A database of aerothermal measurements in hypersonic flow for CFD validation

NASA Technical Reports Server (NTRS)

Holden, M. S.; Moselle, J. R.

1992-01-01

This paper presents an experimental database selected and compiled from aerothermal measurements obtained on basic model configurations on which fundamental flow phenomena could be most easily examined. The experimental studies were conducted in hypersonic flows in 48-inch, 96-inch, and 6-foot shock tunnels. A special computer program was constructed to provide easy access to the measurements in the database as well as the means to plot the measurements and compare them with imported data. The database contains tabulations of model configurations, freestream conditions, and measurements of heat transfer, pressure, and skin friction for each of the studies selected for inclusion. The first segment contains measurements in laminar flow emphasizing shock-wave boundary-layer interaction. In the second segment, measurements in transitional flows over flat plates and cones are given. The third segment comprises measurements in regions of shock-wave/turbulent-boundary-layer interactions. Studies of the effects of surface roughness of nosetips and conical afterbodies are presented in the fourth segment of the database. Detailed measurements in regions of shock/shock boundary layer interaction are contained in the fifth segment. Measurements in regions of wall jet and transpiration cooling are presented in the final two segments.

Monitoring service for the Gran Telescopio Canarias control system

NASA Astrophysics Data System (ADS)

Huertas, Manuel; Molgo, Jordi; Macías, Rosa; Ramos, Francisco

2016-07-01

The Monitoring Service collects, persists and propagates the Telescope and Instrument telemetry, for the Gran Telescopio CANARIAS (GTC), an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). A new version of the Monitoring Service has been developed in order to improve performance, provide high availability, guarantee fault tolerance and scalability to cope with high volume of data. The architecture is based on a distributed in-memory data store with a Product/Consumer pattern design. The producer generates the data samples. The consumers either persists the samples to a database for further analysis or propagates them to the consoles in the control room to monitorize the state of the whole system.

RADS Version 4: An Efficient Way to Analyse the Multi-Mission Altimeter Database

NASA Astrophysics Data System (ADS)

Scharroo, Remko; Leuliette, Eric; Naeije, Marc; Martin-Puig, Cristina; Pires, Nelson

2016-08-01

The Radar Altimeter Database System (RADS) has grown to become a mature altimeter database. Over the last 18 years it is continuously being developed, first at Delft University of Technology, now also at the National Oceanic and Atmospheric Administration (NOAA) and the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT).RADS now serves as a fundamental Climate Data Record for sea level. Because of the multiple users involved in vetting the data and the regular updates to the database, RADS is one of the most accurate and complete databases of satellite altimeter data around.RADS version 4 is a major change from the previous version. While the database is compatible with both software versions, the new software provides new tools, allows easier expansion, and has a better and more standardised interface.

IAU MDC Photographic Meteor Orbits Database: Version 2013

NASA Astrophysics Data System (ADS)

Neslušan, L.; Porubčan, V.; Svoreň, J.

2014-05-01

A new 2013 version of the IAU MDC photographic meteor orbits database which is an upgrade of the current 2003 version (Lindblad et al. 2003, EMP 93:249-260) is presented. To the 2003 version additional 292 orbits are added, thus the new version of the database consists of 4,873 meteors with their geophysical and orbital parameters compiled in 41 catalogues. For storing the data, a new format enabling a more simple treatment with the parameters, including the errors of their determination is applied. The data can be downloaded from the IAU MDC web site: http://www.astro.sk/IAUMDC/Ph2013/

Poly-Pattern Compressive Segmentation of ASTER Data for GIS

NASA Technical Reports Server (NTRS)

Myers, Wayne; Warner, Eric; Tutwiler, Richard

2007-01-01

Pattern-based segmentation of multi-band image data, such as ASTER, produces one-byte and two-byte approximate compressions. This is a dual segmentation consisting of nested coarser and finer level pattern mappings called poly-patterns. The coarser A-level version is structured for direct incorporation into geographic information systems in the manner of a raster map. GIs renderings of this A-level approximation are called pattern pictures which have the appearance of color enhanced images. The two-byte version consisting of thousands of B-level segments provides a capability for approximate restoration of the multi-band data in selected areas or entire scenes. Poly-patterns are especially useful for purposes of change detection and landscape analysis at multiple scales. The primary author has implemented the segmentation methodology in a public domain software suite.

D GIS for Flood Modelling in River Valleys

NASA Astrophysics Data System (ADS)

Tymkow, P.; Karpina, M.; Borkowski, A.

2016-06-01

The objective of this study is implementation of system architecture for collecting and analysing data as well as visualizing results for hydrodynamic modelling of flood flows in river valleys using remote sensing methods, tree-dimensional geometry of spatial objects and GPU multithread processing. The proposed solution includes: spatial data acquisition segment, data processing and transformation, mathematical modelling of flow phenomena and results visualization. Data acquisition segment was based on aerial laser scanning supplemented by images in visible range. Vector data creation was based on automatic and semiautomatic algorithms of DTM and 3D spatial features modelling. Algorithms for buildings and vegetation geometry modelling were proposed or adopted from literature. The implementation of the framework was designed as modular software using open specifications and partially reusing open source projects. The database structure for gathering and sharing vector data, including flood modelling results, was created using PostgreSQL. For the internal structure of feature classes of spatial objects in a database, the CityGML standard was used. For the hydrodynamic modelling the solutions of Navier-Stokes equations in two-dimensional version was implemented. Visualization of geospatial data and flow model results was transferred to the client side application. This gave the independence from server hardware platform. A real-world case in Poland, which is a part of Widawa River valley near Wroclaw city, was selected to demonstrate the applicability of proposed system.

Integrating segmentation methods from the Insight Toolkit into a visualization application.

PubMed

Martin, Ken; Ibáñez, Luis; Avila, Lisa; Barré, Sébastien; Kaspersen, Jon H

2005-12-01

The Insight Toolkit (ITK) initiative from the National Library of Medicine has provided a suite of state-of-the-art segmentation and registration algorithms ideally suited to volume visualization and analysis. A volume visualization application that effectively utilizes these algorithms provides many benefits: it allows access to ITK functionality for non-programmers, it creates a vehicle for sharing and comparing segmentation techniques, and it serves as a visual debugger for algorithm developers. This paper describes the integration of image processing functionalities provided by the ITK into VolView, a visualization application for high performance volume rendering. A free version of this visualization application is publicly available and is available in the online version of this paper. The process for developing ITK plugins for VolView according to the publicly available API is described in detail, and an application of ITK VolView plugins to the segmentation of Abdominal Aortic Aneurysms (AAAs) is presented. The source code of the ITK plugins is also publicly available and it is included in the online version.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

NASA Astrophysics Data System (ADS)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

Automatic lung nodule graph cuts segmentation with deep learning false positive reduction

NASA Astrophysics Data System (ADS)

Sun, Wenqing; Huang, Xia; Tseng, Tzu-Liang Bill; Qian, Wei

2017-03-01

To automatic detect lung nodules from CT images, we designed a two stage computer aided detection (CAD) system. The first stage is graph cuts segmentation to identify and segment the nodule candidates, and the second stage is convolutional neural network for false positive reduction. The dataset contains 595 CT cases randomly selected from Lung Image Database Consortium and Image Database Resource Initiative (LIDC/IDRI) and the 305 pulmonary nodules achieved diagnosis consensus by all four experienced radiologists were our detection targets. Consider each slice as an individual sample, 2844 nodules were included in our database. The graph cuts segmentation was conducted in a two-dimension manner, 2733 lung nodule ROIs are successfully identified and segmented. With a false positive reduction by a seven-layer convolutional neural network, 2535 nodules remain detected while the false positive dropped to 31.6%. The average F-measure of segmented lung nodule tissue is 0.8501.

NASA Tech Briefs, September 2006

NASA Technical Reports Server (NTRS)

2006-01-01

Topics covered include: Improving Thermomechanical Properties of SiC/SiC Composites; Aerogel/Particle Composites for Thermoelectric Devices; Patches for Repairing Ceramics and Ceramic- Matrix Composites; Lower-Conductivity Ceramic Materials for Thermal-Barrier Coatings; An Alternative for Emergency Preemption of Traffic Lights; Vehicle Transponder for Preemption of Traffic Lights; Automated Announcements of Approaching Emergency Vehicles; Intersection Monitor for Traffic-Light-Preemption System; Full-Duplex Digital Communication on a Single Laser Beam; Stabilizing Microwave Frequency of a Photonic Oscillator; Microwave Oscillators Based on Nonlinear WGM Resonators; Pointing Reference Scheme for Free-Space Optical Communications Systems; High-Level Performance Modeling of SAR Systems; Spectral Analysis Tool 6.2 for Windows; Multi-Platform Avionics Simulator; Silicon-Based Optical Modulator with Ferroelectric Layer; Multiplexing Transducers Based on Tunnel-Diode Oscillators; Scheduling with Automated Resolution of Conflicts; Symbolic Constraint Maintenance Grid; Discerning Trends in Performance Across Multiple Events; Magnetic Field Solver; Computing for Aiming a Spaceborne Bistatic- Radar Transmitter; 4-Vinyl-1,3-Dioxolane-2-One as an Additive for Li-Ion Cells; Probabilistic Prediction of Lifetimes of Ceramic Parts; STRANAL-PMC Version 2.0; Micromechanics and Piezo Enhancements of HyperSizer; Single-Phase Rare-Earth Oxide/Aluminum Oxide Glasses; Tilt/Tip/Piston Manipulator with Base-Mounted Actuators; Measurement of Model Noise in a Hard-Wall Wind Tunnel; Loci-STREAM Version 0.9; The Synergistic Engineering Environment; Reconfigurable Software for Controlling Formation Flying; More About the Tetrahedral Unstructured Software System; Computing Flows Using Chimera and Unstructured Grids; Avoiding Obstructions in Aiming a High-Gain Antenna; Analyzing Aeroelastic Stability of a Tilt-Rotor Aircraft; Tracking Positions and Attitudes of Mars Rovers; Stochastic Evolutionary Algorithms for Planning Robot Paths; Compressible Flow Toolbox; Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines; General Flow-Solver Code for Turbomachinery Applications; Code for Multiblock CFD and Heat-Transfer Computations; Rotating-Pump Design Code; Covering a Crucible with Metal Containing Channels; Repairing Fractured Bones by Use of Bioabsorbable Composites; Kalman Filter for Calibrating a Telescope Focal Plane; Electronic Absolute Cartesian Autocollimator; Fiber-Optic Gratings for Lidar Measurements of Water Vapor; Simulating Responses of Gravitational-Wave Instrumentation; SOFTC: A Software Correlator for VLBI; Progress in Computational Simulation of Earthquakes; Database of Properties of Meteors; Computing Spacecraft Solar-Cell Damage by Charged Particles; Thermal Model of a Current-Carrying Wire in a Vacuum; Program for Analyzing Flows in a Complex Network; Program Predicts Performance of Optical Parametric Oscillators; Processing TES Level-1B Data; Automated Camera Calibration; Tracking the Martian CO2 Polar Ice Caps in Infrared Images; Processing TES Level-2 Data; SmaggIce Version 1.8; Solving the Swath Segment Selection Problem; The Spatial Standard Observer; Less-Complex Method of Classifying MPSK; Improvement in Recursive Hierarchical Segmentation of Data; Using Heaps in Recursive Hierarchical Segmentation of Data; Tool for Statistical Analysis and Display of Landing Sites; Automated Assignment of Proposals to Reviewers; Array-Pattern-Match Compiler for Opportunistic Data Analysis; Pre-Processor for Compression of Multispectral Image Data; Compressing Image Data While Limiting the Effects of Data Losses; Flight Operations Analysis Tool; Improvement in Visual Target Tracking for a Mobile Robot; Software for Simulating Air Traffic; Automated Vectorization of Decision-Based Algorithms; Grayscale Optical Correlator Workbench; "One-Stop Shopping" for Ocean Remote-Sensing and Model Data; State Analysis Database Tool; Generating CAHV and CAHVOmages with Shadows in ROAMS; Improving UDP/IP Transmission Without Increasing Congestion; FORTRAN Versions of Reformulated HFGMC Codes; Program for Editing Spacecraft Command Sequences; Flight-Tested Prototype of BEAM Software; Mission Scenario Development Workbench; Marsviewer; Tool for Analysis and Reduction of Scientific Data; ASPEN Version 3.0; Secure Display of Space-Exploration Images; Digital Front End for Wide-Band VLBI Science Receiver; Multifunctional Tanks for Spacecraft; Lightweight, Segmented, Mostly Silicon Telescope Mirror; Assistant for Analyzing Tropical-Rain-Mapping Radar Data; and Anion-Intercalating Cathodes for High-Energy- Density Cells.

X-ray Photoelectron Spectroscopy Database (Version 4.1)

National Institute of Standards and Technology Data Gateway

SRD 20 X-ray Photoelectron Spectroscopy Database (Version 4.1) (Web, free access)   The NIST XPS Database gives access to energies of many photoelectron and Auger-electron spectral lines. The database contains over 22,000 line positions, chemical shifts, doublet splittings, and energy separations of photoelectron and Auger-electron lines.

Schema Versioning for Multitemporal Relational Databases.

ERIC Educational Resources Information Center

De Castro, Cristina; Grandi, Fabio; Scalas, Maria Rita

1997-01-01

Investigates new design options for extended schema versioning support for multitemporal relational databases. Discusses the improved functionalities they may provide. Outlines options and basic motivations for the new design solutions, as well as techniques for the management of proposed schema versioning solutions, includes algorithms and…

The Mars Climate Database (MCD version 5.2)

NASA Astrophysics Data System (ADS)

Millour, E.; Forget, F.; Spiga, A.; Navarro, T.; Madeleine, J.-B.; Montabone, L.; Pottier, A.; Lefevre, F.; Montmessin, F.; Chaufray, J.-Y.; Lopez-Valverde, M. A.; Gonzalez-Galindo, F.; Lewis, S. R.; Read, P. L.; Huot, J.-P.; Desjean, M.-C.; MCD/GCM development Team

2015-10-01

The Mars Climate Database (MCD) is a database of meteorological fields derived from General Circulation Model (GCM) numerical simulations of the Martian atmosphere and validated using available observational data. The MCD includes complementary post-processing schemes such as high spatial resolution interpolation of environmental data and means of reconstructing the variability thereof. We have just completed (March 2015) the generation of a new version of the MCD, MCD version 5.2

Video-assisted segmentation of speech and audio track

NASA Astrophysics Data System (ADS)

Pandit, Medha; Yusoff, Yusseri; Kittler, Josef; Christmas, William J.; Chilton, E. H. S.

1999-08-01

Video database research is commonly concerned with the storage and retrieval of visual information invovling sequence segmentation, shot representation and video clip retrieval. In multimedia applications, video sequences are usually accompanied by a sound track. The sound track contains potential cues to aid shot segmentation such as different speakers, background music, singing and distinctive sounds. These different acoustic categories can be modeled to allow for an effective database retrieval. In this paper, we address the problem of automatic segmentation of audio track of multimedia material. This audio based segmentation can be combined with video scene shot detection in order to achieve partitioning of the multimedia material into semantically significant segments.

Brief Report: Utilization of the First Biosimilar Infliximab Since Its Approval in South Korea.

PubMed

Kim, Seoyoung C; Choi, Nam-Kyong; Lee, Joongyub; Kwon, Kyoung-Eun; Eddings, Wesley; Sung, Yoon-Kyoung; Ji Song, Hong; Kesselheim, Aaron S; Solomon, Daniel H

2016-05-01

The US Food and Drug Administration is considering an application for a biosimilar version of infliximab, which has been available in South Korea since November 2012. The aim of the present study was to examine the utilization patterns of both branded and biosimilar infliximab and other tumor necrosis factor (TNF) inhibitors in South Korea before and after the introduction of this biosimilar infliximab. Using claims data from April 2009 to March 2014 from the Korean Health Insurance Review and Assessment Service database, which includes the entire South Korean population, the number of claims for biosimilar infliximab was assessed. A segmented linear regression model was used to examine the utilization patterns of infliximab (the branded and biosimilar versions) and other TNF inhibitors (adalimumab and etanercept) before and after the introduction of the biosimilar infliximab. In total, 20,976 TNF inhibitor users were identified from the South Korean claims database, including 983 with a prescription claim for biosimilar infliximab. Among all of the claims for any version of infliximab, the proportion of biosimilar infliximab claims increased to 19% through March 2014. Before November 2012, each month there were 33 (95% confidence interval [95% CI] 32, 35) more infliximab claims, 44 (95% CI 40, 48) more etanercept claims, and 50 (95% CI 47, 53) more adalimumab claims. After November 2012, there were significant changes in the slopes for trend in usage, with additional increases in the use of branded and biosimilar infliximab (9 more claims per month, 95% CI 2, 17) and decreases in the use of etanercept (-52 claims per month, 95% CI -66, -38) and adalimumab (-21 claims per month, 95% CI -35, -6). During the first 15 months since its introduction in South Korea, one-fifth of all infliximab claims were for the biosimilar version. Introduction of biosimilar infliximab may affect the use of other TNF inhibitors, and the magnitude of change in usage will likely differ in other countries. © 2016, American College of Rheumatology.

SparCLeS: dynamic l₁ sparse classifiers with level sets for robust beard/moustache detection and segmentation.

PubMed

Le, T Hoang Ngan; Luu, Khoa; Savvides, Marios

2013-08-01

Robust facial hair detection and segmentation is a highly valued soft biometric attribute for carrying out forensic facial analysis. In this paper, we propose a novel and fully automatic system, called SparCLeS, for beard/moustache detection and segmentation in challenging facial images. SparCLeS uses the multiscale self-quotient (MSQ) algorithm to preprocess facial images and deal with illumination variation. Histogram of oriented gradients (HOG) features are extracted from the preprocessed images and a dynamic sparse classifier is built using these features to classify a facial region as either containing skin or facial hair. A level set based approach, which makes use of the advantages of both global and local information, is then used to segment the regions of a face containing facial hair. Experimental results demonstrate the effectiveness of our proposed system in detecting and segmenting facial hair regions in images drawn from three databases, i.e., the NIST Multiple Biometric Grand Challenge (MBGC) still face database, the NIST Color Facial Recognition Technology FERET database, and the Labeled Faces in the Wild (LFW) database.

Operational calibration and validation of landsat data continuity mission (LDCM) sensors using the image assessment system (IAS)

USGS Publications Warehouse

Micijevic, Esad; Morfitt, Ron

2010-01-01

Systematic characterization and calibration of the Landsat sensors and the assessment of image data quality are performed using the Image Assessment System (IAS). The IAS was first introduced as an element of the Landsat 7 (L7) Enhanced Thematic Mapper Plus (ETM+) ground segment and recently extended to Landsat 4 (L4) and 5 (L5) Thematic Mappers (TM) and Multispectral Sensors (MSS) on-board the Landsat 1-5 satellites. In preparation for the Landsat Data Continuity Mission (LDCM), the IAS was developed for the Earth Observer 1 (EO-1) Advanced Land Imager (ALI) with a capability to assess pushbroom sensors. This paper describes the LDCM version of the IAS and how it relates to unique calibration and validation attributes of its on-board imaging sensors. The LDCM IAS system will have to handle a significantly larger number of detectors and the associated database than the previous IAS versions. An additional challenge is that the LDCM IAS must handle data from two sensors, as the LDCM products will combine the Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS) spectral bands.

From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes

PubMed Central

Corcoran, Callan C.; Grady, Cameron R.; Pisitkun, Trairak; Parulekar, Jaya

2017-01-01

The organization of the mammalian genome into gene subsets corresponding to specific functional classes has provided key tools for systems biology research. Here, we have created a web-accessible resource called the Mammalian Metabolic Enzyme Database (https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/MetabolicEnzymeDatabase.html) keyed to the biochemical reactions represented on iconic metabolic pathway wall charts created in the previous century. Overall, we have mapped 1,647 genes to these pathways, representing ~7 percent of the protein-coding genome. To illustrate the use of the database, we apply it to the area of kidney physiology. In so doing, we have created an additional database (Database of Metabolic Enzymes in Kidney Tubule Segments: https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/), mapping mRNA abundance measurements (mined from RNA-Seq studies) for all metabolic enzymes to each of 14 renal tubule segments. We carry out bioinformatics analysis of the enzyme expression pattern among renal tubule segments and mine various data sources to identify vasopressin-regulated metabolic enzymes in the renal collecting duct. PMID:27974320

Numerical Arc Segmentation Algorithm for a Radio Conference-NASARC (version 4.0) technical manual

NASA Technical Reports Server (NTRS)

Whyte, Wayne A., Jr.; Heyward, Ann O.; Ponchak, Denise S.; Spence, Rodney L.; Zuzek, John E.

1988-01-01

The information contained in the NASARC (Version 4.0) Technical Manual and NASARC (Version 4.0) User's Manual relates to the Numerical Arc Segmentation Algorithm for a Radio Conference (NASARC) software development through November 1, 1988. The Technical Manual describes the NASARC concept and the algorithms used to implement the concept. The User's Manual provides information on computer system considerations, installation instructions, description of input files, and program operation instructions. Significant revisions were incorporated in the Version 4.0 software over prior versions. These revisions have further enhanced the modeling capabilities of the NASARC procedure and provide improved arrangements of predetermined arcs within the geostationary orbits. Array dimensions within the software were structured to fit within the currently available 12 megabyte memory capacity of the International Frequency Registration Board (IFRB) computer facility. A piecewise approach to predetermined arc generation in NASARC (Version 4.0) allows worldwide planning problem scenarios to be accommodated within computer run time and memory constraints with enhanced likelihood and ease of solution.

Fast vessel segmentation in retinal images using multi-scale enhancement and second-order local entropy

NASA Astrophysics Data System (ADS)

Yu, H.; Barriga, S.; Agurto, C.; Zamora, G.; Bauman, W.; Soliz, P.

2012-03-01

Retinal vasculature is one of the most important anatomical structures in digital retinal photographs. Accurate segmentation of retinal blood vessels is an essential task in automated analysis of retinopathy. This paper presents a new and effective vessel segmentation algorithm that features computational simplicity and fast implementation. This method uses morphological pre-processing to decrease the disturbance of bright structures and lesions before vessel extraction. Next, a vessel probability map is generated by computing the eigenvalues of the second derivatives of Gaussian filtered image at multiple scales. Then, the second order local entropy thresholding is applied to segment the vessel map. Lastly, a rule-based decision step, which measures the geometric shape difference between vessels and lesions is applied to reduce false positives. The algorithm is evaluated on the low-resolution DRIVE and STARE databases and the publicly available high-resolution image database from Friedrich-Alexander University Erlangen-Nuremberg, Germany). The proposed method achieved comparable performance to state of the art unsupervised vessel segmentation methods with a competitive faster speed on the DRIVE and STARE databases. For the high resolution fundus image database, the proposed algorithm outperforms an existing approach both on performance and speed. The efficiency and robustness make the blood vessel segmentation method described here suitable for broad application in automated analysis of retinal images.

The Consolidated Human Activity Database — Master Version (CHAD-Master) Technical Memorandum

EPA Pesticide Factsheets

This technical memorandum contains information about the Consolidated Human Activity Database -- Master version, including CHAD contents, inventory of variables: Questionnaire files and Event files, CHAD codes, and references.

Assessment of radionuclide databases in CAP88 mainframe version 1.0 and Windows-based version 3.0.

PubMed

LaBone, Elizabeth D; Farfán, Eduardo B; Lee, Patricia L; Jannik, G Timothy; Donnelly, Elizabeth H; Foley, Trevor Q

2009-09-01

In this study the radionuclide databases for two versions of the Clean Air Act Assessment Package-1988 (CAP88) computer model were assessed in detail. CAP88 estimates radiation dose and the risk of health effects to human populations from radionuclide emissions to air. This program is used by several U.S. Department of Energy (DOE) facilities to comply with National Emission Standards for Hazardous Air Pollutants regulations. CAP88 Mainframe, referred to as version 1.0 on the U.S. Environmental Protection Agency Web site (http://www.epa.gov/radiation/assessment/CAP88/), was the very first CAP88 version released in 1988. Some DOE facilities including the Savannah River Site still employ this version (1.0) while others use the more user-friendly personal computer Windows-based version 3.0 released in December 2007. Version 1.0 uses the program RADRISK based on International Commission on Radiological Protection Publication 30 as its radionuclide database. Version 3.0 uses half-life, dose, and risk factor values based on Federal Guidance Report 13. Differences in these values could cause different results for the same input exposure data (same scenario), depending on which version of CAP88 is used. Consequently, the differences between the two versions are being assessed in detail at Savannah River National Laboratory. The version 1.0 and 3.0 database files contain 496 and 838 radionuclides, respectively, and though one would expect the newer version to include all the 496 radionuclides, 35 radionuclides are listed in version 1.0 that are not included in version 3.0. The majority of these has either extremely short or long half-lives or is no longer in production; however, some of the short-lived radionuclides might produce progeny of great interest at DOE sites. In addition, 122 radionuclides were found to have different half-lives in the two versions, with 21 over 3 percent different and 12 over 10 percent different.

The UMIST database for astrochemistry 2006

NASA Astrophysics Data System (ADS)

Woodall, J.; Agúndez, M.; Markwick-Kemper, A. J.; Millar, T. J.

2007-05-01

Aims:We present a new version of the UMIST Database for Astrochemistry, the fourth such version to be released to the public. The current version contains some 4573 binary gas-phase reactions, an increase of 10% from the previous (1999) version, among 420 species, of which 23 are new to the database. Methods: Major updates have been made to ion-neutral reactions, neutral-neutral reactions, particularly at low temperature, and dissociative recombination reactions. We have included for the first time the interstellar chemistry of fluorine. In addition to the usual database, we have also released a reaction set in which the effects of dipole-enhanced ion-neutral rate coefficients are included. Results: These two reactions sets have been used in a dark cloud model and the results of these models are presented and discussed briefly. The database and associated software are available on the World Wide Web at www.udfa.net. Tables 1, 2, 4 and 9 are only available in electronic form at http://www.aanda.org

Towards online iris and periocular recognition under relaxed imaging constraints.

PubMed

Tan, Chun-Wei; Kumar, Ajay

2013-10-01

Online iris recognition using distantly acquired images in a less imaging constrained environment requires the development of a efficient iris segmentation approach and recognition strategy that can exploit multiple features available for the potential identification. This paper presents an effective solution toward addressing such a problem. The developed iris segmentation approach exploits a random walker algorithm to efficiently estimate coarsely segmented iris images. These coarsely segmented iris images are postprocessed using a sequence of operations that can effectively improve the segmentation accuracy. The robustness of the proposed iris segmentation approach is ascertained by providing comparison with other state-of-the-art algorithms using publicly available UBIRIS.v2, FRGC, and CASIA.v4-distance databases. Our experimental results achieve improvement of 9.5%, 4.3%, and 25.7% in the average segmentation accuracy, respectively, for the UBIRIS.v2, FRGC, and CASIA.v4-distance databases, as compared with most competing approaches. We also exploit the simultaneously extracted periocular features to achieve significant performance improvement. The joint segmentation and combination strategy suggest promising results and achieve average improvement of 132.3%, 7.45%, and 17.5% in the recognition performance, respectively, from the UBIRIS.v2, FRGC, and CASIA.v4-distance databases, as compared with the related competing approaches.

A dynamic appearance descriptor approach to facial actions temporal modeling.

PubMed

Jiang, Bihan; Valstar, Michel; Martinez, Brais; Pantic, Maja

2014-02-01

Both the configuration and the dynamics of facial expressions are crucial for the interpretation of human facial behavior. Yet to date, the vast majority of reported efforts in the field either do not take the dynamics of facial expressions into account, or focus only on prototypic facial expressions of six basic emotions. Facial dynamics can be explicitly analyzed by detecting the constituent temporal segments in Facial Action Coding System (FACS) Action Units (AUs)-onset, apex, and offset. In this paper, we present a novel approach to explicit analysis of temporal dynamics of facial actions using the dynamic appearance descriptor Local Phase Quantization from Three Orthogonal Planes (LPQ-TOP). Temporal segments are detected by combining a discriminative classifier for detecting the temporal segments on a frame-by-frame basis with Markov Models that enforce temporal consistency over the whole episode. The system is evaluated in detail over the MMI facial expression database, the UNBC-McMaster pain database, the SAL database, the GEMEP-FERA dataset in database-dependent experiments, in cross-database experiments using the Cohn-Kanade, and the SEMAINE databases. The comparison with other state-of-the-art methods shows that the proposed LPQ-TOP method outperforms the other approaches for the problem of AU temporal segment detection, and that overall AU activation detection benefits from dynamic appearance information.

Performance of an open-source heart sound segmentation algorithm on eight independent databases.

PubMed

Liu, Chengyu; Springer, David; Clifford, Gari D

2017-08-01

Heart sound segmentation is a prerequisite step for the automatic analysis of heart sound signals, facilitating the subsequent identification and classification of pathological events. Recently, hidden Markov model-based algorithms have received increased interest due to their robustness in processing noisy recordings. In this study we aim to evaluate the performance of the recently published logistic regression based hidden semi-Markov model (HSMM) heart sound segmentation method, by using a wider variety of independently acquired data of varying quality. Firstly, we constructed a systematic evaluation scheme based on a new collection of heart sound databases, which we assembled for the PhysioNet/CinC Challenge 2016. This collection includes a total of more than 120 000 s of heart sounds recorded from 1297 subjects (including both healthy subjects and cardiovascular patients) and comprises eight independent heart sound databases sourced from multiple independent research groups around the world. Then, the HSMM-based segmentation method was evaluated using the assembled eight databases. The common evaluation metrics of sensitivity, specificity, accuracy, as well as the [Formula: see text] measure were used. In addition, the effect of varying the tolerance window for determining a correct segmentation was evaluated. The results confirm the high accuracy of the HSMM-based algorithm on a separate test dataset comprised of 102 306 heart sounds. An average [Formula: see text] score of 98.5% for segmenting S1 and systole intervals and 97.2% for segmenting S2 and diastole intervals were observed. The [Formula: see text] score was shown to increases with an increases in the tolerance window size, as expected. The high segmentation accuracy of the HSMM-based algorithm on a large database confirmed the algorithm's effectiveness. The described evaluation framework, combined with the largest collection of open access heart sound data, provides essential resources for evaluators who need to test their algorithms with realistic data and share reproducible results.

From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes.

PubMed

Corcoran, Callan C; Grady, Cameron R; Pisitkun, Trairak; Parulekar, Jaya; Knepper, Mark A

2017-03-01

The organization of the mammalian genome into gene subsets corresponding to specific functional classes has provided key tools for systems biology research. Here, we have created a web-accessible resource called the Mammalian Metabolic Enzyme Database ( https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/MetabolicEnzymeDatabase.html) keyed to the biochemical reactions represented on iconic metabolic pathway wall charts created in the previous century. Overall, we have mapped 1,647 genes to these pathways, representing ~7 percent of the protein-coding genome. To illustrate the use of the database, we apply it to the area of kidney physiology. In so doing, we have created an additional database ( Database of Metabolic Enzymes in Kidney Tubule Segments: https://hpcwebapps.cit.nih.gov/ESBL/Database/MetabolicEnzymes/), mapping mRNA abundance measurements (mined from RNA-Seq studies) for all metabolic enzymes to each of 14 renal tubule segments. We carry out bioinformatics analysis of the enzyme expression pattern among renal tubule segments and mine various data sources to identify vasopressin-regulated metabolic enzymes in the renal collecting duct. Copyright © 2017 the American Physiological Society.

Numerical Arc Segmentation Algorithm for a Radio Conference (NASARC), version 4.0: User's manual

NASA Technical Reports Server (NTRS)

Whyte, Wayne A., Jr.; Heyward, Ann O.; Ponchak, Denise S.; Spence, Rodney L.; Zuzek, John E.

1988-01-01

The information in the NASARC (Version 4.0) Technical Manual (NASA-TM-101453) and NASARC (Version 4.0) User's Manual (NASA-TM-101454) relates to the state of Numerical Arc Segmentation Algorithm for a Radio Conference (NASARC) software development through November 1, 1988. The Technical Manual describes the NASARC concept and the algorithms used to implement the concept. The User's Manual provides information on computer system considerations, installation instructions, description of input files, and program operation instructions. Significant revisions were incorporated in the Version 4.0 software over prior versions. These revisions have further enhanced the modeling capabilities of the NASARC procedure and provide improved arrangements of predetermined arcs within the geostationary orbit. Array dimensions within the software were structured to fit within the currently available 12-megabyte memory capacity of the International Frequency Registration Board (IFRB) computer facility. A piecewise approach to predetermined arc generation in NASARC (Version 4.) allows worldwide planning problem scenarios to be accommodated within computer run time and memory constraints with enhanced likelihood and ease of solution.

Numerical Arc Segmentation Algorithm for a Radio Conference-NASARC, Version 2.0: User's Manual

NASA Technical Reports Server (NTRS)

Whyte, Wayne A., Jr.; Heyward, Ann O.; Ponchak, Denise S.; Spence, Rodney L.; Zuzek, John E.

1987-01-01

The information contained in the NASARC (Version 2.0) Technical Manual (NASA TM-100160) and the NASARC (Version 2.0) User's Manual (NASA TM-100161) relates to the state of the Numerical Arc Segmentation Algorithm for a Radio Conference (NASARC) software development through October 16, 1987. The technical manual describes the NASARC concept and the algorithms which are used to implement it. The User's Manual provides information on computer system considerations, installation instructions, description of input files, and program operation instructions. Significant revisions have been incorporated in the Version 2.0 software over prior versions. These revisions have enhanced the modeling capabilities of the NASARC procedure while greatly reducing the computer run time and memory requirements. Array dimensions within the software have been structured to fit into the currently available 6-megabyte memory capacity of the International Frequency Registration Board (IFRB) computer facility. A piecewise approach to predetermined arc generation in NASARC (Version 2.0) allows worldwide scenarios to be accommodated within these memory constraints while at the same time reducing computer run time.

Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

PubMed

Schlaeger, Sarah; Freitag, Friedemann; Klupp, Elisabeth; Dieckmeyer, Michael; Weidlich, Dominik; Inhuber, Stephanie; Deschauer, Marcus; Schoser, Benedikt; Bublitz, Sarah; Montagnese, Federica; Zimmer, Claus; Rummeny, Ernst J; Karampinos, Dimitrios C; Kirschke, Jan S; Baum, Thomas

2018-01-01

Magnetic resonance imaging (MRI) can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD). Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA) and volume. Proton density fat fraction (PDFF) of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

Web-based Visualization and Query of semantically segmented multiresolution 3D Models in the Field of Cultural Heritage

NASA Astrophysics Data System (ADS)

Auer, M.; Agugiaro, G.; Billen, N.; Loos, L.; Zipf, A.

2014-05-01

Many important Cultural Heritage sites have been studied over long periods of time by different means of technical equipment, methods and intentions by different researchers. This has led to huge amounts of heterogeneous "traditional" datasets and formats. The rising popularity of 3D models in the field of Cultural Heritage in recent years has brought additional data formats and makes it even more necessary to find solutions to manage, publish and study these data in an integrated way. The MayaArch3D project aims to realize such an integrative approach by establishing a web-based research platform bringing spatial and non-spatial databases together and providing visualization and analysis tools. Especially the 3D components of the platform use hierarchical segmentation concepts to structure the data and to perform queries on semantic entities. This paper presents a database schema to organize not only segmented models but also different Levels-of-Details and other representations of the same entity. It is further implemented in a spatial database which allows the storing of georeferenced 3D data. This enables organization and queries by semantic, geometric and spatial properties. As service for the delivery of the segmented models a standardization candidate of the OpenGeospatialConsortium (OGC), the Web3DService (W3DS) has been extended to cope with the new database schema and deliver a web friendly format for WebGL rendering. Finally a generic user interface is presented which uses the segments as navigation metaphor to browse and query the semantic segmentation levels and retrieve information from an external database of the German Archaeological Institute (DAI).

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

PubMed

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

Retinal blood vessel segmentation using fully convolutional network with transfer learning.

PubMed

Jiang, Zhexin; Zhang, Hao; Wang, Yi; Ko, Seok-Bum

2018-04-26

Since the retinal blood vessel has been acknowledged as an indispensable element in both ophthalmological and cardiovascular disease diagnosis, the accurate segmentation of the retinal vessel tree has become the prerequisite step for automated or computer-aided diagnosis systems. In this paper, a supervised method is presented based on a pre-trained fully convolutional network through transfer learning. This proposed method has simplified the typical retinal vessel segmentation problem from full-size image segmentation to regional vessel element recognition and result merging. Meanwhile, additional unsupervised image post-processing techniques are applied to this proposed method so as to refine the final result. Extensive experiments have been conducted on DRIVE, STARE, CHASE_DB1 and HRF databases, and the accuracy of the cross-database test on these four databases is state-of-the-art, which also presents the high robustness of the proposed approach. This successful result has not only contributed to the area of automated retinal blood vessel segmentation but also supports the effectiveness of transfer learning when applying deep learning technique to medical imaging. Copyright © 2018 Elsevier Ltd. All rights reserved.

The NASA Ames PAH IR Spectroscopic Database: Computational Version 3.00 with Updated Content and the Introduction of Multiple Scaling Factors

NASA Astrophysics Data System (ADS)

Bauschlicher, Charles W., Jr.; Ricca, A.; Boersma, C.; Allamandola, L. J.

2018-02-01

Version 3.00 of the library of computed spectra in the NASA Ames PAH IR Spectroscopic Database (PAHdb) is described. Version 3.00 introduces the use of multiple scale factors, instead of the single scaling factor used previously, to align the theoretical harmonic frequencies with the experimental fundamentals. The use of multiple scale factors permits the use of a variety of basis sets; this allows new PAH species to be included in the database, such as those containing oxygen, and yields an improved treatment of strained species and those containing nitrogen. In addition, the computed spectra of 2439 new PAH species have been added. The impact of these changes on the analysis of an astronomical spectrum through database-fitting is considered and compared with a fit using Version 2.00 of the library of computed spectra. Finally, astronomical constraints are defined for the PAH spectral libraries in PAHdb.

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.

PubMed Central

Hansen, J E; Lund, O; Nilsson, J; Rapacki, K; Brunak, S

1998-01-01

O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/ PMID:9399880

The U.S. Geological Survey coal quality (COALQUAL) database version 3.0

USGS Publications Warehouse

Palmer, Curtis A.; Oman, Charles L.; Park, Andy J.; Luppens, James A.

2015-12-21

Because of database size limits during the development of COALQUAL Version 1.3, many analyses of individual bench samples were merged into whole coal bed averages. The methodology for making these composite intervals was not consistent. Size limits also restricted the amount of georeferencing information and forced removal of qualifier notations such as "less than detection limit" (<) information, which can cause problems when using the data. A review of the original data sheets revealed that COALQUAL Version 2.0 was missing information that was needed for a complete understanding of a coal section. Another important database issue to resolve was the USGS "remnant moisture" problem. Prior to 1998, tests for remnant moisture (as-determined moisture in the sample at the time of analysis) were not performed on any USGS major, minor, or trace element coal analyses. Without the remnant moisture, it is impossible to convert the analyses to a usable basis (as-received, dry, etc.). Based on remnant moisture analyses of hundreds of samples of different ranks (and known residual moisture) reported after 1998, it was possible to develop a method to provide reasonable estimates of remnant moisture for older data to make it more useful in COALQUAL Version 3.0. In addition, COALQUAL Version 3.0 is improved by (1) adding qualifiers, including statistical programming to deal with the qualifiers; (2) clarifying the sample compositing problems; and (3) adding associated samples. Version 3.0 of COALQUAL also represents the first attempt to incorporate data verification by mathematically crosschecking certain analytical parameters. Finally, a new database system was designed and implemented to replace the outdated DOS program used in earlier versions of the database.

[DNAStat, version 1.2 -- a software package for processing genetic profile databases and biostatistical calculations].

PubMed

Berent, Jarosław

2007-01-01

This paper presents the new DNAStat version 1.2 for processing genetic profile databases and biostatistical calculations. This new version contains, besides all the options of its predecessor 1.0, a calculation-results file export option in .xls format for Microsoft Office Excel, as well as the option of importing/exporting the population base of systems as .txt files for processing in Microsoft Notepad or EditPad

Users Manual for the Federal Aviation Administration Research and Development Electromagnetic Database (FRED) For Windows: Version 2.0

DOT National Transportation Integrated Search

1998-02-01

This document provides instructional guidelines to users of the Federal Aviation Administration (FAA) Research and Development Electromagnetic Database (FRED) Version 2.0. Instructions are provided on how to access FRED from a compact disk (CD) and h...

FHWA Deep Foundation Load Test Database Version 2.0 User Manual

DOT National Transportation Integrated Search

2016-09-01

The Federal Highway Administration (FHWA) began the development of the first version of the Deep Foundation Load Test Database (DFLTD) in the 1980s. Over 1,500 load tests were collected and stored for various types of piles and drilled shafts in diff...

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants1[W][OA

PubMed Central

Zhang, Peifen; Dreher, Kate; Karthikeyan, A.; Chi, Anjo; Pujar, Anuradha; Caspi, Ron; Karp, Peter; Kirkup, Vanessa; Latendresse, Mario; Lee, Cynthia; Mueller, Lukas A.; Muller, Robert; Rhee, Seung Yon

2010-01-01

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org). PMID:20522724

Spacecraft Orbit Design and Analysis (SODA), version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.; Davis, John S.

1989-01-01

The Spacecraft Orbit Design and Analysis (SODA) computer program, Version 1.0 is described. SODA is a spaceflight mission planning system which consists of five program modules integrated around a common database and user interface. SODA runs on a VAX/VMS computer with an EVANS & SUTHERLAND PS300 graphics workstation. BOEING RIM-Version 7 relational database management system performs transparent database services. In the current version three program modules produce an interactive three dimensional (3D) animation of one or more satellites in planetary orbit. Satellite visibility and sensor coverage capabilities are also provided. One module produces an interactive 3D animation of the solar system. Another module calculates cumulative satellite sensor coverage and revisit time for one or more satellites. Currently Earth, Moon, and Mars systems are supported for all modules except the solar system module.

Numerical arc segmentation algorithm for a radio conference-NASARC (version 2.0) technical manual

NASA Technical Reports Server (NTRS)

Whyte, Wayne A., Jr.; Heyward, Ann O.; Ponchak, Denise S.; Spence, Rodney L.; Zuzek, John E.

1987-01-01

The information contained in the NASARC (Version 2.0) Technical Manual (NASA TM-100160) and NASARC (Version 2.0) User's Manual (NASA TM-100161) relates to the state of NASARC software development through October 16, 1987. The Technical Manual describes the Numerical Arc Segmentation Algorithm for a Radio Conference (NASARC) concept and the algorithms used to implement the concept. The User's Manual provides information on computer system considerations, installation instructions, description of input files, and program operating instructions. Significant revisions have been incorporated in the Version 2.0 software. These revisions have enhanced the modeling capabilities of the NASARC procedure while greatly reducing the computer run time and memory requirements. Array dimensions within the software have been structured to fit within the currently available 6-megabyte memory capacity of the International Frequency Registration Board (IFRB) computer facility. A piecewise approach to predetermined arc generation in NASARC (Version 2.0) allows worldwide scenarios to be accommodated within these memory constraints while at the same time effecting an overall reduction in computer run time.

Completion of the 2006 National Land Cover Database Update for the Conterminous United States

EPA Science Inventory

Under the organization of the Multi-Resolution Land Characteristics (MRLC) Consortium, the National Land Cover Database (NLCD) has been updated to characterize both land cover and land cover change from 2001 to 2006. An updated version of NLCD 2001 (Version 2.0) is also provided....

The 2003 edition of geisa: a spectroscopic database system for the second generation vertical sounders radiance simulation

NASA Astrophysics Data System (ADS)

Jacquinet-Husson, N.; Lmd Team

The GEISA (Gestion et Etude des Informations Spectroscopiques Atmosphériques: Management and Study of Atmospheric Spectroscopic Information) computer accessible database system, in its former 1997 and 2001 versions, has been updated in 2003 (GEISA-03). It is developed by the ARA (Atmospheric Radiation Analysis) group at LMD (Laboratoire de Météorologie Dynamique, France) since 1974. This early effort implemented the so-called `` line-by-line and layer-by-layer '' approach for forward radiative transfer modelling action. The GEISA 2003 system comprises three databases with their associated management softwares: a database of spectroscopic parameters required to describe adequately the individual spectral lines belonging to 42 molecules (96 isotopic species) and located in a spectral range from the microwave to the limit of the visible. The featured molecules are of interest in studies of the terrestrial as well as the other planetary atmospheres, especially those of the Giant Planets. a database of absorption cross-sections of molecules such as chlorofluorocarbons which exhibit unresolvable spectra. a database of refractive indices of basic atmospheric aerosol components. Illustrations will be given of GEISA-03, data archiving method, contents, management softwares and Web access facilities at: http://ara.lmd.polytechnique.fr The performance of instruments like AIRS (Atmospheric Infrared Sounder; http://www-airs.jpl.nasa.gov) in the USA, and IASI (Infrared Atmospheric Sounding Interferometer; http://smsc.cnes.fr/IASI/index.htm) in Europe, which have a better vertical resolution and accuracy, compared to the presently existing satellite infrared vertical sounders, is directly related to the quality of the spectroscopic parameters of the optically active gases, since these are essential input in the forward models used to simulate recorded radiance spectra. For these upcoming atmospheric sounders, the so-called GEISA/IASI sub-database system has been elaborated, from GEISA. Its content, will be described, as well. This work is ongoing, with the purpose of assessing the IASI measurements capabilities and the spectroscopic information quality, within the ISSWG (IASI Sounding Science Working Group), in the frame of the CNES (Centre National d'Etudes Spatiales, France)/EUMETSAT (EUropean organization for the exploitation of METeorological SATellites) Polar System (EPS) project, by simulating high resolution radiances and/or using experimental data. EUMETSAT will implement GEISA/IASI into the EPS ground segment. The IASI soundings spectroscopic data archive requirements will be discussed in the context of comparisons between recorded and calculated experimental spectra, using the ARA/4A forward line-by-line radiative transfer modelling code in its latest version.

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

PubMed

Fourment, Mathieu; Gibbs, Mark J

2008-02-05

Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

ECG signal quality during arrhythmia and its application to false alarm reduction.

PubMed

Behar, Joachim; Oster, Julien; Li, Qiao; Clifford, Gari D

2013-06-01

An automated algorithm to assess electrocardiogram (ECG) quality for both normal and abnormal rhythms is presented for false arrhythmia alarm suppression of intensive care unit (ICU) monitors. A particular focus is given to the quality assessment of a wide variety of arrhythmias. Data from three databases were used: the Physionet Challenge 2011 dataset, the MIT-BIH arrhythmia database, and the MIMIC II database. The quality of more than 33 000 single-lead 10 s ECG segments were manually assessed and another 12 000 bad-quality single-lead ECG segments were generated using the Physionet noise stress test database. Signal quality indices (SQIs) were derived from the ECGs segments and used as the inputs to a support vector machine classifier with a Gaussian kernel. This classifier was trained to estimate the quality of an ECG segment. Classification accuracies of up to 99% on the training and test set were obtained for normal sinus rhythm and up to 95% for arrhythmias, although performance varied greatly depending on the type of rhythm. Additionally, the association between 4050 ICU alarms from the MIMIC II database and the signal quality, as evaluated by the classifier, was studied. Results suggest that the SQIs should be rhythm specific and that the classifier should be trained for each rhythm call independently. This would require a substantially increased set of labeled data in order to train an accurate algorithm.

ERMes: Open Source Simplicity for Your E-Resource Management

ERIC Educational Resources Information Center

Doering, William; Chilton, Galadriel

2009-01-01

ERMes, the latest version of electronic resource management system (ERM), is a relational database; content in different tables connects to, and works with, content in other tables. ERMes requires Access 2007 (Windows) or Access 2008 (Mac) to operate as the database utilizes functionality not available in previous versions of Microsoft Access. The…

ICCS 2009 User Guide for the International Database. Supplement 1: International Version of the ICCS 2009 Questionnaires

ERIC Educational Resources Information Center

Brese, Falk; Jung, Michael; Mirazchiyski, Plamen; Schulz, Wolfram; Zuehlke, Olaf

2011-01-01

This document presents Supplement 1 of "The International Civic and Citizenship Education Study (ICCS) 2009 International Database," which includes data for all questionnaires administered as part of the ICCS 2009 assessment. This supplement contains the international version of the ICCS 2009 questionnaires in the following seven…

New Access Points to ERIC--CD-ROM Versions. ERIC Digest.

