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.

A gene expression atlas of developing oat seeds for enhancing nutritional composition

USDA-ARS?s Scientific Manuscript database

Oat (Avena sativa L.) genome resources are less abundant than for wheat and barley, but next generation sequencing (NGS) technologies have great potential to accelerate new genome information for oat in a cost-effective manner. We are employing RNA-Seq to develop a gene expression atlas of developin...

Physics division annual report 2006.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glover, J.; Physics

2008-02-28

This report highlights the activities of the Physics Division of Argonne National Laboratory in 2006. The Division's programs include the operation as a national user facility of ATLAS, the Argonne Tandem Linear Accelerator System, research in nuclear structure and reactions, nuclear astrophysics, nuclear theory, investigations in medium-energy nuclear physics as well as research and development in accelerator technology. The mission of nuclear physics is to understand the origin, evolution and structure of baryonic matter in the universe--the core of matter, the fuel of stars, and the basic constituent of life itself. The Division's research focuses on innovative new ways tomore » address this mission.« less

Development of an AMS method to study oceanic circulation characteristics using cosmogenic 39Ar

USGS Publications Warehouse

Collon, P.H.; Bichler, M.; Caggiano, J.; Cecil, L.D.; El, Masri Y.; Golser, R.; Jiang, C.L.; Heinz, A.; Henderson, D.; Kutschera, W.; Lehmann, B.E.; Leleux, P.; Loosli, H.H.; Pardo, R.C.; Paul, M.; Rehm, K.E.; Schlosser, P.; Scott, R.H.; Smethie, W.M.; Vondrasek, R.

2004-01-01

Initial experiments at the ATLAS facility [Nucl. Instr. and Meth. B 92 (1994) 241] resulted in a clear detection of cosmogenic 39Ar signal at the natural level. The present paper summarizes the recent developments of 39Ar AMS measurements at ATLAS: the use of an electron cyclotron resonance (ECR) positive ion source equipped with a special quartz liner to reduce 39K background, the development of a gas handling system for small volume argon samples, the acceleration of 39Ar8+ ions to 232 MeV, and the final separation of 39Ar from 39K in a gas-filled spectrograph. The first successful AMS measurements of 39Ar in ocean water samples from the Southern Atlantic ventilation experiment (SAVE) are reported. Published by Elsevier B.V.

Simulation of the Deployment and Orbit Operations of the NPS-SCAT CubeSat

DTIC Science & Technology

2008-04-01

Vehicle EPF Extended Payload Fairings ESPA EELV Secondary Payload Adapter g Gravitational acceleration constant at sea level on the Earth GSO...Cell Measurement System SOC State Of Charge SPL Secondary Payload SRB Solid Rocket Booster XEPF Extended EPF xvii ACKNOWLEDGMENTS...incorporates the flight proven 4 m diameter Atlas V 12.0 m Large Payload Fairing (LPF), the 12.9 m Extended Payload Fairing ( EPF ), or the 13.8 m

Monitoring of computing resource use of active software releases at ATLAS

NASA Astrophysics Data System (ADS)

Limosani, Antonio; ATLAS Collaboration

2017-10-01

The LHC is the world’s most powerful particle accelerator, colliding protons at centre of mass energy of 13 TeV. As the energy and frequency of collisions has grown in the search for new physics, so too has demand for computing resources needed for event reconstruction. We will report on the evolution of resource usage in terms of CPU and RAM in key ATLAS offline reconstruction workflows at the TierO at CERN and on the WLCG. Monitoring of workflows is achieved using the ATLAS PerfMon package, which is the standard ATLAS performance monitoring system running inside Athena jobs. Systematic daily monitoring has recently been expanded to include all workflows beginning at Monte Carlo generation through to end-user physics analysis, beyond that of event reconstruction. Moreover, the move to a multiprocessor mode in production jobs has facilitated the use of tools, such as “MemoryMonitor”, to measure the memory shared across processors in jobs. Resource consumption is broken down into software domains and displayed in plots generated using Python visualization libraries and collected into pre-formatted auto-generated Web pages, which allow the ATLAS developer community to track the performance of their algorithms. This information is however preferentially filtered to domain leaders and developers through the use of JIRA and via reports given at ATLAS software meetings. Finally, we take a glimpse of the future by reporting on the expected CPU and RAM usage in benchmark workflows associated with the High Luminosity LHC and anticipate the ways performance monitoring will evolve to understand and benchmark future workflows.

Astronaut Curtis Brown works with SAMS on Shuttle Atlantis middeck

NASA Image and Video Library

1994-11-14

STS066-14-021 (3-14 Nov 1994) --- On the Space Shuttle Atlantis' mid-deck, astronaut Curtis L. Brown, Jr., pilot, works with the Space Acceleration Measurement System (SAMS), which is making its eleventh Shuttle flight. This system supports the Protein Crystal Growth (PCG) experiments onboard by collecting and recording data characterizing the microgravity environment in the Shuttle mid-deck. Brown joined four other NASA astronauts and a European Space Agency (ESA) astronaut for 11-days aboard Atlantis in support of the Atmospheric Laboratory for Applications and Science (ATLAS-3) mission.

Monitoring of computing resource utilization of the ATLAS experiment

NASA Astrophysics Data System (ADS)

Rousseau, David; Dimitrov, Gancho; Vukotic, Ilija; Aidel, Osman; Schaffer, Rd; Albrand, Solveig

2012-12-01

Due to the good performance of the LHC accelerator, the ATLAS experiment has seen higher than anticipated levels for both the event rate and the average number of interactions per bunch crossing. In order to respond to these changing requirements, the current and future usage of CPU, memory and disk resources has to be monitored, understood and acted upon. This requires data collection at a fairly fine level of granularity: the performance of each object written and each algorithm run, as well as a dozen per-job variables, are gathered for the different processing steps of Monte Carlo generation and simulation and the reconstruction of both data and Monte Carlo. We present a system to collect and visualize the data from both the online Tier-0 system and distributed grid production jobs. Around 40 GB of performance data are expected from up to 200k jobs per day, thus making performance optimization of the underlying Oracle database of utmost importance.

STS-66 Space Shuttle mission report

NASA Technical Reports Server (NTRS)

Fricke, Robert W., Jr.

1995-01-01

The primary objective of this flight was to accomplish complementary science objectives by operating the Atmospheric Laboratory for Applications and Science-3 (ATLAS-3) and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere-Shuttle Pallet Satellite (CRISTA-SPAS). The secondary objectives of this flight were to perform the operations of the Shuttle Solar Backscatter Ultraviolet/A (SSBUV/A) payload, the Experiment of the Sun Complementing the Atlas Payload and Education-II (ESCAPE-II) payload, the Physiological and Anatomical Rodent Experiment/National Institutes of Health Rodents (PARE/NIH-R) payload, the Protein Crystal Growth-Thermal Enclosure System (PCG-TES) payload, the Protein Crystal Growth-Single Locker Thermal Enclosure System (PCG-STES), the Space Tissue/National Institutes of Health Cells STL/N -A payload, the Space Acceleration Measurement Systems (SAMS) Experiment, and Heat Pipe Performance Experiment (HPPE) payload. The 11-day plus 2 contingency day STS-66 mission was flown as planned, with no contingency days used for weather avoidance or Orbiter contingency operations. Appendix A lists the sources of data from which this report was prepared, and Appendix B defines all acronyms and abbreviations used in the report.

STS-66 Space Shuttle mission report

NASA Astrophysics Data System (ADS)

Fricke, Robert W., Jr.

1995-02-01

The primary objective of this flight was to accomplish complementary science objectives by operating the Atmospheric Laboratory for Applications and Science-3 (ATLAS-3) and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere-Shuttle Pallet Satellite (CRISTA-SPAS). The secondary objectives of this flight were to perform the operations of the Shuttle Solar Backscatter Ultraviolet/A (SSBUV/A) payload, the Experiment of the Sun Complementing the Atlas Payload and Education-II (ESCAPE-II) payload, the Physiological and Anatomical Rodent Experiment/National Institutes of Health Rodents (PARE/NIH-R) payload, the Protein Crystal Growth-Thermal Enclosure System (PCG-TES) payload, the Protein Crystal Growth-Single Locker Thermal Enclosure System (PCG-STES), the Space Tissue/National Institutes of Health Cells STL/N -A payload, the Space Acceleration Measurement Systems (SAMS) Experiment, and Heat Pipe Performance Experiment (HPPE) payload. The 11-day plus 2 contingency day STS-66 mission was flown as planned, with no contingency days used for weather avoidance or Orbiter contingency operations. Appendix A lists the sources of data from which this report was prepared, and Appendix B defines all acronyms and abbreviations used in the report.

Construction and Performance Studies of Large Resistive Micromegas Quadruplets

NASA Astrophysics Data System (ADS)

Farina, E.; Iengo, P.; Bianco, M.; Sidiropoulou, O.; Kuger, F.; Sekhniaidze, G.; Vergain, M.; Wotschack, J.; Danielsson, H.; Degrange, J.; De Oliveira, R.; Schott, M.; Lin, Tai-Hua; Valderanis, C.; Düdder, A.

2018-02-01

In view of the use of Micromegas detectors for the upgrade of the ATLAS muon system, two detector quadruplets with an area of 0.3 m2 per plane serving as prototypes for future ATLAS chambers have been constructed. They are based on the resistive-strip technology and thus spark tolerant. The detectors were built in a modular way. The quadruplets consist of two double-sided readout panels and three support (or drift) panels equipped with the micromesh and the drift electrode. The panels are bolted together such that the detector can be opened and cleaned, if required. Two of the readout planes are equipped with readout strips inclined by 1.5 degree. In this talk, we present the results of detailed performance studies based on X-Ray and cosmic ray measurements as well as measurements with 855 MeV electrons at the MAMI accelerator. In particular, results on reconstruction efficiencies, track resolution and gain homogeneity is presented.

COLD-SAT: An orbital cryogenic hydrogen technology experiment

NASA Technical Reports Server (NTRS)

Schuster, J. R.; Wachter, Joseph P.; Powers, Albert G.

1989-01-01

The COLD-SAT spacecraft will perform subcritical liquid hydrogen storage and transfer experiments under low-gravity conditions to provide engineering data for future space transportation missions. Consisting of an experiment module mated to a spacecraft bus, COLD-SAT will be placed in an initial 460 km circular orbit by an Atlas I commercial launch vehicle. After deployment, the three-axis-controlled spacecraft bus will provide electric power, experiment control and data management, communications, and attitude control along with propulsive acceleration levels ranging from 10(-6) to 10(-4)g. These accelerations are an important aspect of some of the experiments, as it is desired to know the effects that low gravity levels might have on the heat and mass transfer processes involved. The experiment module will contain the three liquid hydrogen tanks, valves, pressurization equipment, and instrumentation. At launch all the hydrogen will be in the largest tank, which has helium-purged MLI and is loaded and topped off by the hydrogen tanking system used for the Centaur upper stage of the Atlas. The two smaller tanks will be utilized in orbit for performing some of the experiments. The experiments are grouped into two classes on the basis of their priority, and include six regarded as enabling technology and nine regarded as enhancing technology.

Hydrodynamic and material properties experiments using pulsed power techniques

NASA Astrophysics Data System (ADS)

Reinovsky, R. E.; Trainor, R. J.

2000-04-01

Within the last five years, a new approach to the exploration of dynamic material properties and advanced hydrodynamics at extreme conditions has joined the traditional techniques of high velocity guns and explosives. This new application uses electromagnetic energy to accelerate solid density material to produce shocks in a cylindrical target. The principal tool for producing high energy density environments is the high precision, magnetically imploded, near-solid density cylindrical liner. The most attractive pulsed power system for driving such experiments is an ultrahigh current, low impedance, microsecond time scale source that is economical both to build and to operate. Two families of pulsed power systems can be applied to drive such experiments. The 25-MJ Atlas capacitor bank system currently under construction at Los Alamos is the first system of its scale specifically designed to drive high precision solid liners. Delivering 30 MA, Atlas will provide liner velocities 12-15 km/sec and kinetic energies of 1-2 MJ/cm with extensive diagnostics and excellent reproducibility. Explosive flux compressor technology provides access to currents exceeding 100 MA producing liner velocities above 25 km/sec and kinetic energies of 5-20 MJ/cm in single shot operations

About TCGA - TCGA

Cancer.gov

Find out about The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

Physics division annual report 2000.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thayer, K., ed.

2001-10-04

This report summarizes the research performed in 2000 in the Physics Division of Argonne National Laboratory. The Division's programs include operation of ATLAS as a national user facility, nuclear structure and reaction research, nuclear theory and medium energy physics research, and accelerator research and development. As the Nuclear Science Advisory Committee and the nuclear science community create a new long range plan for the field in 2001, it is clear that the research of the Division is closely aligned with and continues to help define the national goals of our field. The NSAC 2001 Long Range Plan recommends as themore » highest priority for major new construction the Rare Isotope Accelerator (RIA), a bold step forward for nuclear structure and nuclear astrophysics. The accelerator R&D in the Physics Division has made major contributions to almost all aspects of the RIA design concept and the community was convinced that this project is ready to move forward. 2000 saw the end of the first Gammasphere epoch at ATLAS, One hundred Gammasphere experiments were completed between January 1998 and March 2000, 60% of which used the Fragment Mass Analyzer to provide mass identification in the reaction. The experimental program at ATLAS then shifted to other important research avenues including proton radioactivity, mass measurements with the Canadian Penning Trap and measurements of high energy gamma-rays in nuclear reactions with the MSU/ORNL/Texas A&M BaF{sub 2} array. ATLAS provided 5460 beam-research hours for user experiments and maintained an operational reliability of 95%. Radioactive beams accounted for 7% of the beam time. ATLAS also provided a crucial test of a key RIA concept, the ability to accelerate multiple charge states in a superconducting heavy-ion linac. This new capability was immediately used to increase the performance for a scheduled experiment. The medium energy program continued to make strides in examining how the quark-gluon structure of matter impacts the structure of nuclei and extended the exquisite sensitivity of the Atom-Trap-Trace-Analysis technique to new species and applications. All of this progress was built on advances in nuclear theory, which the Division pursues at the quark, hadron, and nuclear collective degrees of freedom levels. These are just a few of the highlights in the Division's research program. The results reflect the talents and dedication of the Physics Division staff and the visitors, guests and students who bring so much to the research.« less

Participation in the definition, conduct, and analysis of particle accelerator experiments for the first Spacelab Mission

NASA Technical Reports Server (NTRS)

Burch, J. L.

1994-01-01

The Space Experiments with Particle Accelerators (SEPAC) is a joint endeavor between NASA and the Institute of Space and Aeronautical Sciences (ISAS) in Japan. Its objectives are to use energetic electron beams to investigate beam-atmosphere interactions and beam-plasma interactions in the earth's upper atmosphere and ionosphere using the shuttle Spacelab. Two flights of SEPAC have occurred to date (Spacelab 1 on STS-9 in Nov.-Dec. 1983 and ATLAS 1 on STS-45 in Mar.-Apr. 1992). The SEPAC instrumentation is available for future missions, and the scientific results of the first two missions justify further investigations; however, at present there are no identifiable future flight opportunities. As specified in the contract, the primary purpose of this report is to review the scientific accomplishments of the ATLAS 1 SEPAC experiments, which have been documented in the published literature, with only a brief review of the earlier Spacelab 1 results. One of the main results of the Spacelab 1 SEPAC experiments was that the ejection of plasma from the magnetoplasmadynamic (MPD) arcjet was effective in maintaining vehicle charge neutralization during electron beam firings, but only for a brief period of 10 ms or so. Therefore, a xenon plasma contactor, which can provide continuous vehicle charge neutralization, was developed for the ATLAS 1 SEPAC experiments. Because of the successful operation of the plasma contactor on ATLAS 1, it was possible to perform experiments on beam-plasma interactions and beam-atmosphere interactions at the highest beam power levels of SEPAC. In addition, the ability of the plasma contactor to eject neutral xenon led to a successful experiment on the critical ionization velocity (CIV) phenomena on ATLAS 1.

New Funding Opportunity from the Human Biomolecular Atlas Program (HuBMAP)! | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) aims to develop a framework for functional mapping the human body with cellular resolution to enhance our understanding of cellular organization-function. HuBMAP will accelerate the development of the next generation of tools and techniques to generate 3D tissue maps using validated high-content, high-throughput imaging and omics assays, and establish an open data platform for integrating, visualizing data to build multi-dimensional maps.

The Eclipsing Binary On-Line Atlas (EBOLA)

NASA Astrophysics Data System (ADS)

Bradstreet, D. H.; Steelman, D. P.; Sanders, S. J.; Hargis, J. R.

2004-05-01

In conjunction with the upcoming release of \\it Binary Maker 3.0, an extensive on-line database of eclipsing binaries is being made available. The purposes of the atlas are: \\begin {enumerate} Allow quick and easy access to information on published eclipsing binaries. Amass a consistent database of light and radial velocity curve solutions to aid in solving new systems. Provide invaluable querying capabilities on all of the parameters of the systems so that informative research can be quickly accomplished on a multitude of published results. Aid observers in establishing new observing programs based upon stars needing new light and/or radial velocity curves. Encourage workers to submit their published results so that others may have easy access to their work. Provide a vast but easily accessible storehouse of information on eclipsing binaries to accelerate the process of understanding analysis techniques and current work in the field. \\end {enumerate} The database will eventually consist of all published eclipsing binaries with light curve solutions. The following information and data will be supplied whenever available for each binary: original light curves in all bandpasses, original radial velocity observations, light curve parameters, RA and Dec, V-magnitudes, spectral types, color indices, periods, binary type, 3D representation of the system near quadrature, plots of the original light curves and synthetic models, plots of the radial velocity observations with theoretical models, and \\it Binary Maker 3.0 data files (parameter, light curve, radial velocity). The pertinent references for each star are also given with hyperlinks directly to the papers via the NASA Abstract website for downloading, if available. In addition the Atlas has extensive searching options so that workers can specifically search for binaries with specific characteristics. The website has more than 150 systems already uploaded. The URL for the site is http://ebola.eastern.edu/.

KSC-2012-1015

NASA Image and Video Library

2012-01-12

CAPE CANAVERAL, Fla. -- This is an artist's conception of the Dream Chaser spacecraft integrated with an Atlas V rocket. Dream Chaser is under development by Sierra Nevada of Centennial, Colo., for NASA's Commercial Crew Program (CCP). In 2011, NASA selected Sierra Nevada during Commercial Crew Development Round 2 (CCDev2) activities to mature the design and development of a crew transportation system with the overall goal of accelerating a United States-led capability to the International Space Station. United Launch Alliance's Atlas V also is being considered under CCDev2. The goal of CCP is to drive down the cost of space travel as well as open up space to more people than ever before by balancing industry’s own innovative capabilities with NASA's 50 years of human spaceflight experience. Five other aerospace companies also are maturing launch vehicle and spacecraft designs under CCDev2, including Alliant Techsystems Inc. (ATK), The Boeing Co., Excalibur Almaz Inc., Blue Origin, and Space Exploration Technologies (SpaceX). For more information, visit www.nasa.gov/commercialcrew. Image credit: Sierra Nevada Corp.

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.

The High-Luminosity upgrade of the LHC: Physics and Technology Challenges for the Accelerator and the Experiments

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard

2016-04-01

In the second phase of the LHC physics program, the accelerator will provide an additional integrated luminosity of about 2500/fb over 10 years of operation to the general purpose detectors ATLAS and CMS. This will substantially enlarge the mass reach in the search for new particles and will also greatly extend the potential to study the properties of the Higgs boson discovered at the LHC in 2012. In order to meet the experimental challenges of unprecedented pp luminosity, the experiments will need to address the aging of the present detectors and to improve the ability to isolate and precisely measure the products of the most interesting collisions. The lectures gave an overview of the physics motivation and described the conceptual designs and the expected performance of the upgrades of the four major experiments, ALICE, ATLAS, CMS and LHCb, along with the plans to develop the appropriate experimental techniques and a brief overview of the accelerator upgrade. Only some key points of the upgrade program of the four major experiments are discussed in this report; more information can be found in the references given at the end.

Ultra-High Sensitivity Techniques for the Determination of 3 He /4 He Abundances in Helium by Accelerator Mass Spectrometry

NASA Astrophysics Data System (ADS)

Mumm, H. P.; Huber, M.; Bauder, W.; Abrams, N.; Deibel, C.; Huffer, C.; Huffman, P.; Schelhammer, K.; Janssens, R.; Jiang, C.; Scott, R.; Pardo, R.; Rehm, K.; Vondrasek, R.; Swank, C.; O'Shaughnessy, C.; Paul, M.; Yang, L.

2017-01-01

We report the development of an Accelerator Mass Spectrometry technique to measure the 3He/4He isotopic ratio using a radio frequency (RF) discharge source and the ATLAS facility at Argonne National Laboratory. Control over 3He/4He ratio in helium several orders of magnitude lower than natural abundance is critical for neutron lifetime and source experiments using liquid helium. Due to low ultimate beam currents, the ATLAS accelerator and beam line were tuned using a succession of species of the same M/q. A unique RF source was developed for the experiment due to large natural 3He backgrounds. Analog H_3 + and DH + molecular ions are eliminated by dissociation via a gold stripper foil near the detector. The stripped ions were dispersed in a magnetic spectrograph and 3He2 + ions counted in the focal plane detector. This technique is sensitive to 3 He /4 He ratios in the regime of 10-12 with backgrounds that appear to be below 10-14. The techniques used to reduce the backgrounds and remaining outstanding problems will be presented along with results from measurements on high purity 4He samples.

Schaltenbrand-Wahren-Talairach-Tournoux brain atlas registration

NASA Astrophysics Data System (ADS)

Nowinski, Wieslaw L.; Fang, Anthony; Nguyen, Bonnie T.

1995-04-01

The CIeMed electronic brain atlas system contains electronic versions of multiple paper brain atlases with 3D extensions; some other 3D brain atlases are under development. Its primary goal is to provide automatic labeling and quantification of brains. The atlas data are digitized, enhanced, color coded, labeled, and organized into volumes. The atlas system provides several tools for registration, 3D display and real-time manipulation, object extraction/editing, quantification, image processing and analysis, reformatting, anatomical index operations, and file handling. The two main stereotactic atlases provided by the system are electronic and enhanced versions of Atlas of Stereotaxy of the Human Brain by Schaltenbrand and Wahren and Co-Planar Stereotactic Atlas of the Human Brain by Talairach and Tournoux. Each of these atlases has its own strengths and their combination has several advantages. First, a complementary information is merged and provided to the user. Second, the user can register data with a single atlas only, as the Schaltenbrand-Wahren-Talairach-Tournoux registration is data-independent. And last but not least, a direct registration of the Schaltenbrand-Wahren microseries with MRI data may not be feasible, since cerebral deep structures are usually not clearly discernible on MRI images. This paper addresses registration of the Schaltenbrand- Wahren and Talairach-Tournoux brain atlases. A modified proportional grid system transformation is introduced and suitable sets of landmarks identifiable in both atlases are defined. The accuracy of registration is discussed. A continuous navigation in the multi- atlas/patient data space is presented.

Note: The design of thin gap chamber simulation signal source based on field programmable gate array.

PubMed

Hu, Kun; Lu, Houbing; Wang, Xu; Li, Feng; Liang, Futian; Jin, Ge

2015-01-01

The Thin Gap Chamber (TGC) is an important part of ATLAS detector and LHC accelerator. Targeting the feature of the output signal of TGC detector, we have designed a simulation signal source. The core of the design is based on field programmable gate array, randomly outputting 256-channel simulation signals. The signal is generated by true random number generator. The source of randomness originates from the timing jitter in ring oscillators. The experimental results show that the random number is uniform in histogram, and the whole system has high reliability.

Note: The design of thin gap chamber simulation signal source based on field programmable gate array

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Kun; Wang, Xu; Li, Feng

The Thin Gap Chamber (TGC) is an important part of ATLAS detector and LHC accelerator. Targeting the feature of the output signal of TGC detector, we have designed a simulation signal source. The core of the design is based on field programmable gate array, randomly outputting 256-channel simulation signals. The signal is generated by true random number generator. The source of randomness originates from the timing jitter in ring oscillators. The experimental results show that the random number is uniform in histogram, and the whole system has high reliability.

AGIS: The ATLAS Grid Information System

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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.

AGIS: Integration of new technologies used in ATLAS Distributed Computing

NASA Astrophysics Data System (ADS)

Anisenkov, Alexey; Di Girolamo, Alessandro; Alandes Pradillo, Maria

2017-10-01

The variety of the ATLAS Distributed Computing infrastructure requires a central information system to define the topology of computing resources and to store different parameters and configuration data which are needed by various ATLAS software components. The ATLAS Grid Information System (AGIS) is the system designed to integrate configuration and status information about resources, services and topology of the computing infrastructure used by ATLAS Distributed Computing applications and services. Being an intermediate middleware system between clients and external information sources (like central BDII, GOCDB, MyOSG), AGIS defines the relations between experiment specific used resources and physical distributed computing capabilities. Being in production during LHC Runl AGIS became the central information system for Distributed Computing in ATLAS and it is continuously evolving to fulfil new user requests, enable enhanced operations and follow the extension of the ATLAS Computing model. The ATLAS Computing model and data structures used by Distributed Computing applications and services are continuously evolving and trend to fit newer requirements from ADC community. In this note, we describe the evolution and the recent developments of AGIS functionalities, related to integration of new technologies recently become widely used in ATLAS Computing, like flexible computing utilization of opportunistic Cloud and HPC resources, ObjectStore services integration for Distributed Data Management (Rucio) and ATLAS workload management (PanDA) systems, unified storage protocols declaration required for PandDA Pilot site movers and others. The improvements of information model and general updates are also shown, in particular we explain how other collaborations outside ATLAS could benefit the system as a computing resources information catalogue. AGIS is evolving towards a common information system, not coupled to a specific experiment.

Astrophysics experiments with radioactive beams at ATLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Back, B. B.; Clark, J. A.; Pardo, R. C.

Reactions involving short-lived nuclei play an important role in nuclear astrophysics, especially in explosive scenarios which occur in novae, supernovae or X-ray bursts. This article describes the nuclear astrophysics program with radioactive ion beams at the ATLAS accelerator at Argonne National Laboratory. The CARIBU facility as well as recent improvements for the in-flight technique are discussed. New detectors which are important for studies of the rapid proton or the rapid neutron-capture processes are described. At the end we briefly mention plans for future upgrades to enhance the intensity, purity and the range of in-flight and CARIBU beams.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium.

PubMed

Grossman, R L; Abel, B; Angiuoli, S; Barrett, J C; Bassett, D; Bramlett, K; Blumenthal, G M; Carlsson, A; Cortese, R; DiGiovanna, J; Davis-Dusenbery, B; Dittamore, R; Eberhard, D A; Febbo, P; Fitzsimons, M; Flamig, Z; Godsey, J; Goswami, J; Gruen, A; Ortuño, F; Han, J; Hayes, D; Hicks, J; Holloway, D; Hovelson, D; Johnson, J; Juhl, H; Kalamegham, R; Kamal, R; Kang, Q; Kelloff, G J; Klozenbuecher, M; Kolatkar, A; Kuhn, P; Langone, K; Leary, R; Loverso, P; Manmathan, H; Martin, A-M; Martini, J; Miller, D; Mitchell, M; Morgan, T; Mulpuri, R; Nguyen, T; Otto, G; Pathak, A; Peters, E; Philip, R; Posadas, E; Reese, D; Reese, M G; Robinson, D; Dei Rossi, A; Sakul, H; Schageman, J; Singh, S; Scher, H I; Schmitt, K; Silvestro, A; Simmons, J; Simmons, T; Sislow, J; Talasaz, A; Tang, P; Tewari, M; Tomlins, S; Toukhy, H; Tseng, H R; Tuck, M; Tzou, A; Vinson, J; Wang, Y; Wells, W; Welsh, A; Wilbanks, J; Wolf, J; Young, L; Lee, Jsh; Leiman, L C

2017-05-01

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays. © 2017 Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mundy, D; Tryggestad, E; Beltran, C

Purpose: To develop daily and monthly quality assurance (QA) programs in support of a new spot-scanning proton treatment facility using a combination of commercial and custom equipment and software. Emphasis was placed on efficiency and evaluation of key quality parameters. Methods: The daily QA program was developed to test output, spot size and position, proton beam energy, and image guidance using the Sun Nuclear Corporation rf-DQA™3 device and Atlas QA software. The program utilizes standard Atlas linear accelerator tests repurposed for proton measurements and a custom jig for indexing the device to the treatment couch. The monthly QA program wasmore » designed to test mechanical performance, image quality, radiation quality, isocenter coincidence, and safety features. Many of these tests are similar to linear accelerator QA counterparts, but many require customized test design and equipment. Coincidence of imaging, laser marker, mechanical, and radiation isocenters, for instance, is verified using a custom film-based device devised and manufactured at our facility. Proton spot size and position as a function of energy are verified using a custom spot pattern incident on film and analysis software developed in-house. More details concerning the equipment and software developed for monthly QA are included in the supporting document. Thresholds for daily and monthly tests were established via perturbation analysis, early experience, and/or proton system specifications and associated acceptance test results. Results: The periodic QA program described here has been in effect for approximately 9 months and has proven efficient and sensitive to sub-clinical variations in treatment delivery characteristics. Conclusion: Tools and professional guidelines for periodic proton system QA are not as well developed as their photon and electron counterparts. The program described here efficiently evaluates key quality parameters and, while specific to the needs of our facility, could be readily adapted to other proton centers.« less

Atlas-based system for functional neurosurgery

NASA Astrophysics Data System (ADS)

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

1997-05-01

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

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

DOE PAGES

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.; ...

2015-08-28

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstratemore » stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this study, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz.« less

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstratemore » stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this study, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz.« less

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostroumov, P. N., E-mail: ostroumov@anl.gov; Barcikowski, A.; Dickerson, C. A.

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstratemore » stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this paper, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz.« less

Development and test of the DAQ system for a Micromegas prototype to be installed in the ATLAS experiment

NASA Astrophysics Data System (ADS)

Bianco, M.; Martoiu, S.; Sidiropoulou, O.; Zibell, A.

2015-12-01

A Micromegas (MM) quadruplet prototype with an active area of 0.5 m2 that adopts the general design foreseen for the upgrade of the innermost forward muon tracking systems (Small Wheels) of the ATLAS detector in 2018-2019, has been built at CERN and is going to be tested in the ATLAS cavern environment during the LHC RUN-II period 2015-2017. The integration of this prototype detector into the ATLAS data acquisition system using custom ATCA equipment is presented. An ATLAS compatible Read Out Driver (ROD) based on the Scalable Readout System (SRS), the Scalable Readout Unit (SRU), will be used in order to transmit the data after generating valid event fragments to the high-level Read Out System (ROS). The SRU will be synchronized with the LHC bunch crossing clock (40.08 MHz) and will receive the Level-1 trigger signals from the Central Trigger Processor (CTP) through the TTCrx receiver ASIC. The configuration of the system will be driven directly from the ATLAS Run Control System. By using the ATLAS TDAQ Software, a dedicated Micromegas segment has been implemented, in order to include the detector inside the main ATLAS DAQ partition. A full set of tests, on the hardware and software aspects, is presented.

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.

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.

AGIS: The ATLAS Grid Information System

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Lunar Orbiter 4 - Photographic Mission Summary. Volume 1

NASA Technical Reports Server (NTRS)

1968-01-01

Photographic summary report of Lunar Orbiter 4 mission. The fourth of five Lunar Orbiter spacecraft was successfully launched from Launch Complex 13 at the Air Force Eastern Test Range by an Atlas-Agena launch vehicle at 22:25 GMT on May 4, 1967. Tracking data from the Cape Kennedy and Grand Bahama tracking stations were used to control and guide the launch vehicle during Atlas powered flight. The Agena-spacecraft combination was boosted to the proper coast ellipse by the Atlas booster prior to separation. Final maneuvering and acceleration to the velocity required to maintain the 100-nauticalmile- altitude Earth orbit was controlled by the preset on-board Agena computer. In addition, the Agena computer determined the maneuver and engine-burn period required to inject the spacecraft on the cislunar trajectory 20 minutes after launch. Tracking data from the downrange stations and the Johannesburg, South Africa station were used to monitor the boost trajectory.

Lunar Orbiter 5. Photographic Mission Summary. Volume 1

NASA Technical Reports Server (NTRS)

1968-01-01

Selected photographs and mission summary of Lunar Orbiter 5. The last of five Lunar Orbiter spacecraft was successfully launched from Launch Complex 13 at the Air Force Eastern Test Range by an Atlas-Agena launch vehicle at 22:33 GMT on August 1, 1967. Tracking data from the Cape Kennedy and Grand Bahama tracking stations were used to control and guide the launch vehicle during Atlas powered flight. The Agena-spacecraft combination was boosted to the proper coast ellipse by the Atlas booster prior to separation. Final maneuvering and acceleration to the velocity required to maintain the 100-nautical-mile-altitude Earth orbit were controlled by the preset on-board Agena computer. In addition, the Agena computer determined the maneuver and engine-bum period required to inject the spacecraft on the cislunar trajectory about 33 minutes after launch. Tracking data from the downrange stations and the Johannesburg, South Africa station were used to monitor the boost trajectory.

Advanced low-beta cavity development for proton and ion accelerators

NASA Astrophysics Data System (ADS)

Conway, Z. A.; Kelly, M. P.; Ostroumov, P. N.

2015-05-01

Recent developments in designing and processing low-beta superconducting cavities at Argonne National Laboratory are very encouraging for future applications requiring compact proton and ion accelerators. One of the major benefits of these accelerating structures is achieving real-estate accelerating gradients greater than 3 MV/m very efficiently either continuously or for long-duty cycle operation (>1%). The technology has been implemented in low-beta accelerator cryomodules for the Argonne ATLAS heavy-ion linac where the cryomodules are required to have real-estate gradients of more than 3 MV/m. In offline testing low-beta cavities with even higher gradients have already been achieved. This paper will review this work where we have achieved surface fields greater than 166 mT magnetic and 117 MV/m electric in a 72 MHz quarter-wave resonator optimized for β = 0.077 ions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thayer, K.J.

The past year has seen several of the Physics Division`s new research projects reach major milestones with first successful experiments and results: the atomic physics station in the Basic Energy Sciences Research Center at the Argonne Advanced Photon Source was used in first high-energy, high-brilliance x-ray studies in atomic and molecular physics; the Short Orbit Spectrometer in Hall C at the Thomas Jefferson National Accelerator (TJNAF) Facility that the Argonne medium energy nuclear physics group was responsible for, was used extensively in the first round of experiments at TJNAF; at ATLAS, several new beams of radioactive isotopes were developed andmore » used in studies of nuclear physics and nuclear astrophysics; the new ECR ion source at ATLAS was completed and first commissioning tests indicate excellent performance characteristics; Quantum Monte Carlo calculations of mass-8 nuclei were performed for the first time with realistic nucleon-nucleon interactions using state-of-the-art computers, including Argonne`s massively parallel IBM SP. At the same time other future projects are well under way: preparations for the move of Gammasphere to ATLAS in September 1997 have progressed as planned. These new efforts are imbedded in, or flowing from, the vibrant ongoing research program described in some detail in this report: nuclear structure and reactions with heavy ions; measurements of reactions of astrophysical interest; studies of nucleon and sub-nucleon structures using leptonic probes at intermediate and high energies; atomic and molecular structure with high-energy x-rays. The experimental efforts are being complemented with efforts in theory, from QCD to nucleon-meson systems to structure and reactions of nuclei. Finally, the operation of ATLAS as a national users facility has achieved a new milestone, with 5,800 hours beam on target for experiments during the past fiscal year.« less

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 minor (<4%) but significant in regions near the skull base. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

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.

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.

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.

Design and development of the redundant launcher stabilization system for the Atlas 2 launch vehicle

NASA Technical Reports Server (NTRS)

Nakamura, M.

1991-01-01

The Launcher Stabilization System (LSS) is a pneumatic/hydraulic ground system used to support an Atlas launch vehicle prior to launch. The redesign and development activity undertaken to achieve an LSS with increased load capacity and a redundant hydraulic system for the Atlas 2 launch vehicle are described.

Overview of ATLAS PanDA Workload Management

NASA Astrophysics Data System (ADS)

Maeno, T.; De, K.; Wenaus, T.; Nilsson, P.; Stewart, G. A.; Walker, R.; Stradling, A.; Caballero, J.; Potekhin, M.; Smith, D.; ATLAS Collaboration

2011-12-01

The Production and Distributed Analysis System (PanDA) plays a key role in the ATLAS distributed computing infrastructure. All ATLAS Monte-Carlo simulation and data reprocessing jobs pass through the PanDA system. We will describe how PanDA manages job execution on the grid using dynamic resource estimation and data replication together with intelligent brokerage in order to meet the scaling and automation requirements of ATLAS distributed computing. PanDA is also the primary ATLAS system for processing user and group analysis jobs, bringing further requirements for quick, flexible adaptation to the rapidly evolving analysis use cases of the early datataking phase, in addition to the high reliability, robustness and usability needed to provide efficient and transparent utilization of the grid for analysis users. We will describe how PanDA meets ATLAS requirements, the evolution of the system in light of operational experience, how the system has performed during the first LHC data-taking phase and plans for the future.

Overview of ATLAS PanDA Workload Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maeno T.; De K.; Wenaus T.

2011-01-01

The Production and Distributed Analysis System (PanDA) plays a key role in the ATLAS distributed computing infrastructure. All ATLAS Monte-Carlo simulation and data reprocessing jobs pass through the PanDA system. We will describe how PanDA manages job execution on the grid using dynamic resource estimation and data replication together with intelligent brokerage in order to meet the scaling and automation requirements of ATLAS distributed computing. PanDA is also the primary ATLAS system for processing user and group analysis jobs, bringing further requirements for quick, flexible adaptation to the rapidly evolving analysis use cases of the early datataking phase, in additionmore » to the high reliability, robustness and usability needed to provide efficient and transparent utilization of the grid for analysis users. We will describe how PanDA meets ATLAS requirements, the evolution of the system in light of operational experience, how the system has performed during the first LHC data-taking phase and plans for the future.« less

Advanced low-beta cavity development for proton and ion accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conway, Z. A.; Kelly, M. P.; Ostroumov, P. N.

2015-05-01

Recent developments in designing and processing low-beta superconducting cavities at Argonne National Laboratory are very encouraging for future applications requiring compact proton and ion accelerators. One of the major benefits of these accelerating structures is achieving real-estate accelerating gradients greater than 3 MV/m very efficiently either continuously or for long-duty cycle operation (>1%). The technology has been implemented in low-beta accelerator cryomodules for the Argonne ATLAS heavy-ion linac where the cryomodules are required to have real-estate gradients of more than 3 MV/m. In offline testing low-beta cavities with even higher gradients have already been achieved. This paper will review thismore » work where we have achieved surface fields greater than 166 mT magnetic and 117 MV/m electric in a 72 MHz quarter-wave resonator optimized for beta = 0.077 ions.« less

YARR - A PCIe based Readout Concept for Current and Future ATLAS Pixel Modules

NASA Astrophysics Data System (ADS)

Heim, Timon

2017-10-01

The Yet Another Rapid Readout (YARR) system is a DAQ system designed for the readout of current generation ATLAS Pixel FE-I4 and next generation chips. It utilises a commercial-off-the-shelf PCIe FPGA card as a reconfigurable I/O interface, which acts as a simple gateway to pipe all data from the Pixel modules via the high speed PCIe connection into the host system’s memory. Relying on modern CPU architectures, which enables the usage of parallelised processing in threads and commercial high speed interfaces in everyday computers, it is possible to perform all processing on a software level in the host CPU. Although FPGAs are very powerful at parallel signal processing their firmware is hard to maintain and constrained by their connected hardware. Software, on the other hand, is very portable and upgraded frequently with new features coming at no cost. A DAQ concept which does not rely on the underlying hardware for acceleration also eases the transition from prototyping in the laboratory to the full scale implementation in the experiment. The overall concept and data flow will be outlined, as well as the challenges and possible bottlenecks which can be encountered when moving the processing from hardware to software.

A Three-Dimensional Atlas of the Honeybee Neck

PubMed Central

Berry, Richard P.; Ibbotson, Michael R.

2010-01-01

Three-dimensional digital atlases are rapidly becoming indispensible in modern biology. We used serial sectioning combined with manual registration and segmentation of images to develop a comprehensive and detailed three-dimensional atlas of the honeybee head-neck system. This interactive atlas includes skeletal structures of the head and prothorax, the neck musculature, and the nervous system. The scope and resolution of the model exceeds atlases previously developed on similar sized animals, and the interactive nature of the model provides a far more accessible means of interpreting and comprehending insect anatomy and neuroanatomy. PMID:20520729

Fast Switching Magnet for Heavy Ion Beam Separation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartzell, Josiah

2017-10-03

Fast magnets for multiplexing ion beams between different beamlines are technologically challenging and expensive, but there is an ever-growing need to develop such systems for beam separation at research and industrial facilities. For example, The Argonne Tandem Linac Accelerator System (ATLAS) is planning to expand its operations as a multi-user facility and there is a clear need, presently unmet by the industry, for a switching magnet system with the sub-millisecond transient times.In response to this problem, RadiaBeam Technologies is developing a novel pulsed switching magnet system capable of producing a 1.1T peak field over 45 cm length with a shortmore » (<1 ms) rise and fall time. The key enabling innovation in this project is an introduction of a solid-state interposed modulator architecture, which enables to improve magnet performance and reliability and reduce the cost to a practical level.« less

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.

National Comprehensive School Reform: An Analysis of Six Reform Models 1980-2000

ERIC Educational Resources Information Center

Feinzimer, Laurie Gault

2009-01-01

This study analyzes six different National Comprehensive Reform Models through multiple lenses. It seeks to discover how the models of ATLAS Communities, Accelerated Schools Plus, Co-nect Schools, Expeditionary Learning Schools Outward Bound, Modern Red SchoolHouse and Urban Learning Centers both restructure and reculture the schools in which they…

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

NASA Astrophysics Data System (ADS)

Vandelli, Wainer; ATLAS TDAQ Collaboration

2010-04-01

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

Readout and Trigger for the AFP Detector at the ATLAS Experiment at LHC

NASA Astrophysics Data System (ADS)

Korcyl, K.; Kocian, M.; Lopez Paz, I.; Avoni, G.

2017-10-01

The ATLAS Forward Proton is a new detector system in ATLAS that allows study of events with protons scattered at very small angles. The final design assumes four stations at distances of 205 and 217 m from the ATLAS interaction point on both sides of the detector exploiting the Roman Pot technology. In 2016 two stations in one arm were installed; installation of the other two is planned for 2017. This article describes details of the installed hardware, firmware and software leading to the full integration with the ATLAS central trigger and data acquisition systems.

The ATLAS Eventlndex: data flow and inclusion of other metadata

NASA Astrophysics Data System (ADS)

Barberis, D.; Cárdenas Zárate, S. E.; Favareto, A.; Fernandez Casani, A.; Gallas, E. J.; Garcia Montoro, C.; Gonzalez de la Hoz, S.; Hrivnac, J.; Malon, D.; Prokoshin, F.; Salt, J.; Sanchez, J.; Toebbicke, R.; Yuan, R.; ATLAS Collaboration

2016-10-01

The ATLAS EventIndex is the catalogue of the event-related metadata for the information collected from the ATLAS detector. The basic unit of this information is the event record, containing the event identification parameters, pointers to the files containing this event as well as trigger decision information. The main use case for the EventIndex is event picking, as well as data consistency checks for large production campaigns. The EventIndex employs the Hadoop platform for data storage and handling, as well as a messaging system for the collection of information. The information for the EventIndex is collected both at Tier-0, when the data are first produced, and from the Grid, when various types of derived data are produced. The EventIndex uses various types of auxiliary information from other ATLAS sources for data collection and processing: trigger tables from the condition metadata database (COMA), dataset information from the data catalogue AMI and the Rucio data management system and information on production jobs from the ATLAS production system. The ATLAS production system is also used for the collection of event information from the Grid jobs. EventIndex developments started in 2012 and in the middle of 2015 the system was commissioned and started collecting event metadata, as a part of ATLAS Distributed Computing operations.

Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box (TTB)

NASA Technical Reports Server (NTRS)

Doyle, Monica; ONeil, Daniel A.; Christensen, Carissa B.

2005-01-01

The Advanced Technology Lifecycle Analysis System (ATLAS) is a decision support tool designed to aid program managers and strategic planners in determining how to invest technology research and development dollars. It is an Excel-based modeling package that allows a user to build complex space architectures and evaluate the impact of various technology choices. ATLAS contains system models, cost and operations models, a campaign timeline and a centralized technology database. Technology data for all system models is drawn from a common database, the ATLAS Technology Tool Box (TTB). The TTB provides a comprehensive, architecture-independent technology database that is keyed to current and future timeframes.

PD2P: PanDA Dynamic Data Placement for ATLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maeno, T.; De, K.; Panitkin, S.

2012-12-13

The PanDA (Production and Distributed Analysis) system plays a key role in the ATLAS distributed computing infrastructure. PanDA is the ATLAS workload management system for processing all Monte-Carlo (MC) simulation and data reprocessing jobs in addition to user and group analysis jobs. The PanDA Dynamic Data Placement (PD2P) system has been developed to cope with difficulties of data placement for ATLAS. We will describe the design of the new system, its performance during the past year of data taking, dramatic improvements it has brought about in the efficient use of storage and processing resources, and plans for the future.

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.

Three-dimensional Talairach-Tournoux brain atlas

NASA Astrophysics Data System (ADS)

Fang, Anthony; Nowinski, Wieslaw L.; Nguyen, Bonnie T.; Bryan, R. Nick

1995-04-01

The Talairach-Tournoux Stereotaxic Atlas of the human brain is a frequently consulted resource in stereotaxic neurosurgery and computer-based neuroradiology. Its primary application lies in the 2-D analysis and interpretation of neurological images. However, for the purpose of the analysis and visualization of shapes and forms, accurate mensuration of volumes, or 3-D models matching, a 3-D representation of the atlas is essential. This paper proposes and describes, along with its difficulties, a 3-D geometric extension of the atlas. We introduce a `zero-potential' surface smoothing technique, along with a space-dependent convolution kernel and space-dependent normalization. The mesh-based atlas structures are hierarchically organized, and anatomically conform to the original atlas. Structures and their constituents can be independently selected and manipulated in real-time within an integrated system. The extended atlas may be navigated by itself, or interactively registered with patient data with the proportional grid system (piecewise linear) transformation. Visualization of the geometric atlas along with patient data gives a remarkable visual `feel' of the biological structures, not usually perceivable to the untrained eyes in conventional 2-D atlas to image analysis.

Role of the ATLAS Grid Information System (AGIS) in Distributed Data Analysis and Simulation

NASA Astrophysics Data System (ADS)

Anisenkov, A. V.

2018-03-01

In modern high-energy physics experiments, particular attention is paid to the global integration of information and computing resources into a unified system for efficient storage and processing of experimental data. Annually, the ATLAS experiment performed at the Large Hadron Collider at the European Organization for Nuclear Research (CERN) produces tens of petabytes raw data from the recording electronics and several petabytes of data from the simulation system. For processing and storage of such super-large volumes of data, the computing model of the ATLAS experiment is based on heterogeneous geographically distributed computing environment, which includes the worldwide LHC computing grid (WLCG) infrastructure and is able to meet the requirements of the experiment for processing huge data sets and provide a high degree of their accessibility (hundreds of petabytes). The paper considers the ATLAS grid information system (AGIS) used by the ATLAS collaboration to describe the topology and resources of the computing infrastructure, to configure and connect the high-level software systems of computer centers, to describe and store all possible parameters, control, configuration, and other auxiliary information required for the effective operation of the ATLAS distributed computing applications and services. The role of the AGIS system in the development of a unified description of the computing resources provided by grid sites, supercomputer centers, and cloud computing into a consistent information model for the ATLAS experiment is outlined. This approach has allowed the collaboration to extend the computing capabilities of the WLCG project and integrate the supercomputers and cloud computing platforms into the software components of the production and distributed analysis workload management system (PanDA, ATLAS).

Accelerated laboratory weathering of acrylic lens materials

NASA Astrophysics Data System (ADS)

Arndt, Thomas; Richter, Steffen; Kogler, René; Pasierb, Mike; Walby, Christopher

2014-09-01

Flat samples from various PMMA formulations subjected to accelerated laboratory weathering in an "Atlas Xenotest Alpha +" weathering device operating at 3 Sun irradiance remain transparent after 6.48GJ/m2 radiant exposure (300 - 400nm). Transmittance is reduced and yellowness index increases. However, the amount of change depends largely on the PMMA formulation. Higher UV absorber concentrations lead to smaller changes in optical properties. Based on a model of CPV efficiency for a particular power train, relative losses of efficiency are between 1 and 28%. Performance regarding these properties can be linked to the UV absorber type and concentrations used.

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondrasek, R.; Kutsaev, Sergey; Delahaye, P.

2012-11-15

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a {sup 252}Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficienciesmore » of both gaseous and solid species including 14.7% for the radioactive species {sup 143}Ba{sup 27+}. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for {sup 23}Na{sup 7+} and 17.9% for {sup 39}K{sup 10+} were obtained injecting stable Na{sup +} and K{sup +} beams from a surface ionization source.« less

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondrasek, R.; Delahaye, P.; Kutsaev, Sergey

2012-11-01

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a 252Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficiencies ofmore » both gaseous and solid species including 14.7% for the radioactive species 143Ba27+. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for 23Na7+ and 17.9% for 39K10+ were obtained injecting stable Na+ and K+ beams from a surface ionization source.« less

Deploying the ATLAS Metadata Interface (AMI) on the cloud with Jenkins

NASA Astrophysics Data System (ADS)

Lambert, F.; Odier, J.; Fulachier, J.; ATLAS Collaboration

2017-10-01

The ATLAS Metadata Interface (AMI) is a mature application of more than 15 years of existence. Mainly used by the ATLAS experiment at CERN, it consists of a very generic tool ecosystem for metadata aggregation and cataloguing. AMI is used by the ATLAS production system, therefore the service must guarantee a high level of availability. We describe our monitoring and administration systems, and the Jenkins-based strategy used to dynamically test and deploy cloud OpenStack nodes on demand.

