WorldWideScience

Sample records for gforge cde browser

  1. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs.

    NARCIS (Netherlands)

    van Wolfswinkel, J.C.; Claycomb, J.M.; Batista, P.J.; Mello, C.C.; Berezikov, E.; Ketting, R.F.

    2009-01-01

    We have studied the function of a conserved germline-specific nucleotidyltransferase protein, CDE-1, in RNAi and chromosome segregation in C. elegans. CDE-1 localizes specifically to mitotic chromosomes in embryos. This localization requires the RdRP EGO-1, which physically interacts with CDE-1, and

  2. Decoding Technology: Web Browsers

    Science.gov (United States)

    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…

  3. Web Browser Programming

    OpenAIRE

    Luján Mora, Sergio

    2006-01-01

    Presentaciones del curso "Web Browser Programming" impartido en la Université M'Hamed Bougara (Bourmerdes, Argelia) en junio de 2006. Proyecto financiado por la Unión Europea: TEMPUS JEP-32102-2004, Licence Professionnelle Technologies des Applications Web (Professional License for Web Application Technologies).

  4. Mixed Reality Browsers

    OpenAIRE

    Lemordant, Jacques

    2011-01-01

    International audience; This paper focuses on Mixed Reality Browsers (MRB) that merge real and virtual worlds somewhere along the virtuality continuum which connects completely real environments to completely virtual ones. We present the audio-visual MRB developed by the WAM project-team of INRIA at Grenoble, which uses a RDF data format for POIs whose URIs refer to content expressed in HTML5 and in a declarartive data format for interactive audio.

  5. Zooming Web browser

    Science.gov (United States)

    Bederson, Benjamin B.; Hollan, James D.; Stewart, Jason B.; Rogers, David; Druin, Allison; Vick, David

    1996-03-01

    The World Wide Web (WWW) is becoming increasingly important for business, education, and entertainment. Popular web browsers make access to Internet information resources relatively easy for novice users. Simply by clicking on a link, a new page of information replaces the current one on the screen. Unfortunately however, after following a number of links, people can have difficulty remembering where they've been and navigating links they have followed. As one's collection of web pages grows and as more information of interest populates the web, effective navigation becomes an issue of fundamental importance. We are developing a prototype zooming browser to explore alternative mechanisms for navigating the WWW. Instead of having a single page visible at a time, multiple pages and the links between them are depicted on a large zoomable information surface. Pages are scaled so that the page in focus is clearly readable with connected pages shown at smaller scales to provide context. As a link is followed the new page becomes the focus and existing pages are dynamically repositioned and scaled. Layout changes are animated so that the focus page moves smoothly to the center of the display surface while contextual information provided by linked pages scales down. While our browser supports multiscale representations of existing HTML pages, we have also extended HTML to support multiscale layout within a page. This extension, Multi-Scale Markup Language, is at an early stage of development. It currently supports inclusion within a page of variable-sized dynamic objects, graphics, and other interface mechanisms from our underlying Pad++ substrate. This provides sophisticated client- side interactions, permits annotations to be added to pages, and allows page constituents to be used as independent graphical objects. In this paper, we describe our prototype web browser and authoring facilities. We show how simple extensions to HTML can support sophisticated client

  6. Web Browser Security Update Effectiveness

    Science.gov (United States)

    Duebendorfer, Thomas; Frei, Stefan

    We analyze the effectiveness of different Web browser update mechanisms on various operating systems; from Google Chrome's silent update mechanism to Opera's update requiring a full re-installation. We use anonymized logs from Google's world wide distributed Web servers. An analysis of the logged HTTP user-agent strings that Web browsers report when requesting any Web page is used to measure the daily browser version shares in active use. To the best of our knowledge, this is the first global scale measurement of Web browser update effectiveness comparing four different Web browser update strategies including Google Chrome. Our measurements prove that silent updates and little dependency on the underlying operating system are most effective to get users of Web browsers to surf the Web with the latest browser version.

  7. Designing, Implementing, and Evaluating Secure Web Browsers

    Science.gov (United States)

    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…

  8. Web Browser Trends and Technologies.

    Science.gov (United States)

    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)

  9. Eco-Health Relationship Browser

    Science.gov (United States)

    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...

  10. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs.

    Science.gov (United States)

    van Wolfswinkel, Josien C; Claycomb, Julie M; Batista, Pedro J; Mello, Craig C; Berezikov, Eugene; Ketting, René F

    2009-10-02

    We have studied the function of a conserved germline-specific nucleotidyltransferase protein, CDE-1, in RNAi and chromosome segregation in C. elegans. CDE-1 localizes specifically to mitotic chromosomes in embryos. This localization requires the RdRP EGO-1, which physically interacts with CDE-1, and the Argonaute protein CSR-1. We found that CDE-1 is required for the uridylation of CSR-1 bound siRNAs, and that in the absence of CDE-1 these siRNAs accumulate to inappropriate levels, accompanied by defects in both meiotic and mitotic chromosome segregation. Elevated siRNA levels are associated with erroneous gene silencing, most likely through the inappropriate loading of CSR-1 siRNAs into other Argonaute proteins. We propose a model in which CDE-1 restricts specific EGO-1-generated siRNAs to the CSR-1 mediated, chromosome associated RNAi pathway, thus separating it from other endogenous RNAi pathways. The conserved nature of CDE-1 suggests that similar sorting mechanisms may operate in other animals, including mammals.

  11. Trajectory Browser Website

    Science.gov (United States)

    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.

  12. JPL Small Body Database Browser

    Data.gov (United States)

    National Aeronautics and Space Administration — The JPL Small-Body Database Browser provides data for all known asteroids and many comets. Newly discovered objects and their orbits are added on a daily basis....

  13. The central role of CDE/CHR promoter elements in the regulation of cell cycle-dependent gene transcription.

    Science.gov (United States)

    Müller, Gerd A; Engeland, Kurt

    2010-02-01

    The cell cycle-dependent element (CDE) and the cell cycle genes homology region (CHR) control the transcription of genes with maximum expression in G(2) phase and in mitosis. Promoters of these genes are repressed by proteins binding to CDE/CHR elements in G(0) and G(1) phases. Relief from repression begins in S phase and continues into G(2) phase and mitosis. Generally, CDE sites are located four nucleotides upstream of CHR elements in TATA-less promoters of genes such as Cdc25C, Cdc2 and cyclin A. However, expression of some other genes, such as human cyclin B1 and cyclin B2, has been shown to be controlled only by a CHR lacking a functional CDE. To date, it is not fully understood which proteins bind to and control CDE/CHR-containing promoters. Recently, components of the DREAM complex were shown to be involved in CDE/CHR-dependent transcriptional regulation. In addition, the expression of genes regulated by CDE/CHR elements is mostly achieved through CCAAT-boxes, which bind heterotrimeric NF-Y proteins as well as the histone acetyltransferase p300. Importantly, many CDE/CHR promoters are downregulated by the tumor suppressor p53. In this review, we define criteria for CDE/CHR-regulated promoters and propose to distinguish two classes of CDE/CHR-regulated genes. The regulation through transcription factors potentially binding to the CDE/CHR is discussed, and recently discovered links to central pathways regulated by E2F, the pRB family and p53 are highlighted.

  14. EVALUATING EFFECTIVENESS OF MOBILE BROWSER SECURITY WARNINGS

    Directory of Open Access Journals (Sweden)

    Ronak Shah

    2016-09-01

    Full Text Available This work precisely evaluates whether browser security warnings are as ineffective as proposed by popular sentiments and past writings. This research used different kinds of Android mobile browsers as well as desktop browsers to evaluate security warnings. Security experts and developers should give emphasis on making a user aware of security warnings and should not neglect aim of communicating this to users. Security experts and system architects should emphasis the goal of communicating security information to end users. In most of the browsers, security warnings are not emphasized, and browsers simply do not show warnings, or there are a number of ways to hide those warnings of malicious sites. This work precisely finds that how inconsistent browsers really are in prompting security warnings. In particular, majority of the modern mobile web browsers are vulnerable to these security threats. We find inconsistency in SSL warnings among web browsers. Based on this work, we make recommendations for warning designers and researchers.

  15. Quantifying the web browser ecosystem.

    Science.gov (United States)

    Ferdman, Sela; Minkov, Einat; Bekkerman, Ron; 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.

  16. The Web Browser as a Simulation Platform

    OpenAIRE

    Darken, Chris

    2012-01-01

    MOVES Research & Education Systems Seminar: Presentation; Session 7: Computer Gaming and Web-Delivered Simulation; Moderator: Perry McDowell; The Web Browser as a Simulation Platform; speaker: Chris Darken WebGL and HTML5 combine to make web browsers capable simulation platforms. Building simulations to run in browsers require skills that are relatively common and easy to obtain. The resulting simulations are easy to share with students, research collaborators and customers. We will disc...

  17. Memoirs of a Browser: A Cross-browser Detection Model for Privacy-breaching Extensions

    NARCIS (Netherlands)

    Giuffrida, C.; Ortolani, S.; Crispo, B.

    2012-01-01

    Web browsers are undoubtedly one of the most popular user applications. This is even more evident in recent times, with Google introducing a platform where the browser is the only application provided to the user. With their modular and extensible architecture, modern browsers are also an appealing

  18. Engineering the ATLAS TAG Browser

    International Nuclear Information System (INIS)

    Zhang Qizhi

    2011-01-01

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

  19. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services a...

  20. Web browser accessibility using open source software

    NARCIS (Netherlands)

    Z. Obrenovic; J.R. van Ossenbruggen (Jacco)

    2007-01-01

    htmlabstractA Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional

  1. The Navigational Power of Web Browsers

    NARCIS (Netherlands)

    Bielecki, M.; Hidders, J.; Paredaens, J.; Spielmann, M.; Tyszkiewicz, J.; Van den Bussche, J.; http://link.springer.com/article/10.1007/s00224-010-9294-3

    2010-01-01

    We investigate the computational capabilities of Web browsers, when equipped with a standard finite automaton. We observe that Web browsers are Turingcomplete. We introduce the notion of a navigational problem, and investigate the complexity of solving Web queries and navigational problems by Web

  2. Line-mode browser development days

    CERN Multimedia

    Anna Pantelia

    2013-01-01

    Twelve talented web developers have travelled to CERN from all over the world to recreate a piece of web history: the line-mode browser. See the line-mode browser simulator that they created here. Read more about the birth of the web here.

  3. Exploring the enjoyment of playing browser games.

    Science.gov (United States)

    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.

  4. myGenomeBrowser: building and sharing your own genome browser.

    Science.gov (United States)

    Carrere, Sébastien; Gouzy, Jérôme

    2017-04-15

    myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data. myGenomeBrowser is freely available at https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser and includes tutorial screencasts. Source code and installation instructions can be found at https://framagit.org/BBRIC/myGenomeBrowser . myGenomeBrowser is open-source and mainly implemented in Perl, JavaScript, Apache and Docker. sebastien.carrere@inra.fr. © The Author 2017. Published by Oxford University Press.

  5. Browsers for Distributed Systems: Universal Paradigm or Siren's Song?

    National Research Council Canada - National Science Library

    Seacord, Robett

    1998-01-01

    Web based browsers are quickly becoming ubiquitous in the workplace. Software development managers are quick to incorporate browsers into a broad range of software development projects, often inappropriately...

  6. The proteome browser web portal.

    Science.gov (United States)

    Goode, Robert J A; Yu, Simon; Kannan, Anitha; Christiansen, Jeffrey H; Beitz, Anthony; Hancock, William S; Nice, Edouard; Smith, A Ian

    2013-01-04

    In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), aimed at identifying and characterizing the proteome of the human body. To support complete coverage, one arm of the project will take a gene- or chromosomal-centric strategy (C-HPP) aimed at identifying at least one protein product from each protein-coding gene. Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates updated pertinent information from each of these data repositories and assembles the information into a searchable format suitable for the type of global proteomics effort proposed by the C-HPP. We have undertaken the goal of producing a data integration and analysis software system and browser for the C-HPP effort and of making data collections from this resource discoverable through metadata repositories, such as Australian National Data Service's Research Data Australia. Here we present our vision and progress toward the goal of developing a comprehensive data integration and analysis software tool that provides a snapshot of currently available proteomic related knowledge around each gene product, which will ultimately assist in analyzing biological function and the study of human physiology in health and disease.

  7. WebPlus: lxplus in your browser

    CERN Multimedia

    CERN. Geneva

    2017-01-01

    This talk will cover the possibility of offering a lxplus like service directly on the browser. How we could rely on containers and schedulers to maintain long lived sessions, and how to offer integration with common CERN services.

  8. The UCSC Genome Browser database: 2015 update

    Science.gov (United States)

    Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S.; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Miga, Karen H.; Nguyen, Ngan; Paten, Benedict; Raney, Brian J.; Smit, Arian F. A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  9. Overexpression of LolCDE allows deletion of the Escherichia coli gene encoding apolipoprotein N-acyltransferase.

    Science.gov (United States)

    Narita, Shin-ichiro; Tokuda, Hajime

    2011-09-01

    Bacterial lipoproteins represent a subset of membrane-associated proteins that are covalently modified with lipids at the N-terminal cysteine. The final step of lipoprotein modification, N-acylation of apolipoproteins, is mediated by apolipoprotein N-acyltransferase (Lnt). Examinations with reconstituted proteoliposomes and a conditional mutant previously indicated that N-acylation of lipoproteins is required for their efficient release from the inner membrane catalyzed by LolA and LolCDE, the lipoprotein-specific chaperone and ABC transporter, respectively. Because Lnt is essential for Escherichia coli, a mutant lacking Lnt activity has not been isolated. However, we report here that lnt-null strains can be constructed when LolCDE is overproduced in strains lacking either the major outer membrane lipoprotein Lpp or transpeptidases that cross-link Lpp with peptidoglycan. Lipoproteins purified from the lnt-null strain exhibited increased mobility on SDS-PAGE compared to those from wild-type cells and could be sequenced by Edman degradation, indicating that lipoproteins in this mutant exist as apolipoproteins that lack N-acylation. Overexpression of Lpp in the lnt-null strain resulted in the accumulation of apoLpp in the inner membrane and caused growth arrest. In contrast to the release of mature Lpp in the presence of LolA and LolCDE, that of apoLpp from the inner membrane was significantly retarded. Furthermore, the amount of lipoproteins copurified with LolCDE was significantly reduced in the lnt-null strain. These results indicate that the affinity of LolCDE for apolipoprotein is very low, and therefore, overexpression of LolCDE is required for its release and sorting to the outer membrane. Copyright © 2011, American Society for Microbiology. All Rights Reserved.

  10. Overexpression of LolCDE Allows Deletion of the Escherichia coli Gene Encoding Apolipoprotein N-Acyltransferase ▿

    Science.gov (United States)

    Narita, Shin-ichiro; Tokuda, Hajime

    2011-01-01

    Bacterial lipoproteins represent a subset of membrane-associated proteins that are covalently modified with lipids at the N-terminal cysteine. The final step of lipoprotein modification, N-acylation of apolipoproteins, is mediated by apolipoprotein N-acyltransferase (Lnt). Examinations with reconstituted proteoliposomes and a conditional mutant previously indicated that N-acylation of lipoproteins is required for their efficient release from the inner membrane catalyzed by LolA and LolCDE, the lipoprotein-specific chaperone and ABC transporter, respectively. Because Lnt is essential for Escherichia coli, a mutant lacking Lnt activity has not been isolated. However, we report here that lnt-null strains can be constructed when LolCDE is overproduced in strains lacking either the major outer membrane lipoprotein Lpp or transpeptidases that cross-link Lpp with peptidoglycan. Lipoproteins purified from the lnt-null strain exhibited increased mobility on SDS-PAGE compared to those from wild-type cells and could be sequenced by Edman degradation, indicating that lipoproteins in this mutant exist as apolipoproteins that lack N-acylation. Overexpression of Lpp in the lnt-null strain resulted in the accumulation of apoLpp in the inner membrane and caused growth arrest. In contrast to the release of mature Lpp in the presence of LolA and LolCDE, that of apoLpp from the inner membrane was significantly retarded. Furthermore, the amount of lipoproteins copurified with LolCDE was significantly reduced in the lnt-null strain. These results indicate that the affinity of LolCDE for apolipoprotein is very low, and therefore, overexpression of LolCDE is required for its release and sorting to the outer membrane. PMID:21742870

  11. Controlling EPICS from a web browser

    International Nuclear Information System (INIS)

    Evans, K. Jr.

    1999-01-01

    An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and with both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM

  12. The UCSC genome browser database: update 2007

    DEFF Research Database (Denmark)

    Kuhn, R M; Karolchik, D; Zweig, A S

    2006-01-01

    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up...... to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities...... for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature...

  13. The UCSC Genome Browser Database: update 2006

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  14. A Lead Provided by Bookmarks - Intelligent Browsers

    Directory of Open Access Journals (Sweden)

    Dan Balanescu

    2015-05-01

    Full Text Available Browsers are applications that allow Internet access. A defining characteristic is their unidirectionality: Navigator-> Internet. The purpose of this article is to support the idea of Intelligent Browsers that is defined by bidirectional: Navigator-> Internet and Internet-> Navigator. The fundamental idea is that the Internet contains huge resources of knowledge, but they are “passive”. The purpose of this article is to propose the “activation” of this knowledge so that they, through “Intelligent Browsers”, to become from Sitting Ducks to Active Mentors. Following this idea, the present article proposes changes to Bookmarks function, from the current status of Favorites to Recommendations. The article presents an analysis of the utility of this function (by presenting a research of web browsing behaviors and in particular finds that the significance of this utility has decreased lately (to the point of becoming almost useless, as will be shown, in terms data-information-knowledge. Finally, it presents the idea of a project which aims to be an applied approach that anticipates the findings of this study and the concept of Intelligent Browsers (or Active Browsers required in the context of the Big Data concept.