ERIC Educational Resources Information Center

McLaughlin, Pamela W.

This digest reviews three CD-ROM (compact disc-read only memory) versions of the ERIC (Educational Resources Information Center) database currently being delivered or tested and provides information for comparison. However, no attempt is made to recommend any one product. The advantages and disadvantages of the acquisition of CD-ROM databases are…

Design of a diagnostic encyclopaedia using AIDA.

PubMed

van Ginneken, A M; Smeulders, A W; Jansen, W

1987-01-01

Diagnostic Encyclopaedia Workstation (DEW) is the name of a digital encyclopaedia constructed to contain reference knowledge with respect to the pathology of the ovary. Comparing DEW with the common sources of reference knowledge (i.e. books) leads to the following advantages of DEW: it contains more verbal knowledge, pictures and case histories, and it offers information adjusted to the needs of the user. Based on an analysis of the structure of this reference knowledge we have chosen AIDA to develop a relational database and we use a video-disc player to contain the pictorial part of the database. The system consists of a database input version and a read-only run version. The design of the database input version is discussed. Reference knowledge for ovary pathology requires 1-3 Mbytes of memory. At present 15% of this amount is available. The design of the run version is based on an analysis of which information must necessarily be specified to the system by the user to access a desired item of information. Finally, the use of AIDA in constructing DEW is evaluated.

MS lesion segmentation using a multi-channel patch-based approach with spatial consistency

NASA Astrophysics Data System (ADS)

Mechrez, Roey; Goldberger, Jacob; Greenspan, Hayit

2015-03-01

This paper presents an automatic method for segmentation of Multiple Sclerosis (MS) in Magnetic Resonance Images (MRI) of the brain. The approach is based on similarities between multi-channel patches (T1, T2 and FLAIR). An MS lesion patch database is built using training images for which the label maps are known. For each patch in the testing image, k similar patches are retrieved from the database. The matching labels for these k patches are then combined to produce an initial segmentation map for the test case. Finally a novel iterative patch-based label refinement process based on the initial segmentation map is performed to ensure spatial consistency of the detected lesions. A leave-one-out evaluation is done for each testing image in the MS lesion segmentation challenge of MICCAI 2008. Results are shown to compete with the state-of-the-art methods on the MICCAI 2008 challenge.

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

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

Boersma, C.; Mattioda, A. L.; Allamandola, L. J.

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysismore » called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.« less

The Human Communication Research Centre dialogue database.

PubMed

Anderson, A H; Garrod, S C; Clark, A; Boyle, E; Mullin, J

1992-10-01

The HCRC dialogue database consists of over 700 transcribed and coded dialogues from pairs of speakers aged from seven to fourteen. The speakers are recorded while tackling co-operative problem-solving tasks and the same pairs of speakers are recorded over two years tackling 10 different versions of our two tasks. In addition there are over 200 dialogues recorded between pairs of undergraduate speakers engaged on versions of the same tasks. Access to the database, and to its accompanying custom-built search software, is available electronically over the JANET system by contacting liz@psy.glasgow.ac.uk, from whom further information about the database and a user's guide to the database can be obtained.

New Embedded Denotes Fuzzy C-Mean Application for Breast Cancer Density Segmentation in Digital Mammograms

NASA Astrophysics Data System (ADS)

Othman, Khairulnizam; Ahmad, Afandi

2016-11-01

In this research we explore the application of normalize denoted new techniques in advance fast c-mean in to the problem of finding the segment of different breast tissue regions in mammograms. The goal of the segmentation algorithm is to see if new denotes fuzzy c- mean algorithm could separate different densities for the different breast patterns. The new density segmentation is applied with multi-selection of seeds label to provide the hard constraint, whereas the seeds labels are selected based on user defined. New denotes fuzzy c- mean have been explored on images of various imaging modalities but not on huge format digital mammograms just yet. Therefore, this project is mainly focused on using normalize denoted new techniques employed in fuzzy c-mean to perform segmentation to increase visibility of different breast densities in mammography images. Segmentation of the mammogram into different mammographic densities is useful for risk assessment and quantitative evaluation of density changes. Our proposed methodology for the segmentation of mammograms on the basis of their region into different densities based categories has been tested on MIAS database and Trueta Database.

Image segmentation evaluation for very-large datasets

NASA Astrophysics Data System (ADS)

Reeves, Anthony P.; Liu, Shuang; Xie, Yiting

2016-03-01

With the advent of modern machine learning methods and fully automated image analysis there is a need for very large image datasets having documented segmentations for both computer algorithm training and evaluation. Current approaches of visual inspection and manual markings do not scale well to big data. We present a new approach that depends on fully automated algorithm outcomes for segmentation documentation, requires no manual marking, and provides quantitative evaluation for computer algorithms. The documentation of new image segmentations and new algorithm outcomes are achieved by visual inspection. The burden of visual inspection on large datasets is minimized by (a) customized visualizations for rapid review and (b) reducing the number of cases to be reviewed through analysis of quantitative segmentation evaluation. This method has been applied to a dataset of 7,440 whole-lung CT images for 6 different segmentation algorithms designed to fully automatically facilitate the measurement of a number of very important quantitative image biomarkers. The results indicate that we could achieve 93% to 99% successful segmentation for these algorithms on this relatively large image database. The presented evaluation method may be scaled to much larger image databases.

Orthographic Transparency Enhances Morphological Segmentation in Children Reading Hebrew Words.

PubMed

Haddad, Laurice; Weiss, Yael; Katzir, Tami; Bitan, Tali

2017-01-01

Morphological processing of derived words develops simultaneously with reading acquisition. However, the reader's engagement in morphological segmentation may depend on the language morphological richness and orthographic transparency, and the readers' reading skills. The current study tested the common idea that morphological segmentation is enhanced in non-transparent orthographies to compensate for the absence of phonological information. Hebrew's rich morphology and the dual version of the Hebrew script (with and without diacritic marks) provides an opportunity to study the interaction of orthographic transparency and morphological segmentation on the development of reading skills in a within-language design. Hebrew speaking 2nd ( N = 27) and 5th ( N = 29) grade children read aloud 96 noun words. Half of the words were simple mono-morphemic words and half were bi-morphemic derivations composed of a productive root and a morphemic pattern. In each list half of the words were presented in the transparent version of the script (with diacritic marks), and half in the non-transparent version (without diacritic marks). Our results show that in both groups, derived bi-morphemic words were identified more accurately than mono-morphemic words, but only for the transparent, pointed, script. For the un-pointed script the reverse was found, namely, that bi-morphemic words were read less accurately than mono-morphemic words, especially in second grade. Second grade children also read mono-morphemic words faster than bi-morphemic words. Finally, correlations with a standardized measure of morphological awareness were found only for second grade children, and only in bi-morphemic words. These results, showing greater morphological effects in second grade compared to fifth grade children suggest that for children raised in a language with a rich morphology, common and easily segmented morphemic units may be more beneficial for younger compared to older readers. Moreover, in contrast to the common hypothesis, our results show that morphemic segmentation does not compensate for the missing phonological information in a non-transparent orthography, but rather that morphological segmentation is most beneficial in the highly transparent script. These results are consistent with the idea that morphological and phonological segmentation processes occur simultaneously and do not constitute alternative pathways to visual word recognition.

Orthographic Transparency Enhances Morphological Segmentation in Children Reading Hebrew Words

PubMed Central

Haddad, Laurice; Weiss, Yael; Katzir, Tami; Bitan, Tali

2018-01-01

Morphological processing of derived words develops simultaneously with reading acquisition. However, the reader’s engagement in morphological segmentation may depend on the language morphological richness and orthographic transparency, and the readers’ reading skills. The current study tested the common idea that morphological segmentation is enhanced in non-transparent orthographies to compensate for the absence of phonological information. Hebrew’s rich morphology and the dual version of the Hebrew script (with and without diacritic marks) provides an opportunity to study the interaction of orthographic transparency and morphological segmentation on the development of reading skills in a within-language design. Hebrew speaking 2nd (N = 27) and 5th (N = 29) grade children read aloud 96 noun words. Half of the words were simple mono-morphemic words and half were bi-morphemic derivations composed of a productive root and a morphemic pattern. In each list half of the words were presented in the transparent version of the script (with diacritic marks), and half in the non-transparent version (without diacritic marks). Our results show that in both groups, derived bi-morphemic words were identified more accurately than mono-morphemic words, but only for the transparent, pointed, script. For the un-pointed script the reverse was found, namely, that bi-morphemic words were read less accurately than mono-morphemic words, especially in second grade. Second grade children also read mono-morphemic words faster than bi-morphemic words. Finally, correlations with a standardized measure of morphological awareness were found only for second grade children, and only in bi-morphemic words. These results, showing greater morphological effects in second grade compared to fifth grade children suggest that for children raised in a language with a rich morphology, common and easily segmented morphemic units may be more beneficial for younger compared to older readers. Moreover, in contrast to the common hypothesis, our results show that morphemic segmentation does not compensate for the missing phonological information in a non-transparent orthography, but rather that morphological segmentation is most beneficial in the highly transparent script. These results are consistent with the idea that morphological and phonological segmentation processes occur simultaneously and do not constitute alternative pathways to visual word recognition. PMID:29403413

Segmentation Fusion Techniques with Application to Plenoptic Images: A Survey.

NASA Astrophysics Data System (ADS)

Evin, D.; Hadad, A.; Solano, A.; Drozdowicz, B.

2016-04-01

The segmentation of anatomical and pathological structures plays a key role in the characterization of clinically relevant evidence from digital images. Recently, plenoptic imaging has emerged as a new promise to enrich the diagnostic potential of conventional photography. Since the plenoptic images comprises a set of slightly different versions of the target scene, we propose to make use of those images to improve the segmentation quality in relation to the scenario of a single image segmentation. The problem of finding a segmentation solution from multiple images of a single scene, is called segmentation fusion. This paper reviews the issue of segmentation fusion in order to find solutions that can be applied to plenoptic images, particularly images from the ophthalmological domain.

Validation of automated white matter hyperintensity segmentation.

PubMed

Smart, Sean D; Firbank, Michael J; O'Brien, John T

2011-01-01

Introduction. White matter hyperintensities (WMHs) are a common finding on MRI scans of older people and are associated with vascular disease. We compared 3 methods for automatically segmenting WMHs from MRI scans. Method. An operator manually segmented WMHs on MRI images from a 3T scanner. The scans were also segmented in a fully automated fashion by three different programmes. The voxel overlap between manual and automated segmentation was compared. Results. Between observer overlap ratio was 63%. Using our previously described in-house software, we had overlap of 62.2%. We investigated the use of a modified version of SPM segmentation; however, this was not successful, with only 14% overlap. Discussion. Using our previously reported software, we demonstrated good segmentation of WMHs in a fully automated fashion.

TIMSS 2011 User Guide for the International Database. Supplement 1: International Version of the TIMSS 2011 Background and Curriculum Questionnaires

ERIC Educational Resources Information Center

Foy, Pierre, Ed.; Arora, Alka, Ed.; Stanco, Gabrielle M., Ed.

2013-01-01

The TIMSS 2011 International Database includes data for all questionnaires administered as part of the TIMSS 2011 assessment. This supplement contains the international version of the TIMSS 2011 background questionnaires and curriculum questionnaires in the following 10 sections: (1) Fourth Grade Student Questionnaire; (2) Fourth Grade Home…

TEDS-M 2008 User Guide for the International Database. Supplement 1: International Version of the TEDS-M Questionnaires

ERIC Educational Resources Information Center

Brese, Falk, Ed.

2012-01-01

The Teacher Education Study in Mathematics (TEDS-M) International Database includes data for all questionnaires administered as part of the TEDS-M study. These consisted of questionnaires administered to future teachers, educators, and institutions with teacher preparation programs. This supplement contains the international version of the TEDS-M…

19 CFR 351.303 - Filing, document identification, format, translation, service, and certification of documents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... submit a public version of a database in pdf format. The public version of the database must be publicly... interested party that files with the Department a request for an expedited antidumping review, an..., whichever is later. If the interested party that files the request is unable to locate a particular exporter...

Jansen-MIDAS: A multi-level photomicrograph segmentation software based on isotropic undecimated wavelets.

PubMed

de Siqueira, Alexandre Fioravante; Cabrera, Flávio Camargo; Nakasuga, Wagner Massayuki; Pagamisse, Aylton; Job, Aldo Eloizo

2018-01-01

Image segmentation, the process of separating the elements within a picture, is frequently used for obtaining information from photomicrographs. Segmentation methods should be used with reservations, since incorrect results can mislead when interpreting regions of interest (ROI). This decreases the success rate of extra procedures. Multi-Level Starlet Segmentation (MLSS) and Multi-Level Starlet Optimal Segmentation (MLSOS) were developed to be an alternative for general segmentation tools. These methods gave rise to Jansen-MIDAS, an open-source software. A scientist can use it to obtain several segmentations of hers/his photomicrographs. It is a reliable alternative to process different types of photomicrographs: previous versions of Jansen-MIDAS were used to segment ROI in photomicrographs of two different materials, with an accuracy superior to 89%. © 2017 Wiley Periodicals, Inc.

Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection.

PubMed

Zhuang, Xiahai; Bai, Wenjia; Song, Jingjing; Zhan, Songhua; Qian, Xiaohua; Shi, Wenzhe; Lian, Yanyun; Rueckert, Daniel

2015-07-01

Cardiac computed tomography (CT) is widely used in clinical diagnosis of cardiovascular diseases. Whole heart segmentation (WHS) plays a vital role in developing new clinical applications of cardiac CT. However, the shape and appearance of the heart can vary greatly across different scans, making the automatic segmentation particularly challenging. The objective of this work is to develop and evaluate a multiatlas segmentation (MAS) scheme using a new atlas ranking and selection algorithm for automatic WHS of CT data. Research on different MAS strategies and their influence on WHS performance are limited. This work provides a detailed comparison study evaluating the impacts of label fusion, atlas ranking, and sizes of the atlas database on the segmentation performance. Atlases in a database were registered to the target image using a hierarchical registration scheme specifically designed for cardiac images. A subset of the atlases were selected for label fusion, according to the authors' proposed atlas ranking criterion which evaluated the performance of each atlas by computing the conditional entropy of the target image given the propagated atlas labeling. Joint label fusion was used to combine multiple label estimates to obtain the final segmentation. The authors used 30 clinical cardiac CT angiography (CTA) images to evaluate the proposed MAS scheme and to investigate different segmentation strategies. The mean WHS Dice score of the proposed MAS method was 0.918 ± 0.021, and the mean runtime for one case was 13.2 min on a workstation. This MAS scheme using joint label fusion generated significantly better Dice scores than the other label fusion strategies, including majority voting (0.901 ± 0.276, p < 0.01), locally weighted voting (0.905 ± 0.0247, p < 0.01), and probabilistic patch-based fusion (0.909 ± 0.0249, p < 0.01). In the atlas ranking study, the proposed criterion based on conditional entropy yielded a performance curve with higher WHS Dice scores compared to the conventional schemes (p < 0.03). In the atlas database study, the authors showed that the MAS using larger atlas databases generated better performance curves than the MAS using smaller ones, indicating larger atlas databases could produce more accurate segmentation. The authors have developed a new MAS framework for automatic WHS of CTA and investigated alternative implementations of MAS. With the proposed atlas ranking algorithm and joint label fusion, the MAS scheme is able to generate accurate segmentation within practically acceptable computation time. This method can be useful for the development of new clinical applications of cardiac CT.

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

PubMed

Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

2008-11-27

The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

PubMed Central

Fourment, Mathieu; Gibbs, Mark J

2008-01-01

Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. PMID:18251994

Word-level recognition of multifont Arabic text using a feature vector matching approach

NASA Astrophysics Data System (ADS)

Erlandson, Erik J.; Trenkle, John M.; Vogt, Robert C., III

1996-03-01

Many text recognition systems recognize text imagery at the character level and assemble words from the recognized characters. An alternative approach is to recognize text imagery at the word level, without analyzing individual characters. This approach avoids the problem of individual character segmentation, and can overcome local errors in character recognition. A word-level recognition system for machine-printed Arabic text has been implemented. Arabic is a script language, and is therefore difficult to segment at the character level. Character segmentation has been avoided by recognizing text imagery of complete words. The Arabic recognition system computes a vector of image-morphological features on a query word image. This vector is matched against a precomputed database of vectors from a lexicon of Arabic words. Vectors from the database with the highest match score are returned as hypotheses for the unknown image. Several feature vectors may be stored for each word in the database. Database feature vectors generated using multiple fonts and noise models allow the system to be tuned to its input stream. Used in conjunction with database pruning techniques, this Arabic recognition system has obtained promising word recognition rates on low-quality multifont text imagery.

Keywords image retrieval in historical handwritten Arabic documents

NASA Astrophysics Data System (ADS)

Saabni, Raid; El-Sana, Jihad

2013-01-01

A system is presented for spotting and searching keywords in handwritten Arabic documents. A slightly modified dynamic time warping algorithm is used to measure similarities between words. Two sets of features are generated from the outer contour of the words/word-parts. The first set is based on the angles between nodes on the contour and the second set is based on the shape context features taken from the outer contour. To recognize a given word, the segmentation-free approach is partially adopted, i.e., continuous word parts are used as the basic alphabet, instead of individual characters or complete words. Additional strokes, such as dots and detached short segments, are classified and used in a postprocessing step to determine the final comparison decision. The search for a keyword is performed by the search for its word parts given in the correct order. The performance of the presented system was very encouraging in terms of efficiency and match rates. To evaluate the presented system its performance is compared to three different systems. Unfortunately, there are no publicly available standard datasets with ground truth for testing Arabic key word searching systems. Therefore, a private set of images partially taken from Juma'a Al-Majid Center in Dubai for evaluation is used, while using a slightly modified version of the IFN/ENIT database for training.

Scale model test results of several STOVL ventral nozzle concepts

NASA Technical Reports Server (NTRS)

Meyer, B. E.; Re, R. J.; Yetter, J. A.

1991-01-01

Short take-off and vertical landing (STOVL) ventral nozzle concepts are investigated by means of a static cold flow scale model at a NASA facility. The internal aerodynamic performance characteristics of the cruise, transition, and vertical lift modes are considered for four ventral nozzle types. The nozzle configurations examined include those with: butterfly-type inner doors and vectoring exit vanes; circumferential inner doors and thrust vectoring vanes; a three-port segmented version with circumferential inner doors; and a two-port segmented version with cylindrical nozzle exit shells. During the testing, internal and external pressure is measured, and the thrust and flow coefficients and resultant vector angles are obtained. The inner door used for ventral nozzle flow control is found to affect performance negatively during the initial phase of transition. The best thrust performance is demonstrated by the two-port segmented ventral nozzle due to the elimination of the inner door.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

PubMed

Gadala-Maria, Daniel; Yaari, Gur; Uduman, Mohamed; Kleinstein, Steven H

2015-02-24

Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses.

[Bioimpedometry and its utilization in dialysis therapy].

PubMed

Lopot, František

2016-01-01

Measurement of living tissue impedance - bioimpedometry - started to be used in medicine some 50 years ago, first exclusively for estimation of extracellular and intracellular compartment volumes. Its most simple single frequency (50 kHz) version works directly with the measured impedance vector. Technically more sophisticated versions convert the measured impedance in values of volumes of different compartments of body fluids and calculate also principal markers of nutritional status (lean body mass, adipose tissue mass). The latest version specifically developed for application in dialysis patients includes body composition modelling and provides even absolute value of overhydration (excess fluid). Still in experimental phase is the bioimpedance exploitation for more precise estimation of residual glomerular filtration. Not yet standardized is also segmental bioimpedance measurement which should enable separate assessment of hydration status of the trunk segment and ultrafiltration capacity of peritoneum in peritoneal dialysis patients.Key words: assessment - bioimpedance - excess fluid - fluid status - glomerular filtration - haemodialysis - nutritional status - peritoneal dialysis.

Reconstruction of ECG signals in presence of corruption.

PubMed

Ganeshapillai, Gartheeban; Liu, Jessica F; Guttag, John

2011-01-01

We present an approach to identifying and reconstructing corrupted regions in a multi-parameter physiological signal. The method, which uses information in correlated signals, is specifically designed to preserve clinically significant aspects of the signals. We use template matching to jointly segment the multi-parameter signal, morphological dissimilarity to estimate the quality of the signal segment, similarity search using features on a database of templates to find the closest match, and time-warping to reconstruct the corrupted segment with the matching template. In experiments carried out on the MIT-BIH Arrhythmia Database, a two-parameter database with many clinically significant arrhythmias, our method improved the classification accuracy of the beat type by more than 7 times on a signal corrupted with white Gaussian noise, and increased the similarity to the original signal, as measured by the normalized residual distance, by more than 2.5 times.

Resources | Division of Cancer Prevention

Cancer.gov

Manual of Operations Version 3, 12/13/2012 (PDF, 162KB) Database Sources Consortium for Functional Glycomics databases Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases (EUROCarbDB) |

PIRLS 2011 User Guide for the International Database. Supplement 1: International Version of the PIRLS 2011, Background Questionnaires and Curriculum Questionnaire

ERIC Educational Resources Information Center

Foy, Pierre, Ed.; Drucker, Kathleen T., Ed.

2013-01-01

The PIRLS 2011 international database includes data for all questionnaires administered as part of the PIRLS 2011 assessment. This supplement contains the international version of the PIRLS 2011 background questionnaires and curriculum questionnaires in the following 5 sections: (1) Student Questionnaire; (2) Home Questionnaire (Learning to Read…

Enhancing atlas based segmentation with multiclass linear classifiers

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

Sdika, Michaël, E-mail: michael.sdika@creatis.insa-lyon.fr

Purpose: To present a method to enrich atlases for atlas based segmentation. Such enriched atlases can then be used as a single atlas or within a multiatlas framework. Methods: In this paper, machine learning techniques have been used to enhance the atlas based segmentation approach. The enhanced atlas defined in this work is a pair composed of a gray level image alongside an image of multiclass classifiers with one classifier per voxel. Each classifier embeds local information from the whole training dataset that allows for the correction of some systematic errors in the segmentation and accounts for the possible localmore » registration errors. The authors also propose to use these images of classifiers within a multiatlas framework: results produced by a set of such local classifier atlases can be combined using a label fusion method. Results: Experiments have been made on the in vivo images of the IBSR dataset and a comparison has been made with several state-of-the-art methods such as FreeSurfer and the multiatlas nonlocal patch based method of Coupé or Rousseau. These experiments show that their method is competitive with state-of-the-art methods while having a low computational cost. Further enhancement has also been obtained with a multiatlas version of their method. It is also shown that, in this case, nonlocal fusion is unnecessary. The multiatlas fusion can therefore be done efficiently. Conclusions: The single atlas version has similar quality as state-of-the-arts multiatlas methods but with the computational cost of a naive single atlas segmentation. The multiatlas version offers a improvement in quality and can be done efficiently without a nonlocal strategy.« less

RESIS-II: An Updated Version of the Original Reservoir Sedimentation Survey Information System (RESIS) Database

USGS Publications Warehouse

Ackerman, Katherine V.; Mixon, David M.; Sundquist, Eric T.; Stallard, Robert F.; Schwarz, Gregory E.; Stewart, David W.

2009-01-01

The Reservoir Sedimentation Survey Information System (RESIS) database, originally compiled by the Soil Conservation Service (now the Natural Resources Conservation Service) in collaboration with the Texas Agricultural Experiment Station, is the most comprehensive compilation of data from reservoir sedimentation surveys throughout the conterminous United States (U.S.). The database is a cumulative historical archive that includes data from as early as 1755 and as late as 1993. The 1,823 reservoirs included in the database range in size from farm ponds to the largest U.S. reservoirs (such as Lake Mead). Results from 6,617 bathymetric surveys are available in the database. This Data Series provides an improved version of the original RESIS database, termed RESIS-II, and a report describing RESIS-II. The RESIS-II relational database is stored in Microsoft Access and includes more precise location coordinates for most of the reservoirs than the original database but excludes information on reservoir ownership. RESIS-II is anticipated to be a template for further improvements in the database.

[3D modeling of the female pelvis by Computer-Assisted Anatomical Dissection: Applications and perspectives].

PubMed

Balaya, V; Uhl, J-F; Lanore, A; Salachas, C; Samoyeau, T; Ngo, C; Bensaid, C; Cornou, C; Rossi, L; Douard, R; Bats, A-S; Lecuru, F; Delmas, V

2016-05-01

To achieve a 3D vectorial model of a female pelvis by Computer-Assisted Anatomical Dissection and to assess educationnal and surgical applications. From the database of "visible female" of Visible Human Project(®) (VHP) of the "national library of medicine" NLM (United States), we used 739 transverse anatomical slices of 0.33mm thickness going from L4 to the trochanters. The manual segmentation of each anatomical structures was done with Winsurf(®) software version 4.3. Each anatomical element was built as a separate vectorial object. The whole colored-rendered vectorial model with realistic textures was exported in 3Dpdf format to allow a real time interactive manipulation with Acrobat(®) pro version 11 software. Each element can be handled separately at any transparency, which allows an anatomical learning by systems: skeleton, pelvic organs, urogenital system, arterial and venous vascularization. This 3D anatomical model can be used as data bank to teach of the fundamental anatomy. This 3D vectorial model, realistic and interactive constitutes an efficient educational tool for the teaching of the anatomy of the pelvis. 3D printing of the pelvis is possible with the new printers. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

The Chandra Source Catalog: Storage and Interfaces

NASA Astrophysics Data System (ADS)

van Stone, David; Harbo, Peter N.; Tibbetts, Michael S.; Zografou, Panagoula; Evans, Ian N.; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Hain, Roger; Hall, Diane M.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph B.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Winkelman, Sherry L.

2009-09-01

The Chandra Source Catalog (CSC) is part of the Chandra Data Archive (CDA) at the Chandra X-ray Center. The catalog contains source properties and associated data objects such as images, spectra, and lightcurves. The source properties are stored in relational databases and the data objects are stored in files with their metadata stored in databases. The CDA supports different versions of the catalog: multiple fixed release versions and a live database version. There are several interfaces to the catalog: CSCview, a graphical interface for building and submitting queries and for retrieving data objects; a command-line interface for property and source searches using ADQL; and VO-compliant services discoverable though the VO registry. This poster describes the structure of the catalog and provides an overview of the interfaces.

Validation of Automated White Matter Hyperintensity Segmentation

PubMed Central

Smart, Sean D.; Firbank, Michael J.; O'Brien, John T.

2011-01-01

Introduction. White matter hyperintensities (WMHs) are a common finding on MRI scans of older people and are associated with vascular disease. We compared 3 methods for automatically segmenting WMHs from MRI scans. Method. An operator manually segmented WMHs on MRI images from a 3T scanner. The scans were also segmented in a fully automated fashion by three different programmes. The voxel overlap between manual and automated segmentation was compared. Results. Between observer overlap ratio was 63%. Using our previously described in-house software, we had overlap of 62.2%. We investigated the use of a modified version of SPM segmentation; however, this was not successful, with only 14% overlap. Discussion. Using our previously reported software, we demonstrated good segmentation of WMHs in a fully automated fashion. PMID:21904678

The new interactive CESAR

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

Fox, P.B.; Yatabe, M.

1987-01-01

In this report the Nuclear Criticality Safety Analytical Methods Resource Center describes a new interactive version of CESAR, a critical experiments storage and retrieval program available on the Nuclear Criticality Information System (NCIS) database at Lawrence Livermore National Laboratory. The original version of CESAR did not include interactive search capabilities. The CESAR database was developed to provide a convenient, readily accessible means of storing and retrieving code input data for the SCALE Criticality Safety Analytical Sequences and the codes comprising those sequences. The database includes data for both cross section preparation and criticality safety calculations. 3 refs., 1 tab.

A User''s Guide to the Zwikker-Kosten Transmission Line Code (ZKTL)

NASA Technical Reports Server (NTRS)

Kelly, J. J.; Abu-Khajeel, H.

1997-01-01

This user's guide documents updates to the Zwikker-Kosten Transmission Line Code (ZKTL). This code was developed for analyzing new liner concepts developed to provide increased sound absorption. Contiguous arrays of multi-degree-of-freedom (MDOF) liner elements serve as the model for these liner configurations, and Zwikker and Kosten's theory of sound propagation in channels is used to predict the surface impedance. Transmission matrices for the various liner elements incorporate both analytical and semi-empirical methods. This allows standard matrix techniques to be employed in the code to systematically calculate the composite impedance due to the individual liner elements. The ZKTL code consists of four independent subroutines: 1. Single channel impedance calculation - linear version (SCIC) 2. Single channel impedance calculation - nonlinear version (SCICNL) 3. Multi-channel, multi-segment, multi-layer impedance calculation - linear version (MCMSML) 4. Multi-channel, multi-segment, multi-layer impedance calculation - nonlinear version (MCMSMLNL) Detailed examples, comments, and explanations for each liner impedance computation module are included. Also contained in the guide are depictions of the interactive execution, input files and output files.

Effect of segmentation algorithms on the performance of computerized detection of lung nodules in CT

PubMed Central

Guo, Wei; Li, Qiang

2014-01-01

Purpose: The purpose of this study is to reveal how the performance of lung nodule segmentation algorithm impacts the performance of lung nodule detection, and to provide guidelines for choosing an appropriate segmentation algorithm with appropriate parameters in a computer-aided detection (CAD) scheme. Methods: The database consisted of 85 CT scans with 111 nodules of 3 mm or larger in diameter from the standard CT lung nodule database created by the Lung Image Database Consortium. The initial nodule candidates were identified as those with strong response to a selective nodule enhancement filter. A uniform viewpoint reformation technique was applied to a three-dimensional nodule candidate to generate 24 two-dimensional (2D) reformatted images, which would be used to effectively distinguish between true nodules and false positives. Six different algorithms were employed to segment the initial nodule candidates in the 2D reformatted images. Finally, 2D features from the segmented areas in the 24 reformatted images were determined, selected, and classified for removal of false positives. Therefore, there were six similar CAD schemes, in which only the segmentation algorithms were different. The six segmentation algorithms included the fixed thresholding (FT), Otsu thresholding (OTSU), fuzzy C-means (FCM), Gaussian mixture model (GMM), Chan and Vese model (CV), and local binary fitting (LBF). The mean Jaccard index and the mean absolute distance (Dmean) were employed to evaluate the performance of segmentation algorithms, and the number of false positives at a fixed sensitivity was employed to evaluate the performance of the CAD schemes. Results: For the segmentation algorithms of FT, OTSU, FCM, GMM, CV, and LBF, the highest mean Jaccard index between the segmented nodule and the ground truth were 0.601, 0.586, 0.588, 0.563, 0.543, and 0.553, respectively, and the corresponding Dmean were 1.74, 1.80, 2.32, 2.80, 3.48, and 3.18 pixels, respectively. With these segmentation results of the six segmentation algorithms, the six CAD schemes reported 4.4, 8.8, 3.4, 9.2, 13.6, and 10.4 false positives per CT scan at a sensitivity of 80%. Conclusions: When multiple algorithms are available for segmenting nodule candidates in a CAD scheme, the “optimal” segmentation algorithm did not necessarily lead to the “optimal” CAD detection performance. PMID:25186393

Unified framework for automated iris segmentation using distantly acquired face images.

PubMed

Tan, Chun-Wei; Kumar, Ajay

2012-09-01

Remote human identification using iris biometrics has high civilian and surveillance applications and its success requires the development of robust segmentation algorithm to automatically extract the iris region. This paper presents a new iris segmentation framework which can robustly segment the iris images acquired using near infrared or visible illumination. The proposed approach exploits multiple higher order local pixel dependencies to robustly classify the eye region pixels into iris or noniris regions. Face and eye detection modules have been incorporated in the unified framework to automatically provide the localized eye region from facial image for iris segmentation. We develop robust postprocessing operations algorithm to effectively mitigate the noisy pixels caused by the misclassification. Experimental results presented in this paper suggest significant improvement in the average segmentation errors over the previously proposed approaches, i.e., 47.5%, 34.1%, and 32.6% on UBIRIS.v2, FRGC, and CASIA.v4 at-a-distance databases, respectively. The usefulness of the proposed approach is also ascertained from recognition experiments on three different publicly available databases.

Developing a Procedure for Segmenting Meshed Heat Networks of Heat Supply Systems without Outflows

NASA Astrophysics Data System (ADS)

Tokarev, V. V.

2018-06-01

The heat supply systems of cities have, as a rule, a ring structure with the possibility of redistributing the flows. Despite the fact that a ring structure is more reliable than a radial one, the operators of heat networks prefer to use them in normal modes according to the scheme without overflows of the heat carrier between the heat mains. With such a scheme, it is easier to adjust the networks and to detect and locate faults in them. The article proposes a formulation of the heat network segmenting problem. The problem is set in terms of optimization with the heat supply system's excessive hydraulic power used as the optimization criterion. The heat supply system computer model has a hierarchically interconnected multilevel structure. Since iterative calculations are only carried out for the level of trunk heat networks, decomposing the entire system into levels allows the dimensionality of the solved subproblems to be reduced by an order of magnitude. An attempt to solve the problem by fully enumerating possible segmentation versions does not seem to be feasible for systems of really existing sizes. The article suggests a procedure for searching rational segmentation of heat supply networks with limiting the search to versions of dividing the system into segments near the flow convergence nodes with subsequent refining of the solution. The refinement is performed in two stages according to the total excess hydraulic power criterion. At the first stage, the loads are redistributed among the sources. After that, the heat networks are divided into independent fragments, and the possibility of increasing the excess hydraulic power in the obtained fragments is checked by shifting the division places inside a fragment. The proposed procedure has been approbated taking as an example a municipal heat supply system involving six heat mains fed from a common source, 24 loops within the feeding mains plane, and more than 5000 consumers. Application of the proposed segmentation procedure made it possible to find a version with required hydraulic power in the heat supply system on 3% less than the one found using the simultaneous segmentation method.

CUNY+ Web: Usability Study of the Web-Based GUI Version of the Bibliographic Database of the City University of New York (CUNY).

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

Describes the usability evaluation of the CUNY (City University of New York) information system in Web and Graphical User Interface (GUI) versions. Compares results to an earlier usability study of the basic information database available on CUNY's wide-area network and describes the applicability of the previous usability instrument to this…

In Praise of Mr. S. Platter and His Marvelous, Magnificent CD ROM Laser Disc Index for ERIC and PSYCHLIT.

ERIC Educational Resources Information Center

Huffman, Robert F.

These instructions are designed to help patrons of the University of Missouri-Columbia library perform searches on PSYCHLIT, a CD-ROM (compact disc, read only memory) version of the Psych Abstracts database, and a CD-ROM version of the ERIC database, both produced by SilverPlatter Information Services. Basic information is provided about the disk…

Geochemical Database for Igneous Rocks of the Ancestral Cascades Arc - Southern Segment, California and Nevada

USGS Publications Warehouse

du Bray, Edward A.; John, David A.; Putirka, Keith; Cousens, Brian L.

2009-01-01

Volcanic rocks that form the southern segment of the Cascades magmatic arc are an important manifestation of Cenozoic subduction and associated magmatism in western North America. Until recently, these rocks had been little studied and no systematic compilation of existing composition data had been assembled. This report is a compilation of all available chemical data for igneous rocks that constitute the southern segment of the ancestral Cascades magmatic arc and complement a previously completed companion compilation that pertains to rocks that constitute the northern segment of the arc. Data for more than 2,000 samples from a diversity of sources were identified and incorporated in the database. The association between these igneous rocks and spatially and temporally associated mineral deposits is well established and suggests a probable genetic relationship. The ultimate goal of the related research is an evaluation of the time-space-compositional evolution of magmatism associated with the southern Cascades arc segment and identification of genetic associations between magmatism and mineral deposits in this region.

Pre-Calculus California Content Standards: Standards Deconstruction Project. Version 1.0

ERIC Educational Resources Information Center

Arnold, Bruce; Cliffe, Karen; Cubillo, Judy; Kracht, Brenda; Leaf, Abi; Legner, Mary; McGinity, Michelle; Orr, Michael; Rocha, Mario; Ross, Judy; Teegarden, Terrie; Thomson, Sarah; Villero, Geri

2008-01-01

This project was coordinated and funded by the California Partnership for Achieving Student Success (Cal-PASS). Cal-PASS is a data sharing system linking all segments of education. Its purpose is to improve student transition and success from one educational segment to the next. Cal-PASS' standards deconstruction project was initiated by the…

Dual-Mode Adhesive Pad

NASA Technical Reports Server (NTRS)

Hartz, Leslie

1994-01-01

Tool helps worker grip and move along large, smooth structure with no handgrips or footholds. Adheres to surface but easily released by actuating simple mechanism. Includes handle and segmented contact-adhesive pad. Bulk of pad made of soft plastic foam conforming to surface of structure. Each segment reinforced with rib. In sticking mode, ribs braced by side catches. In peeling mode, side catches retracted, and segmented adhesive pad loses its stiffness. Modified versions useful in inspecting hulls of ships and scaling walls in rescue operations.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection

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

Zhuang, Xiahai, E-mail: zhuangxiahai@sjtu.edu.cn; Qian, Xiaohua; Bai, Wenjia

Purpose: Cardiac computed tomography (CT) is widely used in clinical diagnosis of cardiovascular diseases. Whole heart segmentation (WHS) plays a vital role in developing new clinical applications of cardiac CT. However, the shape and appearance of the heart can vary greatly across different scans, making the automatic segmentation particularly challenging. The objective of this work is to develop and evaluate a multiatlas segmentation (MAS) scheme using a new atlas ranking and selection algorithm for automatic WHS of CT data. Research on different MAS strategies and their influence on WHS performance are limited. This work provides a detailed comparison study evaluatingmore » the impacts of label fusion, atlas ranking, and sizes of the atlas database on the segmentation performance. Methods: Atlases in a database were registered to the target image using a hierarchical registration scheme specifically designed for cardiac images. A subset of the atlases were selected for label fusion, according to the authors’ proposed atlas ranking criterion which evaluated the performance of each atlas by computing the conditional entropy of the target image given the propagated atlas labeling. Joint label fusion was used to combine multiple label estimates to obtain the final segmentation. The authors used 30 clinical cardiac CT angiography (CTA) images to evaluate the proposed MAS scheme and to investigate different segmentation strategies. Results: The mean WHS Dice score of the proposed MAS method was 0.918 ± 0.021, and the mean runtime for one case was 13.2 min on a workstation. This MAS scheme using joint label fusion generated significantly better Dice scores than the other label fusion strategies, including majority voting (0.901 ± 0.276, p < 0.01), locally weighted voting (0.905 ± 0.0247, p < 0.01), and probabilistic patch-based fusion (0.909 ± 0.0249, p < 0.01). In the atlas ranking study, the proposed criterion based on conditional entropy yielded a performance curve with higher WHS Dice scores compared to the conventional schemes (p < 0.03). In the atlas database study, the authors showed that the MAS using larger atlas databases generated better performance curves than the MAS using smaller ones, indicating larger atlas databases could produce more accurate segmentation. Conclusions: The authors have developed a new MAS framework for automatic WHS of CTA and investigated alternative implementations of MAS. With the proposed atlas ranking algorithm and joint label fusion, the MAS scheme is able to generate accurate segmentation within practically acceptable computation time. This method can be useful for the development of new clinical applications of cardiac CT.« less

Development and Implementation of a Segment/Junction Box Level Database for the ITS Fiber Optic Conduit Network

DOT National Transportation Integrated Search

2012-03-01

This project initiated the development of a computerized database of ITS facilities, including conduits, junction : boxes, cameras, connections, etc. The current system consists of a database of conduit sections of various lengths. : Over the length ...

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

National Transportation Atlas Databases : 1995

DOT National Transportation Integrated Search

1995-01-01

BTS has compiled the initial version of a geographic atlas : database to support research, analysis, and decision making : across all modes of transportation. The atlas databases are : designed primarily to meet the needs of DOT at the national : lev...

Automatic Skin Lesion Segmentation Using Deep Fully Convolutional Networks With Jaccard Distance.

PubMed

Yuan, Yading; Chao, Ming; Lo, Yeh-Chi

2017-09-01

Automatic skin lesion segmentation in dermoscopic images is a challenging task due to the low contrast between lesion and the surrounding skin, the irregular and fuzzy lesion borders, the existence of various artifacts, and various imaging acquisition conditions. In this paper, we present a fully automatic method for skin lesion segmentation by leveraging 19-layer deep convolutional neural networks that is trained end-to-end and does not rely on prior knowledge of the data. We propose a set of strategies to ensure effective and efficient learning with limited training data. Furthermore, we design a novel loss function based on Jaccard distance to eliminate the need of sample re-weighting, a typical procedure when using cross entropy as the loss function for image segmentation due to the strong imbalance between the number of foreground and background pixels. We evaluated the effectiveness, efficiency, as well as the generalization capability of the proposed framework on two publicly available databases. One is from ISBI 2016 skin lesion analysis towards melanoma detection challenge, and the other is the PH2 database. Experimental results showed that the proposed method outperformed other state-of-the-art algorithms on these two databases. Our method is general enough and only needs minimum pre- and post-processing, which allows its adoption in a variety of medical image segmentation tasks.

Michigan urban trunkline segments safety performance functions (SPFs) : final report.

DOT National Transportation Integrated Search

2016-07-01

This study involves the development of safety performance functions (SPFs) for urban and suburban trunkline segments in the : state of Michigan. Extensive databases were developed through the integration of traffic crash information, traffic volumes,...

Analysis of normal human retinal vascular network architecture using multifractal geometry

PubMed Central

Ţălu, Ştefan; Stach, Sebastian; Călugăru, Dan Mihai; Lupaşcu, Carmen Alina; Nicoară, Simona Delia

2017-01-01

AIM To apply the multifractal analysis method as a quantitative approach to a comprehensive description of the microvascular network architecture of the normal human retina. METHODS Fifty volunteers were enrolled in this study in the Ophthalmological Clinic of Cluj-Napoca, Romania, between January 2012 and January 2014. A set of 100 segmented and skeletonised human retinal images, corresponding to normal states of the retina were studied. An automatic unsupervised method for retinal vessel segmentation was applied before multifractal analysis. The multifractal analysis of digital retinal images was made with computer algorithms, applying the standard box-counting method. Statistical analyses were performed using the GraphPad InStat software. RESULTS The architecture of normal human retinal microvascular network was able to be described using the multifractal geometry. The average of generalized dimensions (Dq) for q=0, 1, 2, the width of the multifractal spectrum (Δα=αmax − αmin) and the spectrum arms' heights difference (|Δf|) of the normal images were expressed as mean±standard deviation (SD): for segmented versions, D0=1.7014±0.0057; D1=1.6507±0.0058; D2=1.5772±0.0059; Δα=0.92441±0.0085; |Δf|= 0.1453±0.0051; for skeletonised versions, D0=1.6303±0.0051; D1=1.6012±0.0059; D2=1.5531±0.0058; Δα=0.65032±0.0162; |Δf|= 0.0238±0.0161. The average of generalized dimensions (Dq) for q=0, 1, 2, the width of the multifractal spectrum (Δα) and the spectrum arms' heights difference (|Δf|) of the segmented versions was slightly greater than the skeletonised versions. CONCLUSION The multifractal analysis of fundus photographs may be used as a quantitative parameter for the evaluation of the complex three-dimensional structure of the retinal microvasculature as a potential marker for early detection of topological changes associated with retinal diseases. PMID:28393036

Segmentation of pulmonary nodules in computed tomography using a regression neural network approach and its application to the Lung Image Database Consortium and Image Database Resource Initiative dataset.

PubMed

Messay, Temesguen; Hardie, Russell C; Tuinstra, Timothy R

2015-05-01

We present new pulmonary nodule segmentation algorithms for computed tomography (CT). These include a fully-automated (FA) system, a semi-automated (SA) system, and a hybrid system. Like most traditional systems, the new FA system requires only a single user-supplied cue point. On the other hand, the SA system represents a new algorithm class requiring 8 user-supplied control points. This does increase the burden on the user, but we show that the resulting system is highly robust and can handle a variety of challenging cases. The proposed hybrid system starts with the FA system. If improved segmentation results are needed, the SA system is then deployed. The FA segmentation engine has 2 free parameters, and the SA system has 3. These parameters are adaptively determined for each nodule in a search process guided by a regression neural network (RNN). The RNN uses a number of features computed for each candidate segmentation. We train and test our systems using the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) data. To the best of our knowledge, this is one of the first nodule-specific performance benchmarks using the new LIDC-IDRI dataset. We also compare the performance of the proposed methods with several previously reported results on the same data used by those other methods. Our results suggest that the proposed FA system improves upon the state-of-the-art, and the SA system offers a considerable boost over the FA system. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

An updated version of NPIDB includes new classifications of DNA–protein complexes and their families

PubMed Central

Zanegina, Olga; Kirsanov, Dmitriy; Baulin, Eugene; Karyagina, Anna; Alexeevski, Andrei; Spirin, Sergey

2016-01-01

The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain–DNA complexes and 17 DNA–protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA–protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family. PMID:26656949

19 CFR 351.304 - Establishing business proprietary treatment of information.

Code of Federal Regulations, 2012 CFR

2012-04-01

... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

19 CFR 351.304 - Establishing business proprietary treatment of information.

Code of Federal Regulations, 2013 CFR

2013-04-01

... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

19 CFR 351.304 - Establishing business proprietary treatment of information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

Mission and Assets Database

NASA Technical Reports Server (NTRS)

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

Bit by Bit or All at Once? Splitting up the Inquiry Task to Promote Children's Scientific Reasoning

ERIC Educational Resources Information Center

Lazonder, Ard W.; Kamp, Ellen

2012-01-01

This study examined whether and why assigning children to a segmented inquiry task makes their investigations more productive. Sixty-one upper elementary-school pupils engaged in a simulation-based inquiry assignment either received a multivariable inquiry task (n = 21), a segmented version of this task that addressed the variables in successive…

A comparison of in-cloud HCl concentrations from the NASA/MSFC MDM to measurements for the space shuttle launch

NASA Technical Reports Server (NTRS)

Glasser, M. E.

1981-01-01

The Multilevel Diffusion Model (MDM) Version 5 was modified to include features of more recent versions. The MDM was used to predict in-cloud HCl concentrations for the April 12 launch of the space Shuttle (STS-1). The maximum centerline predictions were compared with measurements of maximum gaseous HCl obtained from aircraft passes through two segments of the fragmented shuttle ground cloud. The model over-predicted the maximum values for gaseous HCl in the lower cloud segment and portrayed the same rate of decay with time as the observed values. However, the decay with time of HCl maximum predicted by the MDM was more rapid than the observed decay for the higher cloud segment, causing the model to under-predict concentrations which were measured late in the life of the cloud. The causes of the tendency for the MDM to be conservative in over-estimating the HCl concentrations in the one case while tending to under-predict concentrations in the other case are discussed.

ASM Based Synthesis of Handwritten Arabic Text Pages

PubMed Central

Al-Hamadi, Ayoub; Elzobi, Moftah; El-etriby, Sherif; Ghoneim, Ahmed

2015-01-01

Document analysis tasks, as text recognition, word spotting, or segmentation, are highly dependent on comprehensive and suitable databases for training and validation. However their generation is expensive in sense of labor and time. As a matter of fact, there is a lack of such databases, which complicates research and development. This is especially true for the case of Arabic handwriting recognition, that involves different preprocessing, segmentation, and recognition methods, which have individual demands on samples and ground truth. To bypass this problem, we present an efficient system that automatically turns Arabic Unicode text into synthetic images of handwritten documents and detailed ground truth. Active Shape Models (ASMs) based on 28046 online samples were used for character synthesis and statistical properties were extracted from the IESK-arDB database to simulate baselines and word slant or skew. In the synthesis step ASM based representations are composed to words and text pages, smoothed by B-Spline interpolation and rendered considering writing speed and pen characteristics. Finally, we use the synthetic data to validate a segmentation method. An experimental comparison with the IESK-arDB database encourages to train and test document analysis related methods on synthetic samples, whenever no sufficient natural ground truthed data is available. PMID:26295059

ASM Based Synthesis of Handwritten Arabic Text Pages.

