content with galaxy luminosity. The images in this Atlas along with the profiles and integrated properties are publicly

  11. The Atlas E/F launch vehicle - An unsung workhorse

    NASA Astrophysics Data System (ADS)

    Powell, J. W.; Richards, G. R.

    1991-05-01

    Over the 22 years ending in April 1990, the USAF and NASA used the 'E/F' version of the venerable Atlas ICBM for 39 launches, using 11 different upper-stage combinations. Beginning in 1983, a number of the Atlas E/F payloads were assigned to the Atlas H launch vehicle derived from the SLV-3D version of the NASA Atlas-Centaur. A complete Atlas E/F and H chronology is presented, in conjunction with a historical account of some of the most significant satellite payloads lofted by these launch vehicles.

  12. Intepretation of tomographic images using automatic atlas lookup

    NASA Astrophysics Data System (ADS)

    Schiemann, Thomas; Hoehne, Karl H.; Koch, Christoph; Pommert, Andreas; Riemer, Martin; Schubert, Rainer; Tiede, Ulf

    1994-09-01

    We describe a system that automates atlas look-up when viewing cross-sectional images at a viewing station. Using simple specification of landmarks a linear transformation to a volume based anatomical atlas is performed. As a result corresponding atlas pictures containing information about structures, function, or blood supply, or classical atlas pages (like Talairach) appear next to the patient data for any chosen slice. In addition the slices are visible in the 3D context of the VOXEL-MAN 3D atlas, providing all its functionality.

  13. The shunt-LDO regulator to power the upgraded ATLAS pixel detector

    NASA Astrophysics Data System (ADS)

    Gonella, L.; Barbero, M.; Hügging, F.; Krüger, H.; Wermes, N.

    2012-01-01

    The shunt-LDO regulator is a new regulator concept which combines a shunt and a Low Drop-Out (LDO) regulator. Designed as an improved shunt regulator to match the needs of serially powered detector systems, it can also be used as a pure LDO regulator for general application in powering schemes requiring linear regulation. The flexibility of the design makes the shunt-LDO regulator a good candidate for use in the powering schemes envisaged for the upgrades of the ATLAS pixel detector. Two shunt-LDO regulators integrated in the prototype of the next ATLAS pixel front-end chip, the FE-I4A, are used to demonstrate the feasibility of the proposed powering solutions.

  14. Calibration and monitoring systems of the ATLAS tile hadron calorimeter

    NASA Astrophysics Data System (ADS)

    Boumediene, D.

    2013-08-01

    The TileCal is the hadronic calorimeter covering the most central region of the ATLAS experiment at LHC. It is a sampling calorimeter with iron plates as absorber and plastic scintillating tiles as the active material. The scintillation light produced by the passage of charged particles is transmitted by wavelength shifting fibers to about 10,000 photomultiplier tubes (PMTs). Integrated to the calorimeter, there is a composite device that allows to monitor and/or equalize the signals at various stages of their formation. This device is based on signal generation from different sources: radioactive, LASER, charge injection and minimum bias events produced in proton-proton collisions. Recent performances of these systems are presented.

  15. ATLAS computing challenges before the next LHC run

    NASA Astrophysics Data System (ADS)

    Barberis, D.; ATLAS Collaboration

    2016-04-01

    ATLAS software and computing is in a period of intensive evolution. The current long shutdown presents an opportunity to assimilate lessons from the very successful Run 1 (2009-2013) and to prepare for the substantially increased computing requirements for Run 2 (from spring 2015). Run 2 will bring a near doubling of the energy and the data rate, high event pile-up levels, and higher event complexity from detector upgrades, meaning the number and complexity of events to be analyzed will increase dramatically. At the same time operational loads must be reduced through greater automation, a wider array of opportunistic resources must be supported, costly storage must be used with greater efficiency, a sophisticated new analysis model must be integrated, and concurrency features of new processors must be exploited. This paper surveys the distributed computing aspects of the upgrade program and the plans for 2014 to exercise the new capabilities in a large scale Data Challenge.

  16. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

    PubMed Central

    Czerwińska, Patrycja; Wiznerowicz, Maciej

    2015-01-01

    The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive “atlas” of cancer genomic profiles. So far, TCGA researchers have analysed large cohorts of over 30 human tumours through large-scale genome sequencing and integrated multi-dimensional analyses. Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis. A major goal of the project was to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer. This review discusses the current status of TCGA Research Network structure, purpose, and achievements. PMID:25691825

  17. The ATLAS Insertable B-Layer (IBL) project

    NASA Astrophysics Data System (ADS)

    Bilbao de Mendizabal, J.

    2013-12-01

    Preparing for the high luminosity LHC phase, the ATLAS experiment will upgrade its Pixel Detector with the installation of a new pixel layer. The new sub detector, called the Insertable B-Layer (IBL), will be installed during the LHC first shut down in 2013-2014, in between the innermost current pixel layer and the beampipe. To cope with the high radiation and pixel occupancy due to the proximity to the interaction point, a new readout chip FE-I4 and two different silicon sensor technologies, planar and 3D have been developed. Furthermore, the physics performance should be improved through the reduction of pixel size and a new mechanical support using lightweight staves. Two pre-series staves were made in order to qualify the assembly procedure, the loaded module electrical integrity and the readout chain before going into production.

  18. 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

  19. 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.

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

    PubMed

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

    2017-03-31

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

  1. Joint Segmentation of Image Ensembles via Latent Atlases

    PubMed Central

    Raviv, Tammy Riklin; Van Leemput, Koen; Wells, William M.; Golland, Polina

    2010-01-01

    Spatial priors, such as probabilistic atlases, play an important role in MRI segmentation. However, the availability of comprehensive, reliable and suitable manual segmentations for atlas construction is limited. We therefore propose a joint segmentation of corresponding, aligned structures in the entire population that does not require a probability atlas. Instead, a latent atlas, initialized by a single manual segmentation, is inferred from the evolving segmentations of the ensemble. The proposed method is based on probabilistic principles but is solved using partial differential equations (PDEs) and energy minimization criteria. We evaluate the method by segmenting 50 brain MR volumes. Segmentation accuracy for cortical and subcortical structures approaches the quality of state-of-the-art atlas-based segmentation results, suggesting that the latent atlas method is a reasonable alternative when existing atlases are not compatible with the data to be processed. PMID:20425997

  2. EnviroAtlas - Paterson, NJ - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  3. EnviroAtlas - Milwaukee, WI - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  4. EnviroAtlas - Tampa, FL - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  5. EnviroAtlas - Fresno, CA - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  6. EnviroAtlas - Cleveland, OH - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas ) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  7. EnviroAtlas - Durham, NC - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas ) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets ).

  8. EnviroAtlas - Memphis, TN - Park Access by Block Group

    EPA Pesticide Factsheets

    This EnviroAtlas dataset shows the block group population that is within and beyond an easy walking distance (500m) of a park entrance. Park entrances were included in this analysis if they were within 5km of the EnviroAtlas community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

  9. EnviroAtlas - Portland, OR - Park Access by Block Group

    EPA Pesticide Factsheets

    This Env