PopHuman: the human population genomics browser

PubMed Central

Mulet, Roger; Villegas-Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid

2018-01-01

Abstract The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat. PMID:29059408

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems

PubMed Central

Sriyudthsak, Kansuporn; Mejia, Ramon Francisco; Arita, Masanori; Hirai, Masami Yokota

2016-01-01

PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems. PMID:27174940

PopHuman: the human population genomics browser.

PubMed

Casillas, Sònia; Mulet, Roger; Villegas-Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid; Barbadilla, Antonio

2018-01-04

The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Trajectory Browser Website

NASA Technical Reports Server (NTRS)

Foster, Cyrus; Jaroux, Belgacem A.

2012-01-01

The Trajectory Browser is a web-based tool developed at the NASA Ames Research Center to be used for the preliminary assessment of trajectories to small-bodies and planets and for providing relevant launch date, time-of-flight and V requirements. The site hosts a database of transfer trajectories from Earth to asteroids and planets for various types of missions such as rendezvous, sample return or flybys. A search engine allows the user to find trajectories meeting desired constraints on the launch window, mission duration and delta V capability, while a trajectory viewer tool allows the visualization of the heliocentric trajectory and the detailed mission itinerary. The anticipated user base of this tool consists primarily of scientists and engineers designing interplanetary missions in the context of pre-phase A studies, particularly for performing accessibility surveys to large populations of small-bodies. The educational potential of the website is also recognized for academia and the public with regards to trajectory design, a field that has generally been poorly understood by the public. The website is currently hosted on NASA-internal URL http://trajbrowser.arc.nasa.gov/ with plans for a public release as soon as development is complete.

RBSE: Product development team research activity deliverables

NASA Technical Reports Server (NTRS)

1992-01-01

The GHG Functions and Extensions to be added to the NASA Electronic Library System (NELS) 1.1 product are described. These functions will implement the 'output request' capability within the Object Browser. The functions will be implemented in two parts. The first part is a code to be added to the Object Browser (X version) to implement menus allowing the user to request that objects be copied to specific media, or that objects be downloaded to the user's system following a specific protocol, or that the object be printed to one of the printers attached to the host system. The second part is shell scripts which support the various menu selections. Additional scripts to support functions within the GHG shell (X version) will also be created along with the X version of the GHG Shell as initial capability for the 27 Mar. prototype. The scripts will be composed of C shell routines that will accept parameters (primary file pathways). Certain limitations in functionality will invoke Mail instead of Oracle Mail since that has yet to be delivered and the NELS invocation will default to the X-Windows version instead of the ASCII version.

The personal receiving document management and the realization of email function in OAS

NASA Astrophysics Data System (ADS)

Li, Biqing; Li, Zhao

2017-05-01

This software is an independent software system, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs. This software is an independent software system, using the current popular B/S (browser/server) structure and ASP.NET technology development, using the Windows 7 operating system, Microsoft SQL Server2005 Visual2008 and database as a development platform, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs.

A Brain-Computer Interface (BCI) system to use arbitrary Windows applications by directly controlling mouse and keyboard.

PubMed

Spuler, Martin

2015-08-01

A Brain-Computer Interface (BCI) allows to control a computer by brain activity only, without the need for muscle control. In this paper, we present an EEG-based BCI system based on code-modulated visual evoked potentials (c-VEPs) that enables the user to work with arbitrary Windows applications. Other BCI systems, like the P300 speller or BCI-based browsers, allow control of one dedicated application designed for use with a BCI. In contrast, the system presented in this paper does not consist of one dedicated application, but enables the user to control mouse cursor and keyboard input on the level of the operating system, thereby making it possible to use arbitrary applications. As the c-VEP BCI method was shown to enable very fast communication speeds (writing more than 20 error-free characters per minute), the presented system is the next step in replacing the traditional mouse and keyboard and enabling complete brain-based control of a computer.

Securing a web-based teleradiology platform according to German law and "best practices".

PubMed

Spitzer, Michael; Ullrich, Tobias; Ueckert, Frank

2009-01-01

The Medical Data and Picture Exchange platform (MDPE), as a teleradiology system, facilitates the exchange of digital medical imaging data among authorized users. It features extensive support of the DICOM standard including networking functions. Since MDPE is designed as a web service, security and confidentiality of data and communication pose an outstanding challenge. To comply with demands of German laws and authorities, a generic data security concept considered as "best practice" in German health telematics was adapted to the specific demands of MDPE. The concept features strict logical and physical separation of diagnostic and identity data and thus an all-encompassing pseudonymization throughout the system. Hence, data may only be merged at authorized clients. MDPE's solution of merging data from separate sources within a web browser avoids technically questionable techniques such as deliberate cross-site scripting. Instead, data is merged dynamically by JavaScriptlets running in the user's browser. These scriptlets are provided by one server, while content and method calls are generated by another server. Additionally, MDPE uses encrypted temporary IDs for communication and merging of data.

Analytical Tools for Cloudscope Ice Measurement

NASA Technical Reports Server (NTRS)

Arnott, W. Patrick

1998-01-01

The cloudscope is a ground or aircraft instrument for viewing ice crystals impacted on a sapphire window. It is essentially a simple optical microscope with an attached compact CCD video camera whose output is recorded on a Hi-8 mm video cassette recorder equipped with digital time and date recording capability. In aircraft operation the window is at a stagnation point of the flow so adiabatic compression heats the window to sublimate the ice crystals so that later impacting crystals can be imaged as well. A film heater is used for ground based operation to provide sublimation, and it can also be used to provide extra heat for aircraft operation. The compact video camera can be focused manually by the operator, and a beam splitter - miniature bulb combination provide illumination for night operation. Several shutter speeds are available to accommodate daytime illumination conditions by direct sunlight. The video images can be directly used to qualitatively assess the crystal content of cirrus clouds and contrails. Quantitative size spectra are obtained with the tools described in this report. Selected portions of the video images are digitized using a PCI bus frame grabber to form a short movie segment or stack using NIH (National Institute of Health) Image software with custom macros developed at DRI. The stack can be Fourier transform filtered with custom, easy to design filters to reduce most objectionable video artifacts. Particle quantification of each slice of the stack is performed using digital image analysis. Data recorded for each particle include particle number and centroid, frame number in the stack, particle area, perimeter, equivalent ellipse maximum and minimum radii, ellipse angle, and pixel number. Each valid particle in the stack is stamped with a unique number. This output can be used to obtain a semiquantitative appreciation of the crystal content. The particle information becomes the raw input for a subsequent program (FORTRAN) that synthesizes each slice and separates the new from the sublimating particles. The new particle information is used to generate quantitative particle concentration, area, and mass size spectra along with total concentration, solar extinction coefficient, and ice water content. This program directly creates output in html format for viewing with a web browser.

Designing, Implementing, and Evaluating Secure Web Browsers

ERIC Educational Resources Information Center

Grier, Christopher L.

2009-01-01

Web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems using browser-based attacks. Efforts that retrofit existing browsers have had limited success since modern browsers are not designed to withstand attack. To enable more secure web browsing, we design and implement new web browsers from the ground…

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

Separation of High Order Harmonics with Fluoride Windows

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

Allison, Tom; van Tilborg, Jeroen; Wright, Travis

2010-08-02

The lower orders produced in high order harmonic generation can be effciently temporally separated into monochromatic pulses by propagation in a Fluoride window while still preserving their femtosecond pulse duration. We present calculations for MgF2, CaF2, and LiF windows for the third, fifth, and seventh harmonics of 800 nm. We demonstrate the use of this simple and inexpensive technique in a femtosecond pump/probe experiment using the fifth harmonic.

Managing multiple image stacks from confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Zerbe, Joerg; Goetze, Christian H.; Zuschratter, Werner

1999-05-01

A major goal in neuroanatomy is to obtain precise information about the functional organization of neuronal assemblies and their interconnections. Therefore, the analysis of histological sections frequently requires high resolution images in combination with an overview about the structure. To overcome this conflict we have previously introduced a software for the automatic acquisition of multiple image stacks (3D-MISA) in confocal laser scanning microscopy. Here, we describe a Windows NT based software for fast and easy navigation through the multiple images stacks (MIS-browser), the visualization of individual channels and layers and the selection of user defined subregions. In addition, the MIS browser provides useful tools for the visualization and evaluation of the datavolume, as for instance brightness and contrast corrections of individual layers and channels. Moreover, it includes a maximum intensity projection, panning and zoom in/out functions within selected channels or focal planes (x/y) and tracking along the z-axis. The import module accepts any tiff-format and reconstructs the original image arrangement after the user has defined the sequence of images in x/y and z and the number of channels. The implemented export module allows storage of user defined subregions (new single image stacks) for further 3D-reconstruction and evaluation.

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online

PubMed Central

Lehmann, Eldon D.; DeWolf, Dennis K.; Novotny, Christopher A.; Reed, Karen; Gotwals, Robert R.

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored “virtual diabetic patients” on the internet or create new “patients” with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required. PMID:24511312

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online.

PubMed

Lehmann, Eldon D; Dewolf, Dennis K; Novotny, Christopher A; Reed, Karen; Gotwals, Robert R

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored "virtual diabetic patients" on the internet or create new "patients" with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required.

Occupant-responsive optimal control of smart facade systems

NASA Astrophysics Data System (ADS)

Park, Cheol-Soo

Windows provide occupants with daylight, direct sunlight, visual contact with the outside and a feeling of openness. Windows enable the use of daylighting and offer occupants a outside view. Glazing may also cause a number of problems: undesired heat gain/loss in winter. An over-lit window can cause glare, which is another major complaint by occupants. Furthermore, cold or hot window surfaces induce asymmetric thermal radiation which can result in thermal discomfort. To reduce the potential problems of window systems, double skin facades and airflow window systems have been introduced in the 1970s. They typically contain interstitial louvers and ventilation openings. The current problem with double skin facades and airflow windows is that their operation requires adequate dynamic control to reach their expected performance. Many studies have recognized that only an optimal control enables these systems to truly act as active energy savers and indoor environment controllers. However, an adequate solution for this dynamic optimization problem has thus far not been developed. The primary objective of this study is to develop occupant responsive optimal control of smart facade systems. The control could be implemented as a smart controller that operates the motorized Venetian blind system and the opening ratio of ventilation openings. The objective of the control is to combine the benefits of large windows with low energy demands for heating and cooling, while keeping visual well-being and thermal comfort at an optimal level. The control uses a simulation model with an embedded optimization routine that allows occupant interaction via the Web. An occupant can access the smart controller from a standard browser and choose a pre-defined mode (energy saving mode, visual comfort mode, thermal comfort mode, default mode, nighttime mode) or set a preferred mode (user-override mode) by moving preference sliders on the screen. The most prominent feature of these systems is the capability of dynamically reacting to the environmental input data through real-time optimization. The proposed occupant responsive optimal control of smart facade systems could provide a breakthrough in this under-developed area and lead to a renewed interest in smart facade systems.

Exchanging the Context between OGC Geospatial Web clients and GIS applications using Atom

NASA Astrophysics Data System (ADS)

Maso, Joan; Díaz, Paula; Riverola, Anna; Pons, Xavier

2013-04-01

Currently, the discovery and sharing of geospatial information over the web still presents difficulties. News distribution through website content was simplified by the use of Really Simple Syndication (RSS) and Atom syndication formats. This communication exposes an extension of Atom to redistribute references to geospatial information in a Spatial Data Infrastructure distributed environment. A geospatial client can save the status of an application that involves several OGC services of different kind and direct data and share this status with other users that need the same information and use different client vendor products in an interoperable way. The extensibility of the Atom format was essential to define a format that could be used in RSS enabled web browser, Mass Market map viewers and emerging geospatial enable integrated clients that support Open Geospatial Consortium (OGC) services. Since OWS Context has been designed as an Atom extension, it is possible to see the document in common places where Atom documents are valid. Internet web browsers are able to present the document as a list of items with title, abstract, time, description and downloading features. OWS Context uses GeoRSS so that, the document can be to be interpreted by both Google maps and Bing Maps as items that have the extent represented in a dynamic map. Another way to explode a OWS Context is to develop an XSLT to transform the Atom feed into an HTML5 document that shows the exact status of the client view window that saved the context document. To accomplish so, we use the width and height of the client window, and the extent of the view in world (geographic) coordinates in order to calculate the scale of the map. Then, we can mix elements in world coordinates (such as CF-NetCDF files or GML) with elements in pixel coordinates (such as WMS maps, WMTS tiles and direct SVG content). A smarter map browser application called MiraMon Map Browser is able to write a context document and read it again to recover the context of the previous view or load a context generated by another application. The possibility to store direct links to direct files in OWS Context is particularly interesting for GIS desktop solutions. This communication also presents the development made in the MiraMon desktop GIS solution to include OWS Context. MiraMon software is able to deal either with local files, web services and database connections. As in any other GIS solution, MiraMon team designed its own file (MiraMon Map MMM) for storing and sharing the status of a GIS session. The new OWS Context format is now adopted as an interoperable substitution of the MMM. The extensibility of the format makes it possible to map concepts in the MMM to current OWS Context elements (such as titles, data links, extent, etc) and to generate new elements that are able to include all extra metadata not currently covered by OWS Context. These developments were done in the nine edition of the OpenGIS Web Services Interoperability Experiment (OWS-9) and are demonstrated in this communication.

Thermoelastic Analysis of Hyper-X Camera Windows Suddenly Exposed to Mach 7 Stagnation Aerothermal Shock

NASA Technical Reports Server (NTRS)

Ko, William L.; Gong, Leslie

2000-01-01

To visually record the initial free flight event of the Hyper-X research flight vehicle immediately after separation from the Pegasus(registered) booster rocket, a video camera was mounted on the bulkhead of the adapter through which Hyper-X rides on Pegasus. The video camera was shielded by a protecting camera window made of heat-resistant quartz material. When Hyper-X separates from Pegasus, this camera window will be suddenly exposed to Mach 7 stagnation thermal shock and dynamic pressure loading (aerothermal loading). To examine the structural integrity, thermoelastic analysis was performed, and the stress distributions in the camera windows were calculated. The critical stress point where the tensile stress reaches a maximum value for each camera window was identified, and the maximum tensile stress level at that critical point was found to be considerably lower than the tensile failure stress of the camera window material.

Enabling interspecies epigenomic comparison with CEpBrowser.

PubMed

Cao, Xiaoyi; Zhong, Sheng

2013-05-01

We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

Creating interactive physics simulations using the power of GeoGebra

NASA Astrophysics Data System (ADS)

Walsh, Tom

2017-05-01

I have long incorporated physics simulations in my physics teaching, and truly appreciate those who have made their simulations available to the public. I often would think of an idea for a simulation I would love to be able to use, but with no real programming background I did not know how I could make my own. That was the case until I discovered GeoGebra, which is an open source software offering "Dynamic Mathematics for Teaching and Learning." GeoGebra is freely available for non-commercial users. It is powerful, easy to learn, and versatile. There are versions for Windows, Mac, and Linux, as well as tablet and phone versions. It can also be run directly from a Chrome browser.

Mobile Monitoring Stations and Web Visualization of Biotelemetric System - Guardian II

NASA Astrophysics Data System (ADS)

Krejcar, Ondrej; Janckulik, Dalibor; Motalova, Leona; Kufel, Jan

The main area of interest of our project is to provide solution which can be used in different areas of health care and which will be available through PDAs (Personal Digital Assistants), web browsers or desktop clients. The realized system deals with an ECG sensor connected to mobile equipment, such as PDA/Embedded, based on Microsoft Windows Mobile operating system. The whole system is based on the architecture of .NET Compact Framework, and Microsoft SQL Server. Visualization possibilities of web interface and ECG data are also discussed and final suggestion is made to Microsoft Silverlight solution along with current screenshot representation of implemented solution. The project was successfully tested in real environment in cryogenic room (-136OC).

75 FR 45166 - Jeld-Wen, Inc., Hawkins Window Division, Including On-Site Leased Workers of Nicolet Staffing...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-02

... Window Division, Including On-Site Leased Workers of Nicolet Staffing, Hawkins, WI; Notice of Negative... imports of wood- and aluminum- clad windows and patio doors did not contribute to worker group separations... of wood- and aluminum-clad windows and patio doors during 2007, 2008, January through April 2008, and...

A Policy Based Approach for the Management of Web Browser Resources to Prevent Anonymity Attacks in Tor

NASA Astrophysics Data System (ADS)

Navarro-Arribas, Guillermo; Garcia-Alfaro, Joaquin

Web browsers are becoming the universal interface to reach applications and services related with these systems. Different browsing contexts may be required in order to reach them, e.g., use of VPN tunnels, corporate proxies, anonymisers, etc. By browsing context we mean how the user browsers the Web, including mainly the concrete configuration of its browser. When the context of the browser changes, its security requirements also change. In this work, we present the use of authorisation policies to automatise the process of controlling the resources of a Web browser when its context changes. The objective of our proposal is oriented towards easing the adaptation to the security requirements of the new context and enforce them in the browser without the need for user intervention. We present a concrete application of our work as a plug-in for the adaption of security requirements in Mozilla/Firefox browser when a context of anonymous navigation through the Tor network is enabled.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

Assessment of Undiscovered Deposits of Gold, Silver, Copper, Lead, and Zinc in the United States: A Portable Document (PDF) Recompilation of USGS Open-File Report 96-96 and Circular 1178

USGS Publications Warehouse

U.S. Geological Survey National Mineral Resource Assessment Team Recompiled by Schruben, Paul G.

2002-01-01

This publication contains the results of a national mineral resource assessment study. The study (1) identifies regional tracts of ground believed to contain most of the nation's undiscovered resources of gold, silver, copper, lead, and zinc in conventional types of deposits; and (2) includes probabilistic estimates of the amounts of these undiscovered resources in most of the tracts. It also contains a table of the significant known deposits in the tracts, and includes descriptions of the mineral deposit models used for the assessment. The assessment was previously released in two major publications. The conterminous United States assessment was published in 1996 as USGS Open-File Report 96-96. Subsequently, the Alaska assessment was combined with the conterminous assessment in 1998 and released as USGS Circular 1178. This new recompilation was undertaken for several reasons. First, the graphical browser software used in Circular 1178 was ONLY compatible with the Microsoft Windows operating system. It was incompatible with the Macintosh operating system, Linux, and other types of Unix computers. Second, the browser on Circular 1178 is much less intuitive to operate, requiring most users to follow a tutorial to understand how to navigate the information on the CD. Third, this release corrects several errors and numbering inconsistencies in Circular 1178.

LightWAVE: Waveform and Annotation Viewing and Editing in a Web Browser.

PubMed

Moody, George B

2013-09-01

This paper describes LightWAVE, recently-developed open-source software for viewing ECGs and other physiologic waveforms and associated annotations (event markers). It supports efficient interactive creation and modification of annotations, capabilities that are essential for building new collections of physiologic signals and time series for research. LightWAVE is constructed of components that interact in simple ways, making it straightforward to enhance or replace any of them. The back end (server) is a common gateway interface (CGI) application written in C for speed and efficiency. It retrieves data from its data repository (PhysioNet's open-access PhysioBank archives by default, or any set of files or web pages structured as in PhysioBank) and delivers them in response to requests generated by the front end. The front end (client) is a web application written in JavaScript. It runs within any modern web browser and does not require installation on the user's computer, tablet, or phone. Finally, LightWAVE's scribe is a tiny CGI application written in Perl, which records the user's edits in annotation files. LightWAVE's data repository, back end, and front end can be located on the same computer or on separate computers. The data repository may be split across multiple computers. For compatibility with the standard browser security model, the front end and the scribe must be loaded from the same domain.

Exploring the enjoyment of playing browser games.

PubMed

Klimmt, Christoph; Schmid, Hannah; Orthmann, Julia

2009-04-01

Browser games--mostly persistent game worlds that can be used without client software and monetary cost with a Web browser--belong to the understudied digital game types, although they attract large player communities and motivate sustained play. The present work reports findings from an online survey of 8,203 players of a German strategy browser game ("Travian"). Results suggest that multiplayer browser games are enjoyed primarily because of the social relationships involved in game play and the specific time and flexibility characteristics ("easy-in, easy-out"). Competition, in contrast, seems to be less important for browser gamers than for users of other game types. Findings are discussed in terms of video game enjoyment and game addiction.

Study of Design Knowledge Capture (DKC) schemes implemented in magnetic bearing applications

NASA Technical Reports Server (NTRS)

1990-01-01

A design knowledge capture (DKC) scheme was implemented using frame-based techniques. The objective of such a system is to capture not only the knowledge which describes a design, but also that which explains how the design decisions were reached. These knowledge types were labelled definitive and explanatory, respectively. Examination of the design process helped determine what knowledge to retain and at what stage that knowledge is used. A discussion of frames resulted in the recognition of their value to knowledge representation and organization. The FORMS frame system was used as a basis for further development, and for examples using magnetic bearing design. The specific contributions made by this research include: determination that frame-based systems provide a useful methodology for management and application of design knowledge; definition of specific user interface requirements, (this consists of a window-based browser); specification of syntax for DKC commands; and demonstration of the feasibility of DKC by applications to existing designs. It was determined that design knowledge capture could become an extremely valuable engineering tool for complicated, long-life systems, but that further work was needed, particularly the development of a graphic, window-based interface.

The DREO Elint Browser Utility (DEBU) reference manual

NASA Astrophysics Data System (ADS)

Ford, Barbara; Jones, David

1992-04-01

An electronic intelligent database browsing tool called DEBU has been developed that allows databases such as ELP, Kilting, EWIR, and AFEWC to be reviewed and analyzed from a user-friendly environment on a personal computer. DEBU's basic function is to allow users to examine the contents of user-selected subfiles of user-selected emitters of user-selected databases. DEBU augments this functionality with support for selecting (filtering) and combining subsets of emitters by user-selected attributes such as name, parameter type, or parameter value. DEBU provides facilities for examining histograms and x-y plots of selected parameters, for doing ambiguity analysis and mode level analysis, and for generating and printing a variety of reports. A manual is provided for users of DEBU, including descriptions and illustrations of menus and windows.

Guide to Mathematics Released Items: Understanding Scoring. 2015

ERIC Educational Resources Information Center

Partnership for Assessment of Readiness for College and Careers, 2015

2015-01-01

The 2014-2015 administrations of the PARCC assessment included two separate test administration windows: the Performance-Based Assessment (PBA) and the End-of-Year (EOY), both of which were administered in paper-based and computer-based formats. The first window was for administration of the PBA, and the second window was for the administration of…

Design and implementation of a P300-based brain-computer interface for controlling an internet browser.

PubMed

Mugler, Emily M; Ruf, Carolin A; Halder, Sebastian; Bensch, Michael; Kubler, Andrea

2010-12-01

An electroencephalographic (EEG) brain-computer interface (BCI) internet browser was designed and evaluated with 10 healthy volunteers and three individuals with advanced amyotrophic lateral sclerosis (ALS), all of whom were given tasks to execute on the internet using the browser. Participants with ALS achieved an average accuracy of 73% and a subsequent information transfer rate (ITR) of 8.6 bits/min and healthy participants with no prior BCI experience over 90% accuracy and an ITR of 14.4 bits/min. We define additional criteria for unrestricted internet access for evaluation of the presented and future internet browsers, and we provide a review of the existing browsers in the literature. The P300-based browser provides unrestricted access and enables free web surfing for individuals with paralysis.

Secure Design Patterns

DTIC Science & Technology

2009-03-01

the Distrustful Decomposition pattern: • a number of separate programs, each running in a separate process . For more complete sepa- ration, each...be used in place of fork(). For example, under various versions of Windows, the CreateProcess() func- tion is used to spawn a child process . Figure...list contains the SIDs of the client processes that are allowed to connect to the server, that is, the Windows service. For more information about

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

2014-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C.

2015-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible. PMID:25628562

Firefox add-ons for medical reference.

PubMed

Hoy, Matthew B

2010-07-01

Firefox is a Web browser created by the Mozilla project, an open-source software group. Features of the browser include automated updates, advanced security and standards compliance, and the ability to add functionality through add-ons and extensions. First introduced in 2004, Firefox now accounts for roughly 30% of the browser market. This article will focus primarily on add-ons and extensions available for the browser that are useful to medical researchers.

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

Conquering technophobia: preparing faculty for today.

PubMed

Richard, P L

1997-01-01

The constantly changing world of technology creates excitement and an obligation for faculty of schools of nursing to address computer literacy in the curricula at all levels. The initial step in the process of meeting the goals was to assist the faculty in becoming computer literate so that they could foster and encourage the same in the students. The implementation of The Cure for Technophobia included basic and advanced computer skills designed to assist the faculty in becoming comfortable and competent computer users. The applications addressed included: introduction to windows, electronic mail, word processing, presentation and database applications, library on-line searches of literature databases, introduction to internet browsers and a computerized testing program. Efforts were made to overcome barriers to computer literacy and promote the learning process. Familiar, competent, computer literate individuals were used to conduct the classes to accomplish this goal.

29. OVERVIEW OF CENTRAL PART, TO WEST, SHOWING CLERESTORY WINDOWS. ...

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

29. OVERVIEW OF CENTRAL PART, TO WEST, SHOWING CLERESTORY WINDOWS. THE WALL AT REAR IS RECENT, SEPARATING TWO TENANTS' SPACES. - United Engineering Company Shipyard, Inspection & Repair Shops, 2900 Main Street, Alameda, Alameda County, CA

Eco-Health Relationship Browser

EPA Science Inventory

The Eco-Health Relationship Browser (Browser) is a web tool designed to portray, in an engaging and intuitive way, the linkages between ecosystems, their services, and potential health outcomes that have been associated with those services in the literature. It functions an inte...

Inside storm window

NASA Astrophysics Data System (ADS)

Kaplan, J. I.

1980-11-01

The work effort to design, build, install, and evaluate an inside storm window (ISW) is presented. The ISW, made of two separated layers of mylar (like a thermopane window) which, when not in use can be rolled up in a shade, is described. The work effort included: development of a prototype model; the development of production facilities to turn out a small number (50) of ISW's; the production of the windows; the installation of the windows into buildings; the building of a test chamber to determine the R value of the ISW and the subsequent determination of the R value; and a survey to determine how the residents of the homes in which ISW's were installed felt about the windows.

Integrating speech in time depends on temporal expectancies and attention.

PubMed

Scharinger, Mathias; Steinberg, Johanna; Tavano, Alessandro

2017-08-01

Sensory information that unfolds in time, such as in speech perception, relies on efficient chunking mechanisms in order to yield optimally-sized units for further processing. Whether or not two successive acoustic events receive a one-unit or a two-unit interpretation seems to depend on the fit between their temporal extent and a stipulated temporal window of integration. However, there is ongoing debate on how flexible this temporal window of integration should be, especially for the processing of speech sounds. Furthermore, there is no direct evidence of whether attention may modulate the temporal constraints on the integration window. For this reason, we here examine how different word durations, which lead to different temporal separations of sound onsets, interact with attention. In an Electroencephalography (EEG) study, participants actively and passively listened to words where word-final consonants were occasionally omitted. Words had either a natural duration or were artificially prolonged in order to increase the separation of speech sound onsets. Omission responses to incomplete speech input, originating in left temporal cortex, decreased when the critical speech sound was separated from previous sounds by more than 250 msec, i.e., when the separation was larger than the stipulated temporal window of integration (125-150 msec). Attention, on the other hand, only increased omission responses for stimuli with natural durations. We complemented the event-related potential (ERP) analyses by a frequency-domain analysis on the stimulus presentation rate. Notably, the power of stimulation frequency showed the same duration and attention effects than the omission responses. We interpret these findings on the background of existing research on temporal integration windows and further suggest that our findings may be accounted for within the framework of predictive coding. Copyright © 2017 Elsevier Ltd. All rights reserved.

CERESVis: A QC Tool for CERES that Leverages Browser Technology for Data Validation

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Doelling, D.

2015-12-01

In this poster, we are going to present three user interfaces that CERES team uses to validate pixel-level data. Besides our home grown tools, we will aslo present the browser technology that we use to provide interactive interfaces, such as jquery, HighCharts and Google Earth. We pass data to the users' browsers and use the browsers to do some simple computations. The three user interfaces are: Thumbnails -- it displays hundrends images to allow users to browse 24-hour data files in few seconds. Multiple-synchronized cursors -- it allows users to compare multiple images side by side. Bounding Boxes and Histograms -- it allows users to draw multiple bounding boxes on an image and the browser computes/display the histograms.

Archive of Boomer and Chirp Seismic Reflection Data Collected During USGS Cruise 01RCE02, Southern Louisiana, April and May 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.

2003-01-01

In April and May of 2001, the U.S. Geological Survey conducted a geophysical study of the Mississippi River Delta, Atchafalaya River Delta, and Shell Island Pass in southern Louisiana. This study was part of a larger USGS River Contaminant Evaluation (RCE) Project. This disc serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, shotpoint navigation maps, observers' logbooks, GIS information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a filtered and gained digital GIF-formatted image of each seismic profile is provided. For your convenience, a list of acronyms and abbreviations frequently used in this report has also been provided. This DVD (Digital Versatile Disc) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information by using a web browser (i.e. Netscape or Internet Explorer). To access the information contained on this disc, open the file 'index.htm' located at the top level of the disc using your web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the internet is available while viewing the DVD. The archived boomer and chirp seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes. Examples of SU processing scripts are provided in the boom.tar and chirp.tar files located in the SU subfolder of the SOFTWARE folder located at the top level of this DVD. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zilhman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, shotpoint navigation maps, logbooks, and formal metadata may be viewed with your web browser.

Feedback about Astronomical Application Developments for Mobile Devices

NASA Astrophysics Data System (ADS)

Schaaff, A.; Boch, T.; Fernique, P.; Houpin, R.; Kaestlé, V.; Royer, M.; Scheffmann, J.; Weiler, A.

2013-10-01

Within a few years, Smartphones have become the standard for mobile telephony, and we are now witnessing a rapid development of Internet tablets. These mobile devices have enough powerful hardware features to run more and more complex applications. In the field of astronomy it is not only possible to use these tools to access data via a simple browser, but also to develop native applications reusing libraries (Java for Android, Objective-C for iOS) developed for desktops. We have been working for two years on mobile application development and we now have the skills in native iOS and Android development, Web development (especially HTML5, JavaScript, CSS3) and conversion tools (PhoneGap) from Web development to native applications. The biggest change comes from human/computer interaction that is radically changed by the use of multitouch. This interaction requires a redesign of interfaces to take advantage of new features (simultaneous selections in different parts of the screen, etc.). In the case of native applications, the distribution is usually done through online stores (App Store, Google Play, etc.) which gives visibility to a wider audience. Our approach is not only to perform testing of materials and developing of prototypes, but also operational applications. The native application development is costly in development time, but the possibilities are broader because it is possible to use native hardware such as the gyroscope and the accelerometer, to point out an object in the sky. Development depends on the Web browser and the rendering and performance are often very different between different browsers. It is also possible to convert Web developments to native applications, but currently it is better to restrict this possibility to light applications in terms of functionality. Developments in HTML5 are promising but are far behind those available on desktops. HTML5 has the advantage of allowing development independent from the evolution of the mobile platforms (“write once, run everywhere”). The upcoming Windows 8 support on desktops and Internet tablets as well as a mobile version for smartphones will further expand the native systems family. This will enhance the interest of Web development.

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

Cassidy looks through window into the PMA-2 during STS-127 Mission

NASA Image and Video Library

2009-07-17

S127-E-006705 (17 July 2009) --- Astronaut Christopher Cassidy, STS-127 mission specialist, peers through a window in the hatch that separates seven Endeavour crew members from six International Space Station inhabitants. But the separation wasn't for long, as soon afterward the hatch was opened and the visitors from Earth moved onto the station to set the population record at 13. More importantly, over a week's worth of joint activities lies ahead for the two crews.

Model MTF for the mosaic window

NASA Astrophysics Data System (ADS)

Xing, Zhenchong; Hong, Yongfeng; Zhang, Bao

2017-10-01

An electro-optical targeting system mounted either within an airframe or housed in separate pods requires a window to form an environmental barrier to the outside world. In current practice, such windows usually use a mosaic or segmented window. When scanning the target, internally gimbaled systems sweep over the window, which can affect the modulation transfer function (MTF) due to wave-front division and optical path differences arising from the thickness/wedge differences between panes. In this paper, a mathematical model of the MTF of the mosaic window is presented that allows an analysis of influencing factors; we show how the model may be integrated into ZEMAX® software for optical design. The model can be used to guide both the design and the tolerance analysis of optical systems that employ a mosaic window.

Development of educational image databases and e-books for medical physics training.

PubMed

Tabakov, S; Roberts, V C; Jonsson, B-A; Ljungberg, M; Lewis, C A; Wirestam, R; Strand, S-E; Lamm, I-L; Milano, F; Simmons, A; Deane, C; Goss, D; Aitken, V; Noel, A; Giraud, J-Y; Sherriff, S; Smith, P; Clarke, G; Almqvist, M; Jansson, T

2005-09-01

Medical physics education and training requires the use of extensive imaging material and specific explanations. These requirements provide an excellent background for application of e-Learning. The EU projects Consortia EMERALD and EMIT developed five volumes of such materials, now used in 65 countries. EMERALD developed e-Learning materials in three areas of medical physics (X-ray diagnostic radiology, nuclear medicine and radiotherapy). EMIT developed e-Learning materials in two further areas: ultrasound and magnetic resonance imaging. This paper describes the development of these e-Learning materials (consisting of e-books and educational image databases). The e-books include tasks helping studying of various equipment and methods. The text of these PDF e-books is hyperlinked with respective images. The e-books are used through the readers' own Internet browser. Each Image Database (IDB) includes a browser, which displays hundreds of images of equipment, block diagrams and graphs, image quality examples, artefacts, etc. Both the e-books and IDB are engraved on five separate CD-ROMs. Demo of these materials can be taken from www.emerald2.net.

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

Ajax and Firefox: New Web Applications and Browsers

ERIC Educational Resources Information Center

Godwin-Jones, Bob

2005-01-01

Alternative browsers are gaining significant market share, and both Apple and Microsoft are releasing OS upgrades which portend some interesting changes in Web development. Of particular interest for language learning professionals may be new developments in the area of Web browser based applications, particularly using an approach dubbed "Ajax."…

Interactive Analysis of General Beam Configurations using Finite Element Methods and JavaScript

NASA Astrophysics Data System (ADS)

Hernandez, Christopher

Advancements in computer technology have contributed to the widespread practice of modelling and solving engineering problems through the use of specialized software. The wide use of engineering software comes with the disadvantage to the user of costs from the required purchase of software licenses. The creation of accurate, trusted, and freely available applications capable of conducting meaningful analysis of engineering problems is a way to mitigate to the costs associated with every-day engineering computations. Writing applications in the JavaScript programming language allows the applications to run within any computer browser, without the need to install specialized software, since all internet browsers are equipped with virtual machines (VM) that allow the browsers to execute JavaScript code. The objective of this work is the development of an application that performs the analysis of a completely general beam through use of the finite element method. The app is written in JavaScript and embedded in a web page so it can be downloaded and executed by a user with an internet connection. This application allows the user to analyze any uniform or non-uniform beam, with any combination of applied forces, moments, distributed loads, and boundary conditions. Outputs for this application include lists the beam deformations and slopes, as well as lateral and slope deformation graphs, bending stress distributions, and shear and a moment diagrams. To validate the methodology of the GBeam finite element app, its results are verified using the results from obtained from two other established finite element solvers for fifteen separate test cases.

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML).

PubMed

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-07-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging.

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML)*

PubMed Central

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-01-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging. PMID:15973760

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

NASA Astrophysics Data System (ADS)

Lahti, Paul M.; Motyka, Eric J.; Lancashire, Robert J.

2000-05-01

A straightforward procedure is described to combine computation of molecular vibrational modes using commonly available molecular modeling programs with visualization of the modes using advanced features of the MDL Information Systems Inc. Chime World Wide Web browser plug-in. Minor editing of experimental spectra that are stored in the JCAMP-DX format allows linkage of IR spectral frequency ranges to Chime molecular display windows. The spectra and animation files can be combined by Hypertext Markup Language programming to allow interactive linkage between experimental spectra and computationally generated vibrational displays. Both the spectra and the molecular displays can be interactively manipulated to allow the user maximum control of the objects being viewed. This procedure should be very valuable not only for aiding students through visual linkage of spectra and various vibrational animations, but also by assisting them in learning the advantages and limitations of computational chemistry by comparison to experiment.

PACS on mobile devices

NASA Astrophysics Data System (ADS)

Parikh, Ashesh; Mehta, Nihal

2015-03-01

Recent advances in internet browser technologies makes it possible to incorporate advanced functionality of a traditional PACS for viewing DICOM medical images on standard web browsers without the need to pre-install any plug-ins, apps or software. We demonstrate some of the capabilities of standard web browsers setting the stage for a cloud-based PACS.

YADBrowser: A Browser for Web-Based Educational Applications

ERIC Educational Resources Information Center

Zaldivar, Vicente Arturo Romero; Arandia, Jon Ander Elorriaga; Brito, Mateo Lezcano

2005-01-01

In this article, the main characteristics of the educational browser YADBrowser are described. One of the main objectives of this project is to define new languages and object models which facilitate the creation of educational applications for the Internet. The fundamental characteristics of the object model of the browser are also described.…

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Optimization and comparison of simultaneous and separate acquisition protocols for dual isotope myocardial perfusion SPECT.

PubMed

Ghaly, Michael; Links, Jonathan M; Frey, Eric C

2015-07-07

Dual-isotope simultaneous-acquisition (DISA) rest-stress myocardial perfusion SPECT (MPS) protocols offer a number of advantages over separate acquisition. However, crosstalk contamination due to scatter in the patient and interactions in the collimator degrade image quality. Compensation can reduce the effects of crosstalk, but does not entirely eliminate image degradations. Optimizing acquisition parameters could further reduce the impact of crosstalk. In this paper we investigate the optimization of the rest Tl-201 energy window width and relative injected activities using the ideal observer (IO), a realistic digital phantom population and Monte Carlo (MC) simulated Tc-99m and Tl-201 projections as a means to improve image quality. We compared performance on a perfusion defect detection task for Tl-201 acquisition energy window widths varying from 4 to 40 keV centered at 72 keV for a camera with a 9% energy resolution. We also investigated 7 different relative injected activities, defined as the ratio of Tc-99m and Tl-201 activities, while keeping the total effective dose constant at 13.5 mSv. For each energy window and relative injected activity, we computed the IO test statistics using a Markov chain Monte Carlo (MCMC) method for an ensemble of 1,620 triplets of fixed and reversible defect-present, and defect-absent noisy images modeling realistic background variations. The volume under the 3-class receiver operating characteristic (ROC) surface (VUS) was estimated and served as the figure of merit. For simultaneous acquisition, the IO suggested that relative Tc-to-Tl injected activity ratios of 2.6-5 and acquisition energy window widths of 16-22% were optimal. For separate acquisition, we observed a broad range of optimal relative injected activities from 2.6 to 12.1 and acquisition energy window of widths 16-22%. A negative correlation between Tl-201 injected activity and the width of the Tl-201 energy window was observed in these ranges. The results also suggested that DISA methods could potentially provide image quality as good as that obtained with separate acquisition protocols. We compared observer performance for the optimized protocols and the current clinical protocol using separate acquisition. The current clinical protocols provided better performance at a cost of injecting the patient with approximately double the injected activity of Tc-99m and Tl-201, resulting in substantially increased radiation dose.

Design challenges and gaps in standards in developing an interoperable zero footprint DI thin client for use in image-enabled electronic health record solutions

NASA Astrophysics Data System (ADS)

Agrawal, Arun; Koff, David; Bak, Peter; Bender, Duane; Castelli, Jane

2015-03-01

The deployment of regional and national Electronic Health Record solutions has been a focus of many countries throughout the past decade. A major challenge for these deployments has been support for ubiquitous image viewing. More specifically, these deployments require an imaging solution that can work over the Internet, leverage any point of service device: desktop, tablet, phone; and access imaging data from any source seamlessly. Whereas standards exist to enable ubiquitous image viewing, few if any solutions exist that leverage these standards and meet the challenge. Rather, most of the currently available web based DI viewing solutions are either proprietary solutions or require special plugins. We developed a true zero foot print browser based DI viewing solution based on the Web Access DICOM Objects (WADO) and Cross-enterprise Document Sharing for Imaging (XDS-I.b) standards to a) demonstrate that a truly ubiquitous image viewer can be deployed; b) identify the gaps in the current standards and the design challenges for developing such a solution. The objective was to develop a viewer, which works on all modern browsers on both desktop and mobile devices. The implementation allows basic viewing functionalities of scroll, zoom, pan and window leveling (limited). The major gaps identified in the current DICOM WADO standards are a lack of ability to allow any kind of 3D reconstruction or MPR views. Other design challenges explored include considerations related to optimization of the solution for response time and low memory foot print.