PubMed

Dinges, Laslo; Al-Hamadi, Ayoub; Elzobi, Moftah; El-Etriby, Sherif; Ghoneim, Ahmed

2015-01-01

Document analysis tasks, as text recognition, word spotting, or segmentation, are highly dependent on comprehensive and suitable databases for training and validation. However their generation is expensive in sense of labor and time. As a matter of fact, there is a lack of such databases, which complicates research and development. This is especially true for the case of Arabic handwriting recognition, that involves different preprocessing, segmentation, and recognition methods, which have individual demands on samples and ground truth. To bypass this problem, we present an efficient system that automatically turns Arabic Unicode text into synthetic images of handwritten documents and detailed ground truth. Active Shape Models (ASMs) based on 28046 online samples were used for character synthesis and statistical properties were extracted from the IESK-arDB database to simulate baselines and word slant or skew. In the synthesis step ASM based representations are composed to words and text pages, smoothed by B-Spline interpolation and rendered considering writing speed and pen characteristics. Finally, we use the synthetic data to validate a segmentation method. An experimental comparison with the IESK-arDB database encourages to train and test document analysis related methods on synthetic samples, whenever no sufficient natural ground truthed data is available.

White blood cell segmentation by color-space-based k-means clustering.

PubMed

Zhang, Congcong; Xiao, Xiaoyan; Li, Xiaomei; Chen, Ying-Jie; Zhen, Wu; Chang, Jun; Zheng, Chengyun; Liu, Zhi

2014-09-01

White blood cell (WBC) segmentation, which is important for cytometry, is a challenging issue because of the morphological diversity of WBCs and the complex and uncertain background of blood smear images. This paper proposes a novel method for the nucleus and cytoplasm segmentation of WBCs for cytometry. A color adjustment step was also introduced before segmentation. Color space decomposition and k-means clustering were combined for segmentation. A database including 300 microscopic blood smear images were used to evaluate the performance of our method. The proposed segmentation method achieves 95.7% and 91.3% overall accuracy for nucleus segmentation and cytoplasm segmentation, respectively. Experimental results demonstrate that the proposed method can segment WBCs effectively with high accuracy.

DNAStat, version 2.1--a computer program for processing genetic profile databases and biostatistical calculations.

PubMed

Berent, Jarosław

2010-01-01

This paper presents the new DNAStat version 2.1 for processing genetic profile databases and biostatistical calculations. The popularization of DNA studies employed in the judicial system has led to the necessity of developing appropriate computer programs. Such programs must, above all, address two critical problems, i.e. the broadly understood data processing and data storage, and biostatistical calculations. Moreover, in case of terrorist attacks and mass natural disasters, the ability to identify victims by searching related individuals is very important. DNAStat version 2.1 is an adequate program for such purposes. The DNAStat version 1.0 was launched in 2005. In 2006, the program was updated to 1.1 and 1.2 versions. There were, however, slight differences between those versions and the original one. The DNAStat version 2.0 was launched in 2007 and the major program improvement was an introduction of the group calculation options with the potential application to personal identification of mass disasters and terrorism victims. The last 2.1 version has the option of language selection--Polish or English, which will enhance the usage and application of the program also in other countries.

Geodemographic segmentation systems for screening health data.

PubMed Central

Openshaw, S; Blake, M

1995-01-01

AIM--To describe how geodemographic segmentation systems might be useful as a quick and easy way of exploring postcoded health databases for potential interesting patterns related to deprivation and other socioeconomic characteristics. DESIGN AND SETTING--This is demonstrated using GB Profiles, a freely available geodemographic classification system developed at Leeds University. It is used here to screen a database of colorectal cancer registrations as a first step in the analysis of that data. RESULTS AND CONCLUSION--Conventional geodemographics is a fairly simple technology and a number of outstanding methodological problems are identified. A solution to some problems is illustrated by using neural net based classifiers and then by reference to a more sophisticated geodemographic approach via a data optimal segmentation technique. Images PMID:8594132

Automatic detection and segmentation of brain metastases on multimodal MR images with a deep convolutional neural network.

PubMed

Charron, Odelin; Lallement, Alex; Jarnet, Delphine; Noblet, Vincent; Clavier, Jean-Baptiste; Meyer, Philippe

2018-04-01

Stereotactic treatments are today the reference techniques for the irradiation of brain metastases in radiotherapy. The dose per fraction is very high, and delivered in small volumes (diameter <1 cm). As part of these treatments, effective detection and precise segmentation of lesions are imperative. Many methods based on deep-learning approaches have been developed for the automatic segmentation of gliomas, but very little for that of brain metastases. We adapted an existing 3D convolutional neural network (DeepMedic) to detect and segment brain metastases on MRI. At first, we sought to adapt the network parameters to brain metastases. We then explored the single or combined use of different MRI modalities, by evaluating network performance in terms of detection and segmentation. We also studied the interest of increasing the database with virtual patients or of using an additional database in which the active parts of the metastases are separated from the necrotic parts. Our results indicated that a deep network approach is promising for the detection and the segmentation of brain metastases on multimodal MRI. Copyright © 2018 Elsevier Ltd. All rights reserved.

A prefiltering version of the Kalman filter with new numerical integration formulas for Riccati equations

NASA Technical Reports Server (NTRS)

Womble, M. E.; Potter, J. E.

1975-01-01

A prefiltering version of the Kalman filter is derived for both discrete and continuous measurements. The derivation consists of determining a single discrete measurement that is equivalent to either a time segment of continuous measurements or a set of discrete measurements. This prefiltering version of the Kalman filter easily handles numerical problems associated with rapid transients and ill-conditioned Riccati matrices. Therefore, the derived technique for extrapolating the Riccati matrix from one time to the next constitutes a new set of integration formulas which alleviate ill-conditioning problems associated with continuous Riccati equations. Furthermore, since a time segment of continuous measurements is converted into a single discrete measurement, Potter's square root formulas can be used to update the state estimate and its error covariance matrix. Therefore, if having the state estimate and its error covariance matrix at discrete times is acceptable, the prefilter extends square root filtering with all its advantages, to continuous measurement problems.

Accelerated Leach Testing of GLASS: ALTGLASS Version 3.0

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

Trivelpiece, Cory L.; Jantzen, Carol M.; Crawford, Charles L.

The Accelerated Leach Testing of GLASS (ALTGLASS) database is a collection of data from short- and long-term product consistency tests (PCT, ASTM C1285 A and B) on high level waste (HLW) as well as low activity waste (LAW) glasses. The database provides both U.S. and international researchers with an archive of experimental data for the purpose of studying, modeling, or validating existing models of nuclear waste glass corrosion. The ALTGLASS database is maintained and updated by researchers at the Savannah River National Laboratory (SRNL). This newest version, ALTGLASS Version 3.0, has been updated with an additional 503 rows of datamore » representing PCT results from corrosion experiments conducted in the United States by the Savannah River National Laboratory, Pacific Northwest National Laboratory, Argonne National Laboratory, and the Vitreous State Laboratory (SRNL, PNNL, ANL, VSL, respectively) as well as the National Nuclear Laboratory (NNL) in the United Kingdom.« less

ThermoData Engine Database - Pure Compounds and Binary Mixtures

National Institute of Standards and Technology Data Gateway

SRD 103b NIST ThermoData Engine Version 6.0 - Pure CompoThermoData Engine Database - Pure Compounds and Binary Mixtures (PC database for purchase)   This database contains property data for more than 21,000 pure compounds, 37,500 binary mixtures, 10,000 ternary mixtures, and 6,000 chemical reactions.

USGS cold-water coral geographic database-Gulf of Mexico and western North Atlantic Ocean, version 1.0

USGS Publications Warehouse

Scanlon, Kathryn M.; Waller, Rhian G.; Sirotek, Alexander R.; Knisel, Julia M.; O'Malley, John; Alesandrini, Stian

2010-01-01

The USGS Cold-Water Coral Geographic Database (CoWCoG) provides a tool for researchers and managers interested in studying, protecting, and/or utilizing cold-water coral habitats in the Gulf of Mexico and western North Atlantic Ocean.  The database makes information about the locations and taxonomy of cold-water corals available to the public in an easy-to-access form while preserving the scientific integrity of the data.  The database includes over 1700 entries, mostly from published scientific literature, museum collections, and other databases.  The CoWCoG database is easy to search in a variety of ways, and data can be quickly displayed in table form and on a map by using only the software included with this publication.  Subsets of the database can be selected on the basis of geographic location, taxonomy, or other criteria and exported to one of several available file formats.  Future versions of the database are being planned to cover a larger geographic area and additional taxa.

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

A review of automatic mass detection and segmentation in mammographic images.

PubMed

Oliver, Arnau; Freixenet, Jordi; Martí, Joan; Pérez, Elsa; Pont, Josep; Denton, Erika R E; Zwiggelaar, Reyer

2010-04-01

The aim of this paper is to review existing approaches to the automatic detection and segmentation of masses in mammographic images, highlighting the key-points and main differences between the used strategies. The key objective is to point out the advantages and disadvantages of the various approaches. In contrast with other reviews which only describe and compare different approaches qualitatively, this review also provides a quantitative comparison. The performance of seven mass detection methods is compared using two different mammographic databases: a public digitised database and a local full-field digital database. The results are given in terms of Receiver Operating Characteristic (ROC) and Free-response Receiver Operating Characteristic (FROC) analysis. Copyright 2009 Elsevier B.V. All rights reserved.

Testing the Abbreviated Food Technology Neophobia Scale and its relation to satisfaction with food-related life in university students.

PubMed

Schnettler, Berta; Grunert, Klaus G; Miranda-Zapata, Edgardo; Orellana, Ligia; Sepúlveda, José; Lobos, Germán; Hueche, Clementina; Höger, Yesli

2017-06-01

The aims of this study were to test the relationships between food neophobia, satisfaction with food-related life and food technology neophobia, distinguishing consumer segments according to these variables and characterizing them according to willingness to purchase food produced with novel technologies. A survey was conducted with 372 university students (mean aged=20.4years, SD=2.4). The questionnaire included the Abbreviated version of the Food Technology Neophobia Scale (AFTNS), Satisfaction with Life Scale (SWLS), and a 6-item version of the Food Neophobia Scale (FNS). Using confirmatory factor analysis, it was confirmed that SWFL correlated inversely with FNS, whereas FNS correlated inversely with AFTNS. No relationship was found between SWFL and AFTNS. Two main segments were identified using cluster analysis; these segments differed according to gender and family size. Group 1 (57.8%) possessed higher AFTNS and FNS scores than Group 2 (28.5%). However, these groups did not differ in their SWFL scores. Group 1 was less willing to purchase foods produced with new technologies than Group 2. The AFTNS and the 6-item version of the FNS are suitable instruments to measure acceptance of foods produced using new technologies in South American developing countries. The AFTNS constitutes a parsimonious alternative for the international study of food technology neophobia. Copyright © 2017 Elsevier Ltd. All rights reserved.

DEVELOPMENT AND APPLICATION OF THE DORIAN (DOSE-RESPONSE INFORMATION ANALYSIS) SYSTEM

EPA Science Inventory

• Migration of ArrayTrack from the proprietary Oracle database to open source Postgres database.
• Making the public version of the ebKB available with provisions for soliciting input from collaborators and outside users.
• Continued development ...

• General Electromagnetic Model for the Analysis of Complex Systems (GEMACS) Computer Code Documentation (Version 3). Volume 3, Part 4.

  DTIC Science & Technology

  1983-09-01

  6ENFRAL. ELECTROMAGNETIC MODEL FOR THE ANALYSIS OF COMPLEX SYSTEMS **%(GEMA CS) Computer Code Documentation ii( Version 3 ). A the BDM Corporation Dr...ANALYSIS FnlTcnclRpr F COMPLEX SYSTEM (GmCS) February 81 - July 83- I TR CODE DOCUMENTATION (Version 3 ) 6.PROMN N.REPORT NUMBER 5. CONTRACT ORGAT97...the ti and t2 directions on the source patch. 3 . METHOD: The electric field at a segment observation point due to the source patch j is given by 1-- lnA

Economic Analysis of Cyber Security

DTIC Science & Technology

2006-07-01

vulnerability databases and track the number of incidents reported by U.S. organizations. Many of these are private organizations, such as the security...VULNERABILITY AND ATTACK ESTIMATES Numerous organizations compile vulnerability databases and patch information, and track the number of reported incidents... database / security focus Databases of vulnerabilities identifying the software versions that are susceptible, including information on the method of

Tree chemistry database (version 1.0)

Treesearch

Linda H. Pardo; Molly Robin-Abbott; Natasha Duarte; Eric K. Miller

2005-01-01

The Tree Chemistry Database is a relational database of C, N, P, K, Ca, Mg, Mn, and Al concentrations in bole bark, bole wood, branches, twigs, and foliage. Compiled from data in 218 articles and publications, the database contains reported nutrient and biomass values for tree species in the Northeastern United States. Nutrient data can be sorted on parameters such as...

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

Reference Fluid Thermodynamic and Transport Properties Database (REFPROP)

National Institute of Standards and Technology Data Gateway

SRD 23 NIST Reference Fluid Thermodynamic and Transport Properties Database (REFPROP) (PC database for purchase)   NIST 23 contains revised data in a Windows version of the database, including 105 pure fluids and allowing mixtures of up to 20 components. The fluids include the environmentally acceptable HFCs, traditional HFCs and CFCs and 'natural' refrigerants like ammonia

Text Detection and Translation from Natural Scenes

DTIC Science & Technology

2001-06-01

is no explicit tags around Chinese words. A module for Chinese word segmentation is included in the system. This segmentor uses a word- frequency ... list to make segmentation decisions. We tested the EBMT based method using randomly selected 50 signs from our database, assuming perfect sign

The Golosiiv on-line plate archive database, management and maintenance

NASA Astrophysics Data System (ADS)

Pakuliak, L.; Sergeeva, T.

2007-08-01

We intend to create online version of the database of the MAO NASU plate archive as VO-compatible structures in accordance with principles, developed by the International Virtual Observatory Alliance in order to make them available for world astronomical community. The online version of the log-book database is constructed by means of MySQL+PHP. Data management system provides a user with user interface, gives a capability of detailed traditional form-filling radial search of plates, obtaining some auxiliary sampling, the listing of each collection and permits to browse the detail descriptions of collections. The administrative tool allows database administrator the data correction, enhancement with new data sets and control of the integrity and consistence of the database as a whole. The VO-compatible database is currently constructing under the demands and in the accordance with principles of international data archives and has to be strongly generalized in order to provide a possibility of data mining by means of standard interfaces and to be the best fitted to the demands of WFPDB Group for databases of the plate catalogues. On-going enhancements of database toward the WFPDB bring the problem of the verification of data to the forefront, as it demands the high degree of data reliability. The process of data verification is practically endless and inseparable from data management owing to a diversity of data errors nature, that means to a variety of ploys of their identification and fixing. The current status of MAO NASU glass archive forces the activity in both directions simultaneously: the enhancement of log-book database with new sets of observational data as well as generalized database creation and the cross-identification between them. The VO-compatible version of the database is supplying with digitized data of plates obtained with MicroTek ScanMaker 9800 XL TMA. The scanning procedure is not total but is conducted selectively in the frames of special projects.

Machine Learning Techniques for the Detection of Shockable Rhythms in Automated External Defibrillators

PubMed Central

Irusta, Unai; Morgado, Eduardo; Aramendi, Elisabete; Ayala, Unai; Wik, Lars; Kramer-Johansen, Jo; Eftestøl, Trygve; Alonso-Atienza, Felipe

2016-01-01

Early recognition of ventricular fibrillation (VF) and electrical therapy are key for the survival of out-of-hospital cardiac arrest (OHCA) patients treated with automated external defibrillators (AED). AED algorithms for VF-detection are customarily assessed using Holter recordings from public electrocardiogram (ECG) databases, which may be different from the ECG seen during OHCA events. This study evaluates VF-detection using data from both OHCA patients and public Holter recordings. ECG-segments of 4-s and 8-s duration were analyzed. For each segment 30 features were computed and fed to state of the art machine learning (ML) algorithms. ML-algorithms with built-in feature selection capabilities were used to determine the optimal feature subsets for both databases. Patient-wise bootstrap techniques were used to evaluate algorithm performance in terms of sensitivity (Se), specificity (Sp) and balanced error rate (BER). Performance was significantly better for public data with a mean Se of 96.6%, Sp of 98.8% and BER 2.2% compared to a mean Se of 94.7%, Sp of 96.5% and BER 4.4% for OHCA data. OHCA data required two times more features than the data from public databases for an accurate detection (6 vs 3). No significant differences in performance were found for different segment lengths, the BER differences were below 0.5-points in all cases. Our results show that VF-detection is more challenging for OHCA data than for data from public databases, and that accurate VF-detection is possible with segments as short as 4-s. PMID:27441719

Machine Learning Techniques for the Detection of Shockable Rhythms in Automated External Defibrillators.

PubMed

Figuera, Carlos; Irusta, Unai; Morgado, Eduardo; Aramendi, Elisabete; Ayala, Unai; Wik, Lars; Kramer-Johansen, Jo; Eftestøl, Trygve; Alonso-Atienza, Felipe

2016-01-01

Early recognition of ventricular fibrillation (VF) and electrical therapy are key for the survival of out-of-hospital cardiac arrest (OHCA) patients treated with automated external defibrillators (AED). AED algorithms for VF-detection are customarily assessed using Holter recordings from public electrocardiogram (ECG) databases, which may be different from the ECG seen during OHCA events. This study evaluates VF-detection using data from both OHCA patients and public Holter recordings. ECG-segments of 4-s and 8-s duration were analyzed. For each segment 30 features were computed and fed to state of the art machine learning (ML) algorithms. ML-algorithms with built-in feature selection capabilities were used to determine the optimal feature subsets for both databases. Patient-wise bootstrap techniques were used to evaluate algorithm performance in terms of sensitivity (Se), specificity (Sp) and balanced error rate (BER). Performance was significantly better for public data with a mean Se of 96.6%, Sp of 98.8% and BER 2.2% compared to a mean Se of 94.7%, Sp of 96.5% and BER 4.4% for OHCA data. OHCA data required two times more features than the data from public databases for an accurate detection (6 vs 3). No significant differences in performance were found for different segment lengths, the BER differences were below 0.5-points in all cases. Our results show that VF-detection is more challenging for OHCA data than for data from public databases, and that accurate VF-detection is possible with segments as short as 4-s.

A database of georeferenced nutrient chemistry data for mountain lakes of the Western United States

PubMed Central

Williams, Jason; Labou, Stephanie G.

2017-01-01

Human activities have increased atmospheric nitrogen and phosphorus deposition rates relative to pre-industrial background. In the Western U.S., anthropogenic nutrient deposition has increased nutrient concentrations and stimulated algal growth in at least some remote mountain lakes. The Georeferenced Lake Nutrient Chemistry (GLNC) Database was constructed to create a spatially-extensive lake chemistry database needed to assess atmospheric nutrient deposition effects on Western U.S. mountain lakes. The database includes nitrogen and phosphorus water chemistry data spanning 1964–2015, with 148,336 chemistry results from 51,048 samples collected across 3,602 lakes in the Western U.S. Data were obtained from public databases, government agencies, scientific literature, and researchers, and were formatted into a consistent table structure. All data are georeferenced to a modified version of the National Hydrography Dataset Plus version 2. The database is transparent and reproducible; R code and input files used to format data are provided in an appendix. The database will likely be useful to those assessing spatial patterns of lake nutrient chemistry associated with atmospheric deposition or other environmental stressors. PMID:28509907

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention. PMID:18387211

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 2.

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

Iversen, C.M.; Powell, A.S.; McCormack, M.L.

The second version of the Fine-Root Ecology Database is available for download! Download the full FRED 2.0 data set, user guidance document, map, and list of data sources here. Prior to downloading the data, please read and follow the Data Use Guidelines, and it's worth checking out some tips for using FRED before you begin your analyses. Also, see here for an updating list of corrections to FRED 2.0.

Joint graph cut and relative fuzzy connectedness image segmentation algorithm.

PubMed

Ciesielski, Krzysztof Chris; Miranda, Paulo A V; Falcão, Alexandre X; Udupa, Jayaram K

2013-12-01

We introduce an image segmentation algorithm, called GC(sum)(max), which combines, in novel manner, the strengths of two popular algorithms: Relative Fuzzy Connectedness (RFC) and (standard) Graph Cut (GC). We show, both theoretically and experimentally, that GC(sum)(max) preserves robustness of RFC with respect to the seed choice (thus, avoiding "shrinking problem" of GC), while keeping GC's stronger control over the problem of "leaking though poorly defined boundary segments." The analysis of GC(sum)(max) is greatly facilitated by our recent theoretical results that RFC can be described within the framework of Generalized GC (GGC) segmentation algorithms. In our implementation of GC(sum)(max) we use, as a subroutine, a version of RFC algorithm (based on Image Forest Transform) that runs (provably) in linear time with respect to the image size. This results in GC(sum)(max) running in a time close to linear. Experimental comparison of GC(sum)(max) to GC, an iterative version of RFC (IRFC), and power watershed (PW), based on a variety medical and non-medical images, indicates superior accuracy performance of GC(sum)(max) over these other methods, resulting in a rank ordering of GC(sum)(max)>PW∼IRFC>GC. Copyright © 2013 Elsevier B.V. All rights reserved.

Automatic cardiac LV segmentation in MRI using modified graph cuts with smoothness and interslice constraints.

PubMed

Albà, Xènia; Figueras I Ventura, Rosa M; Lekadir, Karim; Tobon-Gomez, Catalina; Hoogendoorn, Corné; Frangi, Alejandro F

2014-12-01

Magnetic resonance imaging (MRI), specifically late-enhanced MRI, is the standard clinical imaging protocol to assess cardiac viability. Segmentation of myocardial walls is a prerequisite for this assessment. Automatic and robust multisequence segmentation is required to support processing massive quantities of data. A generic rule-based framework to automatically segment the left ventricle myocardium is presented here. We use intensity information, and include shape and interslice smoothness constraints, providing robustness to subject- and study-specific changes. Our automatic initialization considers the geometrical and appearance properties of the left ventricle, as well as interslice information. The segmentation algorithm uses a decoupled, modified graph cut approach with control points, providing a good balance between flexibility and robustness. The method was evaluated on late-enhanced MRI images from a 20-patient in-house database, and on cine-MRI images from a 15-patient open access database, both using as reference manually delineated contours. Segmentation agreement, measured using the Dice coefficient, was 0.81±0.05 and 0.92±0.04 for late-enhanced MRI and cine-MRI, respectively. The method was also compared favorably to a three-dimensional Active Shape Model approach. The experimental validation with two magnetic resonance sequences demonstrates increased accuracy and versatility. © 2013 Wiley Periodicals, Inc.

Metachronous colorectal cancer following segmental or extended colectomy in Lynch syndrome: a systematic review and meta-analysis.

PubMed

Malik, Salim S; Lythgoe, Mark P; McPhail, Mark; Monahan, Kevin J

2017-11-30

Around 5% of colorectal cancers are due to mutations within DNA mismatch repair genes, resulting in Lynch syndrome (LS). These mutations have a high penetrance with early onset of colorectal cancer at a mean age of 45 years. The mainstay of surgical management is either a segmental or extensive colectomy. Currently there is no unified agreement as to which management strategy is superior due to limited conclusive empirical evidence available. A systematic review and meta- analysis to evaluate the risk of metachronous colorectal cancer (MCC) and mortality in LS following segmental and extensive colectomy. A systematic review of the PubMed database was conducted. Studies were included/ excluded based on pre-specified criteria. To assess the risk of MCC and mortality attributed to segmental or extensive colectomies, relative risks (RR) were calculated and corresponding 95% confidence intervals (CI). Publication bias was investigated using funnel plots. Data about mortality, as well as patient ascertainment [Amsterdam criteria (AC), germline mutation (GM)] were also extracted. Statistical analysis was conducted using the R program (version 3.2.3). The literature search identified 85 studies. After further analysis ten studies were eligible for inclusion in data synthesis. Pooled data identified 1389 patients followed up for a mean of 100.7 months with a mean age of onset of 45.5 years of age. A total 1119 patients underwent segmental colectomies with an absolute risk of MCC in this group of 22.4% at the end of follow-up. The 270 patients who had extensive colectomies had a MCC absolute risk of 4.7% (0% in those with a panproctocolecomy). Segmental colectomy was significantly associated with an increased relative risk of MCC (RR = 5.12; 95% CI 2.88-9.11; Fig. 1), although no significant association with mortality was identified (RR = 1.65; 95% CI 0.90-3.02). There was no statistically significant difference in the risk of MCC between AC and GM cohorts (p = 0.5, Chi-squared test). In LS, segmental colectomy results in a significant increased risk of developing MCC. Despite the choice of segmental or extensive colectomies having no statistically significant impact on mortality, the choice of initial surgical management can impact a patient's requirement for further surgery. An extensive colectomy can result in decreased need for further surgery; reduced hospital stays and associated costs. The significant difference in the risk of MCC, following segmental or extensive colectomies should be discussed with patients when deciding appropriate management. An individualised approach should be utilised, taking into account the patient's age, co-morbidities and genotype. In order to determine likely germline-specific effects, or a difference in survival, larger and more comprehensive studies are required.

The Forest Inventory and Analysis Database: Database description and users manual version 4.0 for Phase 2

Treesearch

Sharon W. Woudenberg; Barbara L. Conkling; Barbara M. O' Connell; Elizabeth B. LaPoint; Jeffery A. Turner; Karen L. Waddell

2010-01-01

This document is based on previous documentation of the nationally standardized Forest Inventory and Analysis database (Hansen and others 1992; Woudenberg and Farrenkopf 1995; Miles and others 2001). Documentation of the structure of the Forest Inventory and Analysis database (FIADB) for Phase 2 data, as well as codes and definitions, is provided. Examples for...

Computer programs to characterize alloys and predict cyclic life using the total strain version of strainrange partitioning: Tutorial and users manual, version 1.0

NASA Technical Reports Server (NTRS)

Saltsman, James F.

1992-01-01

This manual presents computer programs for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the total strain version of Strainrange Partitioning (TS-SRP). An extensive database has also been developed in a parallel effort. This database is probably the largest source of high-temperature, creep-fatigue test data available in the public domain and can be used with other life prediction methods as well. This users manual, software, and database are all in the public domain and are available through COSMIC (382 East Broad Street, Athens, GA 30602; (404) 542-3265, FAX (404) 542-4807). Two disks accompany this manual. The first disk contains the source code, executable files, and sample output from these programs. The second disk contains the creep-fatigue data in a format compatible with these programs.

Associative memory model for searching an image database by image snippet

NASA Astrophysics Data System (ADS)

Khan, Javed I.; Yun, David Y.

1994-09-01

This paper presents an associative memory called an multidimensional holographic associative computing (MHAC), which can be potentially used to perform feature based image database query using image snippet. MHAC has the unique capability to selectively focus on specific segments of a query frame during associative retrieval. As a result, this model can perform search on the basis of featural significance described by a subset of the snippet pixels. This capability is critical for visual query in image database because quite often the cognitive index features in the snippet are statistically weak. Unlike, the conventional artificial associative memories, MHAC uses a two level representation and incorporates additional meta-knowledge about the reliability status of segments of information it receives and forwards. In this paper we present the analysis of focus characteristics of MHAC.

An expert system shell for inferring vegetation characteristics: Changes to the historical cover type database (Task F)

NASA Technical Reports Server (NTRS)

1993-01-01

All the options in the NASA VEGetation Workbench (VEG) make use of a database of historical cover types. This database contains results from experiments by scientists on a wide variety of different cover types. The learning system uses the database to provide positive and negative training examples of classes that enable it to learn distinguishing features between classes of vegetation. All the other VEG options use the database to estimate the error bounds involved in the results obtained when various analysis techniques are applied to the sample of cover type data that is being studied. In the previous version of VEG, the historical cover type database was stored as part of the VEG knowledge base. This database was removed from the knowledge base. It is now stored as a series of flat files that are external to VEG. An interface between VEG and these files was provided. The interface allows the user to select which files of historical data to use. The files are then read, and the data are stored in Knowledge Engineering Environment (KEE) units using the same organization of units as in the previous version of VEG. The interface also allows the user to delete some or all of the historical database units from VEG and load new historical data from a file. This report summarizes the use of the historical cover type database in VEG. It then describes the new interface to the files containing the historical data. It describes minor changes that were made to VEG to enable the externally stored database to be used. Test runs to test the operation of the new interface and also to test the operation of VEG using historical data loaded from external files are described. Task F was completed. A Sun cartridge tape containing the KEE and Common Lisp code for the new interface and the modified version of the VEG knowledge base was delivered to the NASA GSFC technical representative.

On a methodology for robust segmentation of nonideal iris images.

PubMed

Schmid, Natalia A; Zuo, Jinyu

2010-06-01

Iris biometric is one of the most reliable biometrics with respect to performance. However, this reliability is a function of the ideality of the data. One of the most important steps in processing nonideal data is reliable and precise segmentation of the iris pattern from remaining background. In this paper, a segmentation methodology that aims at compensating various nonidealities contained in iris images during segmentation is proposed. The virtue of this methodology lies in its capability to reliably segment nonideal imagery that is simultaneously affected with such factors as specular reflection, blur, lighting variation, occlusion, and off-angle images. We demonstrate the robustness of our segmentation methodology by evaluating ideal and nonideal data sets, namely, the Chinese Academy of Sciences iris data version 3 interval subdirectory, the iris challenge evaluation data, the West Virginia University (WVU) data, and the WVU off-angle data. Furthermore, we compare our performance to that of our implementation of Camus and Wildes's algorithm and Masek's algorithm. We demonstrate considerable improvement in segmentation performance over the formerly mentioned algorithms.

Donor cycle and donor segmentation: new tools for improving blood donor management.

PubMed

Veldhuizen, I; Folléa, G; de Kort, W

2013-07-01

An adequate donor population is of key importance for the entire blood transfusion chain. For good donor management, a detailed overview of the donor database is therefore imperative. This study offers a new description of the donor cycle related to the donor management process. It also presents the outcomes of a European Project, Donor Management IN Europe (DOMAINE), regarding the segmentation of the donor population into donor types. Blood establishments (BEs) from 18 European countries, the Thalassaemia International Federation and a representative from the South-Eastern Europe Health Network joined forces in DOMAINE. A questionnaire assessed blood donor management practices and the composition of the donor population using the newly proposed DOMAINE donor segmentation. 48 BEs in 34 European countries were invited to participate. The response rate was high (88%). However, only 14 BEs could deliver data on the composition of their donor population. The data showed large variations and major imbalances in the donor population. In 79% of the countries, inactive donors formed the dominant donor type. Only in 21%, regular donors were the largest subgroup, and in 29%, the proportion of first-time donors was higher than the proportion of regular donors. Good donor management depends on a thorough insight into the flow of donors through their donor career. Segmentation of the donor database is an essential tool to understand the influx and efflux of donors. The DOMAINE donor segmentation helps BEs in understanding their donor database and to adapt their donor recruitment and retention practices accordingly. Ways to use this new tool are proposed. © 2013 International Society of Blood Transfusion.

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

PubMed

López, Yosvany; Nakai, Kenta; Patil, Ashwini

2015-01-01

HitPredict is a consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein-protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of physical, genetic and predicted interactions. Automated integration of interactions is further complicated by varying levels of accuracy of database content and lack of adherence to standard formats. To address these issues, the latest version of HitPredict provides a manually curated dataset of 398 696 physical associations between 70 808 proteins from 105 species. Manual confirmation was used to resolve all issues encountered during data integration. For improved reliability assessment, this version combines a new score derived from the experimental information of the interactions with the original score based on the features of the interacting proteins. The combined interaction score performs better than either of the individual scores in HitPredict as well as the reliability score of another similar database. HitPredict provides a web interface to search proteins and visualize their interactions, and the data can be downloaded for offline analysis. Data usability has been enhanced by mapping protein identifiers across multiple reference databases. Thus, the latest version of HitPredict provides a significantly larger, more reliable and usable dataset of protein-protein interactions from several species for the study of gene groups. Database URL: http://hintdb.hgc.jp/htp. © The Author(s) 2015. Published by Oxford University Press.

What is new in the 2017 ESC clinical practice guidelines : Management of acute myocardial infarction in patients presenting with ST-segment elevation.

PubMed

Lang, Irene M

2018-05-23

Guidelines and recommendations are designed to guide physicians in making decisions in daily practice. Guidelines provide a condensed summary of all available evidence at the time of the writing process. Recommendations take into account the risk-benefit ratio of particular diagnostic or therapeutic means and the impact on outcome, but not monetary or political considerations. Guidelines are not substitutes but are complementary to textbooks and cover the European Society of Cardiology (ESC) core curriculum topics. The level of evidence and the strength of recommendations of particular treatment options were recently newly weighted and graded according to predefined scales. Guidelines endorsement and implementation strategies are based on abridged pocket guidelines versions, electronic version for digital applications, translations into the national languages or extracts with reference to main changes since the last version. The present article represents a condensed summary of new and practically relevant items contained in the 2017 European Society of Cardiology (ESC) guidelines for the management of acute myocardial infarction in patients with ST-segment elevation, with reference to key citations.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, departs from NASA’s Kennedy Space Center in Florida, with two containers on railcars for transport to the Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, departs from the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida, with two containers on railcars for transport to the NASA Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the RPSF. Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

Automatic CT Brain Image Segmentation Using Two Level Multiresolution Mixture Model of EM

NASA Astrophysics Data System (ADS)

Jiji, G. Wiselin; Dehmeshki, Jamshid

2014-04-01

Tissue classification in computed tomography (CT) brain images is an important issue in the analysis of several brain dementias. A combination of different approaches for the segmentation of brain images is presented in this paper. A multi resolution algorithm is proposed along with scaled versions using Gaussian filter and wavelet analysis that extends expectation maximization (EM) algorithm. It is found that it is less sensitive to noise and got more accurate image segmentation than traditional EM. Moreover the algorithm has been applied on 20 sets of CT of the human brain and compared with other works. The segmentation results show the advantages of the proposed work have achieved more promising results and the results have been tested with Doctors.

High Tech High School Interns Develop a Mid-Ocean Ridge Database for Research and Education

NASA Astrophysics Data System (ADS)

Staudigel, D.; Delaney, R.; Staudigel, H.; Koppers, A. A.; Miller, S. P.

2004-12-01

Mid-ocean ridges (MOR) represent one of the most important geographical and geological features on planet Earth. MORs are the locations where plates spread apart, they are the locations of the majority of the Earths' volcanoes that harbor some of the most extreme life forms. These concepts attract much research, but mid-ocean ridges are still effectively underrepresented in the Earth science class rooms. As two High Tech High School students, we began an internship at Scripps to develop a database for mid-ocean ridges as a resource for science and education. This Ridge Catalog will be accessible via http://earthref.org/databases/RC/ and applies a similar structure, design and data archival principle as the Seamount Catalog under EarthRef.org. Major research goals of this project include the development of (1) an archival structure for multibeam and sidescan data, standard bathymetric maps (including ODP-DSDP drill site and dredge locations) or any other arbitrary digital objects relating to MORs, and (2) to compile a global data set for some of the most defining characteristics of every ridge segment including ridge segment length, depth and azimuth and half spreading rates. One of the challenges included the need of making MOR data useful to the scientist as well as the teacher in the class room. Since the basic structure follows the design of the Seamount Catalog closely, we could move our attention to the basic data population of the database. We have pulled together multibeam data for the MOR segments from various public archives (SIOExplorer, SIO-GDC, NGDC, Lamont), and pre-processed it for public use. In particular, we have created individual bathymetric maps for each ridge segment, while merging the multibeam data with global satellite bathymetry data from Smith & Sandwell (1997). The global scale of this database will give it the ability to be used for any number of applications, from cruise planning to data

SU-D-BRD-06: Automated Population-Based Planning for Whole Brain Radiation Therapy

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

Schreibmann, E; Fox, T; Crocker, I

2014-06-01

Purpose: Treatment planning for whole brain radiation treatment is technically a simple process but in practice it takes valuable clinical time of repetitive and tedious tasks. This report presents a method that automatically segments the relevant target and normal tissues and creates a treatment plan in only a few minutes after patient simulation. Methods: Segmentation is performed automatically through morphological operations on the soft tissue. The treatment plan is generated by searching a database of previous cases for patients with similar anatomy. In this search, each database case is ranked in terms of similarity using a customized metric designed formore » sensitivity by including only geometrical changes that affect the dose distribution. The database case with the best match is automatically modified to replace relevant patient info and isocenter position while maintaining original beam and MLC settings. Results: Fifteen patients were used to validate the method. In each of these cases the anatomy was accurately segmented to mean Dice coefficients of 0.970 ± 0.008 for the brain, 0.846 ± 0.009 for the eyes and 0.672 ± 0.111 for the lens as compared to clinical segmentations. Each case was then subsequently matched against a database of 70 validated treatment plans and the best matching plan (termed auto-planned), was compared retrospectively with the clinical plans in terms of brain coverage and maximum doses to critical structures. Maximum doses were reduced by a maximum of 20.809 Gy for the left eye (mean 3.533), by 13.352 (1.311) for the right eye, and by 27.471 (4.856), 25.218 (6.315) for the left and right lens. Time from simulation to auto-plan was 3-4 minutes. Conclusion: Automated database- based matching is an alternative to classical treatment planning that improves quality while providing a cost—effective solution to planning through modifying previous validated plans to match a current patient's anatomy.« less

Shot boundary detection and label propagation for spatio-temporal video segmentation

NASA Astrophysics Data System (ADS)

Piramanayagam, Sankaranaryanan; Saber, Eli; Cahill, Nathan D.; Messinger, David

2015-02-01

This paper proposes a two stage algorithm for streaming video segmentation. In the first stage, shot boundaries are detected within a window of frames by comparing dissimilarity between 2-D segmentations of each frame. In the second stage, the 2-D segments are propagated across the window of frames in both spatial and temporal direction. The window is moved across the video to find all shot transitions and obtain spatio-temporal segments simultaneously. As opposed to techniques that operate on entire video, the proposed approach consumes significantly less memory and enables segmentation of lengthy videos. We tested our segmentation based shot detection method on the TRECVID 2007 video dataset and compared it with block-based technique. Cut detection results on the TRECVID 2007 dataset indicate that our algorithm has comparable results to the best of the block-based methods. The streaming video segmentation routine also achieves promising results on a challenging video segmentation benchmark database.

Medhost: An encyclopedic bibliography of the host plants of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann),Version 2.0

USDA-ARS?s Scientific Manuscript database

MEDHOST,Version 2.0 is the second revision of:"MEDHOST: An encyclopedic bibliography of the host plants of the Mediterranean fruit fly,Ceratitis capitata(Wiedemann),Version 1.0," which was released in 1998 as a Windows-based executable database and listed all plant species reported as hosts of Medit...

FreeSolv: A database of experimental and calculated hydration free energies, with input files

PubMed Central

Mobley, David L.; Guthrie, J. Peter

2014-01-01

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz. PMID:24928188

Adding glycaemic index and glycaemic load functionality to DietPLUS, a Malaysian food composition database and diet intake calculator.

PubMed

Shyam, Sangeetha; Wai, Tony Ng Kock; Arshad, Fatimah

2012-01-01

This paper outlines the methodology to add glycaemic index (GI) and glycaemic load (GL) functionality to food DietPLUS, a Microsoft Excel-based Malaysian food composition database and diet intake calculator. Locally determined GI values and published international GI databases were used as the source of GI values. Previously published methodology for GI value assignment was modified to add GI and GL calculators to the database. Two popular local low GI foods were added to the DietPLUS database, bringing up the total number of foods in the database to 838 foods. Overall, in relation to the 539 major carbohydrate foods in the Malaysian Food Composition Database, 243 (45%) food items had local Malaysian values or were directly matched to International GI database and another 180 (33%) of the foods were linked to closely-related foods in the GI databases used. The mean ± SD dietary GI and GL of the dietary intake of 63 women with previous gestational diabetes mellitus, calculated using DietPLUS version3 were, 62 ± 6 and 142 ± 45, respectively. These values were comparable to those reported from other local studies. DietPLUS version3, a simple Microsoft Excel-based programme aids calculation of diet GI and GL for Malaysian diets based on food records.

The Forest Inventory and Analysis Database Version 4.0: Database Description and Users Manual for Phase 3

Treesearch

Christopher W. Woodall; Barbara L. Conkling; Michael C. Amacher; John W. Coulston; Sarah Jovan; Charles H. Perry; Beth Schulz; Gretchen C. Smith; Susan Will Wolf

2010-01-01

Describes the structure of the Forest Inventory and Analysis Database (FIADB) 4.0 for phase 3 indicators. The FIADB structure provides a consistent framework for storing forest health monitoring data across all ownerships for the entire United States. These data are available to the public.

A UNIMARC Bibliographic Format Database for ABCD

ERIC Educational Resources Information Center

Megnigbeto, Eustache

2012-01-01

Purpose: ABCD is a web-based open and free software suite for library management derived from the UNESCO CDS/ISIS software technology. The first version was launched officially in December 2009 with a MARC 21 bibliographic format database. This paper aims to detail the building of the UNIMARC bibliographic format database for ABCD.…

Segmentation of lung nodules in computed tomography images using dynamic programming and multidirection fusion techniques.

PubMed

Wang, Qian; Song, Enmin; Jin, Renchao; Han, Ping; Wang, Xiaotong; Zhou, Yanying; Zeng, Jianchao

2009-06-01

The aim of this study was to develop a novel algorithm for segmenting lung nodules on three-dimensional (3D) computed tomographic images to improve the performance of computer-aided diagnosis (CAD) systems. The database used in this study consists of two data sets obtained from the Lung Imaging Database Consortium. The first data set, containing 23 nodules (22% irregular nodules, 13% nonsolid nodules, 17% nodules attached to other structures), was used for training. The second data set, containing 64 nodules (37% irregular nodules, 40% nonsolid nodules, 62% nodules attached to other structures), was used for testing. Two key techniques were developed in the segmentation algorithm: (1) a 3D extended dynamic programming model, with a newly defined internal cost function based on the information between adjacent slices, allowing parameters to be adapted to each slice, and (2) a multidirection fusion technique, which makes use of the complementary relationships among different directions to improve the final segmentation accuracy. The performance of this approach was evaluated by the overlap criterion, complemented by the true-positive fraction and the false-positive fraction criteria. The mean values of the overlap, true-positive fraction, and false-positive fraction for the first data set achieved using the segmentation scheme were 66%, 75%, and 15%, respectively, and the corresponding values for the second data set were 58%, 71%, and 22%, respectively. The experimental results indicate that this segmentation scheme can achieve better performance for nodule segmentation than two existing algorithms reported in the literature. The proposed 3D extended dynamic programming model is an effective way to segment sequential images of lung nodules. The proposed multidirection fusion technique is capable of reducing segmentation errors especially for no-nodule and near-end slices, thus resulting in better overall performance.

Methodology for the Evaluation of the Algorithms for Text Line Segmentation Based on Extended Binary Classification

NASA Astrophysics Data System (ADS)

Brodic, D.

2011-01-01

Text line segmentation represents the key element in the optical character recognition process. Hence, testing of text line segmentation algorithms has substantial relevance. All previously proposed testing methods deal mainly with text database as a template. They are used for testing as well as for the evaluation of the text segmentation algorithm. In this manuscript, methodology for the evaluation of the algorithm for text segmentation based on extended binary classification is proposed. It is established on the various multiline text samples linked with text segmentation. Their results are distributed according to binary classification. Final result is obtained by comparative analysis of cross linked data. At the end, its suitability for different types of scripts represents its main advantage.

Metabolically active tumour volume segmentation from dynamic [(18)F]FLT PET studies in non-small cell lung cancer.

PubMed

Hoyng, Lieke L; Frings, Virginie; Hoekstra, Otto S; Kenny, Laura M; Aboagye, Eric O; Boellaard, Ronald

2015-01-01

Positron emission tomography (PET) with (18)F-3'-deoxy-3'-fluorothymidine ([(18)F]FLT) can be used to assess tumour proliferation. A kinetic-filtering (KF) classification algorithm has been suggested for segmentation of tumours in dynamic [(18)F]FLT PET data. The aim of the present study was to evaluate KF segmentation and its test-retest performance in [(18)F]FLT PET in non-small cell lung cancer (NSCLC) patients. Nine NSCLC patients underwent two 60-min dynamic [(18)F]FLT PET scans within 7 days prior to treatment. Dynamic scans were reconstructed with filtered back projection (FBP) as well as with ordered subsets expectation maximisation (OSEM). Twenty-eight lesions were identified by an experienced physician. Segmentation was performed using KF applied to the dynamic data set and a source-to-background corrected 50% threshold (A50%) was applied to the sum image of the last three frames (45- to 60-min p.i.). Furthermore, several adaptations of KF were tested. Both for KF and A50% test-retest (TRT) variability of metabolically active tumour volume and standard uptake value (SUV) were evaluated. KF performed better on OSEM- than on FBP-reconstructed PET images. The original KF implementation segmented 15 out of 28 lesions, whereas A50% segmented each lesion. Adapted KF versions, however, were able to segment 26 out of 28 lesions. In the best performing adapted versions, metabolically active tumour volume and SUV TRT variability was similar to those of A50%. KF misclassified certain tumour areas as vertebrae or liver tissue, which was shown to be related to heterogeneous [(18)F]FLT uptake areas within the tumour. For [(18)F]FLT PET studies in NSCLC patients, KF and A50% show comparable tumour volume segmentation performance. The KF method needs, however, a site-specific optimisation. The A50% is therefore a good alternative for tumour segmentation in NSCLC [(18)F]FLT PET studies in multicentre studies. Yet, it was observed that KF has the potential to subsegment lesions in high and low proliferative areas.

Comparison of response times of a mobile-web EHRs system using PHP and JSP languages.

PubMed

De la Torre-Díez, Isabel; Antón-Rodríguez, Míriam; Díaz-Pernas, Francisco Javier; Perozo-Rondón, Freddy José

2012-12-01

Performance evaluation is highly important in the Electronic Health Records (EHRs) system implementation. Response time's measurement can be considered as one manner to make that evaluation. In the e-health field, after the creation of EHRs available through different platforms such as Web and/or mobile, a performance evaluation is necessary. The operation of the system in the right way is essential. In this paper, a comparison of the response times for the MEHRmobile system is presented. The first version uses PHP language with a MySQL database and the second one employs JSP with an eXist database. Both versions have got the same functionalities. In addition to the technological aspects, a significant difference is the way the information is stored. The main goal of this paper is choosing the version which offers better response times. We have created a new benchmark to calculate the response times. Better results have been obtained for the PHP version. Nowadays, this version is being used for specialists from Fundación Intras, Spain.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Bossant, M.; Dupont, E.

2014-06-01

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N., E-mail: nicolas.soppera@oecd.org; Bossant, M.; Dupont, E.

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

CALIOP Version 3 Data Products: A Comparison to Version 2

NASA Technical Reports Server (NTRS)

Vaughan, Mark; Omar, Ali; Hunt, Bill; Getzewich, Brian; Tackett, Jason; Powell, Kathy; Avery, Melody; Kuehn, Ralph; Young, Stuart; Hu, Yong;

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

PubMed Central

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S.

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome PMID:26980518

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome. © The Author(s) 2016. Published by Oxford University Press.

Automatic graph-cut based segmentation of bones from knee magnetic resonance images for osteoarthritis research.