  15. Plugin free remote visualization in the browser

    Science.gov (United States)

    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.

  16. DNA deformability changes of single base pair mutants within CDE binding sites in S. Cerevisiae centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries

    Directory of Open Access Journals (Sweden)

    Marx Kenneth A

    2006-03-01

    Full Text Available Abstract Background The centromeres in yeast (S. cerevisiae are organized by short DNA sequences (125 bp on each chromosome consisting of 2 conserved elements: CDEI and CDEIII spaced by a CDEII region. CDEI and CDEIII are critical sequence specific protein binding sites necessary for correct centromere formation and following assembly with proteins, are positioned near each other on a specialized nucleosome. Hegemann et al. BioEssays 1993, 15: 451–460 reported single base DNA mutants within the critical CDEI and CDEIII binding sites on the centromere of chromosome 6 and quantitated centromere loss of function, which they measured as loss rates for the different chromosome 6 mutants during cell division. Olson et al. Proc Natl Acad Sci USA 1998, 95: 11163–11168 reported the use of protein-DNA crystallography data to produce a DNA dinucleotide protein deformability energetic scale (PD-scale that describes local DNA deformability by sequence specific binding proteins. We have used the PD-scale to investigate the DNA sequence dependence of the yeast chromosome 6 mutants' loss rate data. Each single base mutant changes 2 PD-scale values at that changed base position relative to the wild type. In this study, we have utilized these mutants to demonstrate a correlation between the change in DNA deformability of the CDEI and CDEIII core sites and the overall experimentally measured chromosome loss rates of the chromosome 6 mutants. Results In the CDE I and CDEIII core binding regions an increase in the magnitude of change in deformability of chromosome 6 single base mutants with respect to the wild type correlates to an increase in the measured chromosome loss rate. These correlations were found to be significant relative to 105 Monte Carlo randomizations of the dinucleotide PD-scale applied to the same calculation. A net loss of deformability also tends to increase the loss rate. Binding site position specific, 4 data-point correlations were also

  17. Genome Maps, a new generation genome browser

    Science.gov (United States)

    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

  18. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    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.

  19. Online Marketing Strategy for a browser games portal

    OpenAIRE

    Vinaixa Campos, Joan

    2008-01-01

    The Browser games industry: Introduction and description of browser games and browser games portals. Description of the main characteristics that define the browser games industry and its competitive environment. Analysis of all the factors that need to be considered in order to make a successful market entry. Online marketing techniques: Introduction and description to the main online marketing techniques that exist to market a product or service in internet: Search Engine Marketing...

  20. 78 FR 30226 - Accessibility Requirements for Internet Browsers

    Science.gov (United States)

    2013-05-22

    ... accessibility features and capabilities in the ACS web application retrieved and displayed by the browser... or directs the installation of an Internet browser that supports a specific web standard, approved... included Internet browser does not support a particular technology that is needed to make web-based...

  1. A genome browser database for rice ( Oryza sativa ) and Chinese ...

    African Journals Online (AJOL)

    We have constructed an integrated genome browser database for sequence analysis of rice (Oryza sativa) and Chinese cabbage (Brassica rapa) genomes. The genome browser for Arabidopsis (Arabidopsis thaliana) was included to provide the comparative analysis with Chinese cabbage. The genome browser of rice ...

  2. Zbrowse: an interactive GWAS results browser

    Directory of Open Access Journals (Sweden)

    Greg R. Ziegler

    2015-05-01

    Full Text Available The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.

  3. A web browser for LHC design integration

    International Nuclear Information System (INIS)

    Gennaro, Silvano de

    1996-01-01

    This paper describes i3D, a WWW 3D graphic browser which is currently being developed within the scope of the VENUS project at CERN. i3D allows V R style navigation within the LHC Virtual Prototypes (see abstract 103), loaded over standard WWW protocols from the VENUS server. The user can explore these data models, converted from EUCLID to the i3D format, and trigger WWW standard hyperlinks by simply clicking on graphic objects. Some of these objects will cause the loading of new 3D worlds, extending the concept of hyperlinks to the one of hyperworlds. VENUS intends to develop i3D's functionality and performance in order to use it as a graphic model browser within the scope of LHC's Engineering Design Integration. (author)

  4. The UCSC Cancer Genomics Browser: update 2015.

    Science.gov (United States)

    Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun

    2015-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers. The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227,000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. Users can download and upload clinical data, generate Kaplan-Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with others. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. GTB - an online genome tolerance browser.

    Science.gov (United States)

    Shihab, Hashem A; Rogers, Mark F; Ferlaino, Michael; Campbell, Colin; Gaunt, Tom R

    2017-01-06

    Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and prioritize SNVs across the human genome for further investigation. However, no tool exists to visualize the predicted tolerance of the genome to mutation, or the similarities between these methods. We present the Genome Tolerance Browser (GTB, http://gtb.biocompute.org.uk ): an online genome browser for visualizing the predicted tolerance of the genome to mutation. The server summarizes several in silico prediction algorithms and conservation scores: including 13 genome-wide prediction algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specific algorithms. The GTB enables users to visualize the similarities and differences between several prediction algorithms and to upload their own data as additional tracks; thereby facilitating the rapid identification of potential regions of interest.

  6. Aladin Lite: Lightweight sky atlas for browsers

    Science.gov (United States)

    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.

  7. The p53-p21-DREAM-CDE/CHR pathway regulates G2/M cell cycle genes

    Science.gov (United States)

    Fischer, Martin; Quaas, Marianne; Steiner, Lydia; Engeland, Kurt

    2016-01-01

    The tumor suppressor p53 functions predominantly as a transcription factor by activating and downregulating gene expression, leading to cell cycle arrest or apoptosis. p53 was shown to indirectly repress transcription of the CCNB2, KIF23 and PLK4 cell cycle genes through the recently discovered p53-p21-DREAM-CDE/CHR pathway. However, it remained unclear whether this pathway is commonly used. Here, we identify genes regulated by p53 through this pathway in a genome-wide computational approach. The bioinformatic analysis is based on genome-wide DREAM complex binding data, p53-depedent mRNA expression data and a genome-wide definition of phylogenetically conserved CHR promoter elements. We find 210 target genes that are expected to be regulated by the p53-p21-DREAM-CDE/CHR pathway. The target gene list was verified by detailed analysis of p53-dependent repression of the cell cycle genes B-MYB (MYBL2), BUB1, CCNA2, CCNB1, CHEK2, MELK, POLD1, RAD18 and RAD54L. Most of the 210 target genes are essential regulators of G2 phase and mitosis. Thus, downregulation of these genes through the p53-p21-DREAM-CDE/CHR pathway appears to be a principal mechanism for G2/M cell cycle arrest by p53. PMID:26384566

  8. The UCSC Cancer Genomics Browser: update 2013.

    Science.gov (United States)

    Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Zhu, Jingchun

    2013-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. The ability to view multiple datasets together allows users to make comparisons across different data and cancer types. Biological pathways, collections of genes, genomic or clinical information can be used to sort, aggregate and zoom into a group of samples. We currently display an expanding set of data from various sources, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and Stand Up To Cancer. New features include a completely redesigned user interface with an interactive tutorial and updated documentation. We have also added data downloads, additional clinical heatmap features, and an updated Tumor Image Browser based on Google Maps. New security features allow authenticated users access to private datasets hosted by several different consortia through the public website.

  9. QMachine: commodity supercomputing in web browsers

    Science.gov (United States)

    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

  10. QMachine: commodity supercomputing in web browsers.

    Science.gov (United States)

    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.

  11. An application of TOPSIS for ranking internet web browsers

    Directory of Open Access Journals (Sweden)

    Shahram Rostampour

    2012-07-01

    Full Text Available Web browser is one of the most important internet facilities for surfing the internet. A good web browser must incorporate literally tens of features such as integrated search engine, automatic updates, etc. Each year, ten web browsers are formally introduced as top best reviewers by some organizations. In this paper, we propose the implementation of TOPSIS technique to rank ten web browsers. The proposed model of this paper uses five criteria including speed, features, security, technical support and supported configurations. In terms of speed, Safari is the best web reviewer followed by Google Chrome and Internet Explorer while Opera is the best web reviewer when we look into 20 different features. We have also ranked these web browsers using all five categories together and the results indicate that Opera, Internet explorer, Firefox and Google Chrome are the best web browsers to be chosen.

  12. The UCSC Genome Browser database: update 2011

    Science.gov (United States)

    Fujita, Pauline A.; Rhead, Brooke; Zweig, Ann S.; Hinrichs, Angie S.; Karolchik, Donna; Cline, Melissa S.; Goldman, Mary; Barber, Galt P.; Clawson, Hiram; Coelho, Antonio; Diekhans, Mark; Dreszer, Timothy R.; Giardine, Belinda M.; Harte, Rachel A.; Hillman-Jackson, Jennifer; Hsu, Fan; Kirkup, Vanessa; Kuhn, Robert M.; Learned, Katrina; Li, Chin H.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Rosenbloom, Kate R.; Smith, Kayla E.; Haussler, David; Kent, W. James

    2011-01-01

    The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks. PMID:20959295

  13. The UCSC Genome Browser database: 2014 update

    Science.gov (United States)

    Karolchik, Donna; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S.; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hinrichs, Angie S.; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Raney, Brian J.; Rhead, Brooke; Rosenbloom, Kate R.; Sloan, Cricket A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

    2014-01-01

    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 large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation ‘tracks’ for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany. PMID:24270787

  14. The UCSC Genome Browser database: update 2010

    Science.gov (United States)

    Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M.; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Diekhans, Mark; Smith, Kayla E.; Rosenbloom, Kate R.; Raney, Brian J.; Pohl, Andy; Pheasant, Michael; Meyer, Laurence R.; Learned, Katrina; Hsu, Fan; Hillman-Jackson, Jennifer; Harte, Rachel A.; Giardine, Belinda; Dreszer, Timothy R.; Clawson, Hiram; Barber, Galt P.; Haussler, David; Kent, W. James

    2010-01-01

    The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data. As of September 2009, genomic sequence and a basic set of annotation ‘tracks’ are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools. PMID:19906737

  15. Analisis Perbandingan Performansi dan Pemilihan Web Browser (Studi Kasus: Universitas Siliwangi)

    OpenAIRE

    Rachman, Andi Nur; Gufroni, Acep Irham; Hiron, Nurul; Rahmayati, Gina

    2013-01-01

    Semakin berkembangnya browser baik dari segi performansi maupun jumlah yang kerap membuat pengguna bingung untuk memilih dan tidak memanfaatkan fitur yang ditawarkan browser secara penuh. Dengan melakukan analisis perbandingan dan pembuatan panduan pemilihan browser, pengguna browser diharapkan dapat memilih browser secara lebih objektif dan sesuai dengan kebutuhan. Metodologi yang digunakan dalam penelitian ini adalah survey analitik dengan pendekatan cross sectional. Analisis performansi di...

  16. Analisis Perbandingan Performansi Dan Pemilihan Web Browser (Studi Kasus: Universitas Siliwangi)

    OpenAIRE

    Rachman, Andi Nur; Gufroni, Acep Irham; Hiron, Nurul; Rahmayati, Gina

    2013-01-01

    Semakin berkembangnya browser baik dari segi performansi maupun jumlah yang kerap membuat pengguna bingung untuk memilih dan tidak memanfaatkan fitur yang ditawarkan browser secara penuh. Dengan melakukan analisis perbandingan dan pembuatan panduan pemilihan browser, pengguna browser diharapkan dapat memilih browser secara lebih objektif dan sesuai dengan kebutuhan. Metodologi yang digunakan dalam penelitian ini adalah survey analitik dengan pendekatan cross sectional. Analisis performansi di...

  17. The UCSC Genome Browser database: 2018 update.

    Science.gov (United States)

    Casper, Jonathan; Zweig, Ann S; Villarreal, Chris; Tyner, Cath; Speir, Matthew L; Rosenbloom, Kate R; Raney, Brian J; Lee, Christopher M; Lee, Brian T; Karolchik, Donna; Hinrichs, Angie S; Haeussler, Maximilian; Guruvadoo, Luvina; Navarro Gonzalez, Jairo; Gibson, David; Fiddes, Ian T; Eisenhart, Christopher; Diekhans, Mark; Clawson, Hiram; Barber, Galt P; Armstrong, Joel; Haussler, David; Kuhn, Robert M; Kent, W James

    2018-01-04

    The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Xenopus genomic data and browser resources.

    Science.gov (United States)

    Vize, Peter D; Zorn, Aaron M

    2017-06-15

    The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Jet browser model accelerated by GPUs

    Directory of Open Access Journals (Sweden)

    Forster Richárd

    2016-12-01

    Full Text Available In the last centuries the experimental particle physics began to develop thank to growing capacity of computers among others. It is allowed to know the structure of the matter to level of quark gluon. Plasma in the strong interaction. Experimental evidences supported the theory to measure the predicted results. Since its inception the researchers are interested in the track reconstruction. We studied the jet browser model, which was developed for 4π calorimeter. This method works on the measurement data set, which contain the components of interaction points in the detector space and it allows to examine the trajectory reconstruction of the final state particles. We keep the total energy in constant values and it satisfies the Gauss law. Using GPUs the evaluation of the model can be drastically accelerated, as we were able to achieve up to 223 fold speedup compared to a CPU based parallel implementation.

  20. The UCSC Genome Browser Database: 2008 update

    DEFF Research Database (Denmark)

    Karolchik, D; Kuhn, R M; Baertsch, R

    2007-01-01

    and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human......The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate...... variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving...

  1. [The design and realization of Web-view PACS browser].

    Science.gov (United States)

    Yu, Pei-liang; Ye, Zhi-qian

    2006-05-01

    This article analyses the system structure and realization model of Web-view PACS browser in combination with the characteristic of PACS, and presents the realizing process of the web-view PACS browser using JSP mode and B/S model.

  2. Ajax and Firefox: New Web Applications and Browsers

    Science.gov (United States)

    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."…

  3. YADBrowser: A Browser for Web-Based Educational Applications

    Science.gov (United States)

    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.…

  4. MLitB: Machine Learning in the Browser

    NARCIS (Netherlands)

    Meeds, E.; Hendriks, R.; Al Faraby, S.; Bruntink, M.; Welling, M.

    2015-01-01

    With few exceptions, the field of Machine Learning (ML) research has largely ignored the browser as a computational engine. Beyond an educational resource for ML, the browser has vast potential to not only improve the state-of-the-art in ML research, but also, inexpensively and on a massive scale,

  5. Dietary overlap between Boer goats and indigenous browsers in a ...

    African Journals Online (AJOL)

    The winter diet of free ranging Boer goats in Valley Bushveld, KwaZulu-Natal, was determined by direct observations and compared with the diet of indigenous browsers (kudu, eland, giraffe, black rhinoceros) in order to determine which browsers are most compatible with goats for ensuring more efficient use of savanna ...

  6. Interactive metagenomic visualization in a Web browser.

    Science.gov (United States)

    Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

    2011-09-30

    A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  7. Interactive metagenomic visualization in a Web browser

    Directory of Open Access Journals (Sweden)

    Phillippy Adam M

    2011-09-01

    Full Text Available Abstract Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  8. BrainBrowser: distributed, web-based neurological data visualization

    Directory of Open Access Journals (Sweden)

    Tarek eSherif

    2015-01-01

    Full Text Available Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used 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.

  9. BrainBrowser: distributed, web-based neurological data visualization.

    Science.gov (United States)

    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.

  10. Geant4 application in a Web browser

    Science.gov (United States)

    Garnier, Laurent; Geant4 Collaboration

    2014-06-01

    Geant4 is a toolkit for the simulation of the passage of particles through matter. The Geant4 visualization system supports many drivers including OpenGL[1], OpenInventor, HepRep[2], DAWN[3], VRML, RayTracer, gMocren[4] and ASCIITree, with diverse and complementary functionalities. Web applications have an increasing role in our work, and thanks to emerging frameworks such as Wt [5], building a web application on top of a C++ application without rewriting all the code can be done. Because the Geant4 toolkit's visualization and user interface modules are well decoupled from the rest of Geant4, it is straightforward to adapt these modules to render in a web application instead of a computer's native window manager. The API of the Wt framework closely matches that of Qt [6], our experience in building Qt driver will benefit for Wt driver. Porting a Geant4 application to a web application is easy, and with minimal effort, Geant4 users can replicate this process to share their own Geant4 applications in a web browser.

  11. Geant4 application in a Web browser

    International Nuclear Information System (INIS)

    Garnier, Laurent

    2014-01-01

    Geant4 is a toolkit for the simulation of the passage of particles through matter. The Geant4 visualization system supports many drivers including OpenGL[1], OpenInventor, HepRep[2], DAWN[3], VRML, RayTracer, gMocren[4] and ASCIITree, with diverse and complementary functionalities. Web applications have an increasing role in our work, and thanks to emerging frameworks such as Wt [5], building a web application on top of a C++ application without rewriting all the code can be done. Because the Geant4 toolkit's visualization and user interface modules are well decoupled from the rest of Geant4, it is straightforward to adapt these modules to render in a web application instead of a computer's native window manager. The API of the Wt framework closely matches that of Qt [6], our experience in building Qt driver will benefit for Wt driver. Porting a Geant4 application to a web application is easy, and with minimal effort, Geant4 users can replicate this process to share their own Geant4 applications in a web browser.