An easy-to-build, low-budget point-of-care ultrasound simulator: from Linux to a web-based solution.

PubMed

Damjanovic, Domagoj; Goebel, Ulrich; Fischer, Benedikt; Huth, Martin; Breger, Hartmut; Buerkle, Hartmut; Schmutz, Axel

2017-12-01

Hands-on training in point-of-care ultrasound (POC-US) should ideally comprise bedside teaching, as well as simulated clinical scenarios. High-fidelity phantoms and portable ultrasound simulation systems are commercially available, however, at considerable costs. This limits their suitability for medical schools. A Linux-based software for Emergency Department Ultrasound Simulation (edus2TM) was developed by Kulyk and Olszynski in 2011. Its feasibility for POC-US education has been well-documented, and shows good acceptance. An important limitation to an even more widespread use of edus2, however, may be due to the need for a virtual machine for WINDOWS ® systems. Our aim was to adapt the original software toward an HTML-based solution, thus making it affordable and applicable in any simulation setting. We created an HTML browser-based ultrasound simulation application, which reads the input of different sensors, triggering an ultrasound video to be displayed on a respective device. RFID tags, NFC tags, and QR Codes™ have been integrated into training phantoms or were attached to standardized patients. The RFID antenna was hidden in a mock ultrasound probe. The application is independent from the respective device. Our application was used successfully with different trigger/scanner combinations and mounted readily into simulated training scenarios. The application runs independently from operating systems or electronic devices. This low-cost, browser-based ultrasound simulator is easy-to-build, very adaptive, and independent from operating systems. It has the potential to facilitate POC-US training throughout the world, especially in resource-limited areas.

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

Yoshihama, Sachiko; Tateishi, Takaaki; Tabuchi, Naoshi; Matsumoto, Tsutomu

The emergence of Web 2.0 technologies such as Ajax and Mashup has revealed the weakness of the same-origin policy[1], the current de facto standard for the Web browser security model. We propose a new browser security model to allow fine-grained access control in the client-side Web applications for secure mashup and user-generated contents. We propose a browser security model that is based on information-flow-based access control (IBAC) to overcome the dynamic nature of the client-side Web applications and to accurately determine the privilege of scripts in the event-driven programming model.

An Asynchronous P300-Based Brain-Computer Interface Web Browser for Severely Disabled People.

PubMed

Martinez-Cagigal, Victor; Gomez-Pilar, Javier; Alvarez, Daniel; Hornero, Roberto

2017-08-01

This paper presents an electroencephalographic (EEG) P300-based brain-computer interface (BCI) Internet browser. The system uses the "odd-ball" row-col paradigm for generating the P300 evoked potentials on the scalp of the user, which are immediately processed and translated into web browser commands. There were previous approaches for controlling a BCI web browser. However, to the best of our knowledge, none of them was focused on an assistive context, failing to test their applications with a suitable number of end users. In addition, all of them were synchronous applications, where it was necessary to introduce a "read-mode" command in order to avoid a continuous command selection. Thus, the aim of this study is twofold: 1) to test our web browser with a population of multiple sclerosis (MS) patients in order to assess the usefulness of our proposal to meet their daily communication needs; and 2) to overcome the aforementioned limitation by adding a threshold that discerns between control and non-control states, allowing the user to calmly read the web page without undesirable selections. The browser was tested with sixteen MS patients and five healthy volunteers. Both quantitative and qualitative metrics were obtained. MS participants reached an average accuracy of 84.14%, whereas 95.75% was achieved by control subjects. Results show that MS patients can successfully control the BCI web browser, improving their personal autonomy.

Window-closing safety system

DOEpatents

McEwan, Thomas E.

1997-01-01

A safety device includes a wire loop embedded in the glass of a passenger car window and routed near the closing leading-edge of the window. The wire loop carries microwave pulses around the loop to and from a transceiver with separate output and input ports. An evanescent field only and inch or two in radius is created along the wire loop by the pulses. Just about any object coming within the evanescent field will dramatically reduce the energy of the microwave pulses received back by the transceiver. Such a loss in energy is interpreted as a closing area blockage, and electrical interlocks are provided to halt or reverse a power window motor that is actively trying to close the window.

Window-closing safety system

DOEpatents

McEwan, T.E.

1997-08-26

A safety device includes a wire loop embedded in the glass of a passenger car window and routed near the closing leading-edge of the window. The wire loop carries microwave pulses around the loop to and from a transceiver with separate output and input ports. An evanescent field only an inch or two in radius is created along the wire loop by the pulses. Just about any object coming within the evanescent field will dramatically reduce the energy of the microwave pulses received back by the transceiver. Such a loss in energy is interpreted as a closing area blockage, and electrical interlocks are provided to halt or reverse a power window motor that is actively trying to close the window. 5 figs.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

Bi-level microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2004-01-06

A package with an integral window for housing a microelectronic device. The integral window is bonded directly to the package without having a separate layer of adhesive material disposed in-between the window and the package. The device can be a semiconductor chip, CCD chip, CMOS chip, VCSEL chip, laser diode, MEMS device, or IMEMS device. The multilayered package can be formed of a LTCC or HTCC cofired ceramic material, with the integral window being simultaneously joined to the package during LTCC or HTCC processing. The microelectronic device can be flip-chip bonded so that the light-sensitive side is optically accessible through the window. The package has at least two levels of circuits for making electrical interconnections to a pair of microelectronic devices. The result is a compact, low-profile package having an integral window that is hermetically sealed to the package prior to mounting and interconnecting the microelectronic device(s).

Single level microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2003-12-09

A package with an integral window for housing a microelectronic device. The integral window is bonded directly to the package without having a separate layer of adhesive material disposed in-between the window and the package. The device can be a semiconductor chip, CCD chip, CMOS chip, VCSEL chip, laser diode, MEMS device, or IMEMS device. The package can be formed of a multilayered LTCC or HTCC cofired ceramic material, with the integral window being simultaneously joined to the package during cofiring. The microelectronic device can be flip-chip interconnected so that the light-sensitive side is optically accessible through the window. A glob-top encapsulant or protective cover can be used to protect the microelectronic device and electrical interconnections. The result is a compact, low profile package having an integral window that is hermetically sealed to the package prior to mounting and interconnecting the microelectronic device.

HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

Lexicon Sextant: Modeling a Mnemonic System for Customizable Browser Information Organization and Management

ERIC Educational Resources Information Center

Shen, Siu-Tsen

2016-01-01

This paper presents an ongoing study of the development of a customizable web browser information organization and management system, which the author has named Lexicon Sextant (LS). LS is a user friendly, graphical web based add-on to the latest generation of web browsers, such as Google Chrome, making it easier and more intuitive to store and…

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

PubMed

Hallin, Peter F; Stærfeldt, Hans-Henrik; Rotenberg, Eva; Binnewies, Tim T; Benham, Craig J; Ussery, David W

2009-09-25

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/.

Natural Language Processing in aid of FlyBase curators

PubMed Central

Karamanis, Nikiforos; Seal, Ruth; Lewin, Ian; McQuilton, Peter; Vlachos, Andreas; Gasperin, Caroline; Drysdale, Rachel; Briscoe, Ted

2008-01-01

Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully. PMID:18410678

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Are the long-term effects of mesobrowsers on woodland dynamics substitutive or additive to those of elephants?

NASA Astrophysics Data System (ADS)

O'Kane, Christopher A. J.; Duffy, Kevin J.; Page, Bruce R.; Macdonald, David W.

2011-09-01

The large spectrum of existing literature on browser-woodland dynamics, both from savanna and temperate biomes, converges towards concluding that all browsers importantly impact woody plants. In this context a crucial question in the current debate about reintroducing elephant culling, is whether the long-term effects of elephants and mesobrowsers are similar. If the two groups impact the same woody species in the same habitats, sufficiently high biomass-densities of mesobrowsers may, following removal of elephants, continue to heavily impact earlier life-history stages of the same suite of woody plants that elephant impacted, preventing these species from maturing. Thus, as existing mature trees die from natural causes and fade from the system, a similar end-point for woodland structure and composition is achieved. We reviewed 49 years of literature on the savanna browser guild, performing a meta-analysis on the disparate data on the guild's woody plant species use (3677 records) and habitat use (894 records). Mesobrowsers' and elephants' extensive overlap in habitat use and staple woody species diet, together with evidence of their influencing each others' abundance and of their dietary separation increasing with resource depletion, implies that the two groups impact the same core woody species in the same habitats. It therefore seems probable that high biomass-density mesobrowsers may have a long-term substitutive effect to that of elephant on woodland dynamics. Consequently management wanting a particular state of savanna woodland, should consider the biomass-density of both groups, rather than just focus on the system's perceived keystone species. Such principles may also apply to temperate and other systems.

Comparing ungulate dietary proxies using discriminant function analysis.

PubMed

Fraser, Danielle; Theodor, Jessica M

2011-12-01

A variety of tooth-wear and morphological dietary proxies have been proposed for ungulates. In turn, they have been applied to fossil specimens with the purpose of reconstructing the diets of extinct taxa. Although these dietary proxies have been used in isolation and in combination, a consistent set of statistical analyses has never been applied to all of the available datasets. The purpose of this study is to determine how well the most commonly used dietary proxies classify ungulates as browsers, grazers, and mixed feeders individually and in combination. Discriminant function analysis is applied to individual dietary proxies (hypsodonty, mesowear, microwear, and several cranial dietary proxies) and to combinations thereof to compare rates of successful dietary classification. In general, the tooth-wear dietary proxies (mesowear and microwear) perform better than morphological dietary proxies, though none are strong proxies in isolation. The success rates of the cranial dietary proxies are not increased substantially when ruminants and bovids are analyzed separately, and significance among the three dietary guilds is reduced when controlling for phylogenetic relatedness. The combination of hypsodonty, mesowear, and microwear is found to have a high rate of successful dietary classification, but a combination of all commonly used proxies increases the success rate to 100%. In most cases, mixed feeders bear the greatest resemblance to browsers suggesting that a morphology intermediate to browsers and grazers may represent a fitness valley resulting from the inability to exploit both browse and graze efficiently. These results are important for future paleoecological studies and should be used as a guide for determining which dietary proxies are appropriate to the research question. Copyright © 2011 Wiley-Liss, Inc.

The GIS portal based on JSR168 portlet technology and WSRP

NASA Astrophysics Data System (ADS)

Wu, Defu; Chen, Nengcheng; Zhu, Xinyan; Gong, Jianya

2005-10-01

A portal is a powerful Web site that gives users a single point of access to applications and information in a unified interface. A portal lets users view each application or web page in its own window, called a portlet, and a single browser window can contain multiple portlets. The portlet based on JSP168&WSRP is a new technology for interactive, user-facing web services that plug and play with portals. Thanks to the development of Portal&Web GIS, the GIS Poratl is focused on more and more by the researcheres. This paper studies the GIS Portal defined by ESRI and analyzes the development's status, compares with the commercial Portal and points out the great shortage of the ESRI GIS Portal: lack in Personal content and UI. Therefor this paper goes into depth on the discussion of design and implementation scheme of real GIS Portal, and proposes the new idea of developing customized, plug and play GIS Portal Module based on JSP168 Portlet technology and WSRP standard. This way can resolve the difficult problem of the GIS Portal on lacking of content and customization function. According to this idea, this paper plans to use the JaveBeans provided by GeoSurf to develop visual portlet which have basic operating fuction of GIS. Finally deploys the GIS Portal uing the WebLogic Portal.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

A 12,000 year record of changes in herbivore niche separation and palaeoclimate (Wonderwerk Cave, South Africa)

NASA Astrophysics Data System (ADS)

Ecker, Michaela; Brink, James; Horwitz, Liora Kolska; Scott, Louis; Lee-Thorp, Julia A.

2018-01-01

The large mammalian fauna of southern Africa is characterised by strong niche separation into grazer and browser species, with few falling into the intermediate mixed-feeder niche. Moreover, the modern fauna is reduced in species diversity compared to the Pleistocene, following the extinction of several specialized grazers in the late Pleistocene and early Holocene. How did this state develop, and how might it be connected to climatic change during the Holocene? To better understand this development, we obtained extensive carbon and oxygen stable light isotope data from herbivore tooth enamel samples from Wonderwerk Cave, South Africa, spanning about 12,000-500 cal. BP. This is a unique dataset since it is the only site in the southern Kalahari with a robust chronometric record and well-preserved faunal remains for the last 12,000 years without significant gaps. Combining the stable isotopes with pollen and micromammal data from Wonderwerk Cave, we have explored shifts in the proportions of C3 and C4 plants and moisture availability. Although climate remained generally semi-arid for much of this period, the results show significant hydrological and vegetation shifts in the sequence, particularly with the strengthening of summer rainfall in the mid-Holocene. The results for the sixteen herbivore species reveal a reinforcement of the grazer-browser niche partitioning through the Holocene and shows how niche specialization follows changes in local vegetation composition. In the light of this reconstruction of the local ecology we discuss grazer extinctions, human adaptations, and the drivers behind climatic changes in the summer rainfall zone of southern Africa.

Design of the beryllium window for Brookhaven Linac Isotope Producer

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

Nayak, S.; Mapes, M.; Raparia, D.

2015-11-01

In the Brookhaven Linac Isotope Producer (BLIP) beam line, there were two Beryllium (Be) windows with an air gap to separate the high vacuum upstream side from low vacuum downstream side. There had been frequent window failures in the past which affected the machine productivity and increased the radiation dose received by workers due to unplanned maintenance. To improve the window life, design of Be window is reexamined. Detailed structural and thermal simulations are carried out on Be window for different design parameters and loading conditions to come up with better design to improve the window life. The new designmore » removed the air gap and connect the both beam lines with a Be window in-between. The new design has multiple advantages such as 1) reduces the beam energy loss (because of one window with no air gap), 2) reduces air activation due to nuclear radiation and 3) increased the machine reliability as there is no direct pressure load during operation. For quick replacement of this window, an aluminum bellow coupled with load binder was designed. There hasn’t been a single window failure since the new design was implemented in 2012.« less

Electricity Data Browser

EIA Publications

The Electricity Data Browser shows generation, consumption, fossil fuel receipts, stockpiles, retail sales, and electricity prices. The data appear on an interactive web page and are updated each month. The Electricity Data Browser includes all the datasets collected and published in EIA's Electric Power Monthly and allows users to perform dynamic charting of data sets as well as map the data by state. The data browser includes a series of reports that appear in the Electric Power Monthly and allows readers to drill down to plant level statistics, where available. All images and datasets are available for download. Users can also link to the data series in EIA's Application Programming Interface (API). An API makes our data machine-readable and more accessible to users.

Theoretical vibro-acoustic modeling of acoustic noise transmission through aircraft windows

NASA Astrophysics Data System (ADS)

Aloufi, Badr; Behdinan, Kamran; Zu, Jean

2016-06-01

In this paper, a fully vibro-acoustic model for sound transmission across a multi-pane aircraft window is developed. The proposed model is efficiently applied for a set of window models to perform extensive theoretical parametric studies. The studied window configurations generally simulate the passenger window designs of modern aircraft classes which have an exterior multi-Plexiglas pane, an interior single acrylic glass pane and a dimmable glass ("smart" glass), all separated by thin air cavities. The sound transmission loss (STL) characteristics of three different models, triple-, quadruple- and quintuple-paned windows identical in size and surface density, are analyzed for improving the acoustic insulation performances. Typical results describing the influence of several system parameters, such as the thicknesses, number and spacing of the window panes, on the transmission loss are then investigated. In addition, a comparison study is carried out to evaluate the acoustic reduction capability of each window model. The STL results show that the higher frequencies sound transmission loss performance can be improved by increasing the number of window panels, however, the low frequency performance is decreased, particularly at the mass-spring resonances.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

UCSC genome browser: deep support for molecular biomedical research.

PubMed

Mangan, Mary E; Williams, Jennifer M; Lathe, Scott M; Karolchik, Donna; Lathe, Warren C

2008-01-01

The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration. Data can be queried with sequences. Complex database queries are also easily achieved with the Table Browser interface. Associated tools permit additional query types or access to additional data sources such as images of in situ localizations. Support for solving researcher's issues is provided with active discussion mailing lists and by providing updated training materials. The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu).

Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers

PubMed Central

Chiang, Michael F.; Hwang, John C.; Yu, Alexander C.; Casper, Daniel S.; Cimino, James J.; Starren, Justin

2006-01-01

SNOMED-CT has been promoted as a reference terminology for electronic health record (EHR) systems. Many important EHR functions are based on the assumption that medical concepts will be coded consistently by different users. This study is designed to measure agreement among three physicians using two SNOMED-CT terminology browsers to encode 242 concepts from five ophthalmology case presentations in a publicly-available clinical journal. Inter-coder reliability, based on exact coding match by each physician, was 44% using one browser and 53% using the other. Intra-coder reliability testing revealed that a different SNOMED-CT code was obtained up to 55% of the time when the two browsers were used by one user to encode the same concept. These results suggest that the reliability of SNOMED-CT coding is imperfect, and may be a function of browsing methodology. A combination of physician training, terminology refinement, and browser improvement may help increase the reproducibility of SNOMED-CT coding. PMID:17238317

Optimization and comparison of simultaneous and separate acquisition protocols for dual isotope myocardial perfusion SPECT

PubMed Central

Ghaly, Michael; Links, Jonathan M; Frey, Eric C

2015-01-01

Dual-isotope simultaneous-acquisition (DISA) rest-stress myocardial perfusion SPECT (MPS) protocols offer a number of advantages over separate acquisition. However, crosstalk contamination due to scatter in the patient and interactions in the collimator degrade image quality. Compensation can reduce the effects of crosstalk, but does not entirely eliminate image degradations. Optimizing acquisition parameters could further reduce the impact of crosstalk. In this paper we investigate the optimization of the rest Tl-201 energy window width and relative injected activities using the ideal observer (IO), a realistic digital phantom population and Monte Carlo (MC) simulated Tc-99m and Tl-201 projections as a means to improve image quality. We compared performance on a perfusion defect detection task for Tl-201 acquisition energy window widths varying from 4 to 40 keV centered at 72 keV for a camera with a 9% energy resolution. We also investigated 7 different relative injected activities, defined as the ratio of Tc-99m and Tl-201 activities, while keeping the total effective dose constant at 13.5 mSv. For each energy window and relative injected activity, we computed the IO test statistics using a Markov chain Monte Carlo (MCMC) method for an ensemble of 1,620 triplets of fixed and reversible defect-present, and defect-absent noisy images modeling realistic background variations. The volume under the 3-class receiver operating characteristic (ROC) surface (VUS) was estimated and served as the figure of merit. For simultaneous acquisition, the IO suggested that relative Tc-to-Tl injected activity ratios of 2.6–5 and acquisition energy window widths of 16–22% were optimal. For separate acquisition, we observed a broad range of optimal relative injected activities from 2.6 to 12.1 and acquisition energy window of widths 16–22%. A negative correlation between Tl-201 injected activity and the width of the Tl-201 energy window was observed in these ranges. The results also suggested that DISA methods could potentially provide image quality as good as that obtained with separate acquisition protocols. We compared observer performance for the optimized protocols and the current clinical protocol using separate acquisition. The current clinical protocols provided better performance at a cost of injecting the patient with approximately double the injected activity of Tc-99m and Tl-201, resulting in substantially increased radiation dose. PMID:26083239

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

Potential for Bias When Estimating Critical Windows for Air Pollution in Children's Health.

PubMed

Wilson, Ander; Chiu, Yueh-Hsiu Mathilda; Hsu, Hsiao-Hsien Leon; Wright, Robert O; Wright, Rosalind J; Coull, Brent A

2017-12-01

Evidence supports an association between maternal exposure to air pollution during pregnancy and children's health outcomes. Recent interest has focused on identifying critical windows of vulnerability. An analysis based on a distributed lag model (DLM) can yield estimates of a critical window that are different from those from an analysis that regresses the outcome on each of the 3 trimester-average exposures (TAEs). Using a simulation study, we assessed bias in estimates of critical windows obtained using 3 regression approaches: 1) 3 separate models to estimate the association with each of the 3 TAEs; 2) a single model to jointly estimate the association between the outcome and all 3 TAEs; and 3) a DLM. We used weekly fine-particulate-matter exposure data for 238 births in a birth cohort in and around Boston, Massachusetts, and a simulated outcome and time-varying exposure effect. Estimates using separate models for each TAE were biased and identified incorrect windows. This bias arose from seasonal trends in particulate matter that induced correlation between TAEs. Including all TAEs in a single model reduced bias. DLM produced unbiased estimates and added flexibility to identify windows. Analysis of body mass index z score and fat mass in the same cohort highlighted inconsistent estimates from the 3 methods. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Space station proximity operations windows: Human factors design guidelines

NASA Technical Reports Server (NTRS)

Haines, Richard F.

1987-01-01

Proximity operations refers to all activities outside the Space Station which take place within a 1-km radius. Since there will be a large number of different operations involving manned and unmanned vehicles, single- and multiperson crews, automated and manually controlled flight, a wide variety of cargo, and construction/repair activities, accurate and continuous human monitoring of these operations from a specially designed control station on Space Station will be required. Total situational awareness will be required. This paper presents numerous human factors design guidelines and related background information for control windows which will support proximity operations. Separate sections deal with natural and artificial illumination geometry; all basic rendezvous vector approaches; window field-of-view requirements; window size; shape and placement criteria; window optical characteristics as they relate to human perception; maintenance and protection issues; and a comprehensive review of windows installed on U.S. and U.S.S.R. manned vehicles.

Modeling and experimental investigation of x-ray spectra from a liquid metal anode x-ray tube

NASA Astrophysics Data System (ADS)

David, Bernd R.; Thran, Axel; Eckart, Rainer

2004-11-01

This paper presents simulated and measured spectra of a novel type of x-ray tube. The bremsstrahlung generating principle of this tube is based on the interaction of high energetic electrons with a turbulently flowing liquid metal separated from the vacuum by a thin window. We simulated the interaction of 50-150 keV electrons with liquid metal targets composed of the elements Ga, In, Sn, as well as the solid elements C, W and Re used for the electron windows. We obtained x-ray spectra and energy loss curves for various liquid metal/window combinations and thicknesses of the window material. In terms of optimum heat transport a thin diamond window in combination with the liquid metal GaInSn is the best suited system. If photon flux is the optimization criteria, thin tungsten/rhenium windows cooled by GaInSn should be preferred.

Java-based remote viewing and processing of nuclear medicine images: toward "the imaging department without walls".

PubMed

Slomka, P J; Elliott, E; Driedger, A A

2000-01-01

In nuclear medicine practice, images often need to be reviewed and reports prepared from locations outside the department, usually in the form of hard copy. Although hard-copy images are simple and portable, they do not offer electronic data search and image manipulation capabilities. On the other hand, picture archiving and communication systems or dedicated workstations cannot be easily deployed at numerous locations. To solve this problem, we propose a Java-based remote viewing station (JaRViS) for the reading and reporting of nuclear medicine images using Internet browser technology. JaRViS interfaces to the clinical patient database of a nuclear medicine workstation. All JaRViS software resides on a nuclear medicine department server. The contents of the clinical database can be searched by a browser interface after providing a password. Compressed images with the Java applet and color lookup tables are downloaded on the client side. This paradigm does not require nuclear medicine software to reside on remote computers, which simplifies support and deployment of such a system. To enable versatile reporting of the images, color tables and thresholds can be interactively manipulated and images can be displayed in a variety of layouts. Image filtering, frame grouping (adding frames), and movie display are available. Tomographic mode displays are supported, including gated SPECT. The time to display 14 lung perfusion images in 128 x 128 matrix together with the Java applet and color lookup tables over a V.90 modem is <1 min. SPECT and PET slice reorientation is interactive (<1 s). JaRViS could run on a Windows 95/98/NT or a Macintosh platform with Netscape Communicator or Microsoft Intemet Explorer. The performance of Java code for bilinear interpolation, cine display, and filtering approaches that of a standard imaging workstation. It is feasible to set up a remote nuclear medicine viewing station using Java and an Internet or intranet browser. Images can be made easily and cost-effectively available to referring physicians and ambulatory clinics within and outside of the hospital, providing a convenient alternative to film media. We also find this system useful in home reporting of emergency procedures such as lung ventilation-perfusion scans or dynamic studies.

Presentation and response timing accuracy in Adobe Flash and HTML5/JavaScript Web experiments.

PubMed

Reimers, Stian; Stewart, Neil

2015-06-01

Web-based research is becoming ubiquitous in the behavioral sciences, facilitated by convenient, readily available participant pools and relatively straightforward ways of running experiments: most recently, through the development of the HTML5 standard. Although in most studies participants give untimed responses, there is a growing interest in being able to record response times online. Existing data on the accuracy and cross-machine variability of online timing measures are limited, and generally they have compared behavioral data gathered on the Web with similar data gathered in the lab. For this article, we took a more direct approach, examining two ways of running experiments online-Adobe Flash and HTML5 with CSS3 and JavaScript-across 19 different computer systems. We used specialist hardware to measure stimulus display durations and to generate precise response times to visual stimuli in order to assess measurement accuracy, examining effects of duration, browser, and system-to-system variability (such as across different Windows versions), as well as effects of processing power and graphics capability. We found that (a) Flash and JavaScript's presentation and response time measurement accuracy are similar; (b) within-system variability is generally small, even in low-powered machines under high load; (c) the variability of measured response times across systems is somewhat larger; and (d) browser type and system hardware appear to have relatively small effects on measured response times. Modeling of the effects of this technical variability suggests that for most within- and between-subjects experiments, Flash and JavaScript can both be used to accurately detect differences in response times across conditions. Concerns are, however, noted about using some correlational or longitudinal designs online.

Electromagnetic radiation detector

DOEpatents

Benson, Jay L.; Hansen, Gordon J.

1976-01-01

An electromagnetic radiation detector including a collimating window, a cathode member having a photoelectric emissive material surface angularly disposed to said window whereby radiation is impinged thereon at acute angles, an anode, separated from the cathode member by an evacuated space, for collecting photoelectrons emitted from the emissive cathode surface, and a negatively biased, high transmissive grid disposed between the cathode member and anode.

Exploratory Visual Analytics of a Dynamically Built Network of Nodes in a WebGL-Enabled Browser

DTIC Science & Technology

2014-01-01

dimensionality reduction, feature extraction, high-dimensional data, t-distributed stochastic neighbor embedding, neighbor retrieval visualizer, visual...WebGL-enabled rendering is supported natively by browsers such as the latest Mozilla Firefox , Google Chrome, and Microsoft Internet Explorer 11. At the...appropriate names. The resultant 26-node network is displayed in a Mozilla Firefox browser in figure 2 (also see appendix B). 3 Figure 1. The

The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.

PubMed

Kapopoulou, Adamandia; Lew, Jocelyne M; Cole, Stewart T

2011-01-01

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities. Copyright © 2010 Elsevier Ltd. All rights reserved.

Intelligent windows using new thermotropic layers with long-term stability

NASA Astrophysics Data System (ADS)

Watanabe, Haruo

1995-08-01

This paper concerns the autonomous responsive type light adjustment window (intelligent windows) among smart windows which adjust the light upon receiving environmental energy. More specifically, this is a thermotropic window panel that laminates and seals a new type of highly viscous polymer aqueous solution gel. A conventional thermotropic window panel has never been put to practical use since the reversible change between the colorless, transparent state (water-clear) and translucent scattered state (paper-white) with uniformity was not possible. The change involved phase separation and generated non-uniformity. The author, after fundamental studies of hydrophobic bonding, successfully solved the problem by developing a polymer aqueous solution gel with amphiphatic molecule as the third component in addition to water and water-soluble polymer with hydrophobic radical, based on the molecular spacer concept. In addition, the author established peripheral technologies and succeeded in experimentally fabricating a panel type 'Affinity's Intelligent Window (AIW)' that has attained the level of practical use.

X-Windows PVT Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Process Validation Table (PVT) Widget Class ( Class is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing network registration services for Information Sharing Protocol (ISP) graphical-user-interface (GUI) computer programs. Heretofore, ISP PVT programming tasks have required many method calls to identify, query, and interpret the connections and messages exchanged between a client and a PVT server. Normally, programmers have utilized direct access to UNIX socket libraries to implement the PVT protocol queries, necessitating the use of many lines of source code to perform frequent tasks. Now, the X-Windows PVT Widget Class encapsulates ISP client server network registration management tasks within the framework of an X Windows widget. Use of the widget framework enables an X Windows GUI program to interact with PVT services in an abstract way and in the same manner as that of other graphical widgets, making it easier to program PVT clients. Wrapping the PVT services inside the widget framework enables a programmer to treat a PVT server interface as though it were a GUI. Moreover, an alternate subclass could implement another service in a widget of the same type. This program was written by Matthew R. Barry of United Space Alliance for Johnson Space Center. For further information, contact the Johnson Technology Transfer Office at (281) 483-3809. MSC-23582 Shuttle Data Center File- Processing Tool in Java A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67

PubMed Central

2010-01-01

Introduction Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. Methods The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n = 50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n = 50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. Results The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r = 0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n = 123, P = 0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. Conclusions We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens. PMID:20663194

ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.

PubMed

Tuominen, Vilppu J; Ruotoistenmäki, Sanna; Viitanen, Arttu; Jumppanen, Mervi; Isola, Jorma

2010-01-01

Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n = 50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n = 50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r = 0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n = 123, P = 0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.

Multimedia proceedings of the 10th Office Information Technology Conference

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

Hudson, B.

1993-09-10

The CD contains the handouts for all the speakers, demo software from Apple, Adobe, Microsoft, and Zylabs, and video movies of the keynote speakers. Adobe Acrobat is used to provide full-fidelity retrieval of the speakers` slides and Apple`s Quicktime for Macintosh and Windows is used for video playback. ZyIndex is included for Windows users to provide a full-text search engine for selected documents. There are separately labelled installation and operating instructions for Macintosh and Windows users and some general materials common to both sets of users.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

NASA Astrophysics Data System (ADS)

Naito, O.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

A user-centred evaluation framework for the Sealife semantic web browsers

PubMed Central

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-01-01

Background Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. Methods This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. Results It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Conclusion Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues. PMID:19796398

A user-centred evaluation framework for the Sealife semantic web browsers.

PubMed

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-10-01

Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

A browser-based event display for the CMS experiment at the LHC

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

Hategan, M.; McCauley, T.; Nguyen, P.

2012-01-01

The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d.more » The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.« less

Evaluating Web accessibility at different processing phases

NASA Astrophysics Data System (ADS)

Fernandes, N.; Lopes, R.; Carriço, L.

2012-09-01

Modern Web sites use several techniques (e.g. DOM manipulation) that allow for the injection of new content into their Web pages (e.g. AJAX), as well as manipulation of the HTML DOM tree. This has the consequence that the Web pages that are presented to users (i.e. after browser processing) are different from the original structure and content that is transmitted through HTTP communication (i.e. after browser processing). This poses a series of challenges for Web accessibility evaluation, especially on automated evaluation software. This article details an experimental study designed to understand the differences posed by accessibility evaluation after Web browser processing. We implemented a Javascript-based evaluator, QualWeb, that can perform WCAG 2.0 based accessibility evaluations in the two phases of browser processing. Our study shows that, in fact, there are considerable differences between the HTML DOM trees in both phases, which have the consequence of having distinct evaluation results. We discuss the impact of these results in the light of the potential problems that these differences can pose to designers and developers that use accessibility evaluators that function before browser processing.

Theoretical and experimental investigation on magneto-hydrodynamics of plasma window

DOE PAGES

Wang, S. Z.; Zhu, K.; Huang, S.; ...

2016-01-05

As a new device, we designed plasma window to use plasma discharge to separate atmosphere from vacuum with high difference of pressure. It has many excellent properties, being able to be used as available passage for ion beam with negligible energy loss, also impervious to radiation damage and thermal damage. Normally beam focusing by accelerators is not that easy to achieve within channel of small cross section. 10 mm diameter plasma window's experimental realization could contribute to its further application in accelerator system. In this paper, 10 mm diameter 60 mm long plasma window has first been designed and managedmore » to generate arc discharge with argon gas experimentally. Our result proves that it has the ability to separate at least 28.8 kPa (not the upper limit) from 360 Pa with 50 A direct current and 2.5 kW power supplied. Current increase leads to linear inlet pressure increase obviously, while it has less impact on outlet pressure and voltage, coming to the conclusion that the higher current of plasma discharge, the larger pressure difference it creates. Furthermore, theoretical analysis of 10 mm diameter plasma window in axis symmetrical configuration using argon also has been provided, in which a numerical 2D FLUENT-based magneto-hydrodynamic simulation model is settled. It has a good agreement with experimental result on voltage and mass flow rate when inlet pressure is increased.« less

PubMedReco: A Real-Time Recommender System for PubMed Citations.

PubMed

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

The Impact of Changing Cloud Cover on the High Arctic's Primary Cooling-to-space Windows

NASA Astrophysics Data System (ADS)

Mariani, Zen; Rowe, Penny; Strong, Kimberly; Walden, Von; Drummond, James

2014-05-01

In the Arctic, most of the infrared energy emitted by the surface escapes to space in two atmospheric windows at 10 and 20 μm. As the Arctic warms, the 20 μm cooling-to-space window becomes increasingly opaque (or "closed"), trapping more surface infrared radiation in the atmosphere, with implications for the Arctic's radiative energy balance. Since 2006, the Canadian Network for the Detection of Atmospheric Change (CANDAC) has measured downwelling infrared radiance with an Atmospheric Emitted Radiance Interferometer (AERI) at the Polar Environment Atmospheric Research Laboratory (PEARL) at Eureka, Canada, providing the first long-term measurements of the 10 and 20 μm windows in the high Arctic. In this work, measurements of the distribution of downwelling 10 and 20 µm brightness temperatures at Eureka are separated based on cloud cover, providing a comparison to an existing climatology from the Southern Great Plains (SGP). Measurements of the downwelling radiance at both 10 and 20 μm exhibit strong seasonal variability as a result of changes in temperature and water vapour, in addition to variability with cloud cover. When separated by season, brightness temperatures in the 20 µm window are found to be independent of cloud thickness in the summertime, indicating that this window is closed in the summer. Radiance trends in three-month averages are positive and are significantly larger (factor > 5) than the trends detected at the SGP, indicating that changes in the downwelling radiance are accelerated in the high Arctic compared to lower latitudes. This statistically significant increase (> 5% / yr) in radiance at 10 μm occurs only when the 20 μm window is mostly transparent, or "open" (i.e., in all seasons except summer), and may have long-term consequences, particularly as warmer temperatures and increased water vapour "close" the dirty window for a prolonged period. These surface-based measurements of radiative forcing can be used to quantify changes in the high-Arctic energy budget and evaluate general circulation model simulations.

Shift in black rhinoceros diet in the presence of elephant: evidence for competition?

PubMed

Landman, Marietjie; Schoeman, David S; Kerley, Graham I H

2013-01-01

In African large herbivore assemblages, megaherbivores dominate the biomass and utilise the greatest share of available resources. Consequently, they are considered a separate trophic guild that structures the food niches of coexisting large herbivores. However, there exists little empirical evidence on how food resources are shared within this guild, and none for direct competition for food between megaherbivores. Using the histological analysis of faeces, we explore this phenomenon for African elephant Loxodonta africana and black rhinoceros Diceros bicornis in the Addo Elephant National Park, South Africa, where the accumulated impacts of elephant have reduced browse availability. Despite being unable to generalise beyond our study sites, our observations support the predictions of competition theory (as opposed to optimality theory) by showing (1) a clear seasonal separation in resource use between these megaherbivores that increased as resource availability declined, and (2) rhinoceros changed their selectivity in the absence of elephant (using an adjacent site) by expanding and shifting their diet along the grass-browse continuum, and in relation to availability. Although black rhinoceros are generally considered strict browsers, the most significant shift in diet occurred as rhinoceros increased their preferences for grasses in the presence of elephant. We speculate that the lack of specialised grazing adaptations may increase foraging costs in rhinoceros, through reduced harvest- and handling-efficiencies of grasses. In the short-term, this may be off-set by an enhanced tolerance for low quality food and by seasonally mobilising fat reserves; however, the long-term fitness consequences require further study. Our data suggest that managing elephant at high densities may compromise the foraging opportunities of coexisting browsers. This may be particularly important in small, fenced areas and overlapping preferred habitats where impacts intensify.

Investigation on the Frequency Allocation for Radio Astronomy at the L Band

NASA Astrophysics Data System (ADS)

Abidin, Z. Z.; Umar, R.; Ibrahim, Z. A.; Rosli, Z.; Asanok, K.; Gasiprong, N.

2013-09-01

In this paper, the frequency allocation reserved for radio astronomy in the L band set by the International Telecommunication Union (ITU), which is between 1400 and 1427 MHz, is reviewed. We argue that the nearby frequencies are still very important for radio astronomers on the ground by investigating radio objects (H i sources) around 1300-1500 MHz. The L-band window is separated into a group of four windows, namely 1400-1427 MHz (window A), 1380-1400 MHz (window B), 1350-1380 MHz (window C), and 1300-1350 MHz (window D). These windows are selected according to their redshifts from a rest frequency for hydrogen spectral line at 1420.4057 MHz. Radio objects up to z ≈ 0.1 or frequency down to 1300 MHz are examined. We argue that since window B has important radio objects within the four windows, this window should also be given to radio astronomy. They are galaxies, spiral galaxies, and galaxy clusters. This underlines the significance of window B for radio astronomers on the ground. By investigating the severeness of radio frequency interference (RFI) within these windows, we have determined that window B still has significant, consistent RFI. The main RFI sources in the four windows have also been identified. We also found that the Department of Civil Aviation of Malaysia is assigned a frequency range of 1215-1427 MHz, which is transmitted within the four windows and inside the protected frequency for radio astronomy. We also investigated the RFI in the four windows on proposed sites of future radio astronomy observatories in Malaysia and Thailand and found the two best sites as Universiti Pendidikan Sultan Idris (UPSI) and Ubon Ratchathani, respectively. It has also been determined that RFI in window B increases with population density.

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2013 CFR

2013-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2014 CFR

2014-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.

PubMed

Sakurai, Nozomu; Ara, Takeshi; Kanaya, Shigehiko; Nakamura, Yukiko; Iijima, Yoko; Enomoto, Mitsuo; Motegi, Takeshi; Aoki, Koh; Suzuki, Hideyuki; Shibata, Daisuke

2013-01-15

High-accuracy mass values detected by high-resolution mass spectrometry analysis enable prediction of elemental compositions, and thus are used for metabolite annotations in metabolomic studies. Here, we report an application of a relational database to significantly improve the rate of elemental composition predictions. By searching a database of pre-calculated elemental compositions with fixed kinds and numbers of atoms, the approach eliminates redundant evaluations of the same formula that occur in repeated calculations with other tools. When our approach is compared with HR2, which is one of the fastest tools available, our database search times were at least 109 times shorter than those of HR2. When a solid-state drive (SSD) was applied, the search time was 488 times shorter at 5 ppm mass tolerance and 1833 times at 0.1 ppm. Even if the search by HR2 was performed with 8 threads in a high-spec Windows 7 PC, the database search times were at least 26 and 115 times shorter without and with the SSD. These improvements were enhanced in a low spec Windows XP PC. We constructed a web service 'MFSearcher' to query the database in a RESTful manner. Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported. sakurai@kazusa.or.jp Supplementary data are available at Bioinformatics online.

docBUILDER - Building Your Useful Metadata for Earth Science Data and Services.

NASA Astrophysics Data System (ADS)

Weir, H. M.; Pollack, J.; Olsen, L. M.; Major, G. R.