PubMed

Ababneh, Sufyan Y; Prescott, Jeff W; Gurcan, Metin N

2011-08-01

In this paper, a new, fully automated, content-based system is proposed for knee bone segmentation from magnetic resonance images (MRI). The purpose of the bone segmentation is to support the discovery and characterization of imaging biomarkers for the incidence and progression of osteoarthritis, a debilitating joint disease, which affects a large portion of the aging population. The segmentation algorithm includes a novel content-based, two-pass disjoint block discovery mechanism, which is designed to support automation, segmentation initialization, and post-processing. The block discovery is achieved by classifying the image content to bone and background blocks according to their similarity to the categories in the training data collected from typical bone structures. The classified blocks are then used to design an efficient graph-cut based segmentation algorithm. This algorithm requires constructing a graph using image pixel data followed by applying a maximum-flow algorithm which generates a minimum graph-cut that corresponds to an initial image segmentation. Content-based refinements and morphological operations are then applied to obtain the final segmentation. The proposed segmentation technique does not require any user interaction and can distinguish between bone and highly similar adjacent structures, such as fat tissues with high accuracy. The performance of the proposed system is evaluated by testing it on 376 MR images from the Osteoarthritis Initiative (OAI) database. This database included a selection of single images containing the femur and tibia from 200 subjects with varying levels of osteoarthritis severity. Additionally, a full three-dimensional segmentation of the bones from ten subjects with 14 slices each, and synthetic images with background having intensity and spatial characteristics similar to those of bone are used to assess the robustness and consistency of the developed algorithm. The results show an automatic bone detection rate of 0.99 and an average segmentation accuracy of 0.95 using the Dice similarity index. Copyright © 2011 Elsevier B.V. All rights reserved.

A segmentation editing framework based on shape change statistics

NASA Astrophysics Data System (ADS)

Mostapha, Mahmoud; Vicory, Jared; Styner, Martin; Pizer, Stephen

2017-02-01

Segmentation is a key task in medical image analysis because its accuracy significantly affects successive steps. Automatic segmentation methods often produce inadequate segmentations, which require the user to manually edit the produced segmentation slice by slice. Because editing is time-consuming, an editing tool that enables the user to produce accurate segmentations by only drawing a sparse set of contours would be needed. This paper describes such a framework as applied to a single object. Constrained by the additional information enabled by the manually segmented contours, the proposed framework utilizes object shape statistics to transform the failed automatic segmentation to a more accurate version. Instead of modeling the object shape, the proposed framework utilizes shape change statistics that were generated to capture the object deformation from the failed automatic segmentation to its corresponding correct segmentation. An optimization procedure was used to minimize an energy function that consists of two terms, an external contour match term and an internal shape change regularity term. The high accuracy of the proposed segmentation editing approach was confirmed by testing it on a simulated data set based on 10 in-vivo infant magnetic resonance brain data sets using four similarity metrics. Segmentation results indicated that our method can provide efficient and adequately accurate segmentations (Dice segmentation accuracy increase of 10%), with very sparse contours (only 10%), which is promising in greatly decreasing the work expected from the user.

Collaborative SDOCT Segmentation and Analysis Software.

PubMed

Yun, Yeyi; Carass, Aaron; Lang, Andrew; Prince, Jerry L; Antony, Bhavna J

2017-02-01

Spectral domain optical coherence tomography (SDOCT) is routinely used in the management and diagnosis of a variety of ocular diseases. This imaging modality also finds widespread use in research, where quantitative measurements obtained from the images are used to track disease progression. In recent years, the number of available scanners and imaging protocols grown and there is a distinct absence of a unified tool that is capable of visualizing, segmenting, and analyzing the data. This is especially noteworthy in longitudinal studies, where data from older scanners and/or protocols may need to be analyzed. Here, we present a graphical user interface (GUI) that allows users to visualize and analyze SDOCT images obtained from two commonly used scanners. The retinal surfaces in the scans can be segmented using a previously described method, and the retinal layer thicknesses can be compared to a normative database. If necessary, the segmented surfaces can also be corrected and the changes applied. The interface also allows users to import and export retinal layer thickness data to an SQL database, thereby allowing for the collation of data from a number of collaborating sites.

A Review of Large Solid Rocket Motor Free Field Acoustics, Part I

NASA Technical Reports Server (NTRS)

Pilkey, Debbie; Kenny, Robert Jeremy

2011-01-01

At the ATK facility in Utah, large full scale solid rocket motors are tested. The largest is a five segment version of the Reusable Solid Rocket Motor, which is for use on future launch vehicles. Since 2006, Acoustic measurements have been taken on large solid rocket motors at ATK. Both the four segment RSRM and the five segment RSRMV have been instrumented. Measurements are used to update acoustic prediction models and to correlate against vibration responses of the motor. Presentation focuses on two major sections: Part I) Unique challenges associated with measuring rocket acoustics Part II) Acoustic measurements summary over past five years

NASA-Ames three-dimensional potential flow analysis system (POTFAN) equation solver code (SOLN) version 1

NASA Technical Reports Server (NTRS)

Davis, J. E.; Bonnett, W. S.; Medan, R. T.

1976-01-01

A computer program known as SOLN was developed as an independent segment of the NASA-Ames three-dimensional potential flow analysis systems of linear algebraic equations. Methods used include: LU decomposition, Householder's method, a partitioning scheme, and a block successive relaxation method. Due to the independent modular nature of the program, it may be used by itself and not necessarily in conjunction with other segments of the POTFAN system.

Atlas-based fuzzy connectedness segmentation and intensity nonuniformity correction applied to brain MRI.

PubMed

Zhou, Yongxin; Bai, Jing

2007-01-01

A framework that combines atlas registration, fuzzy connectedness (FC) segmentation, and parametric bias field correction (PABIC) is proposed for the automatic segmentation of brain magnetic resonance imaging (MRI). First, the atlas is registered onto the MRI to initialize the following FC segmentation. Original techniques are proposed to estimate necessary initial parameters of FC segmentation. Further, the result of the FC segmentation is utilized to initialize a following PABIC algorithm. Finally, we re-apply the FC technique on the PABIC corrected MRI to get the final segmentation. Thus, we avoid expert human intervention and provide a fully automatic method for brain MRI segmentation. Experiments on both simulated and real MRI images demonstrate the validity of the method, as well as the limitation of the method. Being a fully automatic method, it is expected to find wide applications, such as three-dimensional visualization, radiation therapy planning, and medical database construction.

Age-specific MRI templates for pediatric neuroimaging

PubMed Central

Sanchez, Carmen E.; Richards, John E.; Almli, C. Robert

2012-01-01

This study created a database of pediatric age-specific MRI brain templates for normalization and segmentation. Participants included children from 4.5 through 19.5 years, totaling 823 scans from 494 subjects. Open-source processing programs (FSL, SPM, ANTS) constructed head, brain and segmentation templates in 6 month intervals. The tissue classification (WM, GM, CSF) showed changes over age similar to previous reports. A volumetric analysis of age-related changes in WM and GM based on these templates showed expected increase/decrease pattern in GM and an increase in WM over the sampled ages. This database is available for use for neuroimaging studies (blindedforreview). PMID:22799759

Argonne Geothermal Geochemical Database v2.0

DOE Data Explorer

Harto, Christopher

2013-05-22

A database of geochemical data from potential geothermal sources aggregated from multiple sources as of March 2010. The database contains fields for the location, depth, temperature, pH, total dissolved solids concentration, chemical composition, and date of sampling. A separate tab contains data on non-condensible gas compositions. The database contains records for over 50,000 wells, although many entries are incomplete. Current versions of source documentation are listed in the dataset.

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

Biomechanical effects of maxillary expansion on a patient with cleft palate: A finite element analysis

PubMed Central

Lee, Haofu; Nguyen, Alan; Hong, Christine; Hoang, Paul; Pham, John; Ting, Kang

2017-01-01

Introduction The aims of this study were to evaluate the effects of rapid palatal expansion on the craniofacial skeleton of a patient with unilateral cleft lip and palate (UCLP) and to predict the points of force application for optimal expansion using a 3-dimensional finite element model. Methods A 3-dimensional finite element model of the craniofacial complex with UCLP was generated from spiral computed tomographic scans with imaging software (Mimics, version 13.1; Materialise, Leuven, Belgium). This model was imported into the finite element solver (version 12.0; ANSYS, Canonsburg, Pa) to evaluate transverse expansion forces from rapid palatal expansion. Finite element analysis was performed with transverse expansion to achieve 5 mm of anterolateral expansion of the collapsed minor segment to simulate correction of the anterior crossbite in a patient with UCLP. Results High-stress concentrations were observed at the body of the sphenoid, medial to the orbit, and at the inferior area of the zygomatic process of the maxilla. The craniofacial stress distribution was asymmetric, with higher stress levels on the cleft side. When forces were applied more anteriorly on the collapsed minor segment and more posteriorly on the major segment, there was greater expansion of the anterior region of the minor segment with minimal expansion of the major segment. Conclusions The transverse expansion forces from rapid palatal expansion are distributed to the 3 maxillary buttresses. Finite element analysis is an appropriate tool to study and predict the points of force application for better controlled expansion in patients with UCLP. PMID:27476365

Biomechanical effects of maxillary expansion on a patient with cleft palate: A finite element analysis.

PubMed

Lee, Haofu; Nguyen, Alan; Hong, Christine; Hoang, Paul; Pham, John; Ting, Kang

2016-08-01

The aims of this study were to evaluate the effects of rapid palatal expansion on the craniofacial skeleton of a patient with unilateral cleft lip and palate (UCLP) and to predict the points of force application for optimal expansion using a 3-dimensional finite element model. A 3-dimensional finite element model of the craniofacial complex with UCLP was generated from spiral computed tomographic scans with imaging software (Mimics, version 13.1; Materialise, Leuven, Belgium). This model was imported into the finite element solver (version 12.0; ANSYS, Canonsburg, Pa) to evaluate transverse expansion forces from rapid palatal expansion. Finite element analysis was performed with transverse expansion to achieve 5 mm of anterolateral expansion of the collapsed minor segment to simulate correction of the anterior crossbite in a patient with UCLP. High-stress concentrations were observed at the body of the sphenoid, medial to the orbit, and at the inferior area of the zygomatic process of the maxilla. The craniofacial stress distribution was asymmetric, with higher stress levels on the cleft side. When forces were applied more anteriorly on the collapsed minor segment and more posteriorly on the major segment, there was greater expansion of the anterior region of the minor segment with minimal expansion of the major segment. The transverse expansion forces from rapid palatal expansion are distributed to the 3 maxillary buttresses. Finite element analysis is an appropriate tool to study and predict the points of force application for better controlled expansion in patients with UCLP. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

NGA-West2 Flatfiles and GMPE Reports Now Available! | PEER News

Science.gov Websites

equations (GMPEs) and other research studies supporting GMPE development, along with the NGA-West2 Database NGA-West2 database "flatfiles" used in various research components of NGA-West2 have also database for download have been incorporated into an updated version of the online user-friendly PEER

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, travels along the NASA railroad bridge over the Indian River north of Kennedy Space Center, carrying one of two containers on a railcar for transport to the NASA Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, conracted by Goodloe Transportation of Chicago, travels along the NASA railroad bridge over the Indian River north of Kennedy Space Center, with two containers on railcars for transport to the NASA Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, approaches the raised span of the NASA railroad bridge to continue over the Indian River north of Kennedy Space Center with two containers on railcars for storage at the NASA Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, travels along the NASA railroad bridge over the Indian River north of Kennedy Space Center, carrying one of two containers on a railcar for transport to the NASA Jay Jay railroad yard near the center. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

SLS Pathfinder Segments Car Train Departure

NASA Image and Video Library

2016-03-02

An Iowa Northern locomotive, contracted by Goodloe Transportation of Chicago, continues along the NASA railroad bridge over the Indian River north of Kennedy Space Center, carrying one of two containers on a railcar for transport to the NASA Jay Jay railroad yard. The containers held two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket that were delivered to the Rotation, Processing and Surge Facility (RPSF). Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will conduct a series of lifts, moves and stacking operations using the booster segments, which are inert, to prepare for Exploration Mission-1, deep-space missions and the journey to Mars. The pathfinder booster segments are from Orbital ATK in Utah.

Dentalmaps: Automatic Dental Delineation for Radiotherapy Planning in Head-and-Neck Cancer

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

Thariat, Juliette, E-mail: jthariat@hotmail.com; Ramus, Liliane; INRIA

Purpose: To propose an automatic atlas-based segmentation framework of the dental structures, called Dentalmaps, and to assess its accuracy and relevance to guide dental care in the context of intensity-modulated radiotherapy. Methods and Materials: A multi-atlas-based segmentation, less sensitive to artifacts than previously published head-and-neck segmentation methods, was used. The manual segmentations of a 21-patient database were first deformed onto the query using nonlinear registrations with the training images and then fused to estimate the consensus segmentation of the query. Results: The framework was evaluated with a leave-one-out protocol. The maximum doses estimated using manual contours were considered as groundmore » truth and compared with the maximum doses estimated using automatic contours. The dose estimation error was within 2-Gy accuracy in 75% of cases (with a median of 0.9 Gy), whereas it was within 2-Gy accuracy in 30% of cases only with the visual estimation method without any contour, which is the routine practice procedure. Conclusions: Dose estimates using this framework were more accurate than visual estimates without dental contour. Dentalmaps represents a useful documentation and communication tool between radiation oncologists and dentists in routine practice. Prospective multicenter assessment is underway on patients extrinsic to the database.« less

Reverberation negatively impacts musical sound quality for cochlear implant users.

PubMed

Roy, Alexis T; Vigeant, Michelle; Munjal, Tina; Carver, Courtney; Jiradejvong, Patpong; Limb, Charles J

2015-09-01

Satisfactory musical sound quality remains a challenge for many cochlear implant (CI) users. In particular, questionnaires completed by CI users suggest that reverberation due to room acoustics can negatively impact their music listening experience. The objective of this study was to more specifically characterize of the effect of reverberation on musical sound quality in CI users, normal hearing (NH) non-musicians, and NH musicians using a previously designed assessment method, called Cochlear Implant-MUltiple Stimulus with Hidden Reference and Anchor (CI-MUSHRA). In this method, listeners were randomly presented with an anechoic musical segment and five-versions of this segment in which increasing amounts of reverberation were artificially added. Participants listened to the six reverberation versions and provided sound quality ratings between 0 (very poor) and 100 (excellent). Results demonstrated that on average CI users and NH non-musicians preferred the sound quality of anechoic versions to more reverberant versions. In comparison, NH musicians could be delineated into those who preferred the sound quality of anechoic pieces and those who preferred pieces with some reverberation. This is the first study, to our knowledge, to objectively compare the effects of reverberation on musical sound quality ratings in CI users. These results suggest that musical sound quality for CI users can be improved by non-reverberant listening conditions and musical stimuli in which reverberation is removed.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

PubMed

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-11-27

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

PubMed Central

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-01-01

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

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

Enders, Alexander L.; Lousteau, Angela L.

The Desktop Analysis Reporting Tool (DART) is a software package that allows users to easily view and analyze daily files that span long periods. DART gives users the capability to quickly determine the state of health of a radiation portal monitor (RPM), troubleshoot and diagnose problems, and view data in various time frames to perform trend analysis. In short, it converts the data strings written in the daily files into meaningful tables and plots. The standalone version of DART (“soloDART”) utilizes a database engine that is included with the application; no additional installations are necessary. There is also a networkedmore » version of DART (“polyDART”) that is designed to maximize the benefit of a centralized data repository while distributing the workload to individual desktop machines. This networked approach requires a more complex database manager Structured Query Language (SQL) Server; however, SQL Server is not currently provided with DART. Regardless of which version is used, DART will import daily files from RPMs, store the relevant data in its database, and it can produce reports for status, trend analysis, and reporting purposes.« less

U.S. Geological Survey mineral databases; MRDS and MAS/MILS

USGS Publications Warehouse

McFaul, E.J.; Mason, G.T.; Ferguson, W.B.; Lipin, B.R.

2000-01-01

These two CD-ROM's contain the latest version of the Mineral Resources Data System (MRDS) database and the Minerals Availability System/Minerals Industry Location System (MAS/MILS) database for coverage of North America and the world outside North America. The records in the MRDS database each contain almost 200 data fields describing metallic and nonmetallic mineral resources, deposits, and commodities. The records in the MAS/MILS database each contain almost 100 data fields describing mines and mineral processing plans.

Fast Automatic Segmentation of White Matter Streamlines Based on a Multi-Subject Bundle Atlas.

PubMed

Labra, Nicole; Guevara, Pamela; Duclap, Delphine; Houenou, Josselin; Poupon, Cyril; Mangin, Jean-François; Figueroa, Miguel

2017-01-01

This paper presents an algorithm for fast segmentation of white matter bundles from massive dMRI tractography datasets using a multisubject atlas. We use a distance metric to compare streamlines in a subject dataset to labeled centroids in the atlas, and label them using a per-bundle configurable threshold. In order to reduce segmentation time, the algorithm first preprocesses the data using a simplified distance metric to rapidly discard candidate streamlines in multiple stages, while guaranteeing that no false negatives are produced. The smaller set of remaining streamlines is then segmented using the original metric, thus eliminating any false positives from the preprocessing stage. As a result, a single-thread implementation of the algorithm can segment a dataset of almost 9 million streamlines in less than 6 minutes. Moreover, parallel versions of our algorithm for multicore processors and graphics processing units further reduce the segmentation time to less than 22 seconds and to 5 seconds, respectively. This performance enables the use of the algorithm in truly interactive applications for visualization, analysis, and segmentation of large white matter tractography datasets.

Active fault databases: building a bridge between earthquake geologists and seismic hazard practitioners, the case of the QAFI v.3 database

NASA Astrophysics Data System (ADS)

García-Mayordomo, Julián; Martín-Banda, Raquel; Insua-Arévalo, Juan M.; Álvarez-Gómez, José A.; Martínez-Díaz, José J.; Cabral, João

2017-08-01

Active fault databases are a very powerful and useful tool in seismic hazard assessment, particularly when singular faults are considered seismogenic sources. Active fault databases are also a very relevant source of information for earth scientists, earthquake engineers and even teachers or journalists. Hence, active fault databases should be updated and thoroughly reviewed on a regular basis in order to keep a standard quality and uniformed criteria. Desirably, active fault databases should somehow indicate the quality of the geological data and, particularly, the reliability attributed to crucial fault-seismic parameters, such as maximum magnitude and recurrence interval. In this paper we explain how we tackled these issues during the process of updating and reviewing the Quaternary Active Fault Database of Iberia (QAFI) to its current version 3. We devote particular attention to describing the scheme devised for classifying the quality and representativeness of the geological evidence of Quaternary activity and the accuracy of the slip rate estimation in the database. Subsequently, we use this information as input for a straightforward rating of the level of reliability of maximum magnitude and recurrence interval fault seismic parameters. We conclude that QAFI v.3 is a much better database than version 2 either for proper use in seismic hazard applications or as an informative source for non-specialized users. However, we already envision new improvements for a future update.

UNSODA UNSATURATED SOIL HYDRAULIC DATABASE USER'S MANUAL VERSION 1.0

EPA Science Inventory

This report contains general documentation and serves as a user manual of the UNSODA program. UNSODA is a database of unsaturated soil hydraulic properties (water retention, hydraulic conductivity, and soil water diffusivity), basic soil properties (particle-size distribution, b...

Evaluating the Potential of Commercial GIS for Accelerator Configuration Management

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

T.L. Larrieu; Y.R. Roblin; K. White

2005-10-10

The Geographic Information System (GIS) is a tool used by industries needing to track information about spatially distributed assets. A water utility, for example, must know not only the precise location of each pipe and pump, but also the respective pressure rating and flow rate of each. In many ways, an accelerator such as CEBAF (Continuous Electron Beam Accelerator Facility) can be viewed as an ''electron utility''. Whereas the water utility uses pipes and pumps, the ''electron utility'' uses magnets and RF cavities. At Jefferson lab we are exploring the possibility of implementing ESRI's ArcGIS as the framework for buildingmore » an all-encompassing accelerator configuration database that integrates location, configuration, maintenance, and connectivity details of all hardware and software. The possibilities of doing so are intriguing. From the GIS, software such as the model server could always extract the most-up-to-date layout information maintained by the Survey & Alignment for lattice modeling. The Mechanical Engineering department could use ArcGIS tools to generate CAD drawings of machine segments from the same database. Ultimately, the greatest benefit of the GIS implementation could be to liberate operators and engineers from the limitations of the current system-by-system view of machine configuration and allow a more integrated regional approach. The commercial GIS package provides a rich set of tools for database-connectivity, versioning, distributed editing, importing and exporting, and graphical analysis and querying, and therefore obviates the need for much custom development. However, formidable challenges to implementation exist and these challenges are not only technical and manpower issues, but also organizational ones. The GIS approach would crosscut organizational boundaries and require departments, which heretofore have had free reign to manage their own data, to cede some control and agree to a centralized framework.« less

DOEDEF Software System, Version 2. 2: Operational instructions

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

Meirans, L.

The DOEDEF (Department of Energy Data Exchange Format) Software System is a collection of software routines written to facilitate the manipulation of IGES (Initial Graphics Exchange Specification) data. Typically, the IGES data has been produced by the IGES processors for a Computer-Aided Design (CAD) system, and the data manipulations are user-defined ''flavoring'' operations. The DOEDEF Software System is used in conjunction with the RIM (Relational Information Management) DBMS from Boeing Computer Services (Version 7, UD18 or higher). The three major pieces of the software system are: Parser, reads an ASCII IGES file and converts it to the RIM database equivalent;more » Kernel, provides the user with IGES-oriented interface routines to the database; and Filewriter, writes the RIM database to an IGES file.« less

Poster — Thur Eve — 59: Atlas Selection for Automated Segmentation of Pelvic CT for Prostate Radiotherapy

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

Mallawi, A; Farrell, T; Diamond, K

2014-08-15

Automated atlas-based segmentation has recently been evaluated for use in planning prostate cancer radiotherapy. In the typical approach, the essential step is the selection of an atlas from a database that best matches the target image. This work proposes an atlas selection strategy and evaluates its impact on the final segmentation accuracy. Prostate length (PL), right femoral head diameter (RFHD), and left femoral head diameter (LFHD) were measured in CT images of 20 patients. Each subject was then taken as the target image to which all remaining 19 images were affinely registered. For each pair of registered images, the overlapmore » between prostate and femoral head contours was quantified using the Dice Similarity Coefficient (DSC). Finally, we designed an atlas selection strategy that computed the ratio of PL (prostate segmentation), RFHD (right femur segmentation), and LFHD (left femur segmentation) between the target subject and each subject in the atlas database. Five atlas subjects yielding ratios nearest to one were then selected for further analysis. RFHD and LFHD were excellent parameters for atlas selection, achieving a mean femoral head DSC of 0.82 ± 0.06. PL had a moderate ability to select the most similar prostate, with a mean DSC of 0.63 ± 0.18. The DSC obtained with the proposed selection method were slightly lower than the maximums established using brute force, but this does not include potential improvements expected with deformable registration. Atlas selection based on PL for prostate and femoral diameter for femoral heads provides reasonable segmentation accuracy.« less

Clustering approach for unsupervised segmentation of malarial Plasmodium vivax parasite

NASA Astrophysics Data System (ADS)

Abdul-Nasir, Aimi Salihah; Mashor, Mohd Yusoff; Mohamed, Zeehaida

2017-10-01

Malaria is a global health problem, particularly in Africa and south Asia where it causes countless deaths and morbidity cases. Efficient control and prompt of this disease require early detection and accurate diagnosis due to the large number of cases reported yearly. To achieve this aim, this paper proposes an image segmentation approach via unsupervised pixel segmentation of malaria parasite to automate the diagnosis of malaria. In this study, a modified clustering algorithm namely enhanced k-means (EKM) clustering, is proposed for malaria image segmentation. In the proposed EKM clustering, the concept of variance and a new version of transferring process for clustered members are used to assist the assignation of data to the proper centre during the process of clustering, so that good segmented malaria image can be generated. The effectiveness of the proposed EKM clustering has been analyzed qualitatively and quantitatively by comparing this algorithm with two popular image segmentation techniques namely Otsu's thresholding and k-means clustering. The experimental results show that the proposed EKM clustering has successfully segmented 100 malaria images of P. vivax species with segmentation accuracy, sensitivity and specificity of 99.20%, 87.53% and 99.58%, respectively. Hence, the proposed EKM clustering can be considered as an image segmentation tool for segmenting the malaria images.

Mugshot Identification Database (MID)

National Institute of Standards and Technology Data Gateway

NIST Mugshot Identification Database (MID) (Web, free access)   NIST Special Database 18 is being distributed for use in development and testing of automated mugshot identification systems. The database consists of three CD-ROMs, containing a total of 3248 images of variable size using lossless compression. A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

Dictionary learning-based CT detection of pulmonary nodules

NASA Astrophysics Data System (ADS)

Wu, Panpan; Xia, Kewen; Zhang, Yanbo; Qian, Xiaohua; Wang, Ge; Yu, Hengyong

2016-10-01

Segmentation of lung features is one of the most important steps for computer-aided detection (CAD) of pulmonary nodules with computed tomography (CT). However, irregular shapes, complicated anatomical background and poor pulmonary nodule contrast make CAD a very challenging problem. Here, we propose a novel scheme for feature extraction and classification of pulmonary nodules through dictionary learning from training CT images, which does not require accurately segmented pulmonary nodules. Specifically, two classification-oriented dictionaries and one background dictionary are learnt to solve a two-category problem. In terms of the classification-oriented dictionaries, we calculate sparse coefficient matrices to extract intrinsic features for pulmonary nodule classification. The support vector machine (SVM) classifier is then designed to optimize the performance. Our proposed methodology is evaluated with the lung image database consortium and image database resource initiative (LIDC-IDRI) database, and the results demonstrate that the proposed strategy is promising.

Generation of Fullspan Leading-Edge 3D Ice Shapes for Swept-Wing Aerodynamic Testing

NASA Technical Reports Server (NTRS)

Camello, Stephanie C.; Lee, Sam; Lum, Christopher; Bragg, Michael B.

2016-01-01

The deleterious effect of ice accretion on aircraft is often assessed through dry-air flight and wind tunnel testing with artificial ice shapes. This paper describes a method to create fullspan swept-wing artificial ice shapes from partial span ice segments acquired in the NASA Glenn Icing Reserch Tunnel for aerodynamic wind-tunnel testing. Full-scale ice accretion segments were laser scanned from the Inboard, Midspan, and Outboard wing station models of the 65% scale Common Research Model (CRM65) aircraft configuration. These were interpolated and extrapolated using a weighted averaging method to generate fullspan ice shapes from the root to the tip of the CRM65 wing. The results showed that this interpolation method was able to preserve many of the highly three dimensional features typically found on swept-wing ice accretions. The interpolated fullspan ice shapes were then scaled to fit the leading edge of a 8.9% scale version of the CRM65 wing for aerodynamic wind-tunnel testing. Reduced fidelity versions of the fullspan ice shapes were also created where most of the local three-dimensional features were removed. The fullspan artificial ice shapes and the reduced fidelity versions were manufactured using stereolithography.

Identification of everyday objects on the basis of Gaborized outline versions

PubMed Central

Sassi, Michaël; Vancleef, Kathleen; Machilsen, Bart; Panis, Sven; Wagemans, Johan

2010-01-01

Using outlines derived from a widely used set of line drawings, we created stimuli geared towards the investigation of contour integration and texture segmentation using shapes of everyday objects. Each stimulus consisted of Gabor elements positioned and oriented curvilinearly along the outline of an object, embedded within a larger Gabor array of homogeneous density. We created six versions of the resulting Gaborized outline stimuli by varying the orientations of elements inside and outside the outline. Data from two experiments, in which participants attempted to identify the objects in the stimuli, provide norms for identifiability and name agreement, and show differences in identifiability between stimulus versions. While there was substantial variability between the individual objects in our stimulus set, further analyses suggest a number of stimulus properties which are generally predictive of identification performance. The stimuli and the accompanying normative data, both available on our website (http://www.gestaltrevision.be/sources/gaboroutlines), provide a useful tool to further investigate contour integration and texture segmentation in both normal and clinical populations, especially when top-down influences on these processes, such as the role of prior knowledge of familiar objects, are of main interest. PMID:23145218

Identification of everyday objects on the basis of Gaborized outline versions.

PubMed

Sassi, Michaël; Vancleef, Kathleen; Machilsen, Bart; Panis, Sven; Wagemans, Johan

2010-01-01

Using outlines derived from a widely used set of line drawings, we created stimuli geared towards the investigation of contour integration and texture segmentation using shapes of everyday objects. Each stimulus consisted of Gabor elements positioned and oriented curvilinearly along the outline of an object, embedded within a larger Gabor array of homogeneous density. We created six versions of the resulting Gaborized outline stimuli by varying the orientations of elements inside and outside the outline. Data from two experiments, in which participants attempted to identify the objects in the stimuli, provide norms for identifiability and name agreement, and show differences in identifiability between stimulus versions. While there was substantial variability between the individual objects in our stimulus set, further analyses suggest a number of stimulus properties which are generally predictive of identification performance. The stimuli and the accompanying normative data, both available on our website (http://www.gestaltrevision.be/sources/gaboroutlines), provide a useful tool to further investigate contour integration and texture segmentation in both normal and clinical populations, especially when top-down influences on these processes, such as the role of prior knowledge of familiar objects, are of main interest.

Geologic map of the eastern part of the Challis National Forest and vicinity, Idaho

USGS Publications Warehouse

Wilson, A.B.; Skipp, B.A.

1994-01-01

The paper version of the Geologic Map of the eastern part of the Challis National Forest and vicinity, Idaho was compiled by Anna Wilson and Betty Skipp in 1994. The geology was compiled on a 1:250,000 scale topographic base map. TechniGraphic System, Inc. of Fort Collins Colorado digitized this map under contract for N.Shock. G.Green edited and prepared the digital version for publication as a GIS database. The digital geologic map database can be queried in many ways to produce a variety of geologic maps.

The StarLite Project Prototyping Real-Time Software

DTIC Science & Technology

1991-10-01

multiversion data objects using the prototyping environment. Section 5 concludes the paper. 2. Message-Based Simulation When prototyping distributed...phase locking and priority-based synchronization algorithms, and between a multiversion database and its corresponding single-version database, through...its deadline, since the transaction is only aborted in the validation phase. 4.5. A Multiversion Database System To illustrate the effctivcness of the

NIST/ASME Steam Properties Database

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

GALT protein database: querying structural and functional features of GALT enzyme.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2014-09-01

Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. © 2014 WILEY PERIODICALS, INC.

RREL TREATABILITY DATABASE - VERSION 5.0

EPA Science Inventory

There is no abstract available for this product. If further information is requested, please refer to the bibliographic citation and contact the person listed under Contact field. This database can be obtained by contacting Tom Holdsworth, U.S. EPA, 26 West Martin Luther King D...

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Automatic segmentation of solitary pulmonary nodules based on local intensity structure analysis and 3D neighborhood features in 3D chest CT images

NASA Astrophysics Data System (ADS)

Chen, Bin; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

2012-03-01

This paper presents a solitary pulmonary nodule (SPN) segmentation method based on local intensity structure analysis and neighborhood feature analysis in chest CT images. Automated segmentation of SPNs is desirable for a chest computer-aided detection/diagnosis (CAS) system since a SPN may indicate early stage of lung cancer. Due to the similar intensities of SPNs and other chest structures such as blood vessels, many false positives (FPs) are generated by nodule detection methods. To reduce such FPs, we introduce two features that analyze the relation between each segmented nodule candidate and it neighborhood region. The proposed method utilizes a blob-like structure enhancement (BSE) filter based on Hessian analysis to augment the blob-like structures as initial nodule candidates. Then a fine segmentation is performed to segment much more accurate region of each nodule candidate. FP reduction is mainly addressed by investigating two neighborhood features based on volume ratio and eigenvector of Hessian that are calculates from the neighborhood region of each nodule candidate. We evaluated the proposed method by using 40 chest CT images, include 20 standard-dose CT images that we randomly chosen from a local database and 20 low-dose CT images that were randomly chosen from a public database: LIDC. The experimental results revealed that the average TP rate of proposed method was 93.6% with 12.3 FPs/case.

Emergence of Convolutional Neural Network in Future Medicine: Why and How. A Review on Brain Tumor Segmentation

NASA Astrophysics Data System (ADS)

Alizadeh Savareh, Behrouz; Emami, Hassan; Hajiabadi, Mohamadreza; Ghafoori, Mahyar; Majid Azimi, Seyed

2018-03-01

Manual analysis of brain tumors magnetic resonance images is usually accompanied by some problem. Several techniques have been proposed for the brain tumor segmentation. This study will be focused on searching popular databases for related studies, theoretical and practical aspects of Convolutional Neural Network surveyed in brain tumor segmentation. Based on our findings, details about related studies including the datasets used, evaluation parameters, preferred architectures and complementary steps analyzed. Deep learning as a revolutionary idea in image processing, achieved brilliant results in brain tumor segmentation too. This can be continuing until the next revolutionary idea emerging.

Lessons Learned Implementing DOORS in a Citrix Environment

NASA Technical Reports Server (NTRS)

Bussman, Marie

2005-01-01

NASA's James Web Space Telescope (JWST) Project is a large multi-national project with geographically dispersed contractors that all need access to the Projects requirement database. Initially, the project utilized multiple DOORS databases with the built-in partitions feature to exchange modules amongst the various contractor sites. As the requirements databases matured the use of partitions became extremely difficult. There have been many issues such as incompatible versions of DOORS, inefficient mechanism for sharing modules, security concerns, performance issues, and inconsistent document import and export formats. Deployment of the client software with limited IT resources available was also an issue. The solution chosen by JWST was to integrate the use of a Citrix environment with the DOORS database to address most of the project concerns. The use of the Citrix solution allowed a single Requirements database in a secure environment via a web interface. The Citrix environment allows JWST to upgrade to the most current version of DOORS without having to coordinate multiple sites and user upgrades. The single requirements database eliminates a multitude of Configuration Management concerns and facilitated the standardization of documentation formats. This paper discusses the obstacles and the lessons learned throughout the installation, implementation, usage and deployment process of a centralized DOORS database solution.

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

Members of the news media view the high bay inside the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida. Kerry Chreist, with Jacobs Engineering on the Test and Operations Support Contract, talks with a reporter about the booster segments for NASA’s Space Launch System (SLS) rocket. In the far corner, in the vertical position, is one of two pathfinders, or test versions, of solid rocket booster segments for the SLS rocket. The Ground Systems Development and Operations Program and Jacobs are preparing the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

Members of the news media watch as two cranes are used to lift one of two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System (SLS) rocket into the vertical position inside the Rotation, Processing and Surge Facility at NASA’s Kennedy Space Center in Florida. The pathfinder booster segment will be moved to the other end of the RPSF and secured on a test stand. The Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will prepare the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

How does temporal variability in model parameters affect the risk conclusions from MCnest?

EPA Science Inventory

USEPA recently began using the MCnest model for avian risk for adverse reproductive effects due to pesticide exposure. A more advanced version is currently under development and beta testing for use with threatened and endangered birds. For both versions, a species database has...

"The Incorporation of National Emission Inventories into Version 2 of the Hemispheric Transport of Air Pollutants Inventory"

EPA Science Inventory

EPA’s National Emission Inventory has been incorporated into the Emission Database for Global Atmospheric Research-Hemispheric Transport of Air Pollutants (EDGAR-HTAP) version 2. This work involves the creation of a detailed mapping of EPA Source Classification Codes (SCC) to the...

Serials Information on CD-ROM: A Reference Perspective.

ERIC Educational Resources Information Center

Karch, Linda S.

1990-01-01

Describes Ulrich's PLUS (a CD-ROM version of Ulrich's serials directories) and EBSCO's CD-ROM version of "The Serials Directory," and compares the two in terms of their use as reference tools. Areas discussed include database content, user aids, system features, search features, and a comparison of search results. Equipment requirements…

The Invar tensor package: Differential invariants of Riemann

NASA Astrophysics Data System (ADS)

Martín-García, J. M.; Yllanes, D.; Portugal, R.

2008-10-01

The long standing problem of the relations among the scalar invariants of the Riemann tensor is computationally solved for all 6ṡ10 objects with up to 12 derivatives of the metric. This covers cases ranging from products of up to 6 undifferentiated Riemann tensors to cases with up to 10 covariant derivatives of a single Riemann. We extend our computer algebra system Invar to produce within seconds a canonical form for any of those objects in terms of a basis. The process is as follows: (1) an invariant is converted in real time into a canonical form with respect to the permutation symmetries of the Riemann tensor; (2) Invar reads a database of more than 6ṡ10 relations and applies those coming from the cyclic symmetry of the Riemann tensor; (3) then applies the relations coming from the Bianchi identity, (4) the relations coming from commutations of covariant derivatives, (5) the dimensionally-dependent identities for dimension 4, and finally (6) simplifies invariants that can be expressed as product of dual invariants. Invar runs on top of the tensor computer algebra systems xTensor (for Mathematica) and Canon (for Maple). Program summaryProgram title:Invar Tensor Package v2.0 Catalogue identifier:ADZK_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZK_v2_0.html Program obtainable from:CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:3 243 249 No. of bytes in distributed program, including test data, etc.:939 Distribution format:tar.gz Programming language:Mathematica and Maple Computer:Any computer running Mathematica versions 5.0 to 6.0 or Maple versions 9 and 11 Operating system:Linux, Unix, Windows XP, MacOS RAM:100 Mb Word size:64 or 32 bits Supplementary material:The new database of relations is much larger than that for the previous version and therefore has not been included in the distribution. To obtain the Mathematica and Maple database files click on this link. Classification:1.5, 5 Does the new version supersede the previous version?:Yes. The previous version (1.0) only handled algebraic invariants. The current version (2.0) has been extended to cover differential invariants as well. Nature of problem:Manipulation and simplification of scalar polynomial expressions formed from the Riemann tensor and its covariant derivatives. Solution method:Algorithms of computational group theory to simplify expressions with tensors that obey permutation symmetries. Tables of syzygies of the scalar invariants of the Riemann tensor. Reasons for new version:With this new version, the user can manipulate differential invariants of the Riemann tensor. Differential invariants are required in many physical problems in classical and quantum gravity. Summary of revisions:The database of syzygies has been expanded by a factor of 30. New commands were added in order to deal with the enlarged database and to manipulate the covariant derivative. Restrictions:The present version only handles scalars, and not expressions with free indices. Additional comments:The distribution file for this program is over 53 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time:One second to fully reduce any monomial of the Riemann tensor up to degree 7 or order 10 in terms of independent invariants. The Mathematica notebook included in the distribution takes approximately 5 minutes to run.

GenomeVista

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

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

Multiple Object Retrieval in Image Databases Using Hierarchical Segmentation Tree

ERIC Educational Resources Information Center

Chen, Wei-Bang

2012-01-01

The purpose of this research is to develop a new visual information analysis, representation, and retrieval framework for automatic discovery of salient objects of user's interest in large-scale image databases. In particular, this dissertation describes a content-based image retrieval framework which supports multiple-object retrieval. The…

Concentrations of indoor pollutants (CIP) database user's manual (Version 4. 0)

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

Apte, M.G.; Brown, S.R.; Corradi, C.A.

1990-10-01

This is the latest release of the database and the user manual. The user manual is a tutorial and reference for utilizing the CIP Database system. An installation guide is included to cover various hardware configurations. Numerous examples and explanations of the dialogue between the user and the database program are provided. It is hoped that this resource will, along with on-line help and the menu-driven software, make for a quick and easy learning curve. For the purposes of this manual, it is assumed that the user is acquainted with the goals of the CIP Database, which are: (1) tomore » collect existing measurements of concentrations of indoor air pollutants in a user-oriented database and (2) to provide a repository of references citing measured field results openly accessible to a wide audience of researchers, policy makers, and others interested in the issues of indoor air quality. The database software, as distinct from the data, is contained in two files, CIP. EXE and PFIL.COM. CIP.EXE is made up of a number of programs written in dBase III command code and compiled using Clipper into a single, executable file. PFIL.COM is a program written in Turbo Pascal that handles the output of summary text files and is called from CIP.EXE. Version 4.0 of the CIP Database is current through March 1990.« less

NASA Access Mechanism: Lessons learned document

NASA Technical Reports Server (NTRS)

Burdick, Lisa; Dunbar, Rick; Duncan, Denise; Generous, Curtis; Hunter, Judy; Lycas, John; Taber-Dudas, Ardeth

1994-01-01

The six-month beta test of the NASA Access Mechanism (NAM) prototype was completed on June 30, 1993. This report documents the lessons learned from the use of this Graphical User Interface to NASA databases such as the NASA STI Database, outside databases, Internet resources, and peers in the NASA R&D community. Design decisions, such as the use of XWindows software, a client-server distributed architecture, and use of the NASA Science Internet, are explained. Users' reactions to the interface and suggestions for design changes are reported, as are the changes made by the software developers based on new technology for information discovery and retrieval. The lessons learned section also reports reactions from the public, both at demonstrations and in response to articles in the trade press and journals. Recommendations are included for future versions, such as a World Wide Web (WWW) and Mosaic based interface to heterogeneous databases, and NAM-Lite, a version which allows customization to include utilities provided locally at NASA Centers.

GPU-based relative fuzzy connectedness image segmentation.

PubMed

Zhuge, Ying; Ciesielski, Krzysztof C; Udupa, Jayaram K; Miller, Robert W

2013-01-01

Recently, clinical radiological research and practice are becoming increasingly quantitative. Further, images continue to increase in size and volume. For quantitative radiology to become practical, it is crucial that image segmentation algorithms and their implementations are rapid and yield practical run time on very large data sets. The purpose of this paper is to present a parallel version of an algorithm that belongs to the family of fuzzy connectedness (FC) algorithms, to achieve an interactive speed for segmenting large medical image data sets. The most common FC segmentations, optimizing an [script-l](∞)-based energy, are known as relative fuzzy connectedness (RFC) and iterative relative fuzzy connectedness (IRFC). Both RFC and IRFC objects (of which IRFC contains RFC) can be found via linear time algorithms, linear with respect to the image size. The new algorithm, P-ORFC (for parallel optimal RFC), which is implemented by using NVIDIA's Compute Unified Device Architecture (CUDA) platform, considerably improves the computational speed of the above mentioned CPU based IRFC algorithm. Experiments based on four data sets of small, medium, large, and super data size, achieved speedup factors of 32.8×, 22.9×, 20.9×, and 17.5×, correspondingly, on the NVIDIA Tesla C1060 platform. Although the output of P-ORFC need not precisely match that of IRFC output, it is very close to it and, as the authors prove, always lies between the RFC and IRFC objects. A parallel version of a top-of-the-line algorithm in the family of FC has been developed on the NVIDIA GPUs. An interactive speed of segmentation has been achieved, even for the largest medical image data set. Such GPU implementations may play a crucial role in automatic anatomy recognition in clinical radiology.

GPU-based relative fuzzy connectedness image segmentation

PubMed Central

Zhuge, Ying; Ciesielski, Krzysztof C.; Udupa, Jayaram K.; Miller, Robert W.

2013-01-01

Purpose: Recently, clinical radiological research and practice are becoming increasingly quantitative. Further, images continue to increase in size and volume. For quantitative radiology to become practical, it is crucial that image segmentation algorithms and their implementations are rapid and yield practical run time on very large data sets. The purpose of this paper is to present a parallel version of an algorithm that belongs to the family of fuzzy connectedness (FC) algorithms, to achieve an interactive speed for segmenting large medical image data sets. Methods: The most common FC segmentations, optimizing an ℓ∞-based energy, are known as relative fuzzy connectedness (RFC) and iterative relative fuzzy connectedness (IRFC). Both RFC and IRFC objects (of which IRFC contains RFC) can be found via linear time algorithms, linear with respect to the image size. The new algorithm, P-ORFC (for parallel optimal RFC), which is implemented by using NVIDIA’s Compute Unified Device Architecture (CUDA) platform, considerably improves the computational speed of the above mentioned CPU based IRFC algorithm. Results: Experiments based on four data sets of small, medium, large, and super data size, achieved speedup factors of 32.8×, 22.9×, 20.9×, and 17.5×, correspondingly, on the NVIDIA Tesla C1060 platform. Although the output of P-ORFC need not precisely match that of IRFC output, it is very close to it and, as the authors prove, always lies between the RFC and IRFC objects. Conclusions: A parallel version of a top-of-the-line algorithm in the family of FC has been developed on the NVIDIA GPUs. An interactive speed of segmentation has been achieved, even for the largest medical image data set. Such GPU implementations may play a crucial role in automatic anatomy recognition in clinical radiology. PMID:23298094

Retinal vessel segmentation using the 2-D Gabor wavelet and supervised classification.

PubMed

Soares, João V B; Leandro, Jorge J G; Cesar Júnior, Roberto M; Jelinek, Herbert F; Cree, Michael J

2006-09-01

We present a method for automated segmentation of the vasculature in retinal images. The method produces segmentations by classifying each image pixel as vessel or nonvessel, based on the pixel's feature vector. Feature vectors are composed of the pixel's intensity and two-dimensional Gabor wavelet transform responses taken at multiple scales. The Gabor wavelet is capable of tuning to specific frequencies, thus allowing noise filtering and vessel enhancement in a single step. We use a Bayesian classifier with class-conditional probability density functions (likelihoods) described as Gaussian mixtures, yielding a fast classification, while being able to model complex decision surfaces. The probability distributions are estimated based on a training set of labeled pixels obtained from manual segmentations. The method's performance is evaluated on publicly available DRIVE (Staal et al., 2004) and STARE (Hoover et al., 2000) databases of manually labeled images. On the DRIVE database, it achieves an area under the receiver operating characteristic curve of 0.9614, being slightly superior than that presented by state-of-the-art approaches. We are making our implementation available as open source MATLAB scripts for researchers interested in implementation details, evaluation, or development of methods.

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

PubMed Central

Killion, Patrick J; Sherlock, Gavin; Iyer, Vishwanath R

2003-01-01

Background The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at Conclusions Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. PMID:12930545

Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China.

PubMed

Grunert, Klaus G; Perrea, Toula; Zhou, Yanfeng; Huang, Guang; Sørensen, Bjarne T; Krystallis, Athanasios

2011-04-01

Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the food related lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument, in which a number of dimensions of the original instrument had to be omitted. This revised instrument was tested for statistical robustness and used as a basis for the derivation of consumer segments. Construct validity of the instrument was then investigated by profiling the segments in terms of consumer values, attitudes and purchase behaviour, using frequency of consumption of pork products as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern replicates partly those identified in Western cultures. Moreover, all three segments showed consistent value-attitude-behaviour profiles. The results also suggest which dimensions may be missing in the instrument in a more comprehensive instrument adapted to Chinese conditions, most notably a broader treatment of eating out activities. Copyright © 2010 Elsevier Ltd. All rights reserved.

Denoising and segmentation of retinal layers in optical coherence tomography images

NASA Astrophysics Data System (ADS)

Dash, Puspita; Sigappi, A. N.

2018-04-01

Optical Coherence Tomography (OCT) is an imaging technique used to localize the intra-retinal boundaries for the diagnostics of macular diseases. Due to speckle noise, low image contrast and accurate segmentation of individual retinal layers is difficult. Due to this, a method for retinal layer segmentation from OCT images is presented. This paper proposes a pre-processing filtering approach for denoising and segmentation methods for segmenting retinal layers OCT images using graph based segmentation technique. These techniques are used for segmentation of retinal layers for normal as well as patients with Diabetic Macular Edema. The algorithm based on gradient information and shortest path search is applied to optimize the edge selection. In this paper the four main layers of the retina are segmented namely Internal limiting membrane (ILM), Retinal pigment epithelium (RPE), Inner nuclear layer (INL) and Outer nuclear layer (ONL). The proposed method is applied on a database of OCT images of both ten normal and twenty DME affected patients and the results are found to be promising.

Automatic Structural Parcellation of Mouse Brain MRI Using Multi-Atlas Label Fusion

PubMed Central

Ma, Da; Cardoso, Manuel J.; Modat, Marc; Powell, Nick; Wells, Jack; Holmes, Holly; Wiseman, Frances; Tybulewicz, Victor; Fisher, Elizabeth; Lythgoe, Mark F.; Ourselin, Sébastien

2014-01-01

Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework. PMID:24475148

Distributed Database Control and Allocation. Volume 3. Distributed Database System Designer’s Handbook.