Performance of the ATLAS Trigger System in 2010

NASA Astrophysics Data System (ADS)

Aad, G.; Abbott, B.; Abdallah, J.; Abdelalim, A. A.; Abdesselam, A.; Abdinov, O.; Abi, B.; Abolins, M.; Abramowicz, H.; Abreu, H.; Acerbi, E.; Acharya, B. S.; Adams, D. L.; Addy, T. N.; Adelman, J.; Aderholz, M.; Adomeit, S.; Adragna, P.; Adye, T.; Aefsky, S.; Aguilar-Saavedra, J. A.; Aharrouche, M.; Ahlen, S. P.; Ahles, F.; Ahmad, A.; Ahsan, M.; Aielli, G.; Akdogan, T.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Akiyama, A.; Alam, M. S.; Alam, M. A.; Albrand, S.; Aleksa, M.; Aleksandrov, I. N.; Alessandria, F.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Aliev, M.; Alimonti, G.; Alison, J.; Aliyev, M.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alviggi, M. G.; Amako, K.; Amaral, P.; Amelung, C.; Ammosov, V. V.; Amorim, A.; Amorós, G.; Amram, N.; Anastopoulos, C.; Andari, N.; Andeen, T.; Anders, C. F.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Andrieux, M.-L.; Anduaga, X. S.; Angerami, A.; Anghinolfi, F.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonelli, S.; Antonov, A.; Antos, J.; Anulli, F.; Aoun, S.; Aperio Bella, L.; Apolle, R.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A. T. H.; Archambault, J. P.; Arfaoui, S.; Arguin, J.-F.; Arik, E.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnault, C.; Artamonov, A.; Artoni, G.; Arutinov, D.; Asai, S.; Asfandiyarov, R.; Ask, S.; Åsman, B.; Asquith, L.; Assamagan, K.; Astbury, A.; Astvatsatourov, A.; Atoian, G.; Aubert, B.; Auerbach, B.; Auge, E.; Augsten, K.; Aurousseau, M.; Austin, N.; Avolio, G.; Avramidou, R.; Axen, D.; Ay, C.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Baccaglioni, G.; Bacci, C.; Bach, A. M.; Bachacou, H.; Bachas, K.; Bachy, G.; Backes, M.; Backhaus, M.; Badescu, E.; Bagnaia, P.; Bahinipati, S.; Bai, Y.; Bailey, D. C.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, M. D.; Baker, S.; Baltasar Dos Santos Pedrosa, F.; Banas, E.; Banerjee, P.; Banerjee, Sw.; Banfi, D.; Bangert, A.; Bansal, V.; Bansil, H. S.; Barak, L.; Baranov, S. P.; Barashkou, A.; Barbaro Galtieri, A.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Bardin, D. Y.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Barrillon, P.; Bartoldus, R.; Barton, A. E.; Bartsch, D.; Bartsch, V.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battaglia, A.; Battistin, M.; Battistoni, G.; Bauer, F.; Bawa, H. S.; Beare, B.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Bechtle, P.; Beck, H. P.; Beckingham, M.; Becks, K. H.; Beddall, A. J.; Beddall, A.; Bedikian, S.; Bednyakov, V. A.; Bee, C. P.; Begel, M.; Behar Harpaz, S.; Behera, P. K.; Beimforde, M.; Belanger-Champagne, C.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellagamba, L.; Bellina, F.; Bellomo, M.; Belloni, A.; Beloborodova, O.; Belotskiy, K.; Beltramello, O.; Ben Ami, S.; Benary, O.; Benchekroun, D.; Benchouk, C.; Bendel, M.; Benedict, B. H.; Benekos, N.; Benhammou, Y.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernardet, K.; Bernat, P.; Bernhard, R.; Bernius, C.; Berry, T.; Bertin, A.; Bertinelli, F.; Bertolucci, F.; Besana, M. I.; Besson, N.; Bethke, S.; Bhimji, W.; Bianchi, R. M.; Bianco, M.; Biebel, O.; Bieniek, S. P.; Biesiada, J.; Biglietti, M.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Biscarat, C.; Bitenc, U.; Black, K. M.; Blair, R. E.; Blanchard, J.-B.; Blanchot, G.; Blazek, T.; Blocker, C.; Blocki, J.; Blondel, A.; Blum, W.; Blumenschein, U.; Bobbink, G. J.; Bobrovnikov, V. B.; Bocchetta, S. S.; Bocci, A.; Boddy, C. R.; Boehler, M.; Boek, J.; Boelaert, N.; Böser, S.; Bogaerts, J. A.; Bogdanchikov, A.; Bogouch, A.; Bohm, C.; Boisvert, V.; Bold, T.; Boldea, V.; Bolnet, N. M.; Bona, M.; Bondarenko, V. G.; Boonekamp, M.; Boorman, G.; Booth, C. N.; Bordoni, S.; Borer, C.; Borisov, A.; Borissov, G.; Borjanovic, I.; Borroni, S.; Bos, K.; Boscherini, D.; Bosman, M.; Boterenbrood, H.; Botterill, D.; Bouchami, J.; Boudreau, J.; Bouhova-Thacker, E. V.; Boulahouache, C.; Bourdarios, C.; Bousson, N.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozhko, N. I.; Bozovic-Jelisavcic, I.; Bracinik, J.; Braem, A.; Branchini, P.; Brandenburg, G. W.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Braun, H. M.; Brelier, B.; Bremer, J.; Brenner, R.; Bressler, S.; Breton, D.; Britton, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brodbeck, T. J.; Brodet, E.; Broggi, F.; Bromberg, C.; Brooijmans, G.; Brooks, W. K.; Brown, G.; Brown, H.; Brubaker, E.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruneliere, R.; Brunet, S.; Bruni, A.; Bruni, G.; Bruschi, M.; Buanes, T.; Bucci, F.; Buchanan, J.; Buchanan, N. J.; Buchholz, P.; Buckingham, R. M.; Buckley, A. G.; Buda, S. I.; Budagov, I. A.; Budick, B.; Büscher, V.; Bugge, L.; Buira-Clark, D.; Bulekov, O.; Bunse, M.; Buran, T.; Burckhart, H.; Burdin, S.; Burgess, T.; Burke, S.; Busato, E.; Bussey, P.; Buszello, C. P.; Butin, F.; Butler, B.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Buttinger, W.; Byatt, T.; Cabrera Urbán, S.; Caforio, D.; Cakir, O.; Calafiura, P.; Calderini, G.; Calfayan, P.; Calkins, R.; Caloba, L. P.; Caloi, R.; Calvet, D.; Calvet, S.; Camacho Toro, R.; Camard, A.; Camarri, P.; Cambiaghi, M.; Cameron, D.; Cammin, J.; Campana, S.; Campanelli, M.; Canale, V.; Canelli, F.; Canepa, A.; Cantero, J.; Capasso, L.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capriotti, D.; Capua, M.; Caputo, R.; Caramarcu, C.; Cardarelli, R.; Carli, T.; Carlino, G.; Carminati, L.; Caron, B.; Caron, S.; Carrillo Montoya, G. D.; Carter, A. A.; Carter, J. R.; Carvalho, J.; Casadei, D.; Casado, M. P.; Cascella, M.; Caso, C.; Castaneda Hernandez, A. M.; Castaneda-Miranda, E.; Castillo Gimenez, V.; Castro, N. F.; Cataldi, G.; Cataneo, F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Cattani, G.; Caughron, S.; Cauz, D.; Cavalleri, P.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Cazzato, A.; Ceradini, F.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cetin, S. A.; Cevenini, F.; Chafaq, A.; Chakraborty, D.; Chan, K.; Chapleau, B.; Chapman, J. D.; Chapman, J. W.; Chareyre, E.; Charlton, D. G.; Chavda, V.; Cheatham, S.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, L.; Chen, S.; Chen, T.; Chen, X.; Cheng, S.; Cheplakov, A.; Chepurnov, V. F.; Cherkaoui El Moursli, R.; Chernyatin, V.; Cheu, E.; Cheung, S. L.; Chevalier, L.; Chiefari, G.; Chikovani, L.; Childers, J. T.; Chilingarov, A.; Chiodini, G.; Chislett, R. T.; Chizhov, M. V.; Choudalakis, G.; Chouridou, S.; Christidi, I. A.; Christov, A.; Chromek-Burckhart, D.; Chu, M. L.; Chudoba, J.; Ciapetti, G.; Ciba, K.; Ciftci, A. K.; Ciftci, R.; Cinca, D.; Cindro, V.; Ciobotaru, M. D.; Ciocca, C.; Ciocio, A.; Cirilli, M.; Ciubancan, M.; Clark, A.; Clark, P. J.; Cleland, W.; Clemens, J. C.; Clement, B.; Clement, C.; Clifft, R. W.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coe, P.; Cogan, J. G.; Coggeshall, J.; Cogneras, E.; Cojocaru, C. D.; Colas, J.; Colijn, A. P.; Collard, C.; Collins, N. J.; Collins-Tooth, C.; Collot, J.; Colon, G.; Conde Muiño, P.; Coniavitis, E.; Conidi, M. C.; Consonni, M.; Consorti, V.; Constantinescu, S.; Conta, C.; Conventi, F.; Cook, J.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cooper-Smith, N. J.; Copic, K.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Costin, T.; Côté, D.; Coura Torres, R.; Courneyea, L.; Cowan, G.; Cowden, C.; Cox, B. E.; Cranmer, K.; Crescioli, F.; Cristinziani, M.; Crosetti, G.; Crupi, R.; Crépé-Renaudin, S.; Cuciuc, C.-M.; Cuenca Almenar, C.; Cuhadar Donszelmann, T.; Cuneo, S.; Curatolo, M.; Curtis, C. J.; Cwetanski, P.; Czirr, H.; Czyczula, Z.; D'Auria, S.; D'Onofrio, M.; D'Orazio, A.; Da Rocha Gesualdi Mello, A.; Da Silva, P. V. M.; Da Via, C.; Dabrowski, W.; Dahlhoff, A.; Dai, T.; Dallapiccola, C.; Dam, M.; Dameri, M.; Damiani, D. S.; Danielsson, H. O.; Dannheim, D.; Dao, V.; Darbo, G.; Darlea, G. L.; Daum, C.; Dauvergne, J. P.; Davey, W.; Davidek, T.; Davidson, N.; Davidson, R.; Davies, E.; Davies, M.; Davison, A. R.; Davygora, Y.; Dawe, E.; Dawson, I.; Dawson, J. W.; Daya, R. K.; De, K.; de Asmundis, R.; De Castro, S.; De Castro Faria Salgado, P. E.; De Cecco, S.; de Graat, J.; De Groot, N.; de Jong, P.; De La Taille, C.; De la Torre, H.; De Lotto, B.; De Mora, L.; De Nooij, L.; De Oliveira Branco, M.; De Pedis, D.; de Saintignon, P.; De Salvo, A.; De Sanctis, U.; De Santo, A.; De Vivie De Regie, J. B.; Dean, S.; Dedovich, D. V.; Degenhardt, J.; Dehchar, M.; Deile, M.; Del Papa, C.; Del Peso, J.; Del Prete, T.; Dell'Acqua, A.; Dell'Asta, L.; Della Pietra, M.; della Volpe, D.; Delmastro, M.; Delpierre, P.; Delruelle, N.; Delsart, P. A.; Deluca, C.; Demers, S.; Demichev, M.; Demirkoz, B.; Deng, J.; Denisov, S. P.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Devetak, E.; Deviveiros, P. O.; Dewhurst, A.; DeWilde, B.; Dhaliwal, S.; Dhullipudi, R.; Di Ciaccio, A.; Di Ciaccio, L.; Di Girolamo, A.; Di Girolamo, B.; Di Luise, S.; Di Mattia, A.; Di Micco, B.; Di Nardo, R.; Di Simone, A.; Di Sipio, R.; Diaz, M. A.; Diblen, F.; Diehl, E. B.; Dieli, M. V.; Dietl, H.; Dietrich, J.; Dietzsch, T. A.; Diglio, S.; Dindar Yagci, K.; Dingfelder, J.; Dionisi, C.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djilkibaev, R.; Djobava, T.; do Vale, M. A. B.; Do Valle Wemans, A.; Doan, T. K. O.; Dobbs, M.; Dobinson, R.; Dobos, D.; Dobson, E.; Dobson, M.; Dodd, J.; Dogan, O. B.; Doglioni, C.; Doherty, T.; Doi, Y.; Dolejsi, J.; Dolenc, I.; Dolezal, Z.; Dolgoshein, B. A.; Dohmae, T.; Donadelli, M.; Donega, M.; Donini, J.; Dopke, J.; Doria, A.; Dos Anjos, A.; Dosil, M.; Dotti, A.; Dova, M. T.; Dowell, J. D.; Doxiadis, A. D.; Doyle, A. T.; Drasal, Z.; Drees, J.; Dressnandt, N.; Drevermann, H.; Driouichi, C.; Dris, M.; Dubbert, J.; Dubbs, T.; Dube, S.; Duchovni, E.; Duckeck, G.; Dudarev, A.; Dudziak, F.; Dührssen, M.; Duerdoth, I. P.; Duflot, L.; Dufour, M.-A.; Dunford, M.; Duran Yildiz, H.; Duxfield, R.; Dwuznik, M.; Dydak, F.; Dzahini, D.; Düren, M.; Ebenstein, W. L.; Ebke, J.; Eckert, S.; Eckweiler, S.; Edmonds, K.; Edwards, C. A.; Edwards, N. 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G.; Sarangi, T.; Sarkisyan-Grinbaum, E.; Sarri, F.; Sartisohn, G.; Sasaki, O.; Sasaki, T.; Sasao, N.; Satsounkevitch, I.; Sauvage, G.; Sauvan, J. B.; Savard, P.; Savinov, V.; Savu, D. O.; Savva, P.; Sawyer, L.; Saxon, D. H.; Says, L. P.; Sbarra, C.; Sbrizzi, A.; Scallon, O.; Scannicchio, D. A.; Scarcella, M.; Schaarschmidt, J.; Schacht, P.; Schäfer, U.; Schaepe, S.; Schaetzel, S.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Schamov, A. G.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Scherzer, M. I.; Schiavi, C.; Schieck, J.; Schioppa, M.; Schlenker, S.; Schlereth, J. L.; Schmidt, E.; Schmidt, M. P.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, M.; Schöning, A.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schroeder, C.; Schroer, N.; Schuh, S.; Schuler, G.; Schultes, J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, J. W.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schwemling, Ph.; Schwienhorst, R.; Schwierz, R.; Schwindling, J.; Scott, W. G.; Searcy, J.; Sedykh, E.; Segura, E.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Seliverstov, D. M.; Sellden, B.; Sellers, G.; Seman, M.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Seuster, R.; Severini, H.; Sevior, M. E.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L. Y.; Shank, J. T.; Shao, Q. T.; Shapiro, M.; Shatalov, P. B.; Shaver, L.; Shaw, C.; Shaw, K.; Sherman, D.; Sherwood, P.; Shibata, A.; Shichi, H.; Shimizu, S.; Shimojima, M.; Shin, T.; Shmeleva, A.; Shochet, M. J.; Short, D.; Shupe, M. A.; Sicho, P.; Sidoti, A.; Siebel, A.; Siegert, F.; Siegrist, J.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S. B.; Simak, V.; Simard, O.; Simic, Lj.; Simion, S.; Simmons, B.; Simonyan, M.; Sinervo, P.; Sinev, N. B.; Sipica, V.; Siragusa, G.; Sisakyan, A. N.; Sivoklokov, S. 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K.; Zanello, L.; Zarzhitsky, P.; Zaytsev, A.; Zeitnitz, C.; Zeller, M.; Zemla, A.; Zendler, C.; Zenin, A. V.; Zenin, O.; Ženiš, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; Zevi della Porta, G.; Zhan, Z.; Zhang, D.; Zhang, H.; Zhang, J.; Zhang, X.; Zhang, Z.; Zhao, L.; Zhao, T.; Zhao, Z.; Zhemchugov, A.; Zheng, S.; Zhong, J.; Zhou, B.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, Y.; Zhuang, X.; Zhuravlov, V.; Zieminska, D.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Ziolkowski, M.; Zitoun, R.; Živković, L.; Zmouchko, V. V.; Zobernig, G.; Zoccoli, A.; Zolnierowski, Y.; Zsenei, A.; zur Nedden, M.; Zutshi, V.; Zwalinski, L.

2012-01-01

Proton-proton collisions at sqrt{s}=7 TeV and heavy ion collisions at sqrt{s_{NN}}=2.76 TeV were produced by the LHC and recorded using the ATLAS experiment's trigger system in 2010. The LHC is designed with a maximum bunch crossing rate of 40 MHz and the ATLAS trigger system is designed to record approximately 200 of these per second. The trigger system selects events by rapidly identifying signatures of muon, electron, photon, tau lepton, jet, and B meson candidates, as well as using global event signatures, such as missing transverse energy. An overview of the ATLAS trigger system, the evolution of the system during 2010 and the performance of the trigger system components and selections based on the 2010 collision data are shown. A brief outline of plans for the trigger system in 2011 is presented.

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.

System-of-Systems Technology-Portfolio-Analysis Tool

NASA Technical Reports Server (NTRS)

O'Neil, Daniel; Mankins, John; Feingold, Harvey; Johnson, Wayne

2012-01-01

Advanced Technology Life-cycle Analysis System (ATLAS) is a system-of-systems technology-portfolio-analysis software tool. ATLAS affords capabilities to (1) compare estimates of the mass and cost of an engineering system based on competing technological concepts; (2) estimate life-cycle costs of an outer-space-exploration architecture for a specified technology portfolio; (3) collect data on state-of-the-art and forecasted technology performance, and on operations and programs; and (4) calculate an index of the relative programmatic value of a technology portfolio. ATLAS facilitates analysis by providing a library of analytical spreadsheet models for a variety of systems. A single analyst can assemble a representation of a system of systems from the models and build a technology portfolio. Each system model estimates mass, and life-cycle costs are estimated by a common set of cost models. Other components of ATLAS include graphical-user-interface (GUI) software, algorithms for calculating the aforementioned index, a technology database, a report generator, and a form generator for creating the GUI for the system models. At the time of this reporting, ATLAS is a prototype, embodied in Microsoft Excel and several thousand lines of Visual Basic for Applications that run on both Windows and Macintosh computers.

AGIS: Evolution of Distributed Computing information system for ATLAS

NASA Astrophysics Data System (ADS)

Anisenkov, A.; Di Girolamo, A.; Alandes, M.; Karavakis, E.

2015-12-01

ATLAS, a particle physics experiment at the Large Hadron Collider at CERN, produces petabytes of data annually through simulation production and tens of petabytes of data per year from the detector itself. The ATLAS computing model embraces the Grid paradigm and a high degree of decentralization of computing resources in order to meet the ATLAS requirements of petabytes scale data operations. It has been evolved after the first period of LHC data taking (Run-1) in order to cope with new challenges of the upcoming Run- 2. In this paper we describe the evolution and recent developments of the ATLAS Grid Information System (AGIS), developed in order to integrate configuration and status information about resources, services and topology of the computing infrastructure used by the ATLAS Distributed Computing applications and services.

ATLAS: A High-cadence All-sky Survey System

NASA Astrophysics Data System (ADS)

Tonry, J. L.; Denneau, L.; Heinze, A. N.; Stalder, B.; Smith, K. W.; Smartt, S. J.; Stubbs, C. W.; Weiland, H. J.; Rest, A.

2018-06-01

Technology has advanced to the point that it is possible to image the entire sky every night and process the data in real time. The sky is hardly static: many interesting phenomena occur, including variable stationary objects such as stars or QSOs, transient stationary objects such as supernovae or M dwarf flares, and moving objects such as asteroids and the stars themselves. Funded by NASA, we have designed and built a sky survey system for the purpose of finding dangerous near-Earth asteroids (NEAs). This system, the “Asteroid Terrestrial-impact Last Alert System” (ATLAS), has been optimized to produce the best survey capability per unit cost, and therefore is an efficient and competitive system for finding potentially hazardous asteroids (PHAs) but also for tracking variables and finding transients. While carrying out its NASA mission, ATLAS now discovers more bright (m < 19) supernovae candidates than any ground based survey, frequently detecting very young explosions due to its 2 day cadence. ATLAS discovered the afterglow of a gamma-ray burst independent of the high energy trigger and has released a variable star catalog of 5 × 106 sources. This is the first of a series of articles describing ATLAS, devoted to the design and performance of the ATLAS system. Subsequent articles will describe in more detail the software, the survey strategy, ATLAS-derived NEA population statistics, transient detections, and the first data release of variable stars and transient light curves.

Cryogenic On-Orbit Liquid Depot Storage, Acquisition, and Transfer Satellite (COLD-SAT)

NASA Technical Reports Server (NTRS)

Schuster, John R.; Russ, Edwin J.; Wachter, Joseph P.

1990-01-01

The Cryogenic On-Orbit Liquid Depot Storage, Acquisition, and Transfer Satellite (COLD-SAT) will perform subcritical liquid hydrogen handling experiments under low gravity conditions to provide engineering data for future space transportation missions. Comprising the four Class 1 enabling experiments are tank press control, tank chilldown, tank no-vent fill, and liquid acquisition device fill/refill. The nine Class 2 enhancing experiments are tanker thermal performance, pressurization, low-gravity setting and outflow, liquid acquisition device performance, transfer line chilldown, outflow subcooling, low-gravity vented fill, fluid dumping, and advanced instrumentation. Consisting of an experiment module mated to a spacecraft bus, COLD-SAT will be placed in an initial 1300 km circular orbit by an Atlas commercial launch vehicle, and will perform experiments in a semi-autonomous mode for a period of up to six months. The three-axis controlled spacecraft bus provides electric power, control and data management, communications, and attitude control along with propulsive acceleration levels ranging from 10(exp -6) to 10(exp -4) g. It is desired to understand the effects that low acceleration levels might have on the heat and mass transfer processes involved in some of the experiments. The experiment module contains the three liquid hydrogen tanks, valves, pressurization and pumping equipment, and instrumentation. Within the highly insulated tanks are specialized fluid management equipment that might be used in future space transportation systems. At launch all the liquid hydrogen for the experiments is contained in the largest tank, which has helium-purged insulation to prevent cryo-pumping of air on the launch pad. The tank is loaded by the hydrogen tanking system used for the Centaur upper stage of the Atlas. After reaching orbit the two smaller tanks become receivers for fluid transfers, and when tanked, become the vessels for performing many of the experiments.

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

Performance of the ATLAS Trigger System in 2010

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2012-01-03

Proton-proton collisions atmore » $$\\sqrt{s}$$ = 7 TeV and heavy ion collisions at $$\\sqrt{s}$$$_ {NN}$$ = 2.76 TeV were produced by the LHC and recorded using the ATLAS experiment's trigger system in 2010. The LHC is designed with a maximum bunch crossing rate of 40 MHz and the ATLAS trigger system is designed to record approximately 200 of these per second. The trigger system selects events by rapidly identifying signatures of muon, electron, photon, tau lepton, jet, and B meson candidates, as well as using global event signatures, such as missing transverse energy. An overview of the ATLAS trigger system, the evolution of the system during 2010 and the performance of the trigger system components and selections based on the 2010 collision data are shown. In conclusion, a brief outline of plans for the trigger system in 2011 is presented.« less

Diagnosis - Using automatic test equipment and artificial intelligence expert systems

NASA Astrophysics Data System (ADS)

Ramsey, J. E., Jr.

Three expert systems (ATEOPS, ATEFEXPERS, and ATEFATLAS), which were created to direct automatic test equipment (ATE), are reviewed. The purpose of the project was to develop an expert system to troubleshoot the converter-programmer power supply card for the F-15 aircraft and have that expert system direct the automatic test equipment. Each expert system uses a different knowledge base or inference engine, basing the testing on the circuit schematic, test requirements document, or ATLAS code. Implementing generalized modules allows the expert systems to be used for any different unit under test. Using converted ATLAS to LISP code allows the expert system to direct any ATE using ATLAS. The constraint propagated frame system allows for the expansion of control by creating the ATLAS code, checking the code for good software engineering techniques, directing the ATE, and changing the test sequence as needed (planning).

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.

System Architecture Modeling for Technology Portfolio Management using ATLAS

NASA Technical Reports Server (NTRS)

Thompson, Robert W.; O'Neil, Daniel A.

2006-01-01

Strategic planners and technology portfolio managers have traditionally relied on consensus-based tools, such as Analytical Hierarchy Process (AHP) and Quality Function Deployment (QFD) in planning the funding of technology development. While useful to a certain extent, these tools are limited in the ability to fully quantify the impact of a technology choice on system mass, system reliability, project schedule, and lifecycle cost. The Advanced Technology Lifecycle Analysis System (ATLAS) aims to provide strategic planners a decision support tool for analyzing technology selections within a Space Exploration Architecture (SEA). Using ATLAS, strategic planners can select physics-based system models from a library, configure the systems with technologies and performance parameters, and plan the deployment of a SEA. Key parameters for current and future technologies have been collected from subject-matter experts and other documented sources in the Technology Tool Box (TTB). ATLAS can be used to compare the technical feasibility and economic viability of a set of technology choices for one SEA, and compare it against another set of technology choices or another SEA. System architecture modeling in ATLAS is a multi-step process. First, the modeler defines the system level requirements. Second, the modeler identifies technologies of interest whose impact on an SEA. Third, the system modeling team creates models of architecture elements (e.g. launch vehicles, in-space transfer vehicles, crew vehicles) if they are not already in the model library. Finally, the architecture modeler develops a script for the ATLAS tool to run, and the results for comparison are generated.

New approaches to observation and modeling of fast-moving glaciers and ice streams

NASA Astrophysics Data System (ADS)

Herzfeld, U. C.; Trantow, T.; Markle, M. J.; Medley, G.; Markus, T.; Neumann, T.

2016-12-01

In this paper, we will give an overview of several new approaches to remote-sensing observations and analysis and to modeling of fast glacier flow. The approaches will be applied in case studies of different types of fast-moving glaciers: (1) The Bering-Bagley Glacier System, Alaska (a surge-type glacier system), (2) Jakobshavn Isbræ, Greenland (a tide-water terminating fjord glacier and outlet of the Greenland Inland Ice), and (3) Icelandic Ice Caps (manifestations of the interaction of volcanic and glaciologic processes). On the observational side, we will compare the capabilities of lidar and radar altimeters, including ICESat's Geoscience Laser Altimeter System (GLAS), CryoSat-2's Synthetic Aperture Interferometric Radar Altimeter (SIRAL) and the future ICESat-2 Advanced Topographic Laser Altimeter System (ATLAS), especially regarding retrieval of surface heights over crevassed regions as typical of spatial and temporal acceleration. Properties that can be expected from ICESat-2 ATLAS data will be illustrated based on analyses of data from ICESat-2 simulator instruments: the Slope Imaging Multi-polarization Photon-counting Lidar (SIMPL) and the Multiple Altimeter Beam Experimental Lidar (MABEL). Information from altimeter data will be augmented by an automated surface classification based on image data, which includes satellite imagery such as LANDSAT and WorldView as well as airborne video imagery of ice surfaces. Numerical experiments using Elmer/Ice will be employed to link parameters derived in observations to physical processes during the surge of the Bering Bagley Glacier System. This allows identification of processes that can be explained in an existing framework and processes that may require new concepts for glacier evolution. Topics include zonation of surge progression in a complex glacier system and crevassing as an indication, storage of glacial water, influence of basal topography and the role of friction laws.

ATLAS: Big Data in a Small Package?

NASA Astrophysics Data System (ADS)

Denneau, Larry

2016-01-01

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

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.

The Atlas of Physiology and Pathophysiology: Web-based multimedia enabled interactive simulations.

PubMed

Kofranek, Jiri; Matousek, Stanislav; Rusz, Jan; Stodulka, Petr; Privitzer, Pavol; Matejak, Marek; Tribula, Martin

2011-11-01

The paper is a presentation of the current state of development for the Atlas of Physiology and Pathophysiology (Atlas). Our main aim is to provide a novel interactive multimedia application that can be used for biomedical education where (a) simulations are combined with tutorials and (b) the presentation layer is simplified while the underlying complexity of the model is retained. The development of the Atlas required the cooperation of many professionals including teachers, system analysts, artists, and programmers. During the design of the Atlas, tools were developed that allow for component-based creation of simulation models, creation of interactive multimedia and their final coordination into a compact unit based on the given design. The Atlas is a freely available online application, which can help to explain the function of individual physiological systems and the causes and symptoms of their disorders. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

ATLAS DBM Module Qualification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soha, Aria; Gorisek, Andrej; Zavrtanik, Marko

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 beingmore » 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.« less

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.

Readiness of the ATLAS Trigger and Data Acquisition system for the first LHC beams

NASA Astrophysics Data System (ADS)

Vandelli, W.; Atlas Tdaq Collaboration

2009-12-01

The ATLAS Trigger and Data Acquisition (TDAQ) system is based on O(2k) processing nodes, interconnected by a multi-layer Gigabit network, and consists of a combination of custom electronics and commercial products. In its final configuration, O(20k) applications will provide the needed capabilities in terms of event selection, data flow, local storage and data monitoring. In preparation for the first LHC beams, many TDAQ sub-systems already reached the final configuration and roughly one third of the final processing power has been deployed. Therefore, the current system allows for a sensible evaluation of the performance and scaling properties. In this paper we introduce the ATLAS TDAQ system requirements and architecture and we discuss the status of software and hardware component. We moreover present the results of performance measurements validating the system design and providing a figure for the ATLAS data acquisition capabilities in the initial data taking period.

Measurements and TCAD simulation of novel ATLAS planar pixel detector structures for the HL-LHC upgrade

NASA Astrophysics Data System (ADS)

Nellist, C.; Dinu, N.; Gkougkousis, E.; Lounis, A.

2015-06-01

The LHC accelerator complex will be upgraded between 2020-2022, to the High-Luminosity-LHC, to considerably increase statistics for the various physics analyses. To operate under these challenging new conditions, and maintain excellent performance in track reconstruction and vertex location, the ATLAS pixel detector must be substantially upgraded and a full replacement is expected. Processing techniques for novel pixel designs are optimised through characterisation of test structures in a clean room and also through simulations with Technology Computer Aided Design (TCAD). A method to study non-perpendicular tracks through a pixel device is discussed. Comparison of TCAD simulations with Secondary Ion Mass Spectrometry (SIMS) measurements to investigate the doping profile of structures and validate the simulation process is also presented.

Crustal and lithospheric imaging of the Atlas Mountains of Morocco inferred from magnetotelluric data

NASA Astrophysics Data System (ADS)

Kiyan, D.; Jones, A. G.; Fullea, J.; Hogg, C.; Ledo, J.; Sinischalchi, A.; Campanya, J.; Picasso Phase II Team

2010-12-01

The Atlas System of Morocco is an intra-continental mountain belt extending for more than 2,000 km along the NW African plate with a predominant NE-SW trend. The System comprises three main branches: the High Atlas, the Middle Atlas, and the Anti Atlas. We present the results of a very recent multi-institutional magnetotelluric (MT) experiment across the Atlas Mountains region that started in September, 2009 and ended in February, 2010, comprising acquisition of broadband and long-period MT data. The experiment consisted of two profiles: (1) a N-S oriented profile crossing the Middle Atlas through the Central High Atlas to the east and (2) a NE-SW profile crossing the western High Atlas towards the Anti Atlas to the west. The MT measurements are part of the PICASSO (Program to Investigate Convective Alboran Sea System Overturn) and the concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROCORES TOPO-EUROPE project) projects, to develop a better understanding of the internal structure and evolution of the crust and lithosphere of the Atlas Mountains. The MT data have been processed with robust remote reference methods and submitted to comprehensive strike and dimensionality analysis. Two clearly depth-differentiated strike directions are apparent for crustal (5-35 km) and lithospheric (50-150 km) depth ranges. These two orientations are roughly consistent with the NW-SE Africa-Eurasia convergence acting since the late Cretaceous, and the NNE-SSW Middle Atlas, where Miocene to recent Alkaline volcanism is present. Two-dimensional (2-D) smooth electrical resistivity models were computed independently for both 50 degrees and 20 degrees E of N strike directions. At the crustal scale, our preliminary results reveal a middle to lower-crustal conductive layer stretching from the Middle Atlas southward towards the High Moulouya basin. The most resistive (and therefore potentially thickest) lithosphere is found beneath the Central High Atlas. The inversion results are to be tested against other geophysical observables (i.e. topography, geoid and gravity anomalies, surface heat flow and seismic velocities) using the software package LitMod. This software combines petrological and geophysical modelling of the lithosphere and sub-lithospheric upper mantle within an internally consistent thermodynamic-geophysical framework, where all relevant properties are functions of temperature, pressure and composition.

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.

Charge breeding results and future prospects with electron cyclotron resonance ion source and electron beam ion source (invited)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondrasek, R.; Levand, A.; Pardo, R.

2012-02-15

The Californium Rare Ion Breeder Upgrade (CARIBU) of the Argonne National Laboratory ATLAS facility will provide low-energy and reaccelerated neutron-rich radioactive beams for the nuclear physics program. A 70 mCi {sup 252}Cf source produces fission fragments which are thermalized and collected by a helium gas catcher into a low-energy particle beam with a charge of 1+ or 2+. An electron cyclotron resonance (ECR) ion source functions as a charge breeder in order to raise the ion charge sufficiently for acceleration in the ATLAS linac. The final CARIBU configuration will utilize a 1 Ci {sup 252}Cf source to produce radioactive beamsmore » with intensities up to 10{sup 6} ions/s for use in the ATLAS facility. The ECR charge breeder has been tested with stable beam injection and has achieved charge breeding efficiencies of 3.6% for {sup 23}Na{sup 8+}, 15.6% for {sup 84}Kr{sup 17+}, and 13.7% for {sup 85}Rb{sup 19+} with typical breeding times of 10 ms/charge state. For the first radioactive beams, a charge breeding efficiency of 11.7% has been achieved for {sup 143}Cs{sup 27+} and 14.7% for {sup 143}Ba{sup 27+}. The project has been commissioned with a radioactive beam of {sup 143}Ba{sup 27+} accelerated to 6.1 MeV/u. In order to take advantage of its lower residual contamination, an EBIS charge breeder will replace the ECR charge breeder in the next two years. The advantages and disadvantages of the two techniques are compared taking into account the requirements of the next generation radioactive beam facilities.« less

Controlling feeding behavior by chemical or gene-directed targeting in the brain: what's so spatial about our methods?

PubMed Central

Khan, Arshad M.

2013-01-01

Intracranial chemical injection (ICI) methods have been used to identify the locations in the brain where feeding behavior can be controlled acutely. Scientists conducting ICI studies often document their injection site locations, thereby leaving kernels of valuable location data for others to use to further characterize feeding control circuits. Unfortunately, this rich dataset has not yet been formally contextualized with other published neuroanatomical data. In particular, axonal tracing studies have delineated several neural circuits originating in the same areas where ICI injection feeding-control sites have been documented, but it remains unclear whether these circuits participate in feeding control. Comparing injection sites with other types of location data would require careful anatomical registration between the datasets. Here, a conceptual framework is presented for how such anatomical registration efforts can be performed. For example, by using a simple atlas alignment tool, a hypothalamic locus sensitive to the orexigenic effects of neuropeptide Y (NPY) can be aligned accurately with the locations of neurons labeled by anterograde tracers or those known to express NPY receptors or feeding-related peptides. This approach can also be applied to those intracranial “gene-directed” injection (IGI) methods (e.g., site-specific recombinase methods, RNA expression or interference, optogenetics, and pharmacosynthetics) that involve viral injections to targeted neuronal populations. Spatial alignment efforts can be accelerated if location data from ICI/IGI methods are mapped to stereotaxic brain atlases to allow powerful neuroinformatics tools to overlay different types of data in the same reference space. Atlas-based mapping will be critical for community-based sharing of location data for feeding control circuits, and will accelerate our understanding of structure-function relationships in the brain for mammalian models of obesity and metabolic disorders. PMID:24385950

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.

A practical workflow for making anatomical atlases for biological research.

PubMed

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

2012-01-01

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

LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease.

PubMed

Zhang, Yanqiong; Yang, Chunyuan; Wang, Shaochuang; Chen, Tao; Li, Mansheng; Wang, Xue; Li, Dongsheng; Wang, Kang; Ma, Jie; Wu, Songfeng; Zhang, Xueli; Zhu, Yunping; Wu, Jinsheng; He, Fuchu

2013-09-01

A large amount of liver-related physiological and pathological data exist in publicly available biological and bibliographic databases, which are usually far from comprehensive or integrated. Data collection, integration and mining processes pose a great challenge to scientific researchers and clinicians interested in the liver. To address these problems, we constructed LiverAtlas (http://liveratlas.hupo.org.cn), a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases by incorporating 53 databases. In the present version, LiverAtlas covers data on liver-related genomics, transcriptomics, proteomics, metabolomics and hepatic diseases. Additionally, LiverAtlas provides a wealth of manually curated information, relevant literature citations and cross-references to other databases. Importantly, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate LiverAtlas data. Furthermore, we have demonstrated two examples of applying LiverAtlas data to identify candidate markers for hepatocellular carcinoma (HCC) at the systems level and to develop a systems biology-based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC differential diagnosis. LiverAtlas is the most comprehensive liver and hepatic disease resource, which helps biologists and clinicians to analyse their data at the systems level and will contribute much to the biomarker discovery and diagnostic performance enhancement for liver diseases. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

"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

Trans-cranial opening of the blood-brain barrier in targeted regions using a stereotaxic brain atlas and focused ultrasound energy.

PubMed

Bing, Chenchen; Ladouceur-Wodzak, Michelle; Wanner, Clinton R; Shelton, John M; Richardson, James A; Chopra, Rajiv

2014-01-01

The blood-brain barrier (BBB) protects the brain by preventing the entry of large molecules; this poses a major obstacle for the delivery of drugs to the brain. A novel technique using focused ultrasound (FUS) energy combined with microbubble contrast agents has been widely used for non-invasive trans-cranial BBB opening. Traditionally, FUS research is conducted with magnetic resonance imaging (MRI) guidance, which is expensive and poses physical limitations due to the magnetic field. A system that could allow researchers to test brain therapies without MR intervention could facilitate and accelerate translational research. In this study, we present a novel FUS system that uses a custom-built FUS generator mounted on a motorized stereotaxic apparatus with embedded brain atlas to locally open the BBB in rodents. The system was initially characterized using a tissue-mimicking phantom. Rodent studies were also performed to evaluate whether non-invasive, localized BBB opening could be achieved using brain atlas-based targeting. Brains were exposed to pulsed focused ultrasound energy at 1.06 MHz in rats and 3.23 MHz in mice, with the focal pressure estimated to be 0.5-0.6 MPa through the skull. BBB opening was confirmed in gross tissue sections by the presence of Evans blue leakage in the exposed region of the brain and by histological assessment. The targeting accuracy of the stereotaxic system was better than 0.5 mm in the tissue-mimicking phantom. Reproducible localized BBB opening was verified with Evans blue dye leakage in 32/33 rats and had a targeting accuracy of ±0.3 mm. The use of higher frequency exposures in mice enabled a similar precision of localized BBB opening as was observed with the low frequency in the rat model. With this dedicated small-animal motorized stereotaxic-FUS system, we achieved accurate targeting of focused ultrasound exposures in the brain for non-invasive opening of the BBB. This system can be used as an alternative to MR-guided FUS and offers researchers the ability to perform efficient studies (30 min per experiment including preparation) at a reduced cost in a conventional laboratory environment.

ATLAS tile calorimeter cesium calibration control and analysis software

NASA Astrophysics Data System (ADS)

Solovyanov, O.; Solodkov, A.; Starchenko, E.; Karyukhin, A.; Isaev, A.; Shalanda, N.

2008-07-01

An online control system to calibrate and monitor ATLAS Barrel hadronic calorimeter (TileCal) with a movable radioactive source, driven by liquid flow, is described. To read out and control the system an online software has been developed, using ATLAS TDAQ components like DVS (Diagnostic and Verification System) to verify the hardware before running, IS (Information Server) for data and status exchange between networked computers, and other components like DDC (DCS to DAQ Connection), to connect to PVSS-based slow control systems of Tile Calorimeter, high voltage and low voltage. A system of scripting facilities, based on Python language, is used to handle all the calibration and monitoring processes from hardware perspective to final data storage, including various abnormal situations. A QT based graphical user interface to display the status of the calibration system during the cesium source scan is described. The software for analysis of the detector response, using online data, is discussed. Performance of the system and first experience from the ATLAS pit are presented.

Performance of the ATLAS trigger system in 2015.

PubMed

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Timoshenko, S; Tipton, P; Tisserant, S; Todome, K; Todorov, T; 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; Trefzger, T; 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; 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; Valencic, N; Valentinetti, S; Valero, A; Valery, L; Valkar, S; Valls Ferrer, J A; Van Den Wollenberg, W; Van Der Deijl, P C; van der Graaf, H; van Eldik, N; van Gemmeren, P; Van Nieuwkoop, J; van Vulpen, I; van Woerden, M C; Vanadia, M; Vandelli, W; Vanguri, R; Vaniachine, A; Vankov, P; Vardanyan, G; Vari, R; Varnes, E W; 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, J C; Vest, A; Vetterli, M C; 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; Vittori, C; Vivarelli, I; Vlachos, S; Vlasak, M; Vogel, M; Vokac, P; Volpi, G; Volpi, M; von der Schmitt, H; von Toerne, E; Vorobel, V; Vorobev, K; Vos, M; Voss, R; Vossebeld, J H; Vranjes, N; Vranjes Milosavljevic, M; 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Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zhukov, K; Zibell, A; Zieminska, D; Zimine, N I; Zimmermann, C; Zimmermann, S; Zinonos, Z; Zinser, M; Ziolkowski, M; Živković, L; Zobernig, G; Zoccoli, A; Zur Nedden, M; Zwalinski, L

2017-01-01

During 2015 the ATLAS experiment recorded [Formula: see text] of proton-proton collision data at a centre-of-mass energy of [Formula: see text]. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton-proton collision data.

NASA Technical Interchange Meeting (TIM): Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box

NASA Technical Reports Server (NTRS)

ONeil, D. A.; Craig, D. A.; Christensen, C. B.; Gresham, E. C.

2005-01-01

The objective of this Technical Interchange Meeting was to increase the quantity and quality of technical, cost, and programmatic data used to model the impact of investing in different technologies. The focus of this meeting was the Technology Tool Box (TTB), a database of performance, operations, and programmatic parameters provided by technologists and used by systems engineers. The TTB is the data repository used by a system of models known as the Advanced Technology Lifecycle Analysis System (ATLAS). This report describes the result of the November meeting, and also provides background information on ATLAS and the TTB.

Performance of the ATLAS trigger system in 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

During 2015 the ATLAS experiment recorded 3.8fb –1 of proton–proton collision data at a centre-of-mass energy of 13TeV. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton–proton collision data.

Performance of the ATLAS trigger system in 2015

DOE PAGES

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

2017-05-18

During 2015 the ATLAS experiment recorded 3.8fb –1 of proton–proton collision data at a centre-of-mass energy of 13TeV. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton–proton collision data.

A High-Resolution In Vivo Atlas of the Human Brain's Serotonin System.

PubMed

Beliveau, Vincent; Ganz, Melanie; Feng, Ling; Ozenne, Brice; Højgaard, Liselotte; Fisher, Patrick M; Svarer, Claus; Greve, Douglas N; Knudsen, Gitte M

2017-01-04

The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT 1A , 5-HT 1B , 5-HT 2A , and 5-HT 4 ) and the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of positron emission tomography (PET) and magnetic resonance imaging (MRI) scans acquired in a total of 210 healthy individuals. Comparison of the regional PET binding measures with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (in picomoles per milliliter). We also assessed the regional association between protein concentration and mRNA expression in the human brain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific associations that show the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system of the human brain. We present a high-resolution positron emission tomography (PET)- and magnetic resonance imaging-based human brain atlas of important serotonin receptors and the transporter. The regional PET-derived binding measures correlate strongly with the corresponding autoradiography protein levels. The strong correlation enables the transformation of the PET-derived human brain atlas into a protein density map of the serotonin (5-hydroxytryptamine, 5-HT) system. Next, we compared the regional receptor/transporter protein densities with mRNA levels and uncovered unique associations between protein expression and density at high detail. This new in vivo neuroimaging atlas of the 5-HT system not only provides insight in the human brain's regional protein synthesis, transport, and density, but also represents a valuable source of information for the neuroscience community as a comparative instrument to assess brain disorders. Copyright © 2017 the authors 0270-6474/17/370120-09$15.00/0.

The consistency service of the ATLAS Distributed Data Management system

NASA Astrophysics Data System (ADS)

Serfon, Cédric; Garonne, Vincent; ATLAS Collaboration

2011-12-01

With the continuously increasing volume of data produced by ATLAS and stored on the WLCG sites, the probability of data corruption or data losses, due to software and hardware failures is increasing. In order to ensure the consistency of all data produced by ATLAS a Consistency Service has been developed as part of the DQ2 Distributed Data Management system. This service is fed by the different ATLAS tools, i.e. the analysis tools, production tools, DQ2 site services or by site administrators that report corrupted or lost files. It automatically corrects the errors reported and informs the users in case of irrecoverable file loss.

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases

PubMed Central

Burns, Gully APC; Cheng, Wei-Cheng; Thompson, Richard H; Swanson, Larry W

2006-01-01

Background Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. Results We have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application. Conclusion Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system. PMID:17166289

Atlas Fractures and Atlas Osteosynthesis: A Comprehensive Narrative Review.

PubMed

Kandziora, Frank; Chapman, Jens R; Vaccaro, Alexander R; Schroeder, Gregory D; Scholz, Matti

2017-09-01

Most atlas fractures are the result of compression forces. They are often combined with fractures of the axis and especially with the odontoid process. Multiple classification systems for atlas fractures have been described. For an adequate diagnosis, a computed tomography is mandatory. To distinguish between stable and unstable atlas injury, it is necessary to evaluate the integrity of the transverse atlantal ligament (TAL) by magnetic resonance imaging and to classify the TAL lesion. Studies comparing conservative and operative management of unstable atlas fractures are unfortunately not available in the literature; neither are studies comparing different operative treatment strategies. Hence all treatment recommendations are based on low level evidence. Most of atlas fractures are stable and will be successfully managed by immobilization in a soft/hard collar. Unstable atlas fractures may be treated conservatively by halo-fixation, but nowadays more and more surgeons prefer surgery because of the potential discomfort and complications of halo-traction. Atlas fractures with a midsubstance ligamentous disruption of TAL or severe bony ligamentous avulsion can be treated by a C1/2 fusion. Unstable atlas fractures with moderate bony ligamentous avulsion may be treated by atlas osteosynthesis. Although the evidence for the different treatment strategies of atlas fractures is low, atlas osteosynthesis has the potential to change treatment philosophies. The reasons for this are described in this review.

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

The ATLAS PanDA Pilot in Operation

NASA Astrophysics Data System (ADS)

Nilsson, P.; Caballero, J.; De, K.; Maeno, T.; Stradling, A.; Wenaus, T.; ATLAS Collaboration

2011-12-01

The Production and Distributed Analysis system (PanDA) [1-2] was designed to meet ATLAS [3] requirements for a data-driven workload management system capable of operating at LHC data processing scale. Submitted jobs are executed on worker nodes by pilot jobs sent to the grid sites by pilot factories. This paper provides an overview of the PanDA pilot [4] system and presents major features added in light of recent operational experience, including multi-job processing, advanced job recovery for jobs with output storage failures, gLExec [5-6] based identity switching from the generic pilot to the actual user, and other security measures. The PanDA system serves all ATLAS distributed processing and is the primary system for distributed analysis; it is currently used at over 100 sites worldwide. We analyze the performance of the pilot system in processing real LHC data on the OSG [7], EGI [8] and Nordugrid [9-10] infrastructures used by ATLAS, and describe plans for its evolution.

Large-scale extraction of brain connectivity from the neuroscientific literature

PubMed Central

Richardet, Renaud; Chappelier, Jean-Cédric; Telefont, Martin; Hill, Sean

2015-01-01

Motivation: In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for modern neuroinformatics is finding methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and the integration of such data into computational models. A key example of this is metascale brain connectivity, where results are not reported in a normalized repository. Instead, these experimental results are published in natural language, scattered among individual scientific publications. This lack of normalization and centralization hinders the large-scale integration of brain connectivity results. In this article, we present text-mining models to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience. The brain regions are identified with three different named entity recognizers (NERs) and then normalized against two atlases: the Allen Brain Atlas (ABA) and the atlas from the Brain Architecture Management System (BAMS). We then use three different extractors to assess inter-region connectivity. Results: NERs and connectivity extractors are evaluated against a manually annotated corpus. The complete in litero extraction models are also evaluated against in vivo connectivity data from ABA with an estimated precision of 78%. The resulting database contains over 4 million brain region mentions and over 100 000 (ABA) and 122 000 (BAMS) potential brain region connections. This database drastically accelerates connectivity literature review, by providing a centralized repository of connectivity data to neuroscientists. Availability and implementation: The resulting models are publicly available at github.com/BlueBrain/bluima. Contact: renaud.richardet@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25609795

Reliability and degradation of oxide VCSELs due to reaction to atmospheric water vapor

NASA Astrophysics Data System (ADS)

Dafinca, Alexandru; Weidberg, Anthony R.; McMahon, Steven J.; Grillo, Alexander A.; Farthouat, Philippe; Ziolkowski, Michael; Herrick, Robert W.

2013-03-01

850nm oxide-aperture VCSELs are susceptible to premature failure if operated while exposed to atmospheric water vapor, and not protected by hermetic packaging. The ATLAS detector in CERN's Large Hadron Collider (LHC) has had approximately 6000 channels of Parallel Optic VCSELs fielded under well-documented ambient conditions. Exact time-to-failure data has been collected on this large sample, providing for the first time actual failure data at use conditions. In addition, the same VCSELs were tested under a variety of accelerated conditions to allow us to construct a more accurate acceleration model. Failure analysis information will also be presented to show what we believe causes corrosion-related failure for such VCSELs.

The LHC Experiments

ScienceCinema

Lincoln, Don

2018-01-16

The Large Hadron Collider or LHC is the world’s biggest particle accelerator, but it can only get particles moving very quickly. To make measurements, scientists must employ particle detectors. There are four big detectors at the LHC: ALICE, ATLAS, CMS, and LHCb. In this video, Fermilab’s Dr. Don Lincoln introduces us to these detectors and gives us an idea of each one’s capabilities.

Smashing Protons to Smithereens

ScienceCinema

Pleier, Marc-André

2018-01-05

Pleier discusses the extraordinary research taking place at the Large Hadron Collider (LHC) — the world’s newest, biggest, and highest energy particle accelerator located at CERN. Pleier is one of hundreds of researchers from around the world working on ATLAS, a seven-story particle detector positioned at a point where the LHC’s oppositely circulating beams of protons slam into one another head-on.

Solar System atlas series on the Eötvös University, Budapest, Hungary: textbooks for space and planetary science education

NASA Astrophysics Data System (ADS)

Berczi, Sz.; Hargitai, H.; Horvath, A.; Illes, E.; Kereszturi, A.; Mortl, M.; Sik, A.; Weidinger, T.; Hegyi, S.; Hudoba, Gy.