2005-12-01

The docBUILDER tool, created by NASA's Global Change Master Directory (GCMD), assists the scientific community in efficiently creating quality data and services metadata. Metadata authors are asked to complete five required fields to ensure enough information is provided for users to discover the data and related services they seek. After the metadata record is submitted to the GCMD, it is reviewed for semantic and syntactic consistency. Currently, two versions are available - a Web-based tool accessible with most browsers (docBUILDERweb) and a stand-alone desktop application (docBUILDERsolo). The Web version is available through the GCMD website, at http://gcmd.nasa.gov/User/authoring.html. This version has been updated and now offers: personalized templates to ease entering similar information for multiple data sets/services; automatic population of Data Center/Service Provider URLs based on the selected center/provider; three-color support to indicate required, recommended, and optional fields; an editable text window containing the XML record, to allow for quick editing; and improved overall performance and presentation. The docBUILDERsolo version offers the ability to create metadata records on a computer wherever you are. Except for installation and the occasional update of keywords, data/service providers are not required to have an Internet connection. This freedom will allow users with portable computers (Windows, Mac, and Linux) to create records in field campaigns, whether in Antarctica or the Australian Outback. This version also offers a spell-checker, in addition to all of the features found in the Web version.

Bluff-body drag reduction using a deflector

NASA Astrophysics Data System (ADS)

Fourrié, Grégoire; Keirsbulck, Laurent; Labraga, Larbi; Gilliéron, Patrick

2011-02-01

A passive flow control on a generic car model was experimentally studied. This control consists of a deflector placed on the upper edge of the model rear window. The study was carried out in a wind tunnel at Reynolds numbers based on the model height of 3.1 × 105 and 7.7 × 105. The flow was investigated via standard and stereoscopic particle image velocimetry, Kiel pressure probes and surface flow visualization. The aerodynamic drag was measured using an external balance and calculated using a wake survey method. Drag reductions up to 9% were obtained depending on the deflector angle. The deflector increases the separated region on the rear window. The results show that when this separated region is wide enough, it disrupts the development of the counter-rotating longitudinal vortices appearing on the lateral edges of the rear window. The current study suggests that flow control on such geometries should consider all the flow structures that contribute to the model wake flow.

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

Material separation in x-ray CT with energy resolved photon-counting detectors

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

Wang Xiaolan; Meier, Dirk; Taguchi, Katsuyuki

Purpose: The objective of the study was to demonstrate that, in x-ray computed tomography (CT), more than two types of materials can be effectively separated with the use of an energy resolved photon-counting detector and classification methodology. Specifically, this applies to the case when contrast agents that contain K-absorption edges in the energy range of interest are present in the object. This separation is enabled via the use of recently developed energy resolved photon-counting detectors with multiple thresholds, which allow simultaneous measurements of the x-ray attenuation at multiple energies. Methods: To demonstrate this capability, we performed simulations and physical experimentsmore » using a six-threshold energy resolved photon-counting detector. We imaged mouse-sized cylindrical phantoms filled with several soft-tissue-like and bone-like materials and with iodine-based and gadolinium-based contrast agents. The linear attenuation coefficients were reconstructed for each material in each energy window and were visualized as scatter plots between pairs of energy windows. For comparison, a dual-kVp CT was also simulated using the same phantom materials. In this case, the linear attenuation coefficients at the lower kVp were plotted against those at the higher kVp. Results: In both the simulations and the physical experiments, the contrast agents were easily separable from other soft-tissue-like and bone-like materials, thanks to the availability of the attenuation coefficient measurements at more than two energies provided by the energy resolved photon-counting detector. In the simulations, the amount of separation was observed to be proportional to the concentration of the contrast agents; however, this was not observed in the physical experiments due to limitations of the real detector system. We used the angle between pairs of attenuation coefficient vectors in either the 5-D space (for non-contrast-agent materials using energy resolved photon-counting acquisition) or a 2-D space (for contrast agents using energy resolved photon-counting acquisition and all materials using dual-kVp acquisition) as a measure of the degree of separation. Compared to dual-kVp techniques, an energy resolved detector provided a larger separation and the ability to separate different target materials using measurements acquired in different energy window pairs with a single x-ray exposure. Conclusions: We concluded that x-ray CT with an energy resolved photon-counting detector with more than two energy windows allows the separation of more than two types of materials, e.g., soft-tissue-like, bone-like, and one or more materials with K-edges in the energy range of interest. Separating material types using energy resolved photon-counting detectors has a number of advantages over dual-kVp CT in terms of the degree of separation and the number of materials that can be separated simultaneously.« less

Comparing Commercial WWW Browsers.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

Four commercial World Wide Web browsers are evaluated for features such as handling of WWW protocols and different URLs: FTP, Telnet, Gopher and WAIS, and e-mail and news; bookmark capabilities; navigation features; file management; and security support. (JKP)

US NDC Modernization Iteration E2 Prototyping Report: User Interface Framework

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

Lewis, Jennifer E.; Palmer, Melanie A.; Vickers, James Wallace

2014-12-01

During the second iteration of the US NDC Modernization Elaboration phase (E2), the SNL US NDC Modernization project team completed follow-on Rich Client Platform (RCP) exploratory prototyping related to the User Interface Framework (UIF). The team also developed a survey of browser-based User Interface solutions and completed exploratory prototyping for selected solutions. This report presents the results of the browser-based UI survey, summarizes the E2 browser-based UI and RCP prototyping work, and outlines a path forward for the third iteration of the Elaboration phase (E3).

Cockpit Window Edge Proximity Effects on Judgements of Horizon Vertical Displacement

NASA Technical Reports Server (NTRS)

Haines, R. F.

1984-01-01

To quantify the influence of a spatially fixed edge on vertical displacement threshold, twenty-four males (12 pilots, 12 non-pilots) were presented a series of forced choice, paired comparison trials in which a 32 deg arc wide, thin, luminous horizontal stimulus line moved smoothly downward through five angles from a common starting position within a three second-long period. The five angles were 1.4, 1.7, 2, 2.3, and 2.6 deg. Each angle was presented paired with itself and the other four angles in all combinations in random order. For each pair of trials the observer had to choose which trial possessed the largest displacement. A confidence response also was made. The independent variable was the angular separation between the lower edge of a stable 'window' aperture through which the stimulus was seen to move and the lowest position attained by the stimulus. It was found that vertical displacement accuracy is inversely related to the angle separating the stimulus and the fixed window edge (p = .05). In addition, there is a strong tendency for pilot confidence to be lower than that of non-pilots for each of the three angular separations. These results are discussed in erms of selected cockpit features and as they relate to how pilots judge changes in aircraft pitch attitude.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

PubMed Central

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-01-01

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. PMID:25990738

Theoretical and experimental investigation on magneto-hydrodynamics of plasma window

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

Wang, S. Z.; Zhu, K., E-mail: zhukun@pku.edu.cn; Huang, S.

2016-01-15

As a new device, plasma window has been designed to use plasma discharge to separate atmosphere from vacuum with high difference of pressure. It has many excellent properties, being able to be used as available passage for ion beam with negligible energy loss, also impervious to radiation damage and thermal damage. Normally beam focusing by accelerators is not that easy to achieve within channel of small cross section. 10 mm diameter plasma window's experimental realization could contribute to its further application in accelerator system. In this paper, 10 mm diameter 60 mm long plasma window has first been designed and managed to generatemore » arc discharge with argon gas experimentally. The result proves that it has the ability to separate at least 28.8 kPa (not the upper limit) from 360 Pa with 50 A direct current and 2.5 kW power supplied. Current increase leads to linear inlet pressure increase obviously, while it has less impact on outlet pressure and voltage, coming to the conclusion that the higher current of plasma discharge, the larger pressure difference it creates. Theoretical analysis of 10 mm diameter plasma window in axis symmetrical configuration using argon also has been provided, in which a numerical 2D FLUENT-based magneto-hydrodynamic simulation model is settled. It has a good agreement with experimental result on voltage and mass flow rate when inlet pressure is increased.« less

a Kml-Based Approach for Distributed Collaborative Interpretation of Remote Sensing Images in the Geo-Browser

NASA Astrophysics Data System (ADS)

Huang, L.; Zhu, X.; Guo, W.; Xiang, L.; Chen, X.; Mei, Y.

2012-07-01

Existing implementations of collaborative image interpretation have many limitations for very large satellite imageries, such as inefficient browsing, slow transmission, etc. This article presents a KML-based approach to support distributed, real-time, synchronous collaborative interpretation for remote sensing images in the geo-browser. As an OGC standard, KML (Keyhole Markup Language) has the advantage of organizing various types of geospatial data (including image, annotation, geometry, etc.) in the geo-browser. Existing KML elements can be used to describe simple interpretation results indicated by vector symbols. To enlarge its application, this article expands KML elements to describe some complex image processing operations, including band combination, grey transformation, geometric correction, etc. Improved KML is employed to describe and share interpretation operations and results among interpreters. Further, this article develops some collaboration related services that are collaboration launch service, perceiving service and communication service. The launch service creates a collaborative interpretation task and provides a unified interface for all participants. The perceiving service supports interpreters to share collaboration awareness. Communication service provides interpreters with written words communication. Finally, the GeoGlobe geo-browser (an extensible and flexible geospatial platform developed in LIESMARS) is selected to perform experiments of collaborative image interpretation. The geo-browser, which manage and visualize massive geospatial information, can provide distributed users with quick browsing and transmission. Meanwhile in the geo-browser, GIS data (for example DEM, DTM, thematic map and etc.) can be integrated to assist in improving accuracy of interpretation. Results show that the proposed method is available to support distributed collaborative interpretation of remote sensing image

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences.

PubMed

Inda, Márcia A; van Batenburg, Marinus F; Roos, Marco; Belloum, Adam S Z; Vasunin, Dmitry; Wibisono, Adianto; van Kampen, Antoine H C; Breit, Timo M

2008-08-08

Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential. Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs) in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment. As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the proof-of-principle for the modular e-Science based concept of integrative bioinformatics experimentation.

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

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

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.« less

ToxMystery

MedlinePlus

Accessibility - This is a link to an external javascript file that searchs for a flash browser plug-in and what version of the browser is being used. The javascript is functional ToxMystery uses Adobe Flash Player. If you cannot install Flash Player, please use ...

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services (Las Vegas, NV).

NEVADA GEOSPATICAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services Office (Las Vegas,...

South Platte Data Browser

EPA Science Inventory

The common goal among the developers of the South Platte River Basin Data Browser is to improve decision-making relative to environmental management through the development of applied research. The focus of the research has been to design an integrated system of landscape metri...

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) has developed the Nevada Geospatial Data Browser, a spatial data archive to centralize and distribute the geospatial data used to create the land cover, vertebrate habitat models, and land o...

SAN PEDRO GEODATA BROWSER

EPA Science Inventory

The San Pedro Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV). The goal of the Landscape Sciences Program is to improve decision-making relative to natural and human resource management through the development...

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

PubMed

Harper, Lisa C; Schaeffer, Mary L; Thistle, Jordan; Gardiner, Jack M; Andorf, Carson M; Campbell, Darwin A; Cannon, Ethalinda K S; Braun, Bremen L; Birkett, Scott M; Lawrence, Carolyn J; Sen, Taner Z

2011-01-01

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is 'Using the MaizeGDB Genome Browser', which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database

The UCSC genome browser: what every molecular biologist should know.

PubMed

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C

2009-10-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one's understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes

PubMed Central

Lee, Moon Young; Park, Chanjae; Berent, Robyn M.; Park, Paul J.; Fuchs, Robert; Syn, Hannah; Chin, Albert; Townsend, Jared; Benson, Craig C.; Redelman, Doug; Shen, Tsai-wei; Park, Jong Kun; Miano, Joseph M.; Sanders, Kenton M.; Ro, Seungil

2015-01-01

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies. PMID:26241044

Low functional redundancy among mammalian browsers in regulating an encroaching shrub (Solanum campylacanthum) in African savannah

PubMed Central

Pringle, Robert M.; Goheen, Jacob R.; Palmer, Todd M.; Charles, Grace K.; DeFranco, Elyse; Hohbein, Rhianna; Ford, Adam T.; Tarnita, Corina E.

2014-01-01

Large herbivorous mammals play an important role in structuring African savannahs and are undergoing widespread population declines and local extinctions, with the largest species being the most vulnerable. The impact of these declines on key ecological processes hinges on the degree of functional redundancy within large-herbivore assemblages, a subject that has received little study. We experimentally quantified the effects of three browser species (elephant, impala and dik-dik) on individual- and population-level attributes of Solanum campylacanthum (Solanum incanum sensu lato), an encroaching woody shrub, using semi-permeable exclosures that selectively removed different-sized herbivores. After nearly 5 years, shrub abundance was lowest where all browser species were present and increased with each successive species deletion. Different browsers ate the same plant species in different ways, thereby exerting distinct suites of direct and indirect effects on plant performance and density. Not all of these effects were negative: elephants and impala also dispersed viable seeds and indirectly reduced seed predation by rodents and insects. We integrated these diffuse positive effects with the direct negative effects of folivory using a simple population model, which reinforced the conclusion that different browsers have complementary net effects on plant populations, and further suggested that under some conditions, these net effects may even differ in direction. PMID:24789900

Reaction time effects in lab- versus Web-based research: Experimental evidence.

PubMed

Hilbig, Benjamin E

2016-12-01

Although Web-based research is now commonplace, it continues to spur skepticism from reviewers and editors, especially whenever reaction times are of primary interest. Such persistent preconceptions are based on arguments referring to increased variation, the limits of certain software and technologies, and a noteworthy lack of comparisons (between Web and lab) in fully randomized experiments. To provide a critical test, participants were randomly assigned to complete a lexical decision task either (a) in the lab using standard experimental software (E-Prime), (b) in the lab using a browser-based version (written in HTML and JavaScript), or (c) via the Web using the same browser-based version. The classical word frequency effect was typical in size and corresponded to a very large effect in all three conditions. There was no indication that the Web- or browser-based data collection was in any way inferior. In fact, if anything, a larger effect was obtained in the browser-based conditions than in the condition relying on standard experimental software. No differences between Web and lab (within the browser-based conditions) could be observed, thus disconfirming any substantial influence of increased technical or situational variation. In summary, the present experiment contradicts the still common preconception that reaction time effects of only a few hundred milliseconds cannot be detected in Web experiments.

Archive of Boomer Seismic Reflection Data Collected During USGS Cruises 01SCC01 and 01SCC02, Timbalier Bay and Offshore East Timbalier Island, Louisiana, June-August, 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Kindinger, Jack G.; Wiese, Dana S.

2003-01-01

In June, July, and August of 2001, the U.S. Geological Survey (USGS), in cooperation with the University of New Orleans (UNO), the U.S. Army Corps of Engineers, and the Louisiana Department of Natural Resources, conducted a shallow geophysical and sediment core survey of Timbalier Bay and the Gulf of Mexico offshore East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, trackline navigation maps, observers' logbooks, Geographic Information Systems (GIS) information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a filtered and gained digital Graphics Interchange Format (GIF) image of each seismic profile is provided. Please see Kulp and others (2002), Flocks and others (2003), and Kulp and others (in prep.) for further information about the sediment cores collected and the geophysical results. For convenience, a list of acronyms and abbreviations frequently used in this report is also included. This Digital Versatile Disc (DVD) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information using a web browser (i.e. Netscape, Internet Explorer). To access the information contained on this disc, open the file 'index.htm' located at the top level of the disc using a web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the Internet is available while viewing this DVD. The archived boomer seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes/index.html. Examples of SU processing scripts are provided in the BOOM.tar file located in the SU subfolder of the SOFTWARE folder located at the top level of this disc. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zihlman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, trackline navigation maps, logbooks, and formal metadata may be viewed with a web browser.

Archive of Chirp Seismic Reflection Data Collected During USGS Cruises 01SCC01 and 01SCC02, Timbalier Bay and Offshore East Timbalier Island, Louisiana, June 30 - July 9 and August 1 - 12, 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.; Kindinger, Jack G.

2003-01-01

In June, July, and August of 2001, the U.S. Geological Survey (USGS), in cooperation with the University of New Orleans, the U.S. Army Corps of Engineers, and the Louisiana Department of Natural Resources, conducted a shallow geophysical and sediment core survey of Timbalier Bay and the Gulf of Mexico offshore East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, trackline navigation maps, observers' logbooks, Geographic Information Systems (GIS) information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a gained digital Graphics Interchange Format (GIF) image of each seismic profile is provided. Please see Kulp and others (2002), Flocks and others (2003), and Kulp and others (in prep.) for further information about the sediment cores collected and the geophysical results. For convenience, a list of acronyms and abbreviations frequently used in this report is also included. This Digital Versatile Disc (DVD) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information using a web browser (i.e. Netscape, Internet Explorer). To access the information contained on these discs, open the file 'index.htm' located at the top level of each disc using a web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the internet is available while viewing these DVDs. The archived chirp seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes/index.html. Examples of SU processing scripts are provided in the CHIRP.tar file located in the SU subfolder of the SOFTWARE folder located at the top level of each disc. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zihlman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, trackline navigation maps, logbooks, and formal metadata may be viewed with a web browser.

Development of a Global Marine Environmental Library

DTIC Science & Technology

2010-06-01

Gulf. Marine Geology , 129, 237- 269. [4] Lerner, S., & Maffei, A. (2001). 4DGeoBrowser: A Web-based data browser and server for accessing and...Digital Library as a Catalyst for Collaboration: Voyages across Disciplinary and Institutional Boundaries with SIO Explorer; Digital Scholarship

South Platte River Basin Data Browser Report

EPA Science Inventory

The purpose of this data browser is to provide a spatial toolkit that delivers primary data that can be used for primary input information for assessments related to environmental endpoints, e.g. surface water hydrology and habitat mapping, related to ecosystem services. A neces...

A test of multiple correlation temporal window characteristic of non-Markov processes

NASA Astrophysics Data System (ADS)

Arecchi, F. T.; Farini, A.; Megna, N.

2016-03-01

We introduce a sensitive test of memory effects in successive events. The test consists of a combination K of binary correlations at successive times. K decays monotonically from K = 1 for uncorrelated events as a Markov process. For a monotonic memory fading, K<1 always. Here we report evidence of a K>1 temporal window in cognitive tasks consisting of the visual identification of the front face of the Necker cube after a previous presentation of the same. We speculate that memory effects provide a temporal window with K>1 and this experiment could be a possible first step towards a better comprehension of this phenomenon. The K>1 behaviour is maximal at an inter-measurement time τ around 2s with inter-subject differences. The K>1 persists over a time window of 1s around τ; outside this window the K<1 behaviour is recovered. The universal occurrence of a K>1 window in pairs of successive perceptions suggests that, at variance with single visual stimuli eliciting a suitable response, a pair of stimuli shortly separated in time displays mutual correlations.

Improving the Performance of PbS Quantum Dot Solar Cells by Optimizing ZnO Window Layer

NASA Astrophysics Data System (ADS)

Yang, Xiaokun; Hu, Long; Deng, Hui; Qiao, Keke; Hu, Chao; Liu, Zhiyong; Yuan, Shengjie; Khan, Jahangeer; Li, Dengbing; Tang, Jiang; Song, Haisheng; Cheng, Chun

2017-04-01

Comparing with hot researches in absorber layer, window layer has attracted less attention in PbS quantum dot solar cells (QD SCs). Actually, the window layer plays a key role in exciton separation, charge drifting, and so on. Herein, ZnO window layer was systematically investigated for its roles in QD SCs performance. The physical mechanism of improved performance was also explored. It was found that the optimized ZnO films with appropriate thickness and doping concentration can balance the optical and electrical properties, and its energy band align well with the absorber layer for efficient charge extraction. Further characterizations demonstrated that the window layer optimization can help to reduce the surface defects, improve the heterojunction quality, as well as extend the depletion width. Compared with the control devices, the optimized devices have obtained an efficiency of 6.7% with an enhanced V oc of 18%, J sc of 21%, FF of 10%, and power conversion efficiency of 58%. The present work suggests a useful strategy to improve the device performance by optimizing the window layer besides the absorber layer.

78 FR 30226 - Accessibility Requirements for Internet Browsers

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... products and services with peripheral devices or specialized customer premise equipment commonly used by... the telephone or services that such manufacturer or provider offers is accessible to and usable by... requires certain Internet browsers used for advanced communications services to be accessible to people...

Network Security Risks of Online Social Networking in the Workplace

DTIC Science & Technology

2013-11-01

Facebook explains pornographic shock spam, hints at browser vulnera- bility, nakedsecurity. URL – http://nakedsecurity.sophos.com/2011/11/16/ facebook...explains- pornographic -shock-spam-hints-at-browser-vul nerability/. 22 UNCLASSIFIED UNCLASSIFIED DSTO–GD–0772 44. Blatz, J. (2011) CSRF: attack and

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web

NASA Astrophysics Data System (ADS)

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-03-01

We present here the design key concepts of WEBSLIDE, a software project whose objective is to provide a simple, cheap and efficient solution for showing slides during lessons in computer labs. In fact, WEBSLIDE allows the video monitors of several client machines (the "STUDENTS") to be synchronously updated by the actions of a particular client machine, called the "INSTRUCTOR." The system is based on the World Wide Web and the software components of WEBSLIDE mainly consists in a WWW server, browsers and small Cgi-Bill scripts. What makes WEBSLIDE particularly appealing for small educational institutions is that WEBSLIDE is built with "off the shelf" products: it does not involve using a specifically designed program but any Netscape browser, one of the most popular browsers available on the market, is sufficient. Another possible use is to use our system to implement "guided automatic tours" through several pages or Intranets internal news bulletins: the company Web server can broadcast to all employees relevant information on their browser.

Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

PubMed Central

Bensch, Michael; Karim, Ahmed A.; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

2007-01-01

We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications. PMID:18350132

Tuning the emission of aqueous Cu:ZnSe quantum dots to yellow light window

NASA Astrophysics Data System (ADS)

Wang, Chunlei; Hu, Zhiyang; Xu, Shuhong; Wang, Yanbin; Zhao, Zengxia; Wang, Zhuyuan; Cui, Yiping

2015-07-01

Synthesis of internally doped Cu:ZnSe QDs in an aqueous solution still suffers from narrow tunable emissions from the blue to green light window. In this work, we extended the emission window of aqueous Cu:ZnSe QDs to the yellow light window. Our results show that high solution pH, multiple injections of Zn precursors, and nucleation doping strategy are three key factors for preparing yellow emitted Cu:ZnSe QDs. All these factors can depress the reactivity of CuSe nuclei and Zn monomers, promoting ZnSe growth outside CuSe nuclei rather than form ZnSe nuclei separately. With increased ZnSe QD size, the conduction band and nearby trap state energy levels shift to higher energy sites, causing Cu:ZnSe QDs to have a much longer emission.

The origin of blue-green window and the propagation of radiation in ocean waters

NASA Astrophysics Data System (ADS)

Reghunath, A. T.; Venkataramanan, V.; Suviseshamuthu, D. Victor; Krishnamohan, R.; Prasad, B. Raghavendra

1991-01-01

A review of the present knowledge about the origin of blue-green window in the attenuation spectrum of ocean waters is presented. The various physical mechanisms which contribute to the formation of the window are dealt separately and discussed. The typical values of attenuation coefficient arising out of the various processes are compiled to obtain the total beam attenuation coefficient. These values are then compared with measured values of attenuation coefficient for ocean waters collected from Arabian sea and Bay of Bengal. The region of minimum attenuation in pure particle-free sea water is found to be at 450 to 500 nm. It is shown that in the presence of suspended particles and chlorophyll, the window shifts to longer wavelength side. Some suggestions for future work in this area are also given in the concluding section.

Absorption of solar radiation by alkali vapors. [for efficient high temperature energy converters

NASA Technical Reports Server (NTRS)

Mattick, A. T.

1978-01-01

A theoretical study of the direct absorption of solar radiation by the working fluid of high temperature, high efficiency energy converters has been carried out. Alkali vapors and potassium vapor in particular were found to be very effective solar absorbers and suitable thermodynamically for practical high temperature cycles. Energy loss via reradiation from a solar boiler was shown to reduce the overall efficiency of radiation-heated energy converters, although a simple model of radiation transfer in a potassium vapor solar boiler revealed that self-trapping of the reradiation may reduce this loss considerably. A study was also made of the requirements for a radiation boiler window. It was found that for sapphire, one of the best solar transmitting materials, the severe environment in conjunction with high radiation densities will require some form of window protection. An aerodynamic shield is particularly advantageous in this capacity, separating the window from the absorbing vapor to prevent condensation and window corrosion and to reduce the radiation density at the window.

Method for preparing dosimeter for measuring skin dose

DOEpatents

Jones, Donald E.; Parker, DeRay; Boren, Paul R.

1982-01-01

A personnel dosimeter includes a plurality of compartments containing thermoluminescent dosimeter phosphors for registering radiation dose absorbed in the wearer's sensitive skin layer and for registering more deeply penetrating radiation. Two of the phosphor compartments communicate with thin windows of different thicknesses to obtain a ratio of shallowly penetrating radiation, e.g. beta. A third phosphor is disposed within a compartment communicating with a window of substantially greater thickness than the windows of the first two compartments for estimating the more deeply penetrating radiation dose. By selecting certain phosphors that are insensitive to neutrons and by loading the holder material with neutron-absorbing elements, energetic neutron dose can be estimated separately from other radiation dose. This invention also involves a method of injection molding of dosimeter holders with thin windows of consistent thickness at the corresponding compartments of different holders. This is achieved through use of a die insert having the thin window of precision thickness in place prior to the injection molding step.

Dosimeter for measuring skin dose and more deeply penetrating radiation

DOEpatents

Jones, Donald E.; Parker, DeRay; Boren, Paul R.

1981-01-01

A personnel dosimeter includes a plurality of compartments containing thermoluminescent dosimeter phosphors for registering radiation dose absorbed in the wearer's sensitive skin layer and for registering more deeply penetrating radiation. Two of the phosphor compartments communicate with thin windows of different thicknesses to obtain a ratio of shallowly penetrating radiation, e.g. beta. A third phosphor is disposed within a compartment communicating with a window of substantially greater thickness than the windows of the first two compartments for estimating the more deeply penetrating radiation dose. By selecting certain phosphors that are insensitive to neutrons and by loading the holder material with netruon-absorbing elements, energetic neutron dose can be estimated separately from other radiation dose. This invention also involves a method of injection molding of dosimeter holders with thin windows of consistent thickness at the corresponding compartments of different holders. This is achieved through use of a die insert having the thin window of precision thickness in place prior to the injection molding step.

The UCSC Genome Browser: What Every Molecular Biologist Should Know

PubMed Central

Mangan, Mary E.; Williams, Jennifer M.; Kuhn, Robert M.; Lathe, Warren C.

2016-01-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one’s understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. PMID:19816931

[Design of the image browser for PACS image workstation].

PubMed

Li, Feng; Zhou, He-Qin

2006-09-01

The design of PACS image workstation based on DICOM3.0 is introduced in the paper, then the designing method of the PACS image browser based on the control system theory is presented,focusing on two main units:DICOM analyzer and the information mapping transformer.

NATIONAL LANDSCAPE METRICS BROWSER (V1.0)

EPA Science Inventory

This metric browser website describes and displays wall-to-wall landscape metrics that have been calculated for the entire conterminous U.S. The intent is to provide the user with an overview of the nature and utility of this landscape metric data set. The land cover and pattern ...

International Portal

EIA Publications

The International Energy Portal includes a powerful data browser that provides country-level energy data; many countries have at least 30 years of historical data. The data browser provides users the ability to view and download complete datasets for consumption, production, trade, reserves, and carbon dioxide emissions for different fuels and energy sources.

Introduction to the fathead minnow genome browser and opportunities for collaborative development

EPA Science Inventory

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

Toward Exposing Timing-Based Probing Attacks in Web Applications †

PubMed Central

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-01-01

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach. PMID:28245610

Toward Exposing Timing-Based Probing Attacks in Web Applications.

PubMed

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-02-25

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users' browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

A Tri-Band Frequency Selective Surface (FSS) to Diplex Widely Separated Bands for Millimeter Wave Remote Sensing

NASA Astrophysics Data System (ADS)

Poojali, Jayaprakash; Ray, Shaumik; Pesala, Bala; Chitti, Krishnamurthy V.; Arunachalam, Kavitha

2016-10-01

A substrate-backed frequency selective surface (FSS) is presented for diplexing the widely separated frequency spectrum centered at 55, 89, and 183 GHz with varying bandwidth for spatial separation in the quasi-optical feed network of the millimeter wave sounder. A unit cell composed of a crossed dipole integrated with a circular ring and loaded inside a square ring is optimized for tri-band frequency response with transmission window at 89 GHz and rejection windows at 55 and 183 GHz. The reflection and transmission losses predicted for the optimized unit cell (728 μm × 728 μm) composed of dissimilar resonant shapes is less than 0.5 dB for transverse electric (TE) and transverse magnetic (TM) polarizations and wide angle of incidence (0°-45°). The FSS is fabricated on a 175-μm-thick quartz substrate using microfabrication techniques. The transmission characteristics measured with continuous wave (CW) terahertz transmit receive system are in good agreement with the numerical simulations.

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2005-01-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Web-based hydrodynamics computing

NASA Astrophysics Data System (ADS)

Shimoide, Alan; Lin, Luping; Hong, Tracie-Lynne; Yoon, Ilmi; Aragon, Sergio R.

2004-12-01

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

PubMed

Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

2013-01-01

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

Junction-side illuminated silicon detector arrays

DOEpatents

Iwanczyk, Jan S.; Patt, Bradley E.; Tull, Carolyn

2004-03-30

A junction-side illuminated detector array of pixelated detectors is constructed on a silicon wafer. A junction contact on the front-side may cover the whole detector array, and may be used as an entrance window for light, x-ray, gamma ray and/or other particles. The back-side has an array of individual ohmic contact pixels. Each of the ohmic contact pixels on the back-side may be surrounded by a grid or a ring of junction separation implants. Effective pixel size may be changed by separately biasing different sections of the grid. A scintillator may be coupled directly to the entrance window while readout electronics may be coupled directly to the ohmic contact pixels. The detector array may be used as a radiation hardened detector for high-energy physics research or as avalanche imaging arrays.

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

PubMed

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

[The dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modeling language (VRML)].

PubMed

Yu, Zhengyang; Zheng, Shusen; Chen, Huaiqing; Wang, Jianjun; Xiong, Qingwen; Jing, Wanjun; Zeng, Yu

2006-10-01

This research studies the process of dynamic concision and 3D reconstruction from medical body data using VRML and JavaScript language, focuses on how to realize the dynamic concision of 3D medical model built with VRML. The 2D medical digital images firstly are modified and manipulated by 2D image software. Then, based on these images, 3D mould is built with VRML and JavaScript language. After programming in JavaScript to control 3D model, the function of dynamic concision realized by Script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be formed in high quality near to those got in traditional methods. By this way, with the function of dynamic concision, VRML browser can offer better windows of man-computer interaction in real time environment than before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and has a promising prospect in the fields of medical image.

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

Worldwide Telescope as an earth and planetary science educational platform

NASA Astrophysics Data System (ADS)

Fatland, D. R.; Rush, K.; van Ingen, C.; Wong, C.; Fay, J.; Xu, Y.; Fay, D.

2009-12-01

Worldwide Telescope (WWT) -available at no cost from Microsoft Research as both Windows desktop and web browser applications - enables personal computers to function as virtual telescopes for viewing the earth, the solar system and the cosmos across many wavelengths. Bringing together imagery from ground and space-based telescopes as well as photography from Mars rovers and Apollo astronauts, WWT is designed to work as both a research tool and a platform for educational exploration. Central to the latter purpose is the Tour authoring facility which enables a student or educator to create narrative stories with dynamic perspective, voice-over narrative, background sound and superimposed content. We describe here the application of recent developments in WWT, particularly the 2009 updates, towards planetary science education with particular emphasis on WWT earth models. Two core themes informing this development are the notions of enabling social networking through WWT Communities and including the earth as part of the bigger picture, in effect swinging the telescope around from the deep sky to look back at our observatory. moon, earth (WWT solar system view)

LSST Survey Data: Models for EPO Interaction

NASA Astrophysics Data System (ADS)

Olsen, J. K.; Borne, K. D.

2007-12-01

The potential for education and public outreach with the Large Synoptic Survey Telescope is as far reaching as the telescope itself. LSST data will be available to the public, giving anyone with a web browser a movie-like window on the Universe. The LSST project is unique in designing its data management and data access systems with the public and community users in mind. The enormous volume of data to be generated by LSST is staggering: 30 Terabytes per night, 10 Petabytes per year. The final database of extracted science parameters from the images will also be enormous -- 50-100 Petabytes -- a rich gold mine for data mining and scientific discovery potential. LSST will also generate 100,000 astronomical alerts per night, for 10 years. The LSST EPO team is examining models for EPO interaction with the survey data, particularly in how the community (amateurs, teachers, students, and general public) can participate in the discovery process. We will outline some of our models of community interaction for inquiry-based science using the LSST survey data, and we invite discussion on these topics.

Update on PISCES

NASA Technical Reports Server (NTRS)

Pearson, Don; Hamm, Dustin; Kubena, Brian; Weaver, Jonathan K.

2010-01-01

An updated version of the Platform Independent Software Components for the Exploration of Space (PISCES) software library is available. A previous version was reported in Library for Developing Spacecraft-Mission-Planning Software (MSC-22983), NASA Tech Briefs, Vol. 25, No. 7 (July 2001), page 52. To recapitulate: This software provides for Web-based, collaborative development of computer programs for planning trajectories and trajectory- related aspects of spacecraft-mission design. The library was built using state-of-the-art object-oriented concepts and software-development methodologies. The components of PISCES include Java-language application programs arranged in a hierarchy of classes that facilitates the reuse of the components. As its full name suggests, the PISCES library affords platform-independence: The Java language makes it possible to use the classes and application programs with a Java virtual machine, which is available in most Web-browser programs. Another advantage is expandability: Object orientation facilitates expansion of the library through creation of a new class. Improvements in the library since the previous version include development of orbital-maneuver- planning and rendezvous-launch-window application programs, enhancement of capabilities for propagation of orbits, and development of a desktop user interface.

Human interface to large multimedia databases

NASA Astrophysics Data System (ADS)

Davis, Ben; Marks, Linn; Collins, Dave; Mack, Robert; Malkin, Peter; Nguyen, Tam

1994-04-01

The emergence of high-speed networking for multimedia will have the effect of turning the computer screen into a window on a very large information space. As this information space increases in size and complexity, providing users with easy and intuitive means of accessing information will become increasingly important. Providing access to large amounts of text has been the focus of work for hundreds of years and has resulted in the evolution of a set of standards, from the Dewey Decimal System for libraries to the recently proposed ANSI standards for representing information on-line: KIF, Knowledge Interchange Format, and CG's, Conceptual Graphs. Certain problems remain unsolved by these efforts, though: how to let users know the contents of the information space, so that they know whether or not they want to search it in the first place, how to facilitate browsing, and, more specifically, how to facilitate visual browsing. These issues are particularly important for users in educational contexts and have been the focus of much of our recent work. In this paper we discuss some of the solutions we have prototypes: specifically, visual means, visual browsers, and visual definitional sequences.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

DICOM image integration into an electronic medical record using thin viewing clients

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Taira, Ricky K.

1998-07-01

Purpose -- To integrate radiological DICOM images into our currently existing web-browsable Electronic Medical Record (MINDscape). Over the last five years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A text-based view of this data called the Mini Medical Record (MMR) has been available for three years. MINDscape, unlike the text based MMR, provides a platform independent, web browser view of the MIND dataset that can easily be linked to other information resources on the network. We have now added the integration of radiological images into MINDscape through a DICOM webserver. Methods/New Work -- we have integrated a commercial webserver that acts as a DICOM Storage Class Provider to our, computed radiography (CR), computed tomography (CT), digital fluoroscopy (DF), magnetic resonance (MR) and ultrasound (US) scanning devices. These images can be accessed through CGI queries or by linking the image server database using ODBC or SQL gateways. This allows the use of dynamic HTML links to the images on the DICOM webserver from MINDscape, so that the radiology reports already resident in the MIND repository can be married with the associated images through the unique examination accession number generated by our Radiology Information System (RIS). The web browser plug-in used provides a wavelet decompression engine (up to 16-bits per pixel) and performs the following image manipulation functions: window/level, flip, invert, sort, rotate, zoom, cine-loop and save as JPEG. Results -- Radiological DICOM image sets (CR, CT, MR and US) are displayed with associated exam reports for referring physician and clinicians anywhere within the widespread academic medical center on PCs, Macs, X-terminals and Unix computers. This system is also being used for home teleradiology application. Conclusion -- Radiological DICOM images can be made available medical center wide to physicians quickly using low-cost and ubiquitous, thin client browsing technology and wavelet compression.

Medical high-resolution image sharing and electronic whiteboard system: A pure-web-based system for accessing and discussing lossless original images in telemedicine.

PubMed

Qiao, Liang; Li, Ying; Chen, Xin; Yang, Sheng; Gao, Peng; Liu, Hongjun; Feng, Zhengquan; Nian, Yongjian; Qiu, Mingguo

2015-09-01

There are various medical image sharing and electronic whiteboard systems available for diagnosis and discussion purposes. However, most of these systems ask clients to install special software tools or web plug-ins to support whiteboard discussion, special medical image format, and customized decoding algorithm of data transmission of HRIs (high-resolution images). This limits the accessibility of the software running on different devices and operating systems. In this paper, we propose a solution based on pure web pages for medical HRIs lossless sharing and e-whiteboard discussion, and have set up a medical HRI sharing and e-whiteboard system, which has four-layered design: (1) HRIs access layer: we improved an tile-pyramid model named unbalanced ratio pyramid structure (URPS), to rapidly share lossless HRIs and to adapt to the reading habits of users; (2) format conversion layer: we designed a format conversion engine (FCE) on server side to real time convert and cache DICOM tiles which clients requesting with window-level parameters, to make browsers compatible and keep response efficiency to server-client; (3) business logic layer: we built a XML behavior relationship storage structure to store and share users' behavior, to keep real time co-browsing and discussion between clients; (4) web-user-interface layer: AJAX technology and Raphael toolkit were used to combine HTML and JavaScript to build client RIA (rich Internet application), to meet clients' desktop-like interaction on any pure webpage. This system can be used to quickly browse lossless HRIs, and support discussing and co-browsing smoothly on any web browser in a diversified network environment. The proposal methods can provide a way to share HRIs safely, and may be used in the field of regional health, telemedicine and remote education at a low cost. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

JSXGraph--Dynamic Mathematics with JavaScript

ERIC Educational Resources Information Center

Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

2010-01-01

Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

Vulnerability Assessment of Open Source Wireshark and Chrome Browser

DTIC Science & Technology

2013-08-01

UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

Airborne Hazards and Open Burn Pit Registry

MedlinePlus

... Burn Pit Registry requires a common web browser technology to guide you through the registry questionnaire. You may try a different browser, or you may try from a different computer. You may also see this problem if you are in a high security environment where this is disabled by a network policy. ...

Energy Savings of Low-E Storm Windows and Panels across US Climate Zones

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

Culp, Thomas D.; Cort, Katherine A.

This report builds off of previous modeling work related to low-e storm windows used to create a "Database of U.S. Climate-Based Analysis for Low-E Storm Windows." This work updates similar studies using new fuel costs and examining the separate contributions of reduced air leakage and reduced coefficients of overall heat transfer and solar heat gain. In this report we examine the energy savings and cost effectiveness of low-E storm windows in residential homes across a broad range of U.S. climates, excluding the impact from infiltration reductions, which tend to vary using the National Energy Audit Tool (NEAT) and RESFEN modelmore » calculations. This report includes a summary of the results, NEAT and RESFEN background, methodology, and input assumptions, and an appendix with detailed results and assumptions by climate zone.« less

Resource Sharing in a Network of Personal Computers.

DTIC Science & Technology

1982-12-01

magnetic card, or a more secure identifier such as a machine-read fingerprint or voiceprint. Security and Protection 57 (3) (R, key) (5) (RB’ B, key) (B...operations are invoked via messages, a program and its terminal can easily be located on separate machines. In Spice, an interface process called Canvas ...request of a process. In Canvas , a process can only subdivide windows that it already has. On the other hand, the window manager treats the screen as a

A Deep Ensemble Learning Method for Monaural Speech Separation.