DTIC Science & Technology

1983-10-01

Multiversion Data 2-18 2.7.1 Multiversion Timestamping 2-20 2.T.2 Multiversion Looking 2-20 2.8 Combining the Techniques 2-22 3. Database Recovery Algorithms...See rTHEM79, GIFF79] for details. 2.7 Multiversion Data Let us return to a database system model where each logical data item is stored at one DM...In a multiversion database each Write wifxl, produces a new copy (or version) of x, denoted xi. Thus, the value of z is a set of ver- sions. For each

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.

PubMed

Nagy, Alinda; Hegyi, Hédi; Farkas, Krisztina; Tordai, Hedvig; Kozma, Evelin; Bányai, László; Patthy, László

2008-08-27

Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i) conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii) presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii) co-occurrence of extracellular and nuclear domains; (iv) violation of domain integrity; (v) chimeras encoded by two or more genes located on different chromosomes. Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis) and two protostome species (Caenorhabditis elegans and Drosophila melanogaster) have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON-predicted entries. MisPred works efficiently in identifying errors in predictions generated by the most reliable gene prediction tools such as the EnsEMBL and NCBI's GNOMON pipelines and also guides the correction of errors. We suggest that application of the MisPred approach will significantly improve the quality of gene predictions and the associated databases.

Conventional and Eccentric Uses of Crystallographic Databases in Practical Materials Identification Problems

PubMed Central

Kaduk, James A.

1996-01-01

The crystallographic databases are powerful and cost-effective tools for solving materials identification problems, both individually and in combination. Examples of the conventional and unconventional use of the databases in solving practical problems involving organic, coordination, and inorganic compounds are provided. The creation and use of fully-relational versions of the Powder Diffraction File and NIST Crystal Data are described. PMID:27805165

Synthesis of Common Arabic Handwritings to Aid Optical Character Recognition Research.

PubMed

Dinges, Laslo; Al-Hamadi, Ayoub; Elzobi, Moftah; El-Etriby, Sherif

2016-03-11

Document analysis tasks such as pattern recognition, word spotting or segmentation, require comprehensive databases for training and validation. Not only variations in writing style but also the used list of words is of importance in the case that training samples should reflect the input of a specific area of application. However, generation of training samples is expensive in the sense of manpower and time, particularly if complete text pages including complex ground truth are required. This is why there is a lack of such databases, especially for Arabic, the second most popular language. However, Arabic handwriting recognition involves different preprocessing, segmentation and recognition methods. Each requires particular ground truth or samples to enable optimal training and validation, which are often not covered by the currently available databases. To overcome this issue, we propose a system that synthesizes Arabic handwritten words and text pages and generates corresponding detailed ground truth. We use these syntheses to validate a new, segmentation based system that recognizes handwritten Arabic words. We found that a modification of an Active Shape Model based character classifiers-that we proposed earlier-improves the word recognition accuracy. Further improvements are achieved, by using a vocabulary of the 50,000 most common Arabic words for error correction.

Synthesis of Common Arabic Handwritings to Aid Optical Character Recognition Research

PubMed Central

Dinges, Laslo; Al-Hamadi, Ayoub; Elzobi, Moftah; El-etriby, Sherif

2016-01-01

Document analysis tasks such as pattern recognition, word spotting or segmentation, require comprehensive databases for training and validation. Not only variations in writing style but also the used list of words is of importance in the case that training samples should reflect the input of a specific area of application. However, generation of training samples is expensive in the sense of manpower and time, particularly if complete text pages including complex ground truth are required. This is why there is a lack of such databases, especially for Arabic, the second most popular language. However, Arabic handwriting recognition involves different preprocessing, segmentation and recognition methods. Each requires particular ground truth or samples to enable optimal training and validation, which are often not covered by the currently available databases. To overcome this issue, we propose a system that synthesizes Arabic handwritten words and text pages and generates corresponding detailed ground truth. We use these syntheses to validate a new, segmentation based system that recognizes handwritten Arabic words. We found that a modification of an Active Shape Model based character classifiers—that we proposed earlier—improves the word recognition accuracy. Further improvements are achieved, by using a vocabulary of the 50,000 most common Arabic words for error correction. PMID:26978368

Efficient Algorithms for Segmentation of Item-Set Time Series

NASA Astrophysics Data System (ADS)

Chundi, Parvathi; Rosenkrantz, Daniel J.

We propose a special type of time series, which we call an item-set time series, to facilitate the temporal analysis of software version histories, email logs, stock market data, etc. In an item-set time series, each observed data value is a set of discrete items. We formalize the concept of an item-set time series and present efficient algorithms for segmenting a given item-set time series. Segmentation of a time series partitions the time series into a sequence of segments where each segment is constructed by combining consecutive time points of the time series. Each segment is associated with an item set that is computed from the item sets of the time points in that segment, using a function which we call a measure function. We then define a concept called the segment difference, which measures the difference between the item set of a segment and the item sets of the time points in that segment. The segment difference values are required to construct an optimal segmentation of the time series. We describe novel and efficient algorithms to compute segment difference values for each of the measure functions described in the paper. We outline a dynamic programming based scheme to construct an optimal segmentation of the given item-set time series. We use the item-set time series segmentation techniques to analyze the temporal content of three different data sets—Enron email, stock market data, and a synthetic data set. The experimental results show that an optimal segmentation of item-set time series data captures much more temporal content than a segmentation constructed based on the number of time points in each segment, without examining the item set data at the time points, and can be used to analyze different types of temporal data.

LARCRIM user's guide, version 1.0

NASA Technical Reports Server (NTRS)

Davis, John S.; Heaphy, William J.

1993-01-01

LARCRIM is a relational database management system (RDBMS) which performs the conventional duties of an RDBMS with the added feature that it can store attributes which consist of arrays or matrices. This makes it particularly valuable for scientific data management. It is accessible as a stand-alone system and through an application program interface. The stand-alone system may be executed in two modes: menu or command. The menu mode prompts the user for the input required to create, update, and/or query the database. The command mode requires the direct input of LARCRIM commands. Although LARCRIM is an update of an old database family, its performance on modern computers is quite satisfactory. LARCRIM is written in FORTRAN 77 and runs under the UNIX operating system. Versions have been released for the following computers: SUN (3 & 4), Convex, IRIS, Hewlett-Packard, CRAY 2 & Y-MP.

BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

Document segmentation via oblique cuts

NASA Astrophysics Data System (ADS)

Svendsen, Jeremy; Branzan-Albu, Alexandra

2013-01-01

This paper presents a novel solution for the layout segmentation of graphical elements in Business Intelligence documents. We propose a generalization of the recursive X-Y cut algorithm, which allows for cutting along arbitrary oblique directions. An intermediate processing step consisting of line and solid region removal is also necessary due to presence of decorative elements. The output of the proposed segmentation is a hierarchical structure which allows for the identification of primitives in pie and bar charts. The algorithm was tested on a database composed of charts from business documents. Results are very promising.

Arabic handwritten: pre-processing and segmentation

NASA Astrophysics Data System (ADS)

Maliki, Makki; Jassim, Sabah; Al-Jawad, Naseer; Sellahewa, Harin

2012-06-01

This paper is concerned with pre-processing and segmentation tasks that influence the performance of Optical Character Recognition (OCR) systems and handwritten/printed text recognition. In Arabic, these tasks are adversely effected by the fact that many words are made up of sub-words, with many sub-words there associated one or more diacritics that are not connected to the sub-word's body; there could be multiple instances of sub-words overlap. To overcome these problems we investigate and develop segmentation techniques that first segment a document into sub-words, link the diacritics with their sub-words, and removes possible overlapping between words and sub-words. We shall also investigate two approaches for pre-processing tasks to estimate sub-words baseline, and to determine parameters that yield appropriate slope correction, slant removal. We shall investigate the use of linear regression on sub-words pixels to determine their central x and y coordinates, as well as their high density part. We also develop a new incremental rotation procedure to be performed on sub-words that determines the best rotation angle needed to realign baselines. We shall demonstrate the benefits of these proposals by conducting extensive experiments on publicly available databases and in-house created databases. These algorithms help improve character segmentation accuracy by transforming handwritten Arabic text into a form that could benefit from analysis of printed text.

A multi-scale tensor voting approach for small retinal vessel segmentation in high resolution fundus images.

PubMed

Christodoulidis, Argyrios; Hurtut, Thomas; Tahar, Houssem Ben; Cheriet, Farida

2016-09-01

Segmenting the retinal vessels from fundus images is a prerequisite for many CAD systems for the automatic detection of diabetic retinopathy lesions. So far, research efforts have concentrated mainly on the accurate localization of the large to medium diameter vessels. However, failure to detect the smallest vessels at the segmentation step can lead to false positive lesion detection counts in a subsequent lesion analysis stage. In this study, a new hybrid method for the segmentation of the smallest vessels is proposed. Line detection and perceptual organization techniques are combined in a multi-scale scheme. Small vessels are reconstructed from the perceptual-based approach via tracking and pixel painting. The segmentation was validated in a high resolution fundus image database including healthy and diabetic subjects using pixel-based as well as perceptual-based measures. The proposed method achieves 85.06% sensitivity rate, while the original multi-scale line detection method achieves 81.06% sensitivity rate for the corresponding images (p<0.05). The improvement in the sensitivity rate for the database is 6.47% when only the smallest vessels are considered (p<0.05). For the perceptual-based measure, the proposed method improves the detection of the vasculature by 7.8% against the original multi-scale line detection method (p<0.05). Copyright © 2016 Elsevier Ltd. All rights reserved.

Multi-atlas and label fusion approach for patient-specific MRI based skull estimation.

PubMed

Torrado-Carvajal, Angel; Herraiz, Joaquin L; Hernandez-Tamames, Juan A; San Jose-Estepar, Raul; Eryaman, Yigitcan; Rozenholc, Yves; Adalsteinsson, Elfar; Wald, Lawrence L; Malpica, Norberto

2016-04-01

MRI-based skull segmentation is a useful procedure for many imaging applications. This study describes a methodology for automatic segmentation of the complete skull from a single T1-weighted volume. The skull is estimated using a multi-atlas segmentation approach. Using a whole head computed tomography (CT) scan database, the skull in a new MRI volume is detected by nonrigid image registration of the volume to every CT, and combination of the individual segmentations by label-fusion. We have compared Majority Voting, Simultaneous Truth and Performance Level Estimation (STAPLE), Shape Based Averaging (SBA), and the Selective and Iterative Method for Performance Level Estimation (SIMPLE) algorithms. The pipeline has been evaluated quantitatively using images from the Retrospective Image Registration Evaluation database (reaching an overlap of 72.46 ± 6.99%), a clinical CT-MR dataset (maximum overlap of 78.31 ± 6.97%), and a whole head CT-MRI pair (maximum overlap 78.68%). A qualitative evaluation has also been performed on MRI acquisition of volunteers. It is possible to automatically segment the complete skull from MRI data using a multi-atlas and label fusion approach. This will allow the creation of complete MRI-based tissue models that can be used in electromagnetic dosimetry applications and attenuation correction in PET/MR. © 2015 Wiley Periodicals, Inc.

Brain Tumour Segmentation based on Extremely Randomized Forest with high-level features.

PubMed

Pinto, Adriano; Pereira, Sergio; Correia, Higino; Oliveira, J; Rasteiro, Deolinda M L D; Silva, Carlos A

2015-08-01

Gliomas are among the most common and aggressive brain tumours. Segmentation of these tumours is important for surgery and treatment planning, but also for follow-up evaluations. However, it is a difficult task, given that its size and locations are variable, and the delineation of all tumour tissue is not trivial, even with all the different modalities of the Magnetic Resonance Imaging (MRI). We propose a discriminative and fully automatic method for the segmentation of gliomas, using appearance- and context-based features to feed an Extremely Randomized Forest (Extra-Trees). Some of these features are computed over a non-linear transformation of the image. The proposed method was evaluated using the publicly available Challenge database from BraTS 2013, having obtained a Dice score of 0.83, 0.78 and 0.73 for the complete tumour, and the core and the enhanced regions, respectively. Our results are competitive, when compared against other results reported using the same database.

Bi-model processing for early detection of breast tumor in CAD system

NASA Astrophysics Data System (ADS)

Mughal, Bushra; Sharif, Muhammad; Muhammad, Nazeer

2017-06-01

Early screening of skeptical masses in mammograms may reduce mortality rate among women. This rate can be further reduced upon developing the computer-aided diagnosis system with decrease in false assumptions in medical informatics. This method highlights the early tumor detection in digitized mammograms. For improving the performance of this system, a novel bi-model processing algorithm is introduced. It divides the region of interest into two parts, the first one is called pre-segmented region (breast parenchyma) and other is the post-segmented region (suspicious region). This system follows the scheme of the preprocessing technique of contrast enhancement that can be utilized to segment and extract the desired feature of the given mammogram. In the next phase, a hybrid feature block is presented to show the effective performance of computer-aided diagnosis. In order to assess the effectiveness of the proposed method, a database provided by the society of mammographic images is tested. Our experimental outcomes on this database exhibit the usefulness and robustness of the proposed method.

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Choosing the Right Database Management Program.

ERIC Educational Resources Information Center

Vockell, Edward L.; Kopenec, Donald

1989-01-01

Provides a comparison of four database management programs commonly used in schools: AppleWorks, the DOS 3.3 and ProDOS versions of PFS, and MECC's Data Handler. Topics discussed include information storage, spelling checkers, editing functions, search strategies, graphs, printout formats, library applications, and HyperCard. (LRW)

SPECIATE 4.0: SPECIATION DATABASE DEVELOPMENT DOCUMENTATION--FINAL REPORT

EPA Science Inventory

SPECIATE is the U.S. EPA's repository of total organic compounds (TOC) and particulate matter (PM) speciation profiles of air pollution sources. This report documents how EPA developed the SPECIATE 4.0 database that replaces the prior version, SPECIATE 3.2. SPECIATE 4.0 includes ...

Brain tumor segmentation in multi-spectral MRI using convolutional neural networks (CNN).

PubMed

Iqbal, Sajid; Ghani, M Usman; Saba, Tanzila; Rehman, Amjad

2018-04-01

A tumor could be found in any area of the brain and could be of any size, shape, and contrast. There may exist multiple tumors of different types in a human brain at the same time. Accurate tumor area segmentation is considered primary step for treatment of brain tumors. Deep Learning is a set of promising techniques that could provide better results as compared to nondeep learning techniques for segmenting timorous part inside a brain. This article presents a deep convolutional neural network (CNN) to segment brain tumors in MRIs. The proposed network uses BRATS segmentation challenge dataset which is composed of images obtained through four different modalities. Accordingly, we present an extended version of existing network to solve segmentation problem. The network architecture consists of multiple neural network layers connected in sequential order with the feeding of Convolutional feature maps at the peer level. Experimental results on BRATS 2015 benchmark data thus show the usability of the proposed approach and its superiority over the other approaches in this area of research. © 2018 Wiley Periodicals, Inc.

Ridge 2000 Data Management System

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Carbotte, S. M.; Arko, R. A.; Haxby, W. F.; Ryan, W. B.; Chayes, D. N.; Lehnert, K. A.; Shank, T. M.

2005-12-01

Hosted at Lamont by the marine geoscience Data Management group, mgDMS, the NSF-funded Ridge 2000 electronic database, http://www.marine-geo.org/ridge2000/, is a key component of the Ridge 2000 multi-disciplinary program. The database covers each of the three Ridge 2000 Integrated Study Sites: Endeavour Segment, Lau Basin, and 8-11N Segment. It promotes the sharing of information to the broader community, facilitates integration of the suite of information collected at each study site, and enables comparisons between sites. The Ridge 2000 data system provides easy web access to a relational database that is built around a catalogue of cruise metadata. Any web browser can be used to perform a versatile text-based search which returns basic cruise and submersible dive information, sample and data inventories, navigation, and other relevant metadata such as shipboard personnel and links to NSF program awards. In addition, non-proprietary data files, images, and derived products which are hosted locally or in national repositories, as well as science and technical reports, can be freely downloaded. On the Ridge 2000 database page, our Data Link allows users to search the database using a broad range of parameters including data type, cruise ID, chief scientist, geographical location. The first Ridge 2000 field programs sailed in 2004 and, in addition to numerous data sets collected prior to the Ridge 2000 program, the database currently contains information on fifteen Ridge 2000-funded cruises and almost sixty Alvin dives. Track lines can be viewed using a recently- implemented Web Map Service button labelled Map View. The Ridge 2000 database is fully integrated with databases hosted by the mgDMS group for MARGINS and the Antarctic multibeam and seismic reflection data initiatives. Links are provided to partner databases including PetDB, SIOExplorer, and the ODP Janus system. Improved inter-operability with existing and new partner repositories continues to be strengthened. One major effort involves the gradual unification of the metadata across these partner databases. Standardised electronic metadata forms that can be filled in at sea are available from our web site. Interactive map-based exploration and visualisation of the Ridge 2000 database is provided by GeoMapApp, a freely-available Java(tm) application being developed within the mgDMS group. GeoMapApp includes high-resolution bathymetric grids for the 8-11N EPR segment and allows customised maps and grids for any of the Ridge 2000 ISS to be created. Vent and instrument locations can be plotted and saved as images, and Alvin dive photos are also available.

Oscillatory network with self-organized dynamical connections for synchronization-based image segmentation.

PubMed

Kuzmina, Margarita; Manykin, Eduard; Surina, Irina

2004-01-01

An oscillatory network of columnar architecture located in 3D spatial lattice was recently designed by the authors as oscillatory model of the brain visual cortex. Single network oscillator is a relaxational neural oscillator with internal dynamics tunable by visual image characteristics - local brightness and elementary bar orientation. It is able to demonstrate either activity state (stable undamped oscillations) or "silence" (quickly damped oscillations). Self-organized nonlocal dynamical connections of oscillators depend on oscillator activity levels and orientations of cortical receptive fields. Network performance consists in transfer into a state of clusterized synchronization. At current stage grey-level image segmentation tasks are carried out by 2D oscillatory network, obtained as a limit version of the source model. Due to supplemented network coupling strength control the 2D reduced network provides synchronization-based image segmentation. New results on segmentation of brightness and texture images presented in the paper demonstrate accurate network performance and informative visualization of segmentation results, inherent in the model.

Characterizing and reaching high-risk drinkers using audience segmentation.

PubMed

Moss, Howard B; Kirby, Susan D; Donodeo, Fred

2009-08-01

Market or audience segmentation is widely used in social marketing efforts to help planners identify segments of a population to target for tailored program interventions. Market-based segments are typically defined by behaviors, attitudes, knowledge, opinions, or lifestyles. They are more helpful to health communication and marketing planning than epidemiologically defined groups because market-based segments are similar in respect to how they behave or might react to marketing and communication efforts. However, market segmentation has rarely been used in alcohol research. As an illustration of its utility, we employed commercial data that describes the sociodemographic characteristics of high-risk drinkers as an audience segment, including where they tend to live, lifestyles, interests, consumer behaviors, alcohol consumption behaviors, other health-related behaviors, and cultural values. Such information can be extremely valuable in targeting and planning public health campaigns, targeted mailings, prevention interventions, and research efforts. We described the results of a segmentation analysis of those individuals who self-reported to consume 5 or more drinks per drinking episode at least twice in the last 30 days. The study used the proprietary PRIZM (Claritas, Inc., San Diego, CA) audience segmentation database merged with the Center for Disease Control and Prevention's (CDC) Behavioral Risk Factor Surveillance System (BRFSS) database. The top 10 of the 66 PRIZM audience segments for this risky drinking pattern are described. For five of these segments we provided additional in-depth details about consumer behavior and the estimates of the market areas where these risky drinkers resided. The top 10 audience segments (PRIZM clusters) most likely to engage in high-risk drinking are described. The cluster with the highest concentration of binge-drinking behavior is referred to as the "Cyber Millenials." This cluster is characterized as "the nation's tech-savvy singles and couples living in fashionable neighborhoods on the urban fringe." Almost 65% of Cyber Millenials households are found in the Pacific and Middle Atlantic regions of the United States. Additional consumer behaviors of the Cyber Millenials and other segments are also described. Audience segmentation can assist in identifying and describing target audience segments, as well as identifying places where segments congregate on- or offline. This information can be helpful for recruiting subjects for alcohol prevention research as well as planning health promotion campaigns. Through commercial data about high-risk drinkers as "consumers," planners can develop interventions that have heightened salience in terms of opportunities, perceptions, and motivations, and have better media channel identification.

Characterizing and Reaching High-Risk Drinkers Using Audience Segmentation

PubMed Central

Moss, Howard B.; Kirby, Susan D.; Donodeo, Fred

2010-01-01

Background Market or audience segmentation is widely used in social marketing efforts to help planners identify segments of a population to target for tailored program interventions. Market-based segments are typically defined by behaviors, attitudes, knowledge, opinions, or lifestyles. They are more helpful to health communication and marketing planning than epidemiologically-defined groups because market-based segments are similar in respect to how they behave or might react to marketing and communication efforts. However, market segmentation has rarely been used in alcohol research. As an illustration of its utility, we employed commercial data that describes the sociodemographic characteristics of high-risk drinkers as an audience segment; where they tend to live, lifestyles, interests, consumer behaviors, alcohol consumption behaviors, other health-related behaviors, and cultural values. Such information can be extremely valuable in targeting and planning public health campaigns, targeted mailings, prevention interventions and research efforts. Methods We describe the results of a segmentation analysis of those individuals who self-report consuming five or more drinks per drinking episode at least twice in the last 30-days. The study used the proprietary PRIZM™ audience segmentation database merged with Center for Disease Control and Prevention's (CDC) Behavioral Risk Factor Surveillance System (BRFSS) database. The top ten of the 66 PRIZM™ audience segments for this risky drinking pattern are described. For five of these segments we provide additional in-depth details about consumer behavior and the estimates of the market areas where these risky drinkers reside. Results The top ten audience segments (PRIZM clusters) most likely to engage in high-risk drinking are described. The cluster with the highest concentration of binge drinking behavior is referred to as the “Cyber Millenials.” This cluster is characterized as “the nation's tech-savvy singles and couples living in fashionable neighborhoods on the urban fringe. Almost 65% of Cyber Millenials households are found in the Pacific and Middle Atlantic regions of the U.S. Additional consumer behaviors of the Cyber Millenials and other segments are also described. Conclusions Audience segmentation can assist in identifying and describing target audience segments, as well as identifying places where segments congregate on- or offline. This information can be helpful for recruiting subjects for alcohol prevention research, as well as planning health promotion campaigns. Through commercial data about high-risk drinkers as “consumers,” planners can develop interventions that have heightened salience in terms of opportunities, perceptions, and motivations, and have better media channel identification. PMID:19413650

VizieR Online Data Catalog: Sloan magnitudes for the brightest stars, V2 (Mallama, 2018)

NASA Astrophysics Data System (ADS)

Mallama, A.

2018-05-01

A new version of the Catalog containing Sloan magnitudes for the brightest stars is presented. The accuracy of the data indicates that the Catalog is a reliable source of comparison star magnitudes for astronomical photometry. Version 2 complements the APASS database of fainter stars. (1 data file).

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

PubMed Central

Wang, Ruijia; Nambiar, Ram; Zheng, Dinghai

2018-01-01

Abstract PolyA_DB is a database cataloging cleavage and polyadenylation sites (PASs) in several genomes. Previous versions were based mainly on expressed sequence tags (ESTs), which had a limited amount and could lead to inaccurate PAS identification due to the presence of internal A-rich sequences in transcripts. Here, we present an updated version of the database based solely on deep sequencing data. First, PASs are mapped by the 3′ region extraction and deep sequencing (3′READS) method, ensuring unequivocal PAS identification. Second, a large volume of data based on diverse biological samples increases PAS coverage by 3.5-fold over the EST-based version and provides PAS usage information. Third, strand-specific RNA-seq data are used to extend annotated 3′ ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. Fourth, conservation information of PAS across mammals sheds light on significance of APA sites. The database (URL: http://www.polya-db.org/v3) currently holds PASs in human, mouse, rat and chicken, and has links to the UCSC genome browser for further visualization and for integration with other genomic data. PMID:29069441

Stress distribution pattern of screw-retained restorations with segmented vs. non-segmented abutments: A finite element analysis

PubMed Central

Aalaei, Shima; Rajabi Naraki, Zahra; Nematollahi, Fatemeh; Beyabanaki, Elaheh; Shahrokhi Rad, Afsaneh

2017-01-01

Background. Screw-retained restorations are favored in some clinical situations such as limited inter-occlusal spaces. This study was designed to compare stresses developed in the peri-implant bone in two different types of screw-retained restorations (segmented vs. non-segmented abutment) using a finite element model. Methods. An implant, 4.1 mm in diameter and 10 mm in length, was placed in the first molar site of a mandibular model with 1 mm of cortical bone on the buccal and lingual sides. Segmented and non-segmented screw abutments with their crowns were placed on the simulated implant in each model. After loading (100 N, axial and 45° non-axial), von Mises stress was recorded using ANSYS software, version 12.0.1. Results. The maximum stresses in the non-segmented abutment screw were less than those of segmented abutment (87 vs. 100, and 375 vs. 430 MPa under axial and non-axial loading, respectively). The maximum stresses in the peri-implant bone for the model with segmented abutment were less than those of non-segmented ones (21 vs. 24 MPa, and 31 vs. 126 MPa under vertical and angular loading, respectively). In addition, the micro-strain of peri-implant bone for the segmented abutment restoration was less than that of non-segmented abutment. Conclusion. Under axial and non-axial loadings, non-segmented abutment showed less stress concentration in the screw, while there was less stress and strain in the peri-implant bone in the segmented abutment. PMID:29184629

Artificial neural network retrained to detect myocardial ischemia using a Japanese multicenter database.

PubMed

Nakajima, Kenichi; Okuda, Koichi; Watanabe, Satoru; Matsuo, Shinro; Kinuya, Seigo; Toth, Karin; Edenbrandt, Lars

2018-03-07

An artificial neural network (ANN) has been applied to detect myocardial perfusion defects and ischemia. The present study compares the diagnostic accuracy of a more recent ANN version (1.1) with the initial version 1.0. We examined 106 patients (age, 77 ± 10 years) with coronary angiographic findings, comprising multi-vessel disease (≥ 50% stenosis) (52%) or old myocardial infarction (27%), or who had undergone coronary revascularization (30%). The ANN versions 1.0 and 1.1 were trained in Sweden (n = 1051) and Japan (n = 1001), respectively, using 99m Tc-methoxyisobutylisonitrile myocardial perfusion images. The ANN probabilities (from 0.0 to 1.0) of stress defects and ischemia were calculated in candidate regions of abnormalities. The diagnostic accuracy was compared using receiver-operating characteristics (ROC) analysis and the calculated area under the ROC curve (AUC) using expert interpretation as the gold standard. Although the AUC for stress defects was 0.95 and 0.93 (p = 0.27) for versions 1.1 and 1.0, respectively, that for detecting ischemia was significantly improved in version 1.1 (p = 0.0055): AUC 0.96 for version 1.1 (sensitivity 87%, specificity 96%) vs. 0.89 for version 1.0 (sensitivity 78%, specificity 97%). The improvement in the AUC shown by version 1.1 was also significant for patients with neither coronary revascularization nor old myocardial infarction (p = 0.0093): AUC = 0.98 for version 1.1 (sensitivity 88%, specificity 100%) and 0.88 for version 1.0 (sensitivity 76%, specificity 100%). Intermediate ANN probability between 0.1 and 0.7 was more often calculated by version 1.1 compared with version 1.0, which contributed to the improved diagnostic accuracy. The diagnostic accuracy of the new version was also improved in patients with either single-vessel disease or no stenosis (n = 47; AUC, 0.81 vs. 0.66 vs. p = 0.0060) when coronary stenosis was used as a gold standard. The diagnostic ability of the ANN version 1.1 was improved by retraining using the Japanese database, particularly for identifying ischemia.

Gaussian Multiscale Aggregation Applied to Segmentation in Hand Biometrics

PubMed Central

de Santos Sierra, Alberto; Ávila, Carmen Sánchez; Casanova, Javier Guerra; del Pozo, Gonzalo Bailador

2011-01-01

This paper presents an image segmentation algorithm based on Gaussian multiscale aggregation oriented to hand biometric applications. The method is able to isolate the hand from a wide variety of background textures such as carpets, fabric, glass, grass, soil or stones. The evaluation was carried out by using a publicly available synthetic database with 408,000 hand images in different backgrounds, comparing the performance in terms of accuracy and computational cost to two competitive segmentation methods existing in literature, namely Lossy Data Compression (LDC) and Normalized Cuts (NCuts). The results highlight that the proposed method outperforms current competitive segmentation methods with regard to computational cost, time performance, accuracy and memory usage. PMID:22247658

Gaussian multiscale aggregation applied to segmentation in hand biometrics.

PubMed

de Santos Sierra, Alberto; Avila, Carmen Sánchez; Casanova, Javier Guerra; del Pozo, Gonzalo Bailador

2011-01-01

This paper presents an image segmentation algorithm based on Gaussian multiscale aggregation oriented to hand biometric applications. The method is able to isolate the hand from a wide variety of background textures such as carpets, fabric, glass, grass, soil or stones. The evaluation was carried out by using a publicly available synthetic database with 408,000 hand images in different backgrounds, comparing the performance in terms of accuracy and computational cost to two competitive segmentation methods existing in literature, namely Lossy Data Compression (LDC) and Normalized Cuts (NCuts). The results highlight that the proposed method outperforms current competitive segmentation methods with regard to computational cost, time performance, accuracy and memory usage.

Improved Estimation of Cardiac Function Parameters Using a Combination of Independent Automated Segmentation Results in Cardiovascular Magnetic Resonance Imaging.

PubMed

Lebenberg, Jessica; Lalande, Alain; Clarysse, Patrick; Buvat, Irene; Casta, Christopher; Cochet, Alexandre; Constantinidès, Constantin; Cousty, Jean; de Cesare, Alain; Jehan-Besson, Stephanie; Lefort, Muriel; Najman, Laurent; Roullot, Elodie; Sarry, Laurent; Tilmant, Christophe; Frouin, Frederique; Garreau, Mireille

2015-01-01

This work aimed at combining different segmentation approaches to produce a robust and accurate segmentation result. Three to five segmentation results of the left ventricle were combined using the STAPLE algorithm and the reliability of the resulting segmentation was evaluated in comparison with the result of each individual segmentation method. This comparison was performed using a supervised approach based on a reference method. Then, we used an unsupervised statistical evaluation, the extended Regression Without Truth (eRWT) that ranks different methods according to their accuracy in estimating a specific biomarker in a population. The segmentation accuracy was evaluated by estimating six cardiac function parameters resulting from the left ventricle contour delineation using a public cardiac cine MRI database. Eight different segmentation methods, including three expert delineations and five automated methods, were considered, and sixteen combinations of the automated methods using STAPLE were investigated. The supervised and unsupervised evaluations demonstrated that in most cases, STAPLE results provided better estimates than individual automated segmentation methods. Overall, combining different automated segmentation methods improved the reliability of the segmentation result compared to that obtained using an individual method and could achieve the accuracy of an expert.

Improved Estimation of Cardiac Function Parameters Using a Combination of Independent Automated Segmentation Results in Cardiovascular Magnetic Resonance Imaging

PubMed Central

Lebenberg, Jessica; Lalande, Alain; Clarysse, Patrick; Buvat, Irene; Casta, Christopher; Cochet, Alexandre; Constantinidès, Constantin; Cousty, Jean; de Cesare, Alain; Jehan-Besson, Stephanie; Lefort, Muriel; Najman, Laurent; Roullot, Elodie; Sarry, Laurent; Tilmant, Christophe

2015-01-01

This work aimed at combining different segmentation approaches to produce a robust and accurate segmentation result. Three to five segmentation results of the left ventricle were combined using the STAPLE algorithm and the reliability of the resulting segmentation was evaluated in comparison with the result of each individual segmentation method. This comparison was performed using a supervised approach based on a reference method. Then, we used an unsupervised statistical evaluation, the extended Regression Without Truth (eRWT) that ranks different methods according to their accuracy in estimating a specific biomarker in a population. The segmentation accuracy was evaluated by estimating six cardiac function parameters resulting from the left ventricle contour delineation using a public cardiac cine MRI database. Eight different segmentation methods, including three expert delineations and five automated methods, were considered, and sixteen combinations of the automated methods using STAPLE were investigated. The supervised and unsupervised evaluations demonstrated that in most cases, STAPLE results provided better estimates than individual automated segmentation methods. Overall, combining different automated segmentation methods improved the reliability of the segmentation result compared to that obtained using an individual method and could achieve the accuracy of an expert. PMID:26287691

Use of Knowledge Bases in Education of Database Management

ERIC Educational Resources Information Center

Radványi, Tibor; Kovács, Emod

2008-01-01

In this article we present a segment of Sulinet Digital Knowledgebase curriculum system in which you can find the sections of subject-matter which aid educating the database management. You can follow the order of the course from the beginning when some topics appearance and raise in elementary school, through the topics accomplish in secondary…

DataBase on Demand

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

USER'S GUIDE FOR GLOED VERSION 1.0 - THE GLOBAL EMISSIONS DATABASE

EPA Science Inventory

The document is a user's guide for the EPA-developed, powerful software package, Global Emissions Database (GloED). GloED is a user-friendly, menu-driven tool for storing and retrieving emissions factors and activity data on a country-specific basis. Data can be selected from dat...

Online vs. Print Publications: Users' Opinions.

ERIC Educational Resources Information Center

Wang, Chih

The rapid expansion of online publications has raised some concerns about the use of online databases in comparison with using traditional print publications. To determine the opinions of end users about using Dialog online databases versus their corresponding print versions, three libraries in Atlanta, Georgia--Atlanta-Fulton Public Library,…

BIOREMEDIATION IN THE FIELD SEARCH SYSTEM (BFSS) - VERSION 2.0 (DISKETTE)

EPA Science Inventory

BFSS is a PC-based software product that provides access to a database of information on waste sites in the United States and Canada where bioremediation is being tested or implemented, or has been completed. BFSS allows users to search the database electronically, view data on s...

Discontinued Codes in The USDA Food and Nutrient Database for Dietary Studies

USDA-ARS?s Scientific Manuscript database

For each new version of the Food and Nutrient Database for Dietary Studies (FNDDS), foods and beverages, portions, and nutrient values are reviewed and updated. New food and beverage codes are added based on changes in consumption and the marketplace; additionally, codes are discontinued. To date,...

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

At the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida, members of the news media photograph the process as cranes are used to lift one of two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket. The Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, are preparing the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

At the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida, members of the news media watch as cranes are used to lift one of two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket. The Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, are preparing the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

Modified SSCP method using sequential electrophoresis of multiple nucleic acid segments

DOEpatents

Gatti, Richard A.

2002-10-01

The present invention is directed to a method of screening large, complex, polyexonic eukaryotic genes such as the ATM gene for mutations and polymorphisms by an improved version of single strand conformation polymorphism (SSCP) electrophoresis that allows electrophoresis of two or three amplified segments in a single lane. The present invention also is directed to new mutations and polymorphisms in the ATM gene that are useful in performing more accurate screening of human DNA samples for mutations and in distinguishing mutations from polymorphisms, thereby improving the efficiency of automated screening methods.

Research Directions in Database Security IV

DTIC Science & Technology

1993-07-01

second algorithm, which is based on multiversion timestamp ordering, is that high level transactions can be forced to read arbitrarily old data values...system. The first, the single ver- sion model, stores only the latest veision of each data item, while the second, the 88 multiversion model, stores... Multiversion Database Model In the standard database model, where there is only one version of each data item, all transactions compete for the most recent

Automatic segmentation of tumor-laden lung volumes from the LIDC database

NASA Astrophysics Data System (ADS)

O'Dell, Walter G.

2012-03-01

The segmentation of the lung parenchyma is often a critical pre-processing step prior to application of computer-aided detection of lung nodules. Segmentation of the lung volume can dramatically decrease computation time and reduce the number of false positive detections by excluding from consideration extra-pulmonary tissue. However, while many algorithms are capable of adequately segmenting the healthy lung, none have been demonstrated to work reliably well on tumor-laden lungs. Of particular challenge is to preserve tumorous masses attached to the chest wall, mediastinum or major vessels. In this role, lung volume segmentation comprises an important computational step that can adversely affect the performance of the overall CAD algorithm. An automated lung volume segmentation algorithm has been developed with the goals to maximally exclude extra-pulmonary tissue while retaining all true nodules. The algorithm comprises a series of tasks including intensity thresholding, 2-D and 3-D morphological operations, 2-D and 3-D floodfilling, and snake-based clipping of nodules attached to the chest wall. It features the ability to (1) exclude trachea and bowels, (2) snip large attached nodules using snakes, (3) snip small attached nodules using dilation, (4) preserve large masses fully internal to lung volume, (5) account for basal aspects of the lung where in a 2-D slice the lower sections appear to be disconnected from main lung, and (6) achieve separation of the right and left hemi-lungs. The algorithm was developed and trained to on the first 100 datasets of the LIDC image database.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

PubMed Central

Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin

2010-01-01

JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. PMID:19906716

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

Members of the news media view the high bay inside the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida. Kerry Chreist, with Jacobs Engineering on the Test and Operations Support Contract, explains the various test stands and how they will be used to prepare booster segments for NASA’s Space Launch System (SLS) rocket. In the far corner, in the vertical position, is one of two pathfinders, or test versions, of solid rocket booster segments for the SLS rocket. The Ground Systems Development and Operations Program and Jacobs are preparing the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

Mathematical morphology for automated analysis of remotely sensed objects in radar images

NASA Technical Reports Server (NTRS)

Daida, Jason M.; Vesecky, John F.

1991-01-01

A symbiosis of pyramidal segmentation and morphological transmission is described. The pyramidal segmentation portion of the symbiosis has resulted in low (2.6 percent) misclassification error rate for a one-look simulation. Other simulations indicate lower error rates (1.8 percent for a four-look image). The morphological transformation portion has resulted in meaningful partitions with a minimal loss of fractal boundary information. An unpublished version of Thicken, suitable for watersheds transformations of fractal objects, is also presented. It is demonstrated that the proposed symbiosis works with SAR (synthetic aperture radar) images: in this case, a four-look Seasat image of sea ice. It is concluded that the symbiotic forms of both segmentation and morphological transformation seem well suited for unsupervised geophysical analysis.

Pattern-based, multi-scale segmentation and regionalization of EOSD land cover

NASA Astrophysics Data System (ADS)

Niesterowicz, Jacek; Stepinski, Tomasz F.

2017-10-01

The Earth Observation for Sustainable Development of Forests (EOSD) map is a 25 m resolution thematic map of Canadian forests. Because of its large spatial extent and relatively high resolution the EOSD is difficult to analyze using standard GIS methods. In this paper we propose multi-scale segmentation and regionalization of EOSD as new methods for analyzing EOSD on large spatial scales. Segments, which we refer to as forest land units (FLUs), are delineated as tracts of forest characterized by cohesive patterns of EOSD categories; we delineated from 727 to 91,885 FLUs within the spatial extent of EOSD depending on the selected scale of a pattern. Pattern of EOSD's categories within each FLU is described by 1037 landscape metrics. A shapefile containing boundaries of all FLUs together with an attribute table listing landscape metrics make up an SQL-searchable spatial database providing detailed information on composition and pattern of land cover types in Canadian forest. Shapefile format and extensive attribute table pertaining to the entire legend of EOSD are designed to facilitate broad range of investigations in which assessment of composition and pattern of forest over large areas is needed. We calculated four such databases using different spatial scales of pattern. We illustrate the use of FLU database for producing forest regionalization maps of two Canadian provinces, Quebec and Ontario. Such maps capture the broad scale variability of forest at the spatial scale of the entire province. We also demonstrate how FLU database can be used to map variability of landscape metrics, and thus the character of landscape, over the entire Canada.

Automatic initialization and quality control of large-scale cardiac MRI segmentations.

PubMed

Albà, Xènia; Lekadir, Karim; Pereañez, Marco; Medrano-Gracia, Pau; Young, Alistair A; Frangi, Alejandro F

2018-01-01

Continuous advances in imaging technologies enable ever more comprehensive phenotyping of human anatomy and physiology. Concomitant reduction of imaging costs has resulted in widespread use of imaging in large clinical trials and population imaging studies. Magnetic Resonance Imaging (MRI), in particular, offers one-stop-shop multidimensional biomarkers of cardiovascular physiology and pathology. A wide range of analysis methods offer sophisticated cardiac image assessment and quantification for clinical and research studies. However, most methods have only been evaluated on relatively small databases often not accessible for open and fair benchmarking. Consequently, published performance indices are not directly comparable across studies and their translation and scalability to large clinical trials or population imaging cohorts is uncertain. Most existing techniques still rely on considerable manual intervention for the initialization and quality control of the segmentation process, becoming prohibitive when dealing with thousands of images. The contributions of this paper are three-fold. First, we propose a fully automatic method for initializing cardiac MRI segmentation, by using image features and random forests regression to predict an initial position of the heart and key anatomical landmarks in an MRI volume. In processing a full imaging database, the technique predicts the optimal corrective displacements and positions in relation to the initial rough intersections of the long and short axis images. Second, we introduce for the first time a quality control measure capable of identifying incorrect cardiac segmentations with no visual assessment. The method uses statistical, pattern and fractal descriptors in a random forest classifier to detect failures to be corrected or removed from subsequent statistical analysis. Finally, we validate these new techniques within a full pipeline for cardiac segmentation applicable to large-scale cardiac MRI databases. The results obtained based on over 1200 cases from the Cardiac Atlas Project show the promise of fully automatic initialization and quality control for population studies. Copyright © 2017 Elsevier B.V. All rights reserved.

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

Learning of perceptual grouping for object segmentation on RGB-D data☆

PubMed Central

Richtsfeld, Andreas; Mörwald, Thomas; Prankl, Johann; Zillich, Michael; Vincze, Markus

2014-01-01

Object segmentation of unknown objects with arbitrary shape in cluttered scenes is an ambitious goal in computer vision and became a great impulse with the introduction of cheap and powerful RGB-D sensors. We introduce a framework for segmenting RGB-D images where data is processed in a hierarchical fashion. After pre-clustering on pixel level parametric surface patches are estimated. Different relations between patch-pairs are calculated, which we derive from perceptual grouping principles, and support vector machine classification is employed to learn Perceptual Grouping. Finally, we show that object hypotheses generation with Graph-Cut finds a globally optimal solution and prevents wrong grouping. Our framework is able to segment objects, even if they are stacked or jumbled in cluttered scenes. We also tackle the problem of segmenting objects when they are partially occluded. The work is evaluated on publicly available object segmentation databases and also compared with state-of-the-art work of object segmentation. PMID:24478571

Segmentation by fusion of histogram-based k-means clusters in different color spaces.

PubMed

Mignotte, Max

2008-05-01

This paper presents a new, simple, and efficient segmentation approach, based on a fusion procedure which aims at combining several segmentation maps associated to simpler partition models in order to finally get a more reliable and accurate segmentation result. The different label fields to be fused in our application are given by the same and simple (K-means based) clustering technique on an input image expressed in different color spaces. Our fusion strategy aims at combining these segmentation maps with a final clustering procedure using as input features, the local histogram of the class labels, previously estimated and associated to each site and for all these initial partitions. This fusion framework remains simple to implement, fast, general enough to be applied to various computer vision applications (e.g., motion detection and segmentation), and has been successfully applied on the Berkeley image database. The experiments herein reported in this paper illustrate the potential of this approach compared to the state-of-the-art segmentation methods recently proposed in the literature.

Supplemental Fingerprint Card Data (SFCD) for NIST Special Database 9

National Institute of Standards and Technology Data Gateway

Supplemental Fingerprint Card Data (SFCD) for NIST Special Database 9 (Web, free access)   NIST Special Database 10 (Supplemental Fingerprint Card Data for Special Database 9 - 8-Bit Gray Scale Images) provides a larger sample of fingerprint patterns that have a low natural frequency of occurrence and transitional fingerprint classes in NIST Special Database 9. The software is the same code used with NIST Special Database 4 and 9. A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 1

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

Iversen, C. M.; Powell, A. S.; McCormack, M. L.

To address the need for a centralized root trait database, we are compiling the Fine-Root Ecology Database (FRED) from published literature and unpublished data. FRED Version 1 (FRED 1.0) currently houses more than 70,000 observations of root traits and their associated site, vegetation, edaphic, and climatic conditions from across the globe (see image below, which shows the more than 1000 distinct locations associated with observations in FRED 1.0). Data collection is ongoing and will continue for the foreseeable future. The more than 300 root traits currently housed in FRED 1.0 are described in detail here. FRED is focused on finemore » roots (less than 2 mm), as coarse roots are studied using different methodology, often at very different scales, and have different traits and trait interpretations.« less

Segmentation of pulmonary nodules in three-dimensional CT images by use of a spiral-scanning technique

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

Wang Jiahui; Engelmann, Roger; Li Qiang

2007-12-15

Accurate segmentation of pulmonary nodules in computed tomography (CT) is an important and difficult task for computer-aided diagnosis of lung cancer. Therefore, the authors developed a novel automated method for accurate segmentation of nodules in three-dimensional (3D) CT. First, a volume of interest (VOI) was determined at the location of a nodule. To simplify nodule segmentation, the 3D VOI was transformed into a two-dimensional (2D) image by use of a key 'spiral-scanning' technique, in which a number of radial lines originating from the center of the VOI spirally scanned the VOI from the 'north pole' to the 'south pole'. Themore » voxels scanned by the radial lines provided a transformed 2D image. Because the surface of a nodule in the 3D image became a curve in the transformed 2D image, the spiral-scanning technique considerably simplified the segmentation method and enabled reliable segmentation results to be obtained. A dynamic programming technique was employed to delineate the 'optimal' outline of a nodule in the 2D image, which corresponded to the surface of the nodule in the 3D image. The optimal outline was then transformed back into 3D image space to provide the surface of the nodule. An overlap between nodule regions provided by computer and by the radiologists was employed as a performance metric for evaluating the segmentation method. The database included two Lung Imaging Database Consortium (LIDC) data sets that contained 23 and 86 CT scans, respectively, with 23 and 73 nodules that were 3 mm or larger in diameter. For the two data sets, six and four radiologists manually delineated the outlines of the nodules as reference standards in a performance evaluation for nodule segmentation. The segmentation method was trained on the first and was tested on the second LIDC data sets. The mean overlap values were 66% and 64% for the nodules in the first and second LIDC data sets, respectively, which represented a higher performance level than those of two existing segmentation methods that were also evaluated by use of the LIDC data sets. The segmentation method provided relatively reliable results for pulmonary nodule segmentation and would be useful for lung cancer quantification, detection, and diagnosis.« less

FPGA accelerator for protein secondary structure prediction based on the GOR algorithm

PubMed Central

2011-01-01

Background Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived from its molecular structure. The GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the execution time is still intolerable with the steep growth in protein database. Recently, FPGA chips have emerged as one promising application accelerator to accelerate bioinformatics algorithms by exploiting fine-grained custom design. Results In this paper, we propose a complete fine-grained parallel hardware implementation on FPGA to accelerate the GOR-IV package for 2D protein structure prediction. To improve computing efficiency, we partition the parameter table into small segments and access them in parallel. We aggressively exploit data reuse schemes to minimize the need for loading data from external memory. The whole computation structure is carefully pipelined to overlap the sequence loading, computing and back-writing operations as much as possible. We implemented a complete GOR desktop system based on an FPGA chip XC5VLX330. Conclusions The experimental results show a speedup factor of more than 430x over the original GOR-IV version and 110x speedup over the optimized version with multi-thread SIMD implementation running on a PC platform with AMD Phenom 9650 Quad CPU for 2D protein structure prediction. However, the power consumption is only about 30% of that of current general-propose CPUs. PMID:21342582

Evolution of Fseg/Cseg dimorphism in region III of the Plasmodium falciparum eba-175 gene.