  12. Results from the CDE phase activity on neutron dosimetry for the international fusion materials irradiation facility test cell

    CERN Document Server

    Esposito, B; Maruccia, G; Petrizzi, L; Bignon, G; Blandin, C; Chauffriat, S; Lebrun, A; Recroix, H; Trapp, J P; Kaschuck, Y

    2000-01-01

    The international fusion materials irradiation facility (IFMIF) project deals with the study of an accelerator-based, deuterium-lithium source, producing high energy neutrons at sufficient intensity and irradiation volume to test samples of candidate materials for fusion energy reactors. IFMIF would also provide calibration and validation of data from fission reactor and other accelerator based irradiation tests. This paper describes the activity on neutron/gamma dosimetry (necessary for the characterization of the specimens' irradiation) performed in the frame of the IFMIF conceptual design evaluation (CDE) neutronics tasks. During the previous phase (conceptual design activity (CDA)) the multifoil activation method was proposed for the measurement of the neutron fluence and spectrum and a set of suitable foils was defined. The cross section variances and covariances of this set of foils have now been used for tests on the sensitivity of the IFMIF neutron spectrum determination to cross section uncertainties...

  13. Chromium based Framework to include Gaze Interaction in Web Browser

    OpenAIRE

    Kumar, Chandan; Menges, Raphael; Müller, Daniel; Staab, Steffen

    2017-01-01

    EnablingWeb interaction by non-conventional input sources like eyes has great potential to enhance Web accessibility. In this paper, we present a Chromium based inclusive framework to adapt eye gaze events in Web interfaces. The frameworkprovides more utility and control to develop a full featured interactive browser, compared to the related approaches of additional mouse and keyboard emulation orbrowser extensions. We demonstrate the framework through a sophisticated gaze driven Web browser,...

  14. CompaGB: An open framework for genome browsers comparison

    Directory of Open Access Journals (Sweden)

    Chiapello Hélène

    2011-05-01

    Full Text Available Abstract Background Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. Findings To assist in this task, we propose a community-based framework based on two cornerstones: (i the implementation of industry promoted software qualification method (QSOS adapted for genome browser evaluations, and (ii a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile with features of interest to a community-based framework: easy management of evolving data, user comments... Conclusions The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1 choose a genome browser that would better fit their particular project, (2 visualize features comparatively with easily accessible formats, such as tables or radar plots and (3 perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology

  15. Comparative assembly hubs: Web-accessible browsers for comparative genomics

    Science.gov (United States)

    Nguyen, Ngan; Hickey, Glenn; Raney, Brian J.; Armstrong, Joel; Clawson, Hiram; Zweig, Ann; Karolchik, Donna; Kent, William James; Haussler, David; Paten, Benedict

    2014-01-01

    Motivation: Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers. Results: We introduce a pipeline to easily generate collections of Web-accessible UCSC Genome Browsers interrelated by an alignment. It is intended to democratize our comparative genomic browser resources, serving the broad and growing community of evolutionary genomicists and facilitating easy public sharing via the Internet. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications. To demonstrate this work, we create a comparative assembly hub containing 57 Escherichia coli and 9 Shigella genomes and show examples that highlight their unique biology. Availability and implementation: The source code is available as open source at: https://github.com/glennhickey/progressiveCactus The E.coli and Shigella genome hub is now a public hub listed on the UCSC browser public hubs Web page. Contact: benedict@soe.ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25138168

  16. Teleradiology system accessible through a common web browser.

    Science.gov (United States)

    Luccichenti, Giacomo; Ngo Dinh, Nhan; Cademartiri, Filippo; Evangelisti, Giulio; Paolillo, Andrea; Bastianello, Stefano

    2004-01-01

    To describe a teleradiology system accessible via a PC and a common web browser. A dedicated system is connected to several radiological imagers (DR, US, CT, MR) with DICOM standard and TCP/IP protocol. The images are visualised in a common web browser on a remote PC by connecting to the dedicated web-site. Compressed images are visualised on a web page. Special toolbars allow specific operations to be performed on the images (brightness-contrast, zoom, distance measurement and ROI defining) and the communication with the radiological centre. The graphic interface is user-friendly and does not require any special knowledge, except for basic PC and internet surfing. Image compression can be set to preserve image quality, and image transfer is fast. The system presented overcomes the limitations of conventional teleradiology systems since it requires no special network or dedicated software, allowing for visualisation of a radiological examination on a PC and a common web browser.

  17. An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division

    Science.gov (United States)

    Xiong, Liping; Lan, Ganhui

    2015-01-01

    Sustained molecular oscillations are ubiquitous in biology. The obtained oscillatory patterns provide vital functions as timekeepers, pacemakers and spacemarkers. Models based on control theory have been introduced to explain how specific oscillatory behaviors stem from protein interaction feedbacks, whereas the energy dissipation through the oscillating processes and its role in the regulatory function remain unexplored. Here we developed a general framework to assess an oscillator’s regulation performance at different dissipation levels. Using the Escherichia coli MinCDE oscillator as a model system, we showed that a sufficient amount of energy dissipation is needed to switch on the oscillation, which is tightly coupled to the system’s regulatory performance. Once the dissipation level is beyond this threshold, unlike stationary regulators’ monotonic performance-to-cost relation, excess dissipation at certain steps in the oscillating process damages the oscillator’s regulatory performance. We further discovered that the chemical free energy from ATP hydrolysis has to be strategically assigned to the MinE-aided MinD release and the MinD immobilization steps for optimal performance, and a higher energy budget improves the robustness of the oscillator. These results unfold a novel mode by which living systems trade energy for regulatory function. PMID:26317492

  18. Molecular Events Involved in a Single Cycle of Ligand Transfer from an ATP Binding Cassette Transporter, LolCDE, to a Molecular Chaperone, LolA*

    OpenAIRE

    Taniguchi, Naohiro; Tokuda, Hajime

    2008-01-01

    An ATP binding cassette transporter LolCDE complex releases lipoproteins from the inner membrane of Escherichia coli in an ATP-dependent manner, leading to the formation of a complex between a lipoprotein and a periplasmic chaperone, LolA. LolA is proposed to undergo a conformational change upon the lipoprotein binding. The lipoprotein is then transferred from the LolA-lipoprotein complex to the outer membrane via LolB. Unlike most ATP binding cassette transporters med...

  19. Disruption of lolCDE, Encoding an ATP-Binding Cassette Transporter, Is Lethal for Escherichia coli and Prevents Release of Lipoproteins from the Inner Membrane

    OpenAIRE

    Narita, Shin-ichiro; Tanaka, Kimie; Matsuyama, Shin-ichi; Tokuda, Hajime

    2002-01-01

    ATP-binding cassette transporter LolCDE was previously identified, by using reconstituted proteoliposomes, as an apparatus catalyzing the release of outer membrane-specific lipoproteins from the inner membrane of Escherichia coli. Mutations resulting in defective LolD were previously shown to be lethal for E. coli. The amino acid sequences of LolC and LolE are similar to each other, but the necessity of both proteins for lipoprotein release has not been proved. Moreover, previous reconstituti...

  20. The UCSC Genome Browser database: extensions and updates 2011

    Science.gov (United States)

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

    2012-01-01

    The University of California Santa Cruz 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, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. 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 new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced ‘track data hubs’, which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image. PMID:22086951

  1. The Project Browser : Supporting information access for a project team

    NARCIS (Netherlands)

    Cremers, A.H.M.; Kuijper, I.; Groenewegen, P.L.M.; Post, W.M.

    2007-01-01

    The objective of our study was to design and evaluate a user interface concept for a so-called Project Browser, following a user-centered design method. Previous work has suggested that users prefer to access project-related information instrumental to the task they have to carry out. First, a

  2. Vulnerability Assessment of Open Source Wireshark and Chrome Browser

    Science.gov (United States)

    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

  3. A genome browser database for rice (Oryza sativa) and Chinese ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... Key words: genome browser, Ensembl project, rice database, Chinese cabbage. INTRODUCTION. As a cereal grain, rice ... The B. rapa Genome Project (BrGP, http://www.brassica- rapa.org/) provides the genome .... informatics approach to agricultural biotechnology to extend the usefulness of breeding for ...

  4. A Comparative Performance Analysis of Popular Internet Browsers ...

    African Journals Online (AJOL)

    different types of content. The lack of awareness of available web browser and their characteristics .... pictures, video clips and sound to be included in text pages. The pages also have links to other pages that ... game consoles and interactive televisions. Technology from Opera is also licensed by other companies for use in ...

  5. The project browser: Supporting information access for a project team

    NARCIS (Netherlands)

    Cremers, A.H.M.; Kuiper, I.; Groenewegen, P.; Post, W.M.

    2007-01-01

    Abstract. The objective of our study was to design and evaluate a user interface concept for a so-called Project Browser, following a user-centered design method. Previous work has suggested that users prefer to access project-related information instrumental to the task they have to carry out.

  6. Faecal nitrogen of browser and mixed feeder game species during ...

    African Journals Online (AJOL)

    A practical measure of assessing periods of potential nutritional stress of game species is needed in the management of these species in the Acacia karroo Riparian Thicket of the central Free State. The objectives of the study were to determine Nf concentration of four game species (browsers and mixed feeders) during ...

  7. Quality Search Content: A Reality With Next Generation Browsers

    Digital Repository Service at National Institute of Oceanography (India)

    Lakshminarayana, S.

    moderate user is browsing through at the most 30 to 40 links out of the total delivery set from a search engine. Next Generation browsers are to reach the user with intelligence to address issues related the content filtering, address blocking, user...

  8. STANDARDIZING THE STRUCTURE OF STROKE CLINICAL AND EPIDEMIOLOGIC RESEARCH DATA: THE NINDS STROKE COMMON DATA ELEMENT (CDE) PROJECT

    Science.gov (United States)

    Saver, Jeffrey L.; Warach, Steven; Janis, Scott; Odenkirchen, Joanne; Becker, Kyra; Benavente, Oscar; Broderick, Joseph; Dromerick, Alexander W.; Duncan, Pamela; Elkind, Mitchell S. V.; Johnston, Karen; Kidwell, Chelsea S.; Meschia, James F.; Schwamm, Lee

    2012-01-01

    Background and Purpose The National Institute of Neurological Disorders and Stroke initiated development of stroke-specific Common Data Elements (CDEs) as part of a project to develop data standards for funded clinical research in all fields of neuroscience. Standardizing data elements in translational, clinical and population research in cerebrovascular disease could decrease study start-up time, facilitate data sharing, and promote well-informed clinical practice guidelines. Methods A Working Group of diverse experts in cerebrovascular clinical trials, epidemiology, and biostatistics met regularly to develop a set of Stroke CDEs, selecting among, refining, and adding to existing, field-tested data elements from national registries and funded trials and studies. Candidate elements were revised based on comments from leading national and international neurovascular research organizations and the public. Results The first iteration of the NINDS stroke-specific CDEs comprises 980 data elements spanning nine content areas: 1) Biospecimens and Biomarkers; 2) Hospital Course and Acute Therapies; 3) Imaging; 4) Laboratory Tests and Vital Signs; 5) Long Term Therapies; 6) Medical History and Prior Health Status; 7) Outcomes and Endpoints; 8) Stroke Presentation; 9) Stroke Types and Subtypes. A CDE website provides uniform names and structures for each element, a data dictionary, and template case report forms (CRFs) using the CDEs. Conclusion Stroke-specific CDEs are now available as standardized, scientifically-vetted variable structures to facilitate data collection and data sharing in cerebrovascular patient-oriented research. The CDEs are an evolving resource that will be iteratively improved based on investigator use, new technologies, and emerging concepts and research findings. PMID:22308239

  9. ENCODE whole-genome data in the UCSC Genome Browser

    Science.gov (United States)

    Rosenbloom, Kate R.; Dreszer, Timothy R.; Pheasant, Michael; Barber, Galt P.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Wang, Ting; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Learned, Katrina; Rhead, Brooke; Smith, Kayla E.; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

    2010-01-01

    The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. PMID:19920125

  10. Context Aware Concurrent Execution Framework for Web Browser

    DEFF Research Database (Denmark)

    Saeed, Aamir; Erbad, Aiman Mahmood; Olsen, Rasmus Løvenstein

    Computing hungry multimedia web applications need to efficiently utilize the device resources. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multi-core hardware. HTML5 web workers are implemented by major browser vendors t...... end users better perceived quality of experience for demanding multimedia web based applications....... between web workers via serialized objects. The application performance is measured by measuring the jitter and the number of frames per second. The results showed improvement in performance with lower jitter and high FPS. These techniques can be used by developers to improve the application design giving......Computing hungry multimedia web applications need to efficiently utilize the device resources. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multi-core hardware. HTML5 web workers are implemented by major browser vendors...

  11. Context Aware Concurrent Execution Framework for Web Browsers

    DEFF Research Database (Denmark)

    Saeed, Aamir; Erbad, Aiman; Olsen, Rasmus Løvenstein

    2016-01-01

    Computing hungry multimedia web applications need to efficiently utilize all the resources of a device. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multicore hardware. HTML5 web workers are implemented by major browser v...... the application design, and giving end users better perceived quality of experience for demanding multimedia web based applications.......Computing hungry multimedia web applications need to efficiently utilize all the resources of a device. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multicore hardware. HTML5 web workers are implemented by major browser...... vendors to facilitate concurrent execution in web clients and enhance the quality of ambitious web applications. The concurrent execution in web workers allows parallel processing using available cores at the expense of communication overhead and extra computation. The benefits of concurrent execution can...

  12. Transcriptional Responses of Escherichia coli to a Small-Molecule Inhibitor of LolCDE, an Essential Component of the Lipoprotein Transport Pathway

    Science.gov (United States)

    Lorenz, Christian; Dougherty, Thomas J.

    2016-01-01

    ABSTRACT In Gram-negative bacteria, a dedicated machinery consisting of LolABCDE components targets lipoproteins to the outer membrane. We used a previously identified small-molecule inhibitor of the LolCDE complex of Escherichia coli to assess the global transcriptional consequences of interference with lipoprotein transport. Exposure of E. coli to the LolCDE inhibitor at concentrations leading to minimal and significant growth inhibition, followed by transcriptome sequencing, identified a small group of genes whose transcript levels were decreased and a larger group whose mRNA levels increased 10- to 100-fold compared to those of untreated cells. The majority of the genes whose mRNA concentrations were reduced were part of the flagellar assembly pathway, which contains an essential lipoprotein component. Most of the genes whose transcript levels were elevated encode proteins involved in selected cell stress pathways. Many of these genes are involved with envelope stress responses induced by the mislocalization of outer membrane lipoproteins. Although several of the genes whose RNAs were induced have previously been shown to be associated with the general perturbation of the cell envelope by antibiotics, a small subset was affected only by LolCDE inhibition. Findings from this work suggest that the efficiency of the Lol system function may be coupled to a specific monitoring system, which could be exploited in the development of reporter constructs suitable for use for screening for additional inhibitors of lipoprotein trafficking. IMPORTANCE Inhibition of the lipoprotein transport pathway leads to E. coli death and subsequent lysis. Early significant changes in the levels of RNA for a subset of genes identified to be associated with some periplasmic and envelope stress responses were observed. Together these findings suggest that disruption of this key pathway can have a severe impact on balanced outer membrane synthesis sufficient to affect viability. PMID

  13. Transcriptional Responses of Escherichia coli to a Small-Molecule Inhibitor of LolCDE, an Essential Component of the Lipoprotein Transport Pathway.

    Science.gov (United States)

    Lorenz, Christian; Dougherty, Thomas J; Lory, Stephen

    2016-12-01

    In Gram-negative bacteria, a dedicated machinery consisting of LolABCDE components targets lipoproteins to the outer membrane. We used a previously identified small-molecule inhibitor of the LolCDE complex of Escherichia coli to assess the global transcriptional consequences of interference with lipoprotein transport. Exposure of E. coli to the LolCDE inhibitor at concentrations leading to minimal and significant growth inhibition, followed by transcriptome sequencing, identified a small group of genes whose transcript levels were decreased and a larger group whose mRNA levels increased 10- to 100-fold compared to those of untreated cells. The majority of the genes whose mRNA concentrations were reduced were part of the flagellar assembly pathway, which contains an essential lipoprotein component. Most of the genes whose transcript levels were elevated encode proteins involved in selected cell stress pathways. Many of these genes are involved with envelope stress responses induced by the mislocalization of outer membrane lipoproteins. Although several of the genes whose RNAs were induced have previously been shown to be associated with the general perturbation of the cell envelope by antibiotics, a small subset was affected only by LolCDE inhibition. Findings from this work suggest that the efficiency of the Lol system function may be coupled to a specific monitoring system, which could be exploited in the development of reporter constructs suitable for use for screening for additional inhibitors of lipoprotein trafficking. Inhibition of the lipoprotein transport pathway leads to E. coli death and subsequent lysis. Early significant changes in the levels of RNA for a subset of genes identified to be associated with some periplasmic and envelope stress responses were observed. Together these findings suggest that disruption of this key pathway can have a severe impact on balanced outer membrane synthesis sufficient to affect viability. Copyright © 2016 Lorenz et al.

  14. The UCSC Genome Browser database: extensions and updates 2013

    Science.gov (United States)

    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. PMID:23155063

  15. Using a Web Browser for Environmental and Climate Change Studies

    Science.gov (United States)

    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.

  16. Fiberweb: Diffusion Visualization and Processing in the Browser

    Directory of Open Access Journals (Sweden)

    Louis-Philippe Ledoux

    2017-08-01

    Full Text Available Data visualization is one of the most important tool to explore the brain as we know it. In this work, we introduce a novel browser-based solution for medical imaging data visualization and interaction with diffusion-weighted magnetic resonance imaging (dMRI and tractography data: Fiberweb. It uses a recent technology, WebGL, that has yet to be fully explored for medical imaging purposes. There are currently very few software tools that allow medical imaging data visualization in the browser, and none of these tools support efficient data interaction and processing, such as streamlines selection and real-time deterministic and probabilistic tractography (RTT. With Fiberweb allowing these types of interaction, it is no longer the case. We show results of the visualization of medical imaging data, and demonstrate that our new RTT probabilistic algorithm can compare to a state of the art offline algorithm. Overall, Fiberweb pushes the boundary of interaction combined with scientific visualization, which opens great perspectives for quality control and neurosurgical navigation on browser-based mobile and static devices.