PubMed

Zhang, Xiao-Lei; Wang, DeLiang

2016-03-01

Monaural speech separation is a fundamental problem in robust speech processing. Recently, deep neural network (DNN)-based speech separation methods, which predict either clean speech or an ideal time-frequency mask, have demonstrated remarkable performance improvement. However, a single DNN with a given window length does not leverage contextual information sufficiently, and the differences between the two optimization objectives are not well understood. In this paper, we propose a deep ensemble method, named multicontext networks, to address monaural speech separation. The first multicontext network averages the outputs of multiple DNNs whose inputs employ different window lengths. The second multicontext network is a stack of multiple DNNs. Each DNN in a module of the stack takes the concatenation of original acoustic features and expansion of the soft output of the lower module as its input, and predicts the ratio mask of the target speaker; the DNNs in the same module employ different contexts. We have conducted extensive experiments with three speech corpora. The results demonstrate the effectiveness of the proposed method. We have also compared the two optimization objectives systematically and found that predicting the ideal time-frequency mask is more efficient in utilizing clean training speech, while predicting clean speech is less sensitive to SNR variations.

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

On the Nets. Comparing Web Browsers: Mosaic, Cello, Netscape, WinWeb and InternetWorks Life.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

World Wide Web browsers are compared by speed, setup, hypertext transport protocol (HTTP) handling, management of file transfer protocol (FTP), telnet, gopher, and wide area information server (WAIS); bookmark options; and communication functions. Netscape has the most features, the fastest retrieval, sophisticated bookmark capabilities. (JMV)

Baby Steps: Starting Out on the World Wide Web.

ERIC Educational Resources Information Center

Simpson, Carol; McElmeel, Sharron L.

1997-01-01

While the Internet is the physical medium used to transport data, the World Wide Web is the collection of protocols and standards used to access the information. This article provides a basic explanation of what the Web is and describes common browser commands. Discusses graphic Web browsers; universal resource locators (URLs); file, message,…

The ranking algorithm of the Coach browser for the UMLS metathesaurus.

PubMed Central

Harbourt, A. M.; Syed, E. J.; Hole, W. T.; Kingsland, L. C.

1993-01-01

This paper presents the novel ranking algorithm of the Coach Metathesaurus browser which is a major module of the Coach expert search refinement program. An example shows how the ranking algorithm can assist in creating a list of candidate terms useful in augmenting a suboptimal Grateful Med search of MEDLINE. PMID:8130570

World-Wide Web: Adding Multimedia to Cyberspace.

ERIC Educational Resources Information Center

Descy, Don E.

1994-01-01

Describes the World-Wide Web (WWW), a network information resource based on hypertext. How to access WWW browsers through remote login (telnet) or though free browser software, such as Mosaic, is provided. Eight information sources that can be accessed through the WWW are listed. The address of a listserv reporting on Internet developments is…

Visits, Hits, Caching and Counting on the World Wide Web: Old Wine in New Bottles?

ERIC Educational Resources Information Center

Berthon, Pierre; Pitt, Leyland; Prendergast, Gerard

1997-01-01

Although web browser caching speeds up retrieval, reduces network traffic, and decreases the load on servers and browser's computers, an unintended consequence for marketing research is that Web servers undercount hits. This article explores counting problems, caching, proxy servers, trawler software and presents a series of correction factors…

Decoding Technology: Web Browsers

ERIC Educational Resources Information Center

Walker, Tim; Donohue, Chip

2007-01-01

More than ever, early childhood administrators are relying on the Internet for information. A key to becoming an exceptional Web "surfer" is getting to know the ins and outs of the Web browser being used. There are several options available, and almost all can be downloaded for free. However, many of the functions and features they offer are very…

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software

PubMed Central

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong

2017-01-01

Abstract Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. PMID:28327936

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

GWIPS-viz: development of a ribo-seq genome browser

PubMed Central

Michel, Audrey M.; Fox, Gearoid; M. Kiran, Anmol; De Bo, Christof; O’Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.

2014-01-01

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. PMID:24185699

Multi-Sector Sustainability Browser (MSSB) User Manual: A ...

EPA Pesticide Factsheets

EPA’s Sustainable and Healthy Communities (SHC) Research Program is developing methodologies, resources, and tools to assist community members and local decision makers in implementing policy choices that facilitate sustainable approaches in managing their resources affecting the built environment, natural environment, and human health. In order to assist communities and decision makers in implementing sustainable practices, EPA is developing computer-based systems including models, databases, web tools, and web browsers to help communities decide upon approaches that support their desired outcomes. Communities need access to resources that will allow them to achieve their sustainability objectives through intelligent decisions in four key sustainability areas: • Land Use • Buildings and Infrastructure • Transportation • Materials Management (i.e., Municipal Solid Waste [MSW] processing and disposal) The Multi-Sector Sustainability Browser (MSSB) is designed to support sustainable decision-making for communities, local and regional planners, and policy and decision makers. Document is an EPA Technical Report, which is the user manual for the Multi-Sector Sustainability Browser (MSSB) tool. The purpose of the document is to provide basic guidance on use of the tool for users

Quantifying the web browser ecosystem

PubMed Central

Ferdman, Sela; Minkov, Einat; Gefen, David

2017-01-01

Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to “sneak in” through third party installations or to get “kicked out” by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. PMID:28644833

Winning by a neck: tall giraffes avoid competing with shorter browsers.

PubMed

Cameron, Elissa Z; du Toit, Johan T

2007-01-01

With their vertically elongated body form, giraffes generally feed above the level of other browsers within the savanna browsing guild, despite having access to foliage at lower levels. They ingest more leaf mass per bite when foraging high in the tree, perhaps because smaller, more selective browsers deplete shoots at lower levels or because trees differentially allocate resources to promote shoot growth in the upper canopy. We erected exclosures around individual Acacia nigrescens trees in the greater Kruger ecosystem, South Africa. After a complete growing season, we found no differences in leaf biomass per shoot across height zones in excluded trees but significant differences in control trees. We conclude that giraffes preferentially browse at high levels in the canopy to avoid competition with smaller browsers. Our findings are analogous with those from studies of grazing guilds and demonstrate that resource partitioning can be driven by competition when smaller foragers displace larger foragers from shared resources. This provides the first experimental support for the classic evolutionary hypothesis that vertical elongation of the giraffe body is an outcome of competition within the browsing ungulate guild.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2002-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth s radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth s Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2005-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth's radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth's Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

The UCSC Genome Browser database: extensions and updates 2013.

PubMed

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M; Fujita, Pauline A; Dreszer, Timothy R; Diekhans, Mark; Cline, Melissa S; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James

2013-01-01

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

PubMed

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2017-04-01

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line-based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. © The Authors 2017. Published by Oxford University Press.

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

On the relationship between instantaneous phase synchrony and correlation-based sliding windows for time-resolved fMRI connectivity analysis.

PubMed

Pedersen, Mangor; Omidvarnia, Amir; Zalesky, Andrew; Jackson, Graeme D

2018-06-08

Correlation-based sliding window analysis (CSWA) is the most commonly used method to estimate time-resolved functional MRI (fMRI) connectivity. However, instantaneous phase synchrony analysis (IPSA) is gaining popularity mainly because it offers single time-point resolution of time-resolved fMRI connectivity. We aim to provide a systematic comparison between these two approaches, on both temporal and topological levels. For this purpose, we used resting-state fMRI data from two separate cohorts with different temporal resolutions (45 healthy subjects from Human Connectome Project fMRI data with repetition time of 0.72 s and 25 healthy subjects from a separate validation fMRI dataset with a repetition time of 3 s). For time-resolved functional connectivity analysis, we calculated tapered CSWA over a wide range of different window lengths that were temporally and topologically compared to IPSA. We found a strong association in connectivity dynamics between IPSA and CSWA when considering the absolute values of CSWA. The association between CSWA and IPSA was stronger for a window length of ∼20 s (shorter than filtered fMRI wavelength) than ∼100 s (longer than filtered fMRI wavelength), irrespective of the sampling rate of the underlying fMRI data. Narrow-band filtering of fMRI data (0.03-0.07 Hz) yielded a stronger relationship between IPSA and CSWA than wider-band (0.01-0.1 Hz). On a topological level, time-averaged IPSA and CSWA nodes were non-linearly correlated for both short (∼20 s) and long (∼100 s) windows, mainly because nodes with strong negative correlations (CSWA) displayed high phase synchrony (IPSA). IPSA and CSWA were anatomically similar in the default mode network, sensory cortex, insula and cerebellum. Our results suggest that IPSA and CSWA provide comparable characterizations of time-resolved fMRI connectivity for appropriately chosen window lengths. Although IPSA requires narrow-band fMRI filtering, we recommend the use of IPSA given that it does not mandate a (semi-)arbitrary choice of window length and window overlap. A code for calculating IPSA is provided. Copyright © 2018. Published by Elsevier Inc.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

PubMed

Bakhtiari, M

2012-06-01

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

Microwave window breakdown experiments and simulations on the UM/L-3 relativistic magnetron

NASA Astrophysics Data System (ADS)

Hoff, B. W.; Mardahl, P. J.; Gilgenbach, R. M.; Haworth, M. D.; French, D. M.; Lau, Y. Y.; Franzi, M.

2009-09-01

Experiments have been performed on the UM/L-3 (6-vane, L-band) relativistic magnetron to test a new microwave window configuration designed to limit vacuum side breakdown. In the baseline case, acrylic microwave windows were mounted between three of the waveguide coupling cavities in the anode block vacuum housing and the output waveguides. Each of the six 3 cm deep coupling cavities is separated from its corresponding anode cavity by a 1.75 cm wide aperture. In the baseline case, vacuum side window breakdown was observed to initiate at single waveguide output powers close to 20 MW. In the new window configuration, three Air Force Research Laboratory-designed, vacuum-rated directional coupler waveguide segments were mounted between the coupling cavities and the microwave windows. The inclusion of the vacuum side power couplers moved the microwave windows an additional 30 cm away from the anode apertures. Additionally, the Lucite microwave windows were replaced with polycarbonate windows and the microwave window mounts were redesigned to better maintain waveguide continuity in the region around the microwave windows. No vacuum side window breakdown was observed in the new window configuration at single waveguide output powers of 120+MW (a factor of 3 increase in measured microwave pulse duration and factor of 3 increase in measured peak power over the baseline case). Simulations were performed to investigate likely causes for the window breakdown in the original configuration. Results from these simulations have shown that in the original configuration, at typical operating voltage and magnetic field ranges, electrons emitted from the anode block microwave apertures strike the windows with a mean kinetic energy of 33 keV with a standard deviation of 14 keV. Calculations performed using electron impact angle and energy data predict a first generation secondary electron yield of 65% of the primary electron population. The effects of the primary aperture electron impacts, combined with multiplication of the secondary populations, were determined to be the likely causes of the poor microwave window performance in the original configuration.

Polymer Dispersed Liquid Crystal Displays

NASA Astrophysics Data System (ADS)

Doane, J. William

The following sections are included: * INTRODUCTION AND HISTORICAL DEVELOPMENT * PDLC MATERIALS PREPARATION * Polymerization induced phase separation (PIPS) * Thermally induced phase separation (TIPS) * Solvent induced phase separation (SIPS) * Encapsulation (NCAP) * RESPONSE VOLTAGE * Dielectric and resistive effects * Radial configuration * Bipolar configuration * Other director configurations * RESPONSE TIME * DISPLAY CONTRAST * Light scattering and index matching * Incorporation of dyes * Contrast measurements * PDLC DISPLAY DEVICES AND INNOVATIONS * Reflective direct view displays * Large-scale, flexible displays * Switchable windows * Projection displays * High definition spatial light modulator * Haze-free PDLC shutters: wide angle view displays * ENVIRONMENTAL STABILITY * ACKNOWLEDGEMENTS * REFERENCES

Simultaneous two-wavelength tri-window common-path digital holography

NASA Astrophysics Data System (ADS)

Liu, Lei; Shan, Mingguang; Zhong, Zhi

2018-06-01

Two-wavelength common-path off-axis digital holography is proposed with a tri-window in a single shot. It is established using a standard 4f optical image system with a 2D Ronchi grating placed outside the Fourier plane. The input plane consists of three windows: one for the object and the other two for reference. Aided by a spatial filter together with two orthogonal linear polarizers in the Fourier plane, the two-wavelength information is encoded into a multiplexed hologram with two orthogonal spatial frequencies that enable full separation of spectral information in the digital Fourier space without resolution loss. Theoretical analysis and experimental results illustrate that our approach can simultaneously perform quantitative phase imaging at two wavelengths.

Microcomputed tomography with a second generation photon-counting x-ray detector: contrast analysis and material separation

NASA Astrophysics Data System (ADS)

Wang, X.; Meier, D.; Oya, P.; Maehlum, G. E.; Wagenaar, D. J.; Tsui, B. M. W.; Patt, B. E.; Frey, E. C.

2010-04-01

The overall aim of this work was to evaluate the potential for improving in vivo small animal microCT through the use of an energy resolved photon-counting detector. To this end, we developed and evaluated a prototype microCT system based on a second-generation photon-counting x-ray detector which simultaneously counted photons with energies above six energy thresholds. First, we developed a threshold tuning procedure to reduce the dependence of detector uniformity and to reduce ring artifacts. Next, we evaluated the system in terms of the contrast-to-noise ratio in different energy windows for different target materials. These differences provided the possibility to weight the data acquired in different windows in order to optimize the contrast-to-noise ratio. We also explored the ability of the system to use data from different energy windows to aid in distinguishing various materials. We found that the energy discrimination capability provided the possibility for improved contrast-to-noise ratios and allowed separation of more than two materials, e.g., bone, soft-tissue and one or more contrast materials having K-absorption edges in the energy ranges of interest.

Adiabat_1ph 3.0 and the MAGMA website: educational and research tools for studying the petrology and geochemistry of plate margins

NASA Astrophysics Data System (ADS)

Antoshechkina, P. M.; Asimow, P. D.

2010-12-01

Adiabat_1ph is a menu-driven front-end to the MELTS, pMELTS and pHMELTS models of thermodynamic equilibrium in silicate systems. Its public release in late 2004 was described in a software brief in G3 (doi:10.1029/2004GC000816). The software package is available for Windows, MacOS X, and Linux and includes Perl scripts that, if desired, will allow almost complete automation of the calculation process. Adiabat_1ph 3.0 is scheduled for release in October 2010 and includes, for the first time, an option to double-click the run_adiabat.command script and to drag and drop file names from a browser (e.g. Explorer on Windows, Finder on Mac). This alternative mode of operation is particularly suited for teaching at undergraduate and graduate levels, as well as for quick, ad hoc, calculations for research purposes. The original method of invoking the program from the command line is retained for more intensive applications. Version 3.0 is the first to specifically target the Windows 7 and Snow Leopard platforms. The release also includes new features that are relevant to the study of plate margins. The Marianas Trough forms the southern part of the Izu-Bonin-Marianas (IBM) arc system, one of the chosen areas of focus for the MARGINS Subduction Factory initiative. Attempts to model the complicated hydrous fractionation trends observed in this region were the motivation for adding modified versions of the ‘reverse-fractionation’ and ‘amoeba’ routines (see doi:10.1016/S0012-821X(04)00058-5) into adiabat_1ph. The ‘amoeba’ scheme, which varies a trial parental melt composition until forward fractionation yields a specified target composition, has been extended so the best-fit liquid line of descent of a group of samples can be found. We have tested the adiabat_1ph versions using glass compositions from the 9N area of the East Pacific Rise and melt inclusions from the Siqueiros Fracture Zone (see Antoshechkina et al., this meeting). One of the first user requested features to be incorporated into adiabat_1ph after its release was the ability to simulate flux melting, in which a metasomatic fluid or melt, of fixed composition, was added to the system before each equilibration step. This idea was further developed in the coupled dynamic and petrological subduction zone model GyPSM, so that fluid flux into the wedge was controlled by the location of dehydration reactions in the slab. The adiabat_1ph release candidate includes a similar option so that the user may specify assimilated compositions, which evolve as the calculation proceeds. This added flexibility opens up a number of possibilities, such as more realistic simulations of melt-rock reactions at mid-ocean ridges. Adiabat_1ph files may be downloaded from the MAGMA website at http://magmasource.caltech.edu/ and feedback is welcomed at a dedicated forum, especially ideas for new software features. MAGMA is an online resource for the study of mantle melting and magma evolution, hosted by Caltech. As well as MELTS-related resources, there are tools for visualization of binary and ternary phase diagrams. Flash movies of phase diagrams for adiabatic decompression melting of peridotite and pyroxenite sources can be played in a web browser or downloaded from a server.

BROWSER: An Automatic Indexing On-Line Text Retrieval System. Annual Progress Report.

ERIC Educational Resources Information Center

Williams, J. H., Jr.

The development and testing of the Browsing On-line With Selective Retrieval (BROWSER) text retrieval system allowing a natural language query statement and providing on-line browsing capabilities through an IBM 2260 display terminal is described. The prototype system contains data bases of 25,000 German language patent abstracts, 9,000 English…

Visual Links in the World-Wide Web: The Uses and Limitations of Image Maps.

ERIC Educational Resources Information Center

Cochenour, John J.; And Others

As information delivery systems on the Internet increasingly evolve into World Wide Web browsers, understanding key graphical elements of the browser interface is critical to the design of effective information display and access tools. Image maps are one such element, and this document describes a pilot study that collected, reviewed, and…

USDA Plant Hardiness Zone Map

Science.gov Websites

those with slower Internet access. Users may also simply type in a ZIP Code and find the hardiness zone : Find Javascript is not enabled in this Internet Browser For a better experience throughout this web site, please enable Javascript in your Internet Browser What is a Captcha and why am I seeing one (on

Adaptive synchrosqueezing based on a quilted short-time Fourier transform

NASA Astrophysics Data System (ADS)

Berrian, Alexander; Saito, Naoki

2017-08-01

In recent years, the synchrosqueezing transform (SST) has gained popularity as a method for the analysis of signals that can be broken down into multiple components determined by instantaneous amplitudes and phases. One such version of SST, based on the short-time Fourier transform (STFT), enables the sharpening of instantaneous frequency (IF) information derived from the STFT, as well as the separation of amplitude-phase components corresponding to distinct IF curves. However, this SST is limited by the time-frequency resolution of the underlying window function, and may not resolve signals exhibiting diverse time-frequency behaviors with sufficient accuracy. In this work, we develop a framework for an SST based on a "quilted" short-time Fourier transform (SST-QSTFT), which allows adaptation to signal behavior in separate time-frequency regions through the use of multiple windows. This motivates us to introduce a discrete reassignment frequency formula based on a finite difference of the phase spectrum, ensuring computational accuracy for a wider variety of windows. We develop a theoretical framework for the SST-QSTFT in both the continuous and the discrete settings, and describe an algorithm for the automatic selection of optimal windows depending on the region of interest. Using synthetic data, we demonstrate the superior numerical performance of SST-QSTFT relative to other SST methods in a noisy context. Finally, we apply SST-QSTFT to audio recordings of animal calls to demonstrate the potential of our method for the analysis of real bioacoustic signals.

Heavy liquid metals: Research programs at PSI

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

Takeda, Y.

1996-06-01

The author describes work at PSI on thermohydraulics, thermal shock, and material tests for mechnical properties. In the presentation, the focus is on two main programs. (1) SINQ LBE target: The phase II study program for SINQ is planned. A new LBE loop is being constructed. The study has the following three objectives: (a) Pump study - design work on an electromagnetic pump to be integrated into the target. (b) Heat pipe performance test - the use of heat pipes as an additional component of the target cooling system is being considered, and it may be a way to futhermore » decouple the liquid metal and water coolant loops. (c) Mixed convection experiment - in order to find an optimal configuration of the additional flow guide for window cooling, mixed convection around the window is to be studied. The experiment will be started using water and then with LBE. (2) ESS Mercury target: For ESS target study, the following experimental studies are planned, some of which are exampled by trial experiments. (a) Flow around the window: Flow mapping around the hemi-cylindrical window will be made for optimising the flow channels and structures, (b) Geometry optimisation for minimizing a recirculation zone behind the edge of the flow separator, (c) Flow induced vibration and buckling problem for a optimised structure of the flow separator and (d) Gas-liquid two-phase flow will be studied by starting to establish the new experimental method of measuring various kinds of two-phase flow characteristics.« less

Automatic Dependent Surveillance Broadcast (ADS-B) System for Ownership and Traffic Situational Awareness

NASA Technical Reports Server (NTRS)

Arteaga, Ricardo A. (Inventor)

2016-01-01

The present invention proposes an automatic dependent surveillance broadcast (ADS-B) architecture and process, in which priority aircraft and ADS-B IN traffic information are included in the transmission of data through the telemetry communications to a remote ground control station. The present invention further proposes methods for displaying general aviation traffic information in three and/or four dimension trajectories using an industry standard Earth browser for increased situation awareness and enhanced visual acquisition of traffic for conflict detection. The present invention enable the applications of enhanced visual acquisition of traffic, traffic alerts, and en-route and terminal surveillance used to augment pilot situational awareness through ADS-B IN display and information in three or four dimensions for self-separation awareness.

28. November 1969 CASTIRON DRAGON GROTESQUE BELOW BASE OF COLUMN ...

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

28. November 1969 CAST-IRON DRAGON GROTESQUE BELOW BASE OF COLUMN SEPARATING WINDOWS ON NORTH SIDE OF RIGGS LIBRARY - Georgetown University, Healy Building, Thirty-seventh & O Streets, Northwest, Washington, District of Columbia, DC

Formats and Network Protocols for Browser Access to 2D Raster Data

NASA Astrophysics Data System (ADS)

Plesea, L.

2015-12-01

Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

[RadLex - German version: a radiological lexicon for indexing image and report information].

PubMed

Marwede, D; Daumke, P; Marko, K; Lobsien, D; Schulz, S; Kahn, T

2009-01-01

Since 2003 the Radiological Society of North America (RSNA) has been developing a lexicon of standardized radiological terms (RadLex) intended to support the structured reporting of imaging observations and the indexing of teaching cases. The aim of this study was to translate the first version of the lexicon (1 - 2007) into German and to implement a language-independent online term browser. RadLex version 1 - 2007 contains 6303 terms in nine main categories. Two radiologists independently translated the lexicon using medical dictionaries. Terms translated differently were revised and translated by consensus. For the development of an online term browser, a text processing algorithm called morphosemantic indexing was used which splits up words into small semantic units and compares those units to language-specific subword thesauri. In total 6240 of 6303 terms (99 %) were translated. Of those terms 3965 were German, 1893 were Latin, 359 were multilingual, and 23 were English terms that are also used in German and were therefore maintained. The online term browser supports a language-independent term search in RadLex (German/English) and other common medical terminology (e. g., ICD 10). The term browser displays term hierarchies and translations in different frames and the complexity of the result lists can be adapted by the user. RadLex version 1 - 2007 developed by the RSNA is now available in German and can be accessed online through a term browser with an efficient search function. This is an important precondition for the future comparison of national and international indexed radiological examination results and the interoperability between digital teaching resources.

Addressing an I/O Bottleneck in a Web-Based CERES QC Tool

NASA Astrophysics Data System (ADS)

Heckert, E.; Sun-Mack, S.; Chen, Y.; Chu, C.; Smith, R. A.

2016-12-01

In this poster, we explore the technologies we have used to overcome the problem of transmitting and analyzing large datasets in our web-based CERES Quality Control tool and consider four technologies to potentially adopt for future performance improvements. The CERES team uses this tool to validate pixel-level data from Terra, Aqua, SNPP, MSG, MTSAT, and many geostationary GOES satellites, as well as to develop cloud retrieval algorithms. The tool includes a histogram feature that allows the user to aggregate data from many different timestamps and different scenes globally or locally selected by the user by drawing bounding boxes. In order to provide a better user experience, the tool passes a large amount of data to the user's browser. The browser then processes the data in order to present it to users in various formats, for example as a histogram. In addition to using multiple servers to subset data and pass a smaller set of data to the browser, the tool also makes use of a compression technology, Gzip, to reduce the size of the data. However, sometimes the application in the browser is still slow when dealing with these large sets of data due to the delay in the browser receiving the server's response. To address this I/O bottleneck, we will investigate four alternatives and present the results in this poster: 1) sending uncompressed data, 2) ESRI's Limited Error Raster Compression (LERC), 3) Gzip, and 4) WebSocket protocol. These approaches are compared to each other and to the uncompressed control to determine the optimal solution.

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

New Perspectives on Popular Culture, Science and Technology: Web Browsers and the New Illiteracy

ERIC Educational Resources Information Center

Charters, Elizabeth

2004-01-01

Analysts predict that the knowledge economy of the near future will require people to be both computer literate and print literate. However, some of the reading and thinking habits of current college students suggest that electronic media such as web browsers may be limiting the new generation's ability to absorb and process what they read. Their…

A Freely-Available Authoring System for Browser-Based CALL with Speech Recognition

ERIC Educational Resources Information Center

O'Brien, Myles

2017-01-01

A system for authoring browser-based CALL material incorporating Google speech recognition has been developed and made freely available for download. The system provides a teacher with a simple way to set up CALL material, including an optional image, sound or video, which will elicit spoken (and/or typed) answers from the user and check them…

Browser-Based Online Applications: Something for Everyone!

ERIC Educational Resources Information Center

Descy, Don E.

2007-01-01

Just as many people log onto a Web mail site (Gmail, Yahoo, MSN, etc.) to read, write and store their email, there are Web sites out there with word processing, database, and a myriad of other software applications that are not downloadable but used on the site through a Web browser. The user does not have to download the applications to a…

Enabling Efficient Intelligence Analysis in Degraded Environments

DTIC Science & Technology

2013-06-01

Magnets Grid widget for multidimensional information exploration ; and a record browser of Visual Summary Cards widget for fast visual identification of...evolution analysis; a Magnets Grid widget for multi- dimensional information exploration ; and a record browser of Visual Summary Cards widget for fast...attention and inattentional blindness. It also explores and develops various techniques to represent information in a salient way and provide efficient

The geovisualisation window of the temporal and spatial variability for Volunteered Geographic Information activities

NASA Astrophysics Data System (ADS)

Medynska-Gulij, Beata; Myszczuk, Miłosz

2012-11-01

This study presents an attempt to design geographical visualisation tools that allow to tackle the immensity of spatial data provided by Volunteered Geographic Information (VGI), both in terms of temporal and spatial aspects. In accordance with the assumptions made at the conceptual stage, the final action was the implementation of the window entitled ‘Geovisualisation of the Panoramio.com Activities in District of Poznan 2011’ into the web browser. The concept has been based on a division of the geovisualisation window into three panels, of which the most important - in order to capture spatial variability - have statistical maps at the general level (dot map and choropleth map), while at the detailed level - a dot map on a topographic reference map or tourist map. For two ranges, temporal variability is presented by graphs, while a review of attributes of individual activities of the social website in question is set forward in the table panel. The element that visually interlinks all of the panels is the emphasised individual activity. Problemem podjetym w tych badaniach stało sie wykorzystanie metod z nurtu geograficznej wizualizacji do wskazania cech fenomenu VGI w zakresie zmiennosci czasowo-przestrzennej. Zgodnie z załozeniami poczynionymi w etapie koncepcyjnym finalnym działaniem stało sie zaimplementowanie do przegladarki internetowej okna pod tytułem: ”Geowizualizacja aktywnosci społecznosci Panoramio.com w powiecie poznanskim w 2011 roku”. Koncepcja została oparta na podziale okna geowizualizacji na trzy panele, z których najwazniejsze znaczenie dla uchwycenia zmiennosci przestrzennej na poziomie ogólnym ma kartogram, natomiast na poziomie szczegółowym mapa kropkowa wyswietlana na podkładzie mapy topograficznej lub turystycznej. Zmiennosc czasowa w dwóch zakresach prezentuja wykresy, a przeglad atrybutów poszczególnych aktywnosci prezentowanego portalu społecznosciowego zapewnia tabela. Elementem spajajacym wizualnie wszystkie panele jest wyeksponowana graficznie pojedyncza aktywnosc. Przetwarzanie danych odbyło sie w srodowisku open source, a technologia funkcjonowania aplikacji okna geowizualizacji bazowała na zastosowaniu asynchronicznych zapytan do serwera WWW oraz serwera baz danych co zapewnia sprawne "odswiezanie” poszczególnych paneli.

STAR: an integrated solution to management and visualization of sequencing data

PubMed Central

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W.; Ecker, Joseph R.; Millar, A. Harvey; Ren, Bing; Wang, Wei

2013-01-01

Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser. Contact: wei-wang@ucsd.edu PMID:24078702

Brain-controlled applications using dynamic P300 speller matrices.

PubMed

Halder, Sebastian; Pinegger, Andreas; Käthner, Ivo; Wriessnegger, Selina C; Faller, Josef; Pires Antunes, João B; Müller-Putz, Gernot R; Kübler, Andrea

2015-01-01

Access to the world wide web and multimedia content is an important aspect of life. We present a web browser and a multimedia user interface adapted for control with a brain-computer interface (BCI) which can be used by severely motor impaired persons. The web browser dynamically determines the most efficient P300 BCI matrix size to select the links on the current website. This enables control of the web browser with fewer commands and smaller matrices. The multimedia player was based on an existing software. Both applications were evaluated with a sample of ten healthy participants and three end-users. All participants used a visual P300 BCI with face-stimuli for control. The healthy participants completed the multimedia player task with 90% accuracy and the web browsing task with 85% accuracy. The end-users completed the tasks with 62% and 58% accuracy. All healthy participants and two out of three end-users reported that they felt to be in control of the system. In this study we presented a multimedia application and an efficient web browser implemented for control with a BCI. Both applications provide access to important areas of modern information retrieval and entertainment. Copyright © 2014 Elsevier B.V. All rights reserved.

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

PubMed Central

Grüning, Björn A.; Paszkiewicz, Konrad; Pritchard, Leighton

2013-01-01

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu). PMID:24109552

Usage of Data-Encoded Web Maps with Client Side Color Rendering for Combined Data Access, Visualization and Modeling Purposes

NASA Technical Reports Server (NTRS)

Pliutau, Denis; Prasad, Narashimha S.

2013-01-01

Current approaches to satellite observation data storage and distribution implement separate visualization and data access methodologies which often leads to the need in time consuming data ordering and coding for applications requiring both visual representation as well as data handling and modeling capabilities. We describe an approach we implemented for a data-encoded web map service based on storing numerical data within server map tiles and subsequent client side data manipulation and map color rendering. The approach relies on storing data using the lossless compression Portable Network Graphics (PNG) image data format which is natively supported by web-browsers allowing on-the-fly browser rendering and modification of the map tiles. The method is easy to implement using existing software libraries and has the advantage of easy client side map color modifications, as well as spatial subsetting with physical parameter range filtering. This method is demonstrated for the ASTER-GDEM elevation model and selected MODIS data products and represents an alternative to the currently used storage and data access methods. One additional benefit includes providing multiple levels of averaging due to the need in generating map tiles at varying resolutions for various map magnification levels. We suggest that such merged data and mapping approach may be a viable alternative to existing static storage and data access methods for a wide array of combined simulation, data access and visualization purposes.

Optical effect of the contamination of infrared windows by the outgassing of materials in outer space

NASA Technical Reports Server (NTRS)

Silberman, E.

1975-01-01

The products and kinetics of outgassing from S13G paint were studied by using infrared absorption measurements of the material outgassed (using an evaporation cell and vacuum chamber). Two separate long-term experimental depositions from heated samples of the S13G paint were made. Before each experiment, the vacuum chamber and sample holder were carefully cleaned and outgassed to ensure that subsequent deposits on the colled-window were due only to the products evaporated from the sample. Results of experiments are listed and discussed.

Analysis of and Techniques for Adaptive Equalization for Underwater Acoustic Communication

DTIC Science & Technology

2011-09-01

used and in (b) an averaging window of 1000 samples is used. There was an overlap length of half the averaging window. The solid black line shows the ...array processing by constraining the signal covariance matrix to be realizable when the received signal was a sum of narrowband plane waves. Their goal...u0 −u0 v(u)vH(u)du. (4.4.9) A key part of the proof in [48] uses the Poincare separation theorem to show that the eigenvectors corresponding to the

A Fast Estimation Algorithm for Two-Dimensional Gravity Data (GEOFAST),

DTIC Science & Technology

1979-11-15

to a wide class of problems (Refs. 9 and 17). The major inhibitor to the widespread appli- ( cation of optimal gravity data processing is the severe...extends directly to two dimensions. Define the nln 2xn1 n2 diagonal window matrix W as the Kronecker product of two one-dimensional windows W = W1 0 W2 (B...Inversion of Separable Matrices Consider the linear system y = T x (B.3-1) where T is block Toeplitz of dimension nln 2xnIn 2 . Its fre- quency domain

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

NASA Astrophysics Data System (ADS)

Buszko, Marian L.; Buszko, Dominik; Wang, Daniel C.

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance.

Launch COLA Gap Analysis for Protection of the International Space Station

NASA Astrophysics Data System (ADS)

Jenkin, Alan B.; McVey, John P.; Peterson, Glenn E.; Sorge, Marlon E.

2013-08-01

For launch missions in general, a collision avoidance (COLA) gap exists between the end of the time interval covered by standard launch COLA screening and the time that other spacecraft can clear a collision with the newly launched objects. To address this issue for the International Space Station (ISS), a COLA gap analysis process has been developed. The first part of the process, nodal separation analysis, identifies launch dates and launch window opportunities when the orbit traces of a launched object and the ISS could cross during the COLA gap. The second and newest part of the analysis process, Monte Carlo conjunction probability analysis, is performed closer to the launch dates of concern to reopen some of the launch window opportunities that would be closed by nodal separation analysis alone. Both parts of the process are described and demonstrated on sample missions.

Assessment of candidates for target window material in accelerator-driven molybdenum-99 production

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

Strons, Philip; Bailey, James; Makarashvili, Vakhtang

2016-10-01

NorthStar Medical Technologies is pursuing production of an important medical isotope, Mo-99, through a photo-nuclear reaction of a Mo-100 target using a high-power electron accelerator. The current target utilizes an Inconel 718 window. The purpose of this study was to evaluate other candidate materials for the target window, which separates the high-pressure helium gas inside the target from the vacuum inside the accelerator beamline and is subjected to significant stress. Our initial analysis assessed the properties (density, thermal conductivity, maximum stress, minimum window thickness, maximum temperature, and figure of merit) for a range of materials, from which the three mostmore » promising were chosen: Inconel 718, 250 maraging steel, and standard-grade beryllium. These materials were subjected to further analysis to determine the effects of thermal and mechanical strain versus beam power at varying thicknesses. Both beryllium and the maraging steel were calculated to withstand more than twice as high beam power than Inconel 718.« less

Absolute Position of Targets Measured Through a Chamber Window Using Lidar Metrology Systems

NASA Technical Reports Server (NTRS)

Kubalak, David; Hadjimichael, Theodore; Ohl, Raymond; Slotwinski, Anthony; Telfer, Randal; Hayden, Joseph

2012-01-01

Lidar is a useful tool for taking metrology measurements without the need for physical contact with the parts under test. Lidar instruments are aimed at a target using azimuth and elevation stages, then focus a beam of coherent, frequency modulated laser energy onto the target, such as the surface of a mechanical structure. Energy from the reflected beam is mixed with an optical reference signal that travels in a fiber path internal to the instrument, and the range to the target is calculated based on the difference in the frequency of the returned and reference signals. In cases when the parts are in extreme environments, additional steps need to be taken to separate the operator and lidar from that environment. A model has been developed that accurately reduces the lidar data to an absolute position and accounts for the three media in the testbed air, fused silica, and vacuum but the approach can be adapted for any environment or material. The accuracy of laser metrology measurements depends upon knowing the parameters of the media through which the measurement beam travels. Under normal conditions, this means knowledge of the temperature, pressure, and humidity of the air in the measurement volume. In the past, chamber windows have been used to separate the measuring device from the extreme environment within the chamber and still permit optical measurement, but, so far, only relative changes have been diagnosed. The ability to make accurate measurements through a window presents a challenge as there are a number of factors to consider. In the case of the lidar, the window will increase the time-of-flight of the laser beam causing a ranging error, and refract the direction of the beam causing angular positioning errors. In addition, differences in pressure, temperature, and humidity on each side of the window will cause slight atmospheric index changes and induce deformation and a refractive index gradient within the window. Also, since the window is a dispersive media, the effect of both phase and group indices have to be considered. Taking all these factors into account, a method was developed to measure targets through multiple regions of different materials and produce results that are absolute measurements of target position in three-dimensional space, rather than simply relative position. The environment in which the lidar measurements are taken must be broken down into separate regions of interest and each region solved for separately. In this case, there were three regions of interest: air, fused silica, and vacuum. The angular position of the target inside the chamber is solved using only phase index and phase velocity, while the ranging effects due to travel from air to glass to vacuum/air are solved with group index and group velocity. When all parameters are solved simultaneously, an absolute knowledge of the position of each target within an environmental chamber can be derived. Novel features of this innovation include measuring absolute position of targets through multiple dispersive and non-dispersive media, deconstruction of lidar raw data from a commercial off-the-shelf unit into reworkable parameters, and use of group velocities to reduce range data. Measurement of structures within a vacuum chamber or other harsh environment, such as a furnace, may now be measured as easily as if they were in an ambient laboratory. This analysis permits transformation of the raw data into absolute spatial units (e.g., mm). This technique has also been extended to laser tracker, theodolite, and cathetometer measurements through refractive media.

Effect of multiple spin species on spherical shell neutron transmission analysis

NASA Technical Reports Server (NTRS)

Semler, T. T.

1972-01-01

A series of Monte Carlo calculations were performed in order to evaluate the effect of separated against merged spin statistics on the analysis of spherical shell neutron transmission experiments for gold. It is shown that the use of separated spin statistics results in larger average capture cross sections of gold at 24 KeV. This effect is explained by stronger windows in the total cross section caused by the interference between potential and J(+) resonances and by J(+) and J(-) resonance overlap allowed by the use of separated spin statistics.

A comparative study of linear and nonlinear anomaly detectors for hyperspectral imagery

NASA Astrophysics Data System (ADS)

Goldberg, Hirsh; Nasrabadi, Nasser M.

2007-04-01

In this paper we implement various linear and nonlinear subspace-based anomaly detectors for hyperspectral imagery. First, a dual window technique is used to separate the local area around each pixel into two regions - an inner-window region (IWR) and an outer-window region (OWR). Pixel spectra from each region are projected onto a subspace which is defined by projection bases that can be generated in several ways. Here we use three common pattern classification techniques (Principal Component Analysis (PCA), Fisher Linear Discriminant (FLD) Analysis, and the Eigenspace Separation Transform (EST)) to generate projection vectors. In addition to these three algorithms, the well-known Reed-Xiaoli (RX) anomaly detector is also implemented. Each of the four linear methods is then implicitly defined in a high- (possibly infinite-) dimensional feature space by using a nonlinear mapping associated with a kernel function. Using a common machine-learning technique known as the kernel trick all dot products in the feature space are replaced with a Mercer kernel function defined in terms of the original input data space. To determine how anomalous a given pixel is, we then project the current test pixel spectra and the spectral mean vector of the OWR onto the linear and nonlinear projection vectors in order to exploit the statistical differences between the IWR and OWR pixels. Anomalies are detected if the separation of the projection of the current test pixel spectra and the OWR mean spectra are greater than a certain threshold. Comparisons are made using receiver operating characteristics (ROC) curves.

Highly Flexible, Multipixelated Thermosensitive Smart Windows Made of Tough Hydrogels.

PubMed

La, Thanh-Giang; Li, Xinda; Kumar, Amit; Fu, Yiyang; Yang, Shu; Chung, Hyun-Joong

2017-09-27

In a cold night, a clear window that will become opaque while retaining the indoor heat is highly desirable for both privacy and energy efficiency. A thermally responsive material that controls both the transmittance of solar radiance (predominantly in the visible and near-infrared wavelengths) and blackbody radiation (mainly in the mid-infrared) can realize such windows with minimal energy consumption. Here, we report a smart coating made from polyampholyte hydrogel (PAH) that transforms from a transparency state to opacity to visible radiation and strengthens opacity to mid-infrared when lowering the temperature as a result of phase separation between the water-rich and polymer-rich phases. To match a typical temperature fluctuation during the day, we fine-tune the phase transition temperature between 25 and 55 °C by introducing a small amount of relatively hydrophobic monomers (0.1 to 0.5 wt % to PAH). To further demonstrate an actively controlled, highly flexible, and high-contrast smart window, we build in an array of electric heaters made of printed elastomeric composite. The multipixelated window offers rapid switching, ∼70 s per cycle, whereas the device can withstand high strain (up to 80%) during operations.