PubMed

Yasukochi, Yoshiki; Naka, Izumi; Patarapotikul, Jintana; Hananantachai, Hathairad; Ohashi, Jun

2017-04-01

The 175-kDa erythrocyte binding antigen (EBA-175) of the malaria parasite Plasmodium falciparum is important for its invasion into human erythrocytes. The primary structure of eba-175 is divided into seven regions, namely I to VII. Region III contains highly divergent dimorphic segments, termed Fseg and Cseg. The allele frequencies of segmental dimorphism within a P. falciparum population have been extensively examined; however, the molecular evolution of segmental dimorphism is not well understood. A comprehensive comparison of nucleotide sequences among 32 P. falciparum eba-175 alleles identified in our previous study, two Plasmodium reichenowi, and one P. gaboni orthologous alleles obtained from the GenBank database was conducted to uncover the origin and evolutionary processes of segmental dimorphism in P. falciparum eba-175. In the eba-175 nucleotide sequence derived from a P. reichenowi CDC strain, both Fseg and Cseg were found in region III, which implies that the original eba-175 gene had both segments, and deletions of F- and C-segments generated Cseg and Fseg alleles, respectively. We also confirmed the presence of allele with Fseg and Cseg in another P. reichenowi strain (SY57), by re-mapping short reads obtained from the GenBank database. On the other hand, the segmental sequence of eba-175 ortholog in P. gaboni was quite diverged from those of the other species, suggesting that the original eba-175 dimorphism of P. falciparum can be traced back to the stem linage of P. falciparum and P. reichenowi. Our findings suggest that Fseg and Cseg alleles are derived from a single eba-175 allele containing both segments in the ancestral population of P. falciparum and P. reichenowi, and that the allelic dimorphism of eba-175 was shaped by the independent emergence of similar dimorphic lineage in different species that has never been observed in any evolutionary mode of allelic dimorphism at other loci in malaria genomes. Copyright © 2017 Elsevier B.V. All rights reserved.

Cpp Utility - Version 1.0

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

III, FredOppel; Rigdon, J. Brian

2014-09-08

A collection of general Umbra modules that are reused by other Umbra libraries. These capabilities include line segments, file utilities, color utilities, string utilities (for std::string), list utilities (for std ::vector ), bounding box intersections, range limiters, simple filters, cubic roots solvers and a few other utilities.

A completely automated processing pipeline for lung and lung lobe segmentation and its application to the LIDC-IDRI data base

NASA Astrophysics Data System (ADS)

Blaffert, Thomas; Wiemker, Rafael; Barschdorf, Hans; Kabus, Sven; Klinder, Tobias; Lorenz, Cristian; Schadewaldt, Nicole; Dharaiya, Ekta

2010-03-01

Automated segmentation of lung lobes in thoracic CT images has relevance for various diagnostic purposes like localization of tumors within the lung or quantification of emphysema. Since emphysema is a known risk factor for lung cancer, both purposes are even related to each other. The main steps of the segmentation pipeline described in this paper are the lung detector and the lung segmentation based on a watershed algorithm, and the lung lobe segmentation based on mesh model adaptation. The segmentation procedure was applied to data sets of the data base of the Image Database Resource Initiative (IDRI) that currently contains over 500 thoracic CT scans with delineated lung nodule annotations. We visually assessed the reliability of the single segmentation steps, with a success rate of 98% for the lung detection and 90% for lung delineation. For about 20% of the cases we found the lobe segmentation not to be anatomically plausible. A modeling confidence measure is introduced that gives a quantitative indication of the segmentation quality. For a demonstration of the segmentation method we studied the correlation between emphysema score and malignancy on a per-lobe basis.

miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.

PubMed

Haunsberger, Stefan J; Connolly, Niamh M C; Prehn, Jochen H M

2017-02-15

The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter , available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results. The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor ( http://bioconductor.org/packages/miRNAmeConverter ). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/ . The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor ( http://bioconductor.org/packages/miRBaseVersions.db ). Minimum R version 3.3.0 is required. stefanhaunsberger@rcsi.ie. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

PR-EDB: Power Reactor Embrittlement Database - Version 3

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

Wang, Jy-An John; Subramani, Ranjit

2008-03-01

The aging and degradation of light-water reactor pressure vessels is of particular concern because of their relevance to plant integrity and the magnitude of the expected irradiation embrittlement. The radiation embrittlement of reactor pressure vessel materials depends on many factors, such as neutron fluence, flux, and energy spectrum, irradiation temperature, and preirradiation material history and chemical compositions. These factors must be considered to reliably predict pressure vessel embrittlement and to ensure the safe operation of the reactor. Large amounts of data from surveillance capsules are needed to develop a generally applicable damage prediction model that can be used for industrymore » standards and regulatory guides. Furthermore, the investigations of regulatory issues such as vessel integrity over plant life, vessel failure, and sufficiency of current codes, Standard Review Plans (SRPs), and Guides for license renewal can be greatly expedited by the use of a well-designed computerized database. The Power Reactor Embrittlement Database (PR-EDB) is such a comprehensive collection of data for U.S. designed commercial nuclear reactors. The current version of the PR-EDB lists the test results of 104 heat-affected-zone (HAZ) materials, 115 weld materials, and 141 base materials, including 103 plates, 35 forgings, and 3 correlation monitor materials that were irradiated in 321 capsules from 106 commercial power reactors. The data files are given in dBASE format and can be accessed with any personal computer using the Windows operating system. "User-friendly" utility programs have been written to investigate radiation embrittlement using this database. Utility programs allow the user to retrieve, select and manipulate specific data, display data to the screen or printer, and fit and plot Charpy impact data. The PR-EDB Version 3.0 upgrades Version 2.0. The package was developed based on the Microsoft .NET framework technology and uses Microsoft Access for backend data storage, and Microsoft Excel for plotting graphs. This software package is compatible with Windows (98 or higher) and has been built with a highly versatile user interface. PR-EDB Version 3.0 also contains an "Evaluated Residual File" utility for generating the evaluated processed files used for radiation embrittlement study.« less

Modeling heterogeneous (co)variances from adjacent-SNP groups improves genomic prediction for milk protein composition traits.

PubMed

Gebreyesus, Grum; Lund, Mogens S; Buitenhuis, Bart; Bovenhuis, Henk; Poulsen, Nina A; Janss, Luc G

2017-12-05

Accurate genomic prediction requires a large reference population, which is problematic for traits that are expensive to measure. Traits related to milk protein composition are not routinely recorded due to costly procedures and are considered to be controlled by a few quantitative trait loci of large effect. The amount of variation explained may vary between regions leading to heterogeneous (co)variance patterns across the genome. Genomic prediction models that can efficiently take such heterogeneity of (co)variances into account can result in improved prediction reliability. In this study, we developed and implemented novel univariate and bivariate Bayesian prediction models, based on estimates of heterogeneous (co)variances for genome segments (BayesAS). Available data consisted of milk protein composition traits measured on cows and de-regressed proofs of total protein yield derived for bulls. Single-nucleotide polymorphisms (SNPs), from 50K SNP arrays, were grouped into non-overlapping genome segments. A segment was defined as one SNP, or a group of 50, 100, or 200 adjacent SNPs, or one chromosome, or the whole genome. Traditional univariate and bivariate genomic best linear unbiased prediction (GBLUP) models were also run for comparison. Reliabilities were calculated through a resampling strategy and using deterministic formula. BayesAS models improved prediction reliability for most of the traits compared to GBLUP models and this gain depended on segment size and genetic architecture of the traits. The gain in prediction reliability was especially marked for the protein composition traits β-CN, κ-CN and β-LG, for which prediction reliabilities were improved by 49 percentage points on average using the MT-BayesAS model with a 100-SNP segment size compared to the bivariate GBLUP. Prediction reliabilities were highest with the BayesAS model that uses a 100-SNP segment size. The bivariate versions of our BayesAS models resulted in extra gains of up to 6% in prediction reliability compared to the univariate versions. Substantial improvement in prediction reliability was possible for most of the traits related to milk protein composition using our novel BayesAS models. Grouping adjacent SNPs into segments provided enhanced information to estimate parameters and allowing the segments to have different (co)variances helped disentangle heterogeneous (co)variances across the genome.

Preliminary Geologic Map of the Topanga 7.5' Quadrangle, Southern California: A Digital Database

USGS Publications Warehouse

Yerkes, R.F.; Campbell, R.H.

1995-01-01

INTRODUCTION This Open-File report is a digital geologic map database. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. This digital map database is compiled from previously published sources combined with some new mapping and modifications in nomenclature. The geologic map database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U. S. Geological Survey. For detailed descriptions of the units, their stratigraphic relations and sources of geologic mapping consult Yerkes and Campbell (1994). More specific information about the units may be available in the original sources. The content and character of the database and methods of obtaining it are described herein. The geologic map database itself, consisting of three ARC coverages and one base layer, can be obtained over the Internet or by magnetic tape copy as described below. The processes of extracting the geologic map database from the tar file, and importing the ARC export coverages (procedure described herein), will result in the creation of an ARC workspace (directory) called 'topnga.' The database was compiled using ARC/INFO version 7.0.3, a commercial Geographic Information System (Environmental Systems Research Institute, Redlands, California), with version 3.0 of the menu interface ALACARTE (Fitzgibbon and Wentworth, 1991, Fitzgibbon, 1991, Wentworth and Fitzgibbon, 1991). It is stored in uncompressed ARC export format (ARC/INFO version 7.x) in a compressed UNIX tar (tape archive) file. The tar file was compressed with gzip, and may be uncompressed with gzip, which is available free of charge via the Internet from the gzip Home Page (http://w3.teaser.fr/~jlgailly/gzip). A tar utility is required to extract the database from the tar file. This utility is included in most UNIX systems, and can be obtained free of charge via the Internet from Internet Literacy's Common Internet File Formats Webpage http://www.matisse.net/files/formats.html). ARC/INFO export files (files with the .e00 extension) can be converted into ARC/INFO coverages in ARC/INFO (see below) and can be read by some other Geographic Information Systems, such as MapInfo via ArcLink and ESRI's ArcView (version 1.0 for Windows 3.1 to 3.11 is available for free from ESRI's web site: http://www.esri.com). 1. Different base layer - The original digital database included separates clipped out of the Los Angeles 1:100,000 sheet. This release includes a vectorized scan of a scale-stable negative of the Topanga 7.5 minute quadrangle. 2. Map projection - The files in the original release were in polyconic projection. The projection used in this release is state plane, which allows for the tiling of adjacent quadrangles. 3. File compression - The files in the original release were compressed with UNIX compression. The files in this release are compressed with gzip.

Handwritten text line segmentation by spectral clustering

NASA Astrophysics Data System (ADS)

Han, Xuecheng; Yao, Hui; Zhong, Guoqiang

2017-02-01

Since handwritten text lines are generally skewed and not obviously separated, text line segmentation of handwritten document images is still a challenging problem. In this paper, we propose a novel text line segmentation algorithm based on the spectral clustering. Given a handwritten document image, we convert it to a binary image first, and then compute the adjacent matrix of the pixel points. We apply spectral clustering on this similarity metric and use the orthogonal kmeans clustering algorithm to group the text lines. Experiments on Chinese handwritten documents database (HIT-MW) demonstrate the effectiveness of the proposed method.

MAPS: The Organization of a Spatial Database System Using Imagery, Terrain, and Map Data

DTIC Science & Technology

1983-06-01

segments which share the same pixel position. Finally, in any largo system, a logical partitioning of the database must be performed in order to avoid...34theodore roosevelt memoria entry 0; entry 1: Virginia ’northwest Washington* 2 en 11" ies for "crossover" for ’theodore roosevelt memor i entry 0

TrSDB: a proteome database of transcription factors

PubMed Central

Hermoso, Antoni; Aguilar, Daniel; Aviles, Francesc X.; Querol, Enrique

2004-01-01

TrSDB—TranScout Database—(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Nine eukaryotic proteomes are included in the current version. Extensive and diverse information for each database entry, different analyses considering TranScout classification and similarity relationships are offered for research on transcription factors or gene expression. PMID:14681387

U.S. Geological Survey coal quality (COALQUAL) database; version 2.0

USGS Publications Warehouse

Bragg, L.J.; Oman, J.K.; Tewalt, S.J.; Oman, C.L.; Rega, N.H.; Washington, P.M.; Finkelman, R.B.

1997-01-01

The USGS Coal Quality database is an interactive, computerized component of the NCRDS. It contains comprehensive analyses of more than 13,000 samples of coal and associated rocks from every major coal-bearing basin and coal bed in the U.S. The data in the coal quality database represent analyses of the coal as it exists in the ground. The data commonly are presented on an as-received whole-coal basis.

Development of the geometry database for the CBM experiment

NASA Astrophysics Data System (ADS)

Akishina, E. P.; Alexandrov, E. I.; Alexandrov, I. N.; Filozova, I. A.; Friese, V.; Ivanov, V. V.

2018-01-01

The paper describes the current state of the Geometry Database (Geometry DB) for the CBM experiment. The main purpose of this database is to provide convenient tools for: (1) managing the geometry modules; (2) assembling various versions of the CBM setup as a combination of geometry modules and additional files. The CBM users of the Geometry DB may use both GUI (Graphical User Interface) and API (Application Programming Interface) tools for working with it.

Discriminative dictionary learning for abdominal multi-organ segmentation.

PubMed

Tong, Tong; Wolz, Robin; Wang, Zehan; Gao, Qinquan; Misawa, Kazunari; Fujiwara, Michitaka; Mori, Kensaku; Hajnal, Joseph V; Rueckert, Daniel

2015-07-01

An automated segmentation method is presented for multi-organ segmentation in abdominal CT images. Dictionary learning and sparse coding techniques are used in the proposed method to generate target specific priors for segmentation. The method simultaneously learns dictionaries which have reconstructive power and classifiers which have discriminative ability from a set of selected atlases. Based on the learnt dictionaries and classifiers, probabilistic atlases are then generated to provide priors for the segmentation of unseen target images. The final segmentation is obtained by applying a post-processing step based on a graph-cuts method. In addition, this paper proposes a voxel-wise local atlas selection strategy to deal with high inter-subject variation in abdominal CT images. The segmentation performance of the proposed method with different atlas selection strategies are also compared. Our proposed method has been evaluated on a database of 150 abdominal CT images and achieves a promising segmentation performance with Dice overlap values of 94.9%, 93.6%, 71.1%, and 92.5% for liver, kidneys, pancreas, and spleen, respectively. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

New approach for segmentation and recognition of handwritten numeral strings

NASA Astrophysics Data System (ADS)

Sadri, Javad; Suen, Ching Y.; Bui, Tien D.

2004-12-01

In this paper, we propose a new system for segmentation and recognition of unconstrained handwritten numeral strings. The system uses a combination of foreground and background features for segmentation of touching digits. The method introduces new algorithms for traversing the top/bottom-foreground-skeletons of the touched digits, and for finding feature points on these skeletons, and matching them to build all the segmentation paths. For the first time a genetic representation is used to show all the segmentation hypotheses. Our genetic algorithm tries to search and evolve the population of candidate segmentations and finds the one with the highest confidence for its segmentation and recognition. We have also used a new method for feature extraction which lowers the variations in the shapes of the digits, and then a MLP neural network is utilized to produce the labels and confidence values for those digits. The NIST SD19 and CENPARMI databases are used for evaluating the system. Our system can get a correct segmentation-recognition rate of 96.07% with rejection rate of 2.61% which compares favorably with those that exist in the literature.

New approach for segmentation and recognition of handwritten numeral strings

NASA Astrophysics Data System (ADS)

Sadri, Javad; Suen, Ching Y.; Bui, Tien D.

2005-01-01

In this paper, we propose a new system for segmentation and recognition of unconstrained handwritten numeral strings. The system uses a combination of foreground and background features for segmentation of touching digits. The method introduces new algorithms for traversing the top/bottom-foreground-skeletons of the touched digits, and for finding feature points on these skeletons, and matching them to build all the segmentation paths. For the first time a genetic representation is used to show all the segmentation hypotheses. Our genetic algorithm tries to search and evolve the population of candidate segmentations and finds the one with the highest confidence for its segmentation and recognition. We have also used a new method for feature extraction which lowers the variations in the shapes of the digits, and then a MLP neural network is utilized to produce the labels and confidence values for those digits. The NIST SD19 and CENPARMI databases are used for evaluating the system. Our system can get a correct segmentation-recognition rate of 96.07% with rejection rate of 2.61% which compares favorably with those that exist in the literature.

Sensor-oriented feature usability evaluation in fingerprint segmentation

NASA Astrophysics Data System (ADS)

Li, Ying; Yin, Yilong; Yang, Gongping

2013-06-01

Existing fingerprint segmentation methods usually process fingerprint images captured by different sensors with the same feature or feature set. We propose to improve the fingerprint segmentation result in view of an important fact that images from different sensors have different characteristics for segmentation. Feature usability evaluation, which means to evaluate the usability of features to find the personalized feature or feature set for different sensors to improve the performance of segmentation. The need for feature usability evaluation for fingerprint segmentation is raised and analyzed as a new issue. To address this issue, we present a decision-tree-based feature-usability evaluation method, which utilizes a C4.5 decision tree algorithm to evaluate and pick the best suitable feature or feature set for fingerprint segmentation from a typical candidate feature set. We apply the novel method on the FVC2002 database of fingerprint images, which are acquired by four different respective sensors and technologies. Experimental results show that the accuracy of segmentation is improved, and time consumption for feature extraction is dramatically reduced with selected feature(s).

Northeast Artificial Intelligence Consortium Annual Report for 1987. Volume 4. Research in Automated Photointerpretation

DTIC Science & Technology

1989-03-01

KOWLEDGE INFERENCE IMAGE DAAAEENGINE DATABASE Automated Photointerpretation Testbed. 4.1.7 Fig. .1.1-2 An Initial Segmentation of an Image / zx...MRF) theory provide a powerful alternative texture model and have resulted in intensive research activity in MRF model- based texture analysis...interpretation process. 5. Additional, and perhaps more powerful , features have to be incorporated into the image segmentation procedure. 6. Object detection

Automated cell analysis tool for a genome-wide RNAi screen with support vector machine based supervised learning

NASA Astrophysics Data System (ADS)

Remmele, Steffen; Ritzerfeld, Julia; Nickel, Walter; Hesser, Jürgen

2011-03-01

RNAi-based high-throughput microscopy screens have become an important tool in biological sciences in order to decrypt mostly unknown biological functions of human genes. However, manual analysis is impossible for such screens since the amount of image data sets can often be in the hundred thousands. Reliable automated tools are thus required to analyse the fluorescence microscopy image data sets usually containing two or more reaction channels. The herein presented image analysis tool is designed to analyse an RNAi screen investigating the intracellular trafficking and targeting of acylated Src kinases. In this specific screen, a data set consists of three reaction channels and the investigated cells can appear in different phenotypes. The main issue of the image processing task is an automatic cell segmentation which has to be robust and accurate for all different phenotypes and a successive phenotype classification. The cell segmentation is done in two steps by segmenting the cell nuclei first and then using a classifier-enhanced region growing on basis of the cell nuclei to segment the cells. The classification of the cells is realized by a support vector machine which has to be trained manually using supervised learning. Furthermore, the tool is brightness invariant allowing different staining quality and it provides a quality control that copes with typical defects during preparation and acquisition. A first version of the tool has already been successfully applied for an RNAi-screen containing three hundred thousand image data sets and the SVM extended version is designed for additional screens.

CD-ROMS Step by Step.

ERIC Educational Resources Information Center

Nath, Herbert

This manual consists of sets of guides for six CD-ROM databases: (1) ABI/INFORM, a business administration CD-ROM published by UMI; (2) Books in Print (an outstanding tool for compiling bibliographies on any subject); (3) ERIC (Educational Resources Information Center), an education database in the version published by SilverPlatter; (4) MLA, a…

Archive and Database as Metaphor: Theorizing the Historical Record

ERIC Educational Resources Information Center

Manoff, Marlene

2010-01-01

Digital media increase the visibility and presence of the past while also reshaping our sense of history. We have extraordinary access to digital versions of books, journals, film, television, music, art and popular culture from earlier eras. New theoretical formulations of database and archive provide ways to think creatively about these changes…

The forest inventory and analysis database description and users manual version 1.0

Treesearch

Patrick D. Miles; Gary J. Brand; Carol L. Alerich; Larry F. Bednar; Sharon W. Woudenberg; Joseph F. Glover; Edward N. Ezell

2001-01-01

Describes the structure of the Forest Inventory and Analysis Database (FIADB) and provides information on generating estimates of forest statistics from these data. The FIADB structure provides a consistent framework for storing forest inventory data across all ownerships across the entire United States. These data are available to the public.

Back to the Scriptorium: Database Marketplace 2009

ERIC Educational Resources Information Center

Tenopir, Carol; Baker, Gayle; Grogg, Jill E.

2009-01-01

The 2009 database marketplace is bounded by two extremes: massive digitization projects to increase access, and retrenchment owing to budget worries. Picture medieval monks hunched over their desks in the scriptorium as they labor to copy manuscripts. A 21st-century version of this activity is being repeated daily in the world's libraries and…

Multi-level deep supervised networks for retinal vessel segmentation.

PubMed

Mo, Juan; Zhang, Lei

2017-12-01

Changes in the appearance of retinal blood vessels are an important indicator for various ophthalmologic and cardiovascular diseases, including diabetes, hypertension, arteriosclerosis, and choroidal neovascularization. Vessel segmentation from retinal images is very challenging because of low blood vessel contrast, intricate vessel topology, and the presence of pathologies such as microaneurysms and hemorrhages. To overcome these challenges, we propose a neural network-based method for vessel segmentation. A deep supervised fully convolutional network is developed by leveraging multi-level hierarchical features of the deep networks. To improve the discriminative capability of features in lower layers of the deep network and guide the gradient back propagation to overcome gradient vanishing, deep supervision with auxiliary classifiers is incorporated in some intermediate layers of the network. Moreover, the transferred knowledge learned from other domains is used to alleviate the issue of insufficient medical training data. The proposed approach does not rely on hand-crafted features and needs no problem-specific preprocessing or postprocessing, which reduces the impact of subjective factors. We evaluate the proposed method on three publicly available databases, the DRIVE, STARE, and CHASE_DB1 databases. Extensive experiments demonstrate that our approach achieves better or comparable performance to state-of-the-art methods with a much faster processing speed, making it suitable for real-world clinical applications. The results of cross-training experiments demonstrate its robustness with respect to the training set. The proposed approach segments retinal vessels accurately with a much faster processing speed and can be easily applied to other biomedical segmentation tasks.

Automatic temporal segment detection via bilateral long short-term memory recurrent neural networks

NASA Astrophysics Data System (ADS)

Sun, Bo; Cao, Siming; He, Jun; Yu, Lejun; Li, Liandong

2017-03-01

Constrained by the physiology, the temporal factors associated with human behavior, irrespective of facial movement or body gesture, are described by four phases: neutral, onset, apex, and offset. Although they may benefit related recognition tasks, it is not easy to accurately detect such temporal segments. An automatic temporal segment detection framework using bilateral long short-term memory recurrent neural networks (BLSTM-RNN) to learn high-level temporal-spatial features, which synthesizes the local and global temporal-spatial information more efficiently, is presented. The framework is evaluated in detail over the face and body database (FABO). The comparison shows that the proposed framework outperforms state-of-the-art methods for solving the problem of temporal segment detection.

Heritability and reliability of automatically segmented human hippocampal formation subregions

PubMed Central

Whelan, Christopher D.; Hibar, Derrek P.; van Velzen, Laura S.; Zannas, Anthony S.; Carrillo-Roa, Tania; McMahon, Katie; Prasad, Gautam; Kelly, Sinéad; Faskowitz, Joshua; deZubiracay, Greig; Iglesias, Juan E.; van Erp, Theo G.M.; Frodl, Thomas; Martin, Nicholas G.; Wright, Margaret J.; Jahanshad, Neda; Schmaal, Lianne; Sämann, Philipp G.; Thompson, Paul M.

2016-01-01

The human hippocampal formation can be divided into a set of cytoarchitecturally and functionally distinct subregions, involved in different aspects of memory formation. Neuroanatomical disruptions within these subregions are associated with several debilitating brain disorders including Alzheimer’s disease, major depression, schizophrenia, and bipolar disorder. Multi-center brain imaging consortia, such as the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) consortium, are interested in studying disease effects on these subregions, and in the genetic factors that affect them. For large-scale studies, automated extraction and subsequent genomic association studies of these hippocampal subregion measures may provide additional insight. Here, we evaluated the test–retest reliability and transplatform reliability (1.5 T versus 3 T) of the subregion segmentation module in the FreeSurfer software package using three independent cohorts of healthy adults, one young (Queensland Twins Imaging Study, N = 39), another elderly (Alzheimer’s Disease Neuroimaging Initiative, ADNI-2, N = 163) and another mixed cohort of healthy and depressed participants (Max Planck Institute, MPIP, N = 598). We also investigated agreement between the most recent version of this algorithm (v6.0) and an older version (v5.3), again using the ADNI-2 and MPIP cohorts in addition to a sample from the Netherlands Study for Depression and Anxiety (NESDA) (N = 221). Finally, we estimated the heritability (h2) of the segmented subregion volumes using the full sample of young, healthy QTIM twins (N = 728). Test–retest reliability was high for all twelve subregions in the 3 T ADNI-2 sample (intraclass correlation coefficient (ICC) = 0.70–0.97) and moderate-to-high in the 4 T QTIM sample (ICC = 0.5–0.89). Transplatform reliability was strong for eleven of the twelve subregions (ICC = 0.66–0.96); however, the hippocampal fissure was not consistently reconstructed across 1.5 T and 3 T field strengths (ICC = 0.47–0.57). Between-version agreement was moderate for the hippocampal tail, subiculum and presubiculum (ICC = 0.78–0.84; Dice Similarity Coefficient (DSC) = 0.55–0.70), and poor for all other subregions (ICC = 0.34–0.81; DSC = 0.28–0.51). All hippocampal subregion volumes were highly heritable (h2 = 0.67–0.91). Our findings indicate that eleven of the twelve human hippocampal subregions segmented using FreeSurfer version 6.0 may serve as reliable and informative quantitative phenotypes for future multi-site imaging genetics initiatives such as those of the ENIGMA consortium. PMID:26747746

Six and Three-Hourly Meteorological Observations From 223 Former U.S.S.R. Stations (NPD-048)

DOE Data Explorer

Razuvaev, V. N. [All-Russian Research Institute of Hydrometeorological Information, World Data Center, Russia; Apasova, E. B. [All-Russian Research Institute of Hydrometeorological Information, World Data Center, Russia; Martuganov, R. A. [All-Russian Research Institute of Hydrometeorological Information, World Data Center, Russia; Kaiser, D. P. [CDIAC, Oak Ridge National Laboratory; Marino, G. P. [CDIAC, Oak Ridge National Laboratory

2007-11-01

This database contains 6- and 3-hourly meteorological observations from a 223-station network of the former Soviet Union. These data have been made available through cooperation between the two principal climate data centers of the United States and Russia: the National Climatic Data Center (NCDC), in Asheville, North Carolina, and the All-Russian Research Institute of Hydrometeorological Information-World Data Centre (RIHMI-WDC) in Obninsk, Russia. The first version of this database extended through the mid-1980s (ending year dependent upon station) and was made available in 1995 by the Carbon Dioxide Information Analysis Center (CDIAC) as NDP-048. A second version of the database extended the data records through 1990. This third, and current version of the database includes data through 2000 for over half of the stations (mainly for Russia), whereas the remainder of the stations have records extending through various years of the 1990s. Because of the break up of the Soviet Union in 1991, and since RIHMI-WDC is a Russian institution, only Russain stations are generally available through 2000. The non-Russian station records in this database typically extend through 1991. Station records consist of 6- and 3-hourly observations of some 24 meteorological variables including temperature, past and present weather type, precipitation amount, cloud amount and type, sea level pressure, relative humidity, and wind direction and speed. The 6-hourly observations extend from 1936 through 1965; the 3-hourly observations extend from 1966 through 2000 (or through the latest year available). These data have undergone extensive quality assurance checks by RIHMI-WDC, NCDC, and CDIAC. The database represents a wealth of meteorological information for a large and climatologically important portion of the earth's land area, and should prove extremely useful for a wide variety of regional climate change studies.

Spatial-Orientation Priming Impedes Rather than Facilitates the Spontaneous Control of Hand-Retraction Speeds in Patients with Parkinson’s Disease

PubMed Central

Yanovich, Polina; Isenhower, Robert W.; Sage, Jacob; Torres, Elizabeth B.

2013-01-01

Background Often in Parkinson’s disease (PD) motor-related problems overshadow latent non-motor deficits as it is difficult to dissociate one from the other with commonly used observational inventories. Here we ask if the variability patterns of hand speed and acceleration would be revealing of deficits in spatial-orientation related decisions as patients performed a familiar reach-to-grasp task. To this end we use spatial-orientation priming which normally facilitates motor-program selection and asked whether in PD spatial-orientation priming helps or hinders performance. Methods To dissociate spatial-orientation- and motor-related deficits participants performed two versions of the task. The biomechanical version (DEFAULT) required the same postural- and hand-paths as the orientation-priming version (primed-UP). Any differences in the patients here could not be due to motor issues as the tasks were biomechanically identical. The other priming version (primed-DOWN) however required additional spatial and postural processing. We assessed in all three cases both the forward segment deliberately aimed towards the spatial-target and the retracting segment, spontaneously bringing the hand to rest without an instructed goal. Results and Conclusions We found that forward and retracting segments belonged in two different statistical classes according to the fluctuations of speed and acceleration maxima. Further inspection revealed conservation of the forward (voluntary) control of speed but in PD a discontinuity of this control emerged during the uninstructed retractions which was absent in NC. Two PD groups self-emerged: one group in which priming always affected the retractions and the other in which only the more challenging primed-DOWN condition was affected. These PD-groups self-formed according to the speed variability patterns, which systematically changed along a gradient that depended on the priming, thus dissociating motor from spatial-orientation issues. Priming did not facilitate the motor task in PD but it did reveal a breakdown in the spatial-orientation decision that was independent of the motor-postural path. PMID:23843963

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed

Nadkarni, P M; Miller, P L

1991-01-01

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

Brain tumor classification and segmentation using sparse coding and dictionary learning.

PubMed

Salman Al-Shaikhli, Saif Dawood; Yang, Michael Ying; Rosenhahn, Bodo

2016-08-01

This paper presents a novel fully automatic framework for multi-class brain tumor classification and segmentation using a sparse coding and dictionary learning method. The proposed framework consists of two steps: classification and segmentation. The classification of the brain tumors is based on brain topology and texture. The segmentation is based on voxel values of the image data. Using K-SVD, two types of dictionaries are learned from the training data and their associated ground truth segmentation: feature dictionary and voxel-wise coupled dictionaries. The feature dictionary consists of global image features (topological and texture features). The coupled dictionaries consist of coupled information: gray scale voxel values of the training image data and their associated label voxel values of the ground truth segmentation of the training data. For quantitative evaluation, the proposed framework is evaluated using different metrics. The segmentation results of the brain tumor segmentation (MICCAI-BraTS-2013) database are evaluated using five different metric scores, which are computed using the online evaluation tool provided by the BraTS-2013 challenge organizers. Experimental results demonstrate that the proposed approach achieves an accurate brain tumor classification and segmentation and outperforms the state-of-the-art methods.

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

PubMed Central

2017-01-01

Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the “pair-rule” genes, are still not well understood at the system level. Building on established genetic interactions, I construct a logical model of the Drosophila pair-rule system that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic “gap” inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries and explains the aetiology of the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggests that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods. PMID:28953896

FLAPS (Fatigue Life Analysis Programs): Computer Programs to Predict Cyclic Life Using the Total Strain Version of Strainrange Partitioning and Other Life Prediction Methods. Users' Manual and Example Problems, Version 1.0

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R. (Technical Monitor)

2003-01-01

This manual presents computer programs FLAPS for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the Total Strain version of Strainrange Partitioning (TS-SRP), and several other life prediction methods described in this manual. The user should be thoroughly familiar with the TS-SRP and these life prediction methods before attempting to use any of these programs. Improper understanding can lead to incorrect use of the method and erroneous life predictions. An extensive database has also been developed in a parallel effort. The database is probably the largest source of high-temperature, creep-fatigue test data available in the public domain and can be used with other life-prediction methods as well. This users' manual, software, and database are all in the public domain and can be obtained by contacting the author. The Compact Disk (CD) accompanying this manual contains an executable file for the FLAPS program, two datasets required for the example problems in the manual, and the creep-fatigue data in a format compatible with these programs.

Retinal vascular segmentation using superpixel-based line operator and its application to vascular topology estimation.

PubMed

Na, Tong; Xie, Jianyang; Zhao, Yitian; Zhao, Yifan; Liu, Yue; Wang, Yongtian; Liu, Jiang

2018-05-09

Automatic methods of analyzing of retinal vascular networks, such as retinal blood vessel detection, vascular network topology estimation, and arteries/veins classification are of great assistance to the ophthalmologist in terms of diagnosis and treatment of a wide spectrum of diseases. We propose a new framework for precisely segmenting retinal vasculatures, constructing retinal vascular network topology, and separating the arteries and veins. A nonlocal total variation inspired Retinex model is employed to remove the image intensity inhomogeneities and relatively poor contrast. For better generalizability and segmentation performance, a superpixel-based line operator is proposed as to distinguish between lines and the edges, thus allowing more tolerance in the position of the respective contours. The concept of dominant sets clustering is adopted to estimate retinal vessel topology and classify the vessel network into arteries and veins. The proposed segmentation method yields competitive results on three public data sets (STARE, DRIVE, and IOSTAR), and it has superior performance when compared with unsupervised segmentation methods, with accuracy of 0.954, 0.957, and 0.964, respectively. The topology estimation approach has been applied to five public databases (DRIVE,STARE, INSPIRE, IOSTAR, and VICAVR) and achieved high accuracy of 0.830, 0.910, 0.915, 0.928, and 0.889, respectively. The accuracies of arteries/veins classification based on the estimated vascular topology on three public databases (INSPIRE, DRIVE and VICAVR) are 0.90.9, 0.910, and 0.907, respectively. The experimental results show that the proposed framework has effectively addressed crossover problem, a bottleneck issue in segmentation and vascular topology reconstruction. The vascular topology information significantly improves the accuracy on arteries/veins classification. © 2018 American Association of Physicists in Medicine.

NUBASE2012 Evaluation of Nuclear Properties

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

Wang, M., E-mail: wangm@impcas.ac.cn; CSNSM-Orsay, MPI-K, D-69117 Heidelberg; Audi, G.

NUBASE is a database containing the recommended values for the main properties of all known nuclides in their ground and excited isomeric states. Since the publication of the first version in 1997, NUBASE has been widely used in the nuclear science community. The latest version (NUBASE2012) was published in December 2012. Two specific examples are given to illustrate the evaluation policy of NUBASE2012.

Mass Spectral Library with Search Program, Data Version: NIST v17

National Institute of Standards and Technology Data Gateway

SRD 1A NIST/EPA/NIH Mass Spectral Library with Search Program, Data Version: NIST v17 (PC database for purchase)   Available with full-featured NIST MS Search Program for Windows integrated tools, the NIST '98 is a fully evaluated collection of electron-ionization mass spectra. (147,198 Compounds with Spectra; 147,194 Chemical Structures; 174,948 Spectra )

New Database Manipulation Tools in the Easy-Learning On-Line Platform

ERIC Educational Resources Information Center

Radescu, Radu; Davidescu, Andrei; Pupezescu, Valentin

2011-01-01

The present paper deals with the new ORM (object-relational mapping) tool introduced in the easy-learning platform. Propel 1.5 is the latest version of Propel, one of the ORMs fully compatible with the Symfony framework, and in comparison with the older versions and it has drastically improved the way the easy-learning platform can manipulate its…

Alaska Geochemical Database - Mineral Exploration Tool for the 21st Century - PDF of presentation

USGS Publications Warehouse

Granitto, Matthew; Schmidt, Jeanine M.; Labay, Keith A.; Shew, Nora B.; Gamble, Bruce M.

2012-01-01

The U.S. Geological Survey has created a geochemical database of geologic material samples collected in Alaska. This database is readily accessible to anyone with access to the Internet. Designed as a tool for mineral or environmental assessment, land management, or mineral exploration, the initial version of the Alaska Geochemical Database - U.S. Geological Survey Data Series 637 - contains geochemical, geologic, and geospatial data for 264,158 samples collected from 1962-2009: 108,909 rock samples; 92,701 sediment samples; 48,209 heavy-mineral-concentrate samples; 6,869 soil samples; and 7,470 mineral samples. In addition, the Alaska Geochemical Database contains mineralogic data for 18,138 nonmagnetic-fraction heavy mineral concentrates, making it the first U.S. Geological Survey database of this scope that contains both geochemical and mineralogic data. Examples from the Alaska Range will illustrate potential uses of the Alaska Geochemical Database in mineral exploration. Data from the Alaska Geochemical Database have been extensively checked for accuracy of sample media description, sample site location, and analytical method using U.S. Geological Survey sample-submittal archives and U.S. Geological Survey publications (plus field notebooks and sample site compilation base maps from the Alaska Technical Data Unit in Anchorage, Alaska). The database is also the repository for nearly all previously released U.S. Geological Survey Alaska geochemical datasets. Although the Alaska Geochemical Database is a fully relational database in Microsoft® Access 2003 and 2010 formats, these same data are also provided as a series of spreadsheet files in Microsoft® Excel 2003 and 2010 formats, and as ASCII text files. A DVD version of the Alaska Geochemical Database was released in October 2011, as U.S. Geological Survey Data Series 637, and data downloads are available at http://pubs.usgs.gov/ds/637/. Also, all Alaska Geochemical Database data have been incorporated into the interactive U.S. Geological Survey Mineral Resource Data web portal, available at http://mrdata.usgs.gov/.

Protocol for the E-Area Low Level Waste Facility Disposal Limits Database

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

Swingle, R

2006-01-31

A database has been developed to contain the disposal limits for the E-Area Low Level Waste Facility (ELLWF). This database originates in the form of an EXCEL{copyright} workbook. The pertinent sheets are translated to PDF format using Adobe ACROBAT{copyright}. The PDF version of the database is accessible from the Solid Waste Division web page on SHRINE. In addition to containing the various disposal unit limits, the database also contains hyperlinks to the original references for all limits. It is anticipated that database will be revised each time there is an addition, deletion or revision of any of the ELLWF radionuclidemore » disposal limits.« less

Database of Geoscientific References Through 2007 for Afghanistan, Version 2

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2007-01-01

This report describes an accompanying database of geoscientific references for the country of Afghanistan. Included is an accompanying Microsoft? Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan's energy, mineral, and water resources, and geologic hazards, currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,462) and unpublished (n = 174) references compiled through September, 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable, interface and only minimum knowledge of the use of Microsoft? Access is required.

NOAA Data Rescue of Key Solar Databases and Digitization of Historical Solar Images

NASA Astrophysics Data System (ADS)

Coffey, H. E.

2006-08-01

Over a number of years, the staff at NOAA National Geophysical Data Center (NGDC) has worked to rescue key solar databases by converting them to digital format and making them available via the World Wide Web. NOAA has had several data rescue programs where staff compete for funds to rescue important and critical historical data that are languishing in archives and at risk of being lost due to deteriorating condition, loss of any metadata or descriptive text that describe the databases, lack of interest or funding in maintaining databases, etc. The Solar-Terrestrial Physics Division at NGDC was able to obtain funds to key in some critical historical tabular databases. Recently the NOAA Climate Database Modernization Program (CDMP) funded a project to digitize historical solar images, producing a large online database of historical daily full disk solar images. The images include the wavelengths Calcium K, Hydrogen Alpha, and white light photos, as well as sunspot drawings and the comprehensive drawings of a multitude of solar phenomena on one daily map (Fraunhofer maps and Wendelstein drawings). Included in the digitization are high resolution solar H-alpha images taken at the Boulder Solar Observatory 1967-1984. The scanned daily images document many phases of solar activity, from decadal variation to rotational variation to daily changes. Smaller versions are available online. Larger versions are available by request. See http://www.ngdc.noaa.gov/stp/SOLAR/ftpsolarimages.html. The tabular listings and solar imagery will be discussed.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

A Recommender System in the Cyber Defense Domain

DTIC Science & Technology

2014-03-27

monitoring software is a java based program sending updates to the database on the sensor machine. The host monitoring program gathers information about...3.2.2 Database. A MySQL database located on the sensor machine acts as the storage for the sensors on the network. Snort, Nmap, vulnerability scores, and...machine with the IDS and the recommender is labeled “sensor”. The recommender system code is written in java and compiled using java version 1.6.024

CyanoBase: the cyanobacteria genome database update 2010.

PubMed

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

PubMed Central

Colangelo, Christopher M.; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L.; Carriero, Nicholas J.; Gulcicek, Erol E.; Lam, TuKiet T.; Wu, Terence; Bjornson, Robert D.; Bruce, Can; Nairn, Angus C.; Rinehart, Jesse; Miller, Perry L.; Williams, Kenneth R.

2015-01-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry (LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED’s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. PMID:25712262

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

PubMed

Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

2015-02-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

Members of the news media watch as a crane is used to move one of two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket to a test stand in the Rotation, Processing and Surge Facility at NASA’s Kennedy Space Center in Florida. Inside the RPSF, the Ground Systems Development and Operations Program and Jacobs Engineering, on the Test and Operations Support Contract, will prepare the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

Labor Market Structure and Salary Determination among Professional Basketball Players.

ERIC Educational Resources Information Center

Wallace, Michael

1988-01-01

The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

Ensemble Semi-supervised Frame-work for Brain Magnetic Resonance Imaging Tissue Segmentation.

PubMed

Azmi, Reza; Pishgoo, Boshra; Norozi, Narges; Yeganeh, Samira

2013-04-01

Brain magnetic resonance images (MRIs) tissue segmentation is one of the most important parts of the clinical diagnostic tools. Pixel classification methods have been frequently used in the image segmentation with two supervised and unsupervised approaches up to now. Supervised segmentation methods lead to high accuracy, but they need a large amount of labeled data, which is hard, expensive, and slow to obtain. Moreover, they cannot use unlabeled data to train classifiers. On the other hand, unsupervised segmentation methods have no prior knowledge and lead to low level of performance. However, semi-supervised learning which uses a few labeled data together with a large amount of unlabeled data causes higher accuracy with less trouble. In this paper, we propose an ensemble semi-supervised frame-work for segmenting of brain magnetic resonance imaging (MRI) tissues that it has been used results of several semi-supervised classifiers simultaneously. Selecting appropriate classifiers has a significant role in the performance of this frame-work. Hence, in this paper, we present two semi-supervised algorithms expectation filtering maximization and MCo_Training that are improved versions of semi-supervised methods expectation maximization and Co_Training and increase segmentation accuracy. Afterward, we use these improved classifiers together with graph-based semi-supervised classifier as components of the ensemble frame-work. Experimental results show that performance of segmentation in this approach is higher than both supervised methods and the individual semi-supervised classifiers.

A Multi-Anatomical Retinal Structure Segmentation System for Automatic Eye Screening Using Morphological Adaptive Fuzzy Thresholding

PubMed Central

Elleithy, Khaled; Elleithy, Abdelrahman

2018-01-01

Eye exam can be as efficacious as physical one in determining health concerns. Retina screening can be the very first clue for detecting a variety of hidden health issues including pre-diabetes and diabetes. Through the process of clinical diagnosis and prognosis; ophthalmologists rely heavily on the binary segmented version of retina fundus image; where the accuracy of segmented vessels, optic disc, and abnormal lesions extremely affects the diagnosis accuracy which in turn affect the subsequent clinical treatment steps. This paper proposes an automated retinal fundus image segmentation system composed of three segmentation subsystems follow same core segmentation algorithm. Despite of broad difference in features and characteristics; retinal vessels, optic disc, and exudate lesions are extracted by each subsystem without the need for texture analysis or synthesis. For sake of compact diagnosis and complete clinical insight, our proposed system can detect these anatomical structures in one session with high accuracy even in pathological retina images. The proposed system uses a robust hybrid segmentation algorithm combines adaptive fuzzy thresholding and mathematical morphology. The proposed system is validated using four benchmark datasets: DRIVE and STARE (vessels), DRISHTI-GS (optic disc), and DIARETDB1 (exudates lesions). Competitive segmentation performance is achieved, outperforming a variety of up-to-date systems and demonstrating the capacity to deal with other heterogeneous anatomical structures. PMID:29888146

Remodeling Cildb, a popular database for cilia and links for ciliopathies

PubMed Central

2014-01-01

Background New generation technologies in cell and molecular biology generate large amounts of data hard to exploit for individual proteins. This is particularly true for ciliary and centrosomal research. Cildb is a multi–species knowledgebase gathering high throughput studies, which allows advanced searches to identify proteins involved in centrosome, basal body or cilia biogenesis, composition and function. Combined to localization of genetic diseases on human chromosomes given by OMIM links, candidate ciliopathy proteins can be compiled through Cildb searches. Methods Othology between recent versions of the whole proteomes was computed using Inparanoid and ciliary high throughput studies were remapped on these recent versions. Results Due to constant evolution of the ciliary and centrosomal field, Cildb has been recently upgraded twice, with new species whole proteomes and new ciliary studies, and the latter version displays a novel BioMart interface, much more intuitive than the previous ones. Conclusions This already popular database is designed now for easier use and is up to date in regard to high throughput ciliary studies. PMID:25422781

CHOgenome.org 2.0: Genome resources and website updates.

PubMed

Kremkow, Benjamin G; Baik, Jong Youn; MacDonald, Madolyn L; Lee, Kelvin H

2015-07-01

Chinese hamster ovary (CHO) cells are a major host cell line for the production of therapeutic proteins, and CHO cell and Chinese hamster (CH) genomes have recently been sequenced using next-generation sequencing methods. CHOgenome.org was launched in 2011 (version 1.0) to serve as a database repository and to provide bioinformatics tools for the CHO community. CHOgenome.org (version 1.0) maintained GenBank CHO-K1 genome data, identified CHO-omics literature, and provided a CHO-specific BLAST service. Recent major updates to CHOgenome.org (version 2.0) include new sequence and annotation databases for both CHO and CH genomes, a more user-friendly website, and new research tools, including a proteome browser and a genome viewer. CHO cell-line specific sequences and annotations facilitate cell line development opportunities, several of which are discussed. Moving forward, CHOgenome.org will host the increasing amount of CHO-omics data and continue to make useful bioinformatics tools available to the CHO community. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Biomolecular Crystallization Database Version 4: expanded content and new features.

PubMed

Tung, Michael; Gallagher, D Travis

2009-01-01

The Biological Macromolecular Crystallization Database (BMCD) has been a publicly available resource since 1988, providing a curated archive of information on crystal growth for proteins and other biological macromolecules. The BMCD content has recently been expanded to include 14 372 crystal entries. The resource continues to be freely available at http://xpdb.nist.gov:8060/BMCD4. In addition, the software has been adapted to support the Java-based Lucene query language, enabling detailed searching over specific parameters, and explicit search of parameter ranges is offered for five numeric variables. Extensive tools have been developed for import and handling of data from the RCSB Protein Data Bank. The updated BMCD is called version 4.02 or BMCD4. BMCD4 entries have been expanded to include macromolecule sequence, enabling more elaborate analysis of relations among protein properties, crystal-growth conditions and the geometric and diffraction properties of the crystals. The BMCD version 4.02 contains greatly expanded content and enhanced search capabilities to facilitate scientific analysis and design of crystal-growth strategies.

Breast mass segmentation in mammograms combining fuzzy c-means and active contours

NASA Astrophysics Data System (ADS)

Hmida, Marwa; Hamrouni, Kamel; Solaiman, Basel; Boussetta, Sana

2018-04-01

Segmentation of breast masses in mammograms is a challenging issue due to the nature of mammography and the characteristics of masses. In fact, mammographic images are poor in contrast and breast masses have various shapes and densities with fuzzy and ill-defined borders. In this paper, we propose a method based on a modified Chan-Vese active contour model for mass segmentation in mammograms. We conduct the experiment on mass Regions of Interest (ROI) extracted from the MIAS database. The proposed method consists of mainly three stages: Firstly, the ROI is preprocessed to enhance the contrast. Next, two fuzzy membership maps are generated from the preprocessed ROI based on fuzzy C-Means algorithm. These fuzzy membership maps are finally used to modify the energy of the Chan-Vese model and to perform the final segmentation. Experimental results indicate that the proposed method yields good mass segmentation results.