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

    Science.gov (United States)

    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

  18. ABrowse - a customizable next-generation genome browser framework

    Directory of Open Access Journals (Sweden)

    Kong Lei

    2012-01-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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

  19. Open source MySQL Browser for Open Innovation

    Directory of Open Access Journals (Sweden)

    Radu Bucea-Manea-Tonis

    2014-07-01

    Full Text Available Abstract. Our purpose is to cross-compile MySQL driver source code for Linux on Windows architecture using a tool chain in order to build a neutral valid graphic interface on 32 bits. Once achieving this goal we could say that every possible Open source application can be built and run on Windows with maximum efficiency concerning costs and resource. This browser is an example of open innovation because its source code is free for anybody willing to develop new software apps for business and uses only Open source tools.

  20. MLitB: machine learning in the browser

    Directory of Open Access Journals (Sweden)

    Edward Meeds

    2015-07-01

    Full Text Available With few exceptions, the field of Machine Learning (ML research has largely ignored the browser as a computational engine. Beyond an educational resource for ML, the browser has vast potential to not only improve the state-of-the-art in ML research, but also, inexpensively and on a massive scale, to bring sophisticated ML learning and prediction to the public at large. This paper introduces MLitB, a prototype ML framework written entirely in Javascript, capable of performing large-scale distributed computing with heterogeneous classes of devices. The development of MLitB has been driven by several underlying objectives whose aim is to make ML learning and usage ubiquitous (by using ubiquitous compute devices, cheap and effortlessly distributed, and collaborative. This is achieved by allowing every internet capable device to run training algorithms and predictive models with no software installation and by saving models in universally readable formats. Our prototype library is capable of training deep neural networks with synchronized, distributed stochastic gradient descent. MLitB offers several important opportunities for novel ML research, including: development of distributed learning algorithms, advancement of web GPU algorithms, novel field and mobile applications, privacy preserving computing, and green grid-computing. MLitB is available as open source software.

  1. Aladin Lite: Embed your Sky in the Browser

    Science.gov (United States)

    Boch, T.; Fernique, P.

    2014-05-01

    I will introduce and describe Aladin Lite1, a lightweight interactive sky viewer running natively in the browser. The past five years have seen the emergence of powerful and complex web applications, thanks to major improvements in JavaScript engines and the advent of HTML5. At the same time, browser plugins Java applets, Flash, Silverlight) that were commonly used to run rich Internet applications are declining and are not well suited for mobile devices. The Aladin team took this opportunity to develop Aladin Lite, a lightweight version of Aladin geared towards simple visualization of a sky region. Relying on the widely supported HTML5 canvas element, it provides an intuitive user interface running on desktops and tablets. This first version allows one to interactively visualize multi-resolution HEALPix image and superimpose tabular data and footprints. Aladin Lite is easily embeddable on any web page and may be of interest for data providers which will be able to use it as an interactive previewer for their own image surveys, previously pre-processed as explained in details in the poster "Create & publish your Hierarchical Progressive Survey". I will present the main features of Aladin Lite as well as the JavaScript API which gives the building blocks to create rich interactions between a web page and Aladin Lite.

  2. Timing of transcription during the cell cycle: Protein complexes binding to E2F, E2F/CLE, CDE/CHR, or CHR promoter elements define early and late cell cycle gene expression

    Science.gov (United States)

    Müller, Gerd A.; Stangner, Konstanze; Schmitt, Thomas; Wintsche, Axel; Engeland, Kurt

    2017-01-01

    A central question in cell cycle control is how differential gene expression is regulated. Timing of expression is important for correct progression through the cell cycle. E2F, CDE, and CHR promoter sites have been linked to transcriptional repression in resting cells and activation during the cell cycle. Further, the DREAM complex binds CHR or CDE/CHR elements of G2/M genes resulting in repression during G0/G1. Here, we show that DREAM also binds to E2F sites of S phase genes in quiescence and upon p53 activation. Furthermore, we describe a novel class of promoter sites, the CHR-like elements (CLE), which can support binding of DREAM to E2F elements. Activation of such S phase genes is achieved through binding of E2F1-3/DP complexes to E2F sites. In contrast, the activating MuvB complexes MMB and FOXM1-MuvB bind to CHR elements and mediate peak expression in G2/M. In conclusion, data presented here in combination with earlier results leads us to propose a model that explains how DREAM can repress early cell cycle genes through E2F or E2F/CLE sites and late genes through CHR or CDE/CHR elements. Also p53-dependent indirect transcriptional repression through the p53-p21-Cyclin/CDK-DREAM-E2F/CLE/CDE/CHR pathway requires DREAM binding to E2F or E2F/CLE sites in early cell cycle genes and binding of DREAM to CHR or CDE/CHR elements of late cell cycle genes. Specific timing of activation is achieved through binding of E2F1-3/DP to E2F sites and MMB or FOXM1-MuvB complexes to CHR elements. PMID:29228647

  3. A Hybrid Web Browser Architecture for Mobile Devices

    Directory of Open Access Journals (Sweden)

    CHO, J.

    2014-08-01

    Full Text Available Web browsing on mobile networks is slow in comparison to wired or Wi-Fi networks. Particularly, the connection establishment phase including DNS lookups and TCP handshakes takes a long time on mobile networks due to its long round-trip latency. In this paper, we propose a novel web browser architecture that aims to improve mobile web browsing performance. Our approach delegates the connection establishment and HTTP header field delivery tasks to a dedicated proxy server located at the joint point between the WAN and mobile network. Since the traffic for the connection establishment and HTTP header fields delivery passes only through the WAN between the proxy and web servers, our approach significantly reduces both the number and size of packets on the mobile network. Our evaluation showed that the proposed scheme reduces the number of mobile network packets by up to 42% and, consequently, the average page loading time is shortened by up to 52%.

  4. EMBEDDED LINUX BASED ALBUM BROWSER SYSTEM AT MUSIC STORES

    Directory of Open Access Journals (Sweden)

    Suryadiputra Liawatimena

    2009-01-01

    Full Text Available The goal of this research is the creation of an album browser system at a music store based on embedded Linux. It is expected with this system; it will help the promotion of said music store and make the customers activity at the store simpler and easier. This system uses NFS for networking, database system, ripping software, and GUI development. The research method used are and laboratory experiments to test the system’s hardware using TPC-57 (Touch Panel Computer 5.7" SA2410 ARM-9 Medallion CPU Module and software using QtopiaCore. The result of the research are; 1. The database query process is working properly; 2. The audio data buffering process is working properly. With those experiment results, it can be concluded that the summary of this research is that the system is ready to be implemented and used in the music stores.

  5. Web Pages Content Analysis Using Browser-Based Volunteer Computing

    Directory of Open Access Journals (Sweden)

    Wojciech Turek

    2013-01-01

    Full Text Available Existing solutions to the problem of finding valuable information on the Websuffers from several limitations like simplified query languages, out-of-date in-formation or arbitrary results sorting. In this paper a different approach to thisproblem is described. It is based on the idea of distributed processing of Webpages content. To provide sufficient performance, the idea of browser-basedvolunteer computing is utilized, which requires the implementation of text pro-cessing algorithms in JavaScript. In this paper the architecture of Web pagescontent analysis system is presented, details concerning the implementation ofthe system and the text processing algorithms are described and test resultsare provided.

  6. Integrating heterogeneous open-source software into web browsers using AMICO:WEB

    NARCIS (Netherlands)

    Z. Obrenovic; J.R. van Ossenbruggen (Jacco)

    2007-01-01

    textabstractA web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional

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

    Science.gov (United States)

    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…

  8. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Stærfeldt, Hans Henrik; Rotenberg, Eva

    2009-01-01

    , 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/]....

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

    Science.gov (United States)

    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.…

  10. Rice-Map: a new-generation rice genome browser

    Directory of Open Access Journals (Sweden)

    Luo Jingchu

    2011-03-01

    Full Text Available Abstract Background The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. Description More than one hundred annotation tracks (81 for japonica and 82 for indica have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Conclusions Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

  11. Ungulate browsers promote herbaceous layer diversity in logged temperate forests

    Science.gov (United States)

    Faison, Edward K.; DeStefano, Stephen; Foster, David R.; Motzkin, Glenn; Rapp, Josh

    2016-01-01

    Ungulates are leading drivers of plant communities worldwide, with impacts linked to animal density, disturbance and vegetation structure, and site productivity. Many ecosystems have more than one ungulate species; however, few studies have specifically examined the combined effects of two or more species on plant communities. We examined the extent to which two ungulate browsers (moose [Alces americanus]) and white-tailed deer [Odocoileus virginianus]) have additive (compounding) or compensatory (opposing) effects on herbaceous layer composition and diversity, 5–6 years after timber harvest in Massachusetts, USA. We established three combinations of ungulates using two types of fenced exclosures – none (full exclosure), deer (partial exclosure), and deer + moose (control) in six replicated blocks. Species composition diverged among browser treatments, and changes were generally additive. Plant assemblages characteristic of closed canopy forests were less abundant and assemblages characteristic of open/disturbed habitats were more abundant in deer + moose plots compared with ungulate excluded areas. Browsing by deer + moose resulted in greater herbaceous species richness at the plot scale (169 m2) and greater woody species richness at the subplot scale (1 m2) than ungulate exclusion and deer alone. Browsing by deer + moose resulted in strong changes to the composition, structure, and diversity of forest herbaceous layers, relative to areas free of ungulates and areas browed by white-tailed deer alone. Our results provide evidence that moderate browsing in forest openings can promote both herbaceous and woody plant diversity. These results are consistent with the classic grazing-species richness curve, but have rarely been documented in forests.

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

    Science.gov (United States)

    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.

  13. [A Terahertz Spectral Database Based on Browser/Server Technique].

    Science.gov (United States)

    Zhang, Zhuo-yong; Song, Yue

    2015-09-01

    With the solution of key scientific and technical problems and development of instrumentation, the application of terahertz technology in various fields has been paid more and more attention. Owing to the unique characteristic advantages, terahertz technology has been showing a broad future in the fields of fast, non-damaging detections, as well as many other fields. Terahertz technology combined with other complementary methods can be used to cope with many difficult practical problems which could not be solved before. One of the critical points for further development of practical terahertz detection methods depends on a good and reliable terahertz spectral database. We developed a BS (browser/server) -based terahertz spectral database recently. We designed the main structure and main functions to fulfill practical requirements. The terahertz spectral database now includes more than 240 items, and the spectral information was collected based on three sources: (1) collection and citation from some other abroad terahertz spectral databases; (2) collected from published literatures; and (3) spectral data measured in our laboratory. The present paper introduced the basic structure and fundament functions of the terahertz spectral database developed in our laboratory. One of the key functions of this THz database is calculation of optical parameters. Some optical parameters including absorption coefficient, refractive index, etc. can be calculated based on the input THz time domain spectra. The other main functions and searching methods of the browser/server-based terahertz spectral database have been discussed. The database search system can provide users convenient functions including user registration, inquiry, displaying spectral figures and molecular structures, spectral matching, etc. The THz database system provides an on-line searching function for registered users. Registered users can compare the input THz spectrum with the spectra of database, according to

  14. Cracking ShadowCrypt: Exploring the Limitations of Secure I/O Systems in Internet Browsers

    OpenAIRE

    Freyberger Michael; He Warren; Akhawe Devdatta; Mazurek Michelle L.; Mittal Prateek

    2018-01-01

    An important line of privacy research is investigating the design of systems for secure input and output (I/O) within Internet browsers. These systems would allow for users’ information to be encrypted and decrypted by the browser, and the specific web applications will only have access to the users’ information in encrypted form. The state-of-the-art approach for a secure I/O system within Internet browsers is a system called ShadowCrypt created by UC Berkeley researchers [23]. This paper wi...

  15. Analysis of Using Browser-native Technology to Build Rich Internet Applications for Image Manipulation

    OpenAIRE

    Steenbergen, Thomas; Lew, Michael S.

    2010-01-01

    In this work we investigate whether browser-native technologies can be used to perform photo manipulation tasks e.g cropping, resizing or rotating an image within the current mainstream browser. By the use of a case study we will analyze problems that have occurred during the implementation of a prototype web application that utilizes browser-native web technology in order to create an online version of a real world photo scrapbook. Implementation of a prototype will allows us to analyze the ...

  16. Web-browser encryption of personal health information.

    Science.gov (United States)

    Morse, Richard E; Nadkarni, Prakash; Schoenfeld, David A; Finkelstein, Dianne M

    2011-11-10

    Electronic health records provide access to an unprecedented amount of clinical data for research that can accelerate the development of effective medical practices. However it is important to protect patient confidentiality, as many medical conditions are stigmatized and disclosure could result in personal and/or financial loss. We describe a system for remote data entry that allows the data that would identify the patient to be encrypted in the web browser of the person entering the data. These data cannot be decrypted on the server by the staff at the data center but can be decrypted by the person entering the data or their delegate. We developed this system to solve a problem that arose in the context of clinical research, but it is applicable in a range of situations where sensitive information is stored and updated in a database and it is necessary to ensure that it cannot be viewed by any except those intentionally given access. By developing this system, we are able to centralize the collection of some patient data while minimizing the risk that protected health information be made available to study personnel who are not authorized to use it.

  17. Web-browser encryption of personal health information

    Directory of Open Access Journals (Sweden)

    Morse Richard E

    2011-11-01

    Full Text Available Abstract Background Electronic health records provide access to an unprecedented amount of clinical data for research that can accelerate the development of effective medical practices. However it is important to protect patient confidentiality, as many medical conditions are stigmatized and disclosure could result in personal and/or financial loss. Results We describe a system for remote data entry that allows the data that would identify the patient to be encrypted in the web browser of the person entering the data. These data cannot be decrypted on the server by the staff at the data center but can be decrypted by the person entering the data or their delegate. We developed this system to solve a problem that arose in the context of clinical research, but it is applicable in a range of situations where sensitive information is stored and updated in a database and it is necessary to ensure that it cannot be viewed by any except those intentionally given access. Conclusion By developing this system, we are able to centralize the collection of some patient data while minimizing the risk that protected health information be made available to study personnel who are not authorized to use it.

  18. Mouse Resource Browser--a database of mouse databases.

    Science.gov (United States)

    Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M; Schofield, Paul N; Kollias, George; Aidinis, Vassilis

    2010-07-06

    The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the concomitant need for formalized experimental descriptions, data standardization, database interoperability and integration, a need that has yet to be met. We present here the Mouse Resource Browser (MRB), a database of mouse databases that indexes 217 publicly available mouse resources under 22 categories and uses a standardised database description framework (the CASIMIR DDF) to provide information on their controlled vocabularies (ontologies and minimum information standards), and technical information on programmatic access and data availability. Focusing on interoperability and integration, MRB offers automatic generation of downloadable and re-distributable SOAP application-programming interfaces for resources that provide direct database access. MRB aims to provide useful information to both bench scientists, who can easily navigate and find all mouse related resources in one place, and bioinformaticians, who will be provided with interoperable resources containing data which can be mined and integrated. Database URL: http://bioit.fleming.gr/mrb.

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

    Science.gov (United States)

    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.

  20. Nuun: A System for Developing Platform and Browser Independent Arabic Web Applications

    National Research Council Canada - National Science Library

    Habash, Nizar Y

    2001-01-01

    .... The Nuun toolkit addresses this challenge. Nuun uses an allographic encoding in which each letter form is encoded separately to provide an Arabic display capability in any web browser on any platform...

  1. Comcutejs: A Web Browser Based Platform For Large-Scale Computations

    Directory of Open Access Journals (Sweden)

    Roman Debski

    2013-01-01

    Full Text Available The paper presents a new, cost effective, volunteer computing based platform.It utilizes volunteers’ web browsers as computational nodes. The computationaltasks are delegated to the browsers and executed in the background (indepen-dently of any user interface scripts making use of the HTML5 web workerstechnology. The capabilities of the platform have been proved by experimentsperformed in a wide range of numbers of computational nodes (1–400.

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

    Science.gov (United States)

    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.

  3. Browser Fingerprinting : Exploring Device Diversity to Augment Authentification and Build Client-Side Countermeasures

    OpenAIRE

    Laperdrix , Pierre

    2017-01-01

    Users are presented with an ever-increasing number of choices to connect to the Internet. From desktops, laptops, tablets and smartphones, anyone can find the perfect device that suits his or her needs while factoring mobility, size or processing power. Browser fingerprinting became a reality thanks to the software and hardware diversity that compose every single one of our modem devices. By collecting device-specific information with a simple script running in the browser, a server can fully...

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

    Directory of Open Access Journals (Sweden)

    O. Naito

    2017-01-01

    Full Text Available 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.

  5. Multiple Browsers Structure Tree Recruitment in Logged Temperate Forests.

    Directory of Open Access Journals (Sweden)

    Edward K Faison

    Full Text Available Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus, and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores-no-ungulates (full exclosure, deer (partial exclosure, and deer + moose (control was established. After 6-7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3-6 fold, and species richness by 1.7 species (19%. In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%. Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps, suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were

  6. Multiple Browsers Structure Tree Recruitment in Logged Temperate Forests.

    Science.gov (United States)

    Faison, Edward K; DeStefano, Stephen; Foster, David R; Rapp, Joshua M; Compton, Justin A

    2016-01-01

    Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus), and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus) in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores-no-ungulates (full exclosure), deer (partial exclosure), and deer + moose (control) was established. After 6-7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3-6 fold, and species richness by 1.7 species (19%). In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%). Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps), suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were both large

  7. openBEB: open biological experiment browser for correlative measurements.