Planetary science education needs new forms of teaching. Our group have various initiatives of which a new atlas series about the studies of the Solar System materials, planetary surfaces and atmospheres, instrumental field works with robots (landers, rovers) and other beautiful field work analog studies. Such analog studies are both used in comparative planetology as scientific method and it also plays a key role in planetary science education. With such initiatives the whole system of the knowledge of terrestrial geology can be transformed to the conditions of other planetary worlds. We prepared both courses and their textbooks in Eötvös University in space science education and edited the following educational materials worked out by the members of our space science education and research group: (1): Planetary and Material Maps on: Lunar Rocks, Meteorites (2000); (2): Investigating Planetary Surfaces with the Experimental Space Probe Hunveyor Constructed on the Basis of Surveyor (2001); (3): Atlas of Planetary Bodies (2001); (4): Atlas of Planetary Atmospheres (2002); (5): Space Research and Geometry (2002); (6): Atlas of Micro Environments of Planetary Surfaces (2003); (7): Atlas of Rovers and Activities on Planetary Surfaces (2004); (8): Space Research and Chemistry (2005); (9): Planetary Analog Studies and Simulations: Materials, Terrains, Morphologies, Processes. (2005); References: [1] Bérczi Sz., Hegyi S., Kovács Zs., Fabriczy A., Földi T., Keresztesi M., Cech V., Drommer B., Gránicz K., Hevesi L., Borbola T., Tóth Sz., Németh I., Horváth Cs., Diósy T., Kovács B., Bordás F., Köll˝ Z., Roskó F., Balogh Zs., Koris A., o 1 Imrek Gy. (Bérczi Sz., Kabai S. Eds.) (2002): Concise Atlas of the Solar System (2): From Surveyor to Hunveyor. How we constructed an experimental educational planetary lander model. UNICONSTANT. Budapest-Pécs-Szombathely-Püspökladány. [2] Bérczi Sz., Hargitai H., Illés E., Kereszturi Á., Sik A., Földi T., Hegyi S., Kovács Zs., Mörtl M., Weidinger T. (2004): Concise Atlas of the Solar System (6): Atlas of Microenvironments of Planetary surfaces. ELTE TTK Kozmikus Anyagokat Vizsgáló Ûrkutató Csoport, UNICONSTANT, Budapest-Püspökladány; [3] Szaniszló Bérczi, Henrik Hargitai, Ákos Kereszturi, András Sik (2005): Concise Atlas on the Solar System (3): Atlas of Planetary Bodies. ELTE TTK Kozmikus Anyagokat Vizsgáló Ûrkutató Csoport. Budapest, [4] Szaniszló Bérczi, Tivadar Földi, Péter Gadányi, Arnold Gucsik, Henrik Hargitai, Sándor Hegyi, György Hudoba, Sándor Józsa, Ákos Kereszturi, János Rakonczai, András Sik, György Szakmány, Kálmán Török (2005): Concise Atlas on the Solar System (9): Planetary Analog Studies and Simulations: Materials, Terrains, Morphologies, Processes. (Szaniszló Bérczi, editor) ELTE TTK Kozmikus Anyagokat Vizsgáló Ûrkutató Csoport, UNICONSTANT, Budapest-Püspökladány. 2

Structural styles of the western onshore and offshore termination of the High Atlas, Morocco

NASA Astrophysics Data System (ADS)

Hafid, Mohamad; Zizi, Mahmoud; Bally, Albert W.; Ait Salem, Abdellah

2006-01-01

The present work aims (1) at documenting, by regional seismic transects, how the structural style varies in the western High Atlas system and its prolongation under the present-day Atlantic margin, (2) at understanding how this variation is related to the local geological framework, especially the presence of salt within the sedimentary cover, and (3) at discussing the exact geographic location of the northern front of the western High Atlas and how it links with the most western Atlas front in the offshore Cap Tafelney High Atlas. Previous work showed that the structural style of the Atlas belt changes eastward from a dominantly thick-skinned one in central and eastern High Atlas and Middle Atlas of Morocco to a dominantly thin-skinned one in Algeria and Tunisia. We propose here to show that a similar structural style change can be observed in the other direction of the Atlas Belt within its western termination, where the western High Atlas intersects at right angle the Atlantic passive margin and develops into a distinct segment, namely the High Atlas of Cap Tafelney, where salt/evaporite-based décollement tectonics prevail. To cite this article: M. Hafid et al., C. R. Geoscience 338 (2006).

High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

NASA Astrophysics Data System (ADS)

Huang, Su; Lu, Zhongkang; Huang, Weimin; Seramani, Sankar; Ramasamy, Boominathan; Sekar, Sakthivel; Guan, Cuntai; Bhakoo, Kishore

2016-03-01

Image based atlases for rats brain have a significant impact on pre-clinical research. In this project we acquired T1-weighted images from Wistar rodent brains with fine 59μm isotropical resolution for generation of the atlas template image. By applying post-process procedures using a semi-automatic brain extraction method, we delineated the brain tissues from source data. Furthermore, we applied a symmetric group-wise normalization method to generate an optimized template of T1 image of rodent brain, then aligned our template to the Waxholm Space. In addition, we defined several simple and explicit landmarks to corresponding our template with the well known Paxinos stereotaxic reference system. Anchoring at the origin of the Waxholm Space, we applied piece-wise linear transformation method to map the voxels of the template into the coordinates system in Paxinos' stereotoxic coordinates to facilitate the labelling task. We also cross-referenced our data with both published rodent brain atlas and image atlases available online, methodologically labelling the template to produce a Wistar brain atlas identifying more than 130 structures. Particular attention was paid to the cortex and cerebellum, as these areas encompass the most researched aspects of brain functions. Moreover, we adopted the structure hierarchy and naming nomenclature common to various atlases, so that the names and hierarchy structure presented in the atlas are readily recognised for easy use. It is believed the atlas will present a useful tool in rodent brain functional and pharmaceutical studies.

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.

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:28280284

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.

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.

The Measurement of Spectral Characteristics and Composition of Radiation in Atlas with MEDIPIX2-USB Devices

NASA Astrophysics Data System (ADS)

Campbell, M.; Doležal, Z.; Greiffenberg, D.; Heijne, E.; Holy, T.; Idárraga, J.; Jakůbek, J.; Král, V.; Králík, M.; Lebel, C.; Leroy, C.; Llopart, X.; Lord, G.; Maneuski, D.; Ouellette, O.; Sochor, V.; Pospíšil, S.; Suk, M.; Tlustos, L.; Vykydal, Z.; Wilhelm, I.

2008-06-01

A network of devices to perform real-time measurements of the spectral characteristics and composition of radiation in the ATLAS detector and cavern during its operation is being built. This system of detectors will be a stand alone system fully capable of delivering real-time images of fluxes and spectral composition of different particle species including slow and fast neutrons. The devices are based on MEDIPIX2 pixel silicon detectors that will be operated via active USB cables and USB-Ethernet extenders through an Ethernet network by a PC located in the USA15 ATLAS control room. The installation of 14 devices inside ATLAS (detector and cavern) is in progress.

Application of accelerator sources for pulsed neutron logging of oil and gas wells

NASA Astrophysics Data System (ADS)

Randall, R. R.

1985-05-01

Dresser Atlas introduced the first commercial pulsed neutron oil well log in the early 1960s. This log had the capability of differentiating oil from salt water in a completed well. In the late 1970s the first continuous carbon/oxygen (C/O) log capable of differentiating oil from fresh water was introduced. The sources used in these commercial logs are radial geometry deuterium-tritium reaction devices with Cockcroft-Walton voltage multipliers providing the accelerator voltage. The commercial logging tools using these accelerators are comprised of scintillators detectors, power supplies, line drivers and receivers, and various timing and communications electronics. They are used to measure either the time decay or energy spectra of neutron-induced gamma events. The time decay information is useful in determining the neutron capture cross section, and the energy spectra is used to characterize inelastic neutron events.

High-resolution Ceres Low Altitude Mapping Orbit Atlas derived from Dawn Framing Camera images

NASA Astrophysics Data System (ADS)

Roatsch, Th.; Kersten, E.; Matz, K.-D.; Preusker, F.; Scholten, F.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

2017-06-01

The Dawn spacecraft Framing Camera (FC) acquired over 31,300 clear filter images of Ceres with a resolution of about 35 m/pxl during the eleven cycles in the Low Altitude Mapping Orbit (LAMO) phase between December 16 2015 and August 8 2016. We ortho-rectified the images from the first four cycles and produced a global, high-resolution, uncontrolled photomosaic of Ceres. This global mosaic is the basis for a high-resolution Ceres atlas that consists of 62 tiles mapped at a scale of 1:250,000. The nomenclature used in this atlas was proposed by the Dawn team and was approved by the International Astronomical Union (IAU). The full atlas is available to the public through the Dawn Geographical Information System (GIS) web page [http://dawngis.dlr.de/atlas] and will become available through the NASA Planetary Data System (PDS) (http://pdssbn.astro.umd.edu/).

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, Application and Operational. It is possible to use several variants of the basemap for each stratum. Furthermore, the developed methods of integration allow logically coordinate the application of different types of basemaps into a specific EA/AtIS. For example, such variants of the Conceptual strata basemap as the National map of Ukraine of our production and external resources such as OpenStreetMap are used with the help of meta-system replacement procedures. The authors propose a Conceptual framework of the basemap, which consists of the Conceptual solutions framework of the basemap and few Application solutions frameworks of the basemap. Conceptual framework is intended to be reused in many projects and significantly reduce the resources. We differentiate Application frameworks for mobile and non-mobile environments. The results of the research are applied in few EA produced in 2014-2015 at the Institute of Geography of the National Academy of Sciences of Ukraine. One of them is the Atlas of emergency situations. It includes elements that work on mobile devices. At its core it is "ubiquitous" subset of the Atlas.

ATLAS-plus: Multimedia Instruction in Embryology, Gross Anatomy, and Histology

PubMed Central

Chapman, CM; Miller, JG; Bush, LC; Bruenger, JA; Wysor, WJ; Meininger, ET; Wolf, FM; Fischer, TV; Beaudoin, AR; Burkel, WE; MacCallum, DK; Fisher, DL; Carlson, BM

1992-01-01

ATLAS-plus [Advanced Tools for Learning Anatomical Structure] is a multimedia program used to assist in the teaching of anatomy at the University of Michigan Medical School. ATLAS-plus contains three courses: Histology, Embryology, and Gross Anatomy. In addition to the three courses, a glossary containing terms from the three courses is available. All three courses and the glossary are accessible in the ATLAS-plus environment. The ATLAS-plus environment provides a consistent set of tools and options so that the user can navigate easily and intelligently in and between the various courses and modules in the ATLAS-plus world. The program is a collaboration between anatomy and cell biology faculty, medical students, graphic artists, systems analysts, and instructional designers. PMID:1482964

Complete distributed computing environment for a HEP experiment: experience with ARC-connected infrastructure for ATLAS

NASA Astrophysics Data System (ADS)

Read, A.; Taga, A.; O-Saada, F.; Pajchel, K.; Samset, B. H.; Cameron, D.

2008-07-01

Computing and storage resources connected by the Nordugrid ARC middleware in the Nordic countries, Switzerland and Slovenia are a part of the ATLAS computing Grid. This infrastructure is being commissioned with the ongoing ATLAS Monte Carlo simulation production in preparation for the commencement of data taking in 2008. The unique non-intrusive architecture of ARC, its straightforward interplay with the ATLAS Production System via the Dulcinea executor, and its performance during the commissioning exercise is described. ARC support for flexible and powerful end-user analysis within the GANGA distributed analysis framework is also shown. Whereas the storage solution for this Grid was earlier based on a large, distributed collection of GridFTP-servers, the ATLAS computing design includes a structured SRM-based system with a limited number of storage endpoints. The characteristics, integration and performance of the old and new storage solutions are presented. Although the hardware resources in this Grid are quite modest, it has provided more than double the agreed contribution to the ATLAS production with an efficiency above 95% during long periods of stable operation.

The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain.

PubMed

Schilling, Kurt G; Gao, Yurui; Stepniewska, Iwona; Wu, Tung-Lin; Wang, Feng; Landman, Bennett A; Gore, John C; Chen, Li Min; Anderson, Adam W

2017-10-01

We describe the development of the first digital atlas of the normal squirrel monkey brain and present the resulting product, VALiDATe29. The VALiDATe29 atlas is based on multiple types of magnetic resonance imaging (MRI) contrast acquired on 29 squirrel monkeys, and is created using unbiased, nonlinear registration techniques, resulting in a population-averaged stereotaxic coordinate system. The atlas consists of multiple anatomical templates (proton density, T1, and T2* weighted), diffusion MRI templates (fractional anisotropy and mean diffusivity), and ex vivo templates (fractional anisotropy and a structural MRI). In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. The combination of intensity templates and image segmentations make this atlas suitable for the fundamental atlas applications of spatial normalization and label propagation. Together, this atlas facilitates 3D anatomical localization and region of interest delineation, and enables comparisons of experimental data across different subjects or across different experimental conditions. This article describes the atlas creation and its contents, and demonstrates the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community.

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aad, G.; Abat, E.; Abbott, B.

2011-11-28

The Large Hadron Collider (LHC) at CERN promises a major step forward in the understanding of the fundamental nature of matter. The ATLAS experiment is a general-purpose detector for the LHC, whose design was guided by the need to accommodate the wide spectrum of possible physics signatures. The major remit of the ATLAS experiment is the exploration of the TeV mass scale where groundbreaking discoveries are expected. In the focus are the investigation of the electroweak symmetry breaking and linked to this the search for the Higgs boson as well as the search for Physics beyond the Standard Model. Inmore » this report a detailed examination of the expected performance of the ATLAS detector is provided, with a major aim being to investigate the experimental sensitivity to a wide range of measurements and potential observations of new physical processes. An earlier summary of the expected capabilities of ATLAS was compiled in 1999 [1]. A survey of physics capabilities of the CMS detector was published in [2]. The design of the ATLAS detector has now been finalised, and its construction and installation have been completed [3]. An extensive test-beam programme was undertaken. Furthermore, the simulation and reconstruction software code and frameworks have been completely rewritten. Revisions incorporated reflect improved detector modelling as well as major technical changes to the software technology. Greatly improved understanding of calibration and alignment techniques, and their practical impact on performance, is now in place. The studies reported here are based on full simulations of the ATLAS detector response. A variety of event generators were employed. The simulation and reconstruction of these large event samples thus provided an important operational test of the new ATLAS software system. In addition, the processing was distributed world-wide over the ATLAS Grid facilities and hence provided an important test of the ATLAS computing system - this is the origin of the expression 'CSC studies' ('computing system commissioning'), which is occasionally referred to in these volumes. The work reported does generally assume that the detector is fully operational, and in this sense represents an idealised detector: establishing the best performance of the ATLAS detector with LHC proton-proton collisions is a challenging task for the future. The results summarised here therefore represent the best estimate of ATLAS capabilities before real operational experience of the full detector with beam. Unless otherwise stated, simulations also do not include the effect of additional interactions in the same or other bunch-crossings, and the effect of neutron background is neglected. Thus simulations correspond to the low-luminosity performance of the ATLAS detector. This report is broadly divided into two parts: firstly the performance for identification of physics objects is examined in detail, followed by a detailed assessment of the performance of the trigger system. This part is subdivided into chapters surveying the capabilities for charged particle tracking, each of electron/photon, muon and tau identification, jet and missing transverse energy reconstruction, b-tagging algorithms and performance, and finally the trigger system performance. In each chapter of the report, there is a further subdivision into shorter notes describing different aspects studied. The second major subdivision of the report addresses physics measurement capabilities, and new physics search sensitivities. Individual chapters in this part discuss ATLAS physics capabilities in Standard Model QCD and electroweak processes, in the top quark sector, in b-physics, in searches for Higgs bosons, supersymmetry searches, and finally searches for other new particles predicted in more exotic models.« less

Commissioning of the ATLAS pixel detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 themore » ATLAS pixel system are presented.« less

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 models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

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.

Measurement of the production cross section for Z / γ * in association with jets in p p collisions at s = 7 TeV with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2012-02-28

Results are presented on the production of jets of particles in association with a Z / γ * boson, in proton-proton collisions at √ s = 7 TeV with the ATLAS detector. The analysis includes the full 2010 data set, collected with a low rate of multiple proton-proton collisions in the accelerator, corresponding to an integrated luminosity of 36 pb -1 . Inclusive jet cross sections in Z / γ * events, with Z / γ * decaying into electron or muon pairs, are measured for jets with transverse momentum p T > 30 GeV and jet rapidity | ymore » | < 4.4 . The measurements are compared to next-to-leading-order perturbative QCD calculations, and to predictions from different Monte Carlo generators implementing leading-order matrix elements supplemented by parton showers.« less

El Yunque National Forest Atlas

Treesearch

Maya Quiñones; Isabel K. Parés-Ramos; William A. Gould; Grizelle Gonzalez; Kathleen McGinley; Pedro Ríos

2018-01-01

El Yunque National Forest Atlas is a collaborative effort by the International Institute of Tropical Forestry and El Yunque National Forest to provide upto-date maps and analyses of spatial information of an important natural reserve in Puerto Rico and the only tropical forest in the National Forest System of the United States. El Yunque National Forest Atlas serves as...

Ground Water Atlas of the United States: Introduction and national summary

USGS Publications Warehouse

Miller, James A.

1999-01-01

The Ground Water Atlas of the United States provides a summary of the most important information available for each principal aquifer, or rock unit that will yield usable quantities of water to wells, throughout the 50 States, Puerto Rico, and the U.S. Virgin Islands. The Atlas is an outgrowth of the Regional Aquifer-System Analysis (RASA) program of the U.S. Geological Survey (USGS), a program that investigated 24 of the most important aquifers and aquifer systems of the Nation and one in the Caribbean Islands (fig. 1). The objectives of the RASA program were to define the geologic and hydrologic frameworks of each aquifer system, to assess the geochemistry of the water in the system, to characterize the ground-water flow system, and to describe the effects of development on the flow system. Although the RASA studies did not cover the entire Nation, they compiled much of the data needed to make the National assessments of ground-water resources presented in the Ground Water Atlas of the United States. The Atlas, however, describes the location, extent, and geologic and hydrologic characteristics of all the important aquifers in the United States, including those not studied by the RASA program. The Atlas is written so that it can be understood by readers who are not hydrologists. Simple language is used to explain technical terms. The principles that control the presence, movement, and chemical quality of ground water in different climatic, topographic, and geologic settings are clearly illustrated. The Atlas is, therefore, useful as a teaching tool for introductory courses in hydrology or hydrogeology at the college level and as an overview of ground-water conditions for consultants who need information about an individual aquifer. It also serves as an introduction to regional and National ground-water resources for lawmakers, personnel of local, State, or Federal agencies, or anyone who needs to understand ground-water occurrence, movement, and quality. The purpose of the Ground Water Atlas of the United States is to summarize, in one publication with a common format, the most important ground-water information that has been collected over many years by the USGS, other Federal agencies, and State and local water management agencies. The purpose of this introductory chapter is to describe the content of the Atlas; to discuss the characteristics, use, and limitations of the maps and other types of illustrations used in the different chapters of the book; to summarize the locations of the principal aquifers on a Nationwide map; and to give an example of an aquifer in each principal hydrogeologic setting.

The Belle II imaging Time-of-Propagation (iTOP) detector

NASA Astrophysics Data System (ADS)

Fast, J.; Belle II Barrel Particle Identification Group

2017-12-01

High precision flavor physics measurements are an essential complement to the direct searches for new physics at the LHC ATLAS and CMS experiments. Such measurements will be performed using the upgraded Belle II detector that will take data at the SuperKEKB accelerator. With 40x the luminosity of KEKB, the detector systems must operate efficiently at much higher rates than the original Belle detector. A central element of the upgrade is the barrel particle identification system. Belle II has built and installed an imaging-Time-of-Propagation (iTOP) detector. The iTOP uses quartz optics as Cherenkov radiators. The photons are transported down the quartz bars via total internal reflection with a spherical mirror at the forward end to reflect photons to the backward end where they are imaged onto an array of segmented Micro-Channel Plate Photo-Multiplier Tubes (MCP-PMTs). The system is read out using giga-samples per second waveform sampling Application-Specific Integrated Circuits (ASICs). The combined timing and spatial distribution of the photons for each event are used to determine particle species. This paper provides an overview of the iTOP system.

EARTH SYSTEM ATLAS: A Platform for Access to Peer-Reviewed Information about process and change in the Earth System

NASA Astrophysics Data System (ADS)

Sahagian, D.; Prentice, C.

2004-12-01

A great deal of time, effort and resources have been expended on global change research to date, but dissemination and visualization of the key pertinent data sets has been problematical. Toward that end, we are constructing an Earth System Atlas which will serve as a single compendium describing the state of the art in our understanding of the Earth system and how it has responded to and is likely to respond to natural and anthropogenic perturbations. The Atlas is an interactive web-based system of data bases and data manipulation tools and so is much more than a collection of pre-made maps posted on the web. It represents a tool for assembling, manipulating, and displaying specific data as selected and customized by the user. Maps are created "on the fly" according to user-specified instructions. The information contained in the Atlas represents the growing body of data assembled by the broader Earth system research community, and can be displayed in the form of maps and time series of the various relevant parameters that drive and are driven by changes in the Earth system at various time scales. The Atlas is designed to display the information assembled by the global change research community in the form of maps and time series of all the relevant parameters that drive or are driven by changes in the Earth System at various time scales. This will serve to provide existing data to the community, but also will help to highlight data gaps that may hinder our understanding of critical components of the Earth system. This new approach to handling Earth system data is unique in several ways. First and foremost, data must be peer-reviewed. Further, it is designed to draw on the expertise and products of extensive international research networks rather than on a limited number of projects or institutions. It provides explanatory explanations targeted to the user's needs, and the display of maps and time series can be customize by the user. In general, the Atlas is designed provide the research community with a new opportunity for data observation and manipulation, enabling new scientific discoveries in the coming years. An initial prototype of the Atlas has been developed and can be manipulated in real time.

Second NASA Technical Interchange Meeting (TIM): Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box (TTB)

NASA Technical Reports Server (NTRS)

ONeil, D. A.; Mankins, J. C.; Christensen, C. B.; Gresham, E. C.

2005-01-01

The Advanced Technology Lifecycle Analysis System (ATLAS), a spreadsheet analysis tool suite, applies parametric equations for sizing and lifecycle cost estimation. Performance, operation, and programmatic data used by the equations come from a Technology Tool Box (TTB) database. In this second TTB Technical Interchange Meeting (TIM), technologists, system model developers, and architecture analysts discussed methods for modeling technology decisions in spreadsheet models, identified specific technology parameters, and defined detailed development requirements. This Conference Publication captures the consensus of the discussions and provides narrative explanations of the tool suite, the database, and applications of ATLAS within NASA s changing environment.

Trigger Menu-aware Monitoring for the ATLAS experiment

NASA Astrophysics Data System (ADS)

Hoad, Xanthe; ATLAS Collaboration

2017-10-01

We present a“trigger menu-aware” monitoring system designed for the Run-2 data-taking of the ATLAS experiment at the LHC. Unlike Run-1, where a change in the trigger menu had to be matched by the installation of a new software release at Tier-0, the new monitoring system aims to simplify the ATLAS operational workflows. This is achieved by integrating monitoring updates in a quick and flexible manner via an Oracle DB interface. We present the design and the implementation of the menu-aware monitoring, along with lessons from the operational experience of the new system with the 2016 collision data.

Fine grained event processing on HPCs with the ATLAS Yoda system

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Experience with ATLAS MySQL PanDA database service

NASA Astrophysics Data System (ADS)

Smirnov, Y.; Wlodek, T.; De, K.; Hover, J.; Ozturk, N.; Smith, J.; Wenaus, T.; Yu, D.

2010-04-01

The PanDA distributed production and analysis system has been in production use for ATLAS data processing and analysis since late 2005 in the US, and globally throughout ATLAS since early 2008. Its core architecture is based on a set of stateless web services served by Apache and backed by a suite of MySQL databases that are the repository for all PanDA information: active and archival job queues, dataset and file catalogs, site configuration information, monitoring information, system control parameters, and so on. This database system is one of the most critical components of PanDA, and has successfully delivered the functional and scaling performance required by PanDA, currently operating at a scale of half a million jobs per week, with much growth still to come. In this paper we describe the design and implementation of the PanDA database system, its architecture of MySQL servers deployed at BNL and CERN, backup strategy and monitoring tools. The system has been developed, thoroughly tested, and brought to production to provide highly reliable, scalable, flexible and available database services for ATLAS Monte Carlo production, reconstruction and physics analysis.

Large Scale Software Building with CMake in ATLAS

NASA Astrophysics Data System (ADS)

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

2017-10-01

The offline software of the ATLAS experiment at the Large Hadron Collider (LHC) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector’s trigger system to select LHC collision events during data taking. The ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows, many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications also require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the above mentioned software packages. This also makes it possible to develop and test new and modified packages on top of existing releases. The system also allows one to detect and execute partial rebuilds of the release based on single package changes. The build system makes use of CPack for building RPM packages out of the software releases, and CTest for running unit and integration tests. We report on the migration and integration of the ATLAS software to CMake and show working examples of this large scale project in production.

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

PubMed

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

2014-01-01

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

The SRI24 multichannel brain atlas: construction and applications

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

An Update on the VAMOS Extremes Working Group Activities

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Cavalcanti, Iracema

2011-01-01

We review here the progress of the Variability of the American MOnsoon Systems (VAMOS) extremes working group since it was formed in February of 2010. The goals of the working group are to 1) develop an atlas of warm-season extremes over the Americas, 2) evaluate existing and planned simulations, and 3) suggest new model runs to address mechanisms and predictability of extremes. Substantial progress has been made in the development of an extremes atlas based on gridded observations and several reanalysis products including Modern Era Retrospective-Analysis for Research and Applications (MERRA) and Climate Forecast System Reanalysis (CFSR). The status of the atlas, remaining issues and plans for its expansion to include model data will be discussed. This includes the possibility of adding a companion atlas based on station observations based on the software developed under the World Climate Research Programme (WCRP) Expert Team on Climate Change. Detection and Indices (ETCCDI) activity. We will also review progress on relevant research and plans for the use and validation of the atlas results.

Development, deployment and operations of ATLAS databases

NASA Astrophysics Data System (ADS)

Vaniachine, A. V.; Schmitt, J. G. v. d.

2008-07-01

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

Atlas of Variations in Medical Practice in Spain: the Spanish National Health Service under scrutiny.

PubMed

Bernal-Delgado, Enrique; García-Armesto, Sandra; Peiró, Salvador

2014-01-01

Early in the 2000s, a countrywide health services research initiative was launched under the acronym of Atlas VPM: Atlas of Variations in Medical Practice in the Spanish National Health System. This initiative aimed at describing systematic and unwarranted variations in medical practice at geographic level-building upon the seminal experience of the Dartmouth Atlas of Health Care. The paper aims at explaining the Spanish Atlas experience, built upon the pioneer Dartmouth inspiration. A few selected examples will be used along the following sections to illustrate the outlined conceptual framework, the different factors that may affect variation, and some methodological challenges. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

NASA Astrophysics Data System (ADS)

Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G.; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S.; Ding, Zhaohua; Gore, John C.; Chen, Li min; Landman, Bennett A.; Anderson, Adam W.

2016-03-01

Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

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:25309417

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (Saimiri sciureus) based on diffusion tensor imaging

PubMed Central

Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G.; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S.; Ding, Zhaohua; Gore, John C.; Chen, Li Min; Landman, Bennett A.; Anderson, Adam W.

2016-01-01

Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey – for which the primary published atlases date from the 1960’s. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas. PMID:27064328

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

PubMed

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.

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (Saimiri sciureus) based on diffusion tensor imaging.

PubMed

Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S; Ding, Zhaohua; Gore, John C; Chen, Li Min; Landman, Bennett A; Anderson, Adam W

2016-02-27

Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

Boeing CST-100 Starliner/ULA Atlas V Wind Tunnel Demonstration

NASA Image and Video Library

2016-10-13

An engineer works with a model of a United Launch Alliance Atlas V rocket with a Boeing CST-100 Starliner capsule inside a wind tunnel at NASA's Ames Research Center in California. The Starliner/Atlas V system is under development by Boeing and ULA in partnership with NASA's Commercial Crew Program to launch astronauts to the International Space Station.

The ATLAS Tier-3 in Geneva and the Trigger Development Facility

NASA Astrophysics Data System (ADS)

Gadomski, S.; Meunier, Y.; Pasche, P.; Baud, J.-P.; ATLAS Collaboration

2011-12-01

The ATLAS Tier-3 farm at the University of Geneva provides storage and processing power for analysis of ATLAS data. In addition the facility is used for development, validation and commissioning of the High Level Trigger of ATLAS [1]. The latter purpose leads to additional requirements on the availability of latest software and data, which will be presented. The farm is also a part of the WLCG [2], and is available to all members of the ATLAS Virtual Organization. The farm currently provides 268 CPU cores and 177 TB of storage space. A grid Storage Element, implemented with the Disk Pool Manager software [3], is available and integrated with the ATLAS Distributed Data Management system [4]. The batch system can be used directly by local users, or with a grid interface provided by NorduGrid ARC middleware [5]. In this article we will present the use cases that we support, as well as the experience with the software and the hardware we are using. Results of I/O benchmarking tests, which were done for our DPM Storage Element and for the NFS servers we are using, will also be presented.

Structure and development of the southern Moroccan continental shelf

USGS Publications Warehouse

Dillon, William P.

1974-01-01

The structure of the continental shelf off southern Morocco was studied by means of 2,100 km of seismic reflection profiles, magnetic and bathymetric surveys, and dredge samples. The research area lies off four geologic divisions adjacent to the coast: the Atlas Mountains; the Souss Trough; the Anti-Atlas Mountains; and the Aaiun Basin. The continental shelf, along with the western Atlas Mountains, the western Souss Trough, and the entire Aaiun Basin, has subsided along a normal fault-flexure system. This system runs along the shore at the Anti-Atlas Mountains, and cuts off this cratonic block from the shelf subsidence. The shelf is narrow and characterized by out-building off the Anti-Atlas range, whereas it is broader and characterized by upbuilding to the north and south. Deposition was essentially continuous at least from Early Cretaceous through Eocene time. Published work suggests that the last cycle of sedimentation began during Permian rifting. After Eocene time, most sediments carried to the shelf must have bypassed it and gone to construct the slope and rise or to the deep sea. Tertiary orogenies caused extensive folding of Mesozoic and early Tertiary deposits off the Atlas Mountains. ?? 1974.

Common Accounting System for Monitoring the ATLAS Distributed Computing Resources

NASA Astrophysics Data System (ADS)

Karavakis, E.; Andreeva, J.; Campana, S.; Gayazov, S.; Jezequel, S.; Saiz, P.; Sargsyan, L.; Schovancova, J.; Ueda, I.; Atlas Collaboration

2014-06-01

This paper covers in detail a variety of accounting tools used to monitor the utilisation of the available computational and storage resources within the ATLAS Distributed Computing during the first three years of Large Hadron Collider data taking. The Experiment Dashboard provides a set of common accounting tools that combine monitoring information originating from many different information sources; either generic or ATLAS specific. This set of tools provides quality and scalable solutions that are flexible enough to support the constantly evolving requirements of the ATLAS user community.

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

ATLAS Data Management Accounting with Hadoop Pig and HBase

NASA Astrophysics Data System (ADS)

Lassnig, Mario; Garonne, Vincent; Dimitrov, Gancho; Canali, Luca

2012-12-01

The ATLAS Distributed Data Management system requires accounting of its contents at the metadata layer. This presents a hard problem due to the large scale of the system, the high dimensionality of attributes, and the high rate of concurrent modifications of data. The system must efficiently account more than 90PB of disk and tape that store upwards of 500 million files across 100 sites globally. In this work a generic accounting system is presented, which is able to scale to the requirements of ATLAS. The design and architecture is presented, and the implementation is discussed. An emphasis is placed on the design choices such that the underlying data models are generally applicable to different kinds of accounting, reporting and monitoring.

DISTRIBUTED CONTROL AND DA FOR ATLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

D. SCUDDER; ET AL

1999-05-01

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

An Oracle-based event index for ATLAS

NASA Astrophysics Data System (ADS)

Gallas, E. J.; Dimitrov, G.; Vasileva, P.; Baranowski, Z.; Canali, L.; Dumitru, A.; Formica, A.; ATLAS Collaboration

2017-10-01

The ATLAS Eventlndex System has amassed a set of key quantities for a large number of ATLAS events into a Hadoop based infrastructure for the purpose of providing the experiment with a number of event-wise services. Collecting this data in one place provides the opportunity to investigate various storage formats and technologies and assess which best serve the various use cases as well as consider what other benefits alternative storage systems provide. In this presentation we describe how the data are imported into an Oracle RDBMS (relational database management system), the services we have built based on this architecture, and our experience with it. We’ve indexed about 26 billion real data events thus far and have designed the system to accommodate future data which has expected rates of 5 and 20 billion events per year. We have found this system offers outstanding performance for some fundamental use cases. In addition, profiting from the co-location of this data with other complementary metadata in ATLAS, the system has been easily extended to perform essential assessments of data integrity and completeness and to identify event duplication, including at what step in processing the duplication occurred.

Task Management in the New ATLAS Production System

NASA Astrophysics Data System (ADS)

De, K.; Golubkov, D.; Klimentov, A.; Potekhin, M.; Vaniachine, A.; Atlas Collaboration

2014-06-01

This document describes the design of the new Production System of the ATLAS experiment at the LHC [1]. The Production System is the top level workflow manager which translates physicists' needs for production level processing and analysis into actual workflows executed across over a hundred Grid sites used globally by ATLAS. As the production workload increased in volume and complexity in recent years (the ATLAS production tasks count is above one million, with each task containing hundreds or thousands of jobs) there is a need to upgrade the Production System to meet the challenging requirements of the next LHC run while minimizing the operating costs. In the new design, the main subsystems are the Database Engine for Tasks (DEFT) and the Job Execution and Definition Interface (JEDI). Based on users' requests, DEFT manages inter-dependent groups of tasks (Meta-Tasks) and generates corresponding data processing workflows. The JEDI component then dynamically translates the task definitions from DEFT into actual workload jobs executed in the PanDA Workload Management System [2]. We present the requirements, design parameters, basics of the object model and concrete solutions utilized in building the new Production System and its components.

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 similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holley, W.A.

The goals of the NREL PVMaT program are, among others, to reduce module manufacturing costs and improve the quality, and we might add here the reliability, of manufactured PV products. One component critical to the service life of PV modules is the useful life of the EVA resin-based encapsulant which is employed extensively by module manufacturers on a worldwide basis. This pottant has been in commercial use since 1982, and over that time has proven to be a dependable material from the standpoint of production, module fabrication, and end-use. But despite the widespread acceptance of the EVA resin-based A9918 andmore » similar formulations for PV encapsulation, some module producers, end-users, and investigators have reported a yellowing or browning phenomenon with EVA resin-based encapsulants in the field. Wile the incidence of this discoloration/degradation appeared at comparatively few sites at the time that this present program was conceived, it raised serious concern as to the long term reliability of EVA resin-based encapsulation systems. Consequently, under the NREL PVMaT program, Springborn Laboratories proposed a comprehensive study of the EVA aging and discoloration problem and its possible solution(s). During the first year of this program, accelerated U.V. aging methods were surveyed. On careful review of the various types of accelerated U.V. aging equipment available, an Atlas Ci35A Weather-Ometer Xenon Exposure System was selected as appropriate equipment for this work. The following report summarizes how this accelerated aging technique has been used to develop a family of solutions to the discoloration problem, the most significant of which is a series of EVA-based encapsulants which are resistant to discoloration.« less

An Atlas of ShakeMaps and population exposure catalog for earthquake loss modeling

USGS Publications Warehouse

Allen, T.I.; Wald, D.J.; Earle, P.S.; Marano, K.D.; Hotovec, A.J.; Lin, K.; Hearne, M.G.

2009-01-01

We present an Atlas of ShakeMaps and a catalog of human population exposures to moderate-to-strong ground shaking (EXPO-CAT) for recent historical earthquakes (1973-2007). The common purpose of the Atlas and exposure catalog is to calibrate earthquake loss models to be used in the US Geological Survey's Prompt Assessment of Global Earthquakes for Response (PAGER). The full ShakeMap Atlas currently comprises over 5,600 earthquakes from January 1973 through December 2007, with almost 500 of these maps constrained-to varying degrees-by instrumental ground motions, macroseismic intensity data, community internet intensity observations, and published earthquake rupture models. The catalog of human exposures is derived using current PAGER methodologies. Exposure to discrete levels of shaking intensity is obtained by correlating Atlas ShakeMaps with a global population database. Combining this population exposure dataset with historical earthquake loss data, such as PAGER-CAT, provides a useful resource for calibrating loss methodologies against a systematically-derived set of ShakeMap hazard outputs. We illustrate two example uses for EXPO-CAT; (1) simple objective ranking of country vulnerability to earthquakes, and; (2) the influence of time-of-day on earthquake mortality. In general, we observe that countries in similar geographic regions with similar construction practices tend to cluster spatially in terms of relative vulnerability. We also find little quantitative evidence to suggest that time-of-day is a significant factor in earthquake mortality. Moreover, earthquake mortality appears to be more systematically linked to the population exposed to severe ground shaking (Modified Mercalli Intensity VIII+). Finally, equipped with the full Atlas of ShakeMaps, we merge each of these maps and find the maximum estimated peak ground acceleration at any grid point in the world for the past 35 years. We subsequently compare this "composite ShakeMap" with existing global hazard models, calculating the spatial area of the existing hazard maps exceeded by the combined ShakeMap ground motions. In general, these analyses suggest that existing global, and regional, hazard maps tend to overestimate hazard. Both the Atlas of ShakeMaps and EXPO-CAT have many potential uses for examining earthquake risk and epidemiology. All of the datasets discussed herein are available for download on the PAGER Web page ( http://earthquake.usgs.gov/ eqcenter/pager/prodandref/ ). ?? 2009 Springer Science+Business Media B.V.

ATLAS TDAQ System Administration: evolution and re-design

NASA Astrophysics Data System (ADS)

Ballestrero, S.; Bogdanchikov, A.; Brasolin, F.; Contescu, C.; Dubrov, S.; Fazio, D.; Korol, A.; Lee, C. J.; Scannicchio, D. A.; Twomey, M. S.

2015-12-01

The ATLAS Trigger and Data Acquisition system is responsible for the online processing of live data, streaming from the ATLAS experiment at the Large Hadron Collider at CERN. The online farm is composed of ∼3000 servers, processing the data read out from ∼100 million detector channels through multiple trigger levels. During the two years of the first Long Shutdown there has been a tremendous amount of work done by the ATLAS Trigger and Data Acquisition System Administrators, implementing numerous new software applications, upgrading the OS and the hardware, changing some design philosophies and exploiting the High- Level Trigger farm with different purposes. The OS version has been upgraded to SLC6; for the largest part of the farm, which is composed of net booted nodes, this required a completely new design of the net booting system. In parallel, the migration to Puppet of the Configuration Management systems has been completed for both net booted and local booted hosts; the Post-Boot Scripts system and Quattor have been consequently dismissed. Virtual Machine usage has been investigated and tested and many of the core servers are now running on Virtual Machines. Virtualisation has also been used to adapt the High-Level Trigger farm as a batch system, which has been used for running Monte Carlo production jobs that are mostly CPU and not I/O bound. Finally, monitoring the health and the status of ∼3000 machines in the experimental area is obviously of the utmost importance, so the obsolete Nagios v2 has been replaced with Icinga, complemented by Ganglia as a performance data provider. This paper serves for reporting of the actions taken by the Systems Administrators in order to improve and produce a system capable of performing for the next three years of ATLAS data taking.

ATLAS. Association of Teachers of Latin American Studies. [Newsletter] Volume 3, Number 1. October, 1973.

ERIC Educational Resources Information Center

Association of Teachers of Latin American Studies, Brooklyn, NY.

The October 1973 issue of ATLAS, a newsletter for the Association of Teachers of Latin American Studies, is entered into the ERIC system on a one time basis to acquaint teachers with this resource. This issue reports summer activities and reviews new materials in this subject area. The events of the 1973 summer ATLAS-Fulbright Seminar to Mexico…

Clinical Evaluation of Zero-Echo-Time Attenuation Correction for Brain 18F-FDG PET/MRI: Comparison with Atlas Attenuation Correction.

PubMed

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

2016-12-01

Accurate attenuation correction (AC) on PET/MR is still challenging. The purpose of this study was to evaluate the clinical feasibility of AC based on fast zero-echo-time (ZTE) MRI by comparing it with the default atlas-based AC on a clinical PET/MR scanner. We recruited 10 patients with malignant diseases not located on the brain. In all patients, a clinically indicated whole-body 18 F-FDG PET/CT scan was acquired. In addition, a head PET/MR scan was obtained voluntarily. For each patient, 2 AC maps were generated from the MR images. One was atlas-AC, derived from T1-weighted liver acquisition with volume acceleration flex images (clinical standard). The other was ZTE-AC, derived from proton-density-weighted ZTE images by applying tissue segmentation and assigning continuous attenuation values to the bone. The AC map generated by PET/CT was used as a silver standard. On the basis of each AC map, PET images were reconstructed from identical raw data on the PET/MR scanner. All PET images were normalized to the SPM5 PET template. After that, these images were qualified visually and quantified in 67 volumes of interest (VOIs; automated anatomic labeling, atlas). Relative differences and absolute relative differences between PET images based on each AC were calculated. 18 F-FDG uptake in all 670 VOIs and generalized merged VOIs were compared using a paired t test. Qualitative analysis shows that ZTE-AC was robust to patient variability. Nevertheless, misclassification of air and bone in mastoid and nasal areas led to the overestimation of PET in the temporal lobe and cerebellum (%diff of ZTE-AC, 2.46% ± 1.19% and 3.31% ± 1.70%, respectively). The |%diff| of all 670 VOIs on ZTE was improved by approximately 25% compared with atlas-AC (ZTE-AC vs. atlas-AC, 1.77% ± 1.41% vs. 2.44% ± 1.63%, P < 0.01). In 2 of 7 generalized VOIs, |%diff| on ZTE-AC was significantly smaller than atlas-AC (ZTE-AC vs. atlas-AC: insula and cingulate, 1.06% ± 0.67% vs. 2.22% ± 1.10%, P < 0.01; central structure, 1.03% ± 0.99% vs. 2.54% ± 1.20%, P < 0.05). The ZTE-AC could provide more accurate AC than clinical atlas-AC by improving the estimation of head-skull attenuation. The misclassification in mastoid and nasal areas must be addressed to prevent the overestimation of PET in regions near the skull base. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Developments in the ATLAS Tracking Software ahead of LHC Run 2

NASA Astrophysics Data System (ADS)

Styles, Nicholas; Bellomo, Massimiliano; Salzburger, Andreas; ATLAS Collaboration

2015-05-01

After a hugely successful first run, the Large Hadron Collider (LHC) is currently in a shut-down period, during which essential maintenance and upgrades are being performed on the accelerator. The ATLAS experiment, one of the four large LHC experiments has also used this period for consolidation and further developments of the detector and of its software framework, ahead of the new challenges that will be brought by the increased centre-of-mass energy and instantaneous luminosity in the next run period. This is of particular relevance for the ATLAS Tracking software, responsible for reconstructing the trajectory of charged particles through the detector, which faces a steep increase in CPU consumption due to the additional combinatorics of the high-multiplicity environment. The steps taken to mitigate this increase and stay within the available computing resources while maintaining the excellent performance of the tracking software in terms of the information provided to the physics analyses will be presented. Particular focus will be given to changes to the Event Data Model, replacement of the maths library, and adoption of a new persistent output format. The resulting CPU profiling results will be discussed, as well as the performance of the algorithms for physics processes under the expected conditions for the next LHC run.

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

PubMed

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

2008-01-01

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

Wind Energy Resource Atlas of the Dominican Republic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elliott, D.; Schwartz, M.; George, R.

2001-10-01

The Wind Energy Resource Atlas of the Dominican Republic identifies the wind characteristics and the distribution of the wind resource in this country. This major project is the first of its kind undertaken for the Dominican Republic. The information contained in the atlas is necessary to facilitate the use of wind energy technologies, both for utility-scale power generation and off-grid wind energy applications. A computerized wind mapping system developed by NREL generated detailed wind resource maps for the entire country. This technique uses Geographic Information Systems (GIS) to produce high-resolution (1-square kilometer) annual average wind resource maps.

Distributed Data Collection for the ATLAS EventIndex

NASA Astrophysics Data System (ADS)

Sánchez, J.; Fernández Casaní, A.; González de la Hoz, S.

2015-12-01

The ATLAS EventIndex contains records of all events processed by ATLAS, in all processing stages. These records include the references to the files containing each event (the GUID of the file) and the internal pointer to each event in the file. This information is collected by all jobs that run at Tier-0 or on the Grid and process ATLAS events. Each job produces a snippet of information for each permanent output file. This information is packed and transferred to a central broker at CERN using an ActiveMQ messaging system, and then is unpacked, sorted and reformatted in order to be stored and catalogued into a central Hadoop server. This contribution describes in detail the Producer/Consumer architecture to convey this information from the running jobs through the messaging system to the Hadoop server.

New Release of the High-Resolution Mimas Atlas derived from Cassini-ISS Images

NASA Astrophysics Data System (ADS)

Roatsch, T.; Kersten, E.; Matz, K.-D.; Porco, C. C.

2017-09-01

The Cassini Imaging Science Subsystem (ISS) acquired 128 high-resolution images (< 1 km/pixel) of Mimas during its tour through the Saturnian system since 2004. We combined new images from orbit 249 (Nov. 2016) and orbit 259 (Jan. 2017) with the high-resolution global semi-controlled mosaic of Mimas from 2012. This global mosaic is the baseline for the new high-resolution Mimas atlas that still consists of three tiles mapped at a scale of 1:1,000,000 [1]. The nomenclature used in this atlas was proposed by the Cassini imaging team and was approved by the International Astronomical Union (IAU). The entire atlas will become available to the public through the Imaging Team's website [http://ciclops.org/maps] and the Planetary Data System (PDS) [https://pds- imaging.jpl.nasa.gov/volumes/carto.html].

Conversion of environmental data to a digital-spatial database, Puget Sound area, Washington

USGS Publications Warehouse

Uhrich, M.A.; McGrath, T.S.

1997-01-01

Data and maps from the Puget Sound Environmental Atlas, compiled for the U.S. Environmental Protection Agency, the Puget Sound Water Quality Authority, and the U.S. Army Corps of Engineers, have been converted into a digital-spatial database using a geographic information system. Environmental data for the Puget Sound area,collected from sources other than the Puget SoundEnvironmental Atlas by different Federal, State, andlocal agencies, also have been converted into thisdigital-spatial database. Background on the geographic-information-system planning process, the design and implementation of the geographic information-system database, and the reasons for conversion to this digital-spatial database are included in this report. The Puget Sound Environmental Atlas data layers include information about seabird nesting areas, eelgrass and kelp habitat, marine mammal and fish areas, and shellfish resources and bed certification. Data layers, from sources other than the Puget Sound Environmental Atlas, include the Puget Sound shoreline, the water-body system, shellfish growing areas, recreational shellfish beaches, sewage-treatment outfalls, upland hydrography,watershed and political boundaries, and geographicnames. The sources of data, descriptions of the datalayers, and the steps and errors of processing associated with conversion to a digital-spatial database used in development of the Puget Sound Geographic Information System also are included in this report. The appendixes contain data dictionaries for each of the resource layers and error values for the conversion of Puget SoundEnvironmental Atlas data.

Readout and trigger for the AFP detector at ATLAS experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kocian, M.

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.

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.

A Study of ATLAS Grid Performance for Distributed Analysis

NASA Astrophysics Data System (ADS)

Panitkin, Sergey; Fine, Valery; Wenaus, Torre

2012-12-01

In the past two years the ATLAS Collaboration at the LHC has collected a large volume of data and published a number of ground breaking papers. The Grid-based ATLAS distributed computing infrastructure played a crucial role in enabling timely analysis of the data. We will present a study of the performance and usage of the ATLAS Grid as platform for physics analysis in 2011. This includes studies of general properties as well as timing properties of user jobs (wait time, run time, etc). These studies are based on mining of data archived by the PanDA workload management system.

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 users formulate their requests using a common ontology of metadata terms, called global ontology. A CSW mediator rewrites the user’s request into CSW requests over local CSWs using their own (local) ontologies, collects the results and sends them back to the user. To extend the system, we have recently added global maritime boundaries and are also considering nearshore ocean observing system data. Ongoing work includes adding WFS, error management, and exception handling, enabling Smart Searches, and writing full documentation. This prototype is a central research project of the new International Coastal Atlas Network (ICAN), a group of 30+ organizations from 14 nations (and growing) dedicated to seeking interoperability approaches to CWAs in support of coastal zone management and the translation of coastal science to coastal decision-making.

Commercial Applications Multispectral Sensor System

NASA Technical Reports Server (NTRS)

Birk, Ronald J.; Spiering, Bruce

1993-01-01

NASA's Office of Commercial Programs is funding a multispectral sensor system to be used in the development of remote sensing applications. The Airborne Terrestrial Applications Sensor (ATLAS) is designed to provide versatility in acquiring spectral and spatial information. The ATLAS system will be a test bed for the development of specifications for airborne and spaceborne remote sensing instrumentation for dedicated applications. This objective requires spectral coverage from the visible through thermal infrared wavelengths, variable spatial resolution from 2-25 meters; high geometric and geo-location accuracy; on-board radiometric calibration; digital recording; and optimized performance for minimized cost, size, and weight. ATLAS is scheduled to be available in 3rd quarter 1992 for acquisition of data for applications such as environmental monitoring, facilities management, geographic information systems data base development, and mineral exploration.

The ATLAS Level-1 Calorimeter Trigger: PreProcessor implementation and performance

NASA Astrophysics Data System (ADS)

Åsman, B.; Achenbach, R.; Allbrooke, B. M. M.; Anders, G.; Andrei, V.; Büscher, V.; Bansil, H. S.; Barnett, B. M.; Bauss, B.; Bendtz, K.; Bohm, C.; Bracinik, J.; Brawn, I. P.; Brock, R.; Buttinger, W.; Caputo, R.; Caughron, S.; Cerrito, L.; Charlton, D. G.; Childers, J. T.; Curtis, C. J.; Daniells, A. C.; Davis, A. O.; Davygora, Y.; Dorn, M.; Eckweiler, S.; Edmunds, D.; Edwards, J. P.; Eisenhandler, E.; Ellis, K.; Ermoline, Y.; Föhlisch, F.; Faulkner, P. J. W.; Fedorko, W.; Fleckner, J.; French, S. T.; Gee, C. N. P.; Gillman, A. R.; Goeringer, C.; Hülsing, T.; Hadley, D. R.; Hanke, P.; Hauser, R.; Heim, S.; Hellman, S.; Hickling, R. S.; Hidvégi, A.; Hillier, S. J.; Hofmann, J. I.; Hristova, I.; Ji, W.; Johansen, M.; Keller, M.; Khomich, A.; Kluge, E.-E.; Koll, J.; Laier, H.; Landon, M. P. J.; Lang, V. S.; Laurens, P.; Lepold, F.; Lilley, J. N.; Linnemann, J. T.; Müller, F.; Müller, T.; Mahboubi, K.; Martin, T. A.; Mass, A.; Meier, K.; Meyer, C.; Middleton, R. P.; Moa, T.; Moritz, S.; Morris, J. D.; Mudd, R. D.; Narayan, R.; zur Nedden, M.; Neusiedl, A.; Newman, P. R.; Nikiforov, A.; Ohm, C. C.; Perera, V. J. O.; Pfeiffer, U.; Plucinski, P.; Poddar, S.; Prieur, D. P. F.; Qian, W.; Rieck, P.; Rizvi, E.; Sankey, D. P. C.; Schäfer, U.; Scharf, V.; Schmitt, K.; Schröder, C.; Schultz-Coulon, H.-C.; Schumacher, C.; Schwienhorst, R.; Silverstein, S. B.; Simioni, E.; Snidero, G.; Staley, R. J.; Stamen, R.; Stock, P.; Stockton, M. C.; Tan, C. L. A.; Tapprogge, S.; Thomas, J. P.; Thompson, P. D.; Thomson, M.; True, P.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Weber, P.; Wessels, M.; Wiglesworth, C.; Williams, S. L.

2012-12-01

The PreProcessor system of the ATLAS Level-1 Calorimeter Trigger (L1Calo) receives about 7200 analogue signals from the electromagnetic and hadronic components of the calorimetric detector system. Lateral division results in cells which are pre-summed to so-called Trigger Towers of size 0.1 × 0.1 along azimuth (phi) and pseudorapidity (η). The received calorimeter signals represent deposits of transverse energy. The system consists of 124 individual PreProcessor modules that digitise the input signals for each LHC collision, and provide energy and timing information to the digital processors of the L1Calo system, which identify physics objects forming much of the basis for the full ATLAS first level trigger decision. This paper describes the architecture of the PreProcessor, its hardware realisation, functionality, and performance.

Development of 3D Atlas of Metalworking Equipment

NASA Astrophysics Data System (ADS)

Yevgenyevna Maslennikova, Olga; Borisovna Nazarova, Olga; Aleksandrovna Chudinova, Yulia

2018-05-01

The paper is dedicated to solving the problem of developing innovative educational systems able to train personnel of complex and dangerous manufacturing industries (such as in metallurgy) to control the process not only under regular conditions, but in emergency and pre-emergency situations as well. At that, such educational systems shall transform training of future and current engineers into a professional activity, model both subject matter and social content of their professional labor. Key characteristics of a 3D atlas of equipment as an educational system are given, as it provides immersion of trainees into professional environment. Requirements for such systems are defined (functional, information, software and technical). Stages of development of a 3D atlas of equipment as an automated system are given, allowing one to get closer to yet another problem that of IT specialist training so that they are able to design, implement and deploy such systems.