ECG signal analysis through hidden Markov models.

PubMed

Andreão, Rodrigo V; Dorizzi, Bernadette; Boudy, Jérôme

2006-08-01

This paper presents an original hidden Markov model (HMM) approach for online beat segmentation and classification of electrocardiograms. The HMM framework has been visited because of its ability of beat detection, segmentation and classification, highly suitable to the electrocardiogram (ECG) problem. Our approach addresses a large panel of topics some of them never studied before in other HMM related works: waveforms modeling, multichannel beat segmentation and classification, and unsupervised adaptation to the patient's ECG. The performance was evaluated on the two-channel QT database in terms of waveform segmentation precision, beat detection and classification. Our waveform segmentation results compare favorably to other systems in the literature. We also obtained high beat detection performance with sensitivity of 99.79% and a positive predictivity of 99.96%, using a test set of 59 recordings. Moreover, premature ventricular contraction beats were detected using an original classification strategy. The results obtained validate our approach for real world application.

Blurry-frame detection and shot segmentation in colonoscopy videos

NASA Astrophysics Data System (ADS)

Oh, JungHwan; Hwang, Sae; Tavanapong, Wallapak; de Groen, Piet C.; Wong, Johnny

2003-12-01

Colonoscopy is an important screening procedure for colorectal cancer. During this procedure, the endoscopist visually inspects the colon. Human inspection, however, is not without error. We hypothesize that colonoscopy videos may contain additional valuable information missed by the endoscopist. Video segmentation is the first necessary step for the content-based video analysis and retrieval to provide efficient access to the important images and video segments from a large colonoscopy video database. Based on the unique characteristics of colonoscopy videos, we introduce a new scheme to detect and remove blurry frames, and segment the videos into shots based on the contents. Our experimental results show that the average precision and recall of the proposed scheme are over 90% for the detection of non-blurry images. The proposed method of blurry frame detection and shot segmentation is extensible to the videos captured from other endoscopic procedures such as upper gastrointestinal endoscopy, enteroscopy, cystoscopy, and laparoscopy.

Patch-based automatic retinal vessel segmentation in global and local structural context.

PubMed

Cao, Shuoying; Bharath, Anil A; Parker, Kim H; Ng, Jeffrey

2012-01-01

In this paper, we extend our published work [1] and propose an automated system to segment retinal vessel bed in digital fundus images with enough adaptability to analyze images from fluorescein angiography. This approach takes into account both the global and local context and enables both vessel segmentation and microvascular centreline extraction. These tools should allow researchers and clinicians to estimate and assess vessel diameter, capillary blood volume and microvascular topology for early stage disease detection, monitoring and treatment. Global vessel bed segmentation is achieved by combining phase-invariant orientation fields with neighbourhood pixel intensities in a patch-based feature vector for supervised learning. This approach is evaluated against benchmarks on the DRIVE database [2]. Local microvascular centrelines within Regions-of-Interest (ROIs) are segmented by linking the phase-invariant orientation measures with phase-selective local structure features. Our global and local structural segmentation can be used to assess both pathological structural alterations and microemboli occurrence in non-invasive clinical settings in a longitudinal study.

Compound image segmentation of published biomedical figures.

PubMed

Li, Pengyuan; Jiang, Xiangying; Kambhamettu, Chandra; Shatkay, Hagit

2018-04-01

Images convey essential information in biomedical publications. As such, there is a growing interest within the bio-curation and the bio-databases communities, to store images within publications as evidence for biomedical processes and for experimental results. However, many of the images in biomedical publications are compound images consisting of multiple panels, where each individual panel potentially conveys a different type of information. Segmenting such images into constituent panels is an essential first step toward utilizing images. In this article, we develop a new compound image segmentation system, FigSplit, which is based on Connected Component Analysis. To overcome shortcomings typically manifested by existing methods, we develop a quality assessment step for evaluating and modifying segmentations. Two methods are proposed to re-segment the images if the initial segmentation is inaccurate. Experimental results show the effectiveness of our method compared with other methods. The system is publicly available for use at: https://www.eecis.udel.edu/~compbio/FigSplit. The code is available upon request. shatkay@udel.edu. Supplementary data are available online at Bioinformatics.

CT-based manual segmentation and evaluation of paranasal sinuses.

PubMed

Pirner, S; Tingelhoff, K; Wagner, I; Westphal, R; Rilk, M; Wahl, F M; Bootz, F; Eichhorn, Klaus W G

2009-04-01

Manual segmentation of computed tomography (CT) datasets was performed for robot-assisted endoscope movement during functional endoscopic sinus surgery (FESS). Segmented 3D models are needed for the robots' workspace definition. A total of 50 preselected CT datasets were each segmented in 150-200 coronal slices with 24 landmarks being set. Three different colors for segmentation represent diverse risk areas. Extension and volumetric measurements were performed. Three-dimensional reconstruction was generated after segmentation. Manual segmentation took 8-10 h for each CT dataset. The mean volumes were: right maxillary sinus 17.4 cm(3), left side 17.9 cm(3), right frontal sinus 4.2 cm(3), left side 4.0 cm(3), total frontal sinuses 7.9 cm(3), sphenoid sinus right side 5.3 cm(3), left side 5.5 cm(3), total sphenoid sinus volume 11.2 cm(3). Our manually segmented 3D-models present the patient's individual anatomy with a special focus on structures in danger according to the diverse colored risk areas. For safe robot assistance, the high-accuracy models represent an average of the population for anatomical variations, extension and volumetric measurements. They can be used as a database for automatic model-based segmentation. None of the segmentation methods so far described provide risk segmentation. The robot's maximum distance to the segmented border can be adjusted according to the differently colored areas.

Unraveling Pancreatic Segmentation.

PubMed

Renard, Yohann; de Mestier, Louis; Perez, Manuela; Avisse, Claude; Lévy, Philippe; Kianmanesh, Reza

2018-04-01

Limited pancreatic resections are increasingly performed, but the rate of postoperative fistula is higher than after classical resections. Pancreatic segmentation, anatomically and radiologically identifiable, may theoretically help the surgeon removing selected anatomical portions with their own segmental pancreatic duct and thus might decrease the postoperative fistula rate. We aimed at systematically and comprehensively reviewing the previously proposed pancreatic segmentations and discuss their relevance and limitations. PubMed database was searched for articles investigating pancreatic segmentation, including human or animal anatomy, and cadaveric or surgical studies. Overall, 47/99 articles were selected and grouped into 4 main hypotheses of pancreatic segmentation methodology: anatomic, vascular, embryologic and lymphatic. The head, body and tail segments are gross description without distinct borders. The arterial territories defined vascular segments and isolate an isthmic paucivascular area. The embryological theory relied on the fusion plans of the embryological buds. The lymphatic drainage pathways defined the lymphatic segmentation. These theories had differences, but converged toward separating the head and body/tail parts, and the anterior from posterior and inferior parts of the pancreatic head. The rate of postoperative fistula was not decreased when surgical resection was performed following any of these segmentation theories; hence, none of them appeared relevant enough to guide pancreatic transections. Current pancreatic segmentation theories do not enable defining anatomical-surgical pancreatic segments. Other approaches should be explored, in particular focusing on pancreatic ducts, through pancreatic ducts reconstructions and embryologic 3D modelization.

Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

NASA Astrophysics Data System (ADS)

Munekawa, Yuma; Ino, Fumihiko; Hagihara, Kenichi

This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.

Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm.

PubMed

Harju, Inka; Lange, Christoph; Kostrzewa, Markus; Maier, Thomas; Rantakokko-Jalava, Kaisu; Haanperä, Marjo

2017-03-01

Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcus mitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae , whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper. Copyright © 2017 American Society for Microbiology.

SuBSENSE: a universal change detection method with local adaptive sensitivity.

PubMed

St-Charles, Pierre-Luc; Bilodeau, Guillaume-Alexandre; Bergevin, Robert

2015-01-01

Foreground/background segmentation via change detection in video sequences is often used as a stepping stone in high-level analytics and applications. Despite the wide variety of methods that have been proposed for this problem, none has been able to fully address the complex nature of dynamic scenes in real surveillance tasks. In this paper, we present a universal pixel-level segmentation method that relies on spatiotemporal binary features as well as color information to detect changes. This allows camouflaged foreground objects to be detected more easily while most illumination variations are ignored. Besides, instead of using manually set, frame-wide constants to dictate model sensitivity and adaptation speed, we use pixel-level feedback loops to dynamically adjust our method's internal parameters without user intervention. These adjustments are based on the continuous monitoring of model fidelity and local segmentation noise levels. This new approach enables us to outperform all 32 previously tested state-of-the-art methods on the 2012 and 2014 versions of the ChangeDetection.net dataset in terms of overall F-Measure. The use of local binary image descriptors for pixel-level modeling also facilitates high-speed parallel implementations: our own version, which used no low-level or architecture-specific instruction, reached real-time processing speed on a midlevel desktop CPU. A complete C++ implementation based on OpenCV is available online.

Evaluation of Cross-Cultural Adaptation and Measurement Properties of STarT Back Screening Tool: A Systematic Review.

PubMed

Al Zoubi, Fadi M; Eilayyan, Owis; Mayo, Nancy E; Bussières, André E

2017-10-01

The purpose of this systematic review was to investigate the extent to which the STarT Back Screening Tool (SBST) has been evaluated for (1) the quality of translation of evidence for cross-cultural adaptation and (2) the measurement properties in languages other than English. A systematic search of 8 databases, including Medline, Embase, CINAHL, PsycINFO, AMED, Scopus, PubMed, and Web of Science, was performed. Electronic databases were searched for the period between 2008 and December 27, 2016. We included studies related to cross-cultural adaptation, including translation and assessment of the measurement properties of SBST. Study selection, translation, methodologic and quality assessments, and data extraction were performed independently by 2 reviewers. Of the 1566 citations retrieved, 17 studies were admissible, representing 11 different SBST versions in 10 languages. The quadratic weighted κ statistics of the 2 reviewers, for the translation, methodologic assessment, and quality assessment were 0.85, 0.76, and 0.83, respectively. For translation, only 2 versions (Belgian-French and Mandarin) fulfilled all requirements. None of the versions had tested all the measurement properties, and when performed, these were found to have been conducted inadequately. With regard to quality assessment, overall, the included versions had a "Poor" total summary score except 2 (Persian and Swiss-German), which were rated as "Fair." Few versions fully met the standard criteria for valid translation, and none of the versions tested all the measurement properties. There is a clear need for more accurate cross-cultural adaptation of SBST and greater attention to the quality of psychometric evaluation of the adapted versions of SBST. At this time, caution is recommended when using SBST in languages other than English. Copyright © 2017. Published by Elsevier Inc.

GPU-based relative fuzzy connectedness image segmentation

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

Zhuge Ying; Ciesielski, Krzysztof C.; Udupa, Jayaram K.

2013-01-15

Purpose:Recently, clinical radiological research and practice are becoming increasingly quantitative. Further, images continue to increase in size and volume. For quantitative radiology to become practical, it is crucial that image segmentation algorithms and their implementations are rapid and yield practical run time on very large data sets. The purpose of this paper is to present a parallel version of an algorithm that belongs to the family of fuzzy connectedness (FC) algorithms, to achieve an interactive speed for segmenting large medical image data sets. Methods: The most common FC segmentations, optimizing an Script-Small-L {sub {infinity}}-based energy, are known as relative fuzzymore » connectedness (RFC) and iterative relative fuzzy connectedness (IRFC). Both RFC and IRFC objects (of which IRFC contains RFC) can be found via linear time algorithms, linear with respect to the image size. The new algorithm, P-ORFC (for parallel optimal RFC), which is implemented by using NVIDIA's Compute Unified Device Architecture (CUDA) platform, considerably improves the computational speed of the above mentioned CPU based IRFC algorithm. Results: Experiments based on four data sets of small, medium, large, and super data size, achieved speedup factors of 32.8 Multiplication-Sign , 22.9 Multiplication-Sign , 20.9 Multiplication-Sign , and 17.5 Multiplication-Sign , correspondingly, on the NVIDIA Tesla C1060 platform. Although the output of P-ORFC need not precisely match that of IRFC output, it is very close to it and, as the authors prove, always lies between the RFC and IRFC objects. Conclusions: A parallel version of a top-of-the-line algorithm in the family of FC has been developed on the NVIDIA GPUs. An interactive speed of segmentation has been achieved, even for the largest medical image data set. Such GPU implementations may play a crucial role in automatic anatomy recognition in clinical radiology.« less

Automatic brain tumor segmentation with a fast Mumford-Shah algorithm

NASA Astrophysics Data System (ADS)

Müller, Sabine; Weickert, Joachim; Graf, Norbert

2016-03-01

We propose a fully-automatic method for brain tumor segmentation that does not require any training phase. Our approach is based on a sequence of segmentations using the Mumford-Shah cartoon model with varying parameters. In order to come up with a very fast implementation, we extend the recent primal-dual algorithm of Strekalovskiy et al. (2014) from the 2D to the medically relevant 3D setting. Moreover, we suggest a new confidence refinement and show that it can increase the precision of our segmentations substantially. Our method is evaluated on 188 data sets with high-grade gliomas and 25 with low-grade gliomas from the BraTS14 database. Within a computation time of only three minutes, we achieve Dice scores that are comparable to state-of-the-art methods.

Knee cartilage segmentation using active shape models and local binary patterns

NASA Astrophysics Data System (ADS)

González, Germán.; Escalante-Ramírez, Boris

2014-05-01

Segmentation of knee cartilage has been useful for opportune diagnosis and treatment of osteoarthritis (OA). This paper presents a semiautomatic segmentation technique based on Active Shape Models (ASM) combined with Local Binary Patterns (LBP) and its approaches to describe the surrounding texture of femoral cartilage. The proposed technique is tested on a 16-image database of different patients and it is validated through Leave- One-Out method. We compare different segmentation techniques: ASM-LBP, ASM-medianLBP, and ASM proposed by Cootes. The ASM-LBP approaches are tested with different ratios to decide which of them describes the cartilage texture better. The results show that ASM-medianLBP has better performance than ASM-LBP and ASM. Furthermore, we add a routine which improves the robustness versus two principal problems: oversegmentation and initialization.

A digital version of the 1970 U.S. Geological Survey topographic map of the San Francisco Bay region, three sheets, 1:125,000

USGS Publications Warehouse

Aitken, Douglas S.

1997-01-01

This Open-File report is a digital topographic map database. It contains a digital version of the 1970 U.S. Geological Survey topographic map of the San Francisco Bay Region (3 sheets), at a scale of 1:125,000. These ARC/INFO coverages are in vector format. The vectorization process has distorted characters representing letters and numbers, as well as some road and other symbols, making them difficult to read in some instances. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. The content and character of the database and methods of obtaining it are described herein.

Map showing geologic terranes of the Hailey 1 degree x 2 degrees quadrangle and the western part of the Idaho Falls 1 degree x 2 degrees quadrangle, south-central Idaho

USGS Publications Warehouse

Worl, R.G.; Johnson, K.M.

1995-01-01

The paper version of Map Showing Geologic Terranes of the Hailey 1x2 Quadrangle and the western part of the Idaho Falls 1x2 Quadrangle, south-central Idaho was compiled by Ron Worl and Kate Johnson in 1995. The plate was compiled on a 1:250,000 scale topographic base map. TechniGraphic System, Inc. of Fort Collins Colorado digitized this map under contract for N.Shock. G.Green edited and prepared the digital version for publication as a geographic information system database. The digital geologic map database can be queried in many ways to produce a variety of geologic maps.

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed Central

Nadkarni, P. M.; Miller, P. L.

1991-01-01

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations. PMID:1807632

Curvature and the visual perception of shape: theory on information along object boundaries and the minima rule revisited.

PubMed

Lim, Ik Soo; Leek, E Charles

2012-07-01

Previous empirical studies have shown that information along visual contours is known to be concentrated in regions of high magnitude of curvature, and, for closed contours, segments of negative curvature (i.e., concave segments) carry greater perceptual relevance than corresponding regions of positive curvature (i.e., convex segments). Lately, Feldman and Singh (2005, Psychological Review, 112, 243-252) proposed a mathematical derivation to yield information content as a function of curvature along a contour. Here, we highlight several fundamental errors in their derivation and in its associated implementation, which are problematic in both mathematical and psychological senses. Instead, we propose an alternative mathematical formulation for information measure of contour curvature that addresses these issues. Additionally, unlike in previous work, we extend this approach to 3-dimensional (3D) shape by providing a formal measure of information content for surface curvature and outline a modified version of the minima rule relating to part segmentation using curvature in 3D shape. Copyright 2012 APA, all rights reserved.

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

Not Available

The model is designed to enable decision makers to compare the economics of geothermal projects with the economics of alternative energy systems at an early stage in the decision process. The geothermal engineering and economic feasibility computer model (GEEF) is written in FORTRAN IV language and can be run on a mainframe or a mini-computer system. An abbreviated version of the model is being developed for usage in conjunction with a programmable desk calculator. The GEEF model has two main segments, namely (i) the engineering design/cost segment and (ii) the economic analysis segment. In the engineering segment, the model determinesmore » the numbers of production and injection wells, heat exchanger design, operating parameters for the system, requirement of supplementary system (to augment the working fluid temperature if the resource temperature is not sufficiently high), and the fluid flow rates. The model can handle single stage systems as well as two stage cascaded systems in which the second stage may involve a space heating application after a process heat application in the first stage.« less

Entergy - Monroe Electric Generating Plant Decision

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

North Shore Apartments Petition

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Exxon - Baton Rouge Polyolefins Plant Decision

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

International Soil Carbon Network (ISCN) Database v3-1

DOE Data Explorer

Nave, Luke [University of Michigan] (ORCID:0000000182588335); Johnson, Kris [USDA-Forest Service; van Ingen, Catharine [Microsoft Research; Agarwal, Deborah [Lawrence Berkeley National Laboratory] (ORCID:0000000150452396); Humphrey, Marty [University of Virginia; Beekwilder, Norman [University of Virginia

2016-01-01

The ISCN is an international scientific community devoted to the advancement of soil carbon research. The ISCN manages an open-access, community-driven soil carbon database. This is version 3-1 of the ISCN Database, released in December 2015. It gathers 38 separate dataset contributions, totalling 67,112 sites with data from 71,198 soil profiles and 431,324 soil layers. For more information about the ISCN, its scientific community and resources, data policies and partner networks visit: http://iscn.fluxdata.org/.

Roosevelt Regional Landfill Decision

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Shintech Decision

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Database Management System

NASA Technical Reports Server (NTRS)

1990-01-01

In 1981 Wayne Erickson founded Microrim, Inc, a company originally focused on marketing a microcomputer version of RIM (Relational Information Manager). Dennis Comfort joined the firm and is now vice president, development. The team developed an advanced spinoff from the NASA system they had originally created, a microcomputer database management system known as R:BASE 4000. Microrim added many enhancements and developed a series of R:BASE products for various environments. R:BASE is now the second largest selling line of microcomputer database management software in the world.

Radioactivity and Environmental Security in the Oceans: New Research and Policy Priorities in the Arctic and North Atlantic

DTIC Science & Technology

1993-06-09

within the framework of an update for the computer database "DiaNIK" which has been developed at the Vernadsky Institute of Geochemistry and Analytical...chemical thermodynamic data for minerals and mineral-forming substances. The structure of thermodynamic database "DiaNIK" is based on the principles...in the database . A substantial portion of the thermodynamic values recommended by "DiaNIK" experts for the substances in User Version 3.1 resulted from

Chaffee Landfill... G. Abraham Petition Response

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Chaffee Landfill... NYPIRG Petition Response

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

CyanoBase: the cyanobacteria genome database update 2010

PubMed Central

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly. PMID:19880388

December 19, 2003 Dismissal of Unions Petitions

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Pacificorp's Bridger and Naughton Decision

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

The androgen receptor gene mutations database.

PubMed

Patterson, M N; Hughes, I A; Gottlieb, B; Pinsky, L

1994-09-01

The androgen receptor gene mutations database is a comprehensive listing of mutations published in journals and meetings proceedings. The majority of mutations are point mutations identified in patients with androgen insensitivity syndrome. Information is included regarding the phenotype, the nature and location of the mutations, as well as the effects of the mutations on the androgen binding activity of the receptor. The current version of the database contains 149 entries, of which 114 are unique mutations. The database is available from EMBL (NetServ@EMBL-Heidelberg.DE) or as a Macintosh Filemaker file (mc33001@musica.mcgill.ca).

Insertion algorithms for network model database management systems

NASA Astrophysics Data System (ADS)

Mamadolimov, Abdurashid; Khikmat, Saburov

2017-12-01

The network model is a database model conceived as a flexible way of representing objects and their relationships. Its distinguishing feature is that the schema, viewed as a graph in which object types are nodes and relationship types are arcs, forms partial order. When a database is large and a query comparison is expensive then the efficiency requirement of managing algorithms is minimizing the number of query comparisons. We consider updating operation for network model database management systems. We develop a new sequantial algorithm for updating operation. Also we suggest a distributed version of the algorithm.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

Effects of Iranian Economic Reforms on Equity in Social and Healthcare Financing: A Segmented Regression Analysis.

PubMed

Zandian, Hamed; Takian, Amirhossein; Rashidian, Arash; Bayati, Mohsen; Zahirian Moghadam, Telma; Rezaei, Satar; Olyaeemanesh, Alireza

2018-03-01

One of the main objectives of the Targeted Subsidies Law (TSL) in Iran was to improve equity in healthcare financing. This study aimed at measuring the effects of the TSL, which was implemented in Iran in 2010, on equity in healthcare financing. Segmented regression analysis was applied to assess the effects of TSL implementation on the Gini and Kakwani indices of outcome variables in Iranian households. Data for the years 1977-2014 were retrieved from formal databases. Changes in the levels and trends of the outcome variables before and after TSL implementation were assessed using Stata version 13. In the 33 years before the implementation of the TSL, the Gini index decreased from 0.401 to 0.381. The Gini index and its intercept significantly decreased to 0.362 (p<0.001) 5 years after the implementation of the TSL. There was no statistically significant change in the gross domestic product or inflation rate after TSL implementation. The Kakwani index significantly increased from -0.020 to 0.007 (p<0.001) before the implementation of the TSL, while we observed no statistically significant change (p=0.81) in the Kakwani index after TSL implementation. The TSL reform, which was introduced as part of an economic development plan in Iran in 2010, led to a significant reduction in households' income inequality. However, the TSL did not significantly affect equity in healthcare financing. Hence, while measuring the long-term impact of TSL is paramount, healthcare decision-makers need to consider the efficacy of the TSL in order to develop plans for achieving the desired equity in healthcare financing.

Effects of Iranian Economic Reforms on Equity in Social and Healthcare Financing: A Segmented Regression Analysis

PubMed Central

Bayati, Mohsen

2018-01-01

Objectives One of the main objectives of the Targeted Subsidies Law (TSL) in Iran was to improve equity in healthcare financing. This study aimed at measuring the effects of the TSL, which was implemented in Iran in 2010, on equity in healthcare financing. Methods Segmented regression analysis was applied to assess the effects of TSL implementation on the Gini and Kakwani indices of outcome variables in Iranian households. Data for the years 1977-2014 were retrieved from formal databases. Changes in the levels and trends of the outcome variables before and after TSL implementation were assessed using Stata version 13. Results In the 33 years before the implementation of the TSL, the Gini index decreased from 0.401 to 0.381. The Gini index and its intercept significantly decreased to 0.362 (p<0.001) 5 years after the implementation of the TSL. There was no statistically significant change in the gross domestic product or inflation rate after TSL implementation. The Kakwani index significantly increased from -0.020 to 0.007 (p<0.001) before the implementation of the TSL, while we observed no statistically significant change (p=0.81) in the Kakwani index after TSL implementation. Conclusions The TSL reform, which was introduced as part of an economic development plan in Iran in 2010, led to a significant reduction in households’ income inequality. However, the TSL did not significantly affect equity in healthcare financing. Hence, while measuring the long-term impact of TSL is paramount, healthcare decision-makers need to consider the efficacy of the TSL in order to develop plans for achieving the desired equity in healthcare financing. PMID:29631352

Multi-atlas based segmentation using probabilistic label fusion with adaptive weighting of image similarity measures.

PubMed

Sjöberg, C; Ahnesjö, A

2013-06-01

Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning phase and used to derive fusion weights that are proportional to the probability for each atlas to improve the segmentation result. The method was tested using a leave-one-out strategy on a database of 21 pre-segmented prostate patients for different image registrations combined with different image similarity scorings. The probabilistic weighting yields results that are equal or better compared to both fusion with equal weights and results using the STAPLE algorithm. Results from the experiments demonstrate that label fusion by weighted distance maps is feasible, and that probabilistic weighted fusion improves segmentation quality more the stronger the individual atlas segmentation quality depends on the corresponding registered image similarity. The regions used for evaluation of the image similarity measures were found to be more important than the choice of similarity measure. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A scale self-adapting segmentation approach and knowledge transfer for automatically updating land use/cover change databases using high spatial resolution images

NASA Astrophysics Data System (ADS)

Wang, Zhihua; Yang, Xiaomei; Lu, Chen; Yang, Fengshuo

2018-07-01

Automatic updating of land use/cover change (LUCC) databases using high spatial resolution images (HSRI) is important for environmental monitoring and policy making, especially for coastal areas that connect the land and coast and that tend to change frequently. Many object-based change detection methods are proposed, especially those combining historical LUCC with HSRI. However, the scale parameter(s) segmenting the serial temporal images, which directly determines the average object size, is hard to choose without experts' intervention. And the samples transferred from historical LUCC also need experts' intervention to avoid insufficient or wrong samples. With respect to the scale parameter(s) choosing, a Scale Self-Adapting Segmentation (SSAS) approach based on the exponential sampling of a scale parameter and location of the local maximum of a weighted local variance was proposed to determine the scale selection problem when segmenting images constrained by LUCC for detecting changes. With respect to the samples transferring, Knowledge Transfer (KT), a classifier trained on historical images with LUCC and applied in the classification of updated images, was also proposed. Comparison experiments were conducted in a coastal area of Zhujiang, China, using SPOT 5 images acquired in 2005 and 2010. The results reveal that (1) SSAS can segment images more effectively without intervention of experts. (2) KT can also reach the maximum accuracy of samples transfer without experts' intervention. Strategy SSAS + KT would be a good choice if the temporal historical image and LUCC match, and the historical image and updated image are obtained from the same resource.

Soft computing approach to 3D lung nodule segmentation in CT.

PubMed

Badura, P; Pietka, E

2014-10-01

This paper presents a novel, multilevel approach to the segmentation of various types of pulmonary nodules in computed tomography studies. It is based on two branches of computational intelligence: the fuzzy connectedness (FC) and the evolutionary computation. First, the image and auxiliary data are prepared for the 3D FC analysis during the first stage of an algorithm - the masks generation. Its main goal is to process some specific types of nodules connected to the pleura or vessels. It consists of some basic image processing operations as well as dedicated routines for the specific cases of nodules. The evolutionary computation is performed on the image and seed points in order to shorten the FC analysis and improve its accuracy. After the FC application, the remaining vessels are removed during the postprocessing stage. The method has been validated using the first dataset of studies acquired and described by the Lung Image Database Consortium (LIDC) and by its latest release - the LIDC-IDRI (Image Database Resource Initiative) database. Copyright © 2014 Elsevier Ltd. All rights reserved.

Red Lesion Detection Using Dynamic Shape Features for Diabetic Retinopathy Screening.

PubMed

Seoud, Lama; Hurtut, Thomas; Chelbi, Jihed; Cheriet, Farida; Langlois, J M Pierre

2016-04-01

The development of an automatic telemedicine system for computer-aided screening and grading of diabetic retinopathy depends on reliable detection of retinal lesions in fundus images. In this paper, a novel method for automatic detection of both microaneurysms and hemorrhages in color fundus images is described and validated. The main contribution is a new set of shape features, called Dynamic Shape Features, that do not require precise segmentation of the regions to be classified. These features represent the evolution of the shape during image flooding and allow to discriminate between lesions and vessel segments. The method is validated per-lesion and per-image using six databases, four of which are publicly available. It proves to be robust with respect to variability in image resolution, quality and acquisition system. On the Retinopathy Online Challenge's database, the method achieves a FROC score of 0.420 which ranks it fourth. On the Messidor database, when detecting images with diabetic retinopathy, the proposed method achieves an area under the ROC curve of 0.899, comparable to the score of human experts, and it outperforms state-of-the-art approaches.

K-SPAN: A lexical database of Korean surface phonetic forms and phonological neighborhood density statistics.

PubMed

Holliday, Jeffrey J; Turnbull, Rory; Eychenne, Julien

2017-10-01

This article presents K-SPAN (Korean Surface Phonetics and Neighborhoods), a database of surface phonetic forms and several measures of phonological neighborhood density for 63,836 Korean words. Currently publicly available Korean corpora are limited by the fact that they only provide orthographic representations in Hangeul, which is problematic since phonetic forms in Korean cannot be reliably predicted from orthographic forms. We describe the method used to derive the surface phonetic forms from a publicly available orthographic corpus of Korean, and report on several statistics calculated using this database; namely, segment unigram frequencies, which are compared to previously reported results, along with segment-based and syllable-based neighborhood density statistics for three types of representation: an "orthographic" form, which is a quasi-phonological representation, a "conservative" form, which maintains all known contrasts, and a "modern" form, which represents the pronunciation of contemporary Seoul Korean. These representations are rendered in an ASCII-encoded scheme, which allows users to query the corpus without having to read Korean orthography, and permits the calculation of a wide range of phonological measures.

Event segmentation improves event memory up to one month later.

PubMed

Flores, Shaney; Bailey, Heather R; Eisenberg, Michelle L; Zacks, Jeffrey M

2017-08-01

When people observe everyday activity, they spontaneously parse it into discrete meaningful events. Individuals who segment activity in a more normative fashion show better subsequent memory for the events. If segmenting events effectively leads to better memory, does asking people to attend to segmentation improve subsequent memory? To answer this question, participants viewed movies of naturalistic activity with instructions to remember the activity for a later test, and in some conditions additionally pressed a button to segment the movies into meaningful events or performed a control condition that required button-pressing but not attending to segmentation. In 5 experiments, memory for the movies was assessed at intervals ranging from immediately following viewing to 1 month later. Performing the event segmentation task led to superior memory at delays ranging from 10 min to 1 month. Further, individual differences in segmentation ability predicted individual differences in memory performance for up to a month following encoding. This study provides the first evidence that manipulating event segmentation affects memory over long delays and that individual differences in event segmentation are related to differences in memory over long delays. These effects suggest that attending to how an activity breaks down into meaningful events contributes to memory formation. Instructing people to more effectively segment events may serve as a potential intervention to alleviate everyday memory complaints in aging and clinical populations. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

PubMed Central

Calduch-Giner, Josep A.; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

2016-01-01

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts. PMID:27610085

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax).

PubMed

Calduch-Giner, Josep A; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

2016-01-01

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.

The androgen receptor gene mutations database.

PubMed

Gottlieb, B; Trifiro, M; Lumbroso, R; Pinsky, L

1997-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 212 to 272. We have expanded the database: (i) by adding a large amount of new data on somatic mutations in prostatic cancer tissue; (ii) by defining a new constitutional phenotype, mild androgen insensitivity (MAI); (iii) by placing additional relevant information on an internet site (http://www.mcgill.ca/androgendb/ ). The database has allowed us to examine the contribution of CpG sites to the multiplicity of reports of the same mutation in different families. The database is also available from EMBL (ftp.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker Pro or Word file (MC33@musica,mcgill.ca)

The androgen receptor gene mutations database.

PubMed Central

Gottlieb, B; Trifiro, M; Lumbroso, R; Pinsky, L

1997-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 212 to 272. We have expanded the database: (i) by adding a large amount of new data on somatic mutations in prostatic cancer tissue; (ii) by defining a new constitutional phenotype, mild androgen insensitivity (MAI); (iii) by placing additional relevant information on an internet site (http://www.mcgill.ca/androgendb/ ). The database has allowed us to examine the contribution of CpG sites to the multiplicity of reports of the same mutation in different families. The database is also available from EMBL (ftp.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker Pro or Word file (MC33@musica,mcgill.ca) PMID:9016528

Databases for multilevel biophysiology research available at Physiome.jp.

PubMed

Asai, Yoshiyuki; Abe, Takeshi; Li, Li; Oka, Hideki; Nomura, Taishin; Kitano, Hiroaki

2015-01-01

Physiome.jp (http://physiome.jp) is a portal site inaugurated in 2007 to support model-based research in physiome and systems biology. At Physiome.jp, several tools and databases are available to support construction of physiological, multi-hierarchical, large-scale models. There are three databases in Physiome.jp, housing mathematical models, morphological data, and time-series data. In late 2013, the site was fully renovated, and in May 2015, new functions were implemented to provide information infrastructure to support collaborative activities for developing models and performing simulations within the database framework. This article describes updates to the databases implemented since 2013, including cooperation among the three databases, interactive model browsing, user management, version management of models, management of parameter sets, and interoperability with applications.

Flight Deck Interval Management Display. [Elements, Information and Annunciations Database User Guide

NASA Technical Reports Server (NTRS)

Lancaster, Jeff; Dillard, Michael; Alves, Erin; Olofinboba, Olu

2014-01-01

The User Guide details the Access Database provided with the Flight Deck Interval Management (FIM) Display Elements, Information, & Annunciations program. The goal of this User Guide is to support ease of use and the ability to quickly retrieve and select items of interest from the Database. The Database includes FIM Concepts identified in a literature review preceding the publication of this document. Only items that are directly related to FIM (e.g., spacing indicators), which change or enable FIM (e.g., menu with control buttons), or which are affected by FIM (e.g., altitude reading) are included in the database. The guide has been expanded from previous versions to cover database structure, content, and search features with voiced explanations.

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

PubMed

Ikeda, Shun; Abe, Takashi; Nakamura, Yukiko; Kibinge, Nelson; Hirai Morita, Aki; Nakatani, Atsushi; Ono, Naoaki; Ikemura, Toshimichi; Nakamura, Kensuke; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

2013-05-01

Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.

Dynamics of uniaxially oriented elastomers using dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Hyungki; Fragiadakis, Daniel; Martin, Darren; Runt, James

2009-03-01

We summarize our initial dielectric spectroscopy investigation of the dynamics of oriented segmented polyurethanes and crosslinked polyisoprene elastomers. A specially designed uniaxial stretching rig is used to control the draw ratio, and the electric field is applied normal to the draw direction. For the segmented PUs, we observe a dramatic reduction in relaxation strength of the soft phase segmental process with increasing extension ratio, accompanied by a modest decrease in relaxation frequency. Crosslinking of the polyisoprene was accomplished with dicumyl peroxide and the dynamics of uncrosslinked and crosslinked versions are investigated in the undrawn state and at different extension ratios. Complimentary analysis of the crosslinked PI is conducted with wide angle X- ray diffraction to examine possible strain-induced crystallization, DSC, and swelling experiments. Quantitative analysis of relaxation strengths and shapes as a function of draw ratio will be discussed.

Software Classifications: Trends in Literacy Software Publication and Marketing.

ERIC Educational Resources Information Center

Balajthy, Ernest

First in a continuing series of reports on trends in marketing and publication of software for literacy education, a study explored the development of a database to track the trends and reported on trends seen in 1995. The final version of the 1995 database consisted of 1011 software titles, 165 of which had been published in 1995 and 846…

TEDS-M 2008 User Guide for the International Database. Supplement 2: National Adaptations of the TEDS-M Questionnaires

ERIC Educational Resources Information Center

Brese, Falk, Ed.

2012-01-01

This supplement contains all adaptations made by countries to the international version of the TEDS-M questionnaires under careful supervision of and approval by the TEDS-M International Study Center at Michigan State University. This information provides users of the TEDS-M International Database with a guide to evaluate the availability of…

NCI at Frederick Scientific Library Reintroduces Scientific Publications Database | Poster

Cancer.gov

A 20-year-old database of scientific publications by NCI at Frederick, FNLCR, and affiliated employees has gotten a significant facelift. Maintained by the Scientific Library, the redesigned database—which is linked from each of the Scientific Library’s web pages—offers features that were not available in previous versions, such as additional search limits and non-traditional

Managing hydrological measurements for small and intermediate projects: RObsDat

NASA Astrophysics Data System (ADS)

Reusser, Dominik E.

2014-05-01

Hydrological measurements need good management for the data not to be lost. Multiple, often overlapping files from various loggers with heterogeneous formats need to be merged. Data needs to be validated and cleaned and subsequently converted to the format for the hydrological target application. Preferably, all these steps should be easily tracable. RObsDat is an R package designed to support such data management. It comes with a command line user interface to support hydrologists to enter and adjust their data in a database following the Observations Data Model (ODM) standard by QUASHI. RObsDat helps in the setup of the database within one of the free database engines MySQL, PostgreSQL or SQLite. It imports the controlled water vocabulary from the QUASHI web service and provides a smart interface between the hydrologist and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designes to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. A new development is the use of spacetime objects for subsequent processing.

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

Reconceptualizing Social Work Behaviors from a Human Rights Perspective

ERIC Educational Resources Information Center

Steen, Julie A.

2018-01-01

Although the human rights philosophy has relevance for many segments of the social work curriculum, the latest version of accreditation standards only includes a few behaviors specific to human rights. This deficit can be remedied by incorporating innovations found in the social work literature, which provides a wealth of material for…

MILE Curriculum [and Nine CD-ROM Lessons].

ERIC Educational Resources Information Center

Reiman, John

This curriculum on money management skills for deaf adolescent and young adult students is presented on nine video CD-ROMs as well as in a print version. The curriculum was developed following a survey of the needs of school and rehabilitation programs. It was also piloted and subsequently revised. Each teaching segment is presented in sign…

A Multi-Objective Decision Making Approach for Solving the Image Segmentation Fusion Problem.

PubMed

Khelifi, Lazhar; Mignotte, Max

2017-08-01

Image segmentation fusion is defined as the set of methods which aim at merging several image segmentations, in a manner that takes full advantage of the complementarity of each one. Previous relevant researches in this field have been impeded by the difficulty in identifying an appropriate single segmentation fusion criterion, providing the best possible, i.e., the more informative, result of fusion. In this paper, we propose a new model of image segmentation fusion based on multi-objective optimization which can mitigate this problem, to obtain a final improved result of segmentation. Our fusion framework incorporates the dominance concept in order to efficiently combine and optimize two complementary segmentation criteria, namely, the global consistency error and the F-measure (precision-recall) criterion. To this end, we present a hierarchical and efficient way to optimize the multi-objective consensus energy function related to this fusion model, which exploits a simple and deterministic iterative relaxation strategy combining the different image segments. This step is followed by a decision making task based on the so-called "technique for order performance by similarity to ideal solution". Results obtained on two publicly available databases with manual ground truth segmentations clearly show that our multi-objective energy-based model gives better results than the classical mono-objective one.

Risk Assessment Update: Russian Segment

NASA Technical Reports Server (NTRS)

Christiansen, Eric; Lear, Dana; Hyde, James; Bjorkman, Michael; Hoffman, Kevin

2012-01-01

BUMPER-II version 1.95j source code was provided to RSC-E- and Khrunichev at January 2012 MMOD TIM in Moscow. MEMCxP and ORDEM 3.0 environments implemented as external data files. NASA provided a sample ORDEM 3.0 g."key" & "daf" environment file set for demonstration and benchmarking BUMPER -II v1.95j installation at the Jan-12 TIM. ORDEM 3.0 has been completed and is currently in beta testing. NASA will provide a preliminary set of ORDEM 3.0 ".key" & ".daf" environment files for the years 2012 through 2028. Bumper output files produced using the new ORDEM 3.0 data files are intended for internal use only, not for requirements verification. Output files will contain these words ORDEM FILE DESCRIPTION = PRELIMINARY VERSION: not for production. The projectile density term in many BUMPER-II ballistic limit equations will need to be updated. Cube demo scripts and output files delivered at the Jan-12 TIM have been updated for the new ORDEM 3.0 data files. Risk assessment results based on ORDEM 3.0 and MEM will be presented for the Russian Segment (RS) of ISS.

Food Choice Questionnaire (FCQ) revisited. Suggestions for the development of an enhanced general food motivation model.

PubMed

Fotopoulos, Christos; Krystallis, Athanasios; Vassallo, Marco; Pagiaslis, Anastasios

2009-02-01

Recognising the need for a more statistically robust instrument to investigate general food selection determinants, the research validates and confirms Food Choice Questionnaire (FCQ's) factorial design, develops ad hoc a more robust FCQ version and tests its ability to discriminate between consumer segments in terms of the importance they assign to the FCQ motivational factors. The original FCQ appears to represent a comprehensive and reliable research instrument. However, the empirical data do not support the robustness of its 9-factorial design. On the other hand, segmentation results at the subpopulation level based on the enhanced FCQ version bring about an optimistic message for the FCQ's ability to predict food selection behaviour. The paper concludes that some of the basic components of the original FCQ can be used as a basis for a new general food motivation typology. The development of such a new instrument, with fewer, of higher abstraction FCQ-based dimensions and fewer items per dimension, is a right step forward; yet such a step should be theory-driven, while a rigorous statistical testing across and within population would be necessary.

MedlinePlus FAQ: How Often MedlinePlus is Updated

MedlinePlus

... System Pharmacists is updated monthly. Natural Medicines Comprehensive Database Consumer Version is updated quarterly. Medical Encyclopedia: Updated monthly. ... Guidelines Viewers & Players MedlinePlus Connect for ...

Diet History Questionnaire: Suggested Citations

Cancer.gov

Use of the Diet History Questionnaire and Diet*Calc Analysis Software for publication purposes should contain a citation which includes version information for the software, questionnaire, and nutrient database.

Mortality from idiopathic pulmonary fibrosis: a temporal trend analysis in Brazil, 1979-2014

PubMed Central

Algranti, Eduardo; Saito, Cézar Akiyoshi; Silva, Diego Rodrigues Mendonça e; Carneiro, Ana Paula Scalia; Bussacos, Marco Antonio

2017-01-01

ABSTRACT Objective: To analyze mortality from idiopathic pulmonary fibrosis (IPF) in Brazil over the period 1979-2014. Methods: Microdata were extracted from the Brazilian National Ministry of Health Mortality Database. Only deaths for which the underlying cause was coded as International Classification of Diseases version 9 (ICD-9) 515 or 516.3 (until 1995) or as ICD version 10 (ICD-10) J84.1 (from 1996 onward) were included in our analysis. Standardized mortality rates were calculated for the 2010 Brazilian population. The annual trend in mortality rates was analyzed by joinpoint regression. We calculated risk ratios (RRs) by age group, time period of death, and gender, using a person-years denominator. Results: A total of 32,092 deaths were recorded in the study period. Standardized mortality rates trended upward, rising from 0.24/100,000 population in 1979 to 1.10/100,000 population in 2014. The annual upward trend in mortality rates had two inflection points, in 1992 and 2008, separating three distinct time segments with an annual growth of 2.2%, 6.8%, and 2.4%, respectively. The comparison of RRs for the age groups, using the 50- to 54-year age group as a reference, and for the study period, using 1979-1984 as a reference, were 16.14 (14.44-16.36) and 6.71 (6.34-7.12), respectively. Men compared with women had higher standardized mortality rates (per 100,000 person-years) in all age groups. Conclusion: Brazilian IPF mortality rates are lower than those of other countries, suggesting underdiagnosis or underreporting. The temporal trend is similar to those reported in the literature and is not explained solely by population aging. PMID:29340493

YMDB 2.0: a significantly expanded version of the yeast metabolome database.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Guo, An Chi; Sajed, Tanvir; Wishart, Noah A; Karu, Naama; Djoumbou Feunang, Yannick; Arndt, David; Wishart, David S

2017-01-04

YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDB's web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

sRNAdb: A small non-coding RNA database for gram-positive bacteria

PubMed Central

2012-01-01

Background The class of small non-coding RNA molecules (sRNA) regulates gene expression by different mechanisms and enables bacteria to mount a physiological response due to adaptation to the environment or infection. Over the last decades the number of sRNAs has been increasing rapidly. Several databases like Rfam or fRNAdb were extended to include sRNAs as a class of its own. Furthermore new specialized databases like sRNAMap (gram-negative bacteria only) and sRNATarBase (target prediction) were established. To the best of the authors’ knowledge no database focusing on sRNAs from gram-positive bacteria is publicly available so far. Description In order to understand sRNA’s functional and phylogenetic relationships we have developed sRNAdb and provide tools for data analysis and visualization. The data compiled in our database is assembled from experiments as well as from bioinformatics analyses. The software enables comparison and visualization of gene loci surrounding the sRNAs of interest. To accomplish this, we use a client–server based approach. Offline versions of the database including analyses and visualization tools can easily be installed locally on the user’s computer. This feature facilitates customized local addition of unpublished sRNA candidates and related information such as promoters or terminators using tab-delimited files. Conclusion sRNAdb allows a user-friendly and comprehensive comparative analysis of sRNAs from available sequenced gram-positive prokaryotic replicons. Offline versions including analysis and visualization tools facilitate complex user specific bioinformatics analyses. PMID:22883983

Version 2 of the Protuberance Correlations for the Shuttle-Orbiter Boundary Layer Transition Tool

NASA Technical Reports Server (NTRS)

King, Rudolph A.; Kegerise, Michael A.; Berry, Scott A.

2009-01-01

Orbiter-specific transition data, acquired in four ground-based facilities (LaRC 20-Inch Mach 6 Air Tunnel, LaRC 31-Inch Mach 10 Air Tunnel, LaRC 20-Inch Mach 6 CF4 Tunnel, and CUBRC LENS-I Shock Tunnel) with three wind tunnel model scales (0.75, 0.90, and 1.8%) and from Orbiter historical flight data, have been analyzed to improve a pre-existing engineering tool for reentry transition prediction on the windward side of the Orbiter. Boundary layer transition (BLT) engineering correlations for transition induced by isolated protuberances are presented using a laminar Navier-Stokes (N-S) database to provide the relevant boundary-layer properties. It is demonstrated that the earlier version of the BLT correlation that had been developed using parameters derived from an engineering boundary-layer code has improved data collapse when developed with the N-S database. Of the new correlations examined, the proposed correlation 5, based on boundary-layer edge and wall properties, was found to provide the best overall correlation metrics when the entire database is employed. The second independent correlation (proposed correlation 7) selected is based on properties within the boundary layer at the protuberance height. The Aeroheating Panel selected a process to derive the recommended coefficients for Version 2 of the BLT Tool. The assumptions and limitations of the recommended protuberance BLT Tool V.2 are presented.

Ensemble Semi-supervised Frame-work for Brain Magnetic Resonance Imaging Tissue Segmentation

PubMed Central

Azmi, Reza; Pishgoo, Boshra; Norozi, Narges; Yeganeh, Samira

2013-01-01

Brain magnetic resonance images (MRIs) tissue segmentation is one of the most important parts of the clinical diagnostic tools. Pixel classification methods have been frequently used in the image segmentation with two supervised and unsupervised approaches up to now. Supervised segmentation methods lead to high accuracy, but they need a large amount of labeled data, which is hard, expensive, and slow to obtain. Moreover, they cannot use unlabeled data to train classifiers. On the other hand, unsupervised segmentation methods have no prior knowledge and lead to low level of performance. However, semi-supervised learning which uses a few labeled data together with a large amount of unlabeled data causes higher accuracy with less trouble. In this paper, we propose an ensemble semi-supervised frame-work for segmenting of brain magnetic resonance imaging (MRI) tissues that it has been used results of several semi-supervised classifiers simultaneously. Selecting appropriate classifiers has a significant role in the performance of this frame-work. Hence, in this paper, we present two semi-supervised algorithms expectation filtering maximization and MCo_Training that are improved versions of semi-supervised methods expectation maximization and Co_Training and increase segmentation accuracy. Afterward, we use these improved classifiers together with graph-based semi-supervised classifier as components of the ensemble frame-work. Experimental results show that performance of segmentation in this approach is higher than both supervised methods and the individual semi-supervised classifiers. PMID:24098863

Bayesian inference of stress release models applied to some Italian seismogenic zones

NASA Astrophysics Data System (ADS)

Rotondi, R.; Varini, E.