Development of a browser application to foster research on linking climate and health datasets: Challenges and opportunities.

PubMed

Hajat, Shakoor; Whitmore, Ceri; Sarran, Christophe; Haines, Andy; Golding, Brian; Gordon-Brown, Harriet; Kessel, Anthony; Fleming, Lora E

2017-01-01

Improved data linkages between diverse environment and health datasets have the potential to provide new insights into the health impacts of environmental exposures, including complex climate change processes. Initiatives that link and explore big data in the environment and health arenas are now being established. To encourage advances in this nascent field, this article documents the development of a web browser application to facilitate such future research, the challenges encountered to date, and how they were addressed. A 'storyboard approach' was used to aid the initial design and development of the application. The application followed a 3-tier architecture: a spatial database server for storing and querying data, server-side code for processing and running models, and client-side browser code for user interaction and for displaying data and results. The browser was validated by reproducing previously published results from a regression analysis of time-series datasets of daily mortality, air pollution and temperature in London. Data visualisation and analysis options of the application are presented. The main factors that shaped the development of the browser were: accessibility, open-source software, flexibility, efficiency, user-friendliness, licensing restrictions and data confidentiality, visualisation limitations, cost-effectiveness, and sustainability. Creating dedicated data and analysis resources, such as the one described here, will become an increasingly vital step in improving understanding of the complex interconnections between the environment and human health and wellbeing, whilst still ensuring appropriate confidentiality safeguards. The issues raised in this paper can inform the future development of similar tools by other researchers working in this field. Copyright © 2016 Elsevier B.V. All rights reserved.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

The UCSC genome browser and associated tools

PubMed Central

Haussler, David; Kent, W. James

2013-01-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

The UCSC genome browser and associated tools.

PubMed

Kuhn, Robert M; Haussler, David; Kent, W James

2013-03-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008

Integration and visualization of systems biology data in context of the genome

PubMed Central

2010-01-01

Background High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment. PMID:20642854

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

Dual-Band Modulation of Visible and Near-Infrared Light Transmittance in an All-Solution-Processed Hybrid Micro-Nano Composite Film.

PubMed

Liang, Xiao; Chen, Mei; Guo, Shumeng; Zhang, Lanying; Li, Fasheng; Yang, Huai

2017-11-22

Smart windows with controllable visible and near-infrared light transmittance can significantly improve the building's energy efficiency and inhabitant comfort. However, most of the current smart window technology cannot achieve the target of ideal solar control. Herein, we present a novel all-solution-processed hybrid micronano composite smart material that have four optical states to separately modulate the visible and NIR light transmittance through voltage and temperature, respectively. This dual-band optical modulation was achieved by constructing a phase-separated polymer framework, which contains the microsized liquid crystals domains with a negative dielectric constant and tungsten-doped vanadium dioxide (W-VO 2 ) nanocrystals (NCs). The film with 2.5 wt % W-VO 2 NCs exhibits transparency at normal condition, and the passage of visible light can be reversibly and actively regulated between 60.8% and 1.3% by external applied voltage. Also, the transmittance of NIR light can be reversibly and passively modulated between 59.4% and 41.2% by temperature. Besides, the film also features easy all-solution processability, fast electro-optical (E-O) response time, high mechanical strength, and long-term stability. The as-prepared film provides new opportunities for next-generation smart window technology, and the proposed strategy is conductive to engineering novel hybrid inorganic-organic functional matters.

Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design.

PubMed

Yuan, Shuguang; Chan, H C Stephen; Hu, Zhenquan

2017-06-01

Web browsers have long been recognized as potential platforms for remote macromolecule visualization. However, the difficulty in transferring large-scale data to clients and the lack of native support for hardware-accelerated applications in the local browser undermine the feasibility of such utilities. With the introduction of WebGL and HTML5 technologies in recent years, it is now possible to exploit the power of a graphics-processing unit (GPU) from a browser without any third-party plugin. Many new tools have been developed for biological molecule visualization and modern drug discovery. In contrast to traditional offline tools, real-time computing, interactive data analysis, and cross-platform analyses feature WebGL- and HTML5-based tools, facilitating biological research in a more efficient and user-friendly way. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Genomic HyperBrowser: an analysis web server for genome-scale data

PubMed Central

Sandve, Geir K.; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K.; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje; Rye, Morten B.; Frigessi, Arnoldo; Hovig, Eivind

2013-01-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome. PMID:23632163

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

PubMed

Buszko; Buszko; Wang

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance. Copyright 1998 Academic Press.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

PubMed

Sandve, Geir K; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalas, Matús; Lien, Tonje; Rye, Morten B; Frigessi, Arnoldo; Hovig, Eivind

2013-07-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

Contingency Table Browser - prediction of early stage protein structure.

PubMed

Kalinowska, Barbara; Krzykalski, Artur; Roterman, Irena

2015-01-01

The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table - this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them - analysis of specific protein sequences from the point of view of their structural ambiguity.

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Easy Web Interfaces to IDL Code for NSTX Data Analysis

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

W.M. Davis

Reusing code is a well-known Software Engineering practice to substantially increase the efficiency of code production, as well as to reduce errors and debugging time. A variety of "Web Tools" for the analysis and display of raw and analyzed physics data are in use on NSTX [1], and new ones can be produced quickly from existing IDL [2] code. A Web Tool with only a few inputs, and which calls an IDL routine written in the proper style, can be created in less than an hour; more typical Web Tools with dozens of inputs, and the need for some adaptationmore » of existing IDL code, can be working in a day or so. Efficiency is also increased for users of Web Tools because o f the familiar interface of the web browser, and not needing X-windows, accounts, passwords, etc. Web Tools were adapted for use by PPPL physicists accessing EAST data stored in MDSplus with only a few man-weeks of effort; adapting to additional sites should now be even easier. An overview of Web Tools in use on NSTX, and a list of the most useful features, is also presented.« less

StreamStats: a U.S. geological survey web site for stream information

USGS Publications Warehouse

Kernell, G. Ries; Gray, John R.; Renard, Kenneth G.; McElroy, Stephen A.; Gburek, William J.; Canfield, H. Evan; Scott, Russell L.

2003-01-01

The U.S. Geological Survey has developed a Web application, named StreamStats, for providing streamflow statistics, such as the 100-year flood and the 7-day, 10-year low flow, to the public. Statistics can be obtained for data-collection stations and for ungaged sites. Streamflow statistics are needed for water-resources planning and management; for design of bridges, culverts, and flood-control structures; and for many other purposes. StreamStats users can point and click on data-collection stations shown on a map in their Web browser window to obtain previously determined streamflow statistics and other information for the stations. Users also can point and click on any stream shown on the map to get estimates of streamflow statistics for ungaged sites. StreamStats determines the watershed boundaries and measures physical and climatic characteristics of the watersheds for the ungaged sites by use of a Geographic Information System (GIS), and then it inserts the characteristics into previously determined regression equations to estimate the streamflow statistics. Compared to manual methods, StreamStats reduces the average time needed to estimate streamflow statistics for ungaged sites from several hours to several minutes.

BrainLiner: A Neuroinformatics Platform for Sharing Time-Aligned Brain-Behavior Data

PubMed Central

Takemiya, Makoto; Majima, Kei; Tsukamoto, Mitsuaki; Kamitani, Yukiyasu

2016-01-01

Data-driven neuroscience aims to find statistical relationships between brain activity and task behavior from large-scale datasets. To facilitate high-throughput data processing and modeling, we created BrainLiner as a web platform for sharing time-aligned, brain-behavior data. Using an HDF5-based data format, BrainLiner treats brain activity and data related to behavior with the same salience, aligning both behavioral and brain activity data on a common time axis. This facilitates learning the relationship between behavior and brain activity. Using a common data file format also simplifies data processing and analyses. Properties describing data are unambiguously defined using a schema, allowing machine-readable definition of data. The BrainLiner platform allows users to upload and download data, as well as to explore and search for data from the web platform. A WebGL-based data explorer can visualize highly detailed neurophysiological data from within the web browser, and a data-driven search feature allows users to search for similar time windows of data. This increases transparency, and allows for visual inspection of neural coding. BrainLiner thus provides an essential set of tools for data sharing and data-driven modeling. PMID:26858636

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

World Wide Web Metaphors for Search Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

[Preliminary construction of three-dimensional visual educational system for clinical dentistry based on world wide web webpage].

PubMed

Hu, Jian; Xu, Xiang-yang; Song, En-min; Tan, Hong-bao; Wang, Yi-ning

2009-09-01

To establish a new visual educational system of virtual reality for clinical dentistry based on world wide web (WWW) webpage in order to provide more three-dimensional multimedia resources to dental students and an online three-dimensional consulting system for patients. Based on computer graphics and three-dimensional webpage technologies, the software of 3Dsmax and Webmax were adopted in the system development. In the Windows environment, the architecture of whole system was established step by step, including three-dimensional model construction, three-dimensional scene setup, transplanting three-dimensional scene into webpage, reediting the virtual scene, realization of interactions within the webpage, initial test, and necessary adjustment. Five cases of three-dimensional interactive webpage for clinical dentistry were completed. The three-dimensional interactive webpage could be accessible through web browser on personal computer, and users could interact with the webpage through rotating, panning and zooming the virtual scene. It is technically feasible to implement the visual educational system of virtual reality for clinical dentistry based on WWW webpage. Information related to clinical dentistry can be transmitted properly, visually and interactively through three-dimensional webpage.

Developing cloud applications using the e-Science Central platform.

PubMed

Hiden, Hugo; Woodman, Simon; Watson, Paul; Cala, Jacek

2013-01-28

This paper describes the e-Science Central (e-SC) cloud data processing system and its application to a number of e-Science projects. e-SC provides both software as a service (SaaS) and platform as a service for scientific data management, analysis and collaboration. It is a portable system and can be deployed on both private (e.g. Eucalyptus) and public clouds (Amazon AWS and Microsoft Windows Azure). The SaaS application allows scientists to upload data, edit and run workflows and share results in the cloud, using only a Web browser. It is underpinned by a scalable cloud platform consisting of a set of components designed to support the needs of scientists. The platform is exposed to developers so that they can easily upload their own analysis services into the system and make these available to other users. A representational state transfer-based application programming interface (API) is also provided so that external applications can leverage the platform's functionality, making it easier to build scalable, secure cloud-based applications. This paper describes the design of e-SC, its API and its use in three different case studies: spectral data visualization, medical data capture and analysis, and chemical property prediction.

Developing cloud applications using the e-Science Central platform

PubMed Central

Hiden, Hugo; Woodman, Simon; Watson, Paul; Cala, Jacek

2013-01-01

This paper describes the e-Science Central (e-SC) cloud data processing system and its application to a number of e-Science projects. e-SC provides both software as a service (SaaS) and platform as a service for scientific data management, analysis and collaboration. It is a portable system and can be deployed on both private (e.g. Eucalyptus) and public clouds (Amazon AWS and Microsoft Windows Azure). The SaaS application allows scientists to upload data, edit and run workflows and share results in the cloud, using only a Web browser. It is underpinned by a scalable cloud platform consisting of a set of components designed to support the needs of scientists. The platform is exposed to developers so that they can easily upload their own analysis services into the system and make these available to other users. A representational state transfer-based application programming interface (API) is also provided so that external applications can leverage the platform's functionality, making it easier to build scalable, secure cloud-based applications. This paper describes the design of e-SC, its API and its use in three different case studies: spectral data visualization, medical data capture and analysis, and chemical property prediction. PMID:23230161

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.

PubMed

Kawamura, Takashi; Ohtsubo, Masafumi; Mitsuyama, Susumu; Ohno-Nakamura, Saho; Shimizu, Nobuyoshi; Minoshima, Shinsei

2010-06-01

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

Challenges in the Development and Evolution of Secure Open Architecture Command and Control Systems (Briefing Charts)

DTIC Science & Technology

2013-06-01

widgets for an OA system Design-time architecture: Browser, email, widget, DB, OS Go ogle Instance architecture: Chrome, Gmail, Google...provides functionally similar components or applications compatible with an OA system design Firefox Browser, WP, calendar Opera Instance...architecture: Firefox , AbiWord, Evolution, Fedora GPL Ab1Word Google Docs Instance ardlitecture: Fire fox, OR Google cal., Google Docs, Fedora

Local-Rapid Evaluation of Atmospheric Conditions (L-REAC)

DTIC Science & Technology

2009-01-15

installation available 24/7 to all forms of browser-based access such as mobile blackberry browser. In 2006, the ARL presented data at an International...Oceanic and Atmospheric Administration (NOAA)/Environmental Protection Agency (EPA) Wind Tunnel study with tens-of-meter-scaled measurements sampled around...urban flow in wind tunnels , as well as articles from professional urban meteorological journals. The need to maintain a visual sensor for persons who

Defense AT and L. Volume 44, Number 3

DTIC Science & Technology

2015-06-01

CommunityBrowser.aspx?id=527436 Product Support Key References https://acc.dau.mil/productsupport CLL 011 Performance-Based Life Cycle Product Support (PBL...http://icatalog.dau.mil/onlinecatalog/courses.aspx?crs_id=269 CLL 031 PBL Contracting Strategies http://icatalog.dau.mil/onlinecatalog/courses.aspx...CommunityBrowser.aspx?id=527436 Product Support Key References https://acc.dau.mil/productsupport CLL 011 Performance-Based Life Cycle Product Support (PBL) http

CPTAC Proteomics Data on UCSC Genome Browser | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

Aladin Lite: Lightweight sky atlas for browsers

NASA Astrophysics Data System (ADS)

Boch, Thomas

2014-02-01

Aladin Lite is a lightweight version of the Aladin tool, running in the browser and geared towards simple visualization of a sky region. It allows visualization of image surveys (JPEG multi-resolution HEALPix all-sky surveys) and permits superimposing tabular (VOTable) and footprints (STC-S) data. Aladin Lite is powered by HTML5 canvas technology and is easily embeddable on any web page and can also be controlled through a Javacript API.

A Connection Model between the Positioning Mechanism and Ultrasonic Measurement System via a Web Browser to Assess Acoustic Target Strength

NASA Astrophysics Data System (ADS)

Ishii, Ken; Imaizumi, Tomohito; Abe, Koki; Takao, Yoshimi; Tamura, Shuko

This paper details a network-controlled measurement system for use in fisheries engineering. The target strength (TS) of fish is important in order to convert acoustic integration values obtained during acoustic surveys into estimates of fish abundance. The target strength pattern is measured with the combination of the rotation system for the aspect of the sample and the echo data acquisition system using the underwater supersonic wave. The user interface of the network architecture is designed for collaborative use with researchers in other organizations. The flexible network architecture is based on the web direct-access model for the rotation mechanism. The user interface is available for monitoring and controlling via a web browser that is installed in any terminal PC (personal computer). Previously the combination of two applications was performed not by a web browser but by the exclusive interface program. So a connection model is proposed between two applications by indirect communication via the DCOM (Distributed Component Object Model) server and added in the web direct-access model. A prompt report system in the TS measurement system and a positioning and measurement system using an electric flatcar via a web browser are developed. By a secure network architecture, DCOM communications via both Intranet and LAN are successfully certificated.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

SMC Message Browser Projects

NASA Technical Reports Server (NTRS)

Wichmann, Benjamin C.

2013-01-01

I work directly with the System Monitoring and Control (SMC) software engineers who develop, test and release custom and commercial software in support of the Kennedy Space Center Spaceport Command and Control System. (SCCS). SMC uses Commercial Off-The-Shelf (COTS) Enterprise Management Systems (EMS) software which provides a centralized subsystem for configuring, monitoring, and controlling SCCS hardware and software used in the Control Rooms. There are multiple projects being worked on using the COTS EMS software. I am currently working with the HP Operations Manager for UNIX (OMU) software which allows Master Console Operators (MCO) to access, view and interpret messages regarding the status of the SCCS hardware and software. The OMU message browser gets cluttered with messages which can make it difficult for the MCO to manage. My main project involves determining ways to reduce the number of messages being displayed in the OMU message browser. I plan to accomplish this task in two different ways: (1) by correlating multiple messages into one single message being displayed and (2) to create policies that will determine the significance of each message and whether or not it needs to be displayed to the MCO. The core idea is to lessen the number of messages being sent to the OMU message browser so the MCO can more effectively use it.

Web-based visualization of gridded dataset usings OceanBrowser

NASA Astrophysics Data System (ADS)

Barth, Alexander; Watelet, Sylvain; Troupin, Charles; Beckers, Jean-Marie

2015-04-01

OceanBrowser is a web-based visualization tool for gridded oceanographic data sets. Those data sets are typically four-dimensional (longitude, latitude, depth and time). OceanBrowser allows one to visualize horizontal sections at a given depth and time to examine the horizontal distribution of a given variable. It also offers the possibility to display the results on an arbitrary vertical section. To study the evolution of the variable in time, the horizontal and vertical sections can also be animated. Vertical section can be generated by using a fixed distance from coast or fixed ocean depth. The user can customize the plot by changing the color-map, the range of the color-bar, the type of the plot (linearly interpolated color, simple contours, filled contours) and download the current view as a simple image or as Keyhole Markup Language (KML) file for visualization in applications such as Google Earth. The data products can also be accessed as NetCDF files and through OPeNDAP. Third-party layers from a web map service can also be integrated. OceanBrowser is used in the frame of the SeaDataNet project (http://gher-diva.phys.ulg.ac.be/web-vis/) and EMODNET Chemistry (http://oceanbrowser.net/emodnet/) to distribute gridded data sets interpolated from in situ observation using DIVA (Data-Interpolating Variational Analysis).

Energy dissipation in polymer-polymer adhesion contacts

NASA Astrophysics Data System (ADS)

Garif, Yev Skip

This study focuses on self-adhesion in elastomers as a way of approaching a broader polymer adhesion problem. The model systems studied are cross-linked acrylic pressure-sensitive adhesives (PSA-LNs) synthesized to attain four surface types: neutral, acidic, basic, and polar. As the study progressed, it distinguished itself as the first of its kind to consistently report the effect of temperature on measurable intrinsic parameters of polymer adhesion. The main goal of the study was to understand why the magnitude of the practical adhesion energies of the four PSA-LN systems tested varies disproportionately greater than their respective surface energies. To achieve this goal, continuous sweeps of adhesion energy as a function of rate of interfacial separation were performed using three different adhesion-probing techniques--- peel, micro-scratch, and normal contact. The answer was found in the sub-micron-per-second limit of separation rates. In approaching this limit, the power law behavior of adhesion gradually transitioned into a linear region of markedly weaker sensitivity to rate. Referred to as the "intrinsic window", this linear region was characterized by three parameters: (1) the intrinsic adhesion energy at zero rate of separation; (2) the intrinsic rate sensitivity equal to the proportionality constant of the linear fit; and (3) the critical separation rate in the middle of the transition to the power law. All three were found to be thermally activated. Activation energies suggested that interfacial processes are attributed mainly to dispersive and electrostatic molecular interactions such as hydrogen bonding or van der Waals attraction. Comparative analysis of the intrinsic window of the four PSA-LNs tested showed that an increase in the intrinsic adhesion energy associated with higher surface energy is inherently coupled with an increase in the intrinsic rate sensitivity and reduction in the critical separation rate. When combined, the three parameters reshape the intrinsic window such that the entire power-law portion of the adhesion response is shifted to a level that appears disproportionately high based on the false assumption that there is only one intrinsic parameter contributing to the shift. Thus, the goal of explaining this disproportionality was achieved.

Bias Factor and Therapeutic Window Correlate to Predict Safer Opioid Analgesics.

PubMed

Schmid, Cullen L; Kennedy, Nicole M; Ross, Nicolette C; Lovell, Kimberly M; Yue, Zhizhou; Morgenweck, Jenny; Cameron, Michael D; Bannister, Thomas D; Bohn, Laura M

2017-11-16

Biased agonism has been proposed as a means to separate desirable and adverse drug responses downstream of G protein-coupled receptor (GPCR) targets. Herein, we describe structural features of a series of mu-opioid-receptor (MOR)-selective agonists that preferentially activate receptors to couple to G proteins or to recruit βarrestin proteins. By comparing relative bias for MOR-mediated signaling in each pathway, we demonstrate a strong correlation between the respiratory suppression/antinociception therapeutic window in a series of compounds spanning a wide range of signaling bias. We find that βarrestin-biased compounds, such as fentanyl, are more likely to induce respiratory suppression at weak analgesic doses, while G protein signaling bias broadens the therapeutic window, allowing for antinociception in the absence of respiratory suppression. Copyright © 2017 Elsevier Inc. All rights reserved.

Enclosure for small animals during awake animal imaging

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

Goddard, Jr., James S

An enclosure or burrow restrains an awake animal during an imaging procedure. A tubular body, made from a radiolucent material that does not attenuate x-rays or gamma rays, accepts an awake animal. A proximal end of the body includes an attachment surface that corresponds to an attachment surface of an optically transparent and optically uniform window. An anti-reflective coating may be applied to an inner surface, an outer surface, or both surfaces of the window. Since the window is a separate element of the enclosure and it is not integrally formed as part of the body, it can be mademore » with optically uniform thickness properties for improved motion tracking of markers on the animal with a camera during the imaging procedure. The motion tracking information is then used to compensate for animal movement in the image.« less

International Ultraviolet Explorer (IUE) satellite mission analysis

NASA Technical Reports Server (NTRS)

Cook, R. A.; Griffin, J. H.

1975-01-01

The results are presented of the mission analysis performed by Computer Sciences Corporation (CSC) in support of the International Ultraviolet Explorer (IUE) satellite. The launch window is open for three separate periods (for a total time of 7 months) during the year extending from July 20, 1977, to July 20, 1978. The synchronous orbit shadow constraint limits the launch window to approximately 88 minutes per day. Apogee boost motor fuel was computed to be 455 pounds (206 kilograms) and on-station weight was 931 pounds (422 kilograms). The target orbit is elliptical synchronous, with eccentricity 0.272 and 24 hour period.

Fused silica mirror development for SIRTF

NASA Technical Reports Server (NTRS)

Barnes, W. P., Jr.

1983-01-01

An advanced design, lightweight, fuse-quartz mirror of sandwich construction was evaluated for optical figure performance at cryogenic temperatures. A low temperature shroud was constructed with an integral mirror mount and interface to a cryostat for use in a vacuum chamber. The mirror was tested to 13 K. Cryogenic distortion of the mirror was measured interferometrically. Separate interferometry of the chamber window during the test permitted subtraction of the small window distortions from the data. Results indicate that the imaging performance of helium cooled, infrared telescopes will be improved using this type of mirror without correction of cryogenic distortion of the primary mirror.

Tunable Rare Earth fcu-MOF Platform: Access to Adsorption Kinetics Driven Gas/Vapor Separations via Pore Size Contraction.

PubMed

Xue, Dong-Xu; Belmabkhout, Youssef; Shekhah, Osama; Jiang, Hao; Adil, Karim; Cairns, Amy J; Eddaoudi, Mohamed

2015-04-22

Reticular chemistry approach was successfully employed to deliberately construct new rare-earth (RE, i.e., Eu(3+), Tb(3+), and Y(3+)) fcu metal-organic frameworks (MOFs) with restricted window apertures. Controlled and selective access to the resultant contracted fcu-MOF pores permits the achievement of the requisite sorbate cutoff, ideal for selective adsorption kinetics based separation and/or molecular sieving of gases and vapors. Predetermined reaction conditions that permitted the formation in situ of the 12-connected RE hexanuclear molecular building block (MBB) and the establishment of the first RE-fcu-MOF platform, especially in the presence of 2-fluorobenzoic acid (2-FBA) as a modulator and a structure directing agent, were used to synthesize isostructural RE-1,4-NDC-fcu-MOFs based on a relatively bulkier 2-connected bridging ligand, namely 1,4-naphthalenedicarboxylate (1,4-NDC). The subsequent RE-1,4-NDC-fcu-MOF structural features, contracted windows/pores and high concentration of open metal sites combined with exceptional hydrothermal and chemical stabilities, yielded notable gas/solvent separation properties, driven mostly by adsorption kinetics as exemplified in this work for n-butane/methane, butanol/methanol, and butanol/water pair systems.

Facile fabrication of multilayer separators for lithium-ion battery via multilayer coextrusion and thermal induced phase separation

NASA Astrophysics Data System (ADS)

Li, Yajie; Pu, Hongting

2018-04-01

Polypropylene (PP)/polyethylene (PE) multilayer separators with cellular-like submicron pore structure for lithium-ion battery are efficiently fabricated by the combination of multilayer coextrusion (MC) and thermal induced phase separation (TIPS). The as-prepared separators, referred to as MC-TIPS PP/PE, not only show efficacious thermal shutdown function and wider shutdown temperature window, but also exhibit higher thermal stability than the commercial separator with trilayer construction of PP and PE (Celgard® 2325). The dimensional shrinkage of MC-TIPS PP/PE can be negligible until 160 °C. In addition, compared to the commercial separator, MC-TIPS PP/PE exhibits higher porosity and electrolyte uptake, leading to higher ionic conductivity and better battery performances. The above-mentioned fascinating characteristics with the convenient preparation process make MC-TIPS PP/PE a promising candidate for the application as high performance lithium-ion battery separators.

ISOTOPE SEPARATORS

DOEpatents

Bacon, C.G.

1958-08-26

An improvement is presented in the structure of an isotope separation apparatus and, in particular, is concerned with a magnetically operated shutter associated with a window which is provided for the purpose of enabling the operator to view the processes going on within the interior of the apparatus. The shutier is mounted to close under the force of gravity in the absence of any other force. By closing an electrical circuit to a coil mouated on the shutter the magnetic field of the isotope separating apparatus coacts with the magnetic field of the coil to force the shutter to the open position.

CIS4/403: Design and Implementation of an Intranet-based system for Real-Time Tele-Consultation in Oncology

PubMed Central

Eccher, C; Berloffa, F; Demichelis, F; Larcher, B; Galvagni, M; Sboner, A; Graiff, A; Forti, S

1999-01-01

Introduction This study describes a tele-consultation system (TCS) developed to provide a computing environment over a Wide Area Network (WAN) in North Italy (Province of Trento), that can be used by two or more physicians to share medical data and to work co-operatively on medical records. A pilot study has been carried out in oncology to assess the effectiveness of the system. The aim of this project is to facilitate the management of oncology patients by improving communication among the specialists of central and district hospitals. Methods and Results The TCS is an Intranet-based solution. The Intranet is based on a PC WAN with Windows NT Server, Microsoft SQL Server, and Internet Information Server. TCS is composed of native and custom applications developed in the Microsoft Windows (9x and NT) environment. The basic component of the system is the multimedia digital medical record, structured as a collection of HTML and ASP pages. A distributed relational database will allow users to store and retrieve medical records, accessed by a dedicated Web browser via the Web Server. The medical data to be stored and the presentation architecture of the clinical record had been determined in close collaboration with the clinicians involved in the project. TCS will allow a multi-point tele-consultation (TC) among two or more participants on remote computers, providing synchronized surfing through the clinical report. A set of collaborative and personal tools, whiteboard with drawing tools, point-to-point digital audio-conference, chat, local notepad, e-mail service, are integrated in the system to provide an user friendly environment. TCS has been developed as a client-server architecture. The client part of the system is based on the Microsoft Web Browser control and provides the user interface and the tools described above. The server part, running all the time on a dedicated computer, accepts connection requests and manages the connections among the participants in a TC, allowing multiple TC to run simultaneously. TCS has been developed in Visual C++ environment using MFC library and COM technology; ActiveX controls have been written in Visual Basic to perform dedicated tasks from the inside of the HTML clinical report. Before deploying the system in the hospital departments involved in the project, TCS has been tested in our laboratory by clinicians involved in the project to evaluate the usability of the system. Discussion TCS has the potential to support a "multi-disciplinary distributed virtual oncological meeting". The specialists of different departments and of different hospitals can attend "virtual meetings" and interactively discuss on medical data. An expected benefit of the "virtual meeting" should be the possibility to provide expert remote advice from oncologists to peripheral cancer units in formulating treatment plans, conducting follow-up sessions and supporting clinical research.

Network Analysis of Reconnaissance and Intrusion of an Industrial Control System

DTIC Science & Technology

2016-09-01

simulated a plant engineer using the engineering workstation web browser to authenticate to the vegetable cooker HMI. While the engineer established the...observed the vegetable cooker HMI web display, the attacker stopped capturing network traffic. Acting as the attacker, we searched the attacker’s pcap...manually controlled by human activity. In this testbed network, only web browser traffic (HTTP) is created by an operator to view an HMI status

Coal Data Browser

EIA Publications

The Coal Data Browser gives users easy access to coal information from EIA's electricity and coal surveys as well as data from the Mine Safety and Health Administration and trade information from the U.S. Census Bureau. Users can also see the shipment data from individual mines that deliver coal to the U.S. electric power fleet, have the ability to track supplies delivered to a given power plant, and to see which mines serve each particular plant.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.

PubMed

Lekschas, Fritz; Stachelscheid, Harald; Seltmann, Stefanie; Kurtz, Andreas

2015-03-01

Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users. The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Self-study program on HTML browser--application to Clinical Nursing General Remarks Course.

PubMed

Ochiai, N; Sota, Y; Ezumi, H

1997-01-01

We created a self-study program using HTML browser on the Clinical Nursing General Remarks Course, Eighty-three students each selected a published book on a personal history (written personal reflections from individuals who had undergone medical treatment and hospitalization), read it and submitted reports of their impressions of the histories. Their reports were arranged from a nursing perspective and entered on the home page of our college using HTML browser. We intended that the students would become more interested in reading of the personal histories, and that they would acquire new self-study skills and increase their interest in Internet through use of our program. In addition, we hoped that this program would encourage positive communication and mutual sharing of information. The students were able to easily refer to a personal history according to their interest from a nursing perspective. Therefore this program realized the mutual learning among students and other users.

Use of mobile devices to answer online surveys: implications for research.

PubMed

Cunningham, John A; Neighbors, Clayton; Bertholet, Nicolas; Hendershot, Christian S

2013-07-08

There is a growing use of mobile devices to access the Internet. We examined whether participants who used a mobile device to access a brief online survey were quicker to respond to the survey but also, less likely to complete it than participants using a traditional web browser. Using data from a recently completed online intervention trial, we found that participants using mobile devices were quicker to access the survey but less likely to complete it compared to participants using a traditional web browser. More concerning, mobile device users were also less likely to respond to a request to complete a six week follow-up survey compared to those using traditional web browsers. With roughly a third of participants using mobile devices to answer an online survey in this study, the impact of mobile device usage on survey completion rates is a concern. ClinicalTrials.gov: NCT01521078.

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

[A solution for display and processing of DICOM images in web PACS].

PubMed

Xue, Wei-jing; Lu, Wen; Wang, Hai-yang; Meng, Jian

2009-03-01

Use the technique of Java Applet to realize the supporting of DICOM image in ordinary Web browser, thereby to expand the processing function of medical image. First analyze the format of DICOM file and design a class which can acquire the pixels, then design two Applet classes, of which one is used to disposal the DICOM image, the other is used to display DICOM image that have been disposaled in the first Applet. They all embedded in the View page, and they communicate by Applet Context object. The method designed in this paper can make users display and process DICOM images directly by using ordinary Web browser, which makes Web PACS not only have the advantages of B/S model, but also have the advantages of the C/S model. Java Applet is the key for expanding the Web browser's function in Web PACS, which provides a guideline to sharing of medical images.

JavaScript Access to DICOM Network and Objects in Web Browser.

PubMed

Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

2017-10-01

Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

NASA Interactive Forms Type Interface - NIFTI

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Bill

2005-01-01

A flexible database query, update, modify, and delete tool was developed that provides an easy interface to Oracle forms. This tool - the NASA interactive forms type interface, or NIFTI - features on-the- fly forms creation, forms sharing among users, the capability to query the database from user-entered criteria on forms, traversal of query results, an ability to generate tab-delimited reports, viewing and downloading of reports to the user s workstation, and a hypertext-based help system. NIFTI is a very powerful ad hoc query tool that was developed using C++, X-Windows by a Motif application framework. A unique tool, NIFTI s capabilities appear in no other known commercial-off-the- shelf (COTS) tool, because NIFTI, which can be launched from the user s desktop, is a simple yet very powerful tool with a highly intuitive, easy-to-use graphical user interface (GUI) that will expedite the creation of database query/update forms. NIFTI, therefore, can be used in NASA s International Space Station (ISS) as well as within government and industry - indeed by all users of the widely disseminated Oracle base. And it will provide significant cost savings in the areas of user training and scalability while advancing the art over current COTS browsers. No COTS browser performs all the functions NIFTI does, and NIFTI is easier to use. NIFTI s cost savings are very significant considering the very large database with which it is used and the large user community with varying data requirements it will support. Its ease of use means that personnel unfamiliar with databases (e.g., managers, supervisors, clerks, and others) can develop their own personal reports. For NASA, a tool such as NIFTI was needed to query, update, modify, and make deletions within the ISS vehicle master database (VMDB), a repository of engineering data that includes an indentured parts list and associated resource data (power, thermal, volume, weight, and the like). Since the VMDB is used both as a collection point for data and as a common repository for engineering, integration, and operations teams, a tool such as NIFTI had to be designed that could expedite the creation of database query/update forms which could then be shared among users.

Complexity in African savannas: Direct, indirect, and cascading effects of animal densities, rainfall and vegetation availability

PubMed Central

Leeuwis, Tim; Peel, Mike

2018-01-01

Savanna ecosystems are popular subjects for interaction studies. Multiple studies have been done on the impact of elephants on vegetation, the impact of grass and browse availability on animal densities or on competition between herbivore species. Previous studies showed that elephant densities are frequently negatively correlated with densities of tall trees, and that browse and grass availability are correlated with browser and grazer density respectively. Additionally, a competition effect between browse and grass availability has been reported. These relationships are usually analysed by testing direct relationships between e.g., herbivore densities and food availability, without addressing competition effects or other indirect effects. In this study, multiple interactions in a savanna system have been analysed simultaneously using Partial Least Square-Path Modelling (PLS-PM) using mammal and vegetation data from three different wildlife reserves in southern KwaZulu-Natal. The results showed that the processes that three separate models for the three areas provided the best understanding of the importance of the different interactions. These models suggest that elephants had a negative impact on trees, but also on grass availability. The impact is stronger when elephants are not able to migrate during the dry season. Browsers and grazers were correlated with browse and grass availability, but competition between browse and grass was not detected. This study shows that due to the complexity of the interactions in an ecosystem and differences in environmental factors, these interactions are best studied per area. PLS-PM can be a useful tool for estimating direct, indirect, and cascading effects of changing animal densities in conservation areas. PMID:29768481

Temporal Integration Windows in Neural Processing and Perception Aligned to Saccadic Eye Movements.

PubMed

Wutz, Andreas; Muschter, Evelyn; van Koningsbruggen, Martijn G; Weisz, Nathan; Melcher, David

2016-07-11

When processing dynamic input, the brain balances the opposing needs of temporal integration and sensitivity to change. We hypothesized that the visual system might resolve this challenge by aligning integration windows to the onset of newly arriving sensory samples. In a series of experiments, human participants observed the same sequence of two displays separated by a brief blank delay when performing either an integration or segregation task. First, using magneto-encephalography (MEG), we found a shift in the stimulus-evoked time courses by a 150-ms time window between task signals. After stimulus onset, multivariate pattern analysis (MVPA) decoding of task in occipital-parietal sources remained above chance for almost 1 s, and the task-decoding pattern interacted with task outcome. In the pre-stimulus period, the oscillatory phase in the theta frequency band was informative about both task processing and behavioral outcome for each task separately, suggesting that the post-stimulus effects were caused by a theta-band phase shift. Second, when aligning stimulus presentation to the onset of eye fixations, there was a similar phase shift in behavioral performance according to task demands. In both MEG and behavioral measures, task processing was optimal first for segregation and then integration, with opposite phase in the theta frequency range (3-5 Hz). The best fit to neurophysiological and behavioral data was given by a dampened 3-Hz oscillation from stimulus or eye fixation onset. The alignment of temporal integration windows to input changes found here may serve to actively organize the temporal processing of continuous sensory input. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Modelling the regulatory system for diabetes mellitus with a threshold window

NASA Astrophysics Data System (ADS)

Yang, Jin; Tang, Sanyi; Cheke, Robert A.

2015-05-01

Piecewise (or non-smooth) glucose-insulin models with threshold windows for type 1 and type 2 diabetes mellitus are proposed and analyzed with a view to improving understanding of the glucose-insulin regulatory system. For glucose-insulin models with a single threshold, the existence and stability of regular, virtual, pseudo-equilibria and tangent points are addressed. Then the relations between regular equilibria and a pseudo-equilibrium are studied. Furthermore, the sufficient and necessary conditions for the global stability of regular equilibria and the pseudo-equilibrium are provided by using qualitative analysis techniques of non-smooth Filippov dynamic systems. Sliding bifurcations related to boundary node bifurcations were investigated with theoretical and numerical techniques, and insulin clinical therapies are discussed. For glucose-insulin models with a threshold window, the effects of glucose thresholds or the widths of threshold windows on the durations of insulin therapy and glucose infusion were addressed. The duration of the effects of an insulin injection is sensitive to the variation of thresholds. Our results indicate that blood glucose level can be maintained within a normal range using piecewise glucose-insulin models with a single threshold or a threshold window. Moreover, our findings suggest that it is critical to individualise insulin therapy for each patient separately, based on initial blood glucose levels.

Differential Immunotoxicity Induced by Two Different Windows of Developmental Trichloroethylene Exposure

PubMed Central

Gilbert, Kathleen M.; Woodruff, William; Blossom, Sarah J.

2014-01-01

Developmental exposure to environmental toxicants may induce immune system alterations that contribute to adult stage autoimmune disease. We have shown that continuous exposure of MRL+/+ mice to trichloroethylene (TCE) from gestational day (GD) 0 to postnatal day (PND) 49 alters several aspects of CD4+ T cell function. This window of exposure corresponds to conception-adolescence/young adulthood in humans. More narrowly defining the window of TCE developmental exposure causes immunotoxicity that would establish the stage at which avoidance and/or intervention would be most effective. The current study divided continuous TCE exposure into two separate windows, namely, gestation only (GD0 to birth (PND0)) and early-life only (PND0-PND49). The mice were examined for specific alterations in CD4+ T cell function at PND49. One potentially long-lasting effect of developmental exposure, alterations in retrotransposon expression indicative of epigenetic alterations, was found in peripheral CD4+ T cells from both sets of developmentally exposed mice. Interestingly, certain other effects, such as alterations in thymus cellularity, were only found in mice exposed to TCE during gestation. In contrast, expansion of memory/activation cell subset of peripheral CD4+ T cells were only found in mice exposed to TCE during early life. Different windows of developmental TCE exposure can have different functional consequences. PMID:24696780

Semiclassical spatial correlations in chaotic wave functions.

PubMed

Toscano, Fabricio; Lewenkopf, Caio H

2002-03-01

We study the spatial autocorrelation of energy eigenfunctions psi(n)(q) corresponding to classically chaotic systems in the semiclassical regime. Our analysis is based on the Weyl-Wigner formalism for the spectral average C(epsilon)(q(+),q(-),E) of psi(n)(q(+))psi(*)(n)(q(-)), defined as the average over eigenstates within an energy window epsilon centered at E. In this framework C(epsilon) is the Fourier transform in the momentum space of the spectral Wigner function W(x,E;epsilon). Our study reveals the chord structure that C(epsilon) inherits from the spectral Wigner function showing the interplay between the size of the spectral average window, and the spatial separation scale. We discuss under which conditions is it possible to define a local system independent regime for C(epsilon). In doing so, we derive an expression that bridges the existing formulas in the literature and find expressions for C(epsilon)(q(+),q(-),E) valid for any separation size /q(+)-q(-)/.

Timing of target discrimination in human frontal eye fields.