Planetary Data Systems (PDS) Imaging Node Atlas II

NASA Technical Reports Server (NTRS)

Stanboli, Alice; McAuley, James M.

2013-01-01

The Planetary Image Atlas (PIA) is a Rich Internet Application (RIA) that serves planetary imaging data to the science community and the general public. PIA also utilizes the USGS Unified Planetary Coordinate system (UPC) and the on-Mars map server. The Atlas was designed to provide the ability to search and filter through greater than 8 million planetary image files. This software is a three-tier Web application that contains a search engine backend (MySQL, JAVA), Web service interface (SOAP) between server and client, and a GWT Google Maps API client front end. This application allows for the search, retrieval, and download of planetary images and associated meta-data from the following missions: 2001 Mars Odyssey, Cassini, Galileo, LCROSS, Lunar Reconnaissance Orbiter, Mars Exploration Rover, Mars Express, Magellan, Mars Global Surveyor, Mars Pathfinder, Mars Reconnaissance Orbiter, MESSENGER, Phoe nix, Viking Lander, Viking Orbiter, and Voyager. The Atlas utilizes the UPC to translate mission-specific coordinate systems into a unified coordinate system, allowing the end user to query across missions of similar targets. If desired, the end user can also use a mission-specific view of the Atlas. The mission-specific views rely on the same code base. This application is a major improvement over the initial version of the Planetary Image Atlas. It is a multi-mission search engine. This tool includes both basic and advanced search capabilities, providing a product search tool to interrogate the collection of planetary images. This tool lets the end user query information about each image, and ignores the data that the user has no interest in. Users can reduce the number of images to look at by defining an area of interest with latitude and longitude ranges.

Variability in developmental timings of the knee in young American children as assessed through Pyle and Hoerr's radiographic atlas.

PubMed

Schaefer, Maureen; Hackman, Lucina; Gallagher, John

2016-03-01

This study examines the accuracy of the Pyle and Hoerr radiographic atlas technique in an effort to document the extent of normal variation associated with developmental timings in the knee for purposes of age estimation. The atlas has been previously tested; however, accuracy rates were produced from a dataset, which spread in age from mostly 7-16 years. This study took a closer look at the younger age groups, examining radiographs from 297 children (147 female and 150 male) from birth to 6 years. Standard deviations representing the difference between the skeletal and chronological age were calculated according to two groupings. Each group represents episodes, or time periods, of differential developmental rates as expressed through the number of plates within the atlas dedicated to documenting each year of life. The beginning year of life is characterized by the most rapid of development as represented by the numerous image plates used to depict this time period. Individuals assigned to plates with a skeletal age between birth and 1 year were grouped collectively to document the variation associated with such rapidly changing morphology (SD = 2.5 months in female children; 2.3 months in male children). Years 1-3.8 years (female) and 1-4.5 years (male) were represented by two or three images within the atlas, and therefore, individuals assigned to plates with a skeletal age falling within this range were placed within a second grouping (SD = 5.2 months in female children; 7.0 months in male children). As expected, variation was observed to decrease as developmental processes accelerated in the younger children. The newly calculated standard deviations offer tighter predictions for estimating age in young children while at the same time maintaining an acceptable width that accounts for normal variation in developmental timings.

Readiness of the ATLAS detector: Performance with the first beam and cosmic data

NASA Astrophysics Data System (ADS)

Pastore, F.

2010-05-01

During 2008 the ATLAS experiment went through an intense period of preparation to have the detector fully commissioned for the first beam period. In about 30 h of beam time available to ATLAS in 2008 the systems went through a rapid setup sequence, from successfully recording the first bunch ever reaching ATLAS, to setting up the timing of the trigger system synchronous to the incoming single beams. The so-called splash events were recorded, where the beam was stopped on a collimator 140 m upstream of ATLAS, showering the experiment with millions of particles per beam shot. These events were found to be extremely useful for timing setup. After the stop of the beam operation, the experiment went through an extensive cosmic ray data taking campaign, recording more than 500 million cosmic ray events. These events have been used to make significant progress on the calibration and alignment of the detector. This paper describes the commissioning programme and the results obtained from both the single beam data and the cosmic data recorded in 2008.

The DMLite Rucio Plugin: ATLAS data in a filesystem

NASA Astrophysics Data System (ADS)

Lassnig, M.; van Dongen, D.; Brito Da Rocha, R.; Alvarez Ayllon, A.; Calfayan, P.

2014-06-01

Rucio is the next-generation data management system of the ATLAS experiment. Historically, clients interacted with the data management system via specialised tools, but in Rucio additional methods are provided. To support filesystem-like interaction with all ATLAS data, a plugin to the DMLite software stack has been developed. It is possible to mount Rucio as a filesystem, and execute regular filesystem operations in a POSIX fashion. This is exposed via various protocols, for example, WebDAV or NFS, which then removes any dependency on Rucio for client software. The main challenge for this work is the mapping of the set-like ATLAS namespace into a hierarchical filesystem, whilst preserving the high performance features of the former. This includes listing and searching for data, creation of files, datasets and containers, and the aggregation of existing data - all within directories with potentially millions of entries. This contribution details the design and implementation of the plugin. Furthermore, an evaluation of the performance characteristics is given, to show that this approach can scale to the requirements of ATLAS physics analysis.

Wave Energy Prize - 1/50th Testing - Atlas Ocean Systems

DOE Data Explorer

Wesley Scharmen

2015-12-04

This submission of data includes all the 1/50th scale testing data completed on the Wave Energy Prize for the Atlas Ocean Systems team, and includes: 1/50th test data (raw & processed) 1/50th test data video and pictures 1/50th Test plans and testing documents SSTF_Submission (summarized results)

Interactive 3D visualization tools for stereotactic atlas-based functional neurosurgery

NASA Astrophysics Data System (ADS)

St. Jean, Philippe; Kasrai, Reza; Clonda, Diego; Sadikot, Abbas F.; Evans, Alan C.; Peters, Terence M.

1998-06-01

Many of the critical basal ganglia structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans, even though they differ in functionality. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia has been created from the Shaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be non-linearly deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for pre- and intra-operative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of the leukotome and other surgical tools with respect to the atlas data, as well as pre- registered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intra-operative planning. To date 17 clinical cases have been successfully performed using the described system.

Diagnostic workstation for digital hand atlas in bone age assessment

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente; Ominsky, Steven

1998-06-01

Bone age assessment by a radiological examination of a hand and wrist image is a procedure frequently performed in pediatric patients to evaluate growth disorders, determine growth potential in children and monitor therapy effects. The assessment method currently used in radiological diagnosis is based on atlas matching of the diagnosed hand image with the reference set of atlas patterns, which was developed in 1950s and is not fully applicable for children of today. We intent to implement a diagnostic workstation for creating a new reference set of clinically normal images which will serve as a digital atlas and can be used for a computer-assisted bone age assessment. In this paper, we present the initial data- collection and system setup phase of this five-year research program. We describe the system design, user interface implementation and software tool development for collection, visualization, management and processing of clinically normal hand and wrist images.

ATLAS Eventlndex monitoring system using the Kibana analytics and visualization platform

NASA Astrophysics Data System (ADS)

Barberis, D.; Cárdenas Zárate, S. E.; Favareto, A.; Fernandez Casani, A.; Gallas, E. J.; Garcia Montoro, C.; Gonzalez de la Hoz, S.; Hrivnac, J.; Malon, D.; Prokoshin, F.; Salt, J.; Sanchez, J.; Toebbicke, R.; Yuan, R.; ATLAS Collaboration

2016-10-01

The ATLAS EventIndex is a data catalogue system that stores event-related metadata for all (real and simulated) ATLAS events, on all processing stages. As it consists of different components that depend on other applications (such as distributed storage, and different sources of information) we need to monitor the conditions of many heterogeneous subsystems, to make sure everything is working correctly. This paper describes how we gather information about the EventIndex components and related subsystems: the Producer-Consumer architecture for data collection, health parameters from the servers that run EventIndex components, EventIndex web interface status, and the Hadoop infrastructure that stores EventIndex data. This information is collected, processed, and then displayed using CERN service monitoring software based on the Kibana analytic and visualization package, provided by CERN IT Department. EventIndex monitoring is used both by the EventIndex team and ATLAS Distributed Computing shifts crew.

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.

Evolution of user analysis on the grid in ATLAS

NASA Astrophysics Data System (ADS)

Dewhurst, A.; Legger, F.; ATLAS Collaboration

2017-10-01

More than one thousand physicists analyse data collected by the ATLAS experiment at the Large Hadron Collider (LHC) at CERN through 150 computing facilities around the world. Efficient distributed analysis requires optimal resource usage and the interplay of several factors: robust grid and software infrastructures, and system capability to adapt to different workloads. The continuous automatic validation of grid sites and the user support provided by a dedicated team of expert shifters have been proven to provide a solid distributed analysis system for ATLAS users. Typical user workflows on the grid, and their associated metrics, are discussed. Measurements of user job performance and typical requirements are also shown.

Status of the AFP project in the ATLAS experiment

NASA Astrophysics Data System (ADS)

Taševský, Marek

2015-04-01

Status of the AFP project in the ATLAS experiment is summarized. The AFP system is composed of a tracker to detect intact, diffractively scattered protons, and of a time-of-flight detector serving to suppress background from pile-up interactions. The whole system, located around 210 m from the main ATLAS detector, is placed in Roman Pots which move detectors from and to the incident proton beams. A typical distance of the closest approach of the tracker to these beams is 2-3 mm. The main physics motivation lies in measuring diffractive processes in runs with not a very high amount of pile-up.

The ATLAS Data Acquisition System: from Run 1 to Run 2

NASA Astrophysics Data System (ADS)

Panduro Vazquez, William; ATLAS Collaboration

2016-04-01

The experience gained during the first period of very successful data taking of the ATLAS experiment (Run 1) has inspired a number of ideas for improvement of the Data Acquisition (DAQ) system that are being put in place during the so-called Long Shutdown 1 of the Large Hadron Collider (LHC), in 2013/14. We have updated the data-flow architecture, rewritten an important fraction of the software and replaced hardware, profiting from state of the art technologies. This paper summarizes the main changes that have been applied to the ATLAS DAQ system and highlights the expected performance and functional improvements that will be available for the LHC Run 2. Particular emphasis will be put on explaining the reasons for our architectural and technical choices, as well as on the simulation and testing approach used to validate this system.

Production and integration of the ATLAS Insertable B-Layer

NASA Astrophysics Data System (ADS)

Abbott, B.; Albert, J.; Alberti, F.; Alex, M.; Alimonti, G.; Alkire, S.; Allport, P.; Altenheiner, S.; Ancu, L. S.; Anderssen, E.; Andreani, A.; Andreazza, A.; Axen, B.; Arguin, J.; Backhaus, M.; Balbi, G.; Ballansat, J.; Barbero, M.; Barbier, G.; Bassalat, A.; Bates, R.; Baudin, P.; Battaglia, M.; Beau, T.; Beccherle, R.; Bell, A.; Benoit, M.; Bermgan, A.; Bertsche, C.; Bertsche, D.; Bilbao de Mendizabal, J.; Bindi, F.; Bomben, M.; Borri, M.; Bortolin, C.; Bousson, N.; Boyd, R. G.; Breugnon, P.; Bruni, G.; Brossamer, J.; Bruschi, M.; Buchholz, P.; Budun, E.; Buttar, C.; Cadoux, F.; Calderini, G.; Caminada, L.; Capeans, M.; Carney, R.; Casse, G.; Catinaccio, A.; Cavalli-Sforza, M.; Červ, M.; Cervelli, A.; Chau, C. C.; Chauveau, J.; Chen, S. P.; Chu, M.; Ciapetti, M.; Cindro, V.; Citterio, M.; Clark, A.; Cobal, M.; Coelli, S.; Collot, J.; Crespo-Lopez, O.; Dalla Betta, G. F.; Daly, C.; D'Amen, G.; Dann, N.; Dao, V.; Darbo, G.; DaVia, C.; David, P.; Debieux, S.; Delebecque, P.; De Lorenzi, F.; de Oliveira, R.; Dette, K.; Dietsche, W.; Di Girolamo, B.; Dinu, N.; Dittus, F.; Diyakov, D.; Djama, F.; Dobos, D.; Dondero, P.; Doonan, K.; Dopke, J.; Dorholt, O.; Dube, S.; Dzahini, D.; Egorov, K.; Ehrmann, O.; Einsweiler, K.; Elles, S.; Elsing, M.; Eraud, L.; Ereditato, A.; Eyring, A.; Falchieri, D.; Falou, A.; Fausten, C.; Favareto, A.; Favre, Y.; Feigl, S.; Fernandez Perez, S.; Ferrere, D.; Fleury, J.; Flick, T.; Forshaw, D.; Fougeron, D.; Franconi, L.; Gabrielli, A.; Gaglione, R.; Gallrapp, C.; Gan, K. K.; Garcia-Sciveres, M.; Gariano, G.; Gastaldi, T.; Gavrilenko, I.; Gaudiello, A.; Geffroy, N.; Gemme, C.; Gensolen, F.; George, M.; Ghislain, P.; Giangiacomi, N.; Gibson, S.; Giordani, M. P.; Giugni, D.; Gjersdal, H.; Glitza, K. W.; Gnani, D.; Godlewski, J.; Gonella, L.; Gonzalez-Sevilla, S.; Gorelov, I.; Gorišek, A.; Gössling, C.; Grancagnolo, S.; Gray, H.; Gregor, I.; Grenier, P.; Grinstein, S.; Gris, A.; Gromov, V.; Grondin, D.; Grosse-Knetter, J.; Guescini, F.; Guido, E.; Gutierrez, P.; Hallewell, G.; Hartman, N.; Hauck, S.; Hasi, J.; Hasib, A.; Hegner, F.; Heidbrink, S.; Heim, T.; Heinemann, B.; Hemperek, T.; Hessey, N. P.; Hetmánek, M.; Hinman, R. R.; Hoeferkamp, M.; Holmes, T.; Hostachy, J.; Hsu, S. C.; Hügging, F.; Husi, C.; Iacobucci, G.; Ibragimov, I.; Idarraga, J.; Ikegami, Y.; Ince, T.; Ishmukhametov, R.; Izen, J. M.; Janoška, Z.; Janssen, J.; Jansen, L.; Jeanty, L.; Jensen, F.; Jentzsch, J.; Jezequel, S.; Joseph, J.; Kagan, H.; Kagan, M.; Karagounis, M.; Kass, R.; Kastanas, A.; Kenney, C.; Kersten, S.; Kind, P.; Klein, M.; Klingenberg, R.; Kluit, R.; Kocian, M.; Koffeman, E.; Korchak, O.; Korolkov, I.; Kostyukhina-Visoven, I.; Kovalenko, S.; Kretz, M.; Krieger, N.; Krüger, H.; Kruth, A.; Kugel, A.; Kuykendall, W.; La Rosa, A.; Lai, C.; Lantzsch, K.; Lapoire, C.; Laporte, D.; Lari, T.; Latorre, S.; Leyton, M.; Lindquist, B.; Looper, K.; Lopez, I.; Lounis, A.; Lu, Y.; Lubatti, H. J.; Maeland, S.; Maier, A.; Mallik, U.; Manca, F.; Mandelli, B.; Mandić, I.; Marchand, D.; Marchiori, G.; Marx, M.; Massol, N.; Mättig, P.; Mayer, J.; McGoldrick, G.; Mekkaoui, A.; Menouni, M.; Menu, J.; Meroni, C.; Mesa, J.; Michal, S.; Miglioranzi, S.; Mikuž, M.; Miucci, A.; Mochizuki, K.; Monti, M.; Moore, J.; Morettini, P.; Morley, A.; Moss, J.; Muenstermann, D.; Murray, P.; Nakamura, K.; Nellist, C.; Nelson, D.; Nessi, M.; Nisius, R.; Nordberg, M.; Nuiry, F.; Obermann, T.; Ockenfels, W.; Oide, H.; Oriunno, M.; Ould-Saada, F.; Padilla, C.; Pangaud, P.; Parker, S.; Pelleriti, G.; Pernegger, H.; Piacquadio, G.; Picazio, A.; Pohl, D.; Polini, A.; Pons, X.; Popule, J.; Portell Bueso, X.; Potamianos, K.; Povoli, M.; Puldon, D.; Pylypchenko, Y.; Quadt, A.; Quayle, B.; Rarbi, F.; Ragusa, F.; Rambure, T.; Richards, E.; Riegel, C.; Ristic, B.; Rivière, F.; Rizatdinova, F.; RØhne, O.; Rossi, C.; Rossi, L. P.; Rovani, A.; Rozanov, A.; Rubinskiy, I.; Rudolph, M. S.; Rummler, A.; Ruscino, E.; Sabatini, F.; Salek, D.; Salzburger, A.; Sandaker, H.; Sannino, M.; Sanny, B.; Scanlon, T.; Schipper, J.; Schmidt, U.; Schneider, B.; Schorlemmer, A.; Schroer, N.; Schwemling, P.; Sciuccati, A.; Seidel, S.; Seiden, A.; Šícho, P.; Skubic, P.; Sloboda, M.; Smith, D. S.; Smith, M.; Sood, A.; Spencer, E.; Stramaglia, M.; Strauss, M.; Stucci, S.; Stugu, B.; Stupak, J.; Styles, N.; Su, D.; Takubo, Y.; Tassan, J.; Teng, P.; Teixeira, A.; Terzo, S.; Therry, X.; Todorov, T.; Tomášek, M.; Toms, K.; Travaglini, R.; Trischuk, W.; Troncon, C.; Troska, G.; Tsiskaridze, S.; Tsurin, I.; Tsybychev, D.; Unno, Y.; Vacavant, L.; Verlaat, B.; Vigeolas, E.; Vogt, M.; Vrba, V.; Vuillermet, R.; Wagner, W.; Walkowiak, W.; Wang, R.; Watts, S.; Weber, M. S.; Weber, M.; Weingarten, J.; Welch, S.; Wenig, S.; Wensing, M.; Wermes, N.; Wittig, T.; Wittgen, M.; Yildizkaya, T.; Yang, Y.; Yao, W.; Yi, Y.; Zaman, A.; Zaidan, R.; Zeitnitz, C.; Ziolkowski, M.; Zivkovic, V.; Zoccoli, A.; Zwalinski, L.

2018-05-01

During the shutdown of the CERN Large Hadron Collider in 2013-2014, an additional pixel layer was installed between the existing Pixel detector of the ATLAS experiment and a new, smaller radius beam pipe. The motivation for this new pixel layer, the Insertable B-Layer (IBL), was to maintain or improve the robustness and performance of the ATLAS tracking system, given the higher instantaneous and integrated luminosities realised following the shutdown. Because of the extreme radiation and collision rate environment, several new radiation-tolerant sensor and electronic technologies were utilised for this layer. This paper reports on the IBL construction and integration prior to its operation in the ATLAS detector.

Influence of signal intensity non-uniformity on brain volumetry using an atlas-based method.

PubMed

Goto, Masami; Abe, Osamu; Miyati, Tosiaki; Kabasawa, Hiroyuki; Takao, Hidemasa; Hayashi, Naoto; Kurosu, Tomomi; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Aoki, Shigeki; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

2012-01-01

Many studies have reported pre-processing effects for brain volumetry; however, no study has investigated whether non-parametric non-uniform intensity normalization (N3) correction processing results in reduced system dependency when using an atlas-based method. To address this shortcoming, the present study assessed whether N3 correction processing provides reduced system dependency in atlas-based volumetry. Contiguous sagittal T1-weighted images of the brain were obtained from 21 healthy participants, by using five magnetic resonance protocols. After image preprocessing using the Statistical Parametric Mapping 5 software, we measured the structural volume of the segmented images with the WFU-PickAtlas software. We applied six different bias-correction levels (Regularization 10, Regularization 0.0001, Regularization 0, Regularization 10 with N3, Regularization 0.0001 with N3, and Regularization 0 with N3) to each set of images. The structural volume change ratio (%) was defined as the change ratio (%) = (100 × [measured volume - mean volume of five magnetic resonance protocols] / mean volume of five magnetic resonance protocols) for each bias-correction level. A low change ratio was synonymous with lower system dependency. The results showed that the images with the N3 correction had a lower change ratio compared with those without the N3 correction. The present study is the first atlas-based volumetry study to show that the precision of atlas-based volumetry improves when using N3-corrected images. Therefore, correction for signal intensity non-uniformity is strongly advised for multi-scanner or multi-site imaging trials.

Influence of Signal Intensity Non-Uniformity on Brain Volumetry Using an Atlas-Based Method

PubMed Central

Abe, Osamu; Miyati, Tosiaki; Kabasawa, Hiroyuki; Takao, Hidemasa; Hayashi, Naoto; Kurosu, Tomomi; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Aoki, Shigeki; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

2012-01-01

Objective Many studies have reported pre-processing effects for brain volumetry; however, no study has investigated whether non-parametric non-uniform intensity normalization (N3) correction processing results in reduced system dependency when using an atlas-based method. To address this shortcoming, the present study assessed whether N3 correction processing provides reduced system dependency in atlas-based volumetry. Materials and Methods Contiguous sagittal T1-weighted images of the brain were obtained from 21 healthy participants, by using five magnetic resonance protocols. After image preprocessing using the Statistical Parametric Mapping 5 software, we measured the structural volume of the segmented images with the WFU-PickAtlas software. We applied six different bias-correction levels (Regularization 10, Regularization 0.0001, Regularization 0, Regularization 10 with N3, Regularization 0.0001 with N3, and Regularization 0 with N3) to each set of images. The structural volume change ratio (%) was defined as the change ratio (%) = (100 × [measured volume - mean volume of five magnetic resonance protocols] / mean volume of five magnetic resonance protocols) for each bias-correction level. Results A low change ratio was synonymous with lower system dependency. The results showed that the images with the N3 correction had a lower change ratio compared with those without the N3 correction. Conclusion The present study is the first atlas-based volumetry study to show that the precision of atlas-based volumetry improves when using N3-corrected images. Therefore, correction for signal intensity non-uniformity is strongly advised for multi-scanner or multi-site imaging trials. PMID:22778560

Integration of Titan supercomputer at OLCF with ATLAS Production System

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Studying - Astronaut John H. Glenn, Jr. - Mercury-Atlas (MA)-6 - Cape

NASA Image and Video Library

1961-01-01

S61-04546 (1961) --- Astronaut John H. Glenn Jr., pilot of the Mercury-Atlas 6 (MA-6) "Friendship 7" mission, takes part in spacecraft systems briefing during preflight activity at Cape Canaveral, Florida. Photo credit: NASA

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 satisfied with the system configurations, technology portfolios, and deployment strategies, he or she can present the concepts to a team, which will conduct a detailed, discipline-oriented analysis within a CEE. An analog to this approach is the music industry where a songwriter creates the lyrics and music before entering a recording studio.

The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

NASA Astrophysics Data System (ADS)

Meijs, M.; Debats, O.; Huisman, H.

2015-03-01

In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.

The discovery and measurements of a Higgs boson.

PubMed

Gianotti, F; Virdee, T S

2015-01-13

In July 2012, the ATLAS and CMS collaborations at CERN's Large Hadron Collider announced the discovery of a Higgs-like boson, a new heavy particle at a mass more than 130 times the mass of a proton. Since then, further data have revealed its properties to be strikingly similar to those of the Standard Model Higgs boson, a particle expected from the mechanism introduced almost 50 years ago by six theoreticians including British physicists Peter Higgs from Edinburgh University and Tom Kibble from Imperial College London. The discovery is the culmination of a truly remarkable scientific journey and undoubtedly the most significant scientific discovery of the twenty-first century so far. Its experimental confirmation turned out to be a monumental task requiring the creation of an accelerator and experiments of unprecedented capability and complexity, designed to discern the signatures that correspond to the Higgs boson. Thousands of scientists and engineers, in each of the ATLAS and CMS teams, came together from all four corners of the world to make this massive discovery possible.

Measuring asymmetry load pairs of top quarks-antitop in the final states dileptoniques from D0 and ATLAS detectors (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapelain, Antoine

Particle physics aims to give a coherent description of the nature and the behavior of elementary particles of matter. Particle accelerators (colliders) allow pushing back our know- ledge in this domain producing particles that cannot be observed by other means. This thesis work contributes to this research eld and focuses on the study of the top quark which is the latest brick of matter discovered and the heaviest known elementary particle. The property of the top quark studied here, the charge asymmetry of the top quark-antiquark pairs, has driven a lot of attention in 2011 because of measurements released bymore » Tevatron experiments. These measurements showed deviations with the predictions made in the framework of the standard model of particle physics. New measurements of the charge asymmetry performed at the Tevatron (with the D0 detector) and at the LHC (with the ATLAS detector) are presented in this thesis.« less

Thermal Design, Tvac Testing, and Lessons Learned for Critical GSE of ATLAS and the ICESat-2 Mission

NASA Technical Reports Server (NTRS)

Bradshaw, Heather

2016-01-01

This presentation describes the thermal design of the three main of optical components which comprise the Bench Checkout Equipment (BCE) for the Advanced Topographic Laser Altimeter System (ATLAS) instrument, which is flying on the ICESat-2 mission. Thermal vacuum testing of these components is also described in this presentation, as well as a few lessons learned. These BCE components serve as critical GSE for the mission; their purpose is to verify ATLAS is performing well. It has been said that, in one light, the BCE is the most important part of ATLAS, since, without it, ATLAS cannot be aligned properly or its performance verified before flight. Therefore, careful attention was paid to the BCEs thermal design, development, and component-level Tvac testing prior to its use in instrument-level and spacecraft-level Tvac tests with ATLAS. This presentation describes that thermal design, development, and testing, as well as a few lessons learned.

Mapping human environment connections on the Olympic Peninsula: an atlas of landscape values

Treesearch

R. McLain; L. Cerveny; Paul M. Montesano; André Beaudoin; Guoqing Sun; Hans-Erik Andersen; Michael A. Wulder; S. Rohdy

2015-01-01

The advent of computerized mapping has greatly expanded the ability of land managers to map many aspects of ecological systems, such as tree species, soil types, wildlife habitat, air quality, and water conditions. Mapping the social and cultural aspects of ecological systems, however, has proved much more challenging. This atlas uses the Olympic Peninsula in western...

Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

PubMed Central

2018-01-01

Abstract The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to “Google Maps” for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3‐D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. PMID:29277900

The Belle II imaging Time-of-Propagation (iTOP) detector

DOE PAGES

Fast, J.

2017-02-16

High precision flavor physics measurements are an essential complement to the direct searches for new physics at the LHC ATLAS and CMS experiments. We will perform these measurements using the upgraded Belle II detector that will take data at the SuperKEKB accelerator. With 40x the luminosity of KEKB, the detector systems must operate efficiently at much higher rates than the original Belle detector. A central element of the upgrade is the barrel particle identification system. Belle II has built and installed an imaging-Time-of-Propagation (iTOP) detector. The iTOP uses quartz optics as Cherenkov radiators. The photons are transported down the quartzmore » bars via total internal reflection with a spherical mirror at the forward end to reflect photons to the backward end where they are imaged onto an array of segmented Micro-Channel Plate Photo-Multiplier Tubes (MCP-PMTs). The system is read out using giga-samples per second waveform sampling Application-Specific Integrated Circuits (ASICs). Furthermore, we used the combined timing and spatial distribution of the photons for each event to determine particle species. This paper provides an overview of the iTOP system.« less

Automated 100-Position Specimen Loader and Image Acquisition System for Transmission Electron Microscopy

PubMed Central

Lefman, Jonathan; Morrison, Robert; Subramaniam, Sriram

2007-01-01

We report the development of a novel, multi-specimen imaging system for high-throughput transmission electron microscopy. Our cartridge-based loading system, called the “Gatling”, permits the sequential examination of as many as 100 specimens in the microscope for room temperature electron microscopy using mechanisms for rapid and automated specimen exchange. The software for the operation of the Gatling and automated data acquisition has been implemented in an updated version of our in-house program AutoEM. In the current implementation of the system, the time required to deliver 95 specimens into the microscope and collect overview images from each is about 13 hours. Regions of interest are identified from a low magnification atlas generation from each specimen and an unlimited number of higher magnifications images can be subsequently acquired from these regions using fully automated data acquisition procedures that can be controlled from a remote interface. We anticipate that the availability of the Gatling will greatly accelerate the speed of data acquisition for a variety of applications in biology, materials science and nanotechnology that require rapid screening and image analysis of multiple specimens. PMID:17240161

A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain.

PubMed

Arganda-Carreras, Ignacio; Manoliu, Tudor; Mazuras, Nicolas; Schulze, Florian; Iglesias, Juan E; Bühler, Katja; Jenett, Arnim; Rouyer, François; Andrey, Philippe

2018-01-01

Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila , one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species.

Improving ATLAS grid site reliability with functional tests using HammerCloud

NASA Astrophysics Data System (ADS)

Elmsheuser, Johannes; Legger, Federica; Medrano Llamas, Ramon; Sciacca, Gianfranco; van der Ster, Dan

2012-12-01

With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short lightweight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site performances. Sites that fail or are unable to run the tests are automatically excluded from the PanDA brokerage system, therefore avoiding user or production jobs to be sent to problematic sites.

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.

Low-Temperature Effects on Systems for Composting of Explosives-Contaminated Soils. Part 1. Literature Review

DTIC Science & Technology

1989-12-01

microbial transforma- aerobic metabolism are microbial biov,.ass, carbon tion of compounds ( Atlas and Bartha 1987). Fre- dioxide, water and heat. Conr...41:1040- land, Ohio: CRC Press, vol. II, p 84. 1044. Cathcart, T.P., F.W. Wheaton, R.B. Brinsfield Atlas , R. M. and R. Bartha (1987) Microbial ...odor-free, and gradation under favorable environmental condi- environmentally sound (Finstein et al. 1986b, Ep- tions ( Atlas and Bartha 1987). Moreover

Atlas Career Path Guidebook: Patterns and Common Practices in Systems Engineers’ Development

DTIC Science & Technology

2018-01-16

Overview of Atlas Proficiency Model .............................................................................. 68 5.1.2. Math /Science/General... Math /Science/General Engineering ................................ 72 Figure 42. Distribution for individuals with highest proficiency self...assessment in Math /Science/General Engineering ..................................................................................... 73 Figure 43

An Atlas of ShakeMaps for Landslide and Liquefaction Modeling

NASA Astrophysics Data System (ADS)

Johnson, K. L.; Nowicki, M. A.; Mah, R. T.; Garcia, D.; Harp, E. L.; Godt, J. W.; Lin, K.; Wald, D. J.

2012-12-01

The human consequences of a seismic event are often a result of subsequent hazards induced by the earthquake, such as landslides. While the United States Geological Survey (USGS) ShakeMap and Prompt Assessment of Global Earthquakes for Response (PAGER) systems are, in conjunction, capable of estimating the damage potential of earthquake shaking in near-real time, they do not currently provide estimates for the potential of further damage by secondary processes. We are developing a sound basis for providing estimates of the likelihood and spatial distribution of landslides for any global earthquake under the PAGER system. Here we discuss several important ingredients in this effort. First, we report on the development of a standardized hazard layer from which to calibrate observed landslide distributions; in contrast, prior studies have used a wide variety of means for estimating the hazard input. This layer now takes the form of a ShakeMap, a standardized approach for computing geospatial estimates for a variety of shaking metrics (both peak ground motions and shaking intensity) from any well-recorded earthquake. We have created ShakeMaps for about 20 historical landslide "case history" events, significant in terms of their landslide occurrence, as part of an updated release of the USGS ShakeMap Atlas. We have also collected digitized landslide data from open-source databases for many of the earthquake events of interest. When these are combined with up-to-date topographic and geologic maps, we have the basic ingredients for calibrating landslide probabilities for a significant collection of earthquakes. In terms of modeling, rather than focusing on mechanistic models of landsliding, we adopt a strictly statistical approach to quantify landslide likelihood. We incorporate geology, slope, peak ground acceleration, and landslide data as variables in a logistic regression, selecting the best explanatory variables given the standardized new hazard layers (see Nowicki et al., this meeting, for more detail on the regression). To make the ShakeMap and PAGER systems more comprehensive in terms of secondary losses, we are working to calibrate a similarly constrained regression for liquefaction estimation using a suite of well-studied earthquakes for which detailed, digitized liquefaction datasets are available; here variants of wetness index and soil strength replace geology and slope. We expect that this Atlas of ShakeMaps for landslide and liquefaction case history events, which will soon be publicly available via the internet, will aid in improving the accuracy of loss-modeling systems such as PAGER, as well as allow for a common framework for numerous other mechanistic and empirical studies.

SU-F-T-405: Development of a Rapid Cardiac Contouring Tool Using Landmark-Driven Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pelletier, C; Jung, J; Mosher, E

2016-06-15

Purpose: This study aims to develop a tool to rapidly delineate cardiac substructures for use in dosimetry for large-scale clinical trial or epidemiological investigations. The goal is to produce a system that can semi-automatically delineate nine cardiac structures to a reasonable accuracy within a couple of minutes. Methods: The cardiac contouring tool employs a Most Similar Atlas method, where a selection criterion is used to pre-select the most similar model to the patient from a library of pre-defined atlases. Sixty contrast-enhanced cardiac computed tomography angiography (CTA) scans (30 male and 30 female) were manually contoured to serve as the atlasmore » library. For each CTA 12 structures were delineated. Kabsch algorithm was used to compute the optimum rotation and translation matrices between the patient and atlas. Minimum root mean squared distance between the patient and atlas after transformation was used to select the most-similar atlas. An initial study using 10 CTA sets was performed to assess system feasibility. Leave-one patient out method was performed, and fit criteria were calculated to evaluate the fit accuracy compared to manual contours. Results: For the pilot study, mean dice indices of .895 were achieved for the whole heart, .867 for the ventricles, and .802 for the atria. In addition, mean distance was measured via the chord length distribution (CLD) between ground truth and the atlas structures for the four coronary arteries. The mean CLD for all coronary arteries was below 14mm, with the left circumflex artery showing the best agreement (7.08mm). Conclusion: The cardiac contouring tool is able to delineate cardiac structures with reasonable accuracy in less than 90 seconds. Pilot data indicates that the system is able to delineate the whole heart and ventricles within a reasonable accuracy using even a limited library. We are extending the atlas sets to 60 adult males and females in total.« less

Arctic transitions in the Land - Atmosphere System (ATLAS): Background, objectives, results, and future directions

USGS Publications Warehouse

McGuire, A.D.; Sturm, M.; Chapin, F. S.

2003-01-01

This paper briefly reviews the background, objectives, and results of the Arctic Transitions in the Land-Atmosphere System (ATLAS) Project to date and provides thoughts on future directions. The key goal of the ATLAS Project is to improve understanding of controls over spatial and temporal variability of terrestrial processes in the Arctic that have potential consequences for the climate system, i.e., processes that affect the exchange of water and energy with the atmosphere, the exchange of radiatively active gases with the atmosphere, and the delivery of freshwater to the Arctic Ocean. Three important conclusions have emerged from research associated with the ATLAS Project. First, associated with the observation that the Alaskan Arctic has warmed significantly in the last 30 years, permafrost is warming, shrubs are expanding, and there has been a temporary release of carbon dioxide from tundra soils. Second, the winter is a more important period of biological activity than previously appreciated. Biotic processes, including shrub expansion and decomposition, affect snow structure and accumulation and affect the annual carbon budget of tundra ecosystems. Third, observed vegetation changes can have a significant positive feedback to regional warming. These vegetation effects are, however, less strong than those exerted by land-ocean heating contrasts and the topographic constraints on air mass movements. The papers of this special section provide additional insights related to these conclusions and to the overall goal of ATLAS.

The ATLAS EventIndex: architecture, design choices, deployment and first operation experience

NASA Astrophysics Data System (ADS)

Barberis, D.; Cárdenas Zárate, S. E.; Cranshaw, J.; Favareto, A.; Fernández Casaní, Á.; Gallas, E. J.; Glasman, C.; González de la Hoz, S.; Hřivnáč, J.; Malon, D.; Prokoshin, F.; Salt Cairols, J.; Sánchez, J.; Többicke, R.; Yuan, R.

2015-12-01

The EventIndex is the complete catalogue of all ATLAS events, keeping the references to all files that contain a given event in any processing stage. It replaces the TAG database, which had been in use during LHC Run 1. For each event it contains its identifiers, the trigger pattern and the GUIDs of the files containing it. Major use cases are event picking, feeding the Event Service used on some production sites, and technical checks of the completion and consistency of processing campaigns. The system design is highly modular so that its components (data collection system, storage system based on Hadoop, query web service and interfaces to other ATLAS systems) could be developed separately and in parallel during LSI. The EventIndex is in operation for the start of LHC Run 2. This paper describes the high-level system architecture, the technical design choices and the deployment process and issues. The performance of the data collection and storage systems, as well as the query services, are also reported.

Radial scaling in inclusive jet production at hadron colliders

NASA Astrophysics Data System (ADS)

Taylor, Frank E.

2018-03-01

Inclusive jet production in p-p and p ¯ -p collisions shows many of the same kinematic systematics as observed in single-particle inclusive production at much lower energies. In an earlier study (1974) a phenomenology, called radial scaling, was developed for the single-particle inclusive cross sections that attempted to capture the essential underlying physics of pointlike parton scattering and the fragmentation of partons into hadrons suppressed by the kinematic boundary. The phenomenology was successful in emphasizing the underlying systematics of the inclusive particle productions. Here we demonstrate that inclusive jet production at the Large Hadron Collider (LHC) in high-energy p-p collisions and at the Tevatron in p ¯ -p inelastic scattering shows similar behavior. The ATLAS inclusive jet production plotted as a function of this scaling variable is studied for √s of 2.76, 7 and 13 TeV and is compared to p ¯ -p inclusive jet production at 1.96 TeV measured at the CDF and D0 at the Tevatron and p-Pb inclusive jet production at the LHC ATLAS at √sNN=5.02 TeV . Inclusive single-particle production at Fermi National Accelerator Laboratory fixed target and Intersecting Storage Rings energies are compared to inclusive J /ψ production at the LHC measured in ATLAS, CMS and LHCb. Striking common features of the data are discussed.

Spacelab

NASA Image and Video Library

1994-11-04

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.

A major upgrade of the sediment echosounder ATLAS PARASOUND and the digital acquisition software ParaDigMA for high-resolution sea floor studies

NASA Astrophysics Data System (ADS)

Gerriets, A.; von Lom-Keil, H.; Spiess, V.; Zwanzig, C.; Bruns, R.

2003-04-01

The combination of the ATLAS PARASOUND sediment echosounder, designed by ATLAS Hydrographic, and the digital recording software package ParaDigMA (commercially available as ATLAS PARASTORE-3) for online digitisation, preprocessing and visualisation of recorded seismograms has proven to be a reliable system for high-resolution acoustic sea floor studies. During 10 years of successful operation aboard several research vessels, including R/V Meteor, R/V Sonne and R/V Polarstern, the system has been only slightly modified. Based on this experience, today's PARASOUND/ParaDigMA system has accomplished the step from DOS towards Windows platform and network capability. In cooperation of ATLAS Hydrographic and the Department of Earth Sciences, University of Bremen a major upgrade of the PARASOUND/ParaDigMA system has been developed that adds significant functionality for surveys of sediment structures and sea floor morphology. The innovations primarily concern the control section of the ATLAS PARASOUND echosounder and the ParaDigMA user front end. The previous analogue PARASOUND control terminal has been replaced by a small real time control PC responsible for the control of the echosounder as well as for the continuous digitisation of the data. The control PC communicates via standard network protocols metadata and data with client applications that can display and store the acquired data on different computers on the network. The new network capabilities of the system overcome former limitations and admit a high flexibility with respect to numbers and locations of operator and recording/display PCs. The system now offers a simultaneous parallel registration of the 2.5-5.5kHz parametric signal and the 18kHz NBS signal. This feature in combination with the recording of complete soundings including the entire water column provides the basis for evolving scientific research topics e. g. gas venting. The ParaDigMA recording software now operates on Windows platforms which provide sophisticated possibilities in data visualisation as well as improved methods in data handling. Former approved features as online plot of the preprocessed seismograms have been continued.

A web-based solution to visualize operational monitoring data in the Trigger and Data Acquisition system of the ATLAS experiment at the LHC

NASA Astrophysics Data System (ADS)

Avolio, G.; D'Ascanio, M.; Lehmann-Miotto, G.; Soloviev, I.

2017-10-01

The Trigger and Data Acquisition (TDAQ) system of the ATLAS detector at the Large Hadron Collider at CERN is composed of a large number of distributed hardware and software components (about 3000 computers and more than 25000 applications) which, in a coordinated manner, provide the data-taking functionality of the overall system. During data taking runs, a huge flow of operational data is produced in order to constantly monitor the system and allow proper detection of anomalies or misbehaviours. In the ATLAS trigger and data acquisition system, operational data are archived and made available to applications by the P-BEAST (Persistent Back-End for the Atlas Information System of TDAQ) service, implementing a custom time-series database. The possibility to efficiently visualize both realtime and historical operational data is a great asset facilitating both online identification of problems and post-mortem analysis. This paper will present a web-based solution developed to achieve such a goal: the solution leverages the flexibility of the P-BEAST archiver to retrieve data, and exploits the versatility of the Grafana dashboard builder to offer a very rich user experience. Additionally, particular attention will be given to the way some technical challenges (like the efficient visualization of a huge amount of data and the integration of the P-BEAST data source in Grafana) have been faced and solved.

[The representation of population density in school atlases: a critical examination of population maps].

PubMed

Schroder, P

1997-01-01

The author critiques the way population density is represented in school atlases, focusing on those used in German-speaking countries. After a discussion of the methodological problems underlying such representations, he selects examples from several German atlases to illustrate the transmission of contradictory, misleading, or out-of-date information. He also suggests ways to improve this situation, including better teaching of underlying cartographical issues and the use of a dot system to illustrate population density.

Situational analysis: preliminary regional review of the Mental Health Atlas 2014.

PubMed

Gater, R; Chew, Z; Saeed, K

2015-09-28

The WHO comprehensive Mental Health Action Plan 2013-2020 established goals and objectives that Member States have agreed to meet by 2020. To update the Atlas of Mental Health 2011, specific indicators from the Mental Health Action Plan and additional indicators on service coverage were incorporated into the questionnaire for the Atlas 2014. The data will help facilitate improvement in information gathering and focus efforts towards implementation of the Mental Health Action Plan. The questionnaire was completed by the national mental health focal point of each country. This preliminary review seeks to consolidate data from the initial response to the Atlas 2014 questionnaire by Member States in the Eastern Mediterranean Region. Data for this review were analysed for the whole Region, by health systems groupings and by individual countries. Where possible, data are compared with the Mental Health Atlas 2011 to give a longitudinal perspective.

Three-dimensional interactive and stereotactic atlas of head muscles and glands correlated with cranial nerves and surface and sectional neuroanatomy.

PubMed

Nowinski, Wieslaw L; Chua, Beng Choon; Johnson, Aleksandra; Qian, Guoyu; Poh, Lan Eng; Yi, Su Hnin Wut; Bivi, Aminah; Nowinska, Natalia G

2013-04-30

Three-dimensional (3D) relationships between head muscles and cranial nerves innervating them are complicated. Existing sources present these relationships in illustrations, radiologic scans, or autopsy photographs, which are limited for learning and use. Developed electronic atlases are limited in content, quality, functionality, and/or presentation. We create a truly 3D interactive, stereotactic and high quality atlas, which provides spatial relationships among head muscles, glands and cranial nerves, and correlates them to surface and sectional neuroanatomy. The head muscles and glands were created from a 3T scan by contouring them and generating 3D models. They were named and structured according to Terminologia anatomica. The muscles were divided into: extra-ocular, facial, masticatory and other muscles, and glands into mouth and other glands. The muscles, glands (and also head) were placed in a stereotactic coordinate system. This content was integrated with cranial nerves and neuroanatomy created earlier. To explore this complex content, a scalable user interface was designed with 12 modules including central nervous system (cerebrum, cerebellum, brainstem, spinal cord), cranial nerves, muscles, glands, arterial system, venous system, tracts, deep gray nuclei, ventricles, white matter, visual system, head. Anatomy exploration operations include compositing/decompositing, individual/group selection, 3D view-index mapping, 3D labeling, highlighting, distance measuring, 3D brain cutting, and axial/coronal/sagittal triplanar display. To our best knowledge, this is the first truly 3D, stereotactic, interactive, fairly complete atlas of head muscles, and the first attempt to create a 3D stereotactic atlas of glands. Its use ranges from education of students and patients to research to potential clinical applications. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

The Las Vegas Sustainability Atlas: Modeling Place-based Interactions and Implications in the Las Vegas Valley Bioregion

NASA Astrophysics Data System (ADS)

Ego, H.; McCown, K.; Saghafi, N.; Gross, E.; Hunter, W.; Zawarus, P.; Gann, A.; Piechota, T. C.

2014-12-01

Las Vegas, Nevada, with 2 million residents and 40 million annual visitors, is one of the driest metropolitan environments of its size in the world. The metro imports nearly all of its resources, including energy, water and food. Rapid population increases, drought, and temperature increases due to climate change create challenges for planning resilient systems in the Las Vegas Valley. Because of its growth rate, aridity, Las Vegas, Nevada is a significant and relevant region for the study of the water, energy, food and climate nexus. Cities in the United States and the world are seeing increasing trends in urbanization and water scarcity. How does the water-energy-climate-food nexus affect each metropolitan area? How can this complex information be used for resiliency planning? How can it be related to the public, so they can understand the issues in a way that makes them meaningful participants in the planning process? The topic of our presentation is a 'resiliency atlas.' The atlas is a place-based model tested in Las Vegas to explore bioregional distinctiveness of the water-energy-climate-food nexus, including regional transportation systems. The atlas integrates the systems within a utilitarian organization of information. Systems in this place-based model demonstrate how infrastructure services are efficiently provided for the Las Vegas Valley population. This resiliency atlas can clarify how the nexus applies to place; and how it can be used to spur geographically germane adaption strategies. In the Las Vegas Valley, climate change (drought and high sustained temperatures) and population affect water, energy, and food systems. This clarity of a place based model can help educate the public about the resilience of their place, and facilitate and organize the planning process in the face of uncertainty.

MRI-based treatment planning with pseudo CT generated through atlas registration.

PubMed

Uh, Jinsoo; Merchant, Thomas E; Li, Yimei; Li, Xingyu; Hua, Chiaho

2014-05-01

To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787-0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%-98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the percentage of volume receiving at least 95% of the prescription dose in the planning target volume differed from the original values by less than 2% of the prescription dose (root-mean-square, RMS < 1%). The PRGP scheme did not perform better than the arithmetic mean process with the same number of atlases. Increasing the number of atlases from 6 to 12 often resulted in improvements, but statistical significance was not always found. MRI-based treatment planning with pseudo CTs generated through atlas registration is feasible for pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs, showing dosimetric accuracy within 2% for the PTV when multiple atlases were used. The arithmetic mean process may be a reasonable choice over PRGP for the synthesis scheme considering performance and computational costs.

MRI-based treatment planning with pseudo CT generated through atlas registration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uh, Jinsoo, E-mail: jinsoo.uh@stjude.org; Merchant, Thomas E.; Hua, Chiaho

2014-05-15

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration ofmore » conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the percentage of volume receiving at least 95% of the prescription dose in the planning target volume differed from the original values by less than 2% of the prescription dose (root-mean-square, RMS < 1%). The PRGP scheme did not perform better than the arithmetic mean process with the same number of atlases. Increasing the number of atlases from 6 to 12 often resulted in improvements, but statistical significance was not always found. Conclusions: MRI-based treatment planning with pseudo CTs generated through atlas registration is feasible for pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs, showing dosimetric accuracy within 2% for the PTV when multiple atlases were used. The arithmetic mean process may be a reasonable choice over PRGP for the synthesis scheme considering performance and computational costs.« less

MRI-based treatment planning with pseudo CT generated through atlas registration

PubMed Central

Uh, Jinsoo; Merchant, Thomas E.; Li, Yimei; Li, Xingyu; Hua, Chiaho

2014-01-01

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the percentage of volume receiving at least 95% of the prescription dose in the planning target volume differed from the original values by less than 2% of the prescription dose (root-mean-square, RMS < 1%). The PRGP scheme did not perform better than the arithmetic mean process with the same number of atlases. Increasing the number of atlases from 6 to 12 often resulted in improvements, but statistical significance was not always found. Conclusions: MRI-based treatment planning with pseudo CTs generated through atlas registration is feasible for pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs, showing dosimetric accuracy within 2% for the PTV when multiple atlases were used. The arithmetic mean process may be a reasonable choice over PRGP for the synthesis scheme considering performance and computational costs. PMID:24784377

Artificial auroras in the upper atmosphere. I - Electron beam injections

NASA Technical Reports Server (NTRS)

Burch, J. L.; Mende, S. B.; Kawashima, N.; Roberts, W. T.; Taylor, W. W. L.; Neubert, T.; Gibson, W. C.; Marshall, J. A.; Swenson, G. R.

1993-01-01

The Atlas-1 Spacelab payload's Space Experiments with Particle Accelerators generated artificial electron beams for the stimulation of auroral emissions at southern auroral latitudes. Optical measurements were made by the Shuttle Orbiter's onboard TV cameras, as well as by the Atmospheric Emissions Photometric Imager (in both white light and the 427.8 nm N2(+) emission line). Shuttle-based auroral imaging furnished a novel perspective on the artificial auroras; the emissions were traced from 295 km to the 110 km level along the curved magnetic-field lines.

KSC-2012-4714

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – NASA's Radiation Belt Storm Probes, or RBSP, lift off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida aboard a United Launch Alliance Atlas V rocket at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4752

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4760

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA’s Radiation Belt Storm Probes, or RBSP, is a breath away from lifting off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4753

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifted off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4755

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifted off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4716

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, roars off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4763

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4725

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky

KSC-2012-4765

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifted off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4751

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4750

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4715

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, rumbles off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4764

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4754

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifted off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

Charge breeding of radioactive isotopes at the CARIBU facility with an electron beam ion source

NASA Astrophysics Data System (ADS)

Vondrasek, R. C.; Dickerson, C. A.; Hendricks, M.; Ostroumov, P.; Pardo, R.; Savard, G.; Scott, R.; Zinkann, G.

2018-05-01

An Electron Beam Ion Source Charge Breeder (EBIS-CB) has been developed at Argonne National Laboratory as part of the californium rare ion breeder upgrade. For the past year, the EBIS-CB has been undergoing commissioning as part of the ATLAS accelerator complex. It has delivered both stable and radioactive beams with A/Q < 6, breeding times <30 ms, low background contamination, and charge breeding efficiencies >18% into a single charge state. The operation of this device, challenges during the commissioning phase, and future improvements will be discussed.

Access to the Mars Global Surveyor Data Through the Planetary Image Atlas

NASA Technical Reports Server (NTRS)

Ivanov, A. B.; Duxbury, E. D.; LaVoie, S. K.; McAuley, M.; Woncik, P. J.

2002-01-01

We will present our latest results in providing access to the Mars Global Surveyor Data through the Planetary Image Atlas. This work is a prototype for future Internet based data distribution systems. Additional information is contained in the original extended abstract.

Detector Control System for the AFP detector in ATLAS experiment at CERN

NASA Astrophysics Data System (ADS)

Banaś, E.; Caforio, D.; Czekierda, S.; Hajduk, Z.; Olszowska, J.; Seabra, L.; Šícho, P.