    Science.gov (United States)

    Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas

    2014-03-26

    New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual

  8. Cracking ShadowCrypt: Exploring the Limitations of Secure I/O Systems in Internet Browsers

    Directory of Open Access Journals (Sweden)

    Freyberger Michael

    2018-04-01

    Full Text Available An important line of privacy research is investigating the design of systems for secure input and output (I/O within Internet browsers. These systems would allow for users’ information to be encrypted and decrypted by the browser, and the specific web applications will only have access to the users’ information in encrypted form. The state-of-the-art approach for a secure I/O system within Internet browsers is a system called ShadowCrypt created by UC Berkeley researchers [23]. This paper will explore the limitations of ShadowCrypt in order to provide a foundation for the general principles that must be followed when designing a secure I/O system within Internet browsers. First, we developed a comprehensive UI attack that cannot be mitigated with popular UI defenses, and tested the efficacy of the attack through a user study administered on Amazon Mechanical Turk. Only 1 of the 59 participants who were under attack successfully noticed the UI attack, which validates the stealthiness of the attack. Second, we present multiple attack vectors against Shadow-Crypt that do not rely upon UI deception. These attack vectors expose the privacy weaknesses of Shadow DOM—the key browser primitive leveraged by ShadowCrypt. Finally, we present a sketch of potential countermeasures that can enable the design of future secure I/O systems within Internet browsers.

  9. The HuRef Browser: a web resource for individual human genomics.

    Science.gov (United States)

    Axelrod, Nelson; Lin, Yuan; Ng, Pauline C; Stockwell, Timothy B; Crabtree, Jonathan; Huang, Jiaqi; Kirkness, Ewen; Strausberg, Robert L; Frazier, Marvin E; Venter, J Craig; Kravitz, Saul; Levy, Samuel

    2009-01-01

    The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at http://huref.jcvi.org.

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

    Science.gov (United States)

    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.

  11. Browser impacts in Mapungubwe National Park, South Africa: Should we be worried?

    Directory of Open Access Journals (Sweden)

    Corli Coetsee

    2016-09-01

    Full Text Available This study explores the impact of browsers on vegetation types within the Mapungubwe National Park and specifically whether rocky outcrops or ridges in the park serve as refugia from browsers, particularly elephants. We sampled 80 transects at 20 sites and recorded 1740 plants comprising 65 species. We found that a high proportion (> 80% of the woody vegetation sampled indicated browser utilisation. Although certain woody species (e.g. Albizia harveyi, Boscia albitrunca, Lannea schweinfurthii appeared to be preferred by browsers, browsing levels were relatively high among all woody species. High levels of browsing by herbivores other than elephants suggest that they have a significant impact on the park’s vegetation. We did not find that rocky ridges acted as refugia to browsers, but instead found that vegetation in rocky ridges was more severely impacted by browsers than vegetation in flat areas, despite vegetation being more accessible in flat areas. If elephant numbers continue to increase at the current rate (e.g. elephant numbers doubled between 2007 and 2010, we predict that some of the heavily utilised species will become locally rare over time. Conservation implications: High levels of browsing by both elephant and smaller herbivores contribute to significant impacts on vegetation away from rivers in Mapungubwe National Park. Without management interventions that address both types of impact, structural and species diversity are bound to decrease over the short to medium term.

  12. Functional response of ungulate browsers in disturbed eastern hemlock forests

    Science.gov (United States)

    DeStefano, Stephen

    2015-01-01

    , stem densities were greatest in girdled plots, but proportional browse consumption was highest at intermediate stem densities in logged plots, exhibiting a Type III (rather than a Type II) functional response. Our results revealed shifting top–down control by herbivores at different stages of stand recovery after disturbance and in different understory conditions resulting from logging vs. simulated adelgid attack. If forest managers wish to promote tree regeneration in hemlock stands that is more resistant to ungulate browsers, leaving HWA-infested stands unmanaged may be a better option than preemptively logging them.

  13. gb4gv: a genome browser for geminivirus

    Directory of Open Access Journals (Sweden)

    Eric S. Ho

    2017-04-01

    Full Text Available Background Geminiviruses (family Geminiviridae are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc. Methods We have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases. Results These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser. Discussion With the genomic information readily accessible, we hope that our database

  14. A browser-based tool for visualization and analysis of diffusion MRI data.

    Science.gov (United States)

    Yeatman, Jason D; Richie-Halford, Adam; Smith, Josh K; Keshavan, Anisha; Rokem, Ariel

    2018-03-05

    Human neuroscience research faces several challenges with regards to reproducibility. While scientists are generally aware that data sharing is important, it is not always clear how to share data in a manner that allows other labs to understand and reproduce published findings. Here we report a new open source tool, AFQ-Browser, that builds an interactive website as a companion to a diffusion MRI study. Because AFQ-Browser is portable-it runs in any web-browser-it can facilitate transparency and data sharing. Moreover, by leveraging new web-visualization technologies to create linked views between different dimensions of the dataset (anatomy, diffusion metrics, subject metadata), AFQ-Browser facilitates exploratory data analysis, fueling new discoveries based on previously published datasets. In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, aggregating data across labs, and publishing data alongside manuscripts.

  15. A framework for web browser-based medical simulation using WebGL.

    Science.gov (United States)

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2012-01-01

    This paper presents a web browser-based software framework that provides accessibility, portability, and platform independence for medical simulation. Typical medical simulation systems are restricted to the underlying platform and device, which limits widespread use. Our framework allows realistic and efficient medical simulation using only the web browser for anytime anywhere access using a variety of platforms ranging from desktop PCs to tablets. The framework consists of visualization, simulation, and hardware integration modules that are fundamental components for multimodal interactive simulation. Benchmark tests are performed to validate the rendering and computing performance of our framework with latest web browsers including Chrome and Firefox. The results are quite promising opening up the possibility of developing web-based medical simulation technology.

  16. From legacy systems via client/server to web browser technology in hospital informatics in Finland.

    Science.gov (United States)

    Korpela, M

    1998-01-01

    The majority of hospital information system installations in Finland are based on a legacy technology from the U.S. Department of Veterans Affairs (VA). This paper presents an architecture and a tool set which provide a migration path from terminal-based to client/server technology, conserving much of the investments in existing applications. It is argued, though, that a new technological revolution is required in the form of extending the web browser/server technology to operational information systems in hospitals. A blueprint is presented for a further migration path from client/server to browser/server technology. The browser technology is regarded as a major challenge to hospital information systems in the next few years.

  17. Deco-video: video editing and viewing browser enables to playback movie contents reproduced by using scene scenario

    Science.gov (United States)

    Ishihara, Takashi; Sakamoto, Kunio

    2008-03-01

    The authors developed a prototype video viewing browser. Our video viewer has a function to playback movies on the WWW according to the playing scenario. This scenario makes new scenes from original movies. Our video browser features this scene scenario where you can arrange movie's video clips, insert transition effects, apply colored backgrounds, or add captions and titles. The video movie contents on the WWW are copyrighted. The browser cannot alter web's movie contents owing to its copyright like that a conventional video editing software adds effects to the original. The editing software produces reproductions, but our browser doesn't. The browser adds effects according to the scenario and only shows us a new scene. The scene scenario is written in an XML-like script. The video browser has a function to give effect according to operations of the scenario. In addition, our video viewing browser can provide us with an interactive video art. For example, suppose that a small stream runs down among the rocks. On the browser, if you chose an icon which shows maple leafs and drop it into the stream, a maple leaf starts floating down along the stream.

  18. Enhancing Independent Internet Access for Individuals with Mental Retardation through Use of a Specialized Web Browser: A Pilot Study.

    Science.gov (United States)

    Davies, Daniel K.; Stock, Steven E.; Wehmeyer, Michael L.

    2001-01-01

    In this study, a prototype web browser, called Web Trek, that utilizes multimedia to provide access for individuals with cognitive disabilities was developed and pilot-tested with 12 adults with mental retardation. The Web Trek browser provided greater independence in accessing the Internet compared to Internet Explorer. (Contains references.)…

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

    Science.gov (United States)

    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…

  20. Temporal Manipulation and Sharing of Presentation State in Browser-Embedded Multimedia Documents

    NARCIS (Netherlands)

    D.C.A. Bulterman (Dick); A.J. Jansen (Jack); P.S. Cesar Garcia (Pablo Santiago)

    2008-01-01

    htmlabstractThis paper describes an approach to defining, manipulating and sharing state variables between a web browser and a multimedia presentation engine in functionally compound XML-based documents. This framework, which we call smilState: the SMIL XML State Architecture, is a fully

  1. [Development of a Web-based laboratory data browser integrated with heterogeneous clinical information].

    Science.gov (United States)

    Fujikawa, Jun

    2009-02-01

    To demonstrate the feasibility of a Web-based laboratory data browser integrated with heterogeneous clinical information in a hospital setting. A Java-based web application was developed in-house, using free open-source software. The server side manages queries to heterogeneous hospital databases containing patient data. Order entry information including laboratory test results, drug prescriptions, injection orders, physiological test orders and, imaging test orders, was retrieved from a replication database, and integrated with nursing data from a nursing system database. The result was visualized in a time-series table format, and accessed by web browsers on computers connected to the hospital intranet. The laboratory data browser system achieved practical response times over huge databases (> 90 million records). The medical personnel accepted the system well, and applied the system to various clinical situations. Integrating heterogeneous data from hospital databases in a Web-based laboratory data browser is a practical approach. Presenting relevant medical information simultaneously added value to the laboratory data, and may promote better medical management.

  2. Linking ecosystem services and human health: the Eco-Health Relationship Browser.

    Science.gov (United States)

    Jackson, Laura E; Daniel, Jessica; McCorkle, Betsy; Sears, Alexandra; Bush, Kathleen F

    2013-10-01

    Ecosystems provide multiple services, many of which are linked to positive health outcomes. Review objectives were to identify the set of literature related to this research topic, and to design an interactive, web-based tool highlighting the weight of evidence, thus making the information more accessible. A systematic review was conducted to create the Eco-Health Relationship Browser ( http://www.epa.gov/research/healthscience/browser/introduction.html ). The search was conducted in four stages utilizing Google Scholar, PubMed and Science Direct, targeted journals, and targeted keywords; search results were limited to peer-reviewed journal articles published in English from 1 January 1990 to 31 December 2012. The review identified 344 relevant articles; a subset of 169 articles was included in the Browser. Articles retrieved during the search focused on the buffering and health-promotional aspects of ecosystem services. Landscape and Urban Planning, Urban Forestry and Urban Greening, and Health and Place yielded the most articles relevant to this search. Results from the systematic review were used to populate the Browser, which organizes the diverse literature and allows users to visualize the numerous connections between ecosystem services and human health.

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

    Science.gov (United States)

    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…

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

    International Nuclear Information System (INIS)

    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. 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.

  5. Web Browser History Detection as a Real-World Privacy Threat

    CERN Document Server

    Janc, A

    2010-01-01

    Web browser history detection using CSS $visited$ styles has long been dismissed as an issue of marginal impact. However, due to recent changes in Web usage patterns, coupled with browser performance improvements, the long-standing issue has now become a significant threat to the privacy of Internet users. In this paper we analyze the impact of CSS-based history detection and demonstrate the feasibility of conducting practical attacks with minimal resources. We analyze Web browser behavior and detectability of content loaded via standard protocols and with various HTTP response codes. We develop an algorithm for efficient examination of large link sets and evaluate its performance in modern browsers. Compared to existing methods our approach is up to 6 times faster, and is able to detect up to 30,000 visited links per second. We present a novel Web application capable of effectively detecting clients’ browsing histories and discuss real-world results obtained from 271,576 Internet users. Our results indicat...

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

    Science.gov (United States)

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

    2012-12-01

    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. 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.

  7. Pseudomonas corrugata crpCDE is part of the cyclic lipopeptide corpeptin biosynthetic gene cluster and is involved in bacterial virulence in tomato and in hypersensitive response in Nicotiana benthamiana.

    Science.gov (United States)

    Strano, Cinzia Patricia; Bella, Patrizia; Licciardello, Grazia; Fiore, Alberto; Lo Piero, Angela Roberta; Fogliano, Vincenzo; Venturi, Vittorio; Catara, Vittoria

    2015-06-01

    Pseudomonas corrugata CFBP 5454 produces two kinds of cyclic lipopeptides (CLPs), cormycin A and corpeptins, both of which possess surfactant, antimicrobial and phytotoxic activities. In this study, we identified genes coding for a putative non-ribosomal peptide synthetase and an ABC-type transport system involved in corpeptin production. These genes belong to the same transcriptional unit, designated crpCDE. The genetic organization of this locus is highly similar to other Pseudomonas CLP biosynthetic clusters. Matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis revealed that transporter and synthetase genomic knock-out mutants were unable to produce corpeptins, but continued to produce cormycin A. This suggests that CrpCDE is the only system involved in corpeptin production in P. corrugata CFBP 5454. In addition, phylogenetic analysis revealed that the CrpE ABC transporter clustered with the transporters of CLPs with a long peptide chain. Strains depleted in corpeptin production were significantly less virulent than the wild-type strain when inoculated in tomato plants and induced only chlorosis when infiltrated into Nicotiana benthamiana leaves. Thus, corpeptins are important effectors of P. corrugata interaction with plants. Expression analysis revealed that crpC transcription occurs at high cell density. Two LuxR transcriptional regulators, PcoR and RfiA, have a pivotal role in crpC expression and thus in corpeptin production. © 2014 BSPP AND JOHN WILEY & SONS LTD.

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

    Science.gov (United States)

    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.

  9. Browser App Approach: Can It Be an Answer to the Challenges in Cross-Platform App Development?

    Directory of Open Access Journals (Sweden)

    Minh Q. Huynh

    2017-02-01

    Full Text Available Aim/Purpose: As smartphones proliferate, many different platforms begin to emerge. The challenge to developers as well as IS educators and students is how to learn the skills to design and develop apps to run on cross-platforms. Background: For developers, the purpose of this paper is to describe an alternative to the complex native app development. For IS educators and students, the paper provides a feasible way to learn and develop fully functional mobile apps without technical burdens. Methodology: The methods used in the development of browser-based apps is prototyping. Our proposed approach is browser-based, supports cross-platforms, uses open-source standards, and takes advantage of “write-once-and-run-anywhere” (WORA concept. Contribution: The paper illustrates the application of the browser-based approach to create a series of browser apps without high learning curve. Findings: The results show the potentials for using browser app approach to teach as well as to create new apps. Recommendations for Practitioners\t: Our proposed browser app development approach and example would be useful to mobile app developers/IS educators and non-technical students because the source code as well as documentations in this project are available for downloading. Future Research: For further work, we discuss the use of hybrid development framework to enhance browser apps.

  10. The Open Anatomy Browser: A Collaborative Web-Based Viewer for Interoperable Anatomy Atlases.

    Science.gov (United States)

    Halle, Michael; Demeusy, Valentin; Kikinis, Ron

    2017-01-01

    The Open Anatomy Browser (OABrowser) is an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The viewer includes novel collaborative tools: users can save bookmarks of atlas views for later access and exchange those bookmarks with other users, and dynamic shared views allow groups of users can participate in a collaborative interactive atlas viewing session. We have published several anatomy atlases (an MRI-derived brain atlas and atlases of other parts of the anatomy) to demonstrate OABrowser's functionality. The atlas source data, processing tools, and the source for OABrowser are freely available through GitHub and are distributed under a liberal open source license.

  11. Modeling the HTML DOM and Browser API in Static Analysis of JavaScript Web Applications

    DEFF Research Database (Denmark)

    Jensen, Simon Holm; Madsen, Magnus; Møller, Anders

    2011-01-01

    Developers of JavaScript web applications have little tool support for catching errors early in development. In comparison, an abundance of tools exist for statically typed languages, including sophisticated integrated development environments and specialized static analyses. Transferring...... such technologies to the domain of JavaScript web applications is challenging. In this paper, we discuss the challenges, which include the dynamic aspects of JavaScript and the complex interactions between JavaScript, HTML, and the browser. From this, we present the first static analysis that is capable...... of reasoning about the flow of control and data in modern JavaScript applications that interact with the HTML DOM and browser API. One application of such a static analysis is to detect type-related and dataflow-related programming errors. We report on experiments with a range of modern web applications...

  12. A browser-based multi-user working environment for physicists

    International Nuclear Information System (INIS)

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

    2014-01-01

    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.

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

    Science.gov (United States)

    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 .

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

    Science.gov (United States)

    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.

  15. Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

    Science.gov (United States)

    Kono, Nobuaki; Arakawa, Kazuharu; Ogawa, Ryu; Kido, Nobuhiro; Oshita, Kazuki; Ikegami, Keita; Tamaki, Satoshi; Tomita, Masaru

    2009-11-11

    Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/).

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

    Science.gov (United States)

    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".

  17. Nessi: an EEG-controlled web browser for severely paralyzed patients.

    Science.gov (United States)

    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.

  18. Primates and mouse NumtS in the UCSC Genome Browser

    Directory of Open Access Journals (Sweden)

    Calabrese Francesco Maria

    2012-03-01

    Full Text Available Abstract Background NumtS (Nuclear MiTochondrial Sequences are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses. Results The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance. Conclusions Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.