2007-04-01

In this paper, we evaluate the seismic hazard of a region in southern Italy by analysing stress release models from the Bayesian viewpoint; the data are drawn from the most recent version of the parametric catalogue of Italian earthquakes. For estimation we just use the events up to 1992, then we forecast the date of the next event through a stochastic simulation method and we compare the result with the really occurred shocks in the span 1993-2002. The original version of the stress release model, proposed by Vere-Jones in 1978, transposes Reid's elastic rebound theory in the framework of stochastic point processes. Since the nineties enriched versions of this model have appeared in the literature, applied to historical catalogues from China, Iran, Japan; they envisage the identification of independent or interacting tectonic subunits constituting the region under exam. It follows that the stress release models, designed for regional analyses, are evolving towards studies on fault segments, realizing some degree of convergence to those models that start from an individual fault and, considering the interactions with nearby segments, are driven to studies on regional scale. The optimal performance of the models we consider depends on a set of choices among which: the seismogenic region and possible subzones, the threshold magnitude, the length of the time period. In this paper, we focus our attention on the influence of the subdivision of the region under exam into tectonic units; in the light of the recent studies on the fault segmentation model of Italy we propose a partition of Sannio-Matese-Ofanto-Irpinia, one of the most seismically active region in southern Italy. The results show that the performance of the stress release models improves in terms of both fitting and forecasting when the region is split up into parts including new information about potential seismogenic sources.

Algorithm to calculate proportional area transformation factors for digital geographic databases

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

Edwards, R.

1983-01-01

A computer technique is described for determining proportionate-area factors used to transform thematic data between large geographic areal databases. The number of calculations in the algorithm increases linearly with the number of segments in the polygonal definitions of the databases, and increases with the square root of the total number of chains. Experience is presented in calculating transformation factors for two national databases, the USGS Water Cataloging Unit outlines and DOT county boundaries which consist of 2100 and 3100 polygons respectively. The technique facilitates using thematic data defined on various natural bases (watersheds, landcover units, etc.) in analyses involving economicmore » and other administrative bases (states, counties, etc.), and vice versa.« less

Segmentation of acute pyelonephritis area on kidney SPECT images using binary shape analysis

NASA Astrophysics Data System (ADS)

Wu, Chia-Hsiang; Sun, Yung-Nien; Chiu, Nan-Tsing

1999-05-01

Acute pyelonephritis is a serious disease in children that may result in irreversible renal scarring. The ability to localize the site of urinary tract infection and the extent of acute pyelonephritis has considerable clinical importance. In this paper, we are devoted to segment the acute pyelonephritis area from kidney SPECT images. A two-step algorithm is proposed. First, the original images are translated into binary versions by automatic thresholding. Then the acute pyelonephritis areas are located by finding convex deficiencies in the obtained binary images. This work gives important diagnosis information for physicians and improves the quality of medical care for children acute pyelonephritis disease.

SRB Processing Facilities Media Event

NASA Image and Video Library

2016-03-01

Members of the news media view the high bay inside the Rotation, Processing and Surge Facility (RPSF) at NASA’s Kennedy Space Center in Florida. Inside the RPSF, engineers and technicians with Jacobs Engineering on the Test and Operations Support Contract, explain the various test stands. In the far corner is one of two pathfinders, or test versions, of solid rocket booster segments for NASA’s Space Launch System rocket. The Ground Systems Development and Operations Program and Jacobs are preparing the booster segments, which are inert, for a series of lifts, moves and stacking operations to prepare for Exploration Mission-1, deep-space missions and the journey to Mars.

Should a colon cancer screening decision aid include the option of no testing? A comparative trial of two decision aids

PubMed Central

Griffith, Jennifer M; Fichter, Marlie; Fowler, Floyd J; Lewis, Carmen; Pignone, Michael P

2008-01-01

Background An important question in the development of decision aids about colon cancer (CRC) screening is whether to include an explicit discussion of the option of not being screened. We examined the effect of including or not including an explicit discussion of the option of deciding not to be screened in a CRC screening decision aid on subjective measures of decision aid content; interest in screening; and knowledge. Methods Adults ages 50–85 were assigned to view one of two versions of the decision aid. The two versions differed only in the inclusion of video segments of two men, one of whom decided against being screened. Participants completed questionnaires before and after viewing the decision aid to compare subjective measures of content, screening interest and intent, and knowledge between groups. Likert response categories (5-point) were used for subjective measures of content (eg. clarity, balance in favor/against screening, and overall rating), and screening interest. Knowledge was measured with a three item index and individual questions. Higher scores indicated favorable responses for subjective measures, greater interest, and better knowledge. For the subjective balance, lower numbers were associated with the impression of the decision aid favoring CRC screening. Results 57 viewed the "with" version which included the two segments and 49 viewed the "without" version. After viewing, participants found the "without" version to have better subjective clarity about benefits of screening ("with" 3.4, "without" 4.1, p < 0.01), and to have greater clarity about downsides of screening ("with" 3.2, "without" 3.6, p = 0.03). The "with" version was considered to be less strongly balanced in favor of screening. ("with" 1.8, "without" 1.6, p = 0.05); but the "without" version received a better overall rating ("with" 3.5, "without" 3.8, p = 0.03). Groups did not differ in screening interest after viewing a decision aid or knowledge. Conclusion A decision aid with the explicit discussion of the option of deciding not to be screened appears to increase the impression that the program was not as strongly in favor of screening, but decreases the impression of clarity and resulted in a lower overall rating. We did not observe clinically important or statistically significant differences in interest in screening or knowledge. PMID:18321377

The Latest Mars Climate Database (MCD v5.1)

NASA Astrophysics Data System (ADS)

Millour, Ehouarn; Forget, Francois; Spiga, Aymeric; Navarro, Thomas; Madeleine, Jean-Baptiste; Pottier, Alizée; Montabone, Luca; Kerber, Laura; Lefèvre, Franck; Montmessin, Franck; Chaufray, Jean-Yves; López-Valverde, Miguel; González-Galindo, Francisco; Lewis, Stephen; Read, Peter; Huot, Jean-Paul; Desjean, Marie-Christine; the MCD/GCM development Team

2014-05-01

For many years, several teams around the world have developed GCMs (General Circulation Model or Global Climate Model) to simulate the environment on Mars. The GCM developed at the Laboratoire de Météorologie Dynamique in collaboration with several teams in Europe (LATMOS, France, University of Oxford, The Open University, the Instituto de Astrofisica de Andalucia), and with the support of ESA and CNES is currently used for many applications. Its outputs have also regularly been compiled to build a Mars Climate Database, a freely available tool useful for the scientific and engineering communities. The Mars Climate Database (MCD) has over the years been distributed to more than 150 teams around the world. Following the recent improvements inthe GCM, a new series of reference simulations have been run and compiled into a new version (version5.1) of the Mars Climate Database, released in the first half of 2014. To summarize, MCD v5.1 provides: - Climatologies over a series of dust scenarios: standard year, cold (ie: low dust), warm (ie: dusty atmosphere) and dust storm, all topped by various cases of Extreme UV solar inputs (low, mean or maximum). These scenarios differ from those of previous versions of the MCD (version 4.x) as they have been derived from home-made, instrument-derived (TES, THEMIS, MCS, MERs), dust climatology of the last 8 Martian years. - Mean values and statistics of main meteorological variables (atmospheric temperature, density, pressure and winds), as well as surface pressure and temperature, CO2 ice cover, thermal and solar radiative fluxes, dust column opacity and mixing ratio, [H20] vapor and ice columns, concentrations of many species: [CO], [O2], [O], [N2], [H2], [O3], ... - A high resolution mode which combines high resolution (32 pixel/degree) MOLA topography records and Viking Lander 1 pressure records with raw lower resolution GCM results to yield, within the restriction of the procedure, high resolution values of atmospheric variables. - The possibility to reconstruct realistic conditions by combining the provided climatology with additional large scale and small scale perturbations schemes. At EGU, we will report on the latest improvements in the Mars Climate Database, with comparisons with available measurements from orbit (e.g.: TES, MCS) or landers (Viking, Phoenix, MSL).

High-dynamic-range imaging for cloud segmentation

NASA Astrophysics Data System (ADS)

Dev, Soumyabrata; Savoy, Florian M.; Lee, Yee Hui; Winkler, Stefan

2018-04-01

Sky-cloud images obtained from ground-based sky cameras are usually captured using a fisheye lens with a wide field of view. However, the sky exhibits a large dynamic range in terms of luminance, more than a conventional camera can capture. It is thus difficult to capture the details of an entire scene with a regular camera in a single shot. In most cases, the circumsolar region is overexposed, and the regions near the horizon are underexposed. This renders cloud segmentation for such images difficult. In this paper, we propose HDRCloudSeg - an effective method for cloud segmentation using high-dynamic-range (HDR) imaging based on multi-exposure fusion. We describe the HDR image generation process and release a new database to the community for benchmarking. Our proposed approach is the first using HDR radiance maps for cloud segmentation and achieves very good results.

Geodesic Distance Algorithm for Extracting the Ascending Aorta from 3D CT Images

PubMed Central

Jang, Yeonggul; Jung, Ho Yub; Hong, Youngtaek; Cho, Iksung; Shim, Hackjoon; Chang, Hyuk-Jae

2016-01-01

This paper presents a method for the automatic 3D segmentation of the ascending aorta from coronary computed tomography angiography (CCTA). The segmentation is performed in three steps. First, the initial seed points are selected by minimizing a newly proposed energy function across the Hough circles. Second, the ascending aorta is segmented by geodesic distance transformation. Third, the seed points are effectively transferred through the next axial slice by a novel transfer function. Experiments are performed using a database composed of 10 patients' CCTA images. For the experiment, the ground truths are annotated manually on the axial image slices by a medical expert. A comparative evaluation with state-of-the-art commercial aorta segmentation algorithms shows that our approach is computationally more efficient and accurate under the DSC (Dice Similarity Coefficient) measurements. PMID:26904151

A label field fusion bayesian model and its penalized maximum rand estimator for image segmentation.

PubMed

Mignotte, Max

2010-06-01

This paper presents a novel segmentation approach based on a Markov random field (MRF) fusion model which aims at combining several segmentation results associated with simpler clustering models in order to achieve a more reliable and accurate segmentation result. The proposed fusion model is derived from the recently introduced probabilistic Rand measure for comparing one segmentation result to one or more manual segmentations of the same image. This non-parametric measure allows us to easily derive an appealing fusion model of label fields, easily expressed as a Gibbs distribution, or as a nonstationary MRF model defined on a complete graph. Concretely, this Gibbs energy model encodes the set of binary constraints, in terms of pairs of pixel labels, provided by each segmentation results to be fused. Combined with a prior distribution, this energy-based Gibbs model also allows for definition of an interesting penalized maximum probabilistic rand estimator with which the fusion of simple, quickly estimated, segmentation results appears as an interesting alternative to complex segmentation models existing in the literature. This fusion framework has been successfully applied on the Berkeley image database. The experiments reported in this paper demonstrate that the proposed method is efficient in terms of visual evaluation and quantitative performance measures and performs well compared to the best existing state-of-the-art segmentation methods recently proposed in the literature.

Fast Multiclass Segmentation using Diffuse Interface Methods on Graphs

DTIC Science & Technology

2013-02-01

000 28 × 28 images of handwritten digits 0 through 9. Examples of entries can be found in Figure 6. The task is to classify each of the images into the...database of handwritten digits .” [Online]. Available: http://yann.lecun.com/exdb/mnist/ [36] J. Lellmann, J. H. Kappes, J. Yuan, F. Becker, and C...corresponding digit . The images include digits from 0 to 9; thus, this is a 10 class segmentation problem. To construct the weight matrix, we used N

Global Binary Continuity for Color Face Detection With Complex Background

NASA Astrophysics Data System (ADS)

Belavadi, Bhaskar; Mahendra Prashanth, K. V.; Joshi, Sujay S.; Suprathik, N.

2017-08-01

In this paper, we propose a method to detect human faces in color images, with complex background. The proposed algorithm makes use of basically two color space models, specifically HSV and YCgCr. The color segmented image is filled uniformly with a single color (binary) and then all unwanted discontinuous lines are removed to get the final image. Experimental results on Caltech database manifests that the purported model is able to accomplish far better segmentation for faces of varying orientations, skin color and background environment.

Model-based segmentation of hand radiographs

NASA Astrophysics Data System (ADS)

Weiler, Frank; Vogelsang, Frank

1998-06-01

An important procedure in pediatrics is to determine the skeletal maturity of a patient from radiographs of the hand. There is great interest in the automation of this tedious and time-consuming task. We present a new method for the segmentation of the bones of the hand, which allows the assessment of the skeletal maturity with an appropriate database of reference bones, similar to the atlas based methods. The proposed algorithm uses an extended active contour model for the segmentation of the hand bones, which incorporates a-priori knowledge of shape and topology of the bones in an additional energy term. This `scene knowledge' is integrated in a complex hierarchical image model, that is used for the image analysis task.

Off-lexicon online Arabic handwriting recognition using neural network

NASA Astrophysics Data System (ADS)

Yahia, Hamdi; Chaabouni, Aymen; Boubaker, Houcine; Alimi, Adel M.

2017-03-01

This paper highlights a new method for online Arabic handwriting recognition based on graphemes segmentation. The main contribution of our work is to explore the utility of Beta-elliptic model in segmentation and features extraction for online handwriting recognition. Indeed, our method consists in decomposing the input signal into continuous part called graphemes based on Beta-Elliptical model, and classify them according to their position in the pseudo-word. The segmented graphemes are then described by the combination of geometric features and trajectory shape modeling. The efficiency of the considered features has been evaluated using feed forward neural network classifier. Experimental results using the benchmarking ADAB Database show the performance of the proposed method.

Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum.

PubMed

Wang, Wei; Xia, Minxuan; Chen, Jie; Deng, Fenni; Yuan, Rui; Zhang, Xiaopei; Shen, Fafu

2016-12-01

The data presented in this paper is supporting the research article "Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum" [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), "Bayesian phylogenetic inference under mixed models" [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information." [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, "Pfam: the protein families database" [4].

Hybrid Active/Passive Jet Engine Noise Suppression System

NASA Technical Reports Server (NTRS)

Parente, C. A.; Arcas, N.; Walker, B. E.; Hersh, A. S.; Rice, E. J.

1999-01-01

A novel adaptive segmented liner concept has been developed that employs active control elements to modify the in-duct sound field to enhance the tone-suppressing performance of passive liner elements. This could potentially allow engine designs that inherently produce more tone noise but less broadband noise, or could allow passive liner designs to more optimally address high frequency broadband noise. A proof-of-concept validation program was undertaken, consisting of the development of an adaptive segmented liner that would maximize attenuation of two radial modes in a circular or annular duct. The liner consisted of a leading active segment with dual annuli of axially spaced active Helmholtz resonators, followed by an optimized passive liner and then an array of sensing microphones. Three successively complex versions of the adaptive liner were constructed and their performances tested relative to the performance of optimized uniform passive and segmented passive liners. The salient results of the tests were: The adaptive segmented liner performed well in a high flow speed model fan inlet environment, was successfully scaled to a high sound frequency and successfully attenuated three radial modes using sensor and active resonator arrays that were designed for a two mode, lower frequency environment.

Rapid Maturation of Edge Sensor Technology and Potential Application in Large Space Telescopes with Segmented Primary Mirrors

NASA Technical Reports Server (NTRS)

Montgomery, Edward E., IV; Smith, W. Scott (Technical Monitor)

2002-01-01

This paper explores the history and results of the last two year's efforts to transition inductive edge sensor technology from Technology Readiness Level 2 to Technology Readiness Level 6. Both technical and programmatic challenges were overcome in the design, fabrication, test, and installation of over a thousand sensors making up the Segment Alignment Maintenance System (SAMs) for the 91 segment, 9.2-meter. Hobby Eberly Telescope (HET). The integration of these sensors with the control system will be discussed along with serendipitous leverage they provided for both initialization alignment and operational maintenance. The experience gained important insights into the fundamental motion mechanics of large segmented mirrors, the relative importance of the variance sources of misalignment errors, the efficient conduct of a program to mature the technology to the higher levels. Unanticipated factors required the team to develop new implementation strategies for the edge sensor information which enabled major segmented mirror controller design simplifications. The resulting increase in the science efficiency of HET will be shown. Finally, the on-going effort to complete the maturation of inductive edge sensor by delivering space qualified versions for future IR (infrared radiation) space telescopes.

A Scalable Framework For Segmenting Magnetic Resonance Images

PubMed Central

Hore, Prodip; Goldgof, Dmitry B.; Gu, Yuhua; Maudsley, Andrew A.; Darkazanli, Ammar

2009-01-01

A fast, accurate and fully automatic method of segmenting magnetic resonance images of the human brain is introduced. The approach scales well allowing fast segmentations of fine resolution images. The approach is based on modifications of the soft clustering algorithm, fuzzy c-means, that enable it to scale to large data sets. Two types of modifications to create incremental versions of fuzzy c-means are discussed. They are much faster when compared to fuzzy c-means for medium to extremely large data sets because they work on successive subsets of the data. They are comparable in quality to application of fuzzy c-means to all of the data. The clustering algorithms coupled with inhomogeneity correction and smoothing are used to create a framework for automatically segmenting magnetic resonance images of the human brain. The framework is applied to a set of normal human brain volumes acquired from different magnetic resonance scanners using different head coils, acquisition parameters and field strengths. Results are compared to those from two widely used magnetic resonance image segmentation programs, Statistical Parametric Mapping and the FMRIB Software Library (FSL). The results are comparable to FSL while providing significant speed-up and better scalability to larger volumes of data. PMID:20046893

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

NASA Astrophysics Data System (ADS)

Victorine, John; Watney, W. Lynn; Bhattacharya, Saibal

2005-11-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling.

Spatial Digital Database for the Geologic Map of Oregon

USGS Publications Warehouse

Walker, George W.; MacLeod, Norman S.; Miller, Robert J.; Raines, Gary L.; Connors, Katherine A.

2003-01-01

Introduction This report describes and makes available a geologic digital spatial database (orgeo) representing the geologic map of Oregon (Walker and MacLeod, 1991). The original paper publication was printed as a single map sheet at a scale of 1:500,000, accompanied by a second sheet containing map unit descriptions and ancillary data. A digital version of the Walker and MacLeod (1991) map was included in Raines and others (1996). The dataset provided by this open-file report supersedes the earlier published digital version (Raines and others, 1996). This digital spatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information for use in spatial analysis in a geographic information system (GIS). This database can be queried in many ways to produce a variety of geologic maps. This database is not meant to be used or displayed at any scale larger than 1:500,000 (for example, 1:100,000). This report describes the methods used to convert the geologic map data into a digital format, describes the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. Scanned images of the printed map (Walker and MacLeod, 1991), their correlation of map units, and their explanation of map symbols are also available for download.

Definitions of database files and fields of the Personal Computer-Based Water Data Sources Directory

USGS Publications Warehouse

Green, J. Wayne

1991-01-01

This report describes the data-base files and fields of the personal computer-based Water Data Sources Directory (WDSD). The personal computer-based WDSD was derived from the U.S. Geological Survey (USGS) mainframe computer version. The mainframe version of the WDSD is a hierarchical data-base design. The personal computer-based WDSD is a relational data- base design. This report describes the data-base files and fields of the relational data-base design in dBASE IV (the use of brand names in this abstract is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey) for the personal computer. The WDSD contains information on (1) the type of organization, (2) the major orientation of water-data activities conducted by each organization, (3) the names, addresses, and telephone numbers of offices within each organization from which water data may be obtained, (4) the types of data held by each organization and the geographic locations within which these data have been collected, (5) alternative sources of an organization's data, (6) the designation of liaison personnel in matters related to water-data acquisition and indexing, (7) the volume of water data indexed for the organization, and (8) information about other types of data and services available from the organization that are pertinent to water-resources activities.

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

PubMed

Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

2015-01-01

The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

USGS Publications Warehouse

Victorine, J.; Watney, W.L.; Bhattacharya, S.

2005-01-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling. ?? 2005 Elsevier Ltd. All rights reserved.

[InlineEquation not available: see fulltext.]-Means Based Fingerprint Segmentation with Sensor Interoperability

NASA Astrophysics Data System (ADS)

Yang, Gongping; Zhou, Guang-Tong; Yin, Yilong; Yang, Xiukun

2010-12-01

A critical step in an automatic fingerprint recognition system is the segmentation of fingerprint images. Existing methods are usually designed to segment fingerprint images originated from a certain sensor. Thus their performances are significantly affected when dealing with fingerprints collected by different sensors. This work studies the sensor interoperability of fingerprint segmentation algorithms, which refers to the algorithm's ability to adapt to the raw fingerprints obtained from different sensors. We empirically analyze the sensor interoperability problem, and effectively address the issue by proposing a [InlineEquation not available: see fulltext.]-means based segmentation method called SKI. SKI clusters foreground and background blocks of a fingerprint image based on the [InlineEquation not available: see fulltext.]-means algorithm, where a fingerprint block is represented by a 3-dimensional feature vector consisting of block-wise coherence, mean, and variance (abbreviated as CMV). SKI also employs morphological postprocessing to achieve favorable segmentation results. We perform SKI on each fingerprint to ensure sensor interoperability. The interoperability and robustness of our method are validated by experiments performed on a number of fingerprint databases which are obtained from various sensors.

Fuzzy-C-Means Clustering Based Segmentation and CNN-Classification for Accurate Segmentation of Lung Nodules

PubMed

K, Jalal Deen; R, Ganesan; A, Merline

2017-07-27

Objective: Accurate segmentation of abnormal and healthy lungs is very crucial for a steadfast computer-aided disease diagnostics. Methods: For this purpose a stack of chest CT scans are processed. In this paper, novel methods are proposed for segmentation of the multimodal grayscale lung CT scan. In the conventional methods using Markov–Gibbs Random Field (MGRF) model the required regions of interest (ROI) are identified. Result: The results of proposed FCM and CNN based process are compared with the results obtained from the conventional method using MGRF model. The results illustrate that the proposed method can able to segment the various kinds of complex multimodal medical images precisely. Conclusion: However, in this paper, to obtain an exact boundary of the regions, every empirical dispersion of the image is computed by Fuzzy C-Means Clustering segmentation. A classification process based on the Convolutional Neural Network (CNN) classifier is accomplished to distinguish the normal tissue and the abnormal tissue. The experimental evaluation is done using the Interstitial Lung Disease (ILD) database. Creative Commons Attribution License

Fuzzy-C-Means Clustering Based Segmentation and CNN-Classification for Accurate Segmentation of Lung Nodules

PubMed Central

K, Jalal Deen; R, Ganesan; A, Merline

2017-01-01

Objective: Accurate segmentation of abnormal and healthy lungs is very crucial for a steadfast computer-aided disease diagnostics. Methods: For this purpose a stack of chest CT scans are processed. In this paper, novel methods are proposed for segmentation of the multimodal grayscale lung CT scan. In the conventional methods using Markov–Gibbs Random Field (MGRF) model the required regions of interest (ROI) are identified. Result: The results of proposed FCM and CNN based process are compared with the results obtained from the conventional method using MGRF model. The results illustrate that the proposed method can able to segment the various kinds of complex multimodal medical images precisely. Conclusion: However, in this paper, to obtain an exact boundary of the regions, every empirical dispersion of the image is computed by Fuzzy C-Means Clustering segmentation. A classification process based on the Convolutional Neural Network (CNN) classifier is accomplished to distinguish the normal tissue and the abnormal tissue. The experimental evaluation is done using the Interstitial Lung Disease (ILD) database. PMID:28749127

Unsupervised sputum color image segmentation for lung cancer diagnosis based on a Hopfield neural network

NASA Astrophysics Data System (ADS)

Sammouda, Rachid; Niki, Noboru; Nishitani, Hiroshi; Nakamura, S.; Mori, Shinichiro

1997-04-01

The paper presents a method for automatic segmentation of sputum cells with color images, to develop an efficient algorithm for lung cancer diagnosis based on a Hopfield neural network. We formulate the segmentation problem as a minimization of an energy function constructed with two terms, the cost-term as a sum of squared errors, and the second term a temporary noise added to the network as an excitation to escape certain local minima with the result of being closer to the global minimum. To increase the accuracy in segmenting the regions of interest, a preclassification technique is used to extract the sputum cell regions within the color image and remove those of the debris cells. The former is then given with the raw image to the input of Hopfield neural network to make a crisp segmentation by assigning each pixel to label such as background, cytoplasm, and nucleus. The proposed technique has yielded correct segmentation of complex scene of sputum prepared by ordinary manual staining method in most of the tested images selected from our database containing thousands of sputum color images.

The Starlite Project - Prototyping Real-Time Software.

DTIC Science & Technology

1992-11-01

by ONR under contract ledge of transactions and a temporal data model. A N00014-91-J-l 102, by DOE, and by NOSC. multiversion data object is one...environment. Section 4 presents experimentations of priority-based synchronization algorithms and multiversion data objects using the prototyping environment...priority-based .yn- chronization algorithms and between a multiversion database and its corresponding single- version database, through the sensitivity

Huntington's Disease Research Roster Support with a Microcomputer Database Management System

PubMed Central

Gersting, J. M.; Conneally, P. M.; Beidelman, K.

1983-01-01

This paper chronicles the MEGADATS (Medical Genetics Acquisition and DAta Transfer System) database development effort in collecting, storing, retrieving, and plotting human family pedigrees. The newest system, MEGADATS-3M, is detailed. Emphasis is on the microcomputer version of MEGADATS-3M and its use to support the Huntington's Disease research roster project. Examples of data input and pedigree plotting are included.

Getting Started with AppleWorks Data Base. First Edition.

ERIC Educational Resources Information Center

Schlenker, Richard M.

This manual is a hands-on teaching tool for beginning users of the AppleWorks database software. It was developed to allow Apple IIGS users who are generally familiar with their machine and its peripherals to build a simple AppleWorks database file using version 2.0 or 2.1 of the program, and to store, print, and manipulate the file. The materials…

Near Real-Time Automatic Data Quality Controls for the AERONET Version 3 Database: An Introduction to the New Level 1.5V Aerosol Optical Depth Data Product

NASA Astrophysics Data System (ADS)

Giles, D. M.; Holben, B. N.; Smirnov, A.; Eck, T. F.; Slutsker, I.; Sorokin, M. G.; Espenak, F.; Schafer, J.; Sinyuk, A.

2015-12-01

The Aerosol Robotic Network (AERONET) has provided a database of aerosol optical depth (AOD) measured by surface-based Sun/sky radiometers for over 20 years. AERONET provides unscreened (Level 1.0) and automatically cloud cleared (Level 1.5) AOD in near real-time (NRT), while manually inspected quality assured (Level 2.0) AOD are available after instrument field deployment (Smirnov et al., 2000). The growing need for NRT quality controlled aerosol data has become increasingly important. Applications of AERONET NRT data include the satellite evaluation (e.g., MODIS, VIIRS, MISR, OMI), data synergism (e.g., MPLNET), verification of aerosol forecast models and reanalysis (e.g., GOCART, ICAP, NAAPS, MERRA), input to meteorological models (e.g., NCEP, ECMWF), and field campaign support (e.g., KORUS-AQ, ORACLES). In response to user needs for quality controlled NRT data sets, the new Version 3 (V3) Level 1.5V product was developed with similar quality controls as those applied by hand to the Version 2 (V2) Level 2.0 data set. The AERONET cloud screened (Level 1.5) NRT AOD database can be significantly impacted by data anomalies. The most significant data anomalies include AOD diurnal dependence due to contamination or obstruction of the sensor head windows, anomalous AOD spectral dependence due to problems with filter degradation, instrument gains, or non-linear changes in calibration, and abnormal changes in temperature sensitive wavelengths (e.g., 1020nm) in response to anomalous sensor head temperatures. Other less common AOD anomalies result from loose filters, uncorrected clock shifts, connection and electronic issues, and various solar eclipse episodes. Automatic quality control algorithms are applied to the new V3 Level 1.5 database to remove NRT AOD anomalies and produce the new AERONET V3 Level 1.5V AOD product. Results of the quality control algorithms are presented and the V3 Level 1.5V AOD database is compared to the V2 Level 2.0 AOD database.

(BARS) -- Bibliographic Retrieval System Sandia Shock Compression (SSC) database Shock Physics Index (SPHINX) database. Volume 1: UNIX version query guide customized application for INGRES

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

Herrmann, W.; von Laven, G.M.; Parker, T.

1993-09-01

The Bibliographic Retrieval System (BARS) is a data base management system specially designed to retrieve bibliographic references. Two databases are available, (i) the Sandia Shock Compression (SSC) database which contains over 5700 references to the literature related to stress waves in solids and their applications, and (ii) the Shock Physics Index (SPHINX) which includes over 8000 further references to stress waves in solids, material properties at intermediate and low rates, ballistic and hypervelocity impact, and explosive or shock fabrication methods. There is some overlap in the information in the two data bases.

Mycobacteriophage genome database.

PubMed

Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

2011-01-01

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

An Approach to a Comprehensive Test Framework for Analysis and Evaluation of Text Line Segmentation Algorithms

PubMed Central

Brodic, Darko; Milivojevic, Dragan R.; Milivojevic, Zoran N.

2011-01-01

The paper introduces a testing framework for the evaluation and validation of text line segmentation algorithms. Text line segmentation represents the key action for correct optical character recognition. Many of the tests for the evaluation of text line segmentation algorithms deal with text databases as reference templates. Because of the mismatch, the reliable testing framework is required. Hence, a new approach to a comprehensive experimental framework for the evaluation of text line segmentation algorithms is proposed. It consists of synthetic multi-like text samples and real handwritten text as well. Although the tests are mutually independent, the results are cross-linked. The proposed method can be used for different types of scripts and languages. Furthermore, two different procedures for the evaluation of algorithm efficiency based on the obtained error type classification are proposed. The first is based on the segmentation line error description, while the second one incorporates well-known signal detection theory. Each of them has different capabilities and convenience, but they can be used as supplements to make the evaluation process efficient. Overall the proposed procedure based on the segmentation line error description has some advantages, characterized by five measures that describe measurement procedures. PMID:22164106

Shape based segmentation of MRIs of the bones in the knee using phase and intensity information

NASA Astrophysics Data System (ADS)

Fripp, Jurgen; Bourgeat, Pierrick; Crozier, Stuart; Ourselin, Sébastien

2007-03-01

The segmentation of the bones from MR images is useful for performing subsequent segmentation and quantitative measurements of cartilage tissue. In this paper, we present a shape based segmentation scheme for the bones that uses texture features derived from the phase and intensity information in the complex MR image. The phase can provide additional information about the tissue interfaces, but due to the phase unwrapping problem, this information is usually discarded. By using a Gabor filter bank on the complex MR image, texture features (including phase) can be extracted without requiring phase unwrapping. These texture features are then analyzed using a support vector machine classifier to obtain probability tissue matches. The segmentation of the bone is fully automatic and performed using a 3D active shape model based approach driven using gradient and texture information. The 3D active shape model is automatically initialized using a robust affine registration. The approach is validated using a database of 18 FLASH MR images that are manually segmented, with an average segmentation overlap (Dice similarity coefficient) of 0.92 compared to 0.9 obtained using the classifier only.

3D Multi-segment foot kinematics in children: A developmental study in typically developing boys.

PubMed

Deschamps, Kevin; Staes, Filip; Peerlinck, Kathelijne; Van Geet, Christel; Hermans, Cedric; Matricali, Giovanni Arnoldo; Lobet, Sebastien

2017-02-01

The relationship between age and 3D rotations objectivized with multisegment foot models has not been quantified until now. The purpose of this study was therefore to investigate the relationship between age and multi-segment foot kinematics in a cross-sectional database. Barefoot multi-segment foot kinematics of thirty two typically developing boys, aged 6-20 years, were captured with the Rizzoli Multi-segment Foot Model. One-dimensional statistical parametric mapping linear regression was used to examine the relationship between age and 3D inter-segment rotations of the dominant leg during the full gait cycle. Age was significantly correlated with sagittal plane kinematics of the midfoot and the calcaneus-metatarsus inter-segment angle (p<0.0125). Age was also correlated with the transverse plane kinematics of the calcaneus-metatarsus angle (p<0.0001). Gait labs should consider age related differences and variability if optimal decision making is pursued. It remains unclear if this is of interest for all foot models, however, the current study highlights that this is of particular relevance for foot models which incorporate a separate midfoot segment. Copyright © 2016 Elsevier B.V. All rights reserved.

Retinal Nerve Fiber Layer Segmentation on FD-OCT Scans of Normal Subjects and Glaucoma Patients.

PubMed

Mayer, Markus A; Hornegger, Joachim; Mardin, Christian Y; Tornow, Ralf P

2010-11-08

Automated measurements of the retinal nerve fiber layer thickness on circular OCT B-Scans provide physicians additional parameters for glaucoma diagnosis. We propose a novel retinal nerve fiber layer segmentation algorithm for frequency domain data that can be applied on scans from both normal healthy subjects, as well as glaucoma patients, using the same set of parameters. In addition, the algorithm remains almost unaffected by image quality. The main part of the segmentation process is based on the minimization of an energy function consisting of gradient and local smoothing terms. A quantitative evaluation comparing the automated segmentation results to manually corrected segmentations from three reviewers is performed. A total of 72 scans from glaucoma patients and 132 scans from normal subjects, all from different persons, composed the database for the evaluation of the segmentation algorithm. A mean absolute error per A-Scan of 2.9 µm was achieved on glaucomatous eyes, and 3.6 µm on healthy eyes. The mean absolute segmentation error over all A-Scans lies below 10 µm on 95.1% of the images. Thus our approach provides a reliable tool for extracting diagnostic relevant parameters from OCT B-Scans for glaucoma diagnosis.

Retinal Nerve Fiber Layer Segmentation on FD-OCT Scans of Normal Subjects and Glaucoma Patients

PubMed Central

Mayer, Markus A.; Hornegger, Joachim; Mardin, Christian Y.; Tornow, Ralf P.

2010-01-01

Automated measurements of the retinal nerve fiber layer thickness on circular OCT B-Scans provide physicians additional parameters for glaucoma diagnosis. We propose a novel retinal nerve fiber layer segmentation algorithm for frequency domain data that can be applied on scans from both normal healthy subjects, as well as glaucoma patients, using the same set of parameters. In addition, the algorithm remains almost unaffected by image quality. The main part of the segmentation process is based on the minimization of an energy function consisting of gradient and local smoothing terms. A quantitative evaluation comparing the automated segmentation results to manually corrected segmentations from three reviewers is performed. A total of 72 scans from glaucoma patients and 132 scans from normal subjects, all from different persons, composed the database for the evaluation of the segmentation algorithm. A mean absolute error per A-Scan of 2.9 µm was achieved on glaucomatous eyes, and 3.6 µm on healthy eyes. The mean absolute segmentation error over all A-Scans lies below 10 µm on 95.1% of the images. Thus our approach provides a reliable tool for extracting diagnostic relevant parameters from OCT B-Scans for glaucoma diagnosis. PMID:21258556

An approach to a comprehensive test framework for analysis and evaluation of text line segmentation algorithms.

PubMed

Brodic, Darko; Milivojevic, Dragan R; Milivojevic, Zoran N

2011-01-01

The paper introduces a testing framework for the evaluation and validation of text line segmentation algorithms. Text line segmentation represents the key action for correct optical character recognition. Many of the tests for the evaluation of text line segmentation algorithms deal with text databases as reference templates. Because of the mismatch, the reliable testing framework is required. Hence, a new approach to a comprehensive experimental framework for the evaluation of text line segmentation algorithms is proposed. It consists of synthetic multi-like text samples and real handwritten text as well. Although the tests are mutually independent, the results are cross-linked. The proposed method can be used for different types of scripts and languages. Furthermore, two different procedures for the evaluation of algorithm efficiency based on the obtained error type classification are proposed. The first is based on the segmentation line error description, while the second one incorporates well-known signal detection theory. Each of them has different capabilities and convenience, but they can be used as supplements to make the evaluation process efficient. Overall the proposed procedure based on the segmentation line error description has some advantages, characterized by five measures that describe measurement procedures.

Hidden Markov random field model and Broyden-Fletcher-Goldfarb-Shanno algorithm for brain image segmentation

NASA Astrophysics Data System (ADS)

Guerrout, EL-Hachemi; Ait-Aoudia, Samy; Michelucci, Dominique; Mahiou, Ramdane

2018-05-01

Many routine medical examinations produce images of patients suffering from various pathologies. With the huge number of medical images, the manual analysis and interpretation became a tedious task. Thus, automatic image segmentation became essential for diagnosis assistance. Segmentation consists in dividing the image into homogeneous and significant regions. We focus on hidden Markov random fields referred to as HMRF to model the problem of segmentation. This modelisation leads to a classical function minimisation problem. Broyden-Fletcher-Goldfarb-Shanno algorithm referred to as BFGS is one of the most powerful methods to solve unconstrained optimisation problem. In this paper, we investigate the combination of HMRF and BFGS algorithm to perform the segmentation operation. The proposed method shows very good segmentation results comparing with well-known approaches. The tests are conducted on brain magnetic resonance image databases (BrainWeb and IBSR) largely used to objectively confront the results obtained. The well-known Dice coefficient (DC) was used as similarity metric. The experimental results show that, in many cases, our proposed method approaches the perfect segmentation with a Dice Coefficient above .9. Moreover, it generally outperforms other methods in the tests conducted.

An improved pulse coupled neural network with spectral residual for infrared pedestrian segmentation

NASA Astrophysics Data System (ADS)

He, Fuliang; Guo, Yongcai; Gao, Chao

2017-12-01

Pulse coupled neural network (PCNN) has become a significant tool for the infrared pedestrian segmentation, and a variety of relevant methods have been developed at present. However, these existing models commonly have several problems of the poor adaptability of infrared noise, the inaccuracy of segmentation results, and the fairly complex determination of parameters in current methods. This paper presents an improved PCNN model that integrates the simplified framework and spectral residual to alleviate the above problem. In this model, firstly, the weight matrix of the feeding input field is designed by the anisotropic Gaussian kernels (ANGKs), in order to suppress the infrared noise effectively. Secondly, the normalized spectral residual saliency is introduced as linking coefficient to enhance the edges and structural characteristics of segmented pedestrians remarkably. Finally, the improved dynamic threshold based on the average gray values of the iterative segmentation is employed to simplify the original PCNN model. Experiments on the IEEE OTCBVS benchmark and the infrared pedestrian image database built by our laboratory, demonstrate that the superiority of both subjective visual effects and objective quantitative evaluations in information differences and segmentation errors in our model, compared with other classic segmentation methods.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

A fast and efficient segmentation scheme for cell microscopic image.

PubMed

Lebrun, G; Charrier, C; Lezoray, O; Meurie, C; Cardot, H

2007-04-27

Microscopic cellular image segmentation schemes must be efficient for reliable analysis and fast to process huge quantity of images. Recent studies have focused on improving segmentation quality. Several segmentation schemes have good quality but processing time is too expensive to deal with a great number of images per day. For segmentation schemes based on pixel classification, the classifier design is crucial since it is the one which requires most of the processing time necessary to segment an image. The main contribution of this work is focused on how to reduce the complexity of decision functions produced by support vector machines (SVM) while preserving recognition rate. Vector quantization is used in order to reduce the inherent redundancy present in huge pixel databases (i.e. images with expert pixel segmentation). Hybrid color space design is also used in order to improve data set size reduction rate and recognition rate. A new decision function quality criterion is defined to select good trade-off between recognition rate and processing time of pixel decision function. The first results of this study show that fast and efficient pixel classification with SVM is possible. Moreover posterior class pixel probability estimation is easy to compute with Platt method. Then a new segmentation scheme using probabilistic pixel classification has been developed. This one has several free parameters and an automatic selection must dealt with, but criteria for evaluate segmentation quality are not well adapted for cell segmentation, especially when comparison with expert pixel segmentation must be achieved. Another important contribution in this paper is the definition of a new quality criterion for evaluation of cell segmentation. The results presented here show that the selection of free parameters of the segmentation scheme by optimisation of the new quality cell segmentation criterion produces efficient cell segmentation.

Semantic Segmentation of Building Elements Using Point Cloud Hashing

NASA Astrophysics Data System (ADS)

Chizhova, M.; Gurianov, A.; Hess, M.; Luhmann, T.; Brunn, A.; Stilla, U.

2018-05-01

For the interpretation of point clouds, the semantic definition of extracted segments from point clouds or images is a common problem. Usually, the semantic of geometrical pre-segmented point cloud elements are determined using probabilistic networks and scene databases. The proposed semantic segmentation method is based on the psychological human interpretation of geometric objects, especially on fundamental rules of primary comprehension. Starting from these rules the buildings could be quite well and simply classified by a human operator (e.g. architect) into different building types and structural elements (dome, nave, transept etc.), including particular building parts which are visually detected. The key part of the procedure is a novel method based on hashing where point cloud projections are transformed into binary pixel representations. A segmentation approach released on the example of classical Orthodox churches is suitable for other buildings and objects characterized through a particular typology in its construction (e.g. industrial objects in standardized enviroments with strict component design allowing clear semantic modelling).

Combining deep learning with anatomical analysis for segmentation of the portal vein for liver SBRT planning

NASA Astrophysics Data System (ADS)

Ibragimov, Bulat; Toesca, Diego; Chang, Daniel; Koong, Albert; Xing, Lei

2017-12-01

Automated segmentation of the portal vein (PV) for liver radiotherapy planning is a challenging task due to potentially low vasculature contrast, complex PV anatomy and image artifacts originated from fiducial markers and vasculature stents. In this paper, we propose a novel framework for automated segmentation of the PV from computed tomography (CT) images. We apply convolutional neural networks (CNNs) to learn the consistent appearance patterns of the PV using a training set of CT images with reference annotations and then enhance the PV in previously unseen CT images. Markov random fields (MRFs) were further used to smooth the results of the enhancement of the CNN enhancement and remove isolated mis-segmented regions. Finally, CNN-MRF-based enhancement was augmented with PV centerline detection that relied on PV anatomical properties such as tubularity and branch composition. The framework was validated on a clinical database with 72 CT images of patients scheduled for liver stereotactic body radiation therapy. The obtained accuracy of the segmentation was DSC= 0.83 and \

Automated construction of arterial and venous trees in retinal images.

PubMed

Hu, Qiao; Abràmoff, Michael D; Garvin, Mona K

2015-10-01

While many approaches exist to segment retinal vessels in fundus photographs, only a limited number focus on the construction and disambiguation of arterial and venous trees. Previous approaches are local and/or greedy in nature, making them susceptible to errors or limiting their applicability to large vessels. We propose a more global framework to generate arteriovenous trees in retinal images, given a vessel segmentation. In particular, our approach consists of three stages. The first stage is to generate an overconnected vessel network, named the vessel potential connectivity map (VPCM), consisting of vessel segments and the potential connectivity between them. The second stage is to disambiguate the VPCM into multiple anatomical trees, using a graph-based metaheuristic algorithm. The third stage is to classify these trees into arterial or venous (A/V) trees. We evaluated our approach with a ground truth built based on a public database, showing a pixel-wise classification accuracy of 88.15% using a manual vessel segmentation as input, and 86.11% using an automatic vessel segmentation as input.

Boundary-to-Marker Evidence-Controlled Segmentation and MDL-Based Contour Inference for Overlapping Nuclei.

PubMed

Song, Jie; Xiao, Liang; Lian, Zhichao

2017-03-01

This paper presents a novel method for automated morphology delineation and analysis of cell nuclei in histopathology images. Combining the initial segmentation information and concavity measurement, the proposed method first segments clusters of nuclei into individual pieces, avoiding segmentation errors introduced by the scale-constrained Laplacian-of-Gaussian filtering. After that a nuclear boundary-to-marker evidence computing is introduced to delineate individual objects after the refined segmentation process. The obtained evidence set is then modeled by the periodic B-splines with the minimum description length principle, which achieves a practical compromise between the complexity of the nuclear structure and its coverage of the fluorescence signal to avoid the underfitting and overfitting results. The algorithm is computationally efficient and has been tested on the synthetic database as well as 45 real histopathology images. By comparing the proposed method with several state-of-the-art methods, experimental results show the superior recognition performance of our method and indicate the potential applications of analyzing the intrinsic features of nuclei morphology.

An automatic multi-atlas prostate segmentation in MRI using a multiscale representation and a label fusion strategy

NASA Astrophysics Data System (ADS)

Álvarez, Charlens; Martínez, Fabio; Romero, Eduardo

2015-01-01

The pelvic magnetic Resonance images (MRI) are used in Prostate cancer radiotherapy (RT), a process which is part of the radiation planning. Modern protocols require a manual delineation, a tedious and variable activity that may take about 20 minutes per patient, even for trained experts. That considerable time is an important work ow burden in most radiological services. Automatic or semi-automatic methods might improve the efficiency by decreasing the measure times while conserving the required accuracy. This work presents a fully automatic atlas- based segmentation strategy that selects the more similar templates for a new MRI using a robust multi-scale SURF analysis. Then a new segmentation is achieved by a linear combination of the selected templates, which are previously non-rigidly registered towards the new image. The proposed method shows reliable segmentations, obtaining an average DICE Coefficient of 79%, when comparing with the expert manual segmentation, under a leave-one-out scheme with the training database.

Petition Requesting the Admistrator to Object to Title V Operating Permit Issued to Noranda Alumina

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Sierra Club's Petition to Have the Administrator Object to Citgo Doraville's Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Responding to Petition Requesting the Administrator Object to Permit for Hu Honua Bioenergy, LLC

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

December 19, 2003 Dismissal of Tesoro Refining and Marketing Company's Petition

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Sierra Club Petition to Object to Doe Run Buick Mine and Mill Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to K-Ply Title V Permit From Bonnie Rathod

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Prime Energy Limited Partnership, Dismissal of Untimely Petition to Object to Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to Title V Permit, Louis Dreyfus Agricultural Industries Oil-Seed Plant

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to the Nucor Steel, St. James Parish, Louisiana Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Columbia Gerating Station, Pardeeville, Wisonconsin Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Potlatch Corporation, Order Denying Petition for Objection to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Portland Generating Station, Order Denying Petition for Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Denying Petition for Objection to Siminole Road Municipal Solid Waste Landfill's Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petition to Object to Tanagraphics, Inc. Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petion to Object ot Kings Plaza Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petition to Object to Action Packaging Corp. Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petiton to Object to Rochdale Villiage, Inc. Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petition to Object to Yeshiva University's Albert Einstein College of Medicane Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

NYPIRG Petition to Object to Elmhurst Hospital's Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to the Edgewater Power Plant, Sheboygan County, Wisconsin, Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Public Service Company, Fort St. Vrain Station, Petition For Objection to Issuance of Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to Title V Permit for Marcal Paper Mills, Inc., Elmwood Park, NJ

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to the VIM Recycling, Inc., Elkhart, Indiana, Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Sierra Club's Petition to Have the Administrator Object to Caldewll Tank Alliance's Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

King Finishing, Order Granting Remanded Issue on Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Building an Integrated Environment for Multimedia

NASA Technical Reports Server (NTRS)

1997-01-01

Multimedia courseware on the solar system and earth science suitable for use in elementary, middle, and high schools was developed under this grant. The courseware runs on Silicon Graphics, Incorporated (SGI) workstations and personal computers (PCs). There is also a version of the courseware accessible via the World Wide Web. Accompanying multimedia database systems were also developed to enhance the multimedia courseware. The database systems accompanying the PC software are based on the relational model, while the database systems accompanying the SGI software are based on the object-oriented model.

December 19, 2003 Dismissal of Chevron Products Company's Petition

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Oak Creek Power Plant, Oak Creek, Wisconsin Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition Requesting that the Administrator Object to Dunkirk Steam Generating Station's Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Sullivan County Landfill, Petition to Object to Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Partially Responding to Three Petitions for Luminant Generating Company Title V Permits

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Granting In Part and Denying In Part Three Petitions For Object to Permits

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to Midwest Generation, Romeoville Generating Station Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to Midwest Generation, Joliet Generating Station Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Denying Petition to Object to Operating Permit for TVA's Shawnee Fossil Plant

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.