2017-10-01

The ATLAS Forward Proton (AFP) detector consists of two forward detectors located at 205 m and 217 m on either side of the ATLAS experiment. The aim is to measure the momenta and angles of diffractively scattered protons. In 2016, two detector stations on one side of the ATLAS interaction point were installed and commissioned. The detector infrastructure and necessary services were installed and are supervised by the Detector Control System (DCS), which is responsible for the coherent and safe operation of the detector. A large variety of used equipment represents a considerable challenge for the AFP DCS design. Industrial Supervisory Control and Data Acquisition (SCADA) product Siemens WinCCOA, together with the CERN Joint Control Project (JCOP) framework and standard industrial and custom developed server applications and protocols are used for reading, processing, monitoring and archiving of the detector parameters. Graphical user interfaces allow for overall detector operation and visualization of the detector status. Parameters, important for the detector safety, are used for alert generation and interlock mechanisms.

Lung lobe segmentation based on statistical atlas and graph cuts

NASA Astrophysics Data System (ADS)

Nimura, Yukitaka; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

2012-03-01

This paper presents a novel method that can extract lung lobes by utilizing probability atlas and multilabel graph cuts. Information about pulmonary structures plays very important role for decision of the treatment strategy and surgical planning. The human lungs are divided into five anatomical regions, the lung lobes. Precise segmentation and recognition of lung lobes are indispensable tasks in computer aided diagnosis systems and computer aided surgery systems. A lot of methods for lung lobe segmentation are proposed. However, these methods only target the normal cases. Therefore, these methods cannot extract the lung lobes in abnormal cases, such as COPD cases. To extract lung lobes in abnormal cases, this paper propose a lung lobe segmentation method based on probability atlas of lobe location and multilabel graph cuts. The process consists of three components; normalization based on the patient's physique, probability atlas generation, and segmentation based on graph cuts. We apply this method to six cases of chest CT images including COPD cases. Jaccard index was 79.1%.

A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain

PubMed Central

Arganda-Carreras, Ignacio; Manoliu, Tudor; Mazuras, Nicolas; Schulze, Florian; Iglesias, Juan E.; Bühler, Katja; Jenett, Arnim; Rouyer, François; Andrey, Philippe

2018-01-01

Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila, one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species. PMID:29628885

PC software package to confront multimodality images and a stereotactic atlas in neurosurgery

NASA Astrophysics Data System (ADS)

Barillot, Christian; Lemoine, Didier; Gibaud, Bernard; Toulemont, P. J.; Scarabin, Jean-Marie

1990-07-01

The aim of this application is to interactively transfer information between CT, MRI or DSA data and a 3D stereotactic atlas digitized on a C. Based on a 3D organization of data, this system is devoted to assist a neurosurgeon in surgical planning by numerically cross-assigning information between heterogeneous data (in-vivo or atlas). All these images can be retrieved in digital form from the PACS central archive (SIRENE PACS system). The basic feature of this confrontation is the Talairach's proportional squaring which consists in dividing the 3D cerebral space in independently deformable sub-parts. This 3D model is based on anatomical structures such as the AC-PC line and its two associated vertical lines VAC and VPC. Based on this proportional squaring, the atlas has been digitized in order to get atlas plates along the three orthogonal directions of this geometrical reference (axial, coronal, sagittal). The registration of in-vivo data to the proportional squaring is done by extracting either external framework landmarks or anatomical reference structures (i.e. AC and PC structures on the MRI sagittal mid-plane image). Geometrical transformations and scaling are then recorded for each modality or acquisition according to the proportional squaring. These transformations make for instance possible the transfer of a 3D point of a MRI examination to its 3D location within the proportional squaring and furthermore to its 3D location within another data set (in-vivo or atlas). From that stage, the application gives the choice to the neurosurgeon to select any confrontation between input data (in-vivo images or atlas) and output data (id).

Towards laser spectroscopy of the proton-halo candidate boron-8

NASA Astrophysics Data System (ADS)

Maaß, Bernhard; Müller, Peter; Nörtershäuser, Wilfried; Clark, Jason; Gorges, Christian; Kaufmann, Simon; König, Kristian; Krämer, Jörg; Levand, Anthony; Orford, Rodney; Sánchez, Rodolfo; Savard, Guy; Sommer, Felix

2017-11-01

We propose to determine the nuclear charge radius of 8B by high-resolution laser spectroscopy. 8B (t 1/2 = 770 ms) is perhaps the best candidate of a nucleus exhibiting an extended proton wave-function or "one-proton-halo" in a more descriptive picture. Laser spectroscopic measurements of the isotope shift will be used to probe the change in nuclear charge radius along the three boron isotopes 8B, 10B and 11B. The change in nuclear charge radius directly correlates with the extent of the proton wave function. In-flight production and preparation of sufficient yields of 8B ions at low energies is provided by the Argonne Tandem Linac Accelerator System (ATLAS) at Argonne National Laboratory (ANL) in Chicago, IL, USA. Subsequently, the ions will be guided through a charge exchange cell for neutralization and the fluorescence signal of the atoms which interact with the resonant laser light will be detected. The charge radius can then be extracted from the measured isotope shift by employing highly accurate atomic theory calculations of this five-electron system which are carried out presently.

Memory handling in the ATLAS submission system from job definition to sites limits

NASA Astrophysics Data System (ADS)

Forti, A. C.; Walker, R.; Maeno, T.; Love, P.; Rauschmayr, N.; Filipcic, A.; Di Girolamo, A.

2017-10-01

In the past few years the increased luminosity of the LHC, changes in the linux kernel and a move to a 64bit architecture have affected the ATLAS jobs memory usage and the ATLAS workload management system had to be adapted to be more flexible and pass memory parameters to the batch systems, which in the past wasn’t a necessity. This paper describes the steps required to add the capability to better handle memory requirements, included the review of how each component definition and parametrization of the memory is mapped to the other components, and what changes had to be applied to make the submission chain work. These changes go from the definition of tasks and the way tasks memory requirements are set using scout jobs, through the new memory tool developed to do that, to how these values are used by the submission component of the system and how the jobs are treated by the sites through the CEs, batch systems and ultimately the kernel.

Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

PubMed

Swanson, Larry W

2018-04-15

The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

FELIX: The new detector readout system for the ATLAS experiment

NASA Astrophysics Data System (ADS)

Ryu, Soo; ATLAS TDAQ Collaboration

2017-10-01

After the Phase-I upgrades (2019) of the ATLAS experiment, the Front-End Link eXchange (FELIX) system will be the interface between the data acquisition system and the detector front-end and trigger electronics. FELIX will function as a router between custom serial links and a commodity switch network using standard technologies (Ethernet or Infiniband) to communicate with commercial data collecting and processing components. The system architecture of FELIX will be described and the status of the firmware implementation and hardware development currently in progress will be presented.

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

NASA's Advanced Topographic Laser Altimeter System (ATLAS) will be the single instrument on the ICESat-2 spacecraft which is expected to launch in 2016 with a 3 year mission lifetime. The ICESat-2 orbital altitude will be 500 km with a 92 degree inclination and 91-day repeat tracks. ATLAS is a single photon detection system transmitting at 532nm with a laser repetition rate of 10 kHz and a 6 spot pattern on the Earth's surface. Without some method of eliminating solar background noise in near real-time, the volume of ATLAS telemetry would far exceed the normal X-band downlink capability. To reduce the data volume to an acceptable level a set of onboard Receiver Algorithms has been developed. These Algorithms limit the daily data volume by distinguishing surface echoes from the background noise and allow the instrument to telemeter only a small vertical region about the signal. This is accomplished through the use of an onboard Digital Elevation Model (DEM), signal processing techniques, and an onboard relief map. Similar to what was flown on the ATLAS predecessor GLAS (Geoscience Laser Altimeter System) the DEM provides minimum and maximum heights for each 1 degree x 1 degree tile on the Earth. This information allows the onboard algorithm to limit its signal search to the region between minimum and maximum heights (plus some margin for errors). The understanding that the surface echoes will tend to clump while noise will be randomly distributed led us to histogram the received event times. The selection of the signal locations is based on those histogram bins with statistically significant counts. Once the signal location has been established the onboard Digital Relief Map (DRM) is used to determine the vertical width of the telemetry band about the signal. The ATLAS Receiver Algorithms are nearing completion of the development phase and are currently being tested using a Monte Carlo Software Simulator that models the instrument, the orbit and the environment. 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.

Efficient patient modeling for visuo-haptic VR simulation using a generic patient atlas.

PubMed

Mastmeyer, Andre; Fortmeier, Dirk; Handels, Heinz

2016-08-01

This work presents a new time-saving virtual patient modeling system by way of example for an existing visuo-haptic training and planning virtual reality (VR) system for percutaneous transhepatic cholangio-drainage (PTCD). Our modeling process is based on a generic patient atlas to start with. It is defined by organ-specific optimized models, method modules and parameters, i.e. mainly individual segmentation masks, transfer functions to fill the gaps between the masks and intensity image data. In this contribution, we show how generic patient atlases can be generalized to new patient data. The methodology consists of patient-specific, locally-adaptive transfer functions and dedicated modeling methods such as multi-atlas segmentation, vessel filtering and spline-modeling. Our full image volume segmentation algorithm yields median DICE coefficients of 0.98, 0.93, 0.82, 0.74, 0.51 and 0.48 regarding soft-tissue, liver, bone, skin, blood and bile vessels for ten test patients and three selected reference patients. Compared to standard slice-wise manual contouring time saving is remarkable. Our segmentation process shows out efficiency and robustness for upper abdominal puncture simulation systems. This marks a significant step toward establishing patient-specific training and hands-on planning systems in a clinical environment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peressutti, D; Schipaanboord, B; Kadir, T

Purpose: To investigate the effectiveness of atlas selection methods for improving atlas-based auto-contouring in radiotherapy planning. Methods: 275 H&N clinically delineated cases were employed as an atlas database from which atlases would be selected. A further 40 previously contoured cases were used as test patients against which atlas selection could be performed and evaluated. 26 variations of selection methods proposed in the literature and used in commercial systems were investigated. Atlas selection methods comprised either global or local image similarity measures, computed after rigid or deformable registration, combined with direct atlas search or with an intermediate template image. Workflow Boxmore » (Mirada-Medical, Oxford, UK) was used for all auto-contouring. Results on brain, brainstem, parotids and spinal cord were compared to random selection, a fixed set of 10 “good” atlases, and optimal selection by an “oracle” with knowledge of the ground truth. The Dice score and the average ranking with respect to the “oracle” were employed to assess the performance of the top 10 atlases selected by each method. Results: The fixed set of “good” atlases outperformed all of the atlas-patient image similarity-based selection methods (mean Dice 0.715 c.f. 0.603 to 0.677). In general, methods based on exhaustive comparison of local similarity measures showed better average Dice scores (0.658 to 0.677) compared to the use of either template image (0.655 to 0.672) or global similarity measures (0.603 to 0.666). The performance of image-based selection methods was found to be only slightly better than a random (0.645). Dice scores given relate to the left parotid, but similar results patterns were observed for all organs. Conclusion: Intuitively, atlas selection based on the patient CT is expected to improve auto-contouring performance. However, it was found that published approaches performed marginally better than random and use of a fixed set of representative atlases showed favourable performance. This research was funded via InnovateUK Grant 600277 as part of Eurostars Grant E!9297. DP,BS,MG,TK are employees of Mirada Medical Ltd.« less

Approach for Developing a National Atlas of Vulnerabilities for U.S. Water Quality and Aquatic Ecosystems

EPA Science Inventory

The purpose of the Atlas project is to support national- and regional-scale water quality and aquatic ecosystem vulnerability assessments by providing quantitative information on the relative vulnerability to climate change of different geographic regions and watershed systems ac...

ATLAS and LHC computing on CRAY

NASA Astrophysics Data System (ADS)

Sciacca, F. G.; Haug, S.; ATLAS Collaboration

2017-10-01

Access and exploitation of large scale computing resources, such as those offered by general purpose HPC centres, is one important measure for ATLAS and the other Large Hadron Collider experiments in order to meet the challenge posed by the full exploitation of the future data within the constraints of flat budgets. We report on the effort of moving the Swiss WLCG T2 computing, serving ATLAS, CMS and LHCb, from a dedicated cluster to the large Cray systems at the Swiss National Supercomputing Centre CSCS. These systems do not only offer very efficient hardware, cooling and highly competent operators, but also have large backfill potentials due to size and multidisciplinary usage and potential gains due to economy at scale. Technical solutions, performance, expected return and future plans are discussed.

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.

ATLAS Cloud R&D

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

A new strips tracker for the upgraded ATLAS ITk detector

NASA Astrophysics Data System (ADS)

David, C.

2018-01-01

The ATLAS detector has been designed and developed to function in the environment of the present Large Hadron Collider (LHC). At the next-generation tracking detector proposed for the High Luminosity LHC (HL-LHC), the so-called ATLAS Phase-II Upgrade, the fluences and radiation levels will be higher by as much as a factor of ten. The new sub-detectors must thus be faster, of larger area, more segmented and more radiation hard while the amount of inactive material should be minimized and the power supply to the front-end systems should be increased. For those reasons, the current inner tracker of the ATLAS detector will be fully replaced by an all-silicon tracking system that consists of a pixel detector at small radius close to the beam line and a large area strip tracker surrounding it. This document gives an overview of the design of the strip inner tracker (Strip ITk) and summarises the intensive R&D activities performed over the last years by the numerous institutes within the Strips ITk collaboration. These studies are accompanied with a strong prototyping effort to contribute to the optimisation of the Strip ITk's structure and components. This effort culminated recently in the release of the ATLAS Strips ITk Technical Design Report (TDR).

The Canadian Atlas of Child and Youth Injury: Mobilizing Injury Surveillance Data to Launch a National Knowledge Translation Tool

PubMed Central

Pike, Ian; Smith, Jennifer; Al-Hajj, Samar; Fuselli, Pamela; Macpherson, Alison

2017-01-01

Child and youth injury prevention research in Canada has lagged behind other Organisation for Economic Co-operation and Development nations, despite existing surveillance systems and longitudinal data. A critical need to improve access to the available data, as well as need to tailor its display and interpretation, was identified by injury prevention stakeholders involved in research, policy, and practice. The Canadian Atlas of Child and Youth Injury Prevention (“the Atlas”) was developed to address this need. Following a series of iterative consultation meetings and a pilot testing session, the Atlas was scaled up with national data. Two testing sessions were held to evaluate the tools. The Atlas is comprised of three main components: data, indicators, and visualizations. The accessibility of the dashboard is enhanced by customization of data visualizations and data outputs to suit the user’s needs. Overall feedback indicated that the tools were easy to use, and that the interface was intuitive and visually appealing. The Canadian Atlas of Child and Youth Injury Prevention provides readily accessible information to injury prevention practitioners, policy makers and researchers, helping to chart pathways to success in improving the child and youth injury prevention system in Canada. PMID:28867782

The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.

PubMed

Hesselager, Marianne O; Codrea, Marius C; Sun, Zhi; Deutsch, Eric W; Bennike, Tue B; Stensballe, Allan; Bundgaard, Louise; Moritz, Robert L; Bendixen, Emøke

2016-02-01

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Pig PeptideAtlas: a resource for systems biology in animal production and biomedicine

PubMed Central

Hesselager, Marianne O.; Codrea, Marius C.; Sun, Zhi; Deutsch, Eric W.; Bennike, Tue B.; Stensballe, Allan; Bundgaard, Louise; Moritz, Robert L.; Bendixen, Emøke

2016-01-01

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system wide observations, and cross species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this manuscript demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research. PMID:26699206

Atlas 1.1: An Update to the Theory of Effective Systems Engineers

DTIC Science & Technology

2018-01-16

Proficiency Model ........................................................................................................... 21 5.1.1 Area 1: Math ... Math /Science/General Engineering: Foundational concepts from mathematics, physical sciences, and general engineering; 2. System’s Domain...Table 5. Atlas Proficiency Areas, Categories, and Topics Area Category Topic 1. Math / Science / General Engineering 1.1. Natural Science

InSight Atlas V Fairing Rotate to Vertical

NASA Image and Video Library

2018-02-07

In the Astrotech facility at Vandenberg Air Force Base in California, the payload fairing for the United Launch Alliance (ULA) Atlas V for NASA's upcoming Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars is lifted to the vertical position. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff atop a ULA Atlas V rocket is scheduled for May 5, 2018.

The upgrade of the ATLAS first-level calorimeter trigger

NASA Astrophysics Data System (ADS)

Yamamoto, Shimpei; Atlas Collaboration

2016-07-01

The first-level calorimeter trigger (L1Calo) had operated successfully through the first data taking phase of the ATLAS experiment at the CERN Large Hadron Collider. Towards forthcoming LHC runs, a series of upgrades is planned for L1Calo to face new challenges posed by the upcoming increases of the beam energy and the luminosity. This paper reviews the ATLAS L1Calo trigger upgrade project that introduces new architectures for the liquid-argon calorimeter trigger readout and the L1Calo trigger processing system.

L1 track triggers for ATLAS in the HL-LHC

DOE PAGES

Lipeles, E.

2012-01-01

The HL-LHC, the planned high luminosity upgrade for the LHC, will increase the collision rate in the ATLAS detector approximately a factor of 5 beyond the luminosity for which the detectors were designed, while also increasing the number of pile-up collisions in each event by a similar factor. This means that the level-1 trigger must achieve a higher rejection factor in a more difficult environment. This presentation discusses the challenges that arise in this environment and strategies being considered by ATLAS to include information from the tracking systems in the level-1 decision. The main challenges involve reducing the data volumemore » exported from the tracking system for which two options are under consideration: a region of interest based system and an intelligent sensor method which filters on hits likely to come from higher transverse momentum tracks.« less

Readiness of the ATLAS Tile Calorimeter for LHC collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aad, G.; Abbott, B.; Abdallah, J.

The Tile hadronic calorimeter of the ATLAS detector has undergone extensive testing in the experimental hall since its installation in late 2005. The readout, control and calibration systems have been fully operational since 2007 and the detector has successfully collected data from the LHC single beams in 2008 and first collisions in 2009. This paper gives an overview of the Tile Calorimeter performance as measured using random triggers, calibration data, data from cosmic ray muons and single beam data. The detector operation status, noise characteristics and performance of the calibration systems are presented, as well as the validation of themore » timing and energy calibration carried out with minimum ionising cosmic ray muons data. The calibration systems' precision is well below the design value of 1%. The determination of the global energy scale was performed with an uncertainty of 4%. © 2010 CERN for the benefit of the ATLAS collaboration.« less

Readiness of the ATLAS Tile Calorimeter for LHC collisions

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2010-12-08

The Tile hadronic calorimeter of the ATLAS detector has undergone extensive testing in the experimental hall since its installation in late 2005. The readout, control and calibration systems have been fully operational since 2007 and the detector has successfully collected data from the LHC single beams in 2008 and first collisions in 2009. This paper gives an overview of the Tile Calorimeter performance as measured using random triggers, calibration data, data from cosmic ray muons and single beam data. The detector operation status, noise characteristics and performance of the calibration systems are presented, as well as the validation of themore » timing and energy calibration carried out with minimum ionising cosmic ray muons data. The calibration systems' precision is well below the design value of 1%. The determination of the global energy scale was performed with an uncertainty of 4%. © 2010 CERN for the benefit of the ATLAS collaboration.« less

SU-F-J-171: Robust Atlas Based Segmentation of the Prostate and Peripheral Zone Regions On MRI Utilizing Multiple MRI System Vendors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Padgett, K; Pollack, A; Stoyanova, R

Purpose: Automatically generated prostate MRI contours can be used to aid in image registration with CT or ultrasound and to reduce the burden of contouring for radiation treatment planning. In addition, prostate and zonal contours can assist to automate quantitative imaging features extraction and the analyses of longitudinal MRI studies. These potential gains are limited if the solutions are not compatible across different MRI vendors. The goal of this study is to characterize an atlas based automatic segmentation procedure of the prostate collected on MRI systems from multiple vendors. Methods: The prostate and peripheral zone (PZ) were manually contoured bymore » an expert radiation oncologist on T2-weighted scans acquired on both GE (n=31) and Siemens (n=33) 3T MRI systems. A leave-one-out approach was utilized where the target subject is removed from the atlas before the segmentation algorithm is initiated. The atlas-segmentation method finds the best nine matched atlas subjects and then performs a normalized intensity-based free-form deformable registration of these subjects to the target subject. These nine contours are then merged into a single contour using Simultaneous Truth and Performance Level Estimation (STAPLE). Contour comparisons were made using Dice similarity coefficients (DSC) and Hausdorff distances. Results: Using the T2 FatSat (FS) GE datasets the atlas generated contours resulted in an average DSC of 0.83±0.06 for prostate, 0.57±0.12 for PZ and 0.75±0.09 for CG. Similar results were found when using the Siemens data with a DSC of 0.79±0.14 for prostate, 0.54±0.16 and 0.70±0.9. Contrast between prostate and surrounding anatomy and between the PZ and CG contours for both vendors demonstrated superior contrast separation; significance was found for all comparisons p-value < 0.0001. Conclusion: Atlas-based segmentation yielded promising results for all contours compared to expertly defined contours in both Siemens and GE 3T systems providing fast and automatic segmentation of the prostate. Funding Support, Disclosures, and Conflict of Interest: AS Nelson is a partial owner of MIM Software, Inc. AS Nelson, and A Swallen are current employees at MIM Software, Inc.« less

4D atlas of the mouse embryo for precise morphological staging.

PubMed

Wong, Michael D; van Eede, Matthijs C; Spring, Shoshana; Jevtic, Stefan; Boughner, Julia C; Lerch, Jason P; Henkelman, R Mark

2015-10-15

After more than a century of research, the mouse remains the gold-standard model system, for it recapitulates human development and disease and is quickly and highly tractable to genetic manipulations. Fundamental to the power and success of using a mouse model is the ability to stage embryonic mouse development accurately. Past staging systems were limited by the technologies of the day, such that only surface features, visible with a light microscope, could be recognized and used to define stages. With the advent of high-throughput 3D imaging tools that capture embryo morphology in microscopic detail, we now present the first 4D atlas staging system for mouse embryonic development using optical projection tomography and image registration methods. By tracking 3D trajectories of every anatomical point in the mouse embryo from E11.5 to E14.0, we established the first 4D atlas compiled from ex vivo 3D mouse embryo reference images. The resulting 4D atlas comprises 51 interpolated 3D images in this gestational range, resulting in a temporal resolution of 72 min. From this 4D atlas, any mouse embryo image can be subsequently compared and staged at the global, voxel and/or structural level. Assigning an embryonic stage to each point in anatomy allows for unprecedented quantitative analysis of developmental asynchrony among different anatomical structures in the same mouse embryo. This comprehensive developmental data set offers developmental biologists a new, powerful staging system that can identify and compare differences in developmental timing in wild-type embryos and shows promise for localizing deviations in mutant development. © 2015. Published by The Company of Biologists Ltd.

An Atlas of Far-ultraviolet Spectra of the Zeta Aurigae Binary 31 Cygni with Line Identifications

NASA Astrophysics Data System (ADS)

Hagen Bauer, Wendy; Bennett, Philip D.

2014-04-01

The ζ Aurigae system 31 Cygni (K4 Ib + B4 V) was observed by the FUSE satellite during total eclipse and at three phases during chromospheric eclipse. We present the coadded, calibrated spectra and atlases with line identifications. During total eclipse, emission from high ionization states (e.g., Fe III and Cr III) shows asymmetric profiles redshifted from the systemic velocity, while emission from lower ionization states (e.g., Fe II and O I) appears more symmetric and is centered closer to the systemic velocity. Absorption from neutral and singly ionized elements is detected during chromospheric eclipse. Late in chromospheric eclipse, absorption from the K star wind is detected at a terminal velocity of ~80 km s-1. These atlases will be useful for interpreting the far-UV spectra of other ζ Aur systems, as the observed FUSE spectra of 32 Cyg, KQ Pup, and VV Cep during chromospheric eclipse resemble that of 31 Cyg.

Aptian-Albian boundary in Central Southern Atlas of Tunisia: New tectono-sedimentary facts

NASA Astrophysics Data System (ADS)

Ghanmi, Mohamed Abdelhamid; Barhoumi, Amine; Ghanmi, Mohamed; Zargouni, Fouad

2017-08-01

The Aptian-Albian boundary preserves one of the most important events in Central-Southern Atlas of Tunisia, which belongs to the Southern Tethyan margin. A major sedimentary break was recorded between Early Aptian and Albian series in Bouhedma-Boudouaou Mountains. This major hiatus probably linked to the ''Austrian phase'' and to the Aptian and Albian ''Crisis'' testify a period of major tectonic events. In this paper, field observations on the Mid-Cretaceous stratigraphy combined with seismic profile interpretation were used for the first time to characterize the Aptian-Albian boundary in Central-Southern Atlas of Tunisia. Our new results reveal that Aptian-Albian boundary marks a critical interval not only in Maknassy-Mezzouna orogenic system but also in the Tunisian Atlas. Furthermore, Aptian-Albian series outcrop is marked by the important sedimentary gaps as well as a dramatic thickness change from West to East and predominately from North to South. This is linked to the extensional tectonic features which characterize all the Central-Southern Atlas of Tunisia.

Energy Frontier Research With ATLAS: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, John; Black, Kevin; Ahlen, Steve

2016-06-14

The Boston University (BU) group is playing key roles across the ATLAS experiment: in detector operations, the online trigger, the upgrade, computing, and physics analysis. Our team has been critical to the maintenance and operations of the muon system since its installation. During Run 1 we led the muon trigger group and that responsibility continues into Run 2. BU maintains and operates the ATLAS Northeast Tier 2 computing center. We are actively engaged in the analysis of ATLAS data from Run 1 and Run 2. Physics analyses we have contributed to include Standard Model measurements (W and Z cross sections,more » t\\bar{t} differential cross sections, WWW^* production), evidence for the Higgs decaying to \\tau^+\\tau^-, and searches for new phenomena (technicolor, Z' and W', vector-like quarks, dark matter).« less

Tracking and Data Relay Satellite System configuration and tradeoff study. Volume 3: Atlas Centaur launched TDRSS. Part 2: Final Report, 22 August 1972 - 1 April 1973

NASA Technical Reports Server (NTRS)

1973-01-01

Configuration data and design information for the Atlas Centaur launched configuration are presented. Overall system definition, operations and control, and telecommunication service system, including link budgets, are discussed. A brief description of the user telecommunications equipment and ground station is presented. A summary description of the TDR spacecraft and all the subsystems is included. The data presented are largely in tabular form. A brief treatment of an optional configuration with enhanced telecommunications service is described.

Les dykes basiques du massif ancien de l'Ourika (Atlas de Marrakech, Maroc): géochimie et significationThe basic dykes of the Ourika old massif (High Atlas of Marrakech): Geochemistry and significance

NASA Astrophysics Data System (ADS)

Barakat, Ahmed; Marignac, Christian; Bouabdelli, Mohamed

The Precambrian massif of Ourika is crosscut by two systems of basic dykes, striking N40°E and N90-120°E. Using incompatible trace elements, the two systems form two distinct chemical groups, displaying a continental tholeiitic affinity. The composition variations between the two defined groups can be due to heterogeneities of mantle sources and to contamination, during the magma ascent, by the continental crust. The emplacement of these basic dykes, before the late-PIII formations, can be related to the Neoproterozoic distension generalised to the Anti-Atlas chain. To cite this article: A. Barakat et al., C. R. Geoscience 334 (2002) 827-833.

Testing sTGC with small angle wire edges for the ATLAS new small wheel muon detector upgrade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roth, Itamar; Klier, Amit; Duchovni, Ehud

The LHC upgrade scheduled for 2018 is expected to significantly increase the accelerator's luminosity, and as a result the radiation background rates in the ATLAS Muon Spectrometer will increase too. Some of its components will have to be replaced in order to cope with these high rates. Newly designed small-strip Thin Gap chambers (sTGC) will replace them at the small wheel region. One of the differences between the sTGC and the currently used TGC is the alignment of the wires along the azimuthal direction. As a result, the outermost wires approach the detector's edge with a small angle. Such amore » configuration may be a cause for various problems. Two small dedicated chambers were built and tested in order to study possible edge effects that may arise from the new configuration. The sTGC appears to be stable and no spark have been observed, yet some differences in the detector response near the edge is seen and further studies should be carried out. (authors)« less

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.

The ATLAS Production System Evolution: New Data Processing and Analysis Paradigm for the LHC Run2 and High-Luminosity

NASA Astrophysics Data System (ADS)

Barreiro, F. H.; Borodin, M.; De, K.; Golubkov, D.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Padolski, S.; Wenaus, T.; ATLAS Collaboration

2017-10-01

The second generation of the ATLAS Production System called ProdSys2 is a distributed workload manager that runs daily hundreds of thousands of jobs, from dozens of different ATLAS specific workflows, across more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criteria, such as input and output size, memory requirements and CPU consumption, with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteer-computers. The system dynamically assigns a group of jobs (task) to a group of geographically distributed computing resources. Dynamic assignment and resources utilization is one of the major features of the system, it didn’t exist in the earliest versions of the production system where Grid resources topology was predefined using national or/and geographical pattern. Production System has a sophisticated job fault-recovery mechanism, which efficiently allows to run multi-Terabyte tasks without human intervention. We have implemented “train” model and open-ended production which allow to submit tasks automatically as soon as new set of data is available and to chain physics groups data processing and analysis with central production by the experiment. We present an overview of the ATLAS Production System and its major components features and architecture: task definition, web user interface and monitoring. We describe the important design decisions and lessons learned from an operational experience during the first year of LHC Run2. We also report the performance of the designed system and how various workflows, such as data (re)processing, Monte-Carlo and physics group production, users analysis, are scheduled and executed within one production system on heterogeneous computing resources.

Failure Atlas for Rolling Bearings in Wind Turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tallian, T. E.

2006-01-01

This Atlas is structured as a supplement to the book: T.E. Tallian: Failure Atlas for Hertz Contact Machine Elements, 2nd edition, ASME Press New York, (1999). The content of the atlas comprises plate pages from the book that contain bearing failure images, application data, and descriptions of failure mode, image, and suspected failure causes. Rolling bearings are a critical component of the mainshaft system, gearbox and generator in the rapidly developing technology of power generating wind turbines. The demands for long service life are stringent; the design load, speed and temperature regimes are demanding and the environmental conditions including weather,more » contamination, impediments to monitoring and maintenance are often unfavorable. As a result, experience has shown that the rolling bearings are prone to a variety of failure modes that may prevent achievement of design lives. Morphological failure diagnosis is extensively used in the failure analysis and improvement of bearing operation. Accumulated experience shows that the failure appearance and mode of failure causation in wind turbine bearings has many distinguishing features. The present Atlas is a first effort to collect an interpreted database of specifically wind turbine related rolling bearing failures and make it widely available. This Atlas is structured as a supplement to the book: T. E. Tallian: Failure Atlas for Hertz Contact Machine Elements, 2d edition, ASME Press New York, (1999). The main body of that book is a comprehensive collection of self-contained pages called Plates, containing failure images, bearing and application data, and three descriptions: failure mode, image and suspected failure causes. The Plates are sorted by main failure mode into chapters. Each chapter is preceded by a general technical discussion of the failure mode, its appearance and causes. The Plates part is supplemented by an introductory part, describing the appearance classification and failure classification systems used, and by several indexes. The present Atlas is intended as a supplement to the book. It has the same structure but contains only Plate pages, arranged in chapters, each with a chapter heading page giving a short definition of the failure mode illustrated. Each Plate page is self contained, with images, bearing and application data, and descriptions of the failure mode, the images and the suspected causes. Images are provided in two resolutions: The text page includes 6 by 9 cm images. In addition, high resolution image files are attached, to be retrieved by clicking on their 'push pin' icon. While the material in the present Atlas is self-contained, it is nonetheless a supplement to the book and the complete interpretation of the terse image descriptions and of the system underlying the failure code presupposes familiarity with the book. Since this Atlas is a supplement to the book, its chapter numbering follows that of the book. Not all failure modes covered in the book have been found among the observed wind turbines. For that reason, and because of the omission of introductory matter, the chapter numbers in this Atlas are not a continuous sequence.« less

International Ultraviolet Explorer (IUE) ultraviolet spectral atlas of selected astronomical objects

NASA Technical Reports Server (NTRS)

Wu, Chi-Chao; Reichert, Gail A.; Ake, Thomas B.; Boggess, Albert; Holm, Albert V.; Imhoff, Catherine L.; Kondo, Yoji; Mead, Jaylee M.; Shore, Steven N.

1992-01-01

The IUE Ultraviolet Spectral Atlas of Selected Astronomical Objects (or 'the Atlas'), is based on the data that were available in the IUE archive in 1986, and is intended to be a quick reference for the ultraviolet spectra of many categories of astronomical objects. It shows reflected sunlight from the Moon, planets, and asteroids, and also shows emission from comets. Comprehensive compilations of UV spectra for main sequence, subgiant, giant, bright giant, and supergiant stars are published elsewhere. This Atlas contains the spectra for objects occupying other areas of the Hertzsprung-Russell diagram: pre-main sequence stars, chemically peculiar stars, pulsating variables, subluminous stars, and Wolf-Rayet stars. This Atlas also presents phenomena such as the chromospheric and transition region emissions from late-type stars; composite spectra of stars, gas streams, accretion disks and gas envelopes of binary systems; the behavior of gas ejecta shortly after the outburst of novac and supernovac; and the H II regions, planetary nebulae, and supernova remnants. Population 2 stars, globular clusters, and luminous stars in the Magellanic Clouds, M31, and M33, are also included in this publication. Finally, the Atlas gives the ultraviolet spectra of galaxies of different Hubble types and of active galaxies.

Integration of the Chinese HPC Grid in ATLAS Distributed Computing

NASA Astrophysics Data System (ADS)

Filipčič, A.; ATLAS Collaboration

2017-10-01

Fifteen Chinese High-Performance Computing sites, many of them on the TOP500 list of most powerful supercomputers, are integrated into a common infrastructure providing coherent access to a user through an interface based on a RESTful interface called SCEAPI. These resources have been integrated into the ATLAS Grid production system using a bridge between ATLAS and SCEAPI which translates the authorization and job submission protocols between the two environments. The ARC Computing Element (ARC-CE) forms the bridge using an extended batch system interface to allow job submission to SCEAPI. The ARC-CE was setup at the Institute for High Energy Physics, Beijing, in order to be as close as possible to the SCEAPI front-end interface at the Computing Network Information Center, also in Beijing. This paper describes the technical details of the integration between ARC-CE and SCEAPI and presents results so far with two supercomputer centers, Tianhe-IA and ERA. These two centers have been the pilots for ATLAS Monte Carlo Simulation in SCEAPI and have been providing CPU power since fall 2015.

An electronic atlas on the oceanography of the South China Sea

NASA Astrophysics Data System (ADS)

Rostov, I. D.; Moroz, V. V.; Rudykh, N. I.; Rostov, V. I.

2009-12-01

The digital atlas on CD ROM includes a set of generalized data on the South China Sea oceanography. The data is presented in the form of spreadsheets, graphics, and text. The atlas contains a brief annotated description of the main physical-geographical characteristics and the particularities of the hydrological regime, water masses, tidal phenomena, and water mass circulation. The atlas is an interactive information-reference system including elements of dynamic data visualization. It contains a body of data on the long-term observations of the temperature and salinity; gridded blocks of the average annual, seasonal, and monthly data at the standard depth horizons; and data on the hydrochemical characteristics and water currents obtained by automatic buoy stations (ABS). A list of existing open access data bases and web sites is given where additional online and archived information on a range of special issues and problems related to regional studies and exploitation is provided. The system allows for fast access to specifically selected online or generalized reference information (via the Internet) and for its imaging.

Charting molecular free-energy landscapes with an atlas of collective variables

NASA Astrophysics Data System (ADS)

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2016-11-01

Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and β-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.

Characterisation of novel thin n-in-p planar pixel modules for the ATLAS Inner Tracker upgrade

NASA Astrophysics Data System (ADS)

Beyer, J.-C.; La Rosa, A.; Macchiolo, A.; Nisius, R.; Savic, N.; Taibah, R.

2018-01-01

In view of the high luminosity phase of the LHC (HL-LHC) to start operation around 2026, a major upgrade of the tracker system for the ATLAS experiment is in preparation. The expected neutron equivalent fluence of up to 2.4×1016 1 MeV neq./cm2 at the innermost layer of the pixel detector poses the most severe challenge. Thanks to their low material budget and high charge collection efficiency after irradiation, modules made of thin planar pixel sensors are promising candidates to instrument these layers. To optimise the sensor layout for the decreased pixel cell size of 50×50 μm2, TCAD device simulations are being performed to investigate the charge collection efficiency before and after irradiation. In addition, sensors of 100-150 μm thickness, interconnected to FE-I4 read-out chips featuring the previous generation pixel cell size of 50×250 μm2, are characterised with testbeams at the CERN-SPS and DESY facilities. The performance of sensors with various designs, irradiated up to a fluence of 1×1016 neq./cm2, is compared in terms of charge collection and hit efficiency. A replacement of the two innermost pixel layers is foreseen during the lifetime of HL-LHC . The replacement will require several months of intervention, during which the remaining detector modules cannot be cooled. They are kept at room temperature, thus inducing an annealing. The performance of irradiated modules will be investigated with testbeam campaigns and the method of accelerated annealing at higher temperatures.

How to keep the Grid full and working with ATLAS production and physics jobs

NASA Astrophysics Data System (ADS)

Pacheco Pagés, A.; Barreiro Megino, F. H.; Cameron, D.; Fassi, F.; Filipcic, A.; Di Girolamo, A.; González de la Hoz, S.; Glushkov, I.; Maeno, T.; Walker, R.; Yang, W.; ATLAS Collaboration

2017-10-01

The ATLAS production system provides the infrastructure to process millions of events collected during the LHC Run 1 and the first two years of Run 2 using grid, clouds and high performance computing. We address in this contribution the strategies and improvements that have been implemented to the production system for optimal performance and to achieve the highest efficiency of available resources from operational perspective. We focus on the recent developments.

Computerized Bone Age Estimation Using Deep Learning Based Program: Evaluation of the Accuracy and Efficiency.

PubMed

Kim, Jeong Rye; Shim, Woo Hyun; Yoon, Hee Mang; Hong, Sang Hyup; Lee, Jin Seong; Cho, Young Ah; Kim, Sangki

2017-12-01

The purpose of this study is to evaluate the accuracy and efficiency of a new automatic software system for bone age assessment and to validate its feasibility in clinical practice. A Greulich-Pyle method-based deep-learning technique was used to develop the automatic software system for bone age determination. Using this software, bone age was estimated from left-hand radiographs of 200 patients (3-17 years old) using first-rank bone age (software only), computer-assisted bone age (two radiologists with software assistance), and Greulich-Pyle atlas-assisted bone age (two radiologists with Greulich-Pyle atlas assistance only). The reference bone age was determined by the consensus of two experienced radiologists. First-rank bone ages determined by the automatic software system showed a 69.5% concordance rate and significant correlations with the reference bone age (r = 0.992; p < 0.001). Concordance rates increased with the use of the automatic software system for both reviewer 1 (63.0% for Greulich-Pyle atlas-assisted bone age vs 72.5% for computer-assisted bone age) and reviewer 2 (49.5% for Greulich-Pyle atlas-assisted bone age vs 57.5% for computer-assisted bone age). Reading times were reduced by 18.0% and 40.0% for reviewers 1 and 2, respectively. Automatic software system showed reliably accurate bone age estimations and appeared to enhance efficiency by reducing reading times without compromising the diagnostic accuracy.

Bubble morphology in U 3Si 2 implanted by high-energy Xe ions at 300 °C

DOE PAGES

Miao, Yinbin; Harp, Jason; Mo, Kun; ...

2017-08-02

The microstructure modifications of a high-energy Xe implanted U 3Si 2, a promising accident tolerant fuel candidate, were characterized and are reported upon. The U 3Si 2 pellet was irradiated at Argonne Tandem Linac Accelerator System (ATLAS) by an 84 MeV Xe ion beam at 300 °C. The irradiated specimen was then investigated using a series of transmission electron microscopy (TEM) techniques. A dense distribution of bubbles were observed near the range of the 84 MeV Xe ions. Xe gas was also found to accumulate at multiple types of sinks, such as dislocations and grain boundaries. Bubbles aggregated at thosemore » sinks are slightly larger than intragranular bubbles in lattice. At 300 °C, the gaseous swelling strain is limited as all the bubbles are below 10 nm, implying the promising fission gas behavior of U 3Si 2 under normal operating conditions in light water reactors (LWRs).« less

KSC-2011-8118

NASA Image and Video Library

2011-12-01

CAPE CANAVERAL, Fla. -- This is an artist's conception of a United Launch Alliance (ULA) Atlas V rocket being considered for NASA's Commercial Crew Program (CCP). In 2011, NASA and ULA of Englewood, Colo., entered into an unfunded Space Act Agreement during Commercial Crew Development Round 2 (CCDev2) activities to mature the design and development of a crew transportation system with the overall goal of accelerating a United States-led capability to the International Space Station. The goal of CCP is to drive down the cost of space travel as well as open up space to more people than ever before by balancing industry’s own innovative capabilities with NASA's 50 years of human spaceflight experience. Six other aerospace companies also are maturing launch vehicle and spacecraft designs under CCDev2, including Alliant Techsystems Inc. (ATK), Blue Origin, The Boeing Co., Excalibur Almaz Inc., Sierra Nevada Corp., and Space Exploration Technologies (SpaceX). For more information, visit www.nasa.gov/commercialcrew. Image credit: United Launch Alliance

Stress-triggered atavistic reprogramming (STAR) addiction: driving force behind head and neck cancer?

PubMed Central

Masuda, Muneyuki; Wakasaki, Takahiro; Toh, Satoshi

2016-01-01

Recent results of the Cancer Genome Atlas on head and neck squamous cell carcinoma (HNSCC) revealed that HNSCC lacked predominant gain-of-function mutations in oncogenes, whereas an essential role for epigenetics in oncogenesis has become apparent. In parallel, it has gained general acceptance that cancer is considered as complex adaptive system, which evolves responding environmental selective pressures. This somatic evolution appears to proceed concurrently with the acquisition of an atavistic pluripotent state (i.e., “stemness”), which is inducible by intrinsic epigenetic reprogramming program as demonstrated by induced pluripotent stem (iPS) cells. This Nobel prize-winning discovery has markedly accelerated and expanded cancer stem cell research from the point of epigenetic reprogramming. Taken together, we hypothesize that stress-triggered atavistic reprogramming (STAR) may be the major driving force of HNSCC evolution. In this perspective, we discuss the possible mechanisms of STAR in HNSCC, focusing on recent topics of epigenetic reprogramming in developmental and cancer cell biology. PMID:27429838

Bubble morphology in U3Si2 implanted by high-energy Xe ions at 300 °C

NASA Astrophysics Data System (ADS)

Miao, Yinbin; Harp, Jason; Mo, Kun; Zhu, Shaofei; Yao, Tiankai; Lian, Jie; Yacout, Abdellatif M.

2017-11-01

The microstructure modifications of a high-energy Xe implanted U3Si2, a promising accident tolerant fuel candidate, were characterized and are reported upon. The U3Si2 pellet was irradiated at Argonne Tandem Linac Accelerator System (ATLAS) by an 84 MeV Xe ion beam at 300 °C. The irradiated specimen was then investigated using a series of transmission electron microscopy (TEM) techniques. A dense distribution of bubbles were observed near the range of the 84 MeV Xe ions. Xe gas was also found to accumulate at multiple types of sinks, such as dislocations and grain boundaries. Bubbles aggregated at those sinks are slightly larger than intragranular bubbles in lattice. At 300 °C, the gaseous swelling strain is limited as all the bubbles are below 10 nm, implying the promising fission gas behavior of U3Si2 under normal operating conditions in light water reactors (LWRs).

CAVEman: Standardized anatomical context for biomedical data mapping.

PubMed

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

2008-01-01

The authors have created a software system called the CAVEman, for the visual integration and exploration of heterogeneous anatomical and biomedical data. The CAVEman can be applied for both education and research tasks. The main component of the system is a three-dimensional digital atlas of the adult male human anatomy, structured according to the nomenclature of Terminologia Anatomica. The underlying data-indexing mechanism uses standard ontologies to map a range of biomedical data types onto the atlas. The CAVEman system is now used to visualize genetic processes in the context of the human anatomy and to facilitate visual exploration of the data. Through the use of Javatrade mark software, the atlas-based system is portable to virtually any computer environment, including personal computers and workstations. Existing Java tools for biomedical data analysis have been incorporated into the system. The affordability of virtual-reality installations has increased dramatically over the last several years. This creates new opportunities for educational scenarios that model important processes in a patient's body, including gene expression patterns, metabolic activity, the effects of interventions such as drug treatments, and eventually surgical simulations.

ICESat-2 simulated data from airborne altimetery

NASA Astrophysics Data System (ADS)

Brunt, K. M.; Neumann, T.; Markus, T.; Brenner, A. C.; Barbieri, K.; Field, C.; Sirota, M.

2010-12-01

Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) is scheduled to launch in 2015 and will carry onboard the Advanced Topographic Laser Altimeter System (ATLAS), which represents a new approach to spaceborne determination of surface elevations. Specifically, the current ATLAS design is for a micropulse, multibeam, photon-counting laser altimeter with lower energy, a shorter pulse width, and a higher repetition rate relative to the Geoscience Laser Altimeter (GLAS), the instrument that was onboard ICESat. Given the new and untested technology associated with ATLAS, airborne altimetry data is necessary (1) to test the proposed ATLAS instrument geometry, (2) to validate instrument models, and (3) to assess the atmospheric effects on multibeam altimeters. We present an overview of the airborne instruments and datasets intended to address the ATLAS instrument concept, including data collected over Greenland (July 2009) using an airborne SBIR prototype 100 channel, photon-counting, terrain mapping altimeter, which addresses the first of these 3 scientific concerns. Additionally, we present the plan for further simulator data collection over vegetated and ice covered regions using Multiple Altimeter Beam Experimental Lidar (MABEL), intended to address the latter two scientific concerns. As the ICESAT-2 project is in the design phase, the particular configuration of the ATLAS instrument may change. However, we expect this work to be relevant as long as ATLAS pursues a photon-counting approach.

Discovery through maps: Exploring real-world applications of ...

EPA Pesticide Factsheets

Background/Question/Methods U.S. EPA’s EnviroAtlas provides a collection of interactive tools and resources for exploring ecosystem goods and services. The purpose of EnviroAtlas is to provide better access to consistently derived ecosystems and socio-economic data to facilitate decision-making while also providing data for research and education. EnviroAtlas tools and resources are well-suited for educational use, as they encourage systems thinking, cover a broad range of topics, are freely available, and do not require specialized software to use. To use EnviroAtlas only requires a computer and an internet connection, making it a useful tool for community planning, education, and decision-making at multiple scales. To help users understand how EnviroAtlas resources may be used in different contexts, we provide example use cases. These use cases highlight a real-world issue which EnviroAtlas data, in conjunction with other available data or resources, may be used to address. Here we present three use cases that approach incorporating ecosystem services in decision-making in different decision contexts: 1) to minimize the negative impacts of excessive summer heat due to urbanization in Portland, Oregon 2) to explore selecting a pilot route for a community greenway, and 3) to reduce nutrient loading through a regional manure transport program. Results/Conclusions EnviroAtlas use cases provide step-by-step approaches for using maps and data to address real-wo

Pre-Launch Performance Testing of the ICESat-2/ATLAS Flight Science Receiver Algorithms

NASA Astrophysics Data System (ADS)

Mcgarry, J.; Carabajal, C. C.; Saba, J. L.; Rackley, A.; Holland, S.

2016-12-01

NASA's Advanced Topographic Laser Altimeter System (ATLAS) will be the single instrument on the ICESat-2 spacecraft which is expected to launch in late 2017 with a 3 year mission lifetime. The ICESat-2 planned orbital altitude is 500 km with a 92 degree inclination and 91-day repeat tracks. ATLAS is a single-photon detection system transmitting at 532nm with a laser repetition rate of 10 kHz and a 6 spot pattern on the Earth's surface. Without some method of reducing the received data, the volume of ATLAS telemetry would far exceed the normal X-band downlink capability. To reduce the data volume to an acceptable level a set of onboard Receiver Algorithms has been developed. These Algorithms limit the daily data volume by distinguishing surface echoes from the background noise and allowing the instrument to telemeter data from only a small vertical region about the signal. This is accomplished through the use of an onboard Digital Elevation Model (DEM), signal processing techniques, and onboard relief and surface reference maps. The ATLAS Receiver Algorithms have been completed and have been verified during Instrument testing in the spacecraft assembly area at the Goddard Space Flight Center in late 2015 and early 2016. Testing has been performed at ambient temperature with a pressure of one atmosphere as well as at the expected hot and cold temperatures in a vacuum. 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. Testing with the ATLAS instrument and flight software shows very good agreement with previous Simulator testing and all of the requirements for ATLAS Receiver Algorithms were successfully verified during Run for the Record Testing in December 2015. This poster will describe the performance of the ATLAS Flight Science Receiver Algorithms during the Run for Record and Comprehensive Performance Testing performed at Goddard, which will give insight into the future on-orbit performance of the Algorithms. See the companion poster (Carabajal, et al) in this session.

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

2017-07-01

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 ATAC patientBone (air and tissue from the atlas with patient bone), and PET with ATAC boneless (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 ATAC boneless (-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 ATAC patientBone (-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 Online supplemental material is available for this article.

Single-stage reduction and fixation for atlantoaxial dislocation with atlas assimilation applying occipital plate, C2 screws and rigid cantilever beam system through intraoperative distraction: A retrospective study of 25 cases

NASA Astrophysics Data System (ADS)

Li, Zhonghua; Han, Xuesong; Li, Xiaolei; Qin, Xiaofei

2018-04-01

To report the surgical technique and clinical outcomes for the treatment of AAD with atlas assimilation by single-stage posterior reduction and fixation applying intraoperative distraction between occipital and C2 screws. From April 2008 to January 2014, 25 patients underwent single-stage posterior reduction and fixation applying occipital plate, C2 screws and rigid cantilever beam system through intraoperative distraction between occipital and C2 screws. The pre- and postoperative radiologic parameters and JOA score were examined. Follow-up ranged from 6 to 17months in 25 patients. Clinical symptoms improved in 24 patients (96%) and were stable in 1 patient (4%). Radiologic assessment illustrated that complete reduction was achieved in 24 patients and partial reduction (>60%) in 1 patient. Overall, satisfactory decompression and reduction were showed on postoperative MRT and 3D-CT scans of all 25 patients. The single-stage posterior reduction and fixation applying occipital plate, C2 screws and rigid cantilever beam system through intraoperative distraction between occipital and C2 screws for AAD with atlas assimilation is simple, fast, safe and effective. C1 screws insertion for the treatment of AAD with atlas assimilation should be considered.