  19. A Lifelog Browser for Visualization and Search of Mobile Everyday-Life

    Directory of Open Access Journals (Sweden)

    Keum-Sung Hwang

    2014-01-01

    Full Text Available Mobile devices can now handle a great deal of information thanks to the convergence of diverse functionalities. Mobile environments have already shown great potential in terms of providing customized service to users because they can record meaningful and private information continually for long periods of time. The research for understanding, searching and summarizing the everyday-life of human has received increasing attention in recent years due to the digital convergence. In this paper, we propose a mobile life browser, which visualizes and searches human's mobile life based on the contents and context of lifelog data. The mobile life browser is for searching the personal information effectively collected on his/her mobile device and for supporting the concept-based searching method by using concept networks and Bayesian networks. In the experiments, we collected the real mobile log data from three users for a month and visualized the mobile lives of the users with the mobile life browser developed. Some tests on searching tasks confirmed that the result using the proposed concept-based searching method is promising.

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

    Directory of Open Access Journals (Sweden)

    Michael Bensch

    2007-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  2. SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

    Directory of Open Access Journals (Sweden)

    Kim Seungill

    2008-12-01

    Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

  3. Visualizing Earthquakes in '3D' using the IRIS Earthquake Browser (IEB) Website

    Science.gov (United States)

    Welti, R.; McQuillan, P. J.; Weertman, B. R.

    2012-12-01

    The distribution of earthquakes is often easier to interpret in 3D, but most 3D visualization tools require the installation of specialized software and some practice in their use. To reduce this barrier for students and the general public, a pseudo-3D seismicity viewer has been developed which runs in a web browser as part of the IRIS Earthquake Browser (IEB). IEB is an interactive map for viewing earthquake epicenters all over the world, and is composed of a Google map, HTML, JavaScript and a fast earthquake hypocenter web service. The web service accesses seismic data at IRIS from the early 1960s until present. Users can change the region, the number of events, and the depth and magnitude ranges to display. Earthquakes may also be viewed as a table, or exported to various formats. Predefined regions can be selected and zoomed to, and bookmarks generally preserve whatever region and settings are in effect when bookmarked, allowing the easy sharing of particular "scenarios" with other users. Plate boundaries can be added to the display. The 3DV viewer displays events for the currently-selected IEB region in a separate window. They can be rotated and zoomed, with a fast response for plots of up to several thousand events. Rotation can be done manually by dragging or automatically at a set rate, and tectonic plate boundaries turned on or off. 3DV uses a geographical projection algorithm provided by Gary Pavils and collaborators. It is written in HTML5, and is based on CanvasMol by Branislav Ulicny.; A region SE of Fiji, selected in IRIS Earthquake Browser. ; The same region as viewed in 3D Viewer.

  4. Miocene ungulates and terrestrial primary productivity: where have all the browsers gone?

    Science.gov (United States)

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

    2000-07-05

    Progressive changes are observed in both the composition of mammal faunas and vegetation during the Miocene epoch [24-5 mega-annum (Ma)]. These changes are usually interpreted as a response to climatic changes. In the traditional view, forests or woodlands gradually gave way to more open habitats, with grazing (grass-eating) ungulate (hoofed) mammal species replacing the browsing (leafy-vegetation-eating) species as grasslands expanded. However, data from fossil assemblages in the Great Plains region of North America show that this faunal change was not a one-for-one replacement of browsers by grazers, as usually thought. Typical late early Miocene (17 Ma) fossil communities included extraordinarily high numbers of browsing ungulate species, comprising a fauna that cannot be directly analogized with any present-day community. Both maximum species richness of all ungulates and the proportion of browsers declined steadily in ungulate communities through the middle Miocene, to levels comparable to those of the present by the late Miocene. The resulting dramatic, cumulative loss of browsing species constitutes one of the strongest faunal signals of the late Tertiary (but was not a single "event"). We suggest that the early Miocene browser-rich communities may reflect higher levels of primary productivity in Miocene vegetation, compared with equivalent present-day vegetation types. The observed decline in species richness may represent a gradual decline in primary productivity, which would be consistent with one current hypothesis of a mid-Miocene decrease in atmospheric CO2 concentrations from higher mid-Cenozoic values.

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

    Science.gov (United States)

    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.

  6. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

    Science.gov (United States)

    Raney, Brian J.; Dreszer, Timothy R.; Barber, Galt P.; Clawson, Hiram; Fujita, Pauline A.; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S.; Karolchik, Donna; Kent, W. James

    2014-01-01

    Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu. Contact: donnak@soe.ucsc.edu PMID:24227676

  7. ENCODE whole-genome data in the UCSC Genome Browser: update 2012

    Science.gov (United States)

    Rosenbloom, Kate R.; Dreszer, Timothy R.; Long, Jeffrey C.; Malladi, Venkat S.; Sloan, Cricket A.; Raney, Brian J.; Cline, Melissa S.; Karolchik, Donna; Barber, Galt P.; Clawson, Hiram; Diekhans, Mark; Fujita, Pauline A.; Goldman, Mary; Gravell, Robert C.; Harte, Rachel A.; Hinrichs, Angie S.; Kirkup, Vanessa M.; Kuhn, Robert M.; Learned, Katrina; Maddren, Morgan; Meyer, Laurence R.; Pohl, Andy; Rhead, Brooke; Wong, Matthew C.; Zweig, Ann S.; Haussler, David; Kent, W. James

    2012-01-01

    The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets. PMID:22075998

  8. gEVAL - a web-based browser for evaluating genome assemblies.

    Science.gov (United States)

    Chow, William; Brugger, Kim; Caccamo, Mario; Sealy, Ian; Torrance, James; Howe, Kerstin

    2016-08-15

    For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly. Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin kj2@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

    Science.gov (United States)

    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/

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  12. JavaScript Access to DICOM Network and Objects in Web Browser.

    Science.gov (United States)

    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.

  13. Interactive atlas using web browser: CT and MRI of the temporal bone

    International Nuclear Information System (INIS)

    Chung, Eun Chul; Youn, Eun Kyung; Lee, Young Uk

    2000-01-01

    The purposes of this study were to construct an interactive atlas of the temporal bone using a web-browser and to provide a template for web-based teaching files, using free and shared applets and scripts on the internet. HRCT and MR images of the temporal bone including its normal anatomy, tumors, trauma, inflammation, anomalies and vascular diseases were used in this study. Acquired radiologic images were transformed to GIF/JPG formats and to achieve appropriate image quality, were retouched. Text and image files of normal anatomy and diseases were written by HTML. JavaScript and applets were inserted in the HTML files for the interactive display of images and texts. In order to review anatomic features and diseases, a search index was also attached to the last part of the file. Using interactive images and text, temporal bone anatomy and disorders were displayed. Scripts and applets were also useful for indicating specific points of interest when a mouse was placed over the anatomic sites. The atlas may be viewed in the form of a CD-ROM, or via the internet using any computer platform or web-browser. This web-based teaching file of the temporal bone offers dynamic and interactive education. It can be usefully employed as a template for the production of interactive educational materials, offering JavaScript and providing suitable input for classes. It can replace texts and imaging contents. (author)

  14. Development of childhood fall motion database and browser based on behavior measurements.

    Science.gov (United States)

    Kakara, Hiroyuki; Nishida, Yoshifumi; Yoon, Sang Min; Miyazaki, Yusuke; Koizumi, Yoshinori; Mizoguchi, Hiroshi; Yamanaka, Tatsuhiro

    2013-10-01

    This paper describes the development of a fall motion database and a browser designed to facilitate investigations into fall-related injury risk. First, child-related daily activities were collected at a "sensor home", which is a model of a normal living environment equipped with an embedded video-surveillance system and within which child test subjects were equipped with wearable acceleration-gyro sensors. As of this report, measurements have been conducted for 19 children (months age: mean=23.8, standard deviation=10.5), and data has been obtained on 105 fall incidents. During our research, falls were detected from the accumulated sensor data using a detection algorithm developed by the authors, and then video clips of detected falls were extracted from the recorded video streams automatically. The extracted video clips were then used for fall motion analysis. A computer vision (CV) algorithm, which was developed to automate fall motion analysis, facilitates accumulation of fall motion data into the abovementioned database, and the associated database browser allows users to perform conditional searches of fall data by inputting search conditions, such as child attributes and specific fall situations. Before this study, there was no database which contains child's actual fall motion data, and it has the potential to facilitate injury risk reduction related to falls in daily living environments. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis.

    Science.gov (United States)

    Geistlinger, Ludwig; Csaba, Gergely; Zimmer, Ralf

    2016-01-20

    Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation. We present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks. The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

  16. The Transcriptional Repressor, MtrR, of the mtrCDE Efflux Pump Operon of Neisseria gonorrhoeae Can Also Serve as an Activator of “off Target” Gene (glnE Expression

    Directory of Open Access Journals (Sweden)

    Paul J. T. Johnson

    2015-06-01

    Full Text Available MtrR is a well-characterized repressor of the Neisseria gonorrhoeae mtrCDE efflux pump operon. However, results from a previous transcriptional profiling study suggested that MtrR also represses or activates expression of at least sixty genes outside of the mtr locus. Evidence that MtrR can directly repress so-called “off target” genes has previously been reported; in particular, MtrR was shown to directly repress glnA, which encodes glutamine synthetase. In contrast, evidence for the ability of MtrR to directly activate expression of gonococcal genes has been lacking; herein, we provide such evidence. We now report that MtrR has the ability to directly activate expression of glnE, which encodes the dual functional adenyltransferase/deadenylase enzyme GlnE that modifies GlnA resulting in regulation of its role in glutamine biosynthesis. With its capacity to repress expression of glnA, the results presented herein emphasize the diverse and often opposing regulatory properties of MtrR that likely contributes to the overall physiology and metabolism of N. gonorrhoeae.

  17. Desain prototipe aplikasi sistem monitoring browser ponsel anak untuk menerapkan internet sehat dengan kontrol orang tua

    Directory of Open Access Journals (Sweden)

    Taufik Hidayat

    2017-05-01

    Full Text Available AbstrakPenggunaan internet dikalangan anak-anak saat ini sudah menjadi trend, bahkan banyak orang tua sudah memberikan ponsel android kepada anak-anak dalam melakukan komunikasi sehari-hari. Hal tersebut sangat berdampak kepada anak dalam pemanfaatan teknologi internet yang kurang sehat seperti mendapatkan data dan informasi melalui browsing internet tanpa pemantauan orang tua sehingga anak dengan mudah mendapatkan kata-kata atau informasi yang tidak layak dikonsumsi oleh anak tersebut. Penelitian ini bertujuan untuk mendesain aplikasi sistem monitoring browser ponsel anak untuk menerapkan internet sehat dengan kontrol orang tua menggunakan metode prototipe. Hasil penelitian tersebut berupa rancangan aplikasi monitoring broser anak yang dapat digunakan untuk memantau aktivitas browsing internet pada ponsel anak secara online pada platform android dengan otomatis mengirim pesan notifikasi kepada orang tua dan orang tua dapat memberikan respon atau balasan secara langsung ketika anak sedang mencoba melakukan aktivitas browsing internet yang tidak sehat. Kata kunci: Kontrol orang tua, penelusuran aman, sistem monitoring, aktivitas penelusuran harian  Abstract The use of the internet among children currently have become a trend, even many parents already gives android phones to children in doing everyday communication. It is so impacting to the child in the utilization of internet technologies that are less healthy as get data and information through browsing the internet without monitoring parents so children easily get words or information that is not feasible is consumed by the child. This research aims to design a monitoring system of the mobile browser app to implement a healthy internet parental control method using prototype. The results of such research in the form of a draft application monitoring these children which can be used to monitor the activities of internet browsing on mobile child online on the android platform with automatic

  18. An innovative browser-based data exploration tool with simultaneous scrolling in time and wavelength domains

    Science.gov (United States)

    Slater, Gregory L.; Schiff, David; De Pontieu, Bart; Tarbell, Theodore D.; Freeland, Samuel L.

    2017-08-01

    We present Cruiser, a new web tool for the precision interactive blending of image series across time and wavelength domains. Scrolling in two dimensions enables discovery and investigation of similarities and differences in structure and evolution across multiple wavelengths. Cruiser works in the latest versions of standards compliant browsers on both desktop and IOS platforms. Co-aligned data cubes have been generated for AIA, IRIS, and Hinode SOT FG, and image data from additional instruments, both space-based and ground-based, can be data sources. The tool has several movie playing and image adjustment controls which will be described in the poster and demonstrated on a MacOS notebook and iPad.

  19. Building a Better Book in the Browser (Using Semantic Web technologies and HTML5

    Directory of Open Access Journals (Sweden)

    Jason A. Clark

    2015-07-01

    Full Text Available The library as place and service continues to be shaped by the legacy of the book. The book itself has evolved in recent years, with various technologies vying to become the next dominant book form. In this article, we discuss the design and development of our prototype software from Montana State University (MSU Library for presenting books inside of web browsers. The article outlines the contextual background and technological potential for publishing traditional book content through the web using open standards. Our prototype demonstrates the application of HTML5, structured data with RDFa and Schema.org markup, linked data components using JSON-LD, and an API-driven data model. We examine how this open web model impacts discovery, reading analytics, eBook production, and machine-readability for libraries considering how to unite software development and publishing.

  20. Issues of Page Representation and Organisation in Web Browser's Revisitation Tools

    Directory of Open Access Journals (Sweden)

    Andy Cockburn

    2000-05-01

    Full Text Available Many commercial and research WWW browsers include a variety of graphical revisitation tools that let users return to previously seen pages. Examples include history lists, bookmarks and site maps. In this paper, we examine two fundamental design and usability issues that all graphical tools for revisitation must address. First, how can individual pages be represented to best support page identification? We discuss the problems and prospects of various page representations: the pages themselves, image thumbnails, text labels, and abstract page properties. Second, what display organisation schemes can be used to enhance the visualisation of large sets of previously visited pages? We compare temporal organisations, hub-and spoke dynamic trees, spatial layouts and site maps.

  1. iPiG: integrating peptide spectrum matches into genome browser visualizations.

    Directory of Open Access Journals (Sweden)

    Mathias Kuhring

    Full Text Available Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we introduce iPiG as a tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is simplified and proteomic results can directly be compared to genomic data. iPiG is freely available from https://sourceforge.net/projects/ipig/. It is implemented in Java and can be run as a stand-alone tool with a graphical user-interface or integrated into existing workflows. Supplementary data are available at PLOS ONE online.

  2. A freely-available authoring system for browser-based CALL with speech recognition

    Directory of Open Access Journals (Sweden)

    Myles O'Brien

    2017-06-01

    Full Text Available 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 against a list of specified permitted answers, giving feedback with hints when necessary. The teacher needs no HTML or Javascript expertise, just the facilities and ability to edit text files and upload to the Internet. The structure and functioning of the system are explained in detail, and some suggestions are given for practical use. Finally, some of its limitations are described.

  3. nodeGame: Real-time, synchronous, online experiments in the browser.

    Science.gov (United States)

    Balietti, Stefano

    2017-10-01

    nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform. With zero-install, nodeGame can run on a great variety of devices, from desktop computers to laptops, smartphones, and tablets. The current version of the software is 3.0, and extensive documentation is available on the wiki pages at http://nodegame.org .

  4. A hybrid BCI web browser based on EEG and EOG signals.

    Science.gov (United States)

    Shenghong He; Tianyou Yu; Zhenghui Gu; Yuanqing Li

    2017-07-01

    In this study, we propose a new web browser based on a hybrid brain computer interface (BCI) combining electroencephalographic (EEG) and electrooculography (EOG) signals. Specifically, the user can control the horizontal movement of the mouse by imagining left/right hand motion, and control the vertical movement of the mouse, select/reject a target, or input text in an edit box by blinking eyes in synchrony with the flashes of the corresponding buttons on the GUI. Based on mouse control, target selection and text input, the user can open a web page of interest, select an intended target in the web and read the page content. An online experiment was conducted involving five healthy subjects. The experimental results demonstrated the effectiveness of the proposed method.

  5. Interpolate with DIVA and view the products in OceanBrowser : what's up ?

    Science.gov (United States)

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

    2017-04-01

    The Data-Interpolating Variational Analysis (DIVA) software is a statistical tool designed to reconstruct a continuous field from discrete measurements. This method is based on the numerical implementation of the Variational Inverse Model (VIM), which consists of a minimization of a cost function, allowing the choice of the analyzed field fitting at best the data sets without presenting unrealistic strong variations. The problem is solved efficiently using a finite-element method. This method, equivalent to the Optimal Interpolation, is particularly suited to deal with irregularly-spaced observations and produces outputs on a regular grid (2D, 3D or 4D). The results are stored in NetCDF files, the most widespread format in the earth sciences community. OceanBrowser is a web-service that allows one to visualize gridded fields on-line. Within the SeaDataNet and EMODNET (Chemical lot) projects, several national ocean data centers have created gridded climatologies of different ocean properties using the data analysis software DIVA. In order to give a common viewing service to those interpolated products, the GHER has developed OceanBrowser which is based on open standards from the Open Geospatial Consortium (OGC), in particular Web Map Service (WMS) and Web Feature Service (WFS). These standards define a protocol for describing, requesting and querying two-dimensional maps at a given depth and time. DIVA and OceanBrowser are both softwares tools which are continuously upgraded and distributed for free through frequent version releases. The development is funded by the EMODnet and SeaDataNet projects and include many discussions and feedback from the users community. Here, we present two recent major upgrades. First, we have implemented a "customization" of DIVA analyses following the sea bottom, using the bottom depth gradient as a new source of information. The weaker the slope of the bottom ocean, the higher the correlation length. This correlation length being

  6. Knowledge-based client-server approach to structural information retrieval: the Digital Anatomist Browser.

    Science.gov (United States)

    Brinkley, J F; Eno, K; Sundsten, J W

    1993-06-01

    Structural information can be defined as data and knowledge about biological objects ranging in size from molecules to the whole body. A framework is described for organizing structural information around a well-defined set of terminology and semantic relationships, and for disseminating multimedia structural information by means of a wide-area information server that is accessible over the internet. A Macintosh-based client of this server, called the Digital Anatomist Browser, has been used to teach neuroanatomy for the last 2 years. The client-server approach provides each student unlimited access to a rapidly growing knowledge base of structural biology that, while immediately useful for anatomy teaching, has the potential to be an organizing framework for other kinds of medical knowledge as well.