PubMed

O'Shea, Jacinta; Muggleton, Neil G; Cowey, Alan; Walsh, Vincent

2004-01-01

Frontal eye field (FEF) neurons discharge in response to behaviorally relevant stimuli that are potential targets for saccades. Distinct visual and motor processes have been dissociated in the FEF of macaque monkeys, but little is known about the visual processing capacity of FEF in humans. We used double-pulse transcranial magnetic stimulation [(d)TMS] to investigate the timing of target discrimination during visual conjunction search. We applied dual TMS pulses separated by 40 msec over the right FEF and vertex. These were applied in five timing conditions to sample separate time windows within the first 200 msec of visual processing. (d)TMS impaired search performance, reflected in reduced d' scores. This effect was limited to a time window between 40 and 80 msec after search array onset. These parameters correspond with single-cell activity in FEF that predicts monkeys' behavioral reports on hit, miss, false alarm, and correct rejection trials. Our findings demonstrate a crucial early role for human FEF in visual target discrimination that is independent of saccade programming.

Window Glasses: State and Prospects

NASA Astrophysics Data System (ADS)

Maiorov, V. A.

2018-04-01

Analysis and generalization of the results of investigations devoted to the improvement of optical properties have been carried out, and descriptions of a structure and a reaction mechanism of available and promising window glasses with solar radiation are presented. All devices are divided into groups with static constant and dynamic regulated spectral characteristics. The group of static glasses includes heat-protective and spectrally selective glasses with low-emissivity coatings and infrared filters with dispersed plasmonic nanoparticles. Electrochromic glasses, nanostructured dynamic infrared filters, and glasses with separated regulation of the transmission of visible-light and near-infrared radiation are dynamic devices. It is noted that the use of mesoporous films made of plasmonic nanoparticles open up especially wide possibilities. Their application allows one to realize a dynamic separated regulation of the transmission of visible light and nearinfrared radiation in which, under the gradual increase in the electric potential on the glass, mechanisms of plasmon and polaron reduction of solar radiation gradually change the glass' condition from light warm to light cold and then to dark cold consecutively.

Phase-shifting point diffraction interferometer mask designs

DOEpatents

Goldberg, Kenneth Alan

2001-01-01

In a phase-shifting point diffraction interferometer, different image-plane mask designs can improve the operation of the interferometer. By keeping the test beam window of the mask small compared to the separation distance between the beams, the problem of energy from the reference beam leaking through the test beam window is reduced. By rotating the grating and mask 45.degree., only a single one-dimensional translation stage is required for phase-shifting. By keeping two reference pinholes in the same orientation about the test beam window, only a single grating orientation, and thus a single one-dimensional translation stage, is required. The use of a two-dimensional grating allows for a multiplicity of pinholes to be used about the pattern of diffracted orders of the grating at the mask. Orientation marks on the mask can be used to orient the device and indicate the position of the reference pinholes.

Remote adjustable focus Raman spectroscopy probe

DOEpatents

Schmucker, John E.; Blasi, Raymond J.; Archer, William B.

1999-01-01

A remote adjustable focus Raman spectroscopy probe allows for analyzing Raman scattered light from a point of interest external probe. An environmental barrier including at least one window separates the probe from the point of interest. An optical tube is disposed adjacent to the environmental barrier and includes a long working length compound lens objective next to the window. A beam splitter and a mirror are at the other end. A mechanical means is used to translated the prove body in the X, Y, and Z directions resulting in a variable focus optical apparatus. Laser light is reflected by the beam splitter and directed toward the compound lens objective, then through the window and focused on the point of interest. Raman scattered light is then collected by the compound lens objective and directed through the beam splitter to a mirror. A device for analyzing the light, such as a monochrometer, is coupled to the mirror.

Tunable far-infrared plasmonically induced transparency in graphene based nano-structures

NASA Astrophysics Data System (ADS)

Dolatabady, Alireza; Granpayeh, Nosrat

2018-07-01

In this paper, a structure is proposed to show the phenomenon of tunable far-infrared plasmonically induced transparency. The structure includes a nano-ribbon waveguide side-coupled to nano-stub resonators. The realized effect is due to the coupling between the consecutive nano-stub resonators spaced in properly designed distances, providing a constructive interference in the virtually created Fabry–Perot cavity. Due to the Fabry–Perot like cavity created between two consecutive nano-stubs, periodic values of nano-stubs separation can produce transparency windows. Increasing the number of nano-stubs would increase the number of transparency windows in different frequencies. The structure is theoretically investigated and numerically simulated by using the finite difference time domain method. Owing to the chemical potential dependency of graphene conductivity, the transparency windows can be actively tuned. The proposed component can be extensively utilized in nano-scale switching and slow-light systems.

Extraction-Separation Performance and Dynamic Modeling of Orion Test Vehicles with Adams Simulation: 2nd Edition

NASA Technical Reports Server (NTRS)

Fraire, Usbaldo, Jr.; Anderson, Keith; Varela, Jose G.; Bernatovich, Michael A.

2015-01-01

NASA's Orion Capsule Parachute Assembly System (CPAS) project has advanced into the third generation of its parachute test campaign and requires technically comprehensive modeling capabilities to simulate multi-body dynamics (MBD) of test articles released from a C-17. Safely extracting a 30,000 lbm mated test article from a C-17 and performing stable mid-air separation maneuvers requires an understanding of the interaction between elements in the test configuration and how they are influenced by extraction parachute performance, aircraft dynamics, aerodynamics, separation dynamics, and kinetic energy experienced by the system. During the real-time extraction and deployment sequences, these influences can be highly unsteady and difficult to bound. An avionics logic window based on time, pitch, and pitch rate is used to account for these effects and target a favorable separation state in real time. The Adams simulation has been employed to fine-tune this window, as well as predict and reconstruct the coupled dynamics of the Parachute Test Vehicle (PTV) and Cradle Platform Separation System (CPSS) from aircraft extraction through the mid-air separation event. The test-technique for the extraction of CPAS test articles has evolved with increased complexity and requires new modeling concepts to ensure the test article is delivered to a stable test condition for the programmer phase. Prompted by unexpected dynamics and hardware malfunctions in drop tests, these modeling improvements provide a more accurate loads prediction by incorporating a spring-damper line-model derived from the material properties. The qualification phase of CPAS testing is on the horizon and modeling increasingly complex test-techniques with Adams is vital to successfully qualify the Orion parachute system for human spaceflight.

An Image Understanding Environment for DARPA Supported Research and Applications, Second Annual Report

DTIC Science & Technology

1992-05-01

relatively independent of the 29 30 Basic Objects Support Objects GUI Access Objects Displays Display Mapping Menues Pixel Snapshot Gizmos /Widgets...a user interactively or set from some gizmo /widget, or that a particular browser field is to be updated when some state occurs or a process completes...also want to distinguish tree graph browsers.] 4.3.2 Simplified access to GUI objects "* Gizmos and Widgets: The IUE should provide simplified

The rendering context for stereoscopic 3D web

NASA Astrophysics Data System (ADS)

Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

2014-03-01

3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3D web page, our 3D browser will create two slightly different images, each representing the left-eye view and right-eye view, both to be combined on the 3D display to generate the illusion of depth. And as the result turns out, elements can be manipulated in a truly 3D space.

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

Recalibration of the Multisensory Temporal Window of Integration Results from Changing Task Demands

PubMed Central

Mégevand, Pierre; Molholm, Sophie; Nayak, Ashabari; Foxe, John J.

2013-01-01

The notion of the temporal window of integration, when applied in a multisensory context, refers to the breadth of the interval across which the brain perceives two stimuli from different sensory modalities as synchronous. It maintains a unitary perception of multisensory events despite physical and biophysical timing differences between the senses. The boundaries of the window can be influenced by attention and past sensory experience. Here we examined whether task demands could also influence the multisensory temporal window of integration. We varied the stimulus onset asynchrony between simple, short-lasting auditory and visual stimuli while participants performed two tasks in separate blocks: a temporal order judgment task that required the discrimination of subtle auditory-visual asynchronies, and a reaction time task to the first incoming stimulus irrespective of its sensory modality. We defined the temporal window of integration as the range of stimulus onset asynchronies where performance was below 75% in the temporal order judgment task, as well as the range of stimulus onset asynchronies where responses showed multisensory facilitation (race model violation) in the reaction time task. In 5 of 11 participants, we observed audio-visual stimulus onset asynchronies where reaction time was significantly accelerated (indicating successful integration in this task) while performance was accurate in the temporal order judgment task (indicating successful segregation in that task). This dissociation suggests that in some participants, the boundaries of the temporal window of integration can adaptively recalibrate in order to optimize performance according to specific task demands. PMID:23951203

Pervasive interactions between ungulate browsers and disturbance regimes promote temperate forest herbaceous diversity.

PubMed

Royo, Alejandro A; Collins, Rachel; Adams, Mary Beth; Kirschbaum, Chad; Carson, Walter P

2010-01-01

Disruptions to historic disturbance and herbivory regimes have altered plant assemblages in forests worldwide. An emerging consensus suggests that these disruptions often result in impoverished forest biotas. This is particularly true for eastern U.S. deciduous forests where large gaps and understory fires were once relatively common and browsers were far less abundant. Although much research has focused on how disturbance and browsers affect tree diversity, far less attention has been devoted to forest understories where the vast majority (>75%) of the vascular species reside. Here we test the hypothesis that the reintroduction of disturbances resembling historic disturbance regimes and moderate levels of ungulate browsing enhance plant diversity. We explore whether once-common disturbances and their interaction with the top-down influence of browsers can create conditions favorable for the maintenance of a rich herbaceous layer in a region recognized as a temperate biodiversity hotspot in West Virginia, U.S.A. We tested this hypothesis via a factorial experiment whereby we manipulated canopy gaps (presence/absence) of a size typically found in old-growth stands, low-intensity understory fire (burned/unburned), and deer browsing (fenced/unfenced). We tracked the abundance and diversity of more than 140 herb species for six years. Interactions among our treatments were pervasive. The combination of canopy gaps and understory fire increased herbaceous layer richness, cover, and diversity well beyond either disturbance alone. Furthermore, we documented evidence that deer at moderate levels of abundance promote herbaceous richness and abundance by preferentially browsing fast-growing pioneer species that thrive following co-occurring disturbances (i.e., fire and gaps). This finding sharply contrasts with the negative impact browsers have when their populations reach levels well beyond those that occurred for centuries. Although speculative, our results suggest that interactions among fire, canopy gaps, and browsing provided a variable set of habitats and conditions across the landscape that was potentially capable of maintaining much of the plant diversity found in temperate forests.

Broadband 19F TOCSY using BURBOP-based spin lock

NASA Astrophysics Data System (ADS)

Marchione, Alexander A.; Diaz, Elizabeth L.

2018-01-01

A train of BURBOP universal rotation pulses has been used to generate a spin lock sufficient to observe TOCSY correlations over a 46 kHz 19F spectral window (i.e. 122 ppm on a 9.4 T spectrometer). This spin lock requires lower RF field (γB1 = 15 kHz), and was employed over a wider spectral window, than previously reported DIPSI-2 spin locks. The BURBOP-based spin lock was effected for 80-160 ms periods with a 2% duty cycle without evidence of harm to the RF coil of the probehead. Spectral separation and full set of correlations were obtained for a mixture of perfluorocarbons.

STS-40 Spacelab Life Science 1 (SLS-1) module in OV-102's payload bay (PLB)

NASA Image and Video Library

1991-06-14

STS040-612-005 (5-14 June 1991) --- This view showing the Spacelab Life Sciences (SLS-1) module in Columbia's cargo bay was taken through windows on the aft flight deck. Under some lighting conditions the multi-layered Shuttle windows have internal reflections that provide a kaleidoscopic effect. In this image the sunrays as seen on the clouds also appear to be present in space. Note how the white sunlight toward the Sun at the Earth's limb becomes separated into the colors of the visible spectrum towards that part of the limb further into darkness due to atmosphere acting as a natural prism.

Computer-Aided Writing.

DTIC Science & Technology

1988-04-01

e.g., definitions, references, pictures) on the selected item in a separate window. For example, in a hyper- text document on astronomy , the reader...might arrive at the highlighted word " Copernicus ", select the word with the keyboard or mouse, and then be offered a number of related topics from

CatReg Software for Categorical Regression Analysis (May 2016)

EPA Science Inventory

CatReg 3.0 is a Microsoft Windows enhanced version of the Agency’s categorical regression analysis (CatReg) program. CatReg complements EPA’s existing Benchmark Dose Software (BMDS) by greatly enhancing a risk assessor’s ability to determine whether data from separate toxicologic...

A Voice Enabled Procedure Browser for the International Space Station

NASA Technical Reports Server (NTRS)

Rayner, Manny; Chatzichrisafis, Nikos; Hockey, Beth Ann; Farrell, Kim; Renders, Jean-Michel

2005-01-01

Clarissa, an experimental voice enabled procedure browser that has recently been deployed on the International Space Station (ISS), is to the best of our knowledge the first spoken dialog system in space. This paper gives background on the system and the ISS procedures, then discusses the research developed to address three key problems: grammar-based speech recognition using the Regulus toolkit; SVM based methods for open microphone speech recognition; and robust side-effect free dialogue management for handling undos, corrections and confirmations.

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Surfing for Data: A Gathering Trend in Data Storage Is the Use of Web-Based Applications that Make It Easy for Authorized Users to Access Hosted Server Content with Just a Computing Device and Browser

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

In recent years, the widespread availability of networks and the flexibility of Web browsers have shifted the industry from a client-server model to a Web-based one. In the client-server model of computing, clients run applications locally, with the servers managing storage, printing functions, and network traffic. Because every client is…

Automated design of genomic Southern blot probes

PubMed Central

2010-01-01

Background Sothern blotting is a DNA analysis technique that has found widespread application in molecular biology. It has been used for gene discovery and mapping and has diagnostic and forensic applications, including mutation detection in patient samples and DNA fingerprinting in criminal investigations. Southern blotting has been employed as the definitive method for detecting transgene integration, and successful homologous recombination in gene targeting experiments. The technique employs a labeled DNA probe to detect a specific DNA sequence in a complex DNA sample that has been separated by restriction-digest and gel electrophoresis. Critically for the technique to succeed the probe must be unique to the target locus so as not to cross-hybridize to other endogenous DNA within the sample. Investigators routinely employ a manual approach to probe design. A genome browser is used to extract DNA sequence from the locus of interest, which is searched against the target genome using a BLAST-like tool. Ideally a single perfect match is obtained to the target, with little cross-reactivity caused by homologous DNA sequence present in the genome and/or repetitive and low-complexity elements in the candidate probe. This is a labor intensive process often requiring several attempts to find a suitable probe for laboratory testing. Results We have written an informatic pipeline to automatically design genomic Sothern blot probes that specifically attempts to optimize the resultant probe, employing a brute-force strategy of generating many candidate probes of acceptable length in the user-specified design window, searching all against the target genome, then scoring and ranking the candidates by uniqueness and repetitive DNA element content. Using these in silico measures we can automatically design probes that we predict to perform as well, or better, than our previous manual designs, while considerably reducing design time. We went on to experimentally validate a number of these automated designs by Southern blotting. The majority of probes we tested performed well confirming our in silico prediction methodology and the general usefulness of the software for automated genomic Southern probe design. Conclusions Software and supplementary information are freely available at: http://www.genes2cognition.org/software/southern_blot PMID:20113467

Lagged kernel machine regression for identifying time windows of susceptibility to exposures of complex mixtures.

PubMed

Liu, Shelley H; Bobb, Jennifer F; Lee, Kyu Ha; Gennings, Chris; Claus Henn, Birgit; Bellinger, David; Austin, Christine; Schnaas, Lourdes; Tellez-Rojo, Martha M; Hu, Howard; Wright, Robert O; Arora, Manish; Coull, Brent A

2018-07-01

The impact of neurotoxic chemical mixtures on children's health is a critical public health concern. It is well known that during early life, toxic exposures may impact cognitive function during critical time intervals of increased vulnerability, known as windows of susceptibility. Knowledge on time windows of susceptibility can help inform treatment and prevention strategies, as chemical mixtures may affect a developmental process that is operating at a specific life phase. There are several statistical challenges in estimating the health effects of time-varying exposures to multi-pollutant mixtures, such as: multi-collinearity among the exposures both within time points and across time points, and complex exposure-response relationships. To address these concerns, we develop a flexible statistical method, called lagged kernel machine regression (LKMR). LKMR identifies critical exposure windows of chemical mixtures, and accounts for complex non-linear and non-additive effects of the mixture at any given exposure window. Specifically, LKMR estimates how the effects of a mixture of exposures change with the exposure time window using a Bayesian formulation of a grouped, fused lasso penalty within a kernel machine regression (KMR) framework. A simulation study demonstrates the performance of LKMR under realistic exposure-response scenarios, and demonstrates large gains over approaches that consider each time window separately, particularly when serial correlation among the time-varying exposures is high. Furthermore, LKMR demonstrates gains over another approach that inputs all time-specific chemical concentrations together into a single KMR. We apply LKMR to estimate associations between neurodevelopment and metal mixtures in Early Life Exposures in Mexico and Neurotoxicology, a prospective cohort study of child health in Mexico City.

Ultrafast selective transport of alkali metal ions in metal organic frameworks with subnanometer pores

PubMed Central

Zhang, Huacheng; Hou, Jue; Hu, Yaoxin; Wang, Peiyao; Ou, Ranwen; Jiang, Lei; Liu, Jefferson Zhe; Freeman, Benny D.; Hill, Anita J.; Wang, Huanting

2018-01-01

Porous membranes with ultrafast ion permeation and high ion selectivity are highly desirable for efficient mineral separation, water purification, and energy conversion, but it is still a huge challenge to efficiently separate monatomic ions of the same valence and similar sizes using synthetic membranes. We report metal organic framework (MOF) membranes, including ZIF-8 and UiO-66 membranes with uniform subnanometer pores consisting of angstrom-sized windows and nanometer-sized cavities for ultrafast selective transport of alkali metal ions. The angstrom-sized windows acted as ion selectivity filters for selection of alkali metal ions, whereas the nanometer-sized cavities functioned as ion conductive pores for ultrafast ion transport. The ZIF-8 and UiO-66 membranes showed a LiCl/RbCl selectivity of ~4.6 and ~1.8, respectively, which are much greater than the LiCl/RbCl selectivity of 0.6 to 0.8 measured in traditional porous membranes. Molecular dynamics simulations suggested that ultrafast and selective ion transport in ZIF-8 was associated with partial dehydration effects. This study reveals ultrafast and selective transport of monovalent ions in subnanometer MOF pores and opens up a new avenue to develop unique MOF platforms for efficient ion separations in the future. PMID:29487910

Ultrafast selective transport of alkali metal ions in metal organic frameworks with subnanometer pores.

PubMed

Zhang, Huacheng; Hou, Jue; Hu, Yaoxin; Wang, Peiyao; Ou, Ranwen; Jiang, Lei; Liu, Jefferson Zhe; Freeman, Benny D; Hill, Anita J; Wang, Huanting

2018-02-01

Porous membranes with ultrafast ion permeation and high ion selectivity are highly desirable for efficient mineral separation, water purification, and energy conversion, but it is still a huge challenge to efficiently separate monatomic ions of the same valence and similar sizes using synthetic membranes. We report metal organic framework (MOF) membranes, including ZIF-8 and UiO-66 membranes with uniform subnanometer pores consisting of angstrom-sized windows and nanometer-sized cavities for ultrafast selective transport of alkali metal ions. The angstrom-sized windows acted as ion selectivity filters for selection of alkali metal ions, whereas the nanometer-sized cavities functioned as ion conductive pores for ultrafast ion transport. The ZIF-8 and UiO-66 membranes showed a LiCl/RbCl selectivity of ~4.6 and ~1.8, respectively, which are much greater than the LiCl/RbCl selectivity of 0.6 to 0.8 measured in traditional porous membranes. Molecular dynamics simulations suggested that ultrafast and selective ion transport in ZIF-8 was associated with partial dehydration effects. This study reveals ultrafast and selective transport of monovalent ions in subnanometer MOF pores and opens up a new avenue to develop unique MOF platforms for efficient ion separations in the future.

Low-Rank Matrix Recovery Approach for Clutter Rejection in Real-Time IR-UWB Radar-Based Moving Target Detection

PubMed Central

Sabushimike, Donatien; Na, Seung You; Kim, Jin Young; Bui, Ngoc Nam; Seo, Kyung Sik; Kim, Gil Gyeom

2016-01-01

The detection of a moving target using an IR-UWB Radar involves the core task of separating the waves reflected by the static background and by the moving target. This paper investigates the capacity of the low-rank and sparse matrix decomposition approach to separate the background and the foreground in the trend of UWB Radar-based moving target detection. Robust PCA models are criticized for being batched-data-oriented, which makes them inconvenient in realistic environments where frames need to be processed as they are recorded in real time. In this paper, a novel method based on overlapping-windows processing is proposed to cope with online processing. The method consists of processing a small batch of frames which will be continually updated without changing its size as new frames are captured. We prove that RPCA (via its Inexact Augmented Lagrange Multiplier (IALM) model) can successfully separate the two subspaces, which enhances the accuracy of target detection. The overlapping-windows processing method converges on the optimal solution with its batch counterpart (i.e., processing batched data with RPCA), and both methods prove the robustness and efficiency of the RPCA over the classic PCA and the commonly used exponential averaging method. PMID:27598159

Fourier band-power E/B-mode estimators for cosmic shear

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

Becker, Matthew R.; Rozo, Eduardo

We introduce new Fourier band-power estimators for cosmic shear data analysis and E/B-mode separation. We consider both the case where one performs E/B-mode separation and the case where one does not. The resulting estimators have several nice properties which make them ideal for cosmic shear data analysis. First, they can be written as linear combinations of the binned cosmic shear correlation functions. Secondly, they account for the survey window function in real-space. Thirdly, they are unbiased by shape noise since they do not use correlation function data at zero separation. Fourthly, the band-power window functions in Fourier space are compactmore » and largely non-oscillatory. Fifthly, they can be used to construct band-power estimators with very efficient data compression properties. In particular, we find that all of the information on the parameters Ωm, σ8 and ns in the shear correlation functions in the range of ~10–400 arcmin for single tomographic bin can be compressed into only three band-power estimates. Finally, we can achieve these rates of data compression while excluding small-scale information where the modelling of the shear correlation functions and power spectra is very difficult. Given these desirable properties, these estimators will be very useful for cosmic shear data analysis.« less

Core-shell structured ceramic nonwoven separators by atomic layer deposition for safe lithium-ion batteries

NASA Astrophysics Data System (ADS)

Shen, Xiu; Li, Chao; Shi, Chuan; Yang, Chaochao; Deng, Lei; Zhang, Wei; Peng, Longqing; Dai, Jianhui; Wu, Dezhi; Zhang, Peng; Zhao, Jinbao

2018-05-01

Safety is one of the most factors for lithium-ion batteries (LIBs). In this work, a novel kind of ceramic separator with high safety insurance is proposed. We fabricated the core-shell nanofiber separators for LIBs by atomic layer deposition (ALD) of 30 nm Al2O3 on the electrospinning nonwoven fiber of polyvinylidene fluoride-hexafluoropropylene (PVDF-HFP). The separators show a pretty high heat resistance up to 200 °C without any shrinkage, an excellent fire-resistant property and a wide electrochemical window. Besides, with higher uptake and ionic conductivity, cells assembled with the novel separator shows better electrochemical performance. The ALD produced separators exhibit great potential in elaborate products like 3C communications and in energy field with harsh requirements for safety such as electric vehicles. The application of ALD on polymer fiber membranes brings a new strategy and opportunity for improving the safety of the advanced LIBs.

Auditory Processing Efficiency and Temporal Resolution in Children and Adults.

ERIC Educational Resources Information Center

Hill, Penelope R.; Hartley, Douglas E.H.; Glasberg, Brian R.; Moore, Brian C.J.; Moore, David R.

2004-01-01

Children have higher auditory backward masking (BM) thresholds than adults. One explanation for this is poor temporal resolution, resulting in difficulty separating brief or rapidly presented sounds. This implies that the auditory temporal window is broader in children than in adults. Alternatively, elevated BM thresholds in children may indicate…

Maximizing the Benefits of Training by Example and Direct Instruction

DTIC Science & Technology

2008-01-08

Psychonomic Bulletin & Review , 13, 474-479. This work follows from behavioral and simulation work published in December of 2004 on a similar topic...isolation. Psychonomic Bulletin & Review , 13, 474-479. Jones, M., Love, B. C., & Maddox, W. T. (2006) Recency as a window to generalization: Separating

Worldwide Research, Worldwide Participation: Web-Based Test Logger

NASA Technical Reports Server (NTRS)

Clark, David A.

1998-01-01

Thanks to the World Wide Web, a new paradigm has been born. ESCORT (steady state data system) facilities can now be configured to use a Web-based test logger, enabling worldwide participation in tests. NASA Lewis Research Center's new Web-based test logger for ESCORT automatically writes selected test and facility parameters to a browser and allows researchers to insert comments. All data can be viewed in real time via Internet connections, so anyone with a Web browser and the correct URL (universal resource locator, or Web address) can interactively participate. As the test proceeds and ESCORT data are taken, Web browsers connected to the logger are updated automatically. The use of this logger has demonstrated several benefits. First, researchers are free from manual data entry and are able to focus more on the tests. Second, research logs can be printed in report format immediately after (or during) a test. And finally, all test information is readily available to an international public.

Automatically assisting human memory: a SenseCam browser.

PubMed

Doherty, Aiden R; Moulin, Chris J A; Smeaton, Alan F

2011-10-01

SenseCams have many potential applications as tools for lifelogging, including the possibility of use as a memory rehabilitation tool. Given that a SenseCam can log hundreds of thousands of images per year, it is critical that these be presented to the viewer in a manner that supports the aims of memory rehabilitation. In this article we report a software browser constructed with the aim of using the characteristics of memory to organise SenseCam images into a form that makes the wealth of information stored on SenseCam more accessible. To enable a large amount of visual information to be easily and quickly assimilated by a user, we apply a series of automatic content analysis techniques to structure the images into "events", suggest their relative importance, and select representative images for each. This minimises effort when browsing and searching. We provide anecdotes on use of such a system and emphasise the need for SenseCam images to be meaningfully sorted using such a browser.

BigWig and BigBed: enabling browsing of large distributed datasets.

PubMed

Kent, W J; Zweig, A S; Barber, G; Hinrichs, A S; Karolchik, D

2010-09-01

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, R.; Glaser, C.; Klingebiel, D.; Komm, M.; Müller, G.; Rieger, M.; Steggemann, J.; Urban, M.; Winchen, T.

2014-06-01

Many programs in experimental particle physics do not yet have a graphical interface, or demand strong platform and software requirements. With the most recent development of the VISPA project, we provide graphical interfaces to existing software programs and access to multiple computing clusters through standard web browsers. The scalable clientserver system allows analyses to be performed in sizable teams, and disburdens the individual physicist from installing and maintaining a software environment. The VISPA graphical interfaces are implemented in HTML, JavaScript and extensions to the Python webserver. The webserver uses SSH and RPC to access user data, code and processes on remote sites. As example applications we present graphical interfaces for steering the reconstruction framework OFFLINE of the Pierre-Auger experiment, and the analysis development toolkit PXL. The browser based VISPA system was field-tested in biweekly homework of a third year physics course by more than 100 students. We discuss the system deployment and the evaluation by the students.

EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

PubMed

Loman, Nicholas J; Pallen, Mark J

2010-06-21

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

Launch Control System Master Console Event Message Reduction

NASA Technical Reports Server (NTRS)

Nguyen, Uyen

2014-01-01

System monitoring and control (SMC) message browsers receive so many messages daily that operators do not need to see. Important messages are often mixed up among the less important ones. My job is to reduce the messages displayed in the message browser so that warning and emergency messages can be seen easily and therefore, responded promptly. There are multiple methods to achieve this. Firstly, duplicate messages should not appear many times in the message browser. Instead, the message should appear only once but with a number that counts the times that it appears. This method is called duplicate message suppression. Secondly, messages that update the most recent state (e.g. up/down) of a component should replace the old-state messages. This method is called state based message correlation. Thirdly, messages that display "normal" alarm level should be suppressed unless it's a response to an operator action. In addition to message reduction, I also work on correcting the severity level and text formats on messages.

Using Mobile Devices to Display, Overlay, and Animate Geophysical Data and Imagery

NASA Astrophysics Data System (ADS)

Batzli, S.; Parker, D.

2011-12-01

A major challenge in mobile-device map application development is to offer rich content and features with simple and intuitive controls and fast performance. Our goal is to bring visualization, animation, and notifications of near real-time weather and earth observation information derived from satellite and sensor data to mobile devices. Our robust back-end processing infrastructure can deliver content in the form of images, shapes, standard descriptive formats (eg. KML, JSON) or raw data to a variety of desktop software, browsers, and mobile devices on demand. We have developed custom interfaces for low-bandwidth browsers (including mobile phones) and high-feature browsers (including smartphones), as well as native applications for Android and iOS devices. Mobile devices offer time- and location-awareness and persistent data connections, allowing us to tailor timely notifications and displays to the user's geographic and time context. This presentation includes a live demo of how our mobile apps deliver animation of standard and custom data products in an interactive map interface.

The UCSC Genome Browser: What Every Molecular Biologist Should Know

PubMed Central

Mangan, Mary E.; Williams, Jennifer M.; Kuhn, Robert M.; Lathe, Warren C.

2014-01-01

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data make benchwork much more efficient and drive new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. PMID:24984850

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

Context-Dependent Diversity-Effects of Seaweed Consumption on Coral Reefs in Kenya

PubMed Central

Humphries, Austin T.; McQuaid, Christopher D.; McClanahan, Tim R.

2015-01-01

Consumers and prey diversity, their interactions, and subsequent effects on ecosystem function are important for ecological processes but not well understood in high diversity ecosystems such as coral reefs. Consequently, we tested the potential for diversity-effects with a series of surveys and experiments evaluating the influence of browsing herbivores on macroalgae in Kenya’s fringing reef ecosystem. We surveyed sites and undertook experiments in reefs subject to three levels of human fishing influence: open access fished reefs, small and recently established community-managed marine reserves, and larger, older government-managed marine reserves. Older marine reserves had a greater overall diversity of herbivores and browsers but this was not clearly associated with reduced macroalgal diversity or abundance. Experiments studying succession on hard substrata also found no effects of consumer diversity. Instead, overall browser abundance of either sea urchins or fishes was correlated with declines in macroalgal cover. An exception was that the absence of a key fish browser genus, Naso, which was correlated with the persistence of Sargassum in a marine reserve. Algal selectivity assays showed that macroalgae were consumed at variable rates, a product of strong species-specific feeding and low overlap in the selectivity of browsing fishes. We conclude that the effects of browser and herbivore diversity are less than the influences of key species, whose impacts emerge in different contexts that are influenced by fisheries management. Consequently, identifying key herbivore species and managing to protect them may assist protecting reef functions. PMID:26673609

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

PubMed

Wang, Chunliang; Ritter, Felix; Smedby, Orjan

2010-07-01

To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added <10ms of processing time while the other IPC methods cost 1-5 s in our experiments. The browser-server style communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

Experiments in MPEG-4 content authoring, browsing, and streaming

NASA Astrophysics Data System (ADS)

Puri, Atul; Schmidt, Robert L.; Basso, Andrea; Civanlar, Mehmet R.

2000-12-01

In this paper, within the context of the MPEG-4 standard we report on preliminary experiments in three areas -- authoring of MPEG-4 content, a player/browser for MPEG-4 content, and streaming of MPEG-4 content. MPEG-4 is a new standard for coding of audiovisual objects; the core of MPEG-4 standard is complete while amendments are in various stages of completion. MPEG-4 addresses compression of audio and visual objects, their integration by scene description, and interactivity of users with such objects. MPEG-4 scene description is based on VRML like language for 3D scenes, extended to 2D scenes, and supports integration of 2D and 3D scenes. This scene description language is called BIFS. First, we introduce the basic concepts behind BIFS and then show with an example, textual authoring of different components needed to describe an audiovisual scene in BIFS; the textual BIFS is then saved as compressed binary file/s for storage or transmission. Then, we discuss a high level design of an MPEG-4 player/browser that uses the main components from authoring such as encoded BIFS stream, media files it refers to, and multiplexed object descriptor stream to play an MPEG-4 scene. We also discuss our extensions to such a player/browser. Finally, we present our work in streaming of MPEG-4 -- the payload format, modification to client MPEG-4 player/browser, server-side infrastructure and example content used in our MPEG-4 streaming experiments.

Annoyance, Sleep and Concentration Problems due to Combined Traffic Noise and the Benefit of Quiet Side

PubMed Central

Bodin, Theo; Björk, Jonas; Ardö, Jonas; Albin, Maria

2015-01-01

Background: Access to a quiet side in one’s dwelling is thought to compensate for higher noise levels at the most exposed façade. It has also been indicated that noise from combined traffic sources causes more noise annoyance than equal average levels from either road traffic or railway noise separately. Methods: 2612 persons in Malmö, Sweden, answered to a residential environment survey including questions on outdoor environment, noise sensitivity, noise annoyance, sleep quality and concentration problems. Road traffic and railway noise was modeled using Geographic Information System. Results: Access to a quiet side, i.e., at least one window facing yard, water or green space, was associated with reduced risk of annoyance OR (95%CI) 0.47 (0.38–0.59), and concentration problems 0.76 (0.61–0.95). Bedroom window facing the same environment was associated to reduced risk of reporting of poor sleep quality 0.78 (0.64–1.00). Railway noise was associated with reduced risk of annoyance below 55 dB(A) but not at higher levels of exposure. Conclusions: Having a window facing a yard, water or green space was associated to a substantially reduced risk of noise annoyance and concentration problems. If this window was the bedroom window, sleeping problems were less likely. PMID:25642690

Software for illustrative presentation of basic clinical characteristics of laboratory tests--GraphROC for Windows.

PubMed

Kairisto, V; Poola, A

1995-01-01

GraphROC for Windows is a program for clinical test evaluation. It was designed for the handling of large datasets obtained from clinical laboratory databases. In the user interface, graphical and numerical presentations are combined. For simplicity, numerical data is not shown unless requested. Relevant numbers can be "picked up" from the graph by simple mouse operations. Reference distributions can be displayed by using automatically optimized bin widths. Any percentile of the distribution with corresponding confidence limits can be chosen for display. In sensitivity-specificity analysis, both illness- and health-related distributions are shown in the same graph. The following data for any cutoff limit can be shown in a separate click window: clinical sensitivity and specificity with corresponding confidence limits, positive and negative likelihood ratios, positive and negative predictive values and efficiency. Predictive values and clinical efficiency of the cutoff limit can be updated for any prior probability of disease. Receiver Operating Characteristics (ROC) curves can be generated and combined into the same graph for comparison of several different tests. The area under the curve with corresponding confidence interval is calculated for each ROC curve. Numerical results of analyses and graphs can be printed or exported to other Microsoft Windows programs. GraphROC for Windows also employs a new method, developed by us, for the indirect estimation of health-related limits and change limits from mixed distributions of clinical laboratory data.

On the use of transition matrix methods with extended ensembles.

PubMed

Escobedo, Fernando A; Abreu, Charlles R A

2006-03-14

Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate lambda were formulated so that they employ (i) "variable" sampling window schemes (that include the "successive umbrella sampling" method) to comprehensibly explore the lambda domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy eta landscape (or "importance" weights) associated with lambda. The connection between "acceptance ratio" and transition matrix methods was first established to form the basis of the approach for estimating eta(lambda). The validity and performance of the different NBS schemes were then assessed using as lambda coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of eta is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an "elastic" window of sampling can be used to effectively enact (nonuniform) preferential sampling over the lambda domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a eta surface over a two-dimensional domain.

Science Plan Visualisation for Rosetta

NASA Astrophysics Data System (ADS)

Schmidt, A.; Grieger, B.; Völk, S.

2013-12-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are flexible and particularly complex. To make informed decisions among the many free parameters novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

Communication of Science Plans in the Rosetta Mission

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2014-05-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are both flexible and particularly complex. To make informed decisions among the many free parameters, novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

PubMed

Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2015-10-15

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. brinkman@sfu.ca. © The Author 2015. Published by Oxford University Press.

Cross-standard user description in mobile, medical oriented virtual collaborative environments

NASA Astrophysics Data System (ADS)

Ganji, Rama Rao; Mitrea, Mihai; Joveski, Bojan; Chammem, Afef

2015-03-01

By combining four different open standards belonging to the ISO/IEC JTC1/SC29 WG11 (a.k.a. MPEG) and W3C, this paper advances an architecture for mobile, medical oriented virtual collaborative environments. The various users are represented according to MPEG-UD (MPEG User Description) while the security issues are dealt with by deploying the WebID principles. On the server side, irrespective of their elementary types (text, image, video, 3D, …), the medical data are aggregated into hierarchical, interactive multimedia scenes which are alternatively represented into MPEG-4 BiFS or HTML5 standards. This way, each type of content can be optimally encoded according to its particular constraints (semantic, medical practice, network conditions, etc.). The mobile device should ensure only the displaying of the content (inside an MPEG player or an HTML5 browser) and the capturing of the user interaction. The overall architecture is implemented and tested under the framework of the MEDUSA European project, in partnership with medical institutions. The testbed considers a server emulated by a PC and heterogeneous user devices (tablets, smartphones, laptops) running under iOS, Android and Windows operating systems. The connection between the users and the server is alternatively ensured by WiFi and 3G/4G networks.

PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection

PubMed Central

O’Halloran, Damien M.

2016-01-01

Primer design represents a widely employed gambit in diverse molecular applications including PCR, sequencing, and probe hybridization. Variations of PCR, including primer walking, allele-specific PCR, and nested PCR provide specialized validation and detection protocols for molecular analyses that often require screening large numbers of DNA fragments. In these cases, automated sequence retrieval and processing become important features, and furthermore, a graphic that provides the user with a visual guide to the distribution of designed primers across targets is most helpful in quickly ascertaining primer coverage. To this end, I describe here, PrimerMapper, which provides a comprehensive graphical user interface that designs robust primers from any number of inputted sequences while providing the user with both, graphical maps of primer distribution for each inputted sequence, and also a global assembled map of all inputted sequences with designed primers. PrimerMapper also enables the visualization of graphical maps within a browser and allows the user to draw new primers directly onto the webpage. Other features of PrimerMapper include allele-specific design features for SNP genotyping, a remote BLAST window to NCBI databases, and remote sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely available without restriction. PMID:26853558

EnviroAtlas Connects Urban Ecosystem Services and Human ...

EPA Pesticide Factsheets

Ecosystem services in urban areas can improve public health and well-being by mitigating natural and anthropogenic pollution, and by promoting healthy lifestyles that include engagement with nature and enhanced opportunities for physical activity and social interaction. EPA’s EnviroAtlas online mapping tool identifies urban environmental features linked in the scientific and medical literature to specific aspects of public health and well-being. EnviroAtlas researchers have synthesized newly-generated one-meter resolution landcover data, downscaled census population data, and other existing datasets such as roads and parks. Resulting geospatial metrics represent health-related indicators of urban ecosystem services supply and demand by census block-group and finer scales. EnviroAtlas maps include percent of the population with limited window views of trees, tree cover along walkable roads, overall neighborhood green space, and proximity to parks. Demographic data can be overlaid to perform analyses of disproportionate distribution of urban ecosystem services across population groups. Together with the Eco-Health Relationship Browser, EnviroAtlas data can be linked to numerous aspects of public health and well-being including school performance, physical fitness, social capital, and longevity. EnviroAtlas maps have been developed using consistent methods to allow for comparisons between neighborhoods and across multiple U.S. communities. To feature eco-heal

2D and 3D virtual interactive laboratories of physics on Unity platform

NASA Astrophysics Data System (ADS)

González, J. D.; Escobar, J. H.; Sánchez, H.; De la Hoz, J.; Beltrán, J. R.