A Kalman Filtering Perspective for Multiatlas Segmentation*

PubMed Central

Gao, Yi; Zhu, Liangjia; Cates, Joshua; MacLeod, Rob S.; Bouix, Sylvain; Tannenbaum, Allen

2016-01-01

In multiatlas segmentation, one typically registers several atlases to the novel image, and their respective segmented label images are transformed and fused to form the final segmentation. In this work, we provide a new dynamical system perspective for multiatlas segmentation, inspired by the following fact: The transformation that aligns the current atlas to the novel image can be not only computed by direct registration but also inferred from the transformation that aligns the previous atlas to the image together with the transformation between the two atlases. This process is similar to the global positioning system on a vehicle, which gets position by inquiring from the satellite and by employing the previous location and velocity—neither answer in isolation being perfect. To solve this problem, a dynamical system scheme is crucial to combine the two pieces of information; for example, a Kalman filtering scheme is used. Accordingly, in this work, a Kalman multiatlas segmentation is proposed to stabilize the global/affine registration step. The contributions of this work are twofold. First, it provides a new dynamical systematic perspective for standard independent multiatlas registrations, and it is solved by Kalman filtering. Second, with very little extra computation, it can be combined with most existing multiatlas segmentation schemes for better registration/segmentation accuracy. PMID:26807162

Evolution of the ATLAS PanDA workload management system for exascale computational science

NASA Astrophysics Data System (ADS)

Maeno, T.; De, K.; Klimentov, A.; Nilsson, P.; Oleynik, D.; Panitkin, S.; Petrosyan, A.; Schovancova, J.; Vaniachine, A.; Wenaus, T.; Yu, D.; Atlas Collaboration

2014-06-01

An important foundation underlying the impressive success of data processing and analysis in the ATLAS experiment [1] at the LHC [2] is the Production and Distributed Analysis (PanDA) workload management system [3]. PanDA was designed specifically for ATLAS and proved to be highly successful in meeting all the distributed computing needs of the experiment. However, the core design of PanDA is not experiment specific. The PanDA workload management system is capable of meeting the needs of other data intensive scientific applications. Alpha-Magnetic Spectrometer [4], an astro-particle experiment on the International Space Station, and the Compact Muon Solenoid [5], an LHC experiment, have successfully evaluated PanDA and are pursuing its adoption. In this paper, a description of the new program of work to develop a generic version of PanDA will be given, as well as the progress in extending PanDA's capabilities to support supercomputers and clouds and to leverage intelligent networking. PanDA has demonstrated at a very large scale the value of automated dynamic brokering of diverse workloads across distributed computing resources. The next generation of PanDA will allow other data-intensive sciences and a wider exascale community employing a variety of computing platforms to benefit from ATLAS' experience and proven tools.

Forward-backward multiplicity correlations in pp, p+Pb and Pb+Pb collisions with the ATLAS detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, Jiangyong

2016-12-01

Two-particle pseudorapidity correlations are measured in √s NN = 2.76 TeV Pb+Pb, √s NN = 5.02 TeV p +Pb and √s = 13 TeV pp collisions [ATLAS Collaboration, ATLAS-CONF-2015-051; ATLAS-CONF-2015-020]. Correlation function is measured using charged particles in the pseudorapidity range |η|<2.4 with transverse momentum p T>0.2 GeV, and it is measured as a function of event multiplicity, defined by number of charged particles with |η|<2.5 and p T>0.4 GeV. The correlation function is decomposed into a short-range component (SRC) and a long-range component (LRC). The SRC differs significantly between the opposite-charge pairs and same-charge pairs, and between the threemore » collision systems at similar multiplicity. The LRC is described approximately by 1 + n1n2 in all collision systems over the full multiplicity range. The values of are consistent between the opposite-charge and same-charge pairs, and are similar for the three collision systems at similar multiplicity. The values of and the magnitude of the SRC both follow a power-law dependence on the event multiplicity.« less

The Brain of the Archerfish Toxotes chatareus: A Nissl-Based Neuroanatomical Atlas and Catecholaminergic/Cholinergic Systems

PubMed Central

Karoubi, Naomi; Segev, Ronen; Wullimann, Mario F.

2016-01-01

Over recent years, the seven-spot archerfish (Toxotes chatareus) has emerged as a new model for studies in visual and behavioral neuroscience thanks to its unique hunting strategy. Its natural ability to spit at insects outside of water can be used in the laboratory for well controlled behavioral experiments where the fish is trained to aim at targets on a screen. The need for a documentation of the neuroanatomy of this animal became critical as more research groups use it as a model. Here we present an atlas of adult T. chatareus specimens caught in the wild in South East Asia. The atlas shows representative sections of the brain and specific structures revealed by a classic Nissl staining as well as corresponding schematic drawings. Additional immunostainings for catecholaminergic and cholinergic systems were conducted to corroborate the identification of certain nuclei and the data of a whole brain scanner is available online. We describe the general features of the archerfish brain as well as its specificities, especially for the visual system and compare the neuroanatomy of the archerfish with other teleosts. This atlas of the archerfish brain shows all levels of the neuraxis and intends to provide a solid basis for further neuroscientific research on T. chatareus, in particular electrophysiological studies. PMID:27891081

Reaction Studies With Light, Unstable Nuclei

NASA Astrophysics Data System (ADS)

Ernst Rehm, K.

2006-10-01

The availability of beams of exotic nuclei allows us for the first time to study in a terrestrial laboratory reactions, which occur in stellar explosions, such as Novae, Supernovae or X-ray bursts. In this talk I will present results from recent experiments performed with beams of light, unstable nuclei, which are produced via the in-flight technique at the ATLAs accelerator at Argonne. This work was supported by the US Department of Energy, Nuclear Physics Division, under contract No. W-31-109-ENG-38 and by the NSF Grant No. PHY-02-16783 (Joint Institute for Nuclear Astrophysics).

KSC-2012-4730

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4749

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4735

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4719

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, disappears into the night sky over Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida following liftoff at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Gianni Woods

KSC-2012-4761

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4748

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Rusty Backer

KSC-2012-4717

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, disappears into the night sky over Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4718

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – Exhaust clouds billow across the pad at Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida as the United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Gianni Woods

KSC-2012-4733

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4762

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. - The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Kenny Allen

KSC-2012-4713

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4712

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – Engine ignition under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT signals liftoff of NASA's Radiation Belt Storm Probes, or RBSP, is imminent from Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Jim Grossmann

KSC-2012-4736

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4724

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky

KSC-2012-4727

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4734

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4722

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, rises through the clouds over Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida following liftoff at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky and Gary Thompson

KSC-2012-4737

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4731

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifts off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4728

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4723

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, is a breath away from lifting off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky

KSC-2012-4729

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The engines ignite under the United Launch Alliance Atlas V rocket at 4:05 a.m. EDT lifting NASA's Radiation Belt Storm Probes, or RBSP, off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4732

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA's Radiation Belt Storm Probes, or RBSP, lifted off Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

Being Relevant in Tough Times: TRIUMF's Five-Year Plan

ScienceCinema

Tim, Mayer [TRIUMF

2017-12-09

Perhaps better known to the international community than its own neighbors, TRIUMF is Canada's national laboratory for particle and nuclear physics.  Working with the Canadian scientific community, TRIUMF has formulated a new vision to transform the laboratory and deliver a whole new level of performance and impact.  The plan capitalizes on platform technologies (superconducting RF cavities for accelerator physics and radiotracers in nuclear medicine) and exploits Canada's role in ATLAS and the LHC.  I will describe the key elements of the plan and discuss the science-policy landscape in which TRIUMF must make its case.

X-ray atlas of rheumatic diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dihlmann, W.

1986-01-01

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

InSight Atlas V Fairing Rotate to Vertical

NASA Image and Video Library

2018-02-07

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers inspect the payload fairing for the United Launch Alliance (ULA) Atlas V for NASA's upcoming Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars after it was lifted to the vertical position. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff atop a ULA Atlas V rocket is scheduled for May 5, 2018.

University of Michigan lecture archiving and related activities of the U-M ATLAS Collaboratory Project

NASA Astrophysics Data System (ADS)

Herr, J.; Bhatnagar, T.; Goldfarb, S.; Irrer, J.; McKee, S.; Neal, H. A.

2008-07-01

Large scientific collaborations as well as universities have a growing need for multimedia archiving of meetings and courses. Collaborations need to disseminate training and news to their wide-ranging members, and universities seek to provide their students with more useful studying tools. The University of Michigan ATLAS Collaboratory Project has been involved in the recording and archiving of multimedia lectures since 1999. Our software and hardware architecture has been used to record events for CERN, ATLAS, many units inside the University of Michigan, Fermilab, the American Physical Society and the International Conference on Systems Biology at Harvard. Until 2006 our group functioned primarily as a tiny research/development team with special commitments to the archiving of certain ATLAS events. In 2006 we formed the MScribe project, using a larger scale, and highly automated recording system to record and archive eight University courses in a wide array of subjects. Several robotic carts are wheeled around campus by unskilled student helpers to automatically capture and post to the Web audio, video, slides and chalkboard images. The advances the MScribe project has made in automation of these processes, including a robotic camera operator and automated video processing, are now being used to record ATLAS Collaboration events, making them available more quickly than before and enabling the recording of more events.

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria

PubMed Central

Ibarra-Arellano, Miguel A.; Campos-González, Adrián I.; Treviño-Quintanilla, Luis G.; Tauch, Andreas; Freyre-González, Julio A.

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy (Across-bacteria systems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708 regulons and 1776 systems. All this brings together a large corpus of data that will surely inspire studies to generate hypothesis regarding the principles governing the evolution and organization of systems and the functional architectures controlling them. Database URL: http://abasy.ccg.unam.mx PMID:27242034

ATLAS FTK a - very complex - custom super computer

NASA Astrophysics Data System (ADS)

Kimura, N.; ATLAS Collaboration

2016-10-01

In the LHC environment for high interaction pile-up, advanced techniques of analysing the data in real time are required in order to maximize the rate of physics processes of interest with respect to background processes. The Fast TracKer (FTK) is a track finding implementation at the hardware level that is designed to deliver full-scan tracks with pT above 1 GeV to the ATLAS trigger system for events passing the Level-1 accept (at a maximum rate of 100 kHz). In order to achieve this performance, a highly parallel system was designed and currently it is being commissioned within in ATLAS. Starting in 2016 it will provide tracks for the trigger system in a region covering the central part of the ATLAS detector, and will be extended to the full detector coverage. The system relies on matching hits coming from the silicon tracking detectors against one billion patterns stored in custom ASIC chips (Associative memory chip - AM06). In a first stage, coarse resolution hits are matched against the patterns and the accepted hits undergo track fitting implemented in FPGAs. Tracks with pT > 1GeV are delivered to the High Level Trigger within about 100 ps. Resolution of the tracks coming from FTK is close to the offline tracking and it will allow for reliable detection of primary and secondary vertexes at trigger level and improved trigger performance for b-jets and tau leptons. This contribution will give an overview of the FTK system and present the status of commissioning of the system. Additionally, the expected FTK performance will be briefly described.

Improved segmentation of cerebellar structures in children

PubMed Central

Narayanan, Priya Lakshmi; Boonazier, Natalie; Warton, Christopher; Molteno, Christopher D; Joseph, Jesuchristopher; Jacobson, Joseph L; Jacobson, Sandra W; Zöllei, Lilla; Meintjes, Ernesta M

2016-01-01

Background Consistent localization of cerebellar cortex in a standard coordinate system is important for functional studies and detection of anatomical alterations in studies of morphometry. To date, no pediatric cerebellar atlas is available. New method The probabilistic Cape Town Pediatric Cerebellar Atlas (CAPCA18) was constructed in the age-appropriate National Institute of Health Pediatric Database asymmetric template space using manual tracings of 16 cerebellar compartments in 18 healthy children (9–13 years) from Cape Town, South Africa. The individual atlases of the training subjects were also used to implement multi atlas label fusion using multi atlas majority voting (MAMV) and multi atlas generative model (MAGM) approaches. Segmentation accuracy in 14 test subjects was compared for each method to ‘gold standard’ manual tracings. Results Spatial overlap between manual tracings and CAPCA18 automated segmentation was 73% or higher for all lobules in both hemispheres, except VIIb and X. Automated segmentation using MAGM yielded the best segmentation accuracy over all lobules (mean Dice Similarity Coefficient 0.76; range 0.55–0.91). Comparison with existing methods In all lobules, spatial overlap of CAPCA18 segmentations with manual tracings was similar or higher than those obtained with SUIT (spatially unbiased infra-tentorial template), providing additional evidence of the benefits of an age appropriate atlas. MAGM segmentation accuracy was comparable to values reported recently by Park et al. (2014) in adults (across all lobules mean DSC = 0.73, range 0.40–0.89). Conclusions CAPCA18 and the associated multi atlases of the training subjects yield improved segmentation of cerebellar structures in children. PMID:26743973

Applications of advanced data analysis and expert system technologies in the ATLAS Trigger-DAQ Controls framework

NASA Astrophysics Data System (ADS)

Avolio, G.; Corso Radu, A.; Kazarov, A.; Lehmann Miotto, G.; Magnoni, L.

2012-12-01

The Trigger and Data Acquisition (TDAQ) system of the ATLAS experiment is a very complex distributed computing system, composed of more than 20000 applications running on more than 2000 computers. The TDAQ Controls system has to guarantee the smooth and synchronous operations of all the TDAQ components and has to provide the means to minimize the downtime of the system caused by runtime failures. During data taking runs, streams of information messages sent or published by running applications are the main sources of knowledge about correctness of running operations. The huge flow of operational monitoring data produced is constantly monitored by experts in order to detect problems or misbehaviours. Given the scale of the system and the rates of data to be analyzed, the automation of the system functionality in the areas of operational monitoring, system verification, error detection and recovery is a strong requirement. To accomplish its objective, the Controls system includes some high-level components which are based on advanced software technologies, namely the rule-based Expert System and the Complex Event Processing engines. The chosen techniques allow to formalize, store and reuse the knowledge of experts and thus to assist the shifters in the ATLAS control room during the data-taking activities.

Paleozoic and mesozoic GIS data from the Geologic Atlas of the Rocky Mountain Region: Volume 1

USGS Publications Warehouse

Graeber, Aimee; Gunther, Gregory

2017-01-01

The Rocky Mountain Association of Geologists (RMAG) is, once again, publishing portions of the 1972 Geologic Atlas of the Rocky Mountain Region (Mallory, ed., 1972) as a geospatial map and data package. Georeferenced tiff (Geo TIFF) images of map figures from this atlas has served as the basis for these data products. Shapefiles and file geodatabase features have been generated and cartographically represented for select pages from the following chapters:• Phanerozoic Rocks (page 56)• Cambrian System (page 63)• Ordovician System (pages 78 and 79)• Silurian System (pages 87 - 89)• Devonian System (pages 93, 94, and 96 - 98)• Mississippian System (pages 102 and 103)• Pennsylvanian System (pages 114 and 115)• Permian System (pages 146 and 149 - 154)• Triassic System (pages 168 and 169)• Jurassic System (pages 179 and 180)• Cretaceous System (pages 197 - 201, 207 - 210, 215, - 218, 221, 222, 224, 225, and 227).The primary purpose of this publication is to provide regional-scale, as well as local-scale, geospatial data of the Rocky Mountain Region for use in geoscience studies. An important aspect of this interactive map product is that it does not require extensive GIS experience or highly specialized software.

MRIVIEW: An interactive computational tool for investigation of brain structure and function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranken, D.; George, J.

MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.

PubMed

Calabrese, Evan; Badea, Alexandra; Watson, Charles; Johnson, G Allan

2013-05-01

There has been growing interest in the role of postnatal brain development in the etiology of several neurologic diseases. The rat has long been recognized as a powerful model system for studying neuropathology and the safety of pharmacologic treatments. However, the complex spatiotemporal changes that occur during rat neurodevelopment remain to be elucidated. This work establishes the first magnetic resonance histology (MRH) atlas of the developing rat brain, with an emphasis on quantitation. The atlas comprises five specimens at each of nine time points, imaged with eight distinct MR contrasts and segmented into 26 developmentally defined brain regions. The atlas was used to establish a timeline of morphometric changes and variability throughout neurodevelopment and represents a quantitative database of rat neurodevelopment for characterizing rat models of human neurologic disease. Published by Elsevier Inc.

The long journey to the Higgs boson and beyond at the LHC: Emphasis on ATLAS

NASA Astrophysics Data System (ADS)

Jenni, Peter

2016-09-01

The journey in search for the Higgs boson with the ATLAS and CMS experiments at the Large Hadron Collider (LHC) at CERN started more than two decades ago. But the first discussions motivating the LHC project dream date back even further into the 1980s. This article will recall some of these early historical considerations, mention some of the LHC machine milestones and achievements, focus as an example of a technological challenge on the unique ATLAS superconducting magnet system, and then give an account of the physics results so far, leading to, and featuring particularly, the Higgs boson results, and sketching finally prospects for the future. With its emphasis on the ATLAS experiment it is complementary to the preceding article by Tejinder S. Virdee which focused on the CMS experiment.

The Long Journey to the Higgs Boson and Beyond at the LHC Part II: Emphasis on ATLAS

NASA Astrophysics Data System (ADS)

Jenni, Peter

The journey in search for the Higgs boson with the ATLAS and CMS experiments at the Large Hadron Collider (LHC) at CERN started more than two decades ago. But the first discussions motivating the LHC project dream date back even further into the 1980s. This article will recall some of these early historical considerations, mention some of the LHC machine milestones and achievements, focus as an example of a technological challenge on the unique ATLAS superconducting magnet system, and then give an account of the physics results so far, leading to, and featuring particularly, the Higgs boson results, and sketching finally prospects for the future. With its emphasis on the ATLAS experiment it is complementary to the preceding article by Tejinder S. Virdee which focused on the CMS experiment.

ATLAS software stack on ARM64

NASA Astrophysics Data System (ADS)

Smith, Joshua Wyatt; Stewart, Graeme A.; Seuster, Rolf; Quadt, Arnulf; ATLAS Collaboration

2017-10-01

This paper reports on the port of the ATLAS software stack onto new prototype ARM64 servers. This included building the “external” packages that the ATLAS software relies on. Patches were needed to introduce this new architecture into the build as well as patches that correct for platform specific code that caused failures on non-x86 architectures. These patches were applied such that porting to further platforms will need no or only very little adjustments. A few additional modifications were needed to account for the different operating system, Ubuntu instead of Scientific Linux 6 / CentOS7. Selected results from the validation of the physics outputs on these ARM 64-bit servers will be shown. CPU, memory and IO intensive benchmarks using ATLAS specific environment and infrastructure have been performed, with a particular emphasis on the performance vs. energy consumption.

Development of a custom on-line ultrasonic vapour analyzer and flow meter for the ATLAS inner detector, with application to Cherenkov and gaseous charged particle detectors

NASA Astrophysics Data System (ADS)

Alhroob, M.; Bates, R.; Battistin, M.; Berry, S.; Bitadze, A.; Bonneau, P.; Bousson, N.; Boyd, G.; Bozza, G.; Crespo-Lopez, O.; Degeorge, C.; Deterre, C.; DiGirolamo, B.; Doubek, M.; Favre, G.; Godlewski, J.; Hallewell, G.; Hasib, A.; Katunin, S.; Langevin, N.; Lombard, D.; Mathieu, M.; McMahon, S.; Nagai, K.; O'Rourke, A.; Pearson, B.; Robinson, D.; Rossi, C.; Rozanov, A.; Strauss, M.; Vacek, V.; Zwalinski, L.

2015-03-01

Precision sound velocity measurements can simultaneously determine binary gas composition and flow. We have developed an analyzer with custom microcontroller-based electronics, currently used in the ATLAS Detector Control System, with numerous potential applications. Three instruments monitor C3F8 and CO2 coolant leak rates into the nitrogen envelopes of the ATLAS silicon microstrip and Pixel detectors. Two further instruments will aid operation of the new thermosiphon coolant recirculator: one of these will monitor air leaks into the low pressure condenser while the other will measure return vapour flow along with C3F8/C2F6 blend composition, should blend operation be necessary to protect the ATLAS silicon tracker under increasing LHC luminosity. We describe these instruments and their electronics.

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.

ATLAS Distributed Computing Experience and Performance During the LHC Run-2

NASA Astrophysics Data System (ADS)

Filipčič, A.; ATLAS Collaboration

2017-10-01

ATLAS Distributed Computing during LHC Run-1 was challenged by steadily increasing computing, storage and network requirements. In addition, the complexity of processing task workflows and their associated data management requirements led to a new paradigm in the ATLAS computing model for Run-2, accompanied by extensive evolution and redesign of the workflow and data management systems. The new systems were put into production at the end of 2014, and gained robustness and maturity during 2015 data taking. ProdSys2, the new request and task interface; JEDI, the dynamic job execution engine developed as an extension to PanDA; and Rucio, the new data management system, form the core of Run-2 ATLAS distributed computing engine. One of the big changes for Run-2 was the adoption of the Derivation Framework, which moves the chaotic CPU and data intensive part of the user analysis into the centrally organized train production, delivering derived AOD datasets to user groups for final analysis. The effectiveness of the new model was demonstrated through the delivery of analysis datasets to users just one week after data taking, by completing the calibration loop, Tier-0 processing and train production steps promptly. The great flexibility of the new system also makes it possible to execute part of the Tier-0 processing on the grid when Tier-0 resources experience a backlog during high data-taking periods. The introduction of the data lifetime model, where each dataset is assigned a finite lifetime (with extensions possible for frequently accessed data), was made possible by Rucio. Thanks to this the storage crises experienced in Run-1 have not reappeared during Run-2. In addition, the distinction between Tier-1 and Tier-2 disk storage, now largely artificial given the quality of Tier-2 resources and their networking, has been removed through the introduction of dynamic ATLAS clouds that group the storage endpoint nucleus and its close-by execution satellite sites. All stable ATLAS sites are now able to store unique or primary copies of the datasets. ATLAS Distributed Computing is further evolving to speed up request processing by introducing network awareness, using machine learning and optimisation of the latencies during the execution of the full chain of tasks. The Event Service, a new workflow and job execution engine, is designed around check-pointing at the level of event processing to use opportunistic resources more efficiently. ATLAS has been extensively exploring possibilities of using computing resources extending beyond conventional grid sites in the WLCG fabric to deliver as many computing cycles as possible and thereby enhance the significance of the Monte-Carlo samples to deliver better physics results. The exploitation of opportunistic resources was at an early stage throughout 2015, at the level of 10% of the total ATLAS computing power, but in the next few years it is expected to deliver much more. In addition, demonstrating the ability to use an opportunistic resource can lead to securing ATLAS allocations on the facility, hence the importance of this work goes beyond merely the initial CPU cycles gained. In this paper, we give an overview and compare the performance, development effort, flexibility and robustness of the various approaches.

Infrared Astronomical Satellite (IRAS) Catalogs and Atlases. Explanatory Supplement

NASA Technical Reports Server (NTRS)

Beichman, C. A. (Editor); Neugebauer, G. (Editor); Habing, H. J. (Editor); Clegg, P. E. (Editor); Chester, T. J. (Editor)

1985-01-01

The Infrared Astronomical Satellite (IRAS) mission is described. An overview of the mission, a description of the satellite and its telescope system, and a discussion of the mission design, requirements, and inflight modifications are given. Data reduction, flight tests, flux reconstruction and calibration, data processing, and the formats of the IRAS catalogs and atlases are also considered.

The role of international research projects in the dissemination of innovative technologies in Russia: AgroAtlas case study

USDA-ARS?s Scientific Manuscript database

This paper uses the AgroAtlas project (www.agroatlas.ru) as a case study to illustrate how international projects can be an important resource to help train teachers and scientists in emerging technology including geographic information systems (GIS) software. The paper discusses a series of 10- day...

Development of the Health Atlas of Jalisco: A New Web-Based Service for the Ministry of Health and the Community in Mexico

PubMed Central

Robles, Juan; Fonseca León, Joel

2016-01-01

Background Maps have been widely used to provide a visual representation of information of a geographic area. Health atlases are collections of maps related to conditions, infrastructure or services provided. Various countries have put resources towards producing health atlases that support health decision makers to enhance their services to the communities. Latin America, as well as Spain, have produced several atlases of importance such as the interactive mortality atlas of Andalucía, which is very similar to the one that is presented in this paper. In Mexico, the National Institute of Public Health produced the only health atlas found that is of relevance. It was published online in 2003 and is currently still active. Objective The objective of this work is to describe the methods used to develop the Health Atlas of Jalisco (HAJ), and show its characteristics and how it interactively works with the user as a Web-based service. Methods This work has an ecological design in which the analysis units are the 125 municipalities (counties) of the state of Jalisco, Mexico. We created and published online a geographic health atlas displaying a system based on input from official health database of the Health Ministry of Jalisco (HMJ), and some databases from the National Institute of Statistics and Geography (NISGI). The atlas displays 256 different variables as health-direct or health-related indicators. Instant Atlas software was used to generate the online application. The atlas was developed using these procedures: (1) datasheet processing and base maps generation, (2) software arrangements, and (3) website creation. Results The HAJ is a Web-based service that allows users to interact with health and general data, regions, and categories according to their information needs and generates thematic maps (eg, the total population of the state or of a single municipality grouped by age or sex). The atlas is capable of displaying more than 32,000 different maps by combining categories, indicators, municipalities, and regions. Users can select the entire province, one or several municipalities, and the indicator they require. The atlas then generates and displays the requested map. Conclusions This atlas is a Web-based service that interactively allows users to review health indicators such as structure, supplies, processes, and the impact on public health and related sectors in Jalisco, Mexico. One of the main interests is to reduce the number of information requests that the Ministry of Health receives every week from the general public, media reporters, and other government sectors. The atlas will support transparency, information diffusion, health decision-making, and the formulation of new public policies. Furthermore, the research team intends to promote research and education in public health. PMID:27227146

Development of the Health Atlas of Jalisco: A New Web-Based Service for the Ministry of Health and the Community in Mexico.

PubMed

Ramos Herrera, Igor Martin; Gonzalez Castañeda, Miguel; Robles, Juan; Fonseca León, Joel

2016-01-01

Maps have been widely used to provide a visual representation of information of a geographic area. Health atlases are collections of maps related to conditions, infrastructure or services provided. Various countries have put resources towards producing health atlases that support health decision makers to enhance their services to the communities. Latin America, as well as Spain, have produced several atlases of importance such as the interactive mortality atlas of Andalucía, which is very similar to the one that is presented in this paper. In Mexico, the National Institute of Public Health produced the only health atlas found that is of relevance. It was published online in 2003 and is currently still active. The objective of this work is to describe the methods used to develop the Health Atlas of Jalisco (HAJ), and show its characteristics and how it interactively works with the user as a Web-based service. This work has an ecological design in which the analysis units are the 125 municipalities (counties) of the state of Jalisco, Mexico. We created and published online a geographic health atlas displaying a system based on input from official health database of the Health Ministry of Jalisco (HMJ), and some databases from the National Institute of Statistics and Geography (NISGI). The atlas displays 256 different variables as health-direct or health-related indicators. Instant Atlas software was used to generate the online application. The atlas was developed using these procedures: (1) datasheet processing and base maps generation, (2) software arrangements, and (3) website creation. The HAJ is a Web-based service that allows users to interact with health and general data, regions, and categories according to their information needs and generates thematic maps (eg, the total population of the state or of a single municipality grouped by age or sex). The atlas is capable of displaying more than 32,000 different maps by combining categories, indicators, municipalities, and regions. Users can select the entire province, one or several municipalities, and the indicator they require. The atlas then generates and displays the requested map. This atlas is a Web-based service that interactively allows users to review health indicators such as structure, supplies, processes, and the impact on public health and related sectors in Jalisco, Mexico. One of the main interests is to reduce the number of information requests that the Ministry of Health receives every week from the general public, media reporters, and other government sectors. The atlas will support transparency, information diffusion, health decision-making, and the formulation of new public policies. Furthermore, the research team intends to promote research and education in public health.

ATCA-based ATLAS FTK input interface system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okumura, Yasuyuki; Liu, Tiehui Ted; Olsen, Jamieson

The first stage of the ATLAS Fast TracKer (FTK) is an ATCA-based input interface system, where hits from the entire silicon tracker are clustered and organized into overlapping eta-phi trigger towers before being sent to the tracking engines. First, FTK Input Mezzanine cards receive hit data and perform clustering to reduce data volume. Then, the ATCA-based Data Formatter system will organize the trigger tower data, sharing data among boards over full mesh backplanes and optic fibers. The board and system level design concepts and implementation details, as well as the operation experiences from the FTK full-chain testing, will be presented.

Process Management inside ATLAS DAQ

NASA Astrophysics Data System (ADS)

Alexandrov, I.; Amorim, A.; Badescu, E.; Burckhart-Chromek, D.; Caprini, M.; Dobson, M.; Duval, P. Y.; Hart, R.; Jones, R.; Kazarov, A.; Kolos, S.; Kotov, V.; Liko, D.; Lucio, L.; Mapelli, L.; Mineev, M.; Moneta, L.; Nassiakou, M.; Pedro, L.; Ribeiro, A.; Roumiantsev, V.; Ryabov, Y.; Schweiger, D.; Soloviev, I.; Wolters, H.

2002-10-01

The Process Management component of the online software of the future ATLAS experiment data acquisition system is presented. The purpose of the Process Manager is to perform basic job control of the software components of the data acquisition system. It is capable of starting, stopping and monitoring the status of those components on the data acquisition processors independent of the underlying operating system. Its architecture is designed on the basis of a server client model using CORBA based communication. The server part relies on C++ software agent objects acting as an interface between the local operating system and client applications. Some of the major design challenges of the software agents were to achieve the maximum degree of autonomy possible, to create processes aware of dynamic conditions in their environment and with the ability to determine corresponding actions. Issues such as the performance of the agents in terms of time needed for process creation and destruction, the scalability of the system taking into consideration the final ATLAS configuration and minimizing the use of hardware resources were also of critical importance. Besides the details given on the architecture and the implementation, we also present scalability and performance tests results of the Process Manager system.

Information system to manage anatomical knowledge and image data about brain

NASA Astrophysics Data System (ADS)

Barillot, Christian; Gibaud, Bernard; Montabord, E.; Garlatti, S.; Gauthier, N.; Kanellos, I.

1994-09-01

This paper reports about first results obtained in a project aiming at developing a computerized system to manage knowledge about brain anatomy. The emphasis is put on the design of a knowledge base which includes a symbolic model of cerebral anatomical structures (grey nuclei, cortical structures such as gyri and sulci, verntricles, vessels, etc.) and of hypermedia facilities allowing to retrieve and display information associated with the objects (texts, drawings, images). Atlas plates digitized from a stereotactic atlas are also used to provide natural and effective communication means between the user and the system.

Lessons Learned from the Advanced Topographic Laser Altimeter System

NASA Technical Reports Server (NTRS)

Garrison, Matt; Patel, Deepak; Bradshaw, Heather; Robinson, Frank; Neuberger, Dave

2016-01-01

The ICESat-2 Advanced Topographic Laser Altimeter System (ATLAS) instrument 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 presentation walks through the lessons learned from design, hardware, analysis and testing perspective. ATLAS lessons learned include general thermal design, analysis, hardware, and testing issues as well as lessons specific to laser systems, two-phase thermal control, and optical assemblies with precision alignment requirements.

Interactive energy atlas for Colorado and New Mexico: an online resource for decisionmakers

USGS Publications Warehouse

Carr, Natasha B.; Ignizio, Drew A.; Diffendorfer, James E.; Latysh, Natalie; Matherne, Ann Marie; Linard, Joshua I.; Leib, Kenneth J.; Hawkins, Sarah J.

2013-01-01

Throughout the western United States, increased demand for energy is driving the rapid development of nonrenewable and renewable energy resources. Resource managers must balance the benefits of energy development with the potential consequences for ecological resources and ecosystem services. To facilitate access to geospatial data related to energy resources, energy infrastructure, and natural resources that may be affected by energy development, the U.S. Geological Survey has developed an online Interactive Energy Atlas (Energy Atlas) for Colorado and New Mexico. The Energy Atlas is designed to meet the needs of varied users who seek information about energy in the western United States. The Energy Atlas has two primary capabilities: a geographic information system (GIS) data viewer and an interactive map gallery. The GIS data viewer allows users to preview and download GIS data related to energy potential and development in Colorado and New Mexico. The interactive map gallery contains a collection of maps that compile and summarize thematically related data layers in a user-friendly format. The maps are dynamic, allowing users to explore data at different resolutions and obtain information about the features being displayed. The Energy Atlas also includes an interactive decision-support tool, which allows users to explore the potential consequences of energy development for species that vary in their sensitivity to disturbance.

ATLAS Tile calorimeter calibration and monitoring systems

NASA Astrophysics Data System (ADS)

Chomont, Arthur; ATLAS Collaboration

2017-11-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises cesium radioactive sources, Laser and charge injection elements, and allows for monitoring and equalization of the calorimeter response at each stage of the signal production, from scintillation light to digitization. Based on LHC Run 1 experience, several calibration systems were improved for Run 2. The lessons learned, the modifications, and the current LHC Run 2 performance are discussed.

Catlas: An magnetic resonance imaging-based three-dimensional cortical atlas and tissue probability maps for the domestic cat (Felis catus).

PubMed

Stolzberg, Daniel; Wong, Carmen; Butler, Blake E; Lomber, Stephen G

2017-10-15

Brain atlases play an important role in effectively communicating results from neuroimaging studies in a standardized coordinate system. Furthermore, brain atlases extend analysis of functional magnetic resonance imaging (MRI) data by delineating regions of interest over which to evaluate the extent of functional activation as well as measures of inter-regional connectivity. Here, we introduce a three-dimensional atlas of the cat cerebral cortex based on established cytoarchitectonic and electrophysiological findings. In total, 71 cerebral areas were mapped onto the gray matter (GM) of an averaged T1-weighted structural MRI acquired at 7 T from eight adult domestic cats. In addition, a nonlinear registration procedure was used to generate a common template brain as well as GM, white matter, and cerebral spinal fluid tissue probability maps to facilitate tissue segmentation as part of the standard preprocessing pipeline for MRI data analysis. The atlas and associated files can also be used for planning stereotaxic surgery and for didactic purposes. © 2017 Wiley Periodicals, Inc.

Welcome - TampaBay.WaterAtlas.org

Science.gov Websites

An edition of: WaterAtlas.orgPresented By: USF Water Institute Choose a Water Atlas Charlotte Harbor NEP Water Atlas Hillsborough County Water Atlas Lake County Water Atlas Manatee County Water Atlas Orange County Water Atlas Pinellas County Water Atlas Polk County Water Atlas Sarasota County Water Atlas

Atlas-based analysis of cardiac shape and function: correction of regional shape bias due to imaging protocol for population studies.

PubMed

Medrano-Gracia, Pau; Cowan, Brett R; Bluemke, David A; Finn, J Paul; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Suinesiaputra, Avan; Young, Alistair A

2013-09-13

Cardiovascular imaging studies generate a wealth of data which is typically used only for individual study endpoints. By pooling data from multiple sources, quantitative comparisons can be made of regional wall motion abnormalities between different cohorts, enabling reuse of valuable data. Atlas-based analysis provides precise quantification of shape and motion differences between disease groups and normal subjects. However, subtle shape differences may arise due to differences in imaging protocol between studies. A mathematical model describing regional wall motion and shape was used to establish a coordinate system registered to the cardiac anatomy. The atlas was applied to data contributed to the Cardiac Atlas Project from two independent studies which used different imaging protocols: steady state free precession (SSFP) and gradient recalled echo (GRE) cardiovascular magnetic resonance (CMR). Shape bias due to imaging protocol was corrected using an atlas-based transformation which was generated from a set of 46 volunteers who were imaged with both protocols. Shape bias between GRE and SSFP was regionally variable, and was effectively removed using the atlas-based transformation. Global mass and volume bias was also corrected by this method. Regional shape differences between cohorts were more statistically significant after removing regional artifacts due to imaging protocol bias. Bias arising from imaging protocol can be both global and regional in nature, and is effectively corrected using an atlas-based transformation, enabling direct comparison of regional wall motion abnormalities between cohorts acquired in separate studies.

The digital anatomist information system and its use in the generation and delivery of Web-based anatomy atlases.

PubMed

Brinkley, J F; Bradley, S W; Sundsten, J W; Rosse, C

1997-12-01

Advances in network and imaging technology, coupled with the availability of 3-D datasets such as the Visible Human, provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a half year period from June 1995-January 1997, the on-line atlases were accessed by over 33,000 sites from 94 countries, with an average of over 4000 "hits" per day, and 25,000 hits per day during peak exam periods. The atlases have been linked to by over 500 sites, and have received at least six unsolicited awards by outside rating institutions. The flexibility of the software framework has allowed the information system to evolve with advances in technology and representation methods. Possible new features include knowledge-based image retrieval and tutoring, dynamic generation of 3-D scenes, and eventually, real-time virtual reality navigation through the body. Such features, when coupled with other on-line biomedical information resources, should lead to interesting new ways for managing and accessing structural information in medicine. Copyright 1997 Academic Press.

Launch vehicle tracking enhancement through Global Positioning System Metric Tracking

NASA Astrophysics Data System (ADS)

Moore, T. C.; Li, Hanchu; Gray, T.; Doran, A.

United Launch Alliance (ULA) initiated operational flights of both the Atlas V and Delta IV launch vehicle families in 2002. The Atlas V and Delta IV launch vehicles were developed jointly with the US Air Force (USAF) as part of the Evolved Expendable Launch Vehicle (EELV) program. Both Launch Vehicle (LV) families have provided 100% mission success since their respective inaugural launches and demonstrated launch capability from both Vandenberg Air Force Base (VAFB) on the Western Test Range and Cape Canaveral Air Force Station (CCAFS) on the Eastern Test Range. However, the current EELV fleet communications, tracking, & control architecture & technology, which date back to the origins of the space launch business, require support by a large and high cost ground footprint. The USAF has embarked on an initiative known as Future Flight Safety System (FFSS) that will significantly reduce Test Range Operations and Maintenance (O& M) cost by closing facilities and decommissioning ground assets. In support of the FFSS, a Global Positioning System Metric Tracking (GPS MT) System based on the Global Positioning System (GPS) satellite constellation has been developed for EELV which will allow both Ranges to divest some of their radar assets. The Air Force, ULA and Space Vector have flown the first 2 Atlas Certification vehicles demonstrating the successful operation of the GPS MT System. The first Atlas V certification flight was completed in February 2012 from CCAFS, the second Atlas V certification flight from VAFB was completed in September 2012 and the third certification flight on a Delta IV was completed October 2012 from CCAFS. The GPS MT System will provide precise LV position, velocity and timing information that can replace ground radar tracking resource functionality. The GPS MT system will provide an independent position/velocity S-Band telemetry downlink to support the current man-in-the-loop ground-based commanded destruct of an anomalous flight- The system utilizes a 50 channel digital receiver capable of navigating in high dynamic environments and high altitudes fed by antennas mounted diametrically opposed on the second stage airframe skin. To enhance cost effectiveness, the GPS MT System design implemented existing commercial parts and common environmental and interface requirements for both EELVs. The EELV GPS MT System design is complete, successfully qualified and has demonstrated that the system performs as simulated. This paper summarizes the current development status, system cost comparison, and performance capabilities of the EELV GPS MT System.

ULA's Atlas V for Boeing's Orbital Flight Test

NASA Image and Video Library

2017-10-24

The Atlas V rocket that will launch Boeing’s CST-100 Starliner spacecraft on the company’s uncrewed Orbital Flight Test for NASA’s Commercial Crew Program is coming together inside a United Launch Alliance facility in Decatur, Alabama. The flight test is intended to prove the design of the integrated space system prior to the Crew Flight Test. These events are part of NASA’s required certification process as the company works to regularly fly astronauts to and from the International Space Station. Boeing's Starliner will launch on the United Launch Alliance Atlas V rocket from Space Launch Complex 41 at Cape Canaveral Air Force Station in Florida.

An atlas of ShakeMaps for selected global earthquakes

USGS Publications Warehouse

Allen, Trevor I.; Wald, David J.; Hotovec, Alicia J.; Lin, Kuo-Wan; Earle, Paul S.; Marano, Kristin D.

2008-01-01

An atlas of maps of peak ground motions and intensity 'ShakeMaps' has been developed for almost 5,000 recent and historical global earthquakes. These maps are produced using established ShakeMap methodology (Wald and others, 1999c; Wald and others, 2005) and constraints from macroseismic intensity data, instrumental ground motions, regional topographically-based site amplifications, and published earthquake-rupture models. Applying the ShakeMap methodology allows a consistent approach to combine point observations with ground-motion predictions to produce descriptions of peak ground motions and intensity for each event. We also calculate an estimated ground-motion uncertainty grid for each earthquake. The Atlas of ShakeMaps provides a consistent and quantitative description of the distribution and intensity of shaking for recent global earthquakes (1973-2007) as well as selected historic events. As such, the Atlas was developed specifically for calibrating global earthquake loss estimation methodologies to be used in the U.S. Geological Survey Prompt Assessment of Global Earthquakes for Response (PAGER) Project. PAGER will employ these loss models to rapidly estimate the impact of global earthquakes as part of the USGS National Earthquake Information Center's earthquake-response protocol. The development of the Atlas of ShakeMaps has also led to several key improvements to the Global ShakeMap system. The key upgrades include: addition of uncertainties in the ground motion mapping, introduction of modern ground-motion prediction equations, improved estimates of global seismic-site conditions (VS30), and improved definition of stable continental region polygons. Finally, we have merged all of the ShakeMaps in the Atlas to provide a global perspective of earthquake ground shaking for the past 35 years, allowing comparison with probabilistic hazard maps. The online Atlas and supporting databases can be found at http://earthquake.usgs.gov/eqcenter/shakemap/atlas.php/.

Heavy Ion Results from ATLAS

DOE PAGES

Jia, Jiangyong

2017-09-25

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

Heavy Ion Results from ATLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, Jiangyong

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

Exploiting opportunistic resources for ATLAS with ARC CE and the Event Service

NASA Astrophysics Data System (ADS)

Cameron, D.; Filipčič, A.; Guan, W.; Tsulaia, V.; Walker, R.; Wenaus, T.; ATLAS Collaboration

2017-10-01

With ever-greater computing needs and fixed budgets, big scientific experiments are turning to opportunistic resources as a means to add much-needed extra computing power. These resources can be very different in design from those that comprise the Grid computing of most experiments, therefore exploiting them requires a change in strategy for the experiment. They may be highly restrictive in what can be run or in connections to the outside world, or tolerate opportunistic usage only on condition that tasks may be terminated without warning. The Advanced Resource Connector Computing Element (ARC CE) with its nonintrusive architecture is designed to integrate resources such as High Performance Computing (HPC) systems into a computing Grid. The ATLAS experiment developed the ATLAS Event Service (AES) primarily to address the issue of jobs that can be terminated at any point when opportunistic computing capacity is needed by someone else. This paper describes the integration of these two systems in order to exploit opportunistic resources for ATLAS in a restrictive environment. In addition to the technical details, results from deployment of this solution in the SuperMUC HPC centre in Munich are shown.

A Four-Dimensional Probabilistic Atlas of the Human Brain

PubMed Central

Mazziotta, John; Toga, Arthur; Evans, Alan; Fox, Peter; Lancaster, Jack; Zilles, Karl; Woods, Roger; Paus, Tomas; Simpson, Gregory; Pike, Bruce; Holmes, Colin; Collins, Louis; Thompson, Paul; MacDonald, David; Iacoboni, Marco; Schormann, Thorsten; Amunts, Katrin; Palomero-Gallagher, Nicola; Geyer, Stefan; Parsons, Larry; Narr, Katherine; Kabani, Noor; Le Goualher, Georges; Feidler, Jordan; Smith, Kenneth; Boomsma, Dorret; Pol, Hilleke Hulshoff; Cannon, Tyrone; Kawashima, Ryuta; Mazoyer, Bernard

2001-01-01

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders. PMID:11522763

Measurements of underlying-event properties using neutral and charged particles in pp collisions at $$\\sqrt{s}=900$$ GeV and $$\\sqrt{s}=7$$ TeV with the ATLAS detector at the LHC

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2011-05-10

We present first measurements of charged and neutral particle-flow correlations in pp collisions using the ATLAS calorimeters. Data were collected in 2009 and 2010 at centre-of-mass energies of 900 GeV and 7 TeV. Events were selected using a minimum-bias trigger which required a charged particle in scintillation counters on either side of the interaction point. Particle flows, sensitive to the underlying event, are measured using clusters of energy in the ATLAS calorimeters, taking advantage of their fine granularity. No Monte Carlo generator used in this analysis can accurately describe the measurements. The results are independent of those based on chargedmore » particles measured by the ATLAS tracking systems and can be used to constrain the parameters of Monte Carlo generators.« less

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.

Patient-specific port placement for laparoscopic surgery using atlas-based registration

NASA Astrophysics Data System (ADS)

Enquobahrie, Andinet; Shivaprabhu, Vikas; Aylward, Stephen; Finet, Julien; Cleary, Kevin; Alterovitz, Ron

2013-03-01

Laparoscopic surgery is a minimally invasive surgical approach, in which abdominal surgical procedures are performed through trocars via small incisions. Patients benefit by reduced postoperative pain, shortened hospital stays, improved cosmetic results, and faster recovery times. Optimal port placement can improve surgeon dexterity and avoid the need to move the trocars, which would cause unnecessary trauma to the patient. We are building an intuitive open source visualization system to help surgeons identify ports. Our methodology is based on an intuitive port placement visualization module and atlas-based registration algorithm to transfer port locations to individual patients. The methodology follows three steps:1) Use a port placement visualization module to manually place ports in an abdominal organ atlas. This step generates port-augmented abdominal atlas. This is done only once for a given patient population. 2) Register the atlas data with the patient CT data, to transfer the prescribed ports to the individual patient 3) Review and adjust the transferred port locations using the port placement visualization module. Tool maneuverability and target reachability can be tested using the visualization system. Our methodology would decrease the amount of physician input necessary to optimize port placement for each patient case. In a follow up work, we plan to use the transferred ports as starting point for further optimization of the port locations by formulating a cost function that will take into account factors such as tool dexterity and likelihood of collision between instruments.

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

Atlas-based head modeling and spatial normalization for high-density diffuse optical tomography: in vivo validation against fMRI.

PubMed

Ferradal, Silvina L; Eggebrecht, Adam T; Hassanpour, Mahlega; Snyder, Abraham Z; Culver, Joseph P

2014-01-15

Diffuse optical imaging (DOI) is increasingly becoming a valuable neuroimaging tool when fMRI is precluded. Recent developments in high-density diffuse optical tomography (HD-DOT) overcome previous limitations of sparse DOI systems, providing improved image quality and brain specificity. These improvements in instrumentation prompt the need for advancements in both i) realistic forward light modeling for accurate HD-DOT image reconstruction, and ii) spatial normalization for voxel-wise comparisons across subjects. Individualized forward light models derived from subject-specific anatomical images provide the optimal inverse solutions, but such modeling may not be feasible in all situations. In the absence of subject-specific anatomical images, atlas-based head models registered to the subject's head using cranial fiducials provide an alternative solution. In addition, a standard atlas is attractive because it defines a common coordinate space in which to compare results across subjects. The question therefore arises as to whether atlas-based forward light modeling ensures adequate HD-DOT image quality at the individual and group level. Herein, we demonstrate the feasibility of using atlas-based forward light modeling and spatial normalization methods. Both techniques are validated using subject-matched HD-DOT and fMRI data sets for visual evoked responses measured in five healthy adult subjects. HD-DOT reconstructions obtained with the registered atlas anatomy (i.e. atlas DOT) had an average localization error of 2.7mm relative to reconstructions obtained with the subject-specific anatomical images (i.e. subject-MRI DOT), and 6.6mm relative to fMRI data. At the group level, the localization error of atlas DOT reconstruction was 4.2mm relative to subject-MRI DOT reconstruction, and 6.1mm relative to fMRI. These results show that atlas-based image reconstruction provides a viable approach to individual head modeling for HD-DOT when anatomical imaging is not available. Copyright © 2013. Published by Elsevier Inc.

CephFS: a new generation storage platform for Australian high energy physics

NASA Astrophysics Data System (ADS)

Borges, G.; Crosby, S.; Boland, L.

2017-10-01

This paper presents an implementation of a Ceph file system (CephFS) use case at the ARC Center of Excellence for Particle Physics at the Terascale (CoEPP). CoEPP’s CephFS provides a posix-like file system on top of a Ceph RADOS object store, deployed on commodity hardware and without single points of failure. By delivering a unique file system namespace at different CoEPP centres spread across Australia, local HEP researchers can store, process and share data independently of their geographical locations. CephFS is also used as the back-end file system for a WLCG ATLAS user area at the Australian Tier-2. Dedicated SRM and XROOTD services, deployed on top of CoEPP’s CephFS, integrates it in ATLAS data distributed operations. This setup, while allowing Australian HEP researchers to trigger data movement via ATLAS grid tools, also enables local posix-like read access providing greater control to scientists of their data flows. In this article we will present details on CoEPP’s Ceph/CephFS implementation and report performance I/O metrics collected during the testing/tuning phase of the system.

C3PO - A Dynamic Data Placement Agent for ATLAS Distributed Data Management

NASA Astrophysics Data System (ADS)

Beermann, T.; Lassnig, M.; Barisits, M.; Serfon, C.; Garonne, V.; ATLAS Collaboration

2017-10-01

This paper introduces a new dynamic data placement agent for the ATLAS distributed data management system. This agent is designed to pre-place potentially popular data to make it more widely available. It therefore incorporates information from a variety of sources. Those include input datasets and sites workload information from the ATLAS workload management system, network metrics from different sources like FTS and PerfSonar, historical popularity data collected through a tracer mechanism and more. With this data it decides if, when and where to place new replicas that then can be used by the WMS to distribute the workload more evenly over available computing resources and then ultimately reduce job waiting times. This paper gives an overview of the architecture and the final implementation of this new agent. The paper also includes an evaluation of the placement algorithm by comparing the transfer times and the new replica usage.

Spectral classification with the International Ultraviolet Explorer: An atlas of B-type spectra

NASA Technical Reports Server (NTRS)

Rountree, Janet; Sonneborn, George

1993-01-01

New criteria for the spectral classification of B stars in the ultraviolet show that photospheric absorption lines in the 1200-1900A wavelength region can be used to classify the spectra of B-type dwarfs, subgiants, and giants on a 2-D system consistent with the optical MK system. This atlas illustrates a large number of such spectra at the scale used for classification. These spectra provide a dense matrix of standard stars, and also show the effects of rapid stellar rotation and stellar winds on the spectra and their classification. The observational material consists of high-dispersion spectra from the International Ultraviolet Explorer archives, resampled to a resolution of 0.25 A, uniformly normalized, and plotted at 10 A/cm. The atlas should be useful for the classification of other IUE high-dispersion spectra, especially for stars that have not been observed in the optical.

Commissioning of the ATLAS Muon Spectrometer with cosmic rays

DOE PAGES

Aad, G; Abbott, B; Abdallah, J; ...

2010-12-01

The ATLAS detector at the Large Hadron Collider has collected several hundred million cosmic ray events during 2008 and 2009. These data were used to commission the Muon Spectrometer and to study the performance of the trigger and tracking chambers, their alignment, the detector control system, the data acquisition and the analysis programs. We present the performance in the relevant parameters that determine the quality of the muon measurement. We discuss the single element efficiency, resolution and noise rates, the calibration method of the detector response and of the alignment system, the track reconstruction efficiency and the momentum measurement. Themore » results show that the detector is close to the design performance and that the Muon Spectrometer is ready to detect muons produced in high energy proton-proton collisions. © 2010 CERN for the benefit of the ATLAS collaboration.« less

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.

Feasibility Study of Economics and Performance of Solar PV at the Atlas Industrial Park in Duluth, Minnesota

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steen, M.; Lisell, L.; Mosey, G.

The U.S. Environmental Protection Agency (EPA) Region 5, in accordance with the RE-Powering America's Land initiative, selected the Atlas Industrial Park in Duluth, Minnesota, for a feasibility study of renewable energy production. The EPA provided funding to the National Renewable Energy Laboratory (NREL) to support a feasibility study of solar renewable energy generation at the Atlas Industrial Park. NREL provided technical assistance for this project but did not assess environmental conditions at the site beyond those related to the performance of a photovoltaic (PV) system. The purpose of this study is to assess the site for a possible PV installationmore » and estimate the cost, performance, and site impacts of different PV configurations. In addition, the study evaluates financing options that could assist in the implementation of a PV system at the site.« less

A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

PubMed

Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

2012-01-01

The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

A Molecular atlas of Xenopus respiratory system development.