  7. ROOT I/O in Javascript - Reading ROOT files in a browser

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    A JavaScript version of the ROOT I/O subsystem is being developed, in order to be able to browse (inspect) ROOT files in a platform independent way. This allows the content of ROOT files to be displayed in most web browsers, without having to install ROOT or any other software on the server or on the client. This gives a direct access to ROOT files from new (e.g. portable) devices in a light way. It will be possible to display simple graphical objects such as histograms and graphs (TH1, TH2, TH3, TProfile, TGraph, ...). The rendering will first be done with an external JavaScript graphic library, before investigating a way to produce graphics closer to what ROOT supports on other platforms (X11, Windows).

  8. PopGeV: a web-based large-scale population genome browser.

    Science.gov (United States)

    Shi, Xinyi; Peng, Jing; Yu, Xiaohan; Zhang, Xiaohong; Li, Dongye; Liu, Baohui; Kong, Fanjiang; Yuan, Xiaohui

    2015-09-15

    The development of high-throughput sequencing technology has made it possible for more and more researchers to use population sequencing data to mine genes associated with specific traits. However, the massive amounts of sequencing data have also brought new challenges to the researchers. The question of how to browse population genomic data in an easy and intuitive manner must be addressed. Web-based genome browsers allow user to conveniently view the results of genomic analyses, but heavy usage can reduce the response speed of the webpage, which limits its usefulness in the display of large-scale genome data. IndexedDB technology is a good solution to this problem; it supports web browsers and so creates local databases. In this way, data can be read from the local storage, achieving a smooth display of population genomic data. PopGeV has the following characteristics. First, it uses a new encoding method for compression of population SNP and INDEL data. IndexedDB technology is used to download the results to local storage so that users can browse the results smoothly even when the network traffic is heavy. Second, PopGeV identify similar genomic regions between two individuals based on SNP data. Population diversity indexes are calculated when comparing two populations. Third, user defined annotation information can be integrated for user-friendly mining of gene functions. Simulation shows that PopGeV can smoothly display analysis results of population genome containing over 500 individuals with 2 millions SNP data. PopGeV is available at www.soyomics.com/popgev/ yuanxh@iga.ac.cn. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Identification of transcriptional macromolecular associations in human bone using browser based in silico analysis in a giant correlation matrix.

    Science.gov (United States)

    Reppe, Sjur; Sachse, Daniel; Olstad, Ole K; Gautvik, Vigdis T; Sanderson, Paul; Datta, Harish K; Berg, Jens P; Gautvik, Kaare M

    2013-03-01

    Intracellular signaling is critically dependent on gene regulatory networks comprising physical molecular interactions. Presently, there is a lack of comprehensive databases for most human tissue types to verify such macromolecular interactions. We present a user friendly browser which helps to identify functional macromolecular interactions in human bone as significant correlations at the transcriptional level. The molecular skeletal phenotype has been characterized by transcriptome analysis of iliac crest bone biopsies from 84 postmenopausal women through quantifications of ~23,000 mRNA species. When the signal levels were inter-correlated, an array containing >260 million correlations was generated, thus recognizing the human bone interactome at the RNA level. The matrix correlation and p values were made easily accessible by a freely available online browser. We show that significant correlations within the giant matrix are reproduced in a replica set of 13 male vertebral biopsies. The identified correlations differ somewhat from transcriptional interactions identified in cell culture experiments and transgenic mice, thus demonstrating that care should be taken in extrapolating such results to the in vivo situation in human bone. The current giant matrix and web browser are a valuable tool for easy access to the human bone transcriptome and molecular interactions represented as significant correlations at the RNA-level. The browser and matrix should be a valuable hypothesis generating tool for identification of regulatory mechanisms and serve as a library of transcript relationships in human bone, a relatively inaccessible tissue. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

    Directory of Open Access Journals (Sweden)

    Perez-Rey David

    2012-04-01

    Full Text Available Abstract Background Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs. In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA, (ii identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH, automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard

  11. CDAPubMed: a browser extension to retrieve EHR-based biomedical literature.

    Science.gov (United States)

    Perez-Rey, David; Jimenez-Castellanos, Ana; Garcia-Remesal, Miguel; Crespo, Jose; Maojo, Victor

    2012-04-05

    Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset

  12. ENCODE whole-genome data in the UCSC genome browser (2011 update)

    Science.gov (United States)

    Raney, Brian J.; Cline, Melissa S.; Rosenbloom, Kate R.; Dreszer, Timothy R.; Learned, Katrina; Barber, Galt P.; Meyer, Laurence R.; Sloan, Cricket A.; Malladi, Venkat S.; Roskin, Krishna M.; Suh, Bernard B.; Hinrichs, Angie S.; Clawson, Hiram; Zweig, Ann S.; Kirkup, Vanessa; Fujita, Pauline A.; Rhead, Brooke; Smith, Kayla E.; Pohl, Andy; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

    2011-01-01

    The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access. PMID:21037257

  13. ChromoZoom: a flexible, fluid, web-based genome browser.

    Science.gov (United States)

    Pak, Theodore R; Roth, Frederick P

    2013-02-01

    Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data. ChromoZoom thereby enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets. Human and yeast genome researchers may browse recent assemblies within ChromoZoom at http://chromozoom.org/. Source code is available at http://github.com/rothlab/chromozoom/.

  14. COBE: A Conjunctive Ontology Browser and Explorer for Visualizing SNOMED CT Fragments.

    Science.gov (United States)

    Sun, Mengmeng; Zhu, Wei; Tao, Shiqiang; Cui, Licong; Zhang, Guo-Qiang

    2015-01-01

    Ontology search interfaces can benefit from the latest information retrieval advances. This paper introduces a Conjunctive Ontology Browser and Explorer (COBE) for searching and exploring SNOMED CT concepts and visualizing SNOMED CT fragments. COBE combines navigational exploration (NE) with direct lookup (DL) as two complementary modes for finding specific SNOMED CT concepts. The NE mode allows a user to interactively and incrementally narrow down (hence conjunctive) the search space by adding word stems, one at a time. Such word stems serve as attribute constraints, or "attributes" in Formal Concept Analysis, which allows the user to navigate to specific SNOMED CT concept clusters. The DL mode represents the common search mechanism by using a collection of key words, as well as concept identifiers. With respect to the DL mode, evaluation against manually created reference standard showed that COBE attains an example-based precision of 0.958, recall of 0.917, and F1 measure of 0.875. With respect to the NE mode, COBE leverages 28,371 concepts in non-lattice fragments to construct the stem cloud. With merely 9.37% of the total SNOMED CT stem cloud, our navigational exploration mode covers 98.97% of the entire concept collection.

  15. Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

    LENUS (Irish Health Repository)

    Fitzpatrick, David A

    2010-05-10

    Abstract Background Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome. Results CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging\\/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans. Conclusions Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http:\\/\\/cgob.ucd.ie.

  16. STUDYING STUDENT BEHAVIOR AND CHEMISTRY SKILL USING BROWSER-BASED TOOLS AND EYE-TRACKING HARDWARE

    Directory of Open Access Journals (Sweden)

    Norbert J. Pienta

    Full Text Available Browser-based tools were created to collect quantitative data about university student problem-solving skills. Three of these tools have been described: a word question tool that creates ideal gas law and stoichiometry questions using a set of complexity factors; a Lewis structure drawing tool that enables the user to draw a solution to an ion or molecule assigned to them; and a "spheres" tool that uses spheres to represent atoms and molecules to denote the particulate nature of matter. Results from these studies show that relatively simple questions can be made very complex by the addition of many complexity factors that challenge the cognitive skills. The drawing tools can be used for instruction or to collect data about student understanding; the outcomes suggest that students with more instruction in chemistry are more successful but even the performance of students after four semesters is somewhat disappointing. Eye-tracking hardware enabled the study of the student use of the visual interface of the other tools and to study molecular representation or interpret spectral data.

  17. VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Minovitsky, Simon; Dubchak, Inna; Pennacchio, Len A.

    2006-08-01

    Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimental determination of their in vivo enhanceractivity in transgenic mice (1). These data are available through theVISTA Enhancer Browser (http://enhancer.lbl.gov). This growing databasecurrently contains over 250 experimentally tested DNA fragments, of whichmore than 100 have been validated as tissue-specific enhancers. For eachpositive enhancer, we provide digital images of whole-mount embryostaining at embryonic day 11.5 and an anatomical description of thereporter gene expression pattern. Users can retrieve elements near singlegenes of interest, search for enhancers that target reporter geneexpression to a particular tissue, or download entire collections ofenhancers with a defined tissue specificity or conservation depth. Theseexperimentally validated training sets are expected to provide a basisfor a wide range of downstream computational and functional studies ofenhancer function.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  20. Mass extinction spectra and size distribution measurements of quartz and amorphous silica aerosol at 0.33-19 μm compared to modelled extinction using Mie, CDE, and T-matrix theories

    Science.gov (United States)

    Reed, Benjamin E.; Peters, Daniel M.; McPheat, Robert; Smith, Andrew J. A.; Grainger, R. G.

    2017-09-01

    Simultaneous measurements were made of the spectral extinction (from 0.33-19 μm) and particle size distribution of silica aerosol dispersed in nitrogen gas. Two optical systems were used to measure the extinction spectra over a wide spectral range: a Fourier transform spectrometer in the infrared and two diffraction grating spectrometers covering visible and ultraviolet wavelengths. The particle size distribution was measured using a scanning mobility particle sizer and an optical particle counter. The measurements were applied to one amorphous and two crsystalline silica (quartz) samples. In the infrared peak values of the mass extinction coefficient (MEC) of the crystalline samples were 1.63 ± 0.23 m2g-1 at 9.06 μm and 1.53 ± 0.26 m2g-1 at 9.14 μm with corresponding effective radii of 0.267 and 0.331 μm, respectively. For the amorphous sample the peak MEC value was 1.37 ± 0.18 m2g-1 at 8.98 μm and the effective radius of the particles was 0.374 μm. Using the measured size distribution and literature values of the complex refractive index as inputs, three scattering models were evaluated for modelling the extinction: Mie theory, the Rayleigh continuous distribution of ellipsoids (CDE) model, and T-matrix modelling of a distribution of spheroids. Mie theory provided poor fits to the infrared extinction of quartz (R2 0.82 for crsytalline sillica and R2 = 0.98 for amorphous silica. The T-matrix approach was able to fit the amorphous infrared extinction data with an R2 value of 0.995. Allowing for the possibility of reduced crystallinity in the milled crystal samples, using a mixture of amorphous and crystalline T-matrix cross-sections provided fits with R2 values greater than 0.97 for the infrared extinction of the crystalline samples.

  1. Gbrowse Moby: a Web-based browser for BioMoby Services

    Directory of Open Access Journals (Sweden)

    Wilkinson Mark

    2006-10-01

    Full Text Available Abstract Background The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. Results Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. Conclusion Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment.

  2. Gbrowse Moby: a Web-based browser for BioMoby Services.

    Science.gov (United States)

    Wilkinson, Mark

    2006-10-24

    The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client--Gbrowse Moby--that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment.

  3. Socializing Young People to Ethics via Play Experience: Browser Games and Parental Concerns for Safety Online

    Directory of Open Access Journals (Sweden)

    Divina Meigs

    2009-01-01

    Full Text Available This paper considers an online game and its relation to safety and privacy, in order to examine social and ethical issues raised by parental concern over harmful content. To gain real insights on the responsibility of adults, it develops a hands-on approach that takes into account the major stakeholders, especially young people and the related circle of people around them. Therefore the research question that is raised is: how do browser games provide reassurance to parents about their children’s safety and privacy? The issue of safety online is explored in three parts, using an ethnographic research framework: it explores a specific online game, it provides a profile of participants, it analyses their types of actions in relation to safety and privacy, and discusses the results in terms of incidence of risk, peer-monitoring and community control. The findings show that there is a rather strong tendency to self-regulation, but that tendency is partly due to a strong presence of mediating adults and peers. The results are discussed in terms of incidence of risk, peer-monitoring and networked means of control on the one hand, and in terms of scientific contribution to socialization theory on the other hand. They lead to final considerations on the repertoire of ethical strategies set up online and its meaning for the concerns of adults towards online risk as well as the need for policies on regulation and self-regulation. They also lead to extensions on the socialization to norms and the appropriation of ethics by young people.

  4. Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

    Science.gov (United States)

    Almugbel, Reem; Hung, Ling-Hong; Hu, Jiaming; Almutairy, Abeer; Ortogero, Nicole; Tamta, Yashaswi; Yeung, Ka Yee

    2018-01-01

    Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. WebViz: A web browser based application for collaborative analysis of 3D data

    Science.gov (United States)

    Ruegg, C. S.

    2011-12-01

    In the age of high speed Internet where people can interact instantly, scientific tools have lacked technology which can incorporate this concept of communication using the web. To solve this issue a web application for geological studies has been created, tentatively titled WebViz. This web application utilizes tools provided by Google Web Toolkit to create an AJAX web application capable of features found in non web based software. Using these tools, a web application can be created to act as piece of software from anywhere in the globe with a reasonably speedy Internet connection. An application of this technology can be seen with data regarding the recent tsunami from the major japan earthquakes. After constructing the appropriate data to fit a computer render software called HVR, WebViz can request images of the tsunami data and display it to anyone who has access to the application. This convenience alone makes WebViz a viable solution, but the option to interact with this data with others around the world causes WebViz to be taken as a serious computational tool. WebViz also can be used on any javascript enabled browser such as those found on modern tablets and smart phones over a fast wireless connection. Due to the fact that WebViz's current state is built using Google Web Toolkit the portability of the application is in it's most efficient form. Though many developers have been involved with the project, each person has contributed to increase the usability and speed of the application. In the project's most recent form a dramatic speed increase has been designed as well as a more efficient user interface. The speed increase has been informally noticed in recent uses of the application in China and Australia with the hosting server being located at the University of Minnesota. The user interface has been improved to not only look better but the functionality has been improved. Major functions of the application are rotating the 3D object using buttons

  6. The Pain Genes Database: An interactive web browser of pain-related transgenic knockout studies.

    Science.gov (United States)

    Lacroix-Fralish, Michael L; Ledoux, Jean B; Mogil, Jeffrey S

    2007-09-01

    The transgenic knockout mouse is one of the most important tools of modern biology, and commonly employed by pain researchers to examine the function of genes of interest. Over 400 papers, at a current rate of >60 papers per year, have been published to date describing a statistically significant behavioral pain "phenotype" resulting from the null mutation of a single gene. The standard literature review format is incapable of providing a sufficiently broad and up-to-date overview of the field. We have therefore constructed the Pain Genes Database, an interactive, web-based data browser designed to allow easy access to and analysis of the published pain-related phenotypes of mutant mice (over 200 different mutants at the date of submission). Manuscripts describing results of pain-relevant knockout studies were identified via Medline search. Manuscripts were included in the database if they described the testing of a spontaneous or genetically engineered mutant mouse with null expression of a single gene on a behavioral assay of acute or tonic nociception, injury- or stimulus-induced hypersensitivity (i.e., allodynia or hyperalgesia), or drug- or stress-induced inhibition of nociception (i.e., analgesia), and reported at least one statistically significant difference between the mutant mice and their simultaneously tested wildtype controls. The database features two levels of exploration, one allowing the identification of genes by name, acronym, genomic position or "summary" phenotype, and the other allowing in-depth browsing, paper-by-paper, of specific phenotypes and test parameters. Links to genetic databases and Medline abstracts are provided for each gene and paper. It is our intention to update the database continually based on weekly Medline searches. This database should provide pain researchers with a useful and easy-to-use tool for the generation of novel hypotheses regarding the roles of genes and their protein products in pain processing and modulation

  7. Browser based platform in maintaining clinical activities – use of the iPads in head and neck clinics

    International Nuclear Information System (INIS)

    Yang, W Y; Moore, J; Quon, H; Evans, K; Sharabi, A; Herman, J; Hacker-Prietz, A; McNutt, T

    2014-01-01

    Purpose: Incompatibility between documentation and clinical workflow causes physician resistance in organized data collection, which in turn complicates the use of data in patient care improvement. To resolve the gap, we developed an iPad compatible in situ browser-based platform that integrates clinical activity with data collection and analysis presentation. The ability to perform in-clinic activities and monitor decision making using the iPad was evaluated. Methods: A browser-based platform that can exchange and present analysed data from the MOSAIQ database was developed in situ, the iPads were distributed in head and neck clinics to present the browser for clinical activities, data collection and assessment monitoring. Performance of the iPads for in-clinic activities was observed. Results: All in-clinic documentation activities can be performed without workstation computers. Accessing patient record and previous assessments was significantly faster without having to open the MOSAIQ application. Patient assessments can be completed with the physician facing the patient. Graphical presentation of toxicity progression and patient radiation plans to the patient can be performed in single interface without patient leaving the seating area. Updates in patient treatment status and medical history were presented in real time without having to move paper charts around. Conclusions: The iPad can be used in clinical activities independent of computer workstations. Improvements in clinical workflow can be critical in reducing physician resistance in data maintenance. Using the iPad in providing real-time quality monitoring is intuitive to both providers and patients.