2017-12-01

Using the cross-platform game engine Unity, we develop virtual laboratories for PC, consoles, mobile devices and website as an innovative tool to study physics. There is extensive uptake of ICT in the teaching of science and its impact on the learning, and considering the limited availability of laboratories for physics teaching and the difficulties this causes in the learning of school students, we design the virtual laboratories to enhance studentâĂŹs knowledge of concepts in physics. To achieve this goal, we use Unity due to provide support bump mapping, reflection mapping, parallax mapping, dynamics shadows using shadows maps, full-screen post-processing effects and render-to-texture. Unity can use the best variant for the current video hardware and, if none are compatible, to use an alternative shader that may sacrifice features for performance. The control over delivery to mobile devices, web browsers, consoles and desktops is the main reason Unity is the best option among the same kind cross-platform. Supported platforms include Android, Apple TV, Linux, iOS, Nintendo 3DS line, macOS, PlayStation 4, Windows Phone 8, Wii but also an asset server and Nvidia’s PhysX physics engine which is the most relevant tool on Unity for our PhysLab.

JavaScript DNA translator: DNA-aligned protein translations.

PubMed

Perry, William L

2002-12-01

There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

The dynamics underlying the regeneration and stalling of Hurricane Harvey

NASA Astrophysics Data System (ADS)

Liang, X. S.

2017-12-01

The explosive regeneration and stalling make the hurricane Harvey go from a little-noticed storm to an extremely destructive behemoth in late August 2017 that incurred an estimated economic loss at 70-200 billion USD. In this study, we use a recently developed analysis tool, namely, multiscale window transform (MWT), and the MWT-based theory of canonical transfer, to investigate the dynamics underlying this regeneration and stalling. The atmospheric fields are reconstructed onto three scale ranges or windows, namely, large-scale, tropical cyclone-scale, and cumulus convection-scale windows. The intertwined cyclone-scale nonlinear energy process is uniquely separated into a transport of energy within the cyclone window and an interscale transfer through reconstructing the "atomic" energy fluxes on the multiple scale windows. The resulting transfer bears a Lie bracket form, reminiscent of the Poisson bracket in Hamiltonian mechanics, and is hence referred to as canonical. It is found that within the Gulf of Mexico, Harvey gains much energy from the cumulus convection window through an inverse energy cascade, leading to its explosive growth. In the mean time, there is a barotropic instability (positive canonical transfer) center of the mean circulation in the lower and mid troposphere which lies quasi-steadily over Houston during August 22 through early September. The northwestward propagating Harvey meets that center and then stalls for two days near the coastline, dropping torrential and unprecedented amounts of rainfall and causing catastrophic flooding. It moves out of the instability center by the end of August, and then dissipates quickly in the following days.

Asay window: A new spall diagnostic

NASA Astrophysics Data System (ADS)

McCluskey, Craig W.; Wilke, Mark D.; Anderson, William W.; Byers, Mark E.; Holtkamp, David B.; Rigg, Paulo A.; Furnish, Michael D.; Romero, Vincent T.

2006-11-01

By changing from the metallic foil of the Asay foil diagnostic, which can detect ejecta from a shocked surface, to a lithium fluoride (LiF) or polymethyl methacrylate (PMMA) window, it is possible to detect multiple spall layers and interlayer rubble. Past experiments to demonstrate this diagnostic have used high explosives (HEs) to shock metals to produce multiple spall layers. Because the exact characteristics of HE-induced spall layers cannot be predetermined, two issues exist in the quantitative interpretation of the data. First, to what level of fidelity is the Asay window method capable of providing quantitative information about spall layers, possibly separated by rubble, and second, contingent on the first, can an analytic technique be developed to convert the data to a meaningful description of spall from a given experiment? In this article, we address the first issue. A layered projectile fired from a gas gun was used to test the new diagnostic's accuracy and repeatability. We impacted a LiF or PMMA window viewed by a velocity interferometer system for any reflector (VISAR) probe with a projectile consisting of four thin stainless steel disks spaced apart 200μm with either vacuum or polyethylene. The window/surface interface velocity measured with a VISAR probe was compared with calculations. The good agreement observed between the adjusted calculation and the measured data indicates that, in principle and given enough prior information, it is possible to use the Asay window data to model a density distribution from spalled material with simple hydrodynamic models and only simple adjustments to nominal predictions.

NASA Tech Briefs, November 2010

NASA Technical Reports Server (NTRS)

2010-01-01

Topics covered include: Portable Handheld Optical Window Inspection Device; Salience Assignment for Multiple-Instance Data and Its Application to Crop Yield Prediction; Speech Acquisition and Automatic Speech Recognition for Integrated Spacesuit Audio Systems ; Predicting Long-Range Traversability from Short-Range Stereo-Derived Geometry; Browser-Based Application for Telemetry Monitoring of Robotic Assets; Miniature Low-Noise G-Band I-Q Receiver; Methods of Using a Magnetic Field Response Sensor Within Closed, Electrically Conductive Containers; Differential Resonant Ring YIG Tuned Oscillator; Microfabricated Segmented-Involute-Foil Regenerator for Stirling Engines; Reducing Seal Adhesion in Low Impact Docking Systems; Optimal Flow Control Design; Corrosion-Resistant Container for Molten-Material Processing; Reusable Hot-Wire Cable Cutter; Deployment of a Curved Truss; High-Volume Airborne Fluids Handling Technologies to Fight Wildfires; Modeling of Alkane Oxidation Using Constituents and Species; Fabrication of Lanthanum Telluride 14-1-11 Zintl High-Temperature Thermoelectric Couple; A Computer Model for Analyzing Volatile Removal Assembly; Analysis of Nozzle Jet Plume Effects on Sonic Boom Signature; Optical Sidebands Multiplier; Single Spatial-Mode Room-Temperature-Operated 3.0 to 3.4 micrometer Diode Lasers; Self-Nulling Beam Combiner Using No External Phase Inverter; Portable Dew Point Mass Spectrometry System for Real-Time Gas and Moisture Analysis; Maximum Likelihood Time-of-Arrival Estimation of Optical Pulses via Photon-Counting Photodetectors; Handheld White Light Interferometer for Measuring Defect Depth in Windows; Decomposition Algorithm for Global Reachability on a Time-Varying Graph; Autonomous GN and C for Spacecraft Exploration of Comets and Asteroids; Efficient Web Services Policy Combination; Using CTX Image Features to Predict HiRISE-Equivalent Rock Density; Isolation of the Paenibacillus phoenicis, a Spore-Forming Bacterium; Monolithically Integrated, Mechanically Resilient Carbon-Based Probes for Scanning Probe Microscopy; Cell Radiation Experiment System; Process to Produce Iron Nanoparticle Lunar Dust Simulant Composite; Inversion Method for Early Detection of ARES-1 Case Breach Failure; Use of ILTV Control Laws for LaNCETS Flight Research;and Evaluating Descent and Ascent Trajectories Near Non-Spherical Bodies.

mod_bio: Apache modules for Next-Generation sequencing data.

PubMed

Lindenbaum, Pierre; Redon, Richard

2015-01-01

We describe mod_bio, a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service. https://github.com/lindenb/mod_bio. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

PubMed

Vanderkam, Dan; Aksoy, B Arman; Hodes, Isaac; Perrone, Jaclyn; Hammerbacher, Jeff

2016-08-01

P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license. correspondence@hammerlab.org. © The Author 2016. Published by Oxford University Press.

CliniSpace: a multiperson 3D online immersive training environment accessible through a browser.

PubMed

Dev, Parvati; Heinrichs, W LeRoy; Youngblood, Patricia

2011-01-01

Immersive online medical environments, with dynamic virtual patients, have been shown to be effective for scenario-based learning (1). However, ease of use and ease of access have been barriers to their use. We used feedback from prior evaluation of these projects to design and develop CliniSpace. To improve usability, we retained the richness of prior virtual environments but modified the user interface. To improve access, we used a Software-as-a-Service (SaaS) approach to present a richly immersive 3D environment within a web browser.

Daylighting in Schools: An Investigation into the Relationship between Daylighting and Human Performance. Detailed Report.

ERIC Educational Resources Information Center

Heschong, Lisa

This study examines the effect of daylighting on human performance, focusing on skylighting as a way to isolate daylight as an illumination source, and separate illumination effects from other qualities associated with daylighting from windows. It establishes a statistical connection between daylighting and student performance and between…

Super-Resolution for Color Imagery

DTIC Science & Technology

2017-09-01

separately; however, it requires performing the super-resolution computation 3 times. We transform images in the default red, green, blue (RGB) color space...chrominance components based on ARL’s alias-free image upsampling using Fourier-based windowing methods. A reverse transformation is performed on... Transformation from sRGB to CIELAB............................................... 3 Fig. 2 YCbCr mathematical coordinate transformation

Spectral definition of the ArTeMiS instrument

NASA Astrophysics Data System (ADS)

Haynes, Vic; Maffei, Bruno; Pisano, Giampaolo; Dubreuil, Didier; Delisle, Cyrille; Le Pennec, Jean; Hurtado, Norma

2014-07-01

ArTeMiS is a sub-millimetre camera to be operated, on the Atacama Pathfinder Experiment Telescope (APEX). The ultimate goal is to observe simultaneously in three atmospheric spectral windows in the region of 200, 350 and 450 microns. We present the filtering scheme, which includes the cryostat window, thermal rejection elements, band separation and spectral isolation, which has been adopted for this instrument. This was achieved using a combination of scattering, Yoshinaga filters, organic dyes and Ulrich type embedded metallic mesh devices. Design of the quasi-optical mesh components has been developed by modelling with an in-house developed code. For the band separating dichroics, which are used with an incidence angle of 35 deg, further modelling has been performed with HFSS (Ansoft). Spectral characterization of the components for the 350 and 450 bands have been performed with a Martin-Puplett Polarizing Fourier Transform Spectrometer. While for the first commissioning and observation campaign, one spectral band only was operational (350 microns), we report on the design of the 200, 350 and 450 micron bands.

Wall shear stress characterization of a 3D bluff-body separated flow

NASA Astrophysics Data System (ADS)

Fourrié, Grégoire; Keirsbulck, Laurent; Labraga, Larbi

2013-10-01

Efficient flow control strategies aimed at reducing the aerodynamic drag of road vehicles require a detailed knowledge of the reference flow. In this work, the flow around the rear slanted window of a generic car model was experimentally studied through wall shear stress measurements using an electrochemical method. The mean and fluctuating wall shear stress within the wall impact regions of the recirculation bubble and the main longitudinal vortex structures which develop above the rear window are presented. Correlations allow a more detailed characterization of the recirculation phenomenon within the separation bubble. In the model symmetry plane the recirculation structure compares well with simpler 2D configurations; specific lengths, flapping motion and shedding of large-scale vortices are observed, these similarities diminish when leaving the middle plane due to the strong three-dimensionality of the flow. A specific attention is paid to the convection processes occurring within the recirculation: a downstream convection velocity is observed, in accordance with 2D recirculations from the literature, and an upstream convection is highlighted along the entire bubble length which has not been underlined in some previous canonical configurations.

Fast Human Detection for Intelligent Monitoring Using Surveillance Visible Sensors

PubMed Central

Ko, Byoung Chul; Jeong, Mira; Nam, JaeYeal

2014-01-01

Human detection using visible surveillance sensors is an important and challenging work for intruder detection and safety management. The biggest barrier of real-time human detection is the computational time required for dense image scaling and scanning windows extracted from an entire image. This paper proposes fast human detection by selecting optimal levels of image scale using each level's adaptive region-of-interest (ROI). To estimate the image-scaling level, we generate a Hough windows map (HWM) and select a few optimal image scales based on the strength of the HWM and the divide-and-conquer algorithm. Furthermore, adaptive ROIs are arranged per image scale to provide a different search area. We employ a cascade random forests classifier to separate candidate windows into human and nonhuman classes. The proposed algorithm has been successfully applied to real-world surveillance video sequences, and its detection accuracy and computational speed show a better performance than those of other related methods. PMID:25393782

Lifelong personal health data and application software via virtual machines in the cloud.

PubMed

Van Gorp, Pieter; Comuzzi, Marco

2014-01-01

Personal Health Records (PHRs) should remain the lifelong property of patients, who should be able to show them conveniently and securely to selected caregivers and institutions. In this paper, we present MyPHRMachines, a cloud-based PHR system taking a radically new architectural solution to health record portability. In MyPHRMachines, health-related data and the application software to view and/or analyze it are separately deployed in the PHR system. After uploading their medical data to MyPHRMachines, patients can access them again from remote virtual machines that contain the right software to visualize and analyze them without any need for conversion. Patients can share their remote virtual machine session with selected caregivers, who will need only a Web browser to access the pre-loaded fragments of their lifelong PHR. We discuss a prototype of MyPHRMachines applied to two use cases, i.e., radiology image sharing and personalized medicine.

Image-guided adaptive gating of lung cancer radiotherapy: a computer simulation study

NASA Astrophysics Data System (ADS)

Aristophanous, Michalis; Rottmann, Joerg; Park, Sang-June; Nishioka, Seiko; Shirato, Hiroki; Berbeco, Ross I.

2010-08-01

The purpose of this study is to investigate the effect that image-guided adaptation of the gating window during treatment could have on the residual tumor motion, by simulating different gated radiotherapy techniques. There are three separate components of this simulation: (1) the 'Hokkaido Data', which are previously measured 3D data of lung tumor motion tracks and the corresponding 1D respiratory signals obtained during the entire ungated radiotherapy treatments of eight patients, (2) the respiratory gating protocol at our institution and the imaging performed under that protocol and (3) the actual simulation in which the Hokkaido Data are used to select tumor position information that could have been collected based on the imaging performed under our gating protocol. We simulated treatments with a fixed gating window and a gating window that is updated during treatment. The patient data were divided into different fractions, each with continuous acquisitions longer than 2 min. In accordance to the imaging performed under our gating protocol, we assume that we have tumor position information for the first 15 s of treatment, obtained from kV fluoroscopy, and for the rest of the fractions the tumor position is only available during the beam-on time from MV imaging. The gating window was set according to the information obtained from the first 15 s such that the residual motion was less than 3 mm. For the fixed gating window technique the gate remained the same for the entire treatment, while for the adaptive technique the range of the tumor motion during beam-on time was measured and used to adapt the gating window to keep the residual motion below 3 mm. The algorithm used to adapt the gating window is described. The residual tumor motion inside the gating window was reduced on average by 24% for the patients with regular breathing patterns and the difference was statistically significant (p-value = 0.01). The magnitude of the residual tumor motion depended on the regularity of the breathing pattern suggesting that image-guided adaptive gating should be combined with breath coaching. The adaptive gating window technique was able to track the exhale position of the breathing cycle quite successfully. Out of a total of 53 fractions the duty cycle was greater than 20% for 42 fractions for the fixed gating window technique and for 39 fractions for the adaptive gating window technique. The results of this study suggest that real-time updating of the gating window can result in reliably low residual tumor motion and therefore can facilitate safe margin reduction.

Mid Miocene Terrestrial Ecosystems: Information from Mammalian Herbivore Communities.

NASA Astrophysics Data System (ADS)

Janis, C. M.; Damuth, J.; Theodor, J. M.

2001-05-01

In present day ecosystems the numbers and proportions of different kinds of ecologically distinct ungulates (hoofed mammals) provide an indicator of the nature of the vegetation in the habitat. Different vegetation types (such as forest, savanna, or grassland) are characteristically associated with different arrays of ungulates, with species exhibiting differences in diet, body size, and type of digestive fermentation system. These biological attributes can also be inferred for fossil ungulate species, the first two from quantitative assessment of skull and dental anatomy, and the last from phylogenetic affinity. Thus fossil ungulate communities may be used as indicators of the vegetation types of the habitats in which they lived. Vegetation types, in turn, are determined largely by a number of physical environmental factors. Typical ungulate communities of the late early to early middle Miocene (17 - 15 Ma) from the Great Plains of North America contained a diversity of browsing (leaf-eating) and grazing (grass-eating) species, with proportions of dietary types and a diversity of body sizes indicative of a woodland savanna habitat. Paleobotanical evidence also indicates a woodland savanna type of vegetation. However, these communities included a much larger number of ungulate species than can be found in any present-day community. The "excess" ungulate species were primarily browsers. Throughout the rest of the middle Miocene both species numbers and the proportion of browsers in ungulate communities appear to have declined steadily. During this decline in browser species the numbers of grazer species remained relatively constant. Within-community species numbers comparable to the present day were attained by the late Miocene. We suggest that the early Miocene browser-rich communities, and their subsequent decline, carry an important paleoenvironmental signal. In particular, communities "over rich" in browsers may reflect higher levels of primary productivity in mid Miocene vegetation types in comparison with corresponding, structurally equivalent present-day vegetation types. The observed decline in species numbers may represent a gradual decline in terrestrial primary productivity, which would be consistent with one current hypothesis of a mid-Miocene decrease in atmospheric carbon dioxide concentrations from higher mid-Cenozoic values.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model.

GenColors: annotation and comparative genomics of prokaryotes made easy.

PubMed

Romualdi, Alessandro; Felder, Marius; Rose, Dominic; Gausmann, Ulrike; Schilhabel, Markus; Glöckner, Gernot; Platzer, Matthias; Sühnel, Jürgen

2007-01-01

GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries. PMID:16984652

Concertina browsers: a formative evaluation of user preference.

PubMed

Harper, Simon; Christophorou, Nicola

2008-09-01

Evidence suggests that concertina browsers - browsers with the facility to expand and contract sections of information - are important in providing the reader with an enhanced cognition of small to medium amounts of information. These systems have been shown to be useful for visually disabled users surfing the World Wide Web (Web), and with the development of the Mobile Web, there has been renewed interest in their use. This is due to the similarities of reduced or constrained vision found to exist between visually impaired users and the users of mobile devices. The cognition of information fragments is key to the user experience and the reduction of 'information overload'; as such we are concerned with assisting designers of concertina browsers in providing an enhanced user experience by ascertaining user preference through a formative evaluation of concertina summaries. This aspect of browsing is important because in all concertina systems there is a distinct cognition speed/depth trade-off. Here we investigate a number of these concertina summarization techniques against each other. We describe a formative evaluation which concludes that users prefer concertina summarization of Web documents starting from 6.25% slices of both the top and bottom and expanding from the top in 2% steps to a target maximum of 18.50% (being 12.25% from the top and 6.25% from the bottom). These preferences were found to be representative of documents of less than 600 words of content, and included the preference to not fragment an individual sentence even if that meant slightly increasing the target: Starting, maximum, and step percentage slices.

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

Optimization of the Energy Window for PETbox4, a Preclinical PET Tomograph With a Small Inner Diameter

NASA Astrophysics Data System (ADS)

Gu, Z.; Bao, Q.; Taschereau, R.; Wang, H.; Bai, B.; Chatziioannou, A. F.

2014-06-01

Small animal positron emission tomography (PET) systems are often designed by employing close geometry configurations. Due to the different characteristics caused by geometrical factors, these tomographs require data acquisition protocols that differ from those optimized for conventional large diameter ring systems. In this work we optimized the energy window for data acquisitions with PETbox4, a 50 mm detector separation (box-like geometry) pre-clinical PET scanner, using the Geant4 Application for Tomographic Emission (GATE). The fractions of different types of events were estimated using a voxelized phantom including a mouse as well as its supporting chamber, mimicking a realistic mouse imaging environment. Separate code was developed to extract additional information about the gamma interactions for more accurate event type classification. Three types of detector backscatter events were identified in addition to the trues, phantom scatters and randoms. The energy window was optimized based on the noise equivalent count rate (NECR) and scatter fraction (SF) with lower-level discriminators (LLD) corresponding to energies from 150 keV to 450 keV. The results were validated based on the calculated image uniformity, spillover ratio (SOR) and recovery coefficient (RC) from physical measurements using the National Electrical Manufacturers Association (NEMA) NU-4 image quality phantom. These results indicate that when PETbox4 is operated with a more narrow energy window (350-650 keV), detector backscatter rejection is unnecessary. For the NEMA NU-4 image quality phantom, the SOR for the water chamber decreases by about 45% from 15.1% to 8.3%, and the SOR for the air chamber decreases by 31% from 12.0% to 8.3% at the LLDs of 150 and 350 keV, without obvious change in uniformity, further supporting the simulation based optimization. The optimization described in this work is not limited to PETbox4, but also applicable or helpful to other small inner diameter geometry scanners.

Coaxial microwave electrothermal thruster performance in hydrogen

NASA Technical Reports Server (NTRS)

Richardson, W.; Asmussen, J.; Hawley, M.

1994-01-01

The microwave electro thermal thruster (MET) is an electric propulsion concept that offers the promise of high performance combined with a long lifetime. A unique feature of this electric propulsion concept is its ability to create a microwave plasma discharge separated or floating away from any electrodes or enclosing walls. This allows propellant temperatures that are higher than those in resistojets and reduces electrode and wall erosion. It has been demonstrated that microwave energy is coupled into discharges very efficiently at high input power levels. As a result of these advantages, the MET concept has been identified as a future high power electric propulsion possibility. Recently, two additional improvements have been made to the coaxial MET. The first was concerned with improving the microwave matching. Previous experiments were conducted with 10-30 percent reflected power when incident power was in excess of 600 W(exp 6). Power was reflected back to the generator because the impedance of the MET did not match the 50 ohm impedance of the microwave circuit. To solve this problem, a double stub tuning system has been inserted between the MET and the microwave power supply. The addition of the double stub tuners reduces the reflected power below 1 percent. The other improvement has prepared the coaxial MET for hydrogen experiments. To operate with hydrogen, the vacuum window which separates the coaxial line from the discharge chamber has been changed from teflon to boron nitride. All the microwave energy delivered to the plasma discharge passes through this vacuum window. This material change had caused problems in the past because of the increased microwave reflection coefficients associated with the electrical properties of boron nitride. However, by making the boron nitride window electrically one-half of a wavelength long, power reflection in the window has been eliminated. This technical note summarizes the experimental performance of the improved coaxial MET when operating in nitrogen, helium, and hydrogen gases.

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

PubMed

Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James; Hermida, Leandro; Primig, Michael

2007-01-01

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at http://www.germonline.org/.

Seed Dispersers, Seed Predators, and Browsers Act Synergistically as Biotic Filters in a Mosaic Landscape

PubMed Central

Zamora, Regino; Matías, Luis

2014-01-01

In this study, we analize the functional influence of animals on the plants they interact with in a mediterranean mountain. We hypothesise that seed dispersers, seed predators, and browsers can act as biotic filters for plant communities. We analyse the combined effects of mutualistic (seed dispersal) and antagonistic (seed predation, herbivory) animal interactions in a mosaic landscape of Mediterranean mountains, basing our results on observational and experimental field. Most of the dispersed seeds came from tree species, whereas the population of saplings was composed predominantly of zoochorous shrub species. Seed predators preferentially consumed seeds from tree species, whereas seeds from the dominant fleshy-fruited shrubs had a higher probability of escaping these predators. The same pattern was repeated among the different landscape units by browsers, since they browsed selectively and far more intensely on tree-species saplings than on the surrounding shrubs. In synthesis, our work identifies the major biotic processes that appear to be favoring a community dominated by shrubs versus trees because seed dispersers, predators, and herbivores together favored shrub dispersal and establishment versus trees. PMID:25233342

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

PubMed Central

2010-01-01

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/ PMID:20565938

Natural bounds on herbivorous coral reef fishes

PubMed Central

Hoey, Andrew S.; Williams, Gareth J.; Williams, Ivor D.

2016-01-01

Humans are an increasingly dominant driver of Earth's biological communities, but differentiating human impacts from natural drivers of ecosystem state is crucial. Herbivorous fish play a key role in maintaining coral dominance on coral reefs, and are widely affected by human activities, principally fishing. We assess the relative importance of human and biophysical (habitat and oceanographic) drivers on the biomass of five herbivorous functional groups among 33 islands in the central and western Pacific Ocean. Human impacts were clear for some, but not all, herbivore groups. Biomass of browsers, large excavators, and of all herbivores combined declined rapidly with increasing human population density, whereas grazers, scrapers, and detritivores displayed no relationship. Sea-surface temperature had significant but opposing effects on the biomass of detritivores (positive) and browsers (negative). Similarly, the biomass of scrapers, grazers, and detritivores correlated with habitat structural complexity; however, relationships were group specific. Finally, the biomass of browsers and large excavators was related to island geomorphology, both peaking on low-lying islands and atolls. The substantial variability in herbivore populations explained by natural biophysical drivers highlights the need for locally appropriate management targets on coral reefs. PMID:27881745

The UCSC Genome Browser: What Every Molecular Biologist Should Know.

PubMed

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C

2014-07-01

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. Copyright © 2014 John Wiley & Sons, Inc.

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

PubMed

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Savant Genome Browser 2: visualization and analysis for population-scale genomics

PubMed Central

Smith, Eric J. M.; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M.; Robinson, Mark D.; Wodak, Shoshana J.; Brudno, Michael

2012-01-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com. PMID:22638571

Web Extensible Display Manager

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

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Developmental time windows for axon growth influence neuronal network topology.

PubMed

Lim, Sol; Kaiser, Marcus

2015-04-01

Early brain connectivity development consists of multiple stages: birth of neurons, their migration and the subsequent growth of axons and dendrites. Each stage occurs within a certain period of time depending on types of neurons and cortical layers. Forming synapses between neurons either by growing axons starting at similar times for all neurons (much-overlapped time windows) or at different time points (less-overlapped) may affect the topological and spatial properties of neuronal networks. Here, we explore the extreme cases of axon formation during early development, either starting at the same time for all neurons (parallel, i.e., maximally overlapped time windows) or occurring for each neuron separately one neuron after another (serial, i.e., no overlaps in time windows). For both cases, the number of potential and established synapses remained comparable. Topological and spatial properties, however, differed: Neurons that started axon growth early on in serial growth achieved higher out-degrees, higher local efficiency and longer axon lengths while neurons demonstrated more homogeneous connectivity patterns for parallel growth. Second, connection probability decreased more rapidly with distance between neurons for parallel growth than for serial growth. Third, bidirectional connections were more numerous for parallel growth. Finally, we tested our predictions with C. elegans data. Together, this indicates that time windows for axon growth influence the topological and spatial properties of neuronal networks opening up the possibility to a posteriori estimate developmental mechanisms based on network properties of a developed network.

Highly Efficient Quantum Sieving in Porous Graphene-like Carbon Nitride for Light Isotopes Separation

NASA Astrophysics Data System (ADS)

Qu, Yuanyuan; Li, Feng; Zhou, Hongcai; Zhao, Mingwen

2016-01-01

Light isotopes separation, such as 3He/4He, H2/D2, H2/T2, etc., is crucial for various advanced technologies including isotope labeling, nuclear weapons, cryogenics and power generation. However, their nearly identical chemical properties made the separation challenging. The low productivity of the present isotopes separation approaches hinders the relevant applications. An efficient membrane with high performance for isotopes separation is quite appealing. Based on first-principles calculations, we theoretically demonstrated that highly efficient light isotopes separation, such as 3He/4He, can be reached in a porous graphene-like carbon nitride material via quantum sieving effect. Under moderate tensile strain, the quantum sieving of the carbon nitride membrane can be effectively tuned in a continuous way, leading to a temperature window with high 3He/4He selectivity and permeance acceptable for efficient isotopes harvest in industrial application. This mechanism also holds for separation of other light isotopes, such as H2/D2, H2/T2. Such tunable quantum sieving opens a promising avenue for light isotopes separation for industrial application.

Divorce and Death: Forty Years of the Charleston Heart Study

PubMed Central

Nietert, Paul J.

2010-01-01

Forty years of follow-up data from the Charleston Heart Study (CHS) were used to examine the risk for early mortality associated with marital separation or divorce in a sample of over 1,300 adults assessed on several occasions between 1960 and 2000. Participants who were separated or divorced at study inception evidenced significantly higher rates of early mortality, and these results held after adjusting for baseline health status and other demographic variables. Being separated or divorced throughout the CHS follow-up window was one of the strongest predictors of early mortality. However, the excess mortality risk associated with remaining separated/divorced was completely eliminated when participants were re-classified as having ever experienced a marital separation or divorce. These findings suggest a key determinant of early death is the amount of time people live as separated or divorced and/or dimensions of personality that predict divorce as well as a decreased likelihood of future remarriage. PMID:19076315

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned.

PubMed

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, Aids

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting.

PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

PubMed

Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

2009-11-15

PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

Apollo 14 crewmembers sealed inside a Mobile Quarantine Facility

NASA Technical Reports Server (NTRS)

1971-01-01

Separated by aluminum and glass of their Mobile Quarantine Facility (MQF), the Apollo 14 crewmen visit with their families and friends upon arriving at Ellington Air Force Base in the early morning hours of February 12, 1971. Looking through the MQF window are Astronats Alan B Shepard Jr. (left); Stuart A Roosa (right); and Edgar D. Mitchell.

46 CFR 177.500 - Means of escape.

Code of Federal Regulations, 2012 CFR

2012-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 177.500 - Means of escape.

Code of Federal Regulations, 2013 CFR

2013-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 177.500 - Means of escape.

Code of Federal Regulations, 2014 CFR

2014-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 177.500 - Means of escape.

Code of Federal Regulations, 2011 CFR

2011-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 116.500 - Means of escape.

Code of Federal Regulations, 2010 CFR

2010-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 116.500 - Means of escape.

Code of Federal Regulations, 2014 CFR

2014-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 116.500 - Means of escape.

Code of Federal Regulations, 2011 CFR

2011-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 116.500 - Means of escape.

Code of Federal Regulations, 2012 CFR

2012-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

46 CFR 116.500 - Means of escape.

Code of Federal Regulations, 2013 CFR

2013-10-01

... this section, each space accessible to passengers or used by the crew on a regular basis, must have at... escape must be widely separated and, if possible, at opposite ends or sides of the space to minimize the... windows. (d) The number and dimensions of the means of escape from each space must be sufficient for rapid...

Kerfless epitaxial silicon wafers with 7 ms carrier lifetimes and a wide lift-off process window

NASA Astrophysics Data System (ADS)

Gemmel, Catherin; Hensen, Jan; David, Lasse; Kajari-Schröder, Sarah; Brendel, Rolf

2018-04-01

Silicon wafers contribute significantly to the photovoltaic module cost. Kerfless silicon wafers that grow epitaxially on porous silicon (PSI) and are subsequently detached from the growth substrate are a promising lower cost drop-in replacement for standard Czochralski (Cz) wafers. However, a wide technological processing window appears to be a challenge for this process. This holds in particularly for the etching current density of the separation layer that leads to lift-off failures if it is too large or too low. Here we present kerfless PSI wafers of high electronic quality that we fabricate on weakly reorganized porous Si with etch current densities varying in a wide process window from 110 to 150 mA/cm2. We are able to detach all 17 out of 17 epitaxial wafers. All wafers exhibit charge carrier lifetimes in the range of 1.9 to 4.3 ms at an injection level of 1015 cm-3 without additional high-temperature treatment. We find even higher lifetimes in the range of 4.6 to 7.0 ms after applying phosphorous gettering. These results indicate that a weak reorganization of the porous layer can be beneficial for a large lift-off process window while still allowing for high carrier lifetimes.

Development of a spectro-electrochemical cell for soft X-ray photon-in photon-out spectroscopy

NASA Astrophysics Data System (ADS)

Ishihara, Tomoko; Tokushima, Takashi; Horikawa, Yuka; Kato, Masaru; Yagi, Ichizo

2017-10-01

We developed a spectro-electrochemical cell for X-ray absorption and X-ray emission spectroscopy, which are element-specific methods to study local electronic structures in the soft X-ray region. In the usual electrochemical measurement setup, the electrode is placed in solution, and the surface/interface region of the electrode is not normally accessible by soft X-rays that have low penetration depth in liquids. To realize soft X-ray observation of electrochemical reactions, a 15-nm-thick Pt layer was deposited on a 150-nm-thick film window with an adhesive 3-nm-thick Ti layer for use as both the working electrode and the separator window between vacuum and a sample liquid under atmospheric pressure. The designed three-electrode electrochemical cell consists of a Pt film on a SiC window, a platinized Pt wire, and a commercial Ag|AgCl electrode as the working, counter, and reference electrodes, respectively. The functionality of the cell was tested by cyclic voltammetry and X-ray absorption and emission spectroscopy. As a demonstration, the electroplating of Pb on the Pt/SiC membrane window was measured by X-ray absorption and real-time monitoring of fluorescence intensity at the O 1s excitation.

Perceived Spaciousness and Preference in Sequential Experience.

PubMed

Bokharaei, Saleheh; Nasar, Jack L

2016-11-01

We assessed the perceived spaciousness and preference for a destination space in relation to six attributes (size, lighting, window size, texture, wall mural, and amount of furniture) of it and of the space experienced before it. Studies have examined effects of these attributes but not for dynamic experience or preference. We created 24 virtual reality walks between each possible pair of two levels of each attribute. For each destination space, 31 students (13 men, 18 women) rated spaciousness and 30 students (16 men, 14 women) rated preference. We conducted separate 2 × 2 repeated-measure ANOVAs across each condition for perceived spaciousness and preference. Participants judged the space that was larger, was more brightly lit, with a larger window, or with less furniture as the more spacious. These attributes also increased preference. Consonant with adaptation-level theory, participants judged offices as higher in spaciousness and preference if preceded by a space that was smaller, was more dimly lit, or had smaller windows. The findings suggest that perceived spaciousness varies with size, lightness, window size, and amount of furniture but that perception also depends on the size, lightness, and size of the space experienced before. Designers could use the findings to manipulate features to make a space appear larger or more desirable. © 2016, Human Factors and Ergonomics Society.

[Online endpoint detection algorithm for blending process of Chinese materia medica].

PubMed

Lin, Zhao-Zhou; Yang, Chan; Xu, Bing; Shi, Xin-Yuan; Zhang, Zhi-Qiang; Fu, Jing; Qiao, Yan-Jiang

2017-03-01

Blending process, which is an essential part of the pharmaceutical preparation, has a direct influence on the homogeneity and stability of solid dosage forms. With the official release of Guidance for Industry PAT, online process analysis techniques have been more and more reported in the applications in blending process, but the research on endpoint detection algorithm is still in the initial stage. By progressively increasing the window size of moving block standard deviation (MBSD), a novel endpoint detection algorithm was proposed to extend the plain MBSD from off-line scenario to online scenario and used to determine the endpoint in the blending process of Chinese medicine dispensing granules. By online learning of window size tuning, the status changes of the materials in blending process were reflected in the calculation of standard deviation in a real-time manner. The proposed method was separately tested in the blending processes of dextrin and three other extracts of traditional Chinese medicine. All of the results have shown that as compared with traditional MBSD method, the window size changes according to the proposed MBSD method (progressively increasing the window size) could more clearly reflect the status changes of the materials in blending process, so it is suitable for online application. Copyright© by the Chinese Pharmaceutical Association.

Isolation of chicken embryonic stem cell and preparation of chicken chimeric model.

PubMed

Zhang, Yani; Yang, Haiyan; Zhang, Zhentao; Shi, Qingqing; Wang, Dan; Zheng, Mengmeng; Li, Bichun; Song, Jiuzhou

2013-03-01

Chicken embryonic stem cells (ESCs) were separated from blastoderms at stage-X and cultured in vitro. Alkaline phosphatase activity and stage-specific embryonic antigen-1 staining was conducted to detect ESCs. Then, chicken ESCs were transfected with linearized plasmid pEGFP-N1 in order to produce chimeric chicken. Firstly, the optimal electrotransfection condition was compared; the results showed the highest transfection efficiency was obtained when the field strength and pulse duration was 280 V and 75 μs, respectively. Secondly, the hatchability of shedding methods, drilling a window at the blunt end of egg and drilling a window at the lateral shell of egg was compared, the results showed that the hatchability was the highest for drilling a window at the lateral shell of egg. Thirdly, the hatchability of microinjection (ESCs was microinjected into chick embryo cavity) was compared too, the results showed there were significant difference between the injection group transfected with ESCs and that of other two groups. In addition, five chimeric chickens were obtained in this study and EGFP gene was expressed in some organs, but only two chimeric chicken expressed EGFP gene in the gonad, indicating that the chimeric chicken could be obtained through chick embryo cavity injection by drilling a window at the lateral shell of egg.

Crash forecasting in the Korean stock market based on the log-periodic structure and pattern recognition

NASA Astrophysics Data System (ADS)

Ko, Bonggyun; Song, Jae Wook; Chang, Woojin

2018-02-01

The aim of this research is to propose an alarm index to forecast the crash of the Korean financial market in extension to the idea of Johansen-Ledoit-Sornette model, which uses the log-periodic functions and pattern recognition algorithm. We discover that the crashes of the Korean financial market can be classified into domestic and global crises where each category requires different window length of fitted datasets. Therefore, we add the window length as a new parameter to enhance the performance of alarm index. Distinguishing the domestic and global crises separately, our alarm index demonstrates more robust forecasting than previous model by showing the error diagram and the results of trading performance.

Laser multipass system with interior cell configuration.

PubMed

Borysow, Jacek; Kostinski, Alexander; Fink, Manfred

2011-10-20

We ask whether it is possible to restore a multipass system alignment after a gas cell is inserted in the central region. Indeed, it is possible, and we report on a remarkably simple rearrangement of a laser multipass system, composed of two spherical mirrors and a gas cell with flat windows in the middle. For example, for a window of thickness d and refractive index of n, adjusting the mirror separation by ≈2d(1-1/n) is sufficient to preserve the laser beam alignment and tracing. This expression is in agreement with ray-tracing computations and our laboratory experiment. Insofar as our solution corrects for spherical aberrations, it may also find applications in microscopy. © 2011 Optical Society of America

Toposelective electrochemical desorption of thiol SAMs from neighboring polycrystalline gold surfaces.

PubMed

Tencer, Michal; Berini, Pierre

2008-11-04

We describe a method for the selective desorption of thiol self-assembled monolayers from gold surfaces having micrometer-scale separations on a substrate. In an electrolyte solution, the electrical resistance between the adjacent areas can be much lower than the resistance between a surface and the counter electrode. Also, both reductive and oxidative thiol desorption may occur. Therefore, the potentials of the surfaces must be independently controlled with a multichannel potentiostat and operating windows for a given thiol/electrolyte system must be established. In this study operating windows were established for 1-dodecanethiol-based SAMs in phosphate buffer, phosphate-buffered saline, and sodium hydroxide solution, and selective SAM removal was successfully performed in a four-electrode configuration.

Information transfer rate with serial and simultaneous visual display formats

NASA Astrophysics Data System (ADS)

Matin, Ethel; Boff, Kenneth R.

1988-04-01

Information communication rate for a conventional display with three spatially separated windows was compared with rate for a serial display in which data frames were presented sequentially in one window. For both methods, each frame contained a randomly selected digit with various amounts of additional display 'clutter.' Subjects recalled the digits in a prescribed order. Large rate differences were found, with faster serial communication for all levels of the clutter factors. However, the rate difference was most pronounced for highly cluttered displays. An explanation for the latter effect in terms of visual masking in the retinal periphery was supported by the results of a second experiment. The working hypothesis that serial displays can speed information transfer for automatic but not for controlled processing is discussed.

The evolution of the ISOLDE control system

NASA Astrophysics Data System (ADS)

Jonsson, O. C.; Catherall, R.; Deloose, I.; Drumm, P.; Evensen, A. H. M.; Gase, K.; Focker, G. J.; Fowler, A.; Kugler, E.; Lettry, J.; Olesen, G.; Ravn, H. L.; Isolde Collaboration

The ISOLDE on-line mass separator facility is operating on a Personal Computer based control system since spring 1992. Front End Computers accessing the hardware are controlled from consoles running Microsoft Windows ™ through a Novell NetWare4 ™ local area network. The control system is transparently integrated in the CERN wide office network and makes heavy use of the CERN standard office application programs to control and to document the running of the ISOLDE isotope separators. This paper recalls the architecture of the control system, shows its recent developments and gives some examples of its graphical user interface.

The evolution of the ISOLDE control system

NASA Astrophysics Data System (ADS)

Jonsson, O. C.; Catherall, R.; Deloose, I.; Evensen, A. H. M.; Gase, K.; Focker, G. J.; Fowler, A.; Kugler, E.; Lettry, J.; Olesen, G.; Ravn, H. L.; Drumm, P.

1996-04-01

The ISOLDE on-line mass separator facility is operating on a Personal Computer based control system since spring 1992. Front End Computers accessing the hardware are controlled from consoles running Microsoft Windows® through a Novell NetWare4® local area network. The control system is transparently integrated in the CERN wide office network and makes heavy use of the CERN standard office application programs to control and to document the running of the ISOLDE isotope separators. This paper recalls the architecture of the control system, shows its recent developments and gives some examples of its graphical user interface.

Comparison of home lead dust reduction techniques on hard surfaces: the New Jersey assessment of cleaning techniques trial.

PubMed Central

Rich, David Q; Rhoads, George G; Yiin, Lih-Ming; Zhang, Junfeng; Bai, Zhipeng; Adgate, John L; Ashley, Peter J; Lioy, Paul J

2002-01-01

High efficiency particulate air filter (HEPA) vacuums, which collect particles > 0.3 micro m, and trisodium phosphate (TSP), a detergent claimed to selectively remove lead, have been included in the HUD Guidelines for the Evaluation and Control of Lead Based Paint Hazards in Housing without systematic validation of their effectiveness. At the time the study was initiated, both HEPA vacuums and TSP were relatively expensive, they were not readily found in urban retail centers, and there were environmental concerns about the use and disposal of high-phosphate detergents. A randomized, controlled trial was conducted in urban high-risk homes in northern New Jersey to determine whether a more readily available and less expensive low-phosphate, non-TSP detergent and non-HEPA vacuum could perform as well as TSP and a HEPA vacuum in a cleaning protocol. Homes were randomized to one of three cleaning methods: TSP/HEPA vacuum, TSP/non-HEPA vacuum, or non-TSP/non-HEPA vacuum. Change in log-transformed lead loading was used in mixed models to compare the efficacy of the three cleaning techniques separately for uncarpeted floors, window sills, and window troughs. After we adjusted for baseline lead loading, the non-HEPA vacuum produced larger reductions on hard floors [19%; 95% confidence interval (CI), 3-38%], but the HEPA vacuum produced larger reductions on window sills (22%; 95% CI, 11-32%) and larger reductions on window troughs (16%; 95% CI, -4 to 33%). The non-TSP produced larger reductions on window troughs (21%; 95% CI, -2 to 50%), but TSP produced larger reductions on hard floors (5%; 95% CI, -12 to 19%) and window sills (8%; 95% CI, -5 to 20%). TSP/HEPA produced larger reductions on window sills (28%; 95% CI, 18-37%) and larger reductions on window troughs (2%; 95% CI, -24 to 23%), whereas the non-TSP/non-HEPA method produced larger reductions on hard floors (13%; 95% CI, -5 to 34%). Because neither vacuum nor detergent produced consistent results across surface types, the use of low-phosphate detergents and non-HEPA vacuums in a temporary control measure is supported. PMID:12204823

Comparison of home lead dust reduction techniques on hard surfaces: the New Jersey assessment of cleaning techniques trial.

PubMed

Rich, David Q; Rhoads, George G; Yiin, Lih-Ming; Zhang, Junfeng; Bai, Zhipeng; Adgate, John L; Ashley, Peter J; Lioy, Paul J

2002-09-01

High efficiency particulate air filter (HEPA) vacuums, which collect particles > 0.3 micro m, and trisodium phosphate (TSP), a detergent claimed to selectively remove lead, have been included in the HUD Guidelines for the Evaluation and Control of Lead Based Paint Hazards in Housing without systematic validation of their effectiveness. At the time the study was initiated, both HEPA vacuums and TSP were relatively expensive, they were not readily found in urban retail centers, and there were environmental concerns about the use and disposal of high-phosphate detergents. A randomized, controlled trial was conducted in urban high-risk homes in northern New Jersey to determine whether a more readily available and less expensive low-phosphate, non-TSP detergent and non-HEPA vacuum could perform as well as TSP and a HEPA vacuum in a cleaning protocol. Homes were randomized to one of three cleaning methods: TSP/HEPA vacuum, TSP/non-HEPA vacuum, or non-TSP/non-HEPA vacuum. Change in log-transformed lead loading was used in mixed models to compare the efficacy of the three cleaning techniques separately for uncarpeted floors, window sills, and window troughs. After we adjusted for baseline lead loading, the non-HEPA vacuum produced larger reductions on hard floors [19%; 95% confidence interval (CI), 3-38%], but the HEPA vacuum produced larger reductions on window sills (22%; 95% CI, 11-32%) and larger reductions on window troughs (16%; 95% CI, -4 to 33%). The non-TSP produced larger reductions on window troughs (21%; 95% CI, -2 to 50%), but TSP produced larger reductions on hard floors (5%; 95% CI, -12 to 19%) and window sills (8%; 95% CI, -5 to 20%). TSP/HEPA produced larger reductions on window sills (28%; 95% CI, 18-37%) and larger reductions on window troughs (2%; 95% CI, -24 to 23%), whereas the non-TSP/non-HEPA method produced larger reductions on hard floors (13%; 95% CI, -5 to 34%). Because neither vacuum nor detergent produced consistent results across surface types, the use of low-phosphate detergents and non-HEPA vacuums in a temporary control measure is supported.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation.

PubMed

Pérez-Barbería, F J; Gordon, I J

2001-05-22

In ungulates it is argued that specialization in the consumption of a particular type of food (feeding style) is reflected in morphological adaptations of the organs involved in the selection, processing and digestion of food. We analysed the differences in size and morphology of some oral traits that have been functionally related to food-selection ability (muzzle width, incisor-arcade shape, incisor shape), prehension of food (incisor protrusion), food comminution (molar occlusal surface area, hypsodonty (high-crowned molars)) and intake rate (incisor breadth) between ungulate species with different feeding styles (browser, mixed feeder, grazer). Grazers were characterized by large-body-size species. After controlling only for body mass, we found that grazers had wider muzzles and incisors, more-protruding incisors and more-bulky and higher-crowned molars than did mixed feeders and browsers. When the analyses took into account both body mass and phylogeny, only body mass and two out of the three hypsodonty indexes used remained significantly different between feeding styles. Browsers were smaller, on average, than mixed feeders and grazers, whilst grazers and mixed feeders did not differ in size. Also, browsers had shorter and less-bulky molars than did mixed feeders and grazers; the latter two feeding styles did not differ from each other in any of the hypsodonty indexes. We conclude that the adaptation to different dietary types in most of the oral traits studied is subsumed by the effects of body mass and the sharing of common ancestors. We hypothesize that differences in the ability to exploit different food resources primarily result from differences in body mass between species, and also discuss why hypsodonty characterizes feeding styles.

Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation.

PubMed Central

Pérez-Barbería, F. J.; Gordon, I. J.

2001-01-01

In ungulates it is argued that specialization in the consumption of a particular type of food (feeding style) is reflected in morphological adaptations of the organs involved in the selection, processing and digestion of food. We analysed the differences in size and morphology of some oral traits that have been functionally related to food-selection ability (muzzle width, incisor-arcade shape, incisor shape), prehension of food (incisor protrusion), food comminution (molar occlusal surface area, hypsodonty (high-crowned molars)) and intake rate (incisor breadth) between ungulate species with different feeding styles (browser, mixed feeder, grazer). Grazers were characterized by large-body-size species. After controlling only for body mass, we found that grazers had wider muzzles and incisors, more-protruding incisors and more-bulky and higher-crowned molars than did mixed feeders and browsers. When the analyses took into account both body mass and phylogeny, only body mass and two out of the three hypsodonty indexes used remained significantly different between feeding styles. Browsers were smaller, on average, than mixed feeders and grazers, whilst grazers and mixed feeders did not differ in size. Also, browsers had shorter and less-bulky molars than did mixed feeders and grazers; the latter two feeding styles did not differ from each other in any of the hypsodonty indexes. We conclude that the adaptation to different dietary types in most of the oral traits studied is subsumed by the effects of body mass and the sharing of common ancestors. We hypothesize that differences in the ability to exploit different food resources primarily result from differences in body mass between species, and also discuss why hypsodonty characterizes feeding styles. PMID:11375086

Inter-aquifer Dynamics in and Near a Confining Unit Window in Shelby County, Tennessee, USA

NASA Astrophysics Data System (ADS)

Gentry, R. W.; McKay, L. D.; Larsen, D.; Carmichael, J. K.; Solomon, D. K.; Thonnard, N.; Anderson, J. L.

2003-12-01

An interdisplinary research team is investigating the interaction between the surficial alluvial aquifer and the deeper confined Memphis aquifer in the Memphis area, Shelby County, Tennessee. Previous research has identified a window in the clay-rich, upper Claiborne confining unit that separates the two aquifers near a closed municipal landfill in east-central Shelby County, an area undergoing rapid urbanization. For this investigation, a combination of environmental tracers (tritium/helium-3), major and trace ion geochemistry, hydraulic response testing, measurement of hydraulic gradients, and groundwater flow modeling is being used to quantify recharge of young water from the alluvial aquifer through the window to the Memphis aquifer. The research will provide results to better understand how windows were formed and how they influence recharge and water quality in otherwise confined parts of the Memphis aquifer downdip of its outcrop/subcrop area. Examination of continuous core samples and geophysical logs from wells installed for the study using Rotasonic drilling methods confirmed the existence of a sand-dominated window that may be as much as 1 km in diameter in the upper Claiborne confining unit. The upper Claiborne confining unit is 15 to 20 m thick in most of the study area and is overlain by a 10 to 12 m thick alluvial aquifer. The window is interpreted to have formed as a result of depositional and incisional processes in an Eocene-age deltaic system. Hydraulic gradients of several feet exist vertically between the alluvial and Memphis aquifers within the window, indicating downward flow. Groundwater age-dates from tritium/helium-3 analyses indicate that groundwater in the window at the depth of the base of the surrounding confining unit (approximately 30 m) has an apparent age of 19.8 years, which confirms the occurrence of downward flow. Young groundwater age dates (less than 32 years) also were obtained from wells in the Memphis aquifer at confined sites downgradient of the window, suggesting that a plume of young water is spreading outwards from the window and mixing with the older Memphis aquifer water. Preliminary inverse modeling of the site using a genetic algorithm coupled with a central finite difference flow model indicates a probable steady-state downward flux of about 12,000 m3/d through the window. Collection and analysis of additional groundwater samples are planned to examine geochemical conditions in the confining unit and in the Memphis aquifer upgradient of the window. These analyses will aid in developing a final conceptual model and in subsequent numerical modeling of mixing of the young recharge water with the older Memphis aquifer water.

Recycled Glass and Dredged Materials

DTIC Science & Technology

2007-03-01

stations, and is either source-separated or co-mingled with plastics, aluminum cans, ceramics , or colored glass containers. In the United States in...anything other than container glass ). The debris may contain contaminants including ceramics (from dishware, pottery, window glass , light bulbs...ERDC TN-DOER-T8 March 2007 Recycled Glass and Dredged Materials by Landris T. Lee, Jr. PURPOSE: This technical note explores the concepts

Daylight Makes a Difference: Daylight in the Classroom Can Boost Standardized Test Scores and Learning. [Audiotape].

ERIC Educational Resources Information Center

Kosik, Kenneth S.; Heschong, Lisa

An audiotape presents study analysis of the effect of daylighting on student performance. The study includes a focus on skylighting as a way to isolate daylight as an illumination source, and separate illumination effects from other qualities associated with daylighting from windows. Results from test scores of over 21,000 student records, along…

Expedition 23 State Commission

NASA Image and Video Library

2010-03-31

Expedition 23 Soyuz Commander Alexander Skvortsov says a few words during the State Commission meeting to approve the Soyuz launch of Skvortsov, Expedition 23 Flight Engineer Tracy Caldwell Dyson and Flight Engineer Mikhail Kornienko on Thursday, April 1, 2010 in Baikonur, Kazakhstan. The crew is kept in a separate room with a glass window in order to help maintain their health. Photo Credit: (NASA/Bill Ingalls)

18. VIEW OF PARAPET AT NORTHEAST CORNER. PARAPET IS TREATED ...

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

18. VIEW OF PARAPET AT NORTHEAST CORNER. PARAPET IS TREATED LIKE A CLASSICAL ENTABLATURE WITH DENTILS AND REPETITIVE EGG AND DART ORNAMENTATION BELOW IT. FACE BRICK BELOW SEPARATES THE ARCHED WINDOWS OF THE 11TH FLOOR, PARAPET CORNICE IS ORIGINALLY MADE OF COPPER. PRESENT FINISH LOOKS LIKE STUCCO. - Pacific Telephone & Telegraph Company Building, 1519 Franklin Street, Oakland, Alameda County, CA

Desktop Application Program to Simulate Cargo-Air-Drop Tests

NASA Technical Reports Server (NTRS)

Cuthbert, Peter

2009-01-01

The DSS Application is a computer program comprising a Windows version of the UNIX-based Decelerator System Simulation (DSS) coupled with an Excel front end. The DSS is an executable code that simulates the dynamics of airdropped cargo from first motion in an aircraft through landing. The bare DSS is difficult to use; the front end makes it easy to use. All inputs to the DSS, control of execution of the DSS, and postprocessing and plotting of outputs are handled in the front end. The front end is graphics-intensive. The Excel software provides the graphical elements without need for additional programming. Categories of input parameters are divided into separate tabbed windows. Pop-up comments describe each parameter. An error-checking software component evaluates combinations of parameters and alerts the user if an error results. Case files can be created from inputs, making it possible to build cases from previous ones. Simulation output is plotted in 16 charts displayed on a separate worksheet, enabling plotting of multiple DSS cases with flight-test data. Variables assigned to each plot can be changed. Selected input parameters can be edited from the plot sheet for quick sensitivity studies.

A Modified Empirical Wavelet Transform for Acoustic Emission Signal Decomposition in Structural Health Monitoring.

PubMed

Dong, Shaopeng; Yuan, Mei; Wang, Qiusheng; Liang, Zhiling

2018-05-21

The acoustic emission (AE) method is useful for structural health monitoring (SHM) of composite structures due to its high sensitivity and real-time capability. The main challenge, however, is how to classify the AE data into different failure mechanisms because the detected signals are affected by various factors. Empirical wavelet transform (EWT) is a solution for analyzing the multi-component signals and has been used to process the AE data. In order to solve the spectrum separation problem of the AE signals, this paper proposes a novel modified separation method based on local window maxima (LWM) algorithm. It searches the local maxima of the Fourier spectrum in a proper window, and automatically determines the boundaries of spectrum segmentations, which helps to eliminate the impact of noise interference or frequency dispersion in the detected signal and obtain the meaningful empirical modes that are more related to the damage characteristics. Additionally, both simulation signal and AE signal from the composite structures are used to verify the effectiveness of the proposed method. Finally, the experimental results indicate that the proposed method performs better than the original EWT method in identifying different damage mechanisms of composite structures.

A Modified Empirical Wavelet Transform for Acoustic Emission Signal Decomposition in Structural Health Monitoring

PubMed Central

Dong, Shaopeng; Yuan, Mei; Wang, Qiusheng; Liang, Zhiling

2018-01-01

The acoustic emission (AE) method is useful for structural health monitoring (SHM) of composite structures due to its high sensitivity and real-time capability. The main challenge, however, is how to classify the AE data into different failure mechanisms because the detected signals are affected by various factors. Empirical wavelet transform (EWT) is a solution for analyzing the multi-component signals and has been used to process the AE data. In order to solve the spectrum separation problem of the AE signals, this paper proposes a novel modified separation method based on local window maxima (LWM) algorithm. It searches the local maxima of the Fourier spectrum in a proper window, and automatically determines the boundaries of spectrum segmentations, which helps to eliminate the impact of noise interference or frequency dispersion in the detected signal and obtain the meaningful empirical modes that are more related to the damage characteristics. Additionally, both simulation signal and AE signal from the composite structures are used to verify the effectiveness of the proposed method. Finally, the experimental results indicate that the proposed method performs better than the original EWT method in identifying different damage mechanisms of composite structures. PMID:29883411

Gaussian-windowed frame based method of moments formulation of surface-integral-equation for extended apertures

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

Shlivinski, A., E-mail: amirshli@ee.bgu.ac.il; Lomakin, V., E-mail: vlomakin@eng.ucsd.edu

2016-03-01

Scattering or coupling of electromagnetic beam-field at a surface discontinuity separating two homogeneous or inhomogeneous media with different propagation characteristics is formulated using surface integral equation, which are solved by the Method of Moments with the aid of the Gabor-based Gaussian window frame set of basis and testing functions. The application of the Gaussian window frame provides (i) a mathematically exact and robust tool for spatial-spectral phase-space formulation and analysis of the problem; (ii) a system of linear equations in a transmission-line like form relating mode-like wave objects of one medium with mode-like wave objects of the second medium; (iii)more » furthermore, an appropriate setting of the frame parameters yields mode-like wave objects that blend plane wave properties (as if solving in the spectral domain) with Green's function properties (as if solving in the spatial domain); and (iv) a representation of the scattered field with Gaussian-beam propagators that may be used in many large (in terms of wavelengths) systems.« less

Separation of organic cations using novel background electrolytes by capillary electrophoresis

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

Steiner, S.; Fritz, J.

2008-02-12

A background electrolyte for capillary electrophoresis containing tris(-hydroxymethyl) aminomethane (THAM) and ethanesulfonic acid (ESA) gives excellent efficiency for separation of drug cations with actual theoretical plate numbers as high as 300,000. However, the analyte cations often elute too quickly and consequently offer only a narrow window for separation. The best way to correct this is to induce a reverse electroosmotic flow (EOF) that will spread out the peaks by slowing their migration rates, but this has always been difficult to accomplish in a controlled manner. A new method for producing a variable EOF is described in which a low variablemore » concentration of tributylammonium- or triethylammonium ESA is added to the BGE. The additive equilibrates with the capillary wall to give it a positive charge and thereby produce a controlled opposing EOF. Excellent separations of complex drug mixtures were obtained by this method.« less

DEB: A Diagnostic Experience Browser using similarity networks

NASA Technical Reports Server (NTRS)

Casadaban, Cyprian E.

1990-01-01

Diagnostic Experience Browser (DEB): a fusion of knowledge base and data base that allows users to examine only the data which is most useful to them is described. The system combines a data base of historical cases of diagnostic trouble-shooting experience with similarity networks. A menu-driven natural language interface receives input about the user's current problem. Similarity networks provide the user with references to past cases that are most similar or most related to those they now face. The user can then choose the case that is most pertinent and browse its full textual description which, in turn, may include references to other related cases.

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned

PubMed Central

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M.; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, AIDS

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting. PMID:28149445

Figure summarizer browser extensions for PubMed Central

PubMed Central

Agarwal, Shashank; Yu, Hong

2011-01-01

Summary: Figures in biomedical articles present visual evidence for research facts and help readers understand the article better. However, when figures are taken out of context, it is difficult to understand their content. We developed a summarization algorithm to summarize the content of figures and used it in our figure search engine (http://figuresearch.askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images. Availability: The extensions can be downloaded from http://figuresearch.askhermes.org/articlesearch/extensions.php. Contact: agarwal@uwm.edu PMID:21493658

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

PubMed Central

Harper, Lisa C.; Schaeffer, Mary L.; Thistle, Jordan; Gardiner, Jack M.; Andorf, Carson M.; Campbell, Darwin A.; Cannon, Ethalinda K.S.; Braun, Bremen L.; Birkett, Scott M.; Lawrence, Carolyn J.; Sen, Taner Z.

2011-01-01

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is ‘Using the MaizeGDB Genome Browser’, which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database URL: http://www.maizegdb.org/ PMID:21565781

Performance evaluation of a distance learning program.

PubMed

Dailey, D J; Eno, K R; Brinkley, J F

1994-01-01

This paper presents a performance metric which uses a single number to characterize the response time for a non-deterministic client-server application operating over the Internet. When applied to a Macintosh-based distance learning application called the Digital Anatomist Browser, the metric allowed us to observe that "A typical student doing a typical mix of Browser commands on a typical data set will experience the same delay if they use a slow Macintosh on a local network or a fast Macintosh on the other side of the country accessing the data over the Internet." The methodology presented is applicable to other client-server applications that are rapidly appearing on the Internet.

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

Fulfillment of HTTP Authentication Based on Alcatel OmniSwitch 9700

NASA Astrophysics Data System (ADS)

Liu, Hefu

This paper provides a way of HTTP authentication On Alcatel OmniSwitch 9700. Authenticated VLANs control user access to network resources based on VLAN assignment and user authentication. The user can be authenticated through the switch via any standard Web browser software. Web browser client displays the username and password prompts. Then a way for HTML forms can be given to pass HTTP authentication data when it's submitted. A radius server will provide a database of user information that the switch checks whenever it tries to authenticate through the switch. Before or after authentication, the client can get an address from a Dhcp server.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

PubMed Central

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-01-01

Background Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired. PMID:17877794

Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

With the evolution of web based technologies, especially HTML5 [1], it becomes possible to create web-based control system user interfaces (UI) that are cross-browser and cross-device compatible. This article describes two technologies that facilitate this goal. The first one is the WebOPI [2], which can seamlessly display CSS BOY [3] Operator Interfaces (OPI) in web browsers without modification to the original OPI file. The WebOPI leverages the powerful graphical editing capabilities of BOY and provides the convenience of re-using existing OPI files. On the other hand, it uses generic JavaScript and a generic communication mechanism between the web browser andmore » web server. It is not optimized for a control system, which results in unnecessary network traffic and resource usage. Our second technology is the WebSocket-based Process Data Access (WebPDA) [4]. It is a protocol that provides efficient control system data communication using WebSocket [5], so that users can create web-based control system UIs using standard web page technologies such as HTML, CSS and JavaScript. WebPDA is control system independent, potentially supporting any type of control system.« less

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

GBshape: a genome browser database for DNA shape annotations

PubMed Central

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J.; Parker, Stephen C.J.; Nuzhdin, Sergey V.; Tullius, Thomas D.; Rohs, Remo

2015-01-01

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. PMID:25326329

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Implications for Late Pleistocene Mastodon Diet from Opal Phytoliths in Tooth Calculus

NASA Astrophysics Data System (ADS)

Gobetz, Katrina E.; Bozarth, Steven R.

2001-03-01

Calculus removed from the molar teeth of four American mastodons (Mammut americanum) contained opal phytoliths which reflect major dietary components. Three samples contained abundant grass phytoliths (ca. 86% of total), with long cells and trapezoidal pooid short cells dominant (ca. 25 and 31%, respectively). Dicot phytoliths from hackberry (Celtis sp.) seeds and indeterminate deciduous trees were rare (1-3%), though well preserved, whereas phytoliths from conifer trees were not recognizable in any of the samples. Comparative analysis of calculus from modern and fossil browsers and mixed feeders implies that dicots and conifers are nearly invisible in the phytolith record. This scarcity may result from poor preservation, low silica production in woody taxa, and/or animals' selection of young, silica-poor leaves and shoots. However, abundant grass phytoliths in the mixed feeders suggest that presence versus absence of grass phytoliths may distinguish mixed feeders and grazers from browsers. Mastodons are traditionally considered browsers, but grass phytolith assemblages in three individual mastodons contained similarly high concentrations of pooids, suggesting that these grasses were a significant part of the diet. Abundant pooid phytoliths, in addition to diatoms, indicate that these mastodons grazed in a cool, moist late Pleistocene environment, possibly near water.

Multimedia consultation session recording and playback using Java-based browser in global PACS

NASA Astrophysics Data System (ADS)

Martinez, Ralph; Shah, Pinkesh J.; Yu, Yuan-Pin

1998-07-01

The current version of the Global PACS software system uses a Java-based implementation of the Remote Consultation and Diagnosis (RCD) system. The Java RCD includes a multimedia consultation session between physicians that includes text, static image, image annotation, and audio data. The JAVA RCD allows 2-4 physicians to collaborate on a patient case. It allows physicians to join the session via WWW Java-enabled browsers or stand alone RCD application. The RCD system includes a distributed database archive system for archiving and retrieving patient and session data. The RCD system can be used for store and forward scenarios, case reviews, and interactive RCD multimedia sessions. The RCD system operates over the Internet, telephone lines, or in a private Intranet. A multimedia consultation session can be recorded, and then played back at a later time for review, comments, and education. A session can be played back using Java-enabled WWW browsers on any operating system platform. The JAVA RCD system shows that a case diagnosis can be captured digitally and played back with the original real-time temporal relationships between data streams. In this paper, we describe design and implementation of the RCD session playback.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PubMed

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-09-18

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

Natural bounds on herbivorous coral reef fishes.

PubMed

Heenan, Adel; Hoey, Andrew S; Williams, Gareth J; Williams, Ivor D

2016-11-30

Humans are an increasingly dominant driver of Earth's biological communities, but differentiating human impacts from natural drivers of ecosystem state is crucial. Herbivorous fish play a key role in maintaining coral dominance on coral reefs, and are widely affected by human activities, principally fishing. We assess the relative importance of human and biophysical (habitat and oceanographic) drivers on the biomass of five herbivorous functional groups among 33 islands in the central and western Pacific Ocean. Human impacts were clear for some, but not all, herbivore groups. Biomass of browsers, large excavators, and of all herbivores combined declined rapidly with increasing human population density, whereas grazers, scrapers, and detritivores displayed no relationship. Sea-surface temperature had significant but opposing effects on the biomass of detritivores (positive) and browsers (negative). Similarly, the biomass of scrapers, grazers, and detritivores correlated with habitat structural complexity; however, relationships were group specific. Finally, the biomass of browsers and large excavators was related to island geomorphology, both peaking on low-lying islands and atolls. The substantial variability in herbivore populations explained by natural biophysical drivers highlights the need for locally appropriate management targets on coral reefs. © 2016 The Authors.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model. PMID:25485311

Are there differences in birth weight according to sex and associations with maternal exposure to air pollutants? A cohort study.

PubMed

Fernando Costa Nascimento, Luiz; Blanco Machin, Adrian; Antonio Almeida Dos Santos, Djalma

2017-01-01

Several effects of exposure to air pollutants on human health are known. The aim of this study was to identify whether exposure of pregnant women to air pollutants contributes towards low birth weight and which sex is more affected. Longitudinal study using data on newborns from mothers living in São José do Rio Preto (SP) who were exposed to air pollutants in 2012-2013. A hierarchical model on three levels was built using maternal and newborn variables and environmental concentrations of particulate matter, ozone and nitrogen dioxide in quartiles. Preterm new-borns, twins and newborns with birth defects were excluded and exposure windows of 30, 60 and 90 days before delivery were considered. 8,948 newborns were included: 4,491 males (50.2%) and 4,457 females (49.8%); 301 newborns presented low birth weight (3.4%). The mean weight differed between males (3281.0 g) and females (3146.4 g) (P < 0.001). Exposure to ozone was significantly associated with low birth weight in both sexes in the 30-day window (odds ratio, OR = 1.38) and 90-day window (OR = 1.48); and among females, in the 30-day window (OR = 1.58) and 90-day window (OR = 1.59). Exposure to particulate matter had a paradoxical protective effect. No association was found among male newborns. Female newborns showed greater susceptibility to maternal exposure to air pollutants. Studies on low birth weight in relation to maternal exposure to air pollutants should deal with males and females separately.

Land surface temperature measurements from EOS MODIS data

NASA Technical Reports Server (NTRS)

Wan, Zhengming

1994-01-01

A generalized split-window method for retrieving land-surface temperature (LST) from AVHRR and MODIS data has been developed. Accurate radiative transfer simulations show that the coefficients in the split-window algorithm for LST must depend on the viewing angle, if we are to achieve a LST accuracy of about 1 K for the whole scan swath range (+/-55.4 deg and +/-55 deg from nadir for AVHRR and MODIS, respectively) and for the ranges of surface temperature and atmospheric conditions over land, which are much wider than those over oceans. We obtain these coefficients from regression analysis of radiative transfer simulations, and we analyze sensitivity and error by using results from systematic radiative transfer simulations over wide ranges of surface temperatures and emissivities, and atmospheric water vapor abundance and temperatures. Simulations indicated that as atmospheric column water vapor increases and viewing angle is larger than 45 deg it is necessary to optimize the split-window method by separating the ranges of the atmospheric column water vapor and lower boundary temperature, and the surface temperature into tractable sub-ranges. The atmospheric lower boundary temperature and (vertical) column water vapor values retrieved from HIRS/2 or MODIS atmospheric sounding channels can be used to determine the range where the optimum coefficients of the split-window method are given. This new LST algorithm not only retrieves LST more accurately but also is less sensitive than viewing-angle independent LST algorithms to the uncertainty in the band emissivities of the land-surface in the split-window and to the instrument noise.

Operating Characteristics in DIII-D ELM-Suppressed RMP H-modes with ITER Similar Shapes

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

Evans, T E; Fenstermacher, M E; Jakubowski, M

2008-10-13

Fast energy transients, incident on the DIII-D divertors due to Type-I edge localized modes (ELMs), are eliminated using small dc currents in a simple set of non-axisymmetric coils that produce edge resonant magnetic perturbations (RMP). In ITER similar shaped (ISS) plasmas, with electron pedestal collisionalities matched to those expected in ITER a sharp resonant window in the safety factor at the 95 percent normalized poloidal flux surface is observed for ELM suppression at q{sub 95}=3.57 with a minimum width {delta}q{sub 95} of {+-}0.05. The size of this resonant window has been increased by a factor of 4 in ISS plasmasmore » by increasing the magnitude of the current in an n=3 coil set along with the current in a separate n=1 coil set. The resonant ELM-suppression window is highly reproducible for a given plasma shape, coil configuration and coil current but can vary with other operating conditions such as {beta}{sub N}. Isolated resonant windows have also been found at other q95 values when using different RMP coil configurations. For example, when the I-coil is operated in an n=3 up-down asymmetric configuration rather than an up-down symmetric configuration a resonant window is found near q{sub 95}=7.4. A Fourier analysis of the applied vacuum magnetic field demonstrates a statistical correlation between the Chirikov island overlap parameter and ELM suppression. These results have been used as a guide for RMP coil design studies in various ITER operating scenarios.« less

DNAApp: a mobile application for sequencing data analysis

PubMed Central

Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

2014-01-01

Summary: There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. Availability and implementation: The Android version of DNAApp is available in Google Play Store as ‘DNAApp’, and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. Contact: samuelg@bii.a-star.edu.sg PMID:25095882

DNAApp: a mobile application for sequencing data analysis.

PubMed

Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

2014-11-15

There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. The Android version of DNAApp is available in Google Play Store as 'DNAApp', and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. samuelg@bii.a-star.edu.sg. © The Author 2014. Published by Oxford University Press.

An Internet service for manipulating 3D models of human organs reconstructed from computer tomography and magnetic resonance imaging.

PubMed

Clapworthy, G; Krokos, M; Vasilonikolidakis, N

1997-11-01

Our paper describes an integrated methodology addressing the development of an Internet service for medical professionals, medical students and generally, people interested in medicine. The service (currently developed in the framework of IAEVA, a Telematics Application Programme project of the European Union), incorporates a mechanism for retrieving from a relational database (reference library) 3D volumetric models of human organs reconstructed from computer tomography (CT) and/or magnetic resonance imaging (MRI). Retrieval is implemented in a way transparent to the actual physical location of the database. Prospective users are provided with a Solid Object Viewer that offers them manipulation (rotation, zooming, dissection etc.) of 3D volumetric models. The service constitutes an excellent foundation of understanding for medical professionals/students and a mechanism for broad and rapid dissemination of information related to particular pathological conditions; although pathological conditions of the knee and skin are supported currently, our methodology allows easy service extension into other human organs ultimately covering the entire human body. The service accepts most Internet browsers and supports MS-Windows 32 platforms; no graphics accelerators or any specialised hardware are necessary, thereby allowing service availability to the widest possible audience. Nevertheless, the service operates in near real-time not only over high speed expensive network lines but also over low/medium network connections.

Network Computing Infrastructure to Share Tools and Data in Global Nuclear Energy Partnership

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer-Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP.

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows.

PubMed

Hardie, L C; VandeHaar, M J; Tempelman, R J; Weigel, K A; Armentano, L E; Wiggans, G R; Veerkamp, R F; de Haas, Y; Coffey, M P; Connor, E E; Hanigan, M D; Staples, C; Wang, Z; Dekkers, J C M; Spurlock, D M

2017-11-01

The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain β-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Satellite Data Processing System (SDPS) users manual V1.0

NASA Technical Reports Server (NTRS)

Caruso, Michael; Dunn, Chris

1989-01-01

SDPS is a menu driven interactive program designed to facilitate the display and output of image and line-based data sets common to telemetry, modeling and remote sensing. This program can be used to display up to four separate raster images and overlay line-based data such as coastlines, ship tracks and velocity vectors. The program uses multiple windows to communicate information with the user. At any given time, the program may have up to four image display windows as well as auxiliary windows containing information about each image displayed. SDPS is not a commercial program. It does not contain complete type checking or error diagnostics which may allow the program to crash. Known anomalies will be mentioned in the appropriate section as notes or cautions. SDPS was designed to be used on Sun Microsystems Workstations running SunView1 (Sun Visual/Integrated Environment for Workstations). It was primarily designed to be used on workstations equipped with color monitors, but most of the line-based functions and several of the raster-based functions can be used with monochrome monitors. The program currently runs on Sun 3 series workstations running Sun OS 4.0 and should port easily to Sun 4 and Sun 386 series workstations with SunView1. Users should also be familiar with UNIX, Sun workstations and the SunView window system.

Divorce and death: forty years of the Charleston Heart Study.

PubMed

Sbarra, David A; Nietert, Paul J

2009-01-01

Forty years of follow-up data from the Charleston Heart Study (CHS) were used to examine the risk for early mortality associated with marital separation or divorce in a sample of more than 1,300 adults assessed on several occasions between 1960 and 2000. Participants who were separated or divorced at the start of the study evidenced significantly elevated rates of early mortality, and these results held after adjusting for baseline health status and other demographic variables. Being separated or divorced throughout the CHS follow-up window was one of the strongest predictors of early mortality. However, the excess mortality risk associated with separation or divorce was completely eliminated when participants who had ever experienced a marital separation or divorce during the study were compared with all other participants. These findings suggest that a key predictor of early death is the amount of time people live as separated or divorced. It is possible that the mortality risk conferred by marital dissolution is due to dimensions of personality that predict divorce as well as a decreased likelihood of future remarriage.

The ISOLDE control system

NASA Astrophysics Data System (ADS)

Deloose, I.; Pace, A.

1994-12-01

The two CERN isotope separators named ISOLDE have been running on the new Personal Computer (PC) based control system since April 1992. The new architecture that makes heavy use of the commercial software and hardware of the PC market has been implemented on the 1700 geographically distributed control channels of the two separators and their experimental area. Eleven MSDOS Intel-based PCs with approximately 80 acquisition and control boards are used to access the equipment and are controlled from three PCs running Microsoft Windows used as consoles through a Novell Local Area Network. This paper describes the interesting solutions found and discusses the reduced programming workload and costs that have been obtained.

Dual-opposite injection capillary electrophoresis: Principles and misconceptions.

PubMed

Blackney, Donna M; Foley, Joe P

2017-03-01

Dual-opposite injection capillary electrophoresis (DOI-CE) is a separation technique that utilizes both ends of the capillary for sample introduction. The electroosmotic flow (EOF) is suppressed to allow all ions to reach the detector quickly. Depending on the individual electrophoretic mobilities of the analytes of interest and the effective length that each analyte travels to the detection window, the elution order of analytes in a DOI-CE separation can vary widely. This review discusses the principles, applications, and limitations of dual-opposite injection capillary electrophoresis. Common misconceptions regarding DOI-CE are clarified. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inquiry based learning with a virtual microscope

NASA Astrophysics Data System (ADS)

Kelley, S. P.; Sharples, M.; Tindle, A.; Villasclaras-Fernández, E.

2012-12-01

As part of newly funded initiative, the Wolfson OpenScience Laboratory, we are linking a tool for inquiry based learning, nQuire (http://www.nquire.org.uk) with the virtual microscope for Earth science (http://www.virtualmicroscope.co.uk) to allow students to undertake projects and gain from inquiry based study thin sections of rocks without the need for a laboratory with expensive petrological microscopes. The Virtual Microscope (VM) was developed for undergraduate teaching of petrology and geoscience, allowing students to explore rock hand specimens and thin sections in a browser window. The system is based on HTML5 application and allows students to scan and zoom the rocks in a browser window, view in ppl and xpl conditions, and rotate specific areas to view birefringence and pleochroism. Importantly the VM allows students to gain access to rare specimens such as Moon rocks that might be too precious to suffer loss or damage. Experimentation with such specimens can inspire the learners' interest in science and allows them to investigate relevant science questions. Yet it is challenging for learners to engage in scientific processes, as they may lack scientific investigation skills or have problems in planning their activities; for teachers, managing inquiry activities is a demanding task (Quintana et al., 2004). To facilitate the realization of inquiry activities, the VM is being integrated with the nQuire tool. nQuire is a web tool that guides and supports students through the inquiry process (Mulholland et al., 2011). Learners are encouraged to construct their own personally relevant hypothesis, pose scientific questions, and plan the method to answer them. Then, the system enables users to collect and analyze data, and share their conclusions. Teachers can monitor their students' progress through inquiries, and give them access to new parts of inquiries as they advance. By means of the integration of nQuire and the VM, inquiries that involve collecting data through a microscope can be created and supported. To illustrate the possibilities of these tools, we have designed two inquiries that engage learners in the study of Moon rock samples under the microscope, starting from general questions such as comparison of Moon rocks or determining the origin of meteorites. One is aimed at undergraduate Geology students; the second has been conceived for the general public. Science teachers can reuse these inquiries, adapt them as they need, or create completely new inquiries using nQuire's authoring tool. We will report progress and demonstrate the combination of these two on-line tools to create an open educational resource allowing educators to design and run science inquiries for Earth and planetary science in a range of settings from schools to universities. Quintana, C., Reiser, B. J., Davis, E. A., Krajcik, J., Fretz, E., Duncan, R. G., Kyza, E., et al. (2004). A scaffolding design framework for software to support science inquiry. Journal of the Learning Sciences, 13(3), 337-386. Mulholland, P., Anastopoulou, S., Collins, T., FeiBt, M., Gaved, M., Kerawalla, L., Paxton, M., et al. (2011). nQuire: Technological support for personal inquiry learning. IEEE Transactions on Learning Technologies. First published online, December 5, 2011, http://doi.ieeecomputersociety.org/10.1109/TLT.2011.32.

Fast Color Grouping and Slow Color Inhibition: Evidence for Distinct Temporal Windows for Separate Processes in Preview Search

ERIC Educational Resources Information Center

Braithwaite, Jason J.; Humphreys, Glyn W.; Hulleman, Johan; Watson, Derrick G.

2007-01-01

The authors report 4 experiments that examined color grouping and negative carryover effects in preview search via a probe detection task (J. J. Braithwaite, G. W. Humphreys, & J. Hodsoll, 2003). In Experiment 1, there was evidence of a negative color carryover from the preview to new items, using both search and probe detection measures. There…

Electronic Codebooks for Windows 95/98: 22 ECBs. Electronic Codebook (ECB) Updates for Previously Released Data Files. [CD-ROM].

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

This CD-ROM contains a separate electronic codebook for each of the following National Center for Education Statistics data sets: (1) B94, Baccalaureate and Beyond 1993-94 (restricted); (2) B97, Baccalaureate and Beyond 1993-97 (restricted); (3) BP4, Beginning Postsecondary Students 1990-94 (restricted); (4) FAC, 1992-93 National Student of…

A simple heat-pipe cell for X-ray absorption spectrometry of potassium vapor

NASA Astrophysics Data System (ADS)

Pres̆eren, R.; Kodre, A.; Arc̆on, I.; Padez̆nik Gomils̆ek, J.; Hribar, M.

1999-01-01

The construction and operation of a simple high-temperature X-ray absorption cell for potassium vapor is described. The principle of "spectroscopic heat pipe" is exploited to separate kapton windows, indispensable for good transmission in the low-energy region, from the hot and aggressive vapor. High-resolution spectrum of the K-edge region of atomic potassium reveals fingerprints of multielectron photoexcitations.

Expedition 23 State Commission

NASA Image and Video Library

2010-03-31

Expedition 23 Flight Engineer Mikhail Kornienko says a few words during the State Commission meeting to approve the Soyuz launch of Kornienko, Expedition 23 Soyuz Commander Alexander Skvortsov and Expedition 23 Flight Engineer Tracy Caldwell Dyson on Thursday, April 1, 2010 in Baikonur, Kazakhstan. The crew is kept in a separate room with a glass window in order to help maintain their health. Photo Credit: (NASA/Bill Ingalls)