PubMed

Rankin, Scott A; Thi Tran, Hong; Wlizla, Marcin; Mancini, Pamela; Shifley, Emily T; Bloor, Sean D; Han, Lu; Vleminckx, Kris; Wert, Susan E; Zorn, Aaron M

2015-01-01

Respiratory system development is regulated by a complex series of endoderm-mesoderm interactions that are not fully understood. Recently Xenopus has emerged as an alternative model to investigate early respiratory system development, but the extent to which the morphogenesis and molecular pathways involved are conserved between Xenopus and mammals has not been systematically documented. In this study, we provide a histological and molecular atlas of Xenopus respiratory system development, focusing on Nkx2.1+ respiratory cell fate specification in the developing foregut. We document the expression patterns of Wnt/β-catenin, fibroblast growth factor (FGF), and bone morphogenetic protein (BMP) signaling components in the foregut and show that the molecular mechanisms of respiratory lineage induction are remarkably conserved between Xenopus and mice. Finally, using several functional experiments we refine the epistatic relationships among FGF, Wnt, and BMP signaling in early Xenopus respiratory system development. We demonstrate that Xenopus trachea and lung development, before metamorphosis, is comparable at the cellular and molecular levels to embryonic stages of mouse respiratory system development between embryonic days 8.5 and 10.5. This molecular atlas provides a fundamental starting point for further studies using Xenopus as a model to define the conserved genetic programs controlling early respiratory system development. © 2014 Wiley Periodicals, Inc.

The evolution of the Trigger and Data Acquisition System in the ATLAS experiment

NASA Astrophysics Data System (ADS)

Krasznahorkay, A.; Atlas Collaboration

2014-06-01

The ATLAS experiment, aimed at recording the results of LHC proton-proton collisions, is upgrading its Trigger and Data Acquisition (TDAQ) system during the current LHC first long shutdown. The purpose of the upgrade is to add robustness and flexibility to the selection and the conveyance of the physics data, simplify the maintenance of the infrastructure, exploit new technologies and, overall, make ATLAS data-taking capable of dealing with increasing event rates. The TDAQ system used to date is organised in a three-level selection scheme, including a hardware-based first-level trigger and second- and third-level triggers implemented as separate software systems distributed on separate, commodity hardware nodes. While this architecture was successfully operated well beyond the original design goals, the accumulated experience stimulated interest to explore possible evolutions. We will also be upgrading the hardware of the TDAQ system by introducing new elements to it. For the high-level trigger, the current plan is to deploy a single homogeneous system, which merges the execution of the second and third trigger levels, still separated, on a unique hardware node. Prototyping efforts already demonstrated many benefits to the simplified design. In this paper we report on the design and the development status of this new system.

Thermal Performance of ATLAS Laser Thermal Control System Demonstration Unit

NASA Technical Reports Server (NTRS)

Ku, Jentung; Robinson, Franklin; Patel, Deepak; Ottenstein, Laura

2013-01-01

The second Ice, Cloud, and Land Elevation Satellite mission currently planned by National Aeronautics and Space Administration will measure global ice topography and canopy height using the Advanced Topographic Laser Altimeter System {ATLAS). The ATLAS comprises two lasers; but only one will be used at a time. Each laser will generate between 125 watts and 250 watts of heat, and each laser has its own optimal operating temperature that must be maintained within plus or minus 1 degree Centigrade accuracy by the Laser Thermal Control System (LTCS) consisting of a constant conductance heat pipe (CCHP), a loop heat pipe (LHP) and a radiator. The heat generated by the laser is acquired by the CCHP and transferred to the LHP, which delivers the heat to the radiator for ultimate rejection. The radiator can be exposed to temperatures between minus 71 degrees Centigrade and minus 93 degrees Centigrade. The two lasers can have different operating temperatures varying between plus 15 degrees Centigrade and plus 30 degrees Centigrade, and their operating temperatures are not known while the LTCS is being designed and built. Major challenges of the LTCS include: 1) A single thermal control system must maintain the ATLAS at 15 degrees Centigrade with 250 watts heat load and minus 71 degrees Centigrade radiator sink temperature, and maintain the ATLAS at plus 30 degrees Centigrade with 125 watts heat load and minus 93 degrees Centigrade radiator sink temperature. Furthermore, the LTCS must be qualification tested to maintain the ATLAS between plus 10 degrees Centigrade and plus 35 degrees Centigrade. 2) The LTCS must be shut down to ensure that the ATLAS can be maintained above its lowest desirable temperature of minus 2 degrees Centigrade during the survival mode. No software control algorithm for LTCS can be activated during survival and only thermostats can be used. 3) The radiator must be kept above minus 65 degrees Centigrade to prevent ammonia from freezing using no more than 135 watts of heater power. 4) The LHP reservoir control heater power is limited to 15 watts with a 70 percent duty cycle. 5) The voltage of the power supply can vary between 26 volts direct current and 34 volts direct current during the spacecraft lifetime. A design analysis shows that a single LTCS can satisfy these requirements. However, shutdown of· the LHP is particularly challenging and the shutdown heater must be wired in series with two reservoir thermostats and two CCHP thermostats at different set points. An LTCS demonstration unit has been tested to verify these performance characteristics experimentally prior to proceeding to the final LTCS design and fabrication. Test results showed that the LHP shutdown scheme would be able to shut down the LHP as designed and the reservoir control heater can maintain the ATLAS mass simulator within the plus or minus 1 degrees Centigrade accuracy under various combinations of the heat load, sink temperature, and power supply voltage.

ATLAS Probe: Exploring Frontiers in Galaxy Evolution, Cosmology, and Milky Way Science

NASA Astrophysics Data System (ADS)

Wang, Yun; Robberto, Massimo; Dickinson, Mark; Ferguson, Henry C.; Hillenbrand, Lynne; Hirata, Christopher M.; Cimatti, Andrea; Bartlett, James; Barkhouser, Robert; Benjamin, Robert A.; Brinchmann, Jarle; Chary, Ranga-Ram; Conroy, Charlie; Daddi, Emanuele; Donahue, Megan; Dore, Olivier; Eisenhardt, Peter; Fraser, Wesley C.; Helou, George; Kirkpatrick, J. Davy; Malhotra, Sangeeta; Moscardini, Lauro; Ninkov, Zoran; Ressler, Michael; Rhoads, James; Rhodes, Jason; Shapley, Alice; Smee, Stephen; ATLAS Probe Team

2018-01-01

ATLAS (Astrophysics Telescope for Large Area Spectroscopy) Probe is a concept for a NASA probe-class space mission that leverages WFIRST imaging for targeted spectroscopy. ATLAS Probe will obtain spectra of 90% of all galaxies imaged by the WFIRST High Latitude Survey at z > 0.5, with slit spectra of 300 million galaxies to z = 7. ATLAS Probe and WFIRST together will produce a 3D map of the Universe with Mpc resolution over 2200 sq deg, the definitive data sets for studying galaxy evolution, probing dark matter, dark energy and modification of general relativity, and quantifying the 3D structure and stellar content of the Milky Way.ATLAS Probe science spans four broad categories: (1) Revolutionize galaxy evolution studies by tracing the relation between galaxies and dark matter from the local group to cosmic voids and filaments, from the epoch of reionization through the peak era of galaxy assembly. (2) Open a new window into the Universe by mapping the dark matter filaments using 3D weak lensing with spectroscopic redshifts to unveil the nature of the dark Universe, and obtaining definitive measurements of dark energy and possible modification of general relativity using cosmic large-scale structure. (3) Probe the Milky Way's dust-shrouded regions, reaching the far side of our Galaxy. (4) Characterize asteroids and comets in the outer Solar System.ATLAS Probe is a 1.5m telescope with a field of view (FoV) of 0.4 sq deg, and uses Digital Micromirror Devices (DMDs) as slit selectors. It has a spectroscopic resolution of R = 600, and a wavelength range of 1-4μm. The lack of slit spectroscopy from space over a wide FoV is the obvious gap in current and planned future space missions; ATLAS fills this big gap with an unprecedented spectroscopic capability (with an estimated spectroscopic multiplex factor of 5000-10000). It has an estimated cost under $1B, with a single instrument, a telescope aperture that allows for a lighter launch vehicle, and mature technology (DMDs can reach Technology Readiness Level 6 within two years). ATLAS Probe will lead to transformative science over the entire range of astrophysics: from galaxy evolution to the dark Universe, from Solar System objects to the dusty regions of the Galaxy.

The ATLAS Software Installation System v2: a highly available system to install and validate Grid and Cloud sites via Panda

NASA Astrophysics Data System (ADS)

De Salvo, A.; Kataoka, M.; Sanchez Pineda, A.; Smirnov, Y.

2015-12-01

The ATLAS Installation System v2 is the evolution of the original system, used since 2003. The original tool has been completely re-designed in terms of database backend and components, adding support for submission to multiple backends, including the original Workload Management Service (WMS) and the new PanDA modules. The database engine has been changed from plain MySQL to Galera/Percona and the table structure has been optimized to allow a full High-Availability (HA) solution over Wide Area Network. The servlets, running on each frontend, have been also decoupled from local settings, to allow an easy scalability of the system, including the possibility of an HA system with multiple sites. The clients can also be run in multiple copies and in different geographical locations, and take care of sending the installation and validation jobs to the target Grid or Cloud sites. Moreover, the Installation Database is used as source of parameters by the automatic agents running in CVMFS, in order to install the software and distribute it to the sites. The system is in production for ATLAS since 2013, having as main sites in HA the INFN Roma Tier 2 and the CERN Agile Infrastructure. The Light Job Submission Framework for Installation (LJSFi) v2 engine is directly interfacing with PanDA for the Job Management, the Atlas Grid Information System (AGIS) for the site parameter configurations, and CVMFS for both core components and the installation of the software itself. LJSFi2 is also able to use other plugins, and is essentially Virtual Organization (VO) agnostic, so can be directly used and extended to cope with the requirements of any Grid or Cloud enabled VO. In this work we will present the architecture, performance, status and possible evolutions to the system for the LHC Run2 and beyond.

The COLD-SAT Experiment for Cryogenic Fluid Management Technology

NASA Technical Reports Server (NTRS)

Schuster, J. R.; Wachter, J. P.; Vento, D. M.

1990-01-01

Future national space transportation missions will depend on the use of cryogenic fluid management technology development needs for these missions. In-space testing will be conducted in order to show low gravity cryogenic fluid management concepts and to acquire a technical data base. Liquid H2 is the preferred test fluid due to its propellant use. The design of COLD-SAT (Cryogenic On-orbit Liquid Depot Storage, Acquisition, and Transfer Satellite), an Expendable Launch Vehicle (ELV) launched orbital spacecraft that will perform subcritical liquid H2 storage and transfer experiments under low gravity conditions is studied. An Atlas launch vehicle will place COLD-SAT into a circular orbit, and the 3-axis controlled spacecraft bus will provide electric power, experiment control, and data management, attitude control, and propulsive accelerations for the experiments. Low levels of acceleration will provide data on the effects that low gravity might have on the heat and mass transfer processes used. The experiment module will contain 3 liquid H2 tanks; fluid transfer, pressurization and venting equipment; and instrumentation.

MERCURY-ATLAS (MA)-9 - "FRIENDSHIP 7" SPACECRAFT - PRELAUNCH ACTIVITIES - CAPE

NASA Image and Video Library

1963-02-01

S63-03960 (1 Feb. 1963) --- Astronaut L. Gordon Cooper Jr., prime pilot for the Mercury-Atlas 9 (MA-9) mission, checks over the instrument panel from Mercury spacecraft #20 with Robert Graham, McDonnell Aircraft Corp. spacecraft engineer. It contains the instruments necessary to monitor spacecraft systems and sequencing, the controls required to initiate primary sequences manually, and flight control displays. Photo credit: NASA

Atlas-Centaur AC-18 performance evaluation for Applications Technology Satellite ATS-5 mission

NASA Technical Reports Server (NTRS)

1971-01-01

The Atlas-Centaur with the ATS-5 spacecraft was successfully launched from Eastern Test Range on August 12, 1969, and the ATS-5 was placed in the required highly elliptical transfer orbit with apogee near synchronous altitude. From this orbit the ATS-5, using its apogee motor, achieved the desired near-synchronous circular equatorial orbit. All launch vehicle systems performed satisfactorily.

KSC-2012-4747

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA’s Radiation Belt Storm Probes, or RBSP, spacecraft creates a halo of light at Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida as it lifts off the pad at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4720

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – Spotlights bounce off the clouds over Space Launch Complex 41 on Cape Canaveral Air Force Station as NASA's Radiation Belt Storm Probes, or RBSP, lift off the pad at 4:05 a.m. EDT aboard a United Launch Alliance Atlas V rocket. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky and Gary Thompson

KSC-2012-4746

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA’s Radiation Belt Storm Probes, or RBSP, spacecraft creates a halo of light at Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida as it lifts off the pad at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

KSC-2012-4721

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – Spotlights dance along the clouds over Space Launch Complex 41 on Cape Canaveral Air Force Station as NASA's Radiation Belt Storm Probes, or RBSP, lift off the pad at 4:05 a.m. EDT aboard a United Launch Alliance Atlas V rocket. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Ben Smegelsky and Gary Thompson

KSC-2012-4742

NASA Image and Video Library

2012-08-30

CAPE CANAVERAL, Fla. – The United Launch Alliance Atlas V rocket carrying NASA’s Radiation Belt Storm Probes, or RBSP, spacecraft illuminates Space Launch Complex 41 on Cape Canaveral Air Force Station in Florida as it lifts off the pad at 4:05 a.m. EDT. RBSP will explore changes in Earth's space environment caused by the sun -- known as "space weather" -- that can disable satellites, create power-grid failures and disrupt GPS service. The mission also will provide data on the fundamental radiation and particle acceleration processes throughout the universe. For more information on RBSP, visit http://www.nasa.gov/rbsp. Photo credit: NASA/Tony Gray and Robert Murray

MMS Partial Solar Array Inspection

NASA Image and Video Library

2014-11-14

A plaque affixed to the side of a Magnetospheric Multiscale, or MMS, observatory dedicates the mission to Richard “Richy” D’Antonio, now deceased, in grateful appreciation for his dedicated service to NASA’s MMS mission. MMS, led by a team from NASA's Goddard Space Flight Center, is a Solar Terrestrial Probes mission consisting of four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

MMS Partial Solar Array Inspection

NASA Image and Video Library

2014-11-14

A plaque affixed to the side of a Magnetospheric Multiscale, or MMS, observatory dedicates the mission to Dr. John William Klein, now deceased, who served the MMS team as the standing review board chairman. MMS, led by a team from NASA's Goddard Space Flight Center, is a Solar Terrestrial Probes mission consisting of four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

MMS Partial Solar Array Inspection

NASA Image and Video Library

2014-11-14

A plaque affixed to the side of a Magnetospheric Multiscale, or MMS, observatory dedicates the mission to George S. Moore, now deceased, an engineer who was a beloved colleague and friend to the MMS team. MMS, led by a team from NASA's Goddard Space Flight Center, is a Solar Terrestrial Probes mission consisting of four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

Design and implementation of the web Linguistic and Ethnographic Atlas of Colombia

NASA Astrophysics Data System (ADS)

Rocha S., Luz Angela; Bonilla, Johnatan; Bernal, Julio; Duarte, Catherine; Rodriguez, Alejandro

2018-05-01

The Atlas Lingüístico y Etnográfico de Colombia (Linguistic and Ethnographic Atlas of Colombia), known by "ALEC" is a compilation of popular speaking Spanish of the populations of Colombia; such research was carried out for more than fifty years. The result of this work is a collection of thematic maps organized in six volumes and its supplements in analog format. In that sense was created the project entitles "Interactive ALEC" which main objective is to develop a digital and interactive web version of the ethnographic and Linguistic Atlas of Colombia (1983) and its supplements. In this way the Corpus linguistics research group belonging to the Institute Caro y Cuervo and the research group NIDE of the Universidad Distrital "Francisco José de Caldas" have been working together in the design and development of the Atlas Web, that allows the visualization and consulting of the spatial information contained in the volume III of the analog ALEC Atlas, applying concepts of Geographical Information Systems and web cartography. Therefore, the objective of this paper is to show the process of design and development of the web prototype of the ALEC as a collection of static and dynamic maps, which show spatial information, combined with multimedia content, taking into account that in addition to all maps, the total compendium includes images, illustrations, photographs, audio and text comments. Likewise, the interactive ALEC is a good example of how to use geo-technology tools nowadays, because they are essential for the dissemination of geo linguistic information through internet, achieving more access and distribution of the Atlas web.

Structure, paleogeographic inheritance, and deformation history of the southern Atlas foreland fold and thrust belt of Tunisia

NASA Astrophysics Data System (ADS)

SaïD, Aymen; Baby, Patrice; Chardon, Dominique; Ouali, Jamel

2011-12-01

Structural analysis of the southern Tunisian Atlas was carried out using field observation, seismic interpretation, and cross section balancing. It shows a mix of thick-skinned and thin-skinned tectonics with lateral variations in regional structural geometry and amounts of shortening controlled by NW-SE oblique ramps and tear faults. It confirms the role of the Late Triassic-Early Jurassic rifting inheritance in the structuring of the active foreland fold and thrust belt of the southern Tunisian Atlas, in particular in the development of NW-SE oblique structures such as the Gafsa fault. The Late Triassic-Early Jurassic structural pattern is characterized by a family of first-order NW-SE trending normal faults dipping to the east and by second-order E-W trending normal faults limiting a complex system of grabens and horsts. These faults have been inverted during two contractional tectonic events. The first event occurred between the middle Turonian and the late Maastrichtian and can be correlated with the onset of the convergence between Africa and Eurasia. The second event corresponding to the principal shortening tectonic event in the southern Atlas started in the Serravalian-Tortonian and is still active. During the Neogene, the southern Atlas foreland fold and thrust belt propagated on the evaporitic décollement level infilling the Late Triassic-Early Jurassic rift. The major Eocene "Atlas event," described in hinterland domains and in eastern Tunisia, did not deform significantly the southern Tunisian Atlas, which corresponded in this period to a backbulge broad depozone.

Use of statecharts in the modelling of dynamic behaviour in the ATLAS DAQ prototype-1

NASA Astrophysics Data System (ADS)

Croll, P.; Duval, P.-Y.; Jones, R.; Kolos, S.; Sari, R. F.; Wheeler, S.

1998-08-01

Many applications within the ATLAS DAQ prototype-1 system have complicated dynamic behaviour which can be successfully modelled in terms of states and transitions between states. Previously, state diagrams implemented as finite-state machines have been used. Although effective, they become ungainly as system size increases. Harel statecharts address this problem by implementing additional features such as hierarchy and concurrency. The CHSM object-oriented language system is freeware which implements Harel statecharts as concurrent, hierarchical, finite-state machines (CHSMs). An evaluation of this language system by the ATLAS DAQ group has shown it to be suitable for describing the dynamic behaviour of typical DAQ applications. The language is currently being used to model the dynamic behaviour of the prototype-1 run-control system. The design is specified by means of a CHSM description file, and C++ code is obtained by running the CHSM compiler on the file. In parallel with the modelling work, a code generator has been developed which translates statecharts, drawn using the StP CASE tool, into the CHSM language. C++ code, describing the dynamic behaviour of the run-control system, has been successfully generated directly from StP statecharts using the CHSM generator and compiler. The validity of the design was tested using the simulation features of the Statemate CASE tool.

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 computing facilities infrastructure for High Energy and Nuclear Physics as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.

The informatics of a C57BL/6J mouse brain atlas.

PubMed

MacKenzie-Graham, Allan; Jones, Eagle S; Shattuck, David W; Dinov, Ivo D; Bota, Mihail; Toga, Arthur W

2003-01-01

The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulations by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers' computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at http://www.loni.ucla.edu/MAP.

How to review 4 million lines of ATLAS code

NASA Astrophysics Data System (ADS)

Stewart, Graeme A.; Lampl, Walter; ATLAS Collaboration

2017-10-01

As the ATLAS Experiment prepares to move to a multi-threaded framework (AthenaMT) for Run3, we are faced with the problem of how to migrate 4 million lines of C++ source code. This code has been written over the past 15 years and has often been adapted, re-written or extended to the changing requirements and circumstances of LHC data taking. The code was developed by different authors, many of whom are no longer active, and under the deep assumption that processing ATLAS data would be done in a serial fashion. In order to understand the scale of the problem faced by the ATLAS software community, and to plan appropriately the significant efforts posed by the new AthenaMT framework, ATLAS embarked on a wide ranging review of our offline code, covering all areas of activity: event generation, simulation, trigger, reconstruction. We discuss the difficulties in even logistically organising such reviews in an already busy community, how to examine areas in sufficient depth to learn key areas in need of upgrade, yet also to finish the reviews in a timely fashion. We show how the reviews were organised and how the ouptuts were captured in a way that the sub-system communities could then tackle the problems uncovered on a realistic timeline. Further, we discuss how the review has inuenced the overall planning for the Run 3 ATLAS offline code.

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

EPA Pesticide Factsheets

This EnviroAtlas dataset contains polygons depicting the geographic areas of market-based programs, referred to herein as markets, and projects addressing ecosystem services protection in the United States. Depending upon the type of market or project and data availability, polygons reflect market coverage areas, project footprints, or project primary impact areas in which ecosystem service markets and projects operate. The data were collected via surveys and desk research conducted by Forest Trends' Ecosystem Marketplace from 2008 to 2016 on biodiversity (i.e., imperiled species/habitats; wetlands and streams), carbon, and water markets. Additional biodiversity data were obtained from the Regulatory In-lieu Fee and Bank Information Tracking System (RIBITS) database in 2015. Attribute data include information regarding the methodology, design, and development of biodiversity, carbon, and water markets and projects. This dataset was produced by Forest Trends' Ecosystem Marketplace for EnviroAtlas in order to support public access to and use of information related to environmental markets. 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 thi

Digimouse: a 3D whole body mouse atlas from CT and cryosection data

PubMed Central

Dogdas, Belma; Stout, David; Chatziioannou, Arion F; Leahy, Richard M

2010-01-01

We have constructed a three-dimensional (3D) whole body mouse atlas from coregistered x-ray CT and cryosection data of a normal nude male mouse. High quality PET, x-ray CT and cryosection images were acquired post mortem from a single mouse placed in a stereotactic frame with fiducial markers visible in all three modalities. The image data were coregistered to a common coordinate system using the fiducials and resampled to an isotropic 0.1 mm voxel size. Using interactive editing tools we segmented and labelled whole brain, cerebrum, cerebellum, olfactory bulbs, striatum, medulla, masseter muscles, eyes, lachrymal glands, heart, lungs, liver, stomach, spleen, pancreas, adrenal glands, kidneys, testes, bladder, skeleton and skin surface. The final atlas consists of the 3D volume, in which the voxels are labelled to define the anatomical structures listed above, with coregistered PET, x-ray CT and cryosection images. To illustrate use of the atlas we include simulations of 3D bioluminescence and PET image reconstruction. Optical scatter and absorption values are assigned to each organ to simulate realistic photon transport within the animal for bioluminescence imaging. Similarly, 511 keV photon attenuation values are assigned to each structure in the atlas to simulate realistic photon attenuation in PET. The Digimouse atlas and data are available at http://neuroimage.usc.edu/Digimouse.html. PMID:17228106

Ground Water Atlas of the United States

USGS Publications Warehouse

,

2000-01-01

PrefaceThe Ground Water Atlas of the United States presents a comprehensive summary of the Nation's ground-water resources and is a basic reference for the location, geography, geology, and hydrologic characteristics of the major aquifers in the Nation. The information was collected by the U.S. Geological Survey and other agencies during the course of many years of study. Results of the Regional Aquifer-System Analysis Program, a systematic study of the Nation's major aquifers by the U.S. Geological Survey, were used as a major, but not exclusive, source of information of the Atlas. The Atlas, which is designed in a graphical format that is supported by descriptive discussions, includes 13 chapters, each representing areas that collectively cover the 50 States and Puerto Rico, as well as the U.S. Virgin Islands. Each chapter of the Atlas presents and describes hydrogeologic and hydrologic conditions for the major aquifers in each regional area. The scale of the Atlas does not allow portrayal of minor features of the geology or hydrology of each aquifer presented, nor does it include detailed discussion of minor aquifers. Those readers who seek detailed local information for the aquifers will find extensive lists of references at the end of each chapter. The introductory chapter in this volume presents an overview of ground-water conditions Nationwide and gives an example of an aquifer in each of six hydrogeologic settings.

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

PubMed

Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

2014-07-01

Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. Copyright © 2014 the American Physiological Society.

An interactive toolbox for atlas-based segmentation and coding of volumetric images

NASA Astrophysics Data System (ADS)

Menegaz, G.; Luti, S.; Duay, V.; Thiran, J.-Ph.

2007-03-01

Medical imaging poses the great challenge of having compression algorithms that are lossless for diagnostic and legal reasons and yet provide high compression rates for reduced storage and transmission time. The images usually consist of a region of interest representing the part of the body under investigation surrounded by a "background", which is often noisy and not of diagnostic interest. In this paper, we propose a ROI-based 3D coding system integrating both the segmentation and the compression tools. The ROI is extracted by an atlas based 3D segmentation method combining active contours with information theoretic principles, and the resulting segmentation map is exploited for ROI based coding. The system is equipped with a GUI allowing the medical doctors to supervise the segmentation process and eventually reshape the detected contours at any point. The process is initiated by the user through the selection of either one pre-de.ned reference image or one image of the volume to be used as the 2D "atlas". The object contour is successively propagated from one frame to the next where it is used as the initial border estimation. In this way, the entire volume is segmented based on a unique 2D atlas. The resulting 3D segmentation map is exploited for adaptive coding of the different image regions. Two coding systems were considered: the JPEG3D standard and the 3D-SPITH. The evaluation of the performance with respect to both segmentation and coding proved the high potential of the proposed system in providing an integrated, low-cost and computationally effective solution for CAD and PAC systems.

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

PubMed

Ibarra-Arellano, Miguel A; Campos-González, Adrián I; Treviño-Quintanilla, Luis G; Tauch, Andreas; Freyre-González, Julio A

2016-01-01

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy ( A: cross- BA: cteria SY: stems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708 regulons and 1776 systems. All this brings together a large corpus of data that will surely inspire studies to generate hypothesis regarding the principles governing the evolution and organization of systems and the functional architectures controlling them.Database URL: http://abasy.ccg.unam.mx. © The Author(s) 2016. Published by Oxford University Press.

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.

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.

Lessons learned from the ATLAS performance studies of the Iberian Cloud for the first LHC running period

NASA Astrophysics Data System (ADS)

Sánchez-Martínez, V.; Borges, G.; Borrego, C.; del Peso, J.; Delfino, M.; Gomes, J.; González de la Hoz, S.; Pacheco Pages, A.; Salt, J.; Sedov, A.; Villaplana, M.; Wolters, H.

2014-06-01

In this contribution we describe the performance of the Iberian (Spain and Portugal) ATLAS cloud during the first LHC running period (March 2010-January 2013) in the context of the GRID Computing and Data Distribution Model. The evolution of the resources for CPU, disk and tape in the Iberian Tier-1 and Tier-2s is summarized. The data distribution over all ATLAS destinations is shown, focusing on the number of files transferred and the size of the data. The status and distribution of simulation and analysis jobs within the cloud are discussed. The Distributed Analysis tools used to perform physics analysis are explained as well. Cloud performance in terms of the availability and reliability of its sites is discussed. The effect of the changes in the ATLAS Computing Model on the cloud is analyzed. Finally, the readiness of the Iberian Cloud towards the first Long Shutdown (LS1) is evaluated and an outline of the foreseen actions to take in the coming years is given. The shutdown will be a good opportunity to improve and evolve the ATLAS Distributed Computing system to prepare for the future challenges of the LHC operation.

Observing System Forecast Experiments at the DAO

NASA Technical Reports Server (NTRS)

Atlas, Robert

2001-01-01

Since the advent of meteorological satellites in the 1960's, numerous experiments have been conducted in order to evaluate the impact of these and other data on atmospheric analysis and prediction. Such studies have included both OSE'S and OSSE's. The OSE's were conducted to evaluate the impact of specific observations or classes of observations on analyses and forecasts. Such experiments have been performed for selected types of conventional data and for various satellite data sets as they became available. (See for example the 1989 ECMWF/EUMETSAT workshop proceedings on "The use of satellite data in operational numerical weather prediction" and the references contained therein.) The ODYSSEY were conducted to evaluate the potential for future observing systems to improve Numerical Weather Prediction NWP and to plan for the Global Weather Experiment and more recently for EVANS (Atlas et al., 1985a; Arnold and Day, 1986; Hoffman et al., 1990). In addition, OSSE's have been run to evaluate trade-offs in the design of observing systems and observing networks (Atlas and Emmitt, 1991; Rohaly and Krishnamurti, 1993), and to test new methodology for data assimilation (Atlas and Bloom, 1989).

Upgrade project and plans for the ATLAS detector and trigger

NASA Astrophysics Data System (ADS)

Pastore, Francesca; Atlas Collaboration

2013-08-01

The LHC is expected to under go upgrades over the coming years in order to extend its scientific potential. Through two different phases (namely Phase-I and Phase-II), the average luminosity will be increased by a factor 5-10 above the design luminosity, 1034 cm-2 s-1. Consequently, the LHC experiments will need upgraded detectors and new infrastructure of the trigger and DAQ systems, to take into account the increase of radiation level and of particle rates foreseen at such high luminosity. In this paper we describe the planned changes and the investigations for the ATLAS experiment, focusing on the requirements for the trigger system to handle the increase rate of collisions per beam crossing, while maintaining widely inclusive selections. In different steps, the trigger detectors will improve their selectivity by benefiting from increased granularity. To improve the flexibility of the system, the use of the tracking information in the lower levels of the trigger selection is also discussed. Lastly different scenarios are compared, based on the expected physics potential of ATLAS in this high luminosity regime.

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.

Early Mesozoic rift basin architecture and sediment routing system in the Moroccan High Atlas

NASA Astrophysics Data System (ADS)

Perez, N.; Teixell, A.; Gomez, D.

2016-12-01

Late Permian to Triassic extensional systems associated with Pangea breakup governed the structural framework and rift basin architecture that was inherited by Cenozoic High Atlas Mountains in Morocco. U-Pb detrital zircon geochronologic and mapping results from Permo-Triassic deposits now incorporated into the High Atlas Mountains provide new constraints on the geometry and interconnectivity among synextensional depocenters. U-Pb detrital zircon data provide provenance constraints of Permo-Triassic deposits, highlighting temporal changes in sediment sources and revealing the spatial pattern of sediment routing along the rift. We also characterize the U-Pb detrital zircon geochronologic signature of distinctive interfingering fluvial, tidal, and aeolian facies that are preferentially preserved near the controlling normal faults. These results highlight complex local sediment mixing patterns potentially linked to the interplay between fault motion, eustatic, and erosion/transport processes. We compare our U-Pb geochronologic results with existing studies of Gondwanan and Laurentian cratonic blocks to investigate continent scale sediment routing pathways, and with analogous early Mesozoic extensional systems situated in South America (Mitu basin, Peru) and North America (Newark Basin) to assess sediment mixing patterns in rift basins.

ATLAS EventIndex general dataflow and monitoring infrastructure

NASA Astrophysics Data System (ADS)

Fernández Casaní, Á.; Barberis, D.; Favareto, A.; García Montoro, C.; González de la Hoz, S.; Hřivnáč, J.; Prokoshin, F.; Salt, J.; Sánchez, J.; Többicke, R.; Yuan, R.; ATLAS Collaboration

2017-10-01

The ATLAS EventIndex has been running in production since mid-2015, reliably collecting information worldwide about all produced events and storing them in a central Hadoop infrastructure at CERN. A subset of this information is copied to an Oracle relational database for fast dataset discovery, event-picking, crosschecks with other ATLAS systems and checks for event duplication. The system design and its optimization is serving event picking from requests of a few events up to scales of tens of thousand of events, and in addition, data consistency checks are performed for large production campaigns. Detecting duplicate events with a scope of physics collections has recently arisen as an important use case. This paper describes the general architecture of the project and the data flow and operation issues, which are addressed by recent developments to improve the throughput of the overall system. In this direction, the data collection system is reducing the usage of the messaging infrastructure to overcome the performance shortcomings detected during production peaks; an object storage approach is instead used to convey the event index information, and messages to signal their location and status. Recent changes in the Producer/Consumer architecture are also presented in detail, as well as the monitoring infrastructure.

Recent uplift of the Atlantic Atlas (offshore West Morocco): Tectonic arch and submarine terraces

NASA Astrophysics Data System (ADS)

Benabdellouahed, M.; Klingelhoefer, F.; Gutscher, M.-A.; Rabineau, M.; Biari, Y.; Hafid, M.; Duarte, J. C.; Schnabel, M.; Baltzer, A.; Pedoja, K.; Le Roy, P.; Reichert, C.; Sahabi, M.

2017-06-01

Re-examination of marine geophysical data from the continental margin of West Morocco reveals a broad zone characterized by deformation, active faults and updoming offshore the High Atlas (Morocco margin), situated next to the Tafelney Plateau. Both seismic reflection and swath-bathymetric data, acquired during Mirror marine geophysical survey in 2011, indicate recent uplift of the margin including uplift of the basement. This deformation, which we propose to name the Atlantic Atlas tectonic arch, is interpreted to result largely through uplift of the basement, which originated during the Central Atlantic rifting stage - or even during phases of Hercynian deformation. This has produced a large number of closely spaced normal and reverse faults, ;piano key faults;, originating from the basement and affecting the entire sedimentary sequence, as well as the seafloor. The presence of four terraces in the Essaouira canyon system at about 3500 meters water depth and ;piano key faults; and the fact that these also affect the seafloor, indicate that the Atlantic Atlas is still active north of Agadir canyon. We propose that recent uplift is causing morphogenesis of four terraces in the Essaouira canyon system. In this paper the role of both Canary plume migration and ongoing convergence between the African and Eurasian plates in the formation of the Atlantic Atlas are discussed as possibilities to explain the presence of a tectonic arch in the region. The process of reactivation of passive margins is still not well understood. The region north of Agadir canyon represents a key area to better understand this process.

A Sundial-Atlas Precursor to the TIMED Mission: A Quick-Response Global Investigation into Coupled Lower Thermospheric, Ionospheric, and Mesospheric Physics

NASA Technical Reports Server (NTRS)

Szuszczewicz, E. P.

1996-01-01

The SUNDIAL-ATLAS effort was a global-scale investigation which responded to the science priorities of the ITM Panel, the Integrated SPD Strategy Implementation Plan as a whole, and the need for potential cost-saving design criteria for the TIMED mission. The investigation focused on coupling processes in the ionospheric-thermospheric system, taking advantage of the timelines of the ATLAS-1 mission (March 1992), and the global-scale ground-based measurement and modeling activities of the SUNDIAL program. The collaborative SUNDIAL-ATLAS activity was the first opportunity for global measurements of the chemistry, kinetics, and electrodynamics which couple the E-, Fl-, and F2-regions into a single interactive system. As such, the program represented an important first step in studying global issues; and accordingly, was an important proof of concept experiment relevant to the strategic mission plans for the ITM community and the upcoming intermediate class satellite program called TIMED. To meet its projected goals, TIMED must perform a number of critical measurements and execute a number of correlations that were to be tried and tested for the first time in the SUNDIAL-ATLAS investigation. This was designed to include global correlations of thermospheric and ionospheric composition during quiet and disturbed conditions and the co-registration of global-scale ground-based measurements with along-track satellite diagnostics. The SUNDIAL component of the current investigation addressed this need by acquiring, reducing, and analyzing a multi-sensor database that complemented and extended that which was generated in the ATLAS mission (Atmospheric Laboratory for Applications and Science). The SUNDIAL data defined the state and condition of the global-scale ionosphere in the altitude range from 100 km to the F2-peak. These data specified the peak heights and densities of the E-, Fl-, and F2-regions, along with the global distributions of intermediate, descending, and sequential layers which play a critical role in the dynamo region of the lower ionospheric-thermospheric domain. The data were collected by the SUNDIAL network of more than 50 ground-based stations utilizing ionosondes, radars, photometers, Fabry-Perot interferometers, and total electron content measurements. The data were acquired during a three-week period centered on the eight-day ATLAS-1 mission, which provided image and photometric sensing of the altitude distributions of the major and minor ions and neutrals in the ITM system. This report focuses on the scientific contributions of the SUNDIAL component of the overall investigation. Specific findings are described in seven papers (attached) published in the Journal of Geophysical Research.

The evolution of computer monitoring of real time data during the Atlas Centaur launch countdown

NASA Technical Reports Server (NTRS)

Thomas, W. F.

1981-01-01

In the last decade, improvements in computer technology have provided new 'tools' for controlling and monitoring critical missile systems. In this connection, computers have gradually taken a large role in monitoring all flights and ground systems on the Atlas Centaur. The wide body Centaur which will be launched in the Space Shuttle Cargo Bay will use computers to an even greater extent. It is planned to use the wide body Centaur to boost the Galileo spacecraft toward Jupiter in 1985. The critical systems which must be monitored prior to liftoff are examined. Computers have now been programmed to monitor all critical parameters continuously. At this time, there are two separate computer systems used to monitor these parameters.

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 autosegmentation accuracy. In this study, the optimal number of selected atlases used was six, but for definitive conclusions about the optimal number of atlases and to improve the autosegmentation accuracy for clinical use, more atlases need to be included.

Intelligent operations of the data acquisition system of the ATLAS experiment at LHC

NASA Astrophysics Data System (ADS)

Anders, G.; Avolio, G.; Lehmann Miotto, G.; Magnoni, L.

2015-05-01

The ATLAS experiment at the Large Hadron Collider at CERN relies on a complex and highly distributed Trigger and Data Acquisition (TDAQ) system to gather and select particle collision data obtained at unprecedented energy and rates. The Run Control (RC) system is the component steering the data acquisition by starting and stopping processes and by carrying all data-taking elements through well-defined states in a coherent way. Taking into account all the lessons learnt during LHC's Run 1, the RC has been completely re-designed and re-implemented during the LHC Long Shutdown 1 (LS1) phase. As a result of the new design, the RC is assisted by the Central Hint and Information Processor (CHIP) service that can be truly considered its “brain”. CHIP is an intelligent system able to supervise the ATLAS data taking, take operational decisions and handle abnormal conditions. In this paper, the design, implementation and performances of the RC/CHIP system will be described. A particular emphasis will be put on the way the RC and CHIP cooperate and on the huge benefits brought by the Complex Event Processing engine. Additionally, some error recovery scenarios will be analysed for which the intervention of human experts is now rendered unnecessary.

The ATLAS PanDA Monitoring System and its Evolution

NASA Astrophysics Data System (ADS)

Klimentov, A.; Nevski, P.; Potekhin, M.; Wenaus, T.

2011-12-01

The PanDA (Production and Distributed Analysis) Workload Management System is used for ATLAS distributed production and analysis worldwide. The needs of ATLAS global computing imposed challenging requirements on the design of PanDA in areas such as scalability, robustness, automation, diagnostics, and usability for both production shifters and analysis users. Through a system-wide job database, the PanDA monitor provides a comprehensive and coherent view of the system and job execution, from high level summaries to detailed drill-down job diagnostics. It is (like the rest of PanDA) an Apache-based Python application backed by Oracle. The presentation layer is HTML code generated on the fly in the Python application which is also responsible for managing database queries. However, this approach is lacking in user interface flexibility, simplicity of communication with external systems, and ease of maintenance. A decision was therefore made to migrate the PanDA monitor server to Django Web Application Framework and apply JSON/AJAX technology in the browser front end. This allows us to greatly reduce the amount of application code, separate data preparation from presentation, leverage open source for tools such as authentication and authorization mechanisms, and provide a richer and more dynamic user experience. We describe our approach, design and initial experience with the migration process.

ORIGIN OF THE CHAOTIC MOTION OF THE SATURNIAN SATELLITE ATLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renner, S.; Vienne, A.; Cooper, N. J.

2016-05-01

We revisit the dynamics of Atlas. Using Cassini ISS astrometric observations spanning 2004 February to 2013 August, Cooper et al. found evidence that Atlas is currently perturbed by both a 54:53 corotation eccentricity resonance (CER) and a 54:53 Lindblad eccentricity resonance (LER) with Prometheus. They demonstrated that the orbit of Atlas is chaotic, with a Lyapunov time of order 10 years, as a direct consequence of the coupled resonant interaction (CER/LER) with Prometheus. Here we investigate the interactions between the two resonances using the CoraLin analytical model, showing that the chaotic zone fills almost all the corotation sites occupied bymore » the satellite's orbit. Four 70:67 apse-type mean motion resonances with Pandora are also overlapping, but these resonances have a much weaker effect. Frequency analysis allows us to highlight the coupling between the 54:53 resonances, and confirms that a simplified system including the perturbations due to Prometheus and Saturn's oblateness only captures the essential features of the dynamics.« less

Situational analysis: regional review of the substance use Atlas 2015.

PubMed

Gehring, Elise; Saeed, Khalid

2017-05-01

The Atlas project on substance use is a global WHO project that aims to collect and disseminate data on resources for the prevention and treatment of substance use disorders. Information on resources available in the WHO Eastern Mediterranean Region was first published in 2012. The Atlas questionnaire was updated in 2014 and data were collected in all WHO Member States. All countries of the Region submitted the Atlas questionnaire. This report presents the latest key information on resources for the prevention and treatment of substance use disorders in the Eastern Mediterranean Region based on the responses of the countries to the questionnaire. Current estimates show that the burden attributable to drug use disorders in the Region is high. Health system resources for the prevention and treatment of substance use disorders vary across countries, but are generally still insufficient to provide adequate care and treatment for people with these disorders. Countries need to strengthen prevention and treatment of substance use disorders, particularly by increasing coverage of treatment interventions.

In Brief: New atlas of Africa

NASA Astrophysics Data System (ADS)

Showstack, Randy

2008-07-01

A newly revised atlas of Africa features more than 300 satellite images that show striking before and after photographs of environmental changes spanning about 35 years. Africa: Atlas of Our Changing Environment, compiled by the United Nations Environment Programme (UNEP), provides visual evidence of how development choices, population growth, climate change, and, in some cases, conflicts affect Africa, often negatively. The book includes photographs of shrinking glaciers on Mount Kilimanjaro as well as on Uganda's Rwenzori Mountains; deforestation along an expanding road system in the Congo; the drying up of Lake Chad; and the expansion of urban areas such as Cape Town, South Africa, and Dakar, Senegal. Satellite images also indicate some positive signs of environmental management, including action to stop overgrazing in a Tunisian national park, the effects of a management plan for a dam in Zambia that has helped restore seasonal flooding, and positive impacts of wetlands expansion around a national park in Mauritania. For more information, visit http://www.unep.org/dewa/africa/AfricaAtlas.

Origin of the Chaotic Motion of the Saturnian Satellite Atlas

NASA Astrophysics Data System (ADS)

Renner, S.; Cooper, N. J.; El Moutamid, M.; Sicardy, B.; Vienne, A.; Murray, C. D.; Saillenfest, M.

2016-05-01

We revisit the dynamics of Atlas. Using Cassini ISS astrometric observations spanning 2004 February to 2013 August, Cooper et al. found evidence that Atlas is currently perturbed by both a 54:53 corotation eccentricity resonance (CER) and a 54:53 Lindblad eccentricity resonance (LER) with Prometheus. They demonstrated that the orbit of Atlas is chaotic, with a Lyapunov time of order 10 years, as a direct consequence of the coupled resonant interaction (CER/LER) with Prometheus. Here we investigate the interactions between the two resonances using the CoraLin analytical model, showing that the chaotic zone fills almost all the corotation sites occupied by the satellite's orbit. Four 70:67 apse-type mean motion resonances with Pandora are also overlapping, but these resonances have a much weaker effect. Frequency analysis allows us to highlight the coupling between the 54:53 resonances, and confirms that a simplified system including the perturbations due to Prometheus and Saturn's oblateness only captures the essential features of the dynamics.

Waxholm space: an image-based reference for coordinating mouse brain research.

PubMed

Johnson, G Allan; Badea, Alexandra; Brandenburg, Jeffrey; Cofer, Gary; Fubara, Boma; Liu, Song; Nissanov, Jonathan

2010-11-01

We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 mum (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web. Copyright 2010 Elsevier Inc. All rights reserved.

High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas.

PubMed

Saygin, Z M; Kliemann, D; Iglesias, J E; van der Kouwe, A J W; Boyd, E; Reuter, M; Stevens, A; Van Leemput, K; McKee, A; Frosch, M P; Fischl, B; Augustinack, J C

2017-07-15

The amygdala is composed of multiple nuclei with unique functions and connections in the limbic system and to the rest of the brain. However, standard in vivo neuroimaging tools to automatically delineate the amygdala into its multiple nuclei are still rare. By scanning postmortem specimens at high resolution (100-150µm) at 7T field strength (n = 10), we were able to visualize and label nine amygdala nuclei (anterior amygdaloid, cortico-amygdaloid transition area; basal, lateral, accessory basal, central, cortical medial, paralaminar nuclei). We created an atlas from these labels using a recently developed atlas building algorithm based on Bayesian inference. This atlas, which will be released as part of FreeSurfer, can be used to automatically segment nine amygdala nuclei from a standard resolution structural MR image. We applied this atlas to two publicly available datasets (ADNI and ABIDE) with standard resolution T1 data, used individual volumetric data of the amygdala nuclei as the measure and found that our atlas i) discriminates between Alzheimer's disease participants and age-matched control participants with 84% accuracy (AUC=0.915), and ii) discriminates between individuals with autism and age-, sex- and IQ-matched neurotypically developed control participants with 59.5% accuracy (AUC=0.59). For both datasets, the new ex vivo atlas significantly outperformed (all p < .05) estimations of the whole amygdala derived from the segmentation in FreeSurfer 5.1 (ADNI: 75%, ABIDE: 54% accuracy), as well as classification based on whole amygdala volume (using the sum of all amygdala nuclei volumes; ADNI: 81%, ABIDE: 55% accuracy). This new atlas and the segmentation tools that utilize it will provide neuroimaging researchers with the ability to explore the function and connectivity of the human amygdala nuclei with unprecedented detail in healthy adults as well as those with neurodevelopmental and neurodegenerative disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

The AAL project: automated monitoring and intelligent analysis for the ATLAS data taking infrastructure

NASA Astrophysics Data System (ADS)

Kazarov, A.; Lehmann Miotto, G.; Magnoni, L.

2012-06-01

The Trigger and Data Acquisition (TDAQ) system of the ATLAS experiment at CERN is the infrastructure responsible for collecting and transferring ATLAS experimental data from detectors to the mass storage system. It relies on a large, distributed computing environment, including thousands of computing nodes with thousands of application running concurrently. In such a complex environment, information analysis is fundamental for controlling applications behavior, error reporting and operational monitoring. During data taking runs, streams of messages sent by applications via the message reporting system together with data published from applications via information services are the main sources of knowledge about correctness of running operations. The flow of data produced (with an average rate of O(1-10KHz)) is constantly monitored by experts to detect problem or misbehavior. This requires strong competence and experience in understanding and discovering problems and root causes, and often the meaningful information is not in the single message or update, but in the aggregated behavior in a certain time-line. The AAL project is meant at reducing the man power needs and at assuring a constant high quality of problem detection by automating most of the monitoring tasks and providing real-time correlation of data-taking and system metrics. This project combines technologies coming from different disciplines, in particular it leverages on an Event Driven Architecture to unify the flow of data from the ATLAS infrastructure, on a Complex Event Processing (CEP) engine for correlation of events and on a message oriented architecture for components integration. The project is composed of 2 main components: a core processing engine, responsible for correlation of events through expert-defined queries and a web based front-end to present real-time information and interact with the system. All components works in a loose-coupled event based architecture, with a message broker to centralize all communication between modules. The result is an intelligent system able to extract and compute relevant information from the flow of operational data to provide real-time feedback to human experts who can promptly react when needed. The paper presents the design and implementation of the AAL project, together with the results of its usage as automated monitoring assistant for the ATLAS data taking infrastructure.

Atlas-based automatic measurements of the morphology of the tibiofemoral joint

NASA Astrophysics Data System (ADS)

Brehler, M.; Thawait, G.; Shyr, W.; Ramsay, J.; Siewerdsen, J. H.; Zbijewski, W.

2017-03-01

Purpose: Anatomical metrics of the tibiofemoral joint support assessment of joint stability and surgical planning. We propose an automated, atlas-based algorithm to streamline the measurements in 3D images of the joint and reduce userdependence of the metrics arising from manual identification of the anatomical landmarks. Methods: The method is initialized with coarse registrations of a set of atlas images to the fixed input image. The initial registrations are then refined separately for the tibia and femur and the best matching atlas is selected. Finally, the anatomical landmarks of the best matching atlas are transformed onto the input image by deforming a surface model of the atlas to fit the shape of the tibial plateau in the input image (a mesh-to-volume registration). We apply the method to weight-bearing volumetric images of the knee obtained from 23 subjects using an extremity cone-beam CT system. Results of the automated algorithm were compared to an expert radiologist for measurements of Static Alignment (SA), Medial Tibial Slope (MTS) and Lateral Tibial Slope (LTS). Results: Intra-reader variability as high as 10% for LTS and 7% for MTS (ratio of standard deviation to the mean in repeated measurements) was found for expert radiologist, illustrating the potential benefits of an automated approach in improving the precision of the metrics. The proposed method achieved excellent registration of the atlas mesh to the input volumes. The resulting automated measurements yielded high correlations with expert radiologist, as indicated by correlation coefficients of 0.72 for MTS, 0.8 for LTS, and 0.89 for SA. Conclusions: The automated method for measurement of anatomical metrics of the tibiofemoral joint achieves high correlation with expert radiologist without the need for time consuming and error prone manual selection of landmarks.

Atlas-based automatic measurements of the morphology of the tibiofemoral joint.

PubMed

Brehler, M; Thawait, G; Shyr, W; Ramsay, J; Siewerdsen, J H; Zbijewski, W

2017-02-11

Anatomical metrics of the tibiofemoral joint support assessment of joint stability and surgical planning. We propose an automated, atlas-based algorithm to streamline the measurements in 3D images of the joint and reduce user-dependence of the metrics arising from manual identification of the anatomical landmarks. The method is initialized with coarse registrations of a set of atlas images to the fixed input image. The initial registrations are then refined separately for the tibia and femur and the best matching atlas is selected. Finally, the anatomical landmarks of the best matching atlas are transformed onto the input image by deforming a surface model of the atlas to fit the shape of the tibial plateau in the input image (a mesh-to-volume registration). We apply the method to weight-bearing volumetric images of the knee obtained from 23 subjects using an extremity cone-beam CT system. Results of the automated algorithm were compared to an expert radiologist for measurements of Static Alignment (SA), Medial Tibial Slope (MTS) and Lateral Tibial Slope (LTS). Intra-reader variability as high as ~10% for LTS and 7% for MTS (ratio of standard deviation to the mean in repeated measurements) was found for expert radiologist, illustrating the potential benefits of an automated approach in improving the precision of the metrics. The proposed method achieved excellent registration of the atlas mesh to the input volumes. The resulting automated measurements yielded high correlations with expert radiologist, as indicated by correlation coefficients of 0.72 for MTS, 0.8 for LTS, and 0.89 for SA. The automated method for measurement of anatomical metrics of the tibiofemoral joint achieves high correlation with expert radiologist without the need for time consuming and error prone manual selection of landmarks.

High-Performance Scalable Information Service for the ATLAS Experiment

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Microstructure investigations of U3Si2 implanted by high-energy Xe ions at 600 °C

NASA Astrophysics Data System (ADS)

Miao, Yinbin; Harp, Jason; Mo, Kun; Kim, Yeon Soo; Zhu, Shaofei; Yacout, Abdellatif M.