  8. Browser Based Platform in Maintaining Clinical Activities - Use of The iPads in Head and Neck Clinics

    Science.gov (United States)

    Yang, W. Y.; Moore, J.; Quon, H.; Evans, K.; Sharabi, A.; Herman, J.; Hacker-Prietz, A.; McNutt, T.

    2014-03-01

    Purpose: Incompatibility between documentation and clinical workflow causes physician resistance in organized data collection, which in turn complicates the use of data in patient care improvement. To resolve the gap, we developed an iPad compatible in situ browser-based platform that integrates clinical activity with data collection and analysis presentation. The ability to perform in-clinic activities and monitor decision making using the iPad was evaluated. Methods: A browser-based platform that can exchange and present analysed data from the MOSAIQ database was developed in situ, the iPads were distributed in head and neck clinics to present the browser for clinical activities, data collection and assessment monitoring. Performance of the iPads for in-clinic activities was observed. Results: All in-clinic documentation activities can be performed without workstation computers. Accessing patient record and previous assessments was significantly faster without having to open the MOSAIQ application. Patient assessments can be completed with the physician facing the patient. Graphical presentation of toxicity progression and patient radiation plans to the patient can be performed in single interface without patient leaving the seating area. Updates in patient treatment status and medical history were presented in real time without having to move paper charts around. Conclusions: The iPad can be used in clinical activities independent of computer workstations. Improvements in clinical workflow can be critical in reducing physician resistance in data maintenance. Using the iPad in providing real-time quality monitoring is intuitive to both providers and patients.

  9. PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

    Science.gov (United States)

    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/.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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 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.

  12. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila

    Directory of Open Access Journals (Sweden)

    Parrish Jodi R

    2006-04-01

    Full Text Available Abstract Background Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. Description Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes

  13. 3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data.

    Science.gov (United States)

    Li, Ruifeng; Liu, Yifang; Li, Tingting; Li, Cheng

    2016-10-13

    Chromosomal rearrangement (CR) events have been implicated in many tumor and non-tumor human diseases. CR events lead to their associated diseases by disrupting gene and protein structures. Also, they can lead to diseases through changes in chromosomal 3D structure and gene expression. In this study, we search for CR-associated diseases potentially caused by chromosomal 3D structure alteration by integrating Hi-C and ChIP-seq data. Our algorithm rediscovers experimentally verified disease-associated CRs (polydactyly diseases) that alter gene expression by disrupting chromosome 3D structure. Interestingly, we find that intellectual disability may be a candidate disease caused by 3D chromosome structure alteration. We also develop a Web server (3Disease Browser, http://3dgb.cbi.pku.edu.cn/disease/) for integrating and visualizing disease-associated CR events and chromosomal 3D structure.

  14. A Web services-based distributed system with browser-client architecture to promote tele-audiology assessment.

    Science.gov (United States)

    Yao, Jianchu; Givens, Gregg D; Wan, Yongbo

    2009-10-01

    The purpose of this research was to extend applications of the Internet and other telecommunication means to the assessment of hearing. The newly developed distributed system consists primarily of an application server and its database, and Web services under browser-server architecture to support remote hearing assessment. A pilot study was conducted: three independent audiologists assessed hearing of 25 subjects using testing approaches with different data communication configurations. Analysis of the results demonstrated the feasibility of replacing conventional "face-to-face" tests with the remote hearing tests using the distributed system. Because of its distributed architecture, the present system supports a new service model and separates technical maintenance and clinical services. Consequently, the system shows great potential to benefit the clinical hearing care profession. Future research is planned to apply this system to medical facilities and for distance applications.

  15. pWeb: A High-Performance, Parallel-Computing Framework for Web-Browser-Based Medical Simulation.

    Science.gov (United States)

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2014-01-01

    This work presents a pWeb - a new language and compiler for parallelization of client-side compute intensive web applications such as surgical simulations. The recently introduced HTML5 standard has enabled creating unprecedented applications on the web. Low performance of the web browser, however, remains the bottleneck of computationally intensive applications including visualization of complex scenes, real time physical simulations and image processing compared to native ones. The new proposed language is built upon web workers for multithreaded programming in HTML5. The language provides fundamental functionalities of parallel programming languages as well as the fork/join parallel model which is not supported by web workers. The language compiler automatically generates an equivalent parallel script that complies with the HTML5 standard. A case study on realistic rendering for surgical simulations demonstrates enhanced performance with a compact set of instructions.

  16. Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

    Science.gov (United States)

    Lyapin, Sergey; Kukovyakin, Alexey

    Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

  17. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

    Directory of Open Access Journals (Sweden)

    Guillermo Barturen

    2013-01-01

    Full Text Available Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.

  18. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

    Science.gov (United States)

    Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi

    2014-07-01

    For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.

    Science.gov (United States)

    Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, Avi

    2014-11-15

    Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB CONTACT: avi.maayan@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

    Science.gov (United States)

    Barturen, Guillermo; Dios, Francisco; Hamberg, E. J. Maarten; Oliver, José L.

    2013-01-01

    Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website. PMID:24205506

  1. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

    Science.gov (United States)

    Mei, Shenglin; Qin, Qian; Wu, Qiu; Sun, Hanfei; Zheng, Rongbin; Zang, Chongzhi; Zhu, Muyuan; Wu, Jiaxin; Shi, Xiaohui; Taing, Len; Liu, Tao; Brown, Myles; Meyer, Clifford A; Liu, X Shirley

    2017-01-04

    Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser.

    Science.gov (United States)

    Müller, R Dietmar; Qin, Xiaodong; Sandwell, David T; Dutkiewicz, Adriana; Williams, Simon E; Flament, Nicolas; Maus, Stefan; Seton, Maria

    2016-01-01

    The pace of scientific discovery is being transformed by the availability of 'big data' and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org) is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a high-resolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth's gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to stimulate teaching and learning and novel avenues of inquiry.

  3. The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data.

    Science.gov (United States)

    Awale, Mahendra; Reymond, Jean-Louis

    2017-01-01

    Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictions in each case rely on similarities computed from only one or two fps. Considering that structural similarity and therefore the predicted targets strongly depend on the method used for comparison, it would be highly desirable to predict targets using a broader set of fps simultaneously. Herein, we present the polypharmacology browser (PPB), a web-based platform which predicts possible targets for small molecules by searching for nearest neighbors using ten different fps describing composition, substructures, molecular shape and pharmacophores. PPB searches through 4613 groups of at least 10 same target annotated bioactive molecules from ChEMBL and returns a list of predicted targets ranked by consensus voting scheme and p value. A validation study across 670 drugs with up to 20 targets showed that combining the predictions from all 10 fps gives the best results, with on average 50% of the known targets of a drug being correctly predicted with a hit rate of 25%. Furthermore, when profiling a new inhibitor of the calcium channel TRPV6 against 24 targets taken from a safety screen panel, we observed inhibition in 5 out of 5 targets predicted by PPB and in 7 out of 18 targets not predicted by PPB. The rate of correct (5/12) and incorrect (0/12) predictions for this compound by PPB was comparable to that of other web-based prediction tools. PPB offers a versatile platform for target prediction based on multi-fingerprint comparisons, and is freely accessible at www.gdb.unibe.ch as a valuable support for drug discovery.Graphical abstract.

  4. A browser-based 3D Visualization Tool designed for comparing CERES/CALIOP/CloudSAT level-2 data sets.

    Science.gov (United States)

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

    2017-12-01

    In Langley NASA, Clouds and the Earth's Radiant Energy System (CERES) and Moderate Resolution Imaging Spectroradiometer (MODIS) are merged with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat Cloud Profiling Radar (CPR). The CERES merged product (C3M) matches up to three CALIPSO footprints with each MODIS pixel along its ground track. It then assigns the nearest CloudSat footprint to each of those MODIS pixels. The cloud properties from MODIS, retrieved using the CERES algorithms, are included in C3M with the matched CALIPSO and CloudSat products along with radiances from 18 MODIS channels. The dataset is used to validate the CERES retrieved MODIS cloud properties and the computed TOA and surface flux difference using MODIS or CALIOP/CloudSAT retrieved clouds. This information is then used to tune the computed fluxes to match the CERES observed TOA flux. A visualization tool will be invaluable to determine the cause of these large cloud and flux differences in order to improve the methodology. This effort is part of larger effort to allow users to order the CERES C3M product sub-setted by time and parameter as well as the previously mentioned visualization capabilities. This presentation will show a new graphical 3D-interface, 3D-CERESVis, that allows users to view both passive remote sensing satellites (MODIS and CERES) and active satellites (CALIPSO and CloudSat), such that the detailed vertical structures of cloud properties from CALIPSO and CloudSat are displayed side by side with horizontally retrieved cloud properties from MODIS and CERES. Similarly, the CERES computed profile fluxes whether using MODIS or CALIPSO and CloudSat clouds can also be compared. 3D-CERESVis is a browser-based visualization tool that makes uses of techniques such as multiple synchronized cursors, COLLADA format data and Cesium.

  5. The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser.

    Directory of Open Access Journals (Sweden)

    R Dietmar Müller

    Full Text Available The pace of scientific discovery is being transformed by the availability of 'big data' and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a high-resolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth's gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to stimulate teaching and learning and novel avenues of inquiry.

  6. A New Browser-based, Ontology-driven Tool for Generating Standardized, Deep Descriptions of Geoscience Models

    Science.gov (United States)

    Peckham, S. D.; Kelbert, A.; Rudan, S.; Stoica, M.

    2016-12-01

    Standardized metadata for models is the key to reliable and greatly simplified coupling in model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System). This model metadata also helps model users to understand the important details that underpin computational models and to compare the capabilities of different models. These details include simplifying assumptions on the physics, governing equations and the numerical methods used to solve them, discretization of space (the grid) and time (the time-stepping scheme), state variables (input or output), model configuration parameters. This kind of metadata provides a "deep description" of a computational model that goes well beyond other types of metadata (e.g. author, purpose, scientific domain, programming language, digital rights, provenance, execution) and captures the science that underpins a model. While having this kind of standardized metadata for each model in a repository opens up a wide range of exciting possibilities, it is difficult to collect this information and a carefully conceived "data model" or schema is needed to store it. Automated harvesting and scraping methods can provide some useful information, but they often result in metadata that is inaccurate or incomplete, and this is not sufficient to enable the desired capabilities. In order to address this problem, we have developed a browser-based tool called the MCM Tool (Model Component Metadata) which runs on notebooks, tablets and smart phones. This tool was partially inspired by the TurboTax software, which greatly simplifies the necessary task of preparing tax documents. It allows a model developer or advanced user to provide a standardized, deep description of a computational geoscience model, including hydrologic models. Under the hood, the tool uses a new ontology for models built on the CSDMS Standard Names, expressed as a collection of RDF files (Resource Description Framework). This ontology is based on core concepts

  7. Taking advantage of HTML5 browsers to realize the concepts of session state and workflow sharing in web-tool applications

    Science.gov (United States)

    Suftin, I.; Read, J. S.; Walker, J.

    2013-12-01

    Scientists prefer not having to be tied down to a specific machine or operating system in order to analyze local and remote data sets or publish work. Increasingly, analysis has been migrating to decentralized web services and data sets, using web clients to provide the analysis interface. While simplifying workflow access, analysis, and publishing of data, the move does bring with it its own unique set of issues. Web clients used for analysis typically offer workflows geared towards a single user, with steps and results that are often difficult to recreate and share with others. Furthermore, workflow results often may not be easily used as input for further analysis. Older browsers further complicate things by having no way to maintain larger chunks of information, often offloading the job of storage to the back-end server or trying to squeeze it into a cookie. It has been difficult to provide a concept of "session storage" or "workflow sharing" without a complex orchestration of the back-end for storage depending on either a centralized file system or database. With the advent of HTML5, browsers gained the ability to store more information through the use of the Web Storage API (a browser-cookie holds a maximum of 4 kilobytes). Web Storage gives us the ability to store megabytes of arbitrary data in-browser either with an expiration date or just for a session. This allows scientists to create, update, persist and share their workflow without depending on the backend to store session information, providing the flexibility for new web-based workflows to emerge. In the DSASWeb portal ( http://cida.usgs.gov/DSASweb/ ), using these techniques, the representation of every step in the analyst's workflow is stored as plain-text serialized JSON, which we can generate as a text file and provide to the analyst as an upload. This file may then be shared with others and loaded back into the application, restoring the application to the state it was in when the session file

  8. Comparative Analysis of the ABO and Rh CDE Phenotype ...

    African Journals Online (AJOL)

    Data presented in this report further evaluate the distribution and inter-ethnic phenotypic variability of the ABO and Rh blood groups among students of a tertiary institution in Port Harcourt. Standard haemagglutination procedures were used. ABO blood group frequencies were obtained as follows: 23.8% for blood group A, ...

  9. 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

    Science.gov (United States)

    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…

  10. Erratum: Google Earth as Geoscience Data Browser Project: Development of a Tool to Convert JAMSTEC Research Vessel Navigation Data to KML [Data Science Journal, Volume 8, 30 March 2009. S85-S91

    Directory of Open Access Journals (Sweden)

    Y Yamagishi

    2009-07-01

    Full Text Available The following PDF indicates errata for the original article entitled "Google Earth as Geoscience Data Browser Project: Development of a Tool to Convert JAMSTEC Research Vessel Navigation Data to KML" by Y Yamagishi, H Nagao, K Suzuki, H Tamura, T Hatakeyama, H Yanaka and S Tsuboi.

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

    Science.gov (United States)

    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

  12. The GPlates Portal: Cloud-based interactive 3D and 4D visualization of global geological and geophysical data and models in a browser

    Science.gov (United States)

    Müller, Dietmar; Qin, Xiaodong; Sandwell, David; Dutkiewicz, Adriana; Williams, Simon; Flament, Nicolas; Maus, Stefan; Seton, Maria

    2017-04-01

    The pace of scientific discovery is being transformed by the availability of 'big data' and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other, and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org) is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a high-resolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth's gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The portal has been visited over half a million times since its inception in October 2015, as tracked by google analytics, and the globes have been featured in numerous media articles around the world. This demonstrates the high demand for fast visualization of global spatial big data, both for the present-day as well as through geological time. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to

  13. Evaluation of radiological workstations and web-browser-based image distribution clients for a PACS project in hands-on workshops

    International Nuclear Information System (INIS)

    Boehm, Thomas; Handgraetinger, Oliver; Voellmy, Daniel R.; Marincek, Borut; Wildermuth, Simon; Link, Juergen; Ploner, Ricardo

    2004-01-01

    The methodology and outcome of a hands-on workshop for the evaluation of PACS (picture archiving and communication system) software for a multihospital PACS project are described. The following radiological workstations and web-browser-based image distribution software clients were evaluated as part of a multistep evaluation of PACS vendors in March 2001: Impax DS 3000 V 4.1/Impax Web1000 (Agfa-Gevaert, Mortsel, Belgium); PathSpeed V 8.0/PathSpeed Web (GE Medical Systems, Milwaukee, Wis., USA); ID Report/ID Web (Image Devices, Idstein, Germany); EasyVision DX/EasyWeb (Philips Medical Systems, Eindhoven, Netherlands); and MagicView 1000 VB33a/MagicWeb (Siemens Medical Systems, Erlangen, Germany). A set of anonymized DICOM test data was provided to enable direct image comparison. Radiologists (n=44) evaluated the radiological workstations and nonradiologists (n=53) evaluated the image distribution software clients using different questionnaires. One vendor was not able to import the provided DICOM data set. Another vendor had problems in displaying imported cross-sectional studies in the correct stack order. Three vendors (Agfa-Gevaert, GE, Philips) presented server-client solutions with web access. Two (Siemens, Image Devices) presented stand-alone solutions. The highest scores in the class of radiological workstations were achieved by ID Report from Image Devices (p<0.005). In the class of image distribution clients, the differences were statistically not significant. Questionnaire-based evaluation was shown to be useful for guaranteeing systematic assessment. The workshop was a great success in raising interest in the PACS project in a large group of future clinical users. The methodology used in the present study may be useful for other hospitals evaluating PACS. (orig.)

  14. Response to dietary tannin challenges in view of the browser/grazer dichotomy in an Ethiopian setting: Bonga sheep versus Kaffa goats.

    Science.gov (United States)

    Yisehak, Kechero; Kibreab, Yoseph; Taye, Tolemariam; Lourenço, Marta Ribeiro Alves; Janssens, Geert Paul Jules

    2016-01-01

    It has been suggested that goats (typical browser) are better adapted to digest tannin-rich diets than sheep (typical grazer). To evaluate this, Bonga sheep and Kaffa goats were used in a 2 × 3 randomized crossover design with two species, three diets, and three periods (15-day adaptation + 7-day collection). The dietary treatments consisted of grass-based hay only (tannin-free diet = FT), a high-tannin diet (36% Albizia schimperiana (AS) + 9% Ficus elastica (FE) + 55% FT (HT)), and HT + polyethylene glycol 6000 (PEG). Animals were individually fed at 50 g dry matter (DM)/kg body weight (BW) and had free access to clean drinking water and mineralized salt licks. Nutrient intake, apparent nutrient digestibility, nutrient conversion ratios, and live weight changes were determined. Condensed tannin concentrations in AS and FE were 110 and 191 g/kg DM, respectively. Both sheep and goats ate 47% more of HT than FT, and dry matter intake further increased by 9% when PEG was added, with clear difference in effect size between goats and sheep (P tannin-rich diet and PEG addition were similarly positive for DM digestibility between sheep and goats, but crude protein (CP) digestibility was higher in HT + PEG-fed goats than in sheep fed the same diet. However, PEG addition induced a larger improvement in growth performance and feed efficiency ratio in sheep than in goat (P tannin binder improved digestion and performance in both species, but with the highest effect size in sheep.

  15. Comparison of Three Browser Performances

    Directory of Open Access Journals (Sweden)

    Stefanus