2018-05-01

The microstructure investigations on a high-energy Xe-implanted U3Si2 pellet were performed. The promising accident tolerant fuel (ATF) candidate, U3Si2, was irradiated by 84 MeV Xe ions at 600 °C at Argonne Tandem Linac Accelerator System (ATLAS). The characterizations of the Xe implanted sample were conducted using advanced transmission electron microscopy (TEM) techniques. An oxidation layer was observed on the sample surface after irradiation under the ∼10-5 Pa vacuum. The study on the oxidation layer not only unveils the readily oxidation behavior of U3Si2 under high-temperature irradiation conditions, but also develops an understanding of its oxidation mechanism. Intragranular Xe bubbles with bimodal size distribution were observed within the Xe deposition region of the sample induced by 84 MeV Xe ion implantation. At the irradiation temperature of 600 °C, the gaseous swelling strain contributed by intragranular bubbles was found to be insignificant, indicating an acceptable fission gas behavior of U3Si2 as a light water reactor (LWR) fuel operating at such a temperature.

Warping an atlas derived from serial histology to 5 high-resolution MRIs.

PubMed

Tullo, Stephanie; Devenyi, Gabriel A; Patel, Raihaan; Park, Min Tae M; Collins, D Louis; Chakravarty, M Mallar

2018-06-19

Previous work from our group demonstrated the use of multiple input atlases to a modified multi-atlas framework (MAGeT-Brain) to improve subject-based segmentation accuracy. Currently, segmentation of the striatum, globus pallidus and thalamus are generated from a single high-resolution and -contrast MRI atlas derived from annotated serial histological sections. Here, we warp this atlas to five high-resolution MRI templates to create five de novo atlases. The overall goal of this work is to use these newly warped atlases as input to MAGeT-Brain in an effort to consolidate and improve the workflow presented in previous manuscripts from our group, allowing for simultaneous multi-structure segmentation. The work presented details the methodology used for the creation of the atlases using a technique previously proposed, where atlas labels are modified to mimic the intensity and contrast profile of MRI to facilitate atlas-to-template nonlinear transformation estimation. Dice's Kappa metric was used to demonstrate high quality registration and segmentation accuracy of the atlases. The final atlases are available at https://github.com/CobraLab/atlases/tree/master/5-atlas-subcortical.

The ATLAS Diamond Beam Monitor: Luminosity detector at the LHC

NASA Astrophysics Data System (ADS)

Schaefer, D. M.; ATLAS Collaboration

2016-07-01

After the first three years of the LHC running, the ATLAS experiment extracted its pixel detector system to refurbish and re-position the optical readout drivers and install a new barrel layer of pixels. The experiment has also taken advantage of this access to install a set of beam monitoring telescopes with pixel sensors, four each in the forward and backward regions. These telescopes are based on chemical vapor deposited (CVD) diamond sensors to survive in this high radiation environment without needing extensive cooling. This paper describes the lessons learned in construction and commissioning of the ATLAS Diamond Beam Monitor (DBM). We show results from the construction quality assurance tests and commissioning performance, including results from cosmic ray running in early 2015.

Atlasmaker: A Grid-based Implementation of the Hyperatlas

NASA Astrophysics Data System (ADS)

Williams, R.; Djorgovski, S. G.; Feldmann, M. T.; Jacob, J.

2004-07-01

The Atlasmaker project is using Grid technology, in combination with NVO interoperability, to create new knowledge resources in astronomy. The product is a multi-faceted, multi-dimensional, scientifically trusted image atlas of the sky, made by federating many different surveys at different wavelengths, times, resolutions, polarizations, etc. The Atlasmaker software does resampling and mosaicking of image collections, and is well-suited to operate with the Hyperatlas standard. Requests can be satisfied via on-demand computations or by accessing a data cache. Computed data is stored in a distributed virtual file system, such as the Storage Resource Broker (SRB). We expect these atlases to be a new and powerful paradigm for knowledge extraction in astronomy, as well as a magnificent way to build educational resources. The system is being incorporated into the data analysis pipeline of the Palomar-Quest synoptic survey, and is being used to generate all-sky atlases from the 2MASS, SDSS, and DPOSS surveys for joint object detection.

Technical and Organizational Considerations for the Long-Term Maintenance and Development of Digital Brain Atlases and Web-Based Databases

PubMed Central

Ito, Kei

2010-01-01

Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job. PMID:20661458

Systems for Arctic Spill Response. Volume II. Appendices.

DTIC Science & Technology

1978-03-01

Microbial Degradation of Oil Pollutants, Center for Wetland Resources. Pub. No. LSU-SG-73-O1 , 1973, p. 153. 6. Atlas , R. and E. Schofield , •U petroleum... Atlas , R. and R. Bartha , “Degradation and Mineralization of Petroleum in in Sea Water: Limitation by Nitrogen and Phosphorus ,” Biotechnology, B...iNFORMATION SOURCES USED IN THE PREPARATION OF MAPS OF ECOLOGICAL SENSITIVITY A- i APPENDIX B - APPLICATION OF EXISTING AND PLANNED OIL SPILL

InSight Atlas V LVOS

NASA Image and Video Library

2018-03-03

A United Launch Alliance Atlas V booster arrives at Space Launch Complex 3 at Vandenberg Air Force Base in California. The rocket will launch NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff is scheduled for May 5, 2018.

Computational and mathematical methods in brain atlasing.

PubMed

Nowinski, Wieslaw L

2017-12-01

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

Evolution of the ATLAS PanDA Production and Distributed Analysis System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maeno, T.; De, K.; Wenaus, T.

2012-12-13

Evolution of the ATLAS PanDA Production and Distributed Analysis System T Maeno1,5, K De2, T Wenaus1, P Nilsson2, R Walker3, A Stradling2, V Fine1, M Potekhin1, S Panitkin1 and G Compostella4 Published under licence by IOP Publishing Ltd Journal of Physics: Conference Series, Volume 396, Part 3 Article PDF References Citations Metrics 101 Total downloads Cited by 8 articles Turn on MathJax Share this article Article information Abstract The PanDA (Production and Distributed Analysis) system has been developed to meet ATLAS production and analysis requirements for a data-driven workload management system capable of operating at LHC data processing scale. PanDAmore » has performed well with high reliability and robustness during the two years of LHC data-taking, while being actively evolved to meet the rapidly changing requirements for analysis use cases. We will present an overview of system evolution including automatic rebrokerage and reattempt for analysis jobs, adaptation for the CernVM File System, support for the multi-cloud model through which Tier-2 sites act as members of multiple clouds, pledged resource management and preferential brokerage, and monitoring improvements. We will also describe results from the analysis of two years of PanDA usage statistics, current issues, and plans for the future.« less

Computer-aided bone age assessment for ethnically diverse older children using integrated fuzzy logic system

NASA Astrophysics Data System (ADS)

Ma, Kevin; Moin, Paymann; Zhang, Aifeng; Liu, Brent

2010-03-01

Bone Age Assessment (BAA) of children is a clinical procedure frequently performed in pediatric radiology to evaluate the stage of skeletal maturation based on the left hand x-ray radiograph. The current BAA standard in the US is using the Greulich & Pyle (G&P) Hand Atlas, which was developed fifty years ago and was only based on Caucasian population from the Midwest US. To bring the BAA procedure up-to-date with today's population, a Digital Hand Atlas (DHA) consisting of 1400 hand images of normal children of different ethnicities, age, and gender. Based on the DHA and to solve inter- and intra-observer reading discrepancies, an automatic computer-aided bone age assessment system has been developed and tested in clinical environments. The algorithm utilizes features extracted from three regions of interests: phalanges, carpal, and radius. The features are aggregated into a fuzzy logic system, which outputs the calculated bone age. The previous BAA system only uses features from phalanges and carpal, thus BAA result for children over age of 15 is less accurate. In this project, the new radius features are incorporated into the overall BAA system. The bone age results, calculated from the new fuzzy logic system, are compared against radiologists' readings based on G&P atlas, and exhibits an improvement in reading accuracy for older children.

Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus

NASA Astrophysics Data System (ADS)

Sun, Peizhen; Parvathaneni, Prasanna; Schilling, Kurt G.; Gao, Yurui; Janve, Vaibhav; Anderson, Adam; Landman, Bennett A.

2015-03-01

This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 μm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 μm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.

The ShakeMap Atlas for the City of Naples, Italy

NASA Astrophysics Data System (ADS)

Pierdominici, Simona; Faenza, Licia; Camassi, Romano; Michelini, Alberto; Ercolani, Emanuela; Lauciani, Valentino

2016-04-01

Naples is one of the most vulnerable cities in the world because it is threatened by several natural and man-made hazards: earthquakes, volcanic eruptions, tsunamis, landslides, hydrogeological disasters, and morphologic alterations due to human interference. In addition, the risk is increased by the high density of population (Naples and the surrounding area are among the most populated in Italy), and by the type and condition of buildings and monuments. In light of this, it is crucial to assess the ground shaking suffered by the city. We take into account and integrate data information from five Italian databases and catalogues (DBMI11; CPTI11; CAMAL11; MOLAL08; ITACA) to build a reliable ShakeMap atlas for the area and to recreate the seismic history of the city from historical to recent times (1293 to 1999). This large amount of data gives the opportunity to explore several sources of information, expanding the completeness of our data set in both time and magnitude. 84 earthquakes have been analyzed and for each event, a Shakemap set has been computed using an ad hoc implementation developed for this application: (1) specific ground-motion prediction equations (GMPEs) accounting for the different attenuation properties in volcanic areas compared with the tectonic ones, and (2) detailed local microzonation to include the site effects. The ShakeMap atlas has two main applications: a) it is an important instrument in seismic risk management. It quantifies the level of shaking suffered by a city during its history, and it could be implemented to the quantification of the number of people exposed to certain degrees of shaking. Intensity data provide the evaluation of the damage caused by earthquakes; the damage is closely linked with the ground shaking, building type, and vulnerability, and it is not possible to separate these contributions; b) the Atlas can be used as starting point for Bayesian estimation of seismic hazard. This technique allows for the merging of the more standard approach adopted in the compilation of the national hazard map of Italy. These Shakemaps are provided in terms of Mercalli-Cancani-Sieberg intensity (MCS hereinafter) and peak ground acceleration (PGA).

EnviroAtlas - Austin, TX - Demographics by Block Group Web Service

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas dataset is a summary of key demographic groups for 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).

Using Solid State Disk Array as a Cache for LHC ATLAS Data Analysis

NASA Astrophysics Data System (ADS)

Yang, W.; Hanushevsky, A. B.; Mount, R. P.; Atlas Collaboration

2014-06-01

User data analysis in high energy physics presents a challenge to spinning-disk based storage systems. The analysis is data intense, yet reads are small, sparse and cover a large volume of data files. It is also unpredictable due to users' response to storage performance. We describe here a system with an array of Solid State Disk as a non-conventional, standalone file level cache in front of the spinning disk storage to help improve the performance of LHC ATLAS user analysis at SLAC. The system uses several days of data access records to make caching decisions. It can also use information from other sources such as a work-flow management system. We evaluate the performance of the system both in terms of caching and its impact on user analysis jobs. The system currently uses Xrootd technology, but the technique can be applied to any storage system.

Microallopatry caused strong diversification in Buthus scorpions (Scorpiones: Buthidae) in the Atlas Mountains (NW Africa).

PubMed

Habel, Jan C; Husemann, Martin; Schmitt, Thomas; Zachos, Frank E; Honnen, Ann-Christin; Petersen, Britt; Parmakelis, Aristeidis; Stathi, Iasmi

2012-01-01

The immense biodiversity of the Atlas Mountains in North Africa might be the result of high rates of microallopatry caused by mountain barriers surpassing 4000 meters leading to patchy habitat distributions. We test the influence of geographic structures on the phylogenetic patterns among Buthus scorpions using mtDNA sequences. We sampled 91 individuals of the genus Buthus from 51 locations scattered around the Atlas Mountains (Antiatlas, High Atlas, Middle Atlas and Jebel Sahro). We sequenced 452 bp of the Cytochrome Oxidase I gene which proved to be highly variable within and among Buthus species. Our phylogenetic analysis yielded 12 distinct genetic groups one of which comprised three subgroups mostly in accordance with the orographic structure of the mountain systems. Main clades overlap with each other, while subclades are distributed parapatrically. Geographic structures likely acted as long-term barriers among populations causing restriction of gene flow and allowing for strong genetic differentiation. Thus, genetic structure and geographical distribution of genetic (sub)clusters follow the classical theory of allopatric differentiation where distinct groups evolve without range overlap until reproductive isolation and ecological differentiation has built up. Philopatry and low dispersal ability of Buthus scorpions are the likely causes for the observed strong genetic differentiation at this small geographic scale.

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.

Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra provides reduced effect of scanner for cortex volumetry with atlas-based method in healthy subjects.

PubMed

Goto, Masami; Abe, Osamu; Aoki, Shigeki; Hayashi, Naoto; Miyati, Tosiaki; Takao, Hidemasa; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

2013-07-01

This study aimed to investigate whether the effect of scanner for cortex volumetry with atlas-based method is reduced using Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) normalization compared with standard normalization. Three-dimensional T1-weighted magnetic resonance images (3D-T1WIs) of 21 healthy subjects were obtained and evaluated for effect of scanner in cortex volumetry. 3D-T1WIs of the 21 subjects were obtained with five MRI systems. Imaging of each subject was performed on each of five different MRI scanners. We used the Voxel-Based Morphometry 8 tool implemented in Statistical Parametric Mapping 8 and WFU PickAtlas software (Talairach brain atlas theory). The following software default settings were used as bilateral region-of-interest labels: "Frontal Lobe," "Hippocampus," "Occipital Lobe," "Orbital Gyrus," "Parietal Lobe," "Putamen," and "Temporal Lobe." Effect of scanner for cortex volumetry using the atlas-based method was reduced with DARTEL normalization compared with standard normalization in Frontal Lobe, Occipital Lobe, Orbital Gyrus, Putamen, and Temporal Lobe; was the same in Hippocampus and Parietal Lobe; and showed no increase with DARTEL normalization for any region of interest (ROI). DARTEL normalization reduces the effect of scanner, which is a major problem in multicenter studies.

Microallopatry Caused Strong Diversification in Buthus scorpions (Scorpiones: Buthidae) in the Atlas Mountains (NW Africa)

PubMed Central

Habel, Jan C.; Husemann, Martin; Schmitt, Thomas; Zachos, Frank E.; Honnen, Ann-Christin; Petersen, Britt; Parmakelis, Aristeidis; Stathi, Iasmi

2012-01-01

The immense biodiversity of the Atlas Mountains in North Africa might be the result of high rates of microallopatry caused by mountain barriers surpassing 4000 meters leading to patchy habitat distributions. We test the influence of geographic structures on the phylogenetic patterns among Buthus scorpions using mtDNA sequences. We sampled 91 individuals of the genus Buthus from 51 locations scattered around the Atlas Mountains (Antiatlas, High Atlas, Middle Atlas and Jebel Sahro). We sequenced 452 bp of the Cytochrome Oxidase I gene which proved to be highly variable within and among Buthus species. Our phylogenetic analysis yielded 12 distinct genetic groups one of which comprised three subgroups mostly in accordance with the orographic structure of the mountain systems. Main clades overlap with each other, while subclades are distributed parapatrically. Geographic structures likely acted as long-term barriers among populations causing restriction of gene flow and allowing for strong genetic differentiation. Thus, genetic structure and geographical distribution of genetic (sub)clusters follow the classical theory of allopatric differentiation where distinct groups evolve without range overlap until reproductive isolation and ecological differentiation has built up. Philopatry and low dispersal ability of Buthus scorpions are the likely causes for the observed strong genetic differentiation at this small geographic scale. PMID:22383951

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. Copyright © 2015 Elsevier Inc. All rights reserved.

An extensive assessment of network alignment algorithms for comparison of brain connectomes.

PubMed

Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario

2017-06-06

Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.

Multi atlas based segmentation: Should we prefer the best atlas group over the group of best atlases?

PubMed

Zaffino, Paolo; Ciardo, Delia; Raudaschl, Patrik; Fritscher, Karl; Ricotti, Rosalinda; Alterio, Daniela; Marvaso, Giulia; Fodor, Cristiana; Baroni, Guido; Amato, Francesco; Orecchia, Roberto; Jereczek-Fossa, Barbara Alicja; Sharp, Gregory C; Spadea, Maria Francesca

2018-05-22

Multi Atlas Based Segmentation (MABS) uses a database of atlas images, and an atlas selection process is used to choose an atlas subset for registration and voting. In the current state of the art, atlases are chosen according to a similarity criterion between the target subject and each atlas in the database. In this paper, we propose a new concept for atlas selection that relies on selecting the best performing group of atlases rather than the group of highest scoring individual atlases. Experiments were performed using CT images of 50 patients, with contours of brainstem and parotid glands. The dataset was randomly split in 2 groups: 20 volumes were used as an atlas database and 30 served as target subjects for testing. Classic oracle group selection, where atlases are chosen by the highest Dice Similarity Coefficient (DSC) with the target, was performed. This was compared to oracle Group selection, where all the combinations of atlas subgroups were considered and scored by computing DSC with the target subject. Subsequently, Convolutional Neural Networks (CNNs) were designed to predict the best group of atlases. The results were compared also with the selection strategy based on Normalized Mutual Information (NMI). Oracle group was proved to be significantly better that classic oracle selection (p<10-5). Atlas group selection led to a median±interquartile DSC of 0.740±0.084, 0.718±0.086 and 0.670±0.097 for brainstem and left/right parotid glands respectively, outperforming NMI selection 0.676±0.113, 0.632±0.104 and 0.606±0.118 (p<0.001) as well as classic oracle selection. The implemented methodology is a proof of principle that selecting the atlases by considering the performance of the entire group of atlases instead of each single atlas leads to higher segmentation accuracy, being even better then current oracle strategy. This finding opens a new discussion about the most appropriate atlas selection criterion for MABS. © 2018 Institute of Physics and Engineering in Medicine.

MMS Spacecraft Uncrated & Moved

NASA Image and Video Library

2014-10-29

Two of the observatories, the lower stack, mini-stack number 1, for NASA's Magnetospheric Multiscale Observatory, or MMS, arrive in the Building 1 airlock at the Astrotech payload processing facility in Titusville, Florida, near Kennedy Space Center. The MMS upper stack, mini-stack number 2, is scheduled to arrive in about two weeks. MMS is a Solar Terrestrial Probes mission comprising four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

MMS Uncovering of Spacecraft

NASA Image and Video Library

2014-10-30

Technicians remove the protective covering from the lower stack, mini-stack number 1, two of the observatories for NASA's Magnetospheric Multiscale Observatory, or MMS, in Building 1 D high bay at the Astrotech payload processing facility in Titusville, Florida, near Kennedy Space Center. The MMS upper stack, mini-stack number 2, is scheduled to arrive in about two weeks. MMS is a Solar Terrestrial Probes mission comprising four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

MMS Spacecraft Uncrated & Moved

NASA Image and Video Library

2014-10-29

Two of the observatories, the lower stack, mini-stack number 1, for NASA's Magnetospheric Multiscale Observatory, or MMS, roll into the Building 1 airlock at the Astrotech payload processing facility in Titusville, Florida, near Kennedy Space Center. The MMS upper stack, mini-stack number 2, is scheduled to arrive in about two weeks. MMS is a Solar Terrestrial Probes mission comprising four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

MMS Spacecraft Uncrated & Moved

NASA Image and Video Library

2014-10-29

Workers position two of the observatories, the lower stack, mini-stack number 1 for NASA's Magnetospheric Multiscale Observatory, or MMS, onto a payload dolly in the Building 2 south encapsulation bay at the Astrotech payload processing facility in Titusville, Florida, near Kennedy Space Center. The MMS upper stack, mini-stack number 2, is scheduled to arrive in about two weeks. MMS is a Solar Terrestrial Probes mission comprising four identically instrumented spacecraft that will use Earth’s magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes: magnetic reconnection, energetic particle acceleration and turbulence. Launch aboard a United Launch Alliance Atlas V rocket from Space Launch Complex 41 on Cape Canaveral Air Force Station is targeted for March 12, 2015.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

De, K; Jha, S; Klimentov, A

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 Managementmore » 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 was tested with a variety of Monte-Carlo workloads on several supercomputing platforms for ALICE and ATLAS experiments and it is in full production for the ATLAS experiment since September 2015. We will present our current accomplishments with running PanDA WMS at supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facilities infrastructure for High Energy and Nuclear Physics as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.« less

The ADAM project: a generic web interface for retrieval and display of ATLAS TDAQ information

NASA Astrophysics Data System (ADS)

Harwood, A.; Lehmann Miotto, G.; Magnoni, L.; Vandelli, W.; Savu, D.

2012-06-01

This paper describes a new approach to the visualization of information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers to the network utilization are stored in several databases for later analysis. Although the ability to view these data-sets individually is already in place, currently there is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple providers that have different structures. It is capable of aggregating and correlating the data according to user defined criteria. Finally, it visualizes the collected data using a flexible and interactive front-end web system. Structurally, the project comprises of 3 main levels of the data collection cycle: The Level 0 represents the information sources within ATLAS. These providers do not store information in a uniform fashion. The first step of the project was to define a common interface with which to expose stored data. The interface designed for the project originates from the Google Data Protocol API. The idea is to allow read-only access to data providers, through HTTP requests similar in format to the SQL query structure. This provides a standardized way to access this different information sources within ATLAS. The Level 1 can be considered the engine of the system. The primary task of the Level 1 is to gather data from multiple data sources via the common interface, to correlate this data together, or over a defined time series, and expose the combined data as a whole to the Level 2 web interface. The Level 2 is designed to present the data in a similar style and aesthetic, despite the different data sources. Pages can be constructed, edited and personalized by users to suit the specific data being shown. Pages can show a collection of graphs displaying data potentially coming from multiple sources. The project as a whole has a great amount of scope thanks to the uniform approach chosen for exposing data, and the flexibility of the Level 2 in presenting results. The paper will describe in detail the design and implementation of this new tool. In particular we will go through the project architecture, the implementation choices and the examples of usage of the system in place within the ATLAS TDAQ infrastructure.

ATLAS jet trigger update for the LHC run II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delgado, A. T.

The CERN Large Hadron Collider is the biggest and most powerful particle collider ever built. It produces up to 40 million proton-proton collisions per second at unprecedented energies to explore the fundamental laws and properties of Nature. The ATLAS experiment is one of the detectors that analyses and records these collisions. It generates dozens of GB/s of data that has to be reduced before it can be permanently stored, the event selection is made by the ATLAS trigger system, which reduces the data volume by a factor of 105. The trigger system has to be highly configurable in order tomore » adapt to changing running conditions and maximize the physics output whilst keeping the output rate under control. A particularly interesting pattern generated during collisions consists of a collimated spray of particles, known as a hadronic jet. To retain the interesting jets and efficiently reject the overwhelming background, optimal jet energy resolution is needed. Therefore the Jet trigger software requires CPU-intensive reconstruction algorithms. In order to reduce the resources needed for the reconstruction step, a partial detector readout scheme was developed, which effectively suppresses the low activity regions of the calorimeter. In this paper we describe the overall ATLAS trigger software, and the jet trigger in particular, along with the improvements made on the system. We then focus on detailed studies of the algorithm timing and the performance impact of the full and partial calorimeter readout schemes. We conclude with an outlook of the jet trigger plans for the next LHC data-taking period. (authors)« less

EnviroAtlas - Austin, TX - Atlas Area Boundary

EPA Pesticide Factsheets

This EnviroAtlas dataset shows the boundary of the Austin, TX Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area.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).

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.

Mirror denudation pattern on both sides of the Central Atlantic - a trace of the Pangea break-up?

NASA Astrophysics Data System (ADS)

Ruiz, G.; Saddiqi, O.; Sebti, S.; Negro, F.; Stuart, F.; Foeken, J.; Frizon de Lamotte, D.; Kramers, J.

2009-04-01

The target area of this project is the WSW- ENE oriented intra-continental Atlas chain in Morocco located between the West Africa Craton and the Betic-Rif system. It is a key natural laboratory because it 1) is the southernmost expression of Alpine deformation in Africa, and 2) encompasses Pre-Cambrian to recent evolution of the region. The presence of high surface elevations today in the High-Atlas (>4000m) and Anti-Atlas (>2500m) to the south is subject to discussions because there is little quantitative data available at present. Phases of uplift are thus ill constrained as places where the associated erosion products were accumulated. To better constrain the most recent orogenic growth of the Atlas chain, we selected a section located to the SW of Morocco, and investigated the time-Temperature paths from the different morpho-structural domains using low-temperature thermochronology analyses. These are Fission-Track analysis on Apatite (120-60°C), Zircon (270-210°C) and U-Th/He analysis still on Apatite (80-45°C) and Zircon (200-170°C) minerals. Results are much contrasted from one domain to the other: Pre-Cambrian bedrocks from the Anti-Atlas domain yield old thermochronological Fission-Track ages on zircon (380-300 Ma) and apatite (180-120 Ma) minerals that are associated with slightly younger (U-Th)/He ages on apatite (150-110 Ma). U-Th/He ages on apatite from the High-Atlas are much younger (~35-5 Ma) with a clear alpine signature. Apatite Fission-Track ages from the Meseta region further north are also relatively old ranging between 200 and 140 Ma. We here concentrate on the interpretation of old thermochronological ages from the Meseta and Anti-Atlas regions leaving the Alpine signal for another contribution. There are two direct, possibly inter fingering, interpretations for the preservation of such old thermal record in the Anti-Atlas and Meseta regions. First they remained "stable" being unaffected by 'Alpine' deformation that took place in the High-Atlas. Second, they are being affected "now" but no level with such record is yet exposed. Thermal modelling was performed to decipher between the 2 scenarios using our new thermochronological and available geological constraints. Models suggest that the first scenario is most likely with a clear Triassic to Late Jurassic phase of heating until ~100-90°C that was followed by a phase of cooling until the Middle Cretaceous. These results suggest that the Meseta was buried by a 2-3 kilometres thick sedimentary pile until ~180 Ma and as a result that the concept of a topographic high limiting the Tethysian from the Atlantic has to be reconsidered. Further, denudation patterns from the mirror image of the Atlas system on the other side of the Atlantic ocean are almost identical (Grist and Zentilli, 2003) suggesting that the patterns we constrained for the Triassic until Middle Cretaceous in SW Morocco have to be related to the break-up of the Pangea and oceanization in the Central Atlantic from ~180 Ma.

InSight Atlas V Booster Transport

NASA Image and Video Library

2018-03-02

A United Launch Alliance Atlas V booster is transported to Space Launch Complex 3 at Vandenberg Air Force Base in California. The rocket will launch NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff is scheduled for May 5, 2018.

InSight Atlas V LVOS

NASA Image and Video Library

2018-03-03

A crane lifts a United Launch Alliance Atlas V booster at Space Launch Complex 3 at Vandenberg Air Force Base in California. The rocket will launch NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff is scheduled for May 5, 2018.

InSight Atlas V Fairing Arrival, Offload, and Unbagging

NASA Image and Video Library

2018-01-31

The United Launch Alliance (ULA) payload fairing for NASA's upcoming Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, mission to land on Mars arrives at Vandenberg Air Force Base in California. InSight is the first mission to explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth. Liftoff atop a ULA Atlas V rocket is scheduled for May 5, 2018.

Development, Validation and Integration of the ATLAS Trigger System Software in Run 2

NASA Astrophysics Data System (ADS)

Keyes, Robert; ATLAS Collaboration

2017-10-01

The trigger system of the ATLAS detector at the LHC is a combination of hardware, firmware, and software, associated to various sub-detectors that must seamlessly cooperate in order to select one collision of interest out of every 40,000 delivered by the LHC every millisecond. These proceedings discuss the challenges, organization and work flow of the ongoing trigger software development, validation, and deployment. The goal of this development is to ensure that the most up-to-date algorithms are used to optimize the performance of the experiment. The goal of the validation is to ensure the reliability and predictability of the software performance. Integration tests are carried out to ensure that the software deployed to the online trigger farm during data-taking run as desired. Trigger software is validated by emulating online conditions using a benchmark run and mimicking the reconstruction that occurs during normal data-taking. This exercise is computationally demanding and thus runs on the ATLAS high performance computing grid with high priority. Performance metrics ranging from low-level memory and CPU requirements, to distributions and efficiencies of high-level physics quantities are visualized and validated by a range of experts. This is a multifaceted critical task that ties together many aspects of the experimental effort and thus directly influences the overall performance of the ATLAS experiment.

Increased-resolution OCT thickness mapping of the human macula: a statistically based registration.

PubMed

Bernardes, Rui; Santos, Torcato; Cunha-Vaz, José

2008-05-01

To describe the development of a technique that enhances spatial resolution of retinal thickness maps of the Stratus OCT (Carl Zeiss Meditec, Inc., Dublin, CA). A retinal thickness atlas (RT-atlas) template was calculated, and a macular coordinate system was established, to pursue this objective. The RT-atlas was developed from principal component analysis of retinal thickness analyzer (RTA) maps acquired from healthy volunteers. The Stratus OCT radial thickness measurements were registered on the RT-atlas, from which an improved macular thickness map was calculated. Thereafter, Stratus OCT circular scans were registered on the previously calculated map to enhance spatial resolution. The developed technique was applied to Stratus OCT thickness data from healthy volunteers and from patients with diabetic retinopathy (DR) or age-related macular degeneration (AMD). Results showed that for normal, or close to normal, macular thickness maps from healthy volunteers and patients with DR, this technique can be an important aid in determining retinal thickness. Efforts are under way to improve the registration of retinal thickness data in patients with AMD. The developed technique enhances the evaluation of data acquired by the Stratus OCT, helping the detection of early retinal thickness abnormalities. Moreover, a normative database of retinal thickness measurements gained from this technique, as referenced to the macular coordinate system, can be created without errors induced by missed fixation and eye tilt.

Complex terrain experiments in the New European Wind Atlas.

PubMed

Mann, J; Angelou, N; Arnqvist, J; Callies, D; Cantero, E; Arroyo, R Chávez; Courtney, M; Cuxart, J; Dellwik, E; Gottschall, J; Ivanell, S; Kühn, P; Lea, G; Matos, J C; Palma, J M L M; Pauscher, L; Peña, A; Rodrigo, J Sanz; Söderberg, S; Vasiljevic, N; Rodrigues, C Veiga

2017-04-13

The New European Wind Atlas project will create a freely accessible wind atlas covering Europe and Turkey, develop the model chain to create the atlas and perform a series of experiments on flow in many different kinds of complex terrain to validate the models. This paper describes the experiments of which some are nearly completed while others are in the planning stage. All experiments focus on the flow properties that are relevant for wind turbines, so the main focus is the mean flow and the turbulence at heights between 40 and 300 m. Also extreme winds, wind shear and veer, and diurnal and seasonal variations of the wind are of interest. Common to all the experiments is the use of Doppler lidar systems to supplement and in some cases replace completely meteorological towers. Many of the lidars will be equipped with scan heads that will allow for arbitrary scan patterns by several synchronized systems. Two pilot experiments, one in Portugal and one in Germany, show the value of using multiple synchronized, scanning lidar, both in terms of the accuracy of the measurements and the atmospheric physical processes that can be studied. The experimental data will be used for validation of atmospheric flow models and will by the end of the project be freely available.This article is part of the themed issue 'Wind energy in complex terrains'. © 2017 The Authors.

Complex terrain experiments in the New European Wind Atlas

PubMed Central

Angelou, N.; Callies, D.; Cantero, E.; Arroyo, R. Chávez; Courtney, M.; Cuxart, J.; Dellwik, E.; Gottschall, J.; Ivanell, S.; Kühn, P.; Lea, G.; Matos, J. C.; Palma, J. M. L. M.; Peña, A.; Rodrigo, J. Sanz; Söderberg, S.; Vasiljevic, N.; Rodrigues, C. Veiga

2017-01-01

The New European Wind Atlas project will create a freely accessible wind atlas covering Europe and Turkey, develop the model chain to create the atlas and perform a series of experiments on flow in many different kinds of complex terrain to validate the models. This paper describes the experiments of which some are nearly completed while others are in the planning stage. All experiments focus on the flow properties that are relevant for wind turbines, so the main focus is the mean flow and the turbulence at heights between 40 and 300 m. Also extreme winds, wind shear and veer, and diurnal and seasonal variations of the wind are of interest. Common to all the experiments is the use of Doppler lidar systems to supplement and in some cases replace completely meteorological towers. Many of the lidars will be equipped with scan heads that will allow for arbitrary scan patterns by several synchronized systems. Two pilot experiments, one in Portugal and one in Germany, show the value of using multiple synchronized, scanning lidar, both in terms of the accuracy of the measurements and the atmospheric physical processes that can be studied. The experimental data will be used for validation of atmospheric flow models and will by the end of the project be freely available. This article is part of the themed issue ‘Wind energy in complex terrains’. PMID:28265025

Multi-Atlas-Based Attenuation Correction for Brain 18F-FDG PET Imaging Using a Time-of-Flight PET/MR Scanner: Comparison with Clinical Single-Atlas- and CT-Based Attenuation Correction.

PubMed

Sekine, Tetsuro; Burgos, Ninon; Warnock, Geoffrey; Huellner, Martin; Buck, Alfred; Ter Voert, Edwin E G W; Cardoso, M Jorge; Hutton, Brian F; Ourselin, Sebastien; Veit-Haibach, Patrick; Delso, Gaspar

2016-08-01

In this work, we assessed the feasibility of attenuation correction (AC) based on a multi-atlas-based method (m-Atlas) by comparing it with a clinical AC method (single-atlas-based method [s-Atlas]), on a time-of-flight (TOF) PET/MRI scanner. We enrolled 15 patients. The median patient age was 59 y (age range, 31-80). 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/MRI scan of the head (no additional tracer being injected). For each patient, 3 AC maps were generated. Both s-Atlas and m-Atlas AC maps were generated from the same patient-specific LAVA-Flex T1-weighted images being acquired by default on the PET/MRI scanner during the first 18 s of the PET scan. An s-Atlas AC map was extracted by the PET/MRI scanner, and an m-Atlas AC map was created using a Web service tool that automatically generates m-Atlas pseudo-CT images. For comparison, the AC map generated by PET/CT was registered and used as a gold standard. PET images were reconstructed from raw data on the TOF PET/MRI 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 (%diff) and absolute differences (|%diff|) between images based on each atlas AC and CT-AC were calculated. (18)F-FDG uptake in all VOIs and generalized merged VOIs were compared using the paired t test and Bland-Altman test. The range of error on m-Atlas in all 1,005 VOIs was -4.99% to 4.09%. The |%diff| on the m-Atlas was improved by about 20% compared with s-Atlas (s-Atlas vs. m-Atlas: 1.49% ± 1.06% vs. 1.21% ± 0.89%, P < 0.01). In generalized VOIs, %diff on m-Atlas in the temporal lobe and cerebellum was significantly smaller (s-Atlas vs. m-Atlas: temporal lobe, 1.49% ± 1.37% vs. -0.37% ± 1.41%, P < 0.01; cerebellum, 1.55% ± 1.97% vs. -1.15% ± 1.72%, P < 0.01). The errors introduced using either s-Atlas or m-Atlas did not exceed 5% in any brain region investigated. When compared with the clinical s-Atlas, m-Atlas is more accurate, especially in regions close to the skull base. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-02-11

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

Keeping Current and Increasing The Effectiveness of the Decision-Making Process and the Interoperability in the Digital Age: Geospatial Intelligence and Geospatial Information Systems’ Applications in the Military and Intelligence Fields for the Mexican Navy

DTIC Science & Technology

2008-12-01

Guide, 3rd ed. (London; Thousand Oaks, Calif: Sage Publications, 1999), 228, http://www.loc.gov/catdir/ toc /fy042/99214121.html; (accessed date 6/25...analysis in the GEOINT context is the Sistema Nacional de Seguridad Pública, SNSP (National System of Public Security) with the implementation of the...named Sistema de Información Geográfica del Atlas Nacional de Riesgos (GIS national risk atlas) that is under the “direction of research” of that

Acquisition/expulsion system for earth orbital propulsion system study. Volume 4: Flight test article

NASA Technical Reports Server (NTRS)

1973-01-01

Two orbital test plans were prepared to verify one of the passive cryogenic storage tank/feedline candidate designs. One plan considered the orbital test article to be launched as a dedicated payload using an Atlas F burner launching configuration. The second plan proposed to launch the orbital test article as a secondary payload on the Titan E/Centaur proof flight. The secondary payload concept was pursued until January 1973, when work to build the hardware for this phase of the contract was terminated for lack of a sponsor for the flight. The dedicated payload launched on an Atlas F is described.

The Error Reporting in the ATLAS TDAQ System

NASA Astrophysics Data System (ADS)

Kolos, Serguei; Kazarov, Andrei; Papaevgeniou, Lykourgos

2015-05-01

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

Trigger readout electronics upgrade for the ATLAS Liquid Argon Calorimeters

NASA Astrophysics Data System (ADS)

Dinkespiler, B.

2017-09-01

The upgrade of the Large Hadron Collider (LHC) scheduled for the 2019-2020 shut-down period, referred to as Phase-I upgrade, will increase the instantaneous luminosity to about three times the design value. Since the current ATLAS trigger system does not allow sufficient increase of the trigger rate, an improvement of the trigger system is required. The Liquid Argon (LAr) Calorimeter read-out will therefore be modified to deliver digital trigger signals with a higher spatial granularity in order to improve the identification efficiencies of electrons, photons, tau, jets and missing energy, at high background rejection rates at the Level-1 trigger. The new trigger signals will be arranged in 34000 so-called Super Cells which achieves 5-10 times better granularity than the trigger towers currently used and allows an improved background rejection. The readout of the trigger signals will process the signal of the Super Cells at every LHC bunch-crossing at 12-bit precision and a frequency of 40 MHz. The data will be transmitted to the Back End using a custom serializer and optical converter and 5.12 Gb/s optical links. In order to verify the full functionality of the future Liquid Argon trigger system, a demonstrator set-up has been installed on the ATLAS detector and is operated in parallel to the regular ATLAS data taking during the LHC Run-2 in 2015 and 2016. Noise level and linearity on the energy measurement have been verified to be within our requirements. In addition, we have collected data from 13 TeV proton collisions during the LHC 2015 and 2016 runs, and have observed real pulses from the detector through the demonstrator system. The talk will give an overview of the Phase-I Upgrade of the ATLAS Liquid Argon Calorimeter readout and present the custom developed hardware including their role in real-time data processing and fast data transfer. This contribution will also report on the performance of the newly developed ASICs including their radiation tolerance and on the performance of the prototype boards in the demonstrator system based on various measurements with the 13 TeV collision data. Results of the high-speed link test with the prototypes of the final electronic boards will be also reported.

High-Throughput Study of Diffusion and Phase Transformation Kinetics of Magnesium-Based Systems for Automotive Cast Magnesium Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Alan A; Zhao, Ji-Cheng; Riggi, Adrienne

The objective of the proposed study is to establish a scientific foundation on kinetic modeling of diffusion, phase precipitation, and casting/solidification, in order to accelerate the design and optimization of cast magnesium (Mg) alloys for weight reduction of U.S. automotive fleet. The team has performed the following tasks: 1) study diffusion kinetics of various Mg-containing binary systems using high-throughput diffusion multiples to establish reliable diffusivity and mobility databases for the Mg-aluminum (Al)-zinc (Zn)-tin (Sn)-calcium (Ca)-strontium (Sr)-manganese (Mn) systems; 2) study the precipitation kinetics (nucleation, growth and coarsening) using both innovative dual-anneal diffusion multiples and cast model alloys to provide largemore » amounts of kinetic data (including interfacial energy) and microstructure atlases to enable implementation of the Kampmann-Wagner numerical model to simulate phase transformation kinetics of non-spherical/non-cuboidal precipitates in Mg alloys; 3) implement a micromodel to take into account back diffusion in the solid phase in order to predict microstructure and microsegregation in multicomponent Mg alloys during dendritic solidification especially under high pressure die-casting (HPDC) conditions; and, 4) widely disseminate the data, knowledge and information using the Materials Genome Initiative infrastructure (http://www.mgidata.org) as well as publications and digital data sharing to enable researchers to identify new pathways/routes to better cast Mg alloys.« less

FELIX: a PCIe based high-throughput approach for interfacing front-end and trigger electronics in the ATLAS Upgrade framework

NASA Astrophysics Data System (ADS)

Anderson, J.; Bauer, K.; Borga, A.; Boterenbrood, H.; Chen, H.; Chen, K.; Drake, G.; Dönszelmann, M.; Francis, D.; Guest, D.; Gorini, B.; Joos, M.; Lanni, F.; Lehmann Miotto, G.; Levinson, L.; Narevicius, J.; Panduro Vazquez, W.; Roich, A.; Ryu, S.; Schreuder, F.; Schumacher, J.; Vandelli, W.; Vermeulen, J.; Whiteson, D.; Wu, W.; Zhang, J.

2016-12-01

The ATLAS Phase-I upgrade (2019) requires a Trigger and Data Acquisition (TDAQ) system able to trigger and record data from up to three times the nominal LHC instantaneous luminosity. The Front-End LInk eXchange (FELIX) system provides an infrastructure to achieve this in a scalable, detector agnostic and easily upgradeable way. It is a PC-based gateway, interfacing custom radiation tolerant optical links from front-end electronics, via PCIe Gen3 cards, to a commodity switched Ethernet or InfiniBand network. FELIX enables reducing custom electronics in favour of software running on commercial servers. The FELIX system, the design of the PCIe prototype card and the integration test results are presented in this paper.

A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

NASA Astrophysics Data System (ADS)

Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

2014-03-01

The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

A Complete UV Atlas of Standard Stars

NASA Technical Reports Server (NTRS)

Wu, Chi-Chao

2000-01-01

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

KSC-2012-6187

NASA Image and Video Library

2012-11-05

CAPE CANAVERAL, Fla. -- A Ukrainian Antonov-124 transport aircraft arrives at Cape Canaveral Air Force Station in Florida with the first stage of the Atlas V rocket that will carry the Tracking and Data Relay Satellite, TDRS-K, into orbit. The booster stage, arriving from the United Launch Alliance manufacturing plant in Decatur, Ala., will be taken to the hangar at the Atlas Spaceflight Operations Center at Cape Canaveral. Launch of the TDRS-K on the Atlas V rocket is planned for January 2013 from Space Launch Complex 41. The TDRS-K spacecraft is part of the next-generation series in the Tracking and Data Relay Satellite System, a constellation of space-based communication satellites providing tracking, telemetry, command and high-bandwidth data return services. For more information, visit http://tdrs.gsfc.nasa.gov/. Photo credit: NASA/Tim Jacobs

Atlas of susceptibility to pollution in marinas. Application to the Spanish coast.

PubMed

Gómez, Aina G; Ondiviela, Bárbara; Fernández, María; Juanes, José A

2017-01-15

An atlas of susceptibility to pollution of 320 Spanish marinas is provided. Susceptibility is assessed through a simple, fast and low cost empirical method estimating the flushing capacity of marinas. The Complexity Tidal Range Index (CTRI) was selected among eleven empirical methods. The CTRI method was selected by means of statistical analyses because: it contributes to explain the system's variance; it is highly correlated to numerical model results; and, it is sensitive to marinas' location and typology. The process of implementation to the Spanish coast confirmed its usefulness, versatility and adaptability as a tool for the environmental management of marinas worldwide. The atlas of susceptibility, assessed through CTRI values, is an appropriate instrument to prioritize environmental and planning strategies at a regional scale. Copyright © 2016 Elsevier Ltd. All rights reserved.

Charge collection and field profile studies of heavily irradiated strip sensors for the ATLAS inner tracker upgrade

NASA Astrophysics Data System (ADS)

Hara, K.; Allport, P. P.; Baca, M.; Broughton, J.; Chisholm, A.; Nikolopoulos, K.; Pyatt, S.; Thomas, J. P.; Wilson, J. A.; Kierstead, J.; Kuczewski, P.; Lynn, D.; Arratia, M.; Hommels, L. B. A.; Ullan, M.; Bloch, I.; Gregor, I. M.; Tackmann, K.; Trofimov, A.; Yildirim, E.; Hauser, M.; Jakobs, K.; Kuehn, S.; Mahboubi, K.; Mori, R.; Parzefall, U.; Clark, A.; Ferrere, D.; Gonzalez Sevilla, S.; Ashby, J.; Blue, A.; Bates, R.; Buttar, C.; Doherty, F.; McMullen, T.; McEwan, F.; O'Shea, V.; Kamada, S.; Yamamura, K.; Ikegami, Y.; Nakamura, K.; Takubo, Y.; Unno, Y.; Takashima, R.; Chilingarov, A.; Fox, H.; Affolder, A. A.; Casse, G.; Dervan, P.; Forshaw, D.; Greenall, A.; Wonsak, S.; Wormald, M.; Cindro, V.; Kramberger, G.; Mandić, I.; Mikuž, M.; Gorelov, I.; Hoeferkamp, M.; Palni, P.; Seidel, S.; Taylor, A.; Toms, K.; Wang, R.; Hessey, N. P.; Valencic, N.; Hanagaki, K.; Dolezal, Z.; Kodys, P.; Bohm, J.; Mikestikova, M.; Bevan, A.; Beck, G.; Milke, C.; Domingo, M.; Fadeyev, V.; Galloway, Z.; Hibbard-Lubow, D.; Liang, Z.; Sadrozinski, H. F.-W.; Seiden, A.; To, K.; French, R.; Hodgson, P.; Marin-Reyes, H.; Parker, K.; Jinnouchi, O.; Hara, K.; Sato, K.; Sato, K.; Hagihara, M.; Iwabuchi, S.; Bernabeu, J.; Civera, J. V.; Garcia, C.; Lacasta, C.; Marti i. Garcia, S.; Rodriguez, D.; Santoyo, D.; Solaz, C.; Soldevila, U.

2016-09-01

The ATLAS group has evaluated the charge collection in silicon microstrip sensors irradiated up to a fluence of 1 ×1016 neq/cm2, exceeding the maximum of 1.6 ×1015 neq/cm2 expected for the strip tracker during the high luminosity LHC (HL-LHC) period including a safety factor of 2. The ATLAS12, n+-on-p type sensor, which is fabricated by Hamamatsu Photonics (HPK) on float zone (FZ) substrates, is the latest barrel sensor prototype. The charge collection from the irradiated 1×1 cm2 barrel test sensors has been evaluated systematically using penetrating β-rays and an Alibava readout system. The data obtained at different measurement sites are compared with each other and with the results obtained from the previous ATLAS07 design. The results are very consistent, in particular, when the deposit charge is normalized by the sensor's active thickness derived from the edge transient current technique (edge-TCT) measurements. The measurements obtained using β-rays are verified to be consistent with the measurements using an electron beam. The edge-TCT is also effective for evaluating the field profiles across the depth. The differences between the irradiated ATLAS07 and ATLAS12 samples have been examined along with the differences among the samples irradiated with different radiation sources: neutrons, protons, and pions. The studies of the bulk properties of the devices show that the devices can yield a sufficiently large signal for the expected fluence range in the HL-LHC, thereby acting as precision tracking sensors.

Atlas-guided cluster analysis of large tractography datasets.

PubMed

Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

2013-01-01

Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment.

Segmenting the thoracic, abdominal and pelvic musculature on CT scans combining atlas-based model and active contour model

NASA Astrophysics Data System (ADS)

Zhang, Weidong; Liu, Jiamin; Yao, Jianhua; Summers, Ronald M.

2013-03-01

Segmentation of the musculature is very important for accurate organ segmentation, analysis of body composition, and localization of tumors in the muscle. In research fields of computer assisted surgery and computer-aided diagnosis (CAD), muscle segmentation in CT images is a necessary pre-processing step. This task is particularly challenging due to the large variability in muscle structure and the overlap in intensity between muscle and internal organs. This problem has not been solved completely, especially for all of thoracic, abdominal and pelvic regions. We propose an automated system to segment the musculature on CT scans. The method combines an atlas-based model, an active contour model and prior segmentation of fat and bones. First, body contour, fat and bones are segmented using existing methods. Second, atlas-based models are pre-defined using anatomic knowledge at multiple key positions in the body to handle the large variability in muscle shape. Third, the atlas model is refined using active contour models (ACM) that are constrained using the pre-segmented bone and fat. Before refining using ACM, the initialized atlas model of next slice is updated using previous atlas. The muscle is segmented using threshold and smoothed in 3D volume space. Thoracic, abdominal and pelvic CT scans were used to evaluate our method, and five key position slices for each case were selected and manually labeled as the reference. Compared with the reference ground truth, the overlap ratio of true positives is 91.1%+/-3.5%, and that of false positives is 5.5%+/-4.2%.

Development of representative magnetic resonance imaging-based atlases of the canine brain and evaluation of three methods for atlas-based segmentation.

PubMed

Milne, Marjorie E; Steward, Christopher; Firestone, Simon M; Long, Sam N; O'Brien, Terrence J; Moffat, Bradford A

2016-04-01

To develop representative MRI atlases of the canine brain and to evaluate 3 methods of atlas-based segmentation (ABS). 62 dogs without clinical signs of epilepsy and without MRI evidence of structural brain disease. The MRI scans from 44 dogs were used to develop 4 templates on the basis of brain shape (brachycephalic, mesaticephalic, dolichocephalic, and combined mesaticephalic and dolichocephalic). Atlas labels were generated by segmenting the brain, ventricular system, hippocampal formation, and caudate nuclei. The MRI scans from the remaining 18 dogs were used to evaluate 3 methods of ABS (manual brain extraction and application of a brain shape-specific template [A], automatic brain extraction and application of a brain shape-specific template [B], and manual brain extraction and application of a combined template [C]). The performance of each ABS method was compared by calculation of the Dice and Jaccard coefficients, with manual segmentation used as the gold standard. Method A had the highest mean Jaccard coefficient and was the most accurate ABS method assessed. Measures of overlap for ABS methods that used manual brain extraction (A and C) ranged from 0.75 to 0.95 and compared favorably with repeated measures of overlap for manual extraction, which ranged from 0.88 to 0.97. Atlas-based segmentation was an accurate and repeatable method for segmentation of canine brain structures. It could be performed more rapidly than manual segmentation, which should allow the application of computer-assisted volumetry to large data sets and clinical cases and facilitate neuroimaging research and disease diagnosis.

Localized-atlas-based segmentation of breast MRI in a decision-making framework.

PubMed

Fooladivanda, Aida; Shokouhi, Shahriar B; Ahmadinejad, Nasrin

2017-03-01

Breast-region segmentation is an important step for density estimation and Computer-Aided Diagnosis (CAD) systems in Magnetic Resonance Imaging (MRI). Detection of breast-chest wall boundary is often a difficult task due to similarity between gray-level values of fibroglandular tissue and pectoral muscle. This paper proposes a robust breast-region segmentation method which is applicable for both complex cases with fibroglandular tissue connected to the pectoral muscle, and simple cases with high contrast boundaries. We present a decision-making framework based on geometric features and support vector machine (SVM) to classify breasts in two main groups, complex and simple. For complex cases, breast segmentation is done using a combination of intensity-based and atlas-based techniques; however, only intensity-based operation is employed for simple cases. A novel atlas-based method, that is called localized-atlas, accomplishes the processes of atlas construction and registration based on the region of interest (ROI). Atlas-based segmentation is performed by relying on the chest wall template. Our approach is validated using a dataset of 210 cases. Based on similarity between automatic and manual segmentation results, the proposed method achieves Dice similarity coefficient, Jaccard coefficient, total overlap, false negative, and false positive values of 96.3, 92.9, 97.4, 2.61 and 4.77%, respectively. The localization error of the breast-chest wall boundary is 1.97 mm, in terms of averaged deviation distance. The achieved results prove that the suggested framework performs the breast segmentation with negligible errors and efficient computational time for different breasts from the viewpoints of size, shape, and density pattern.

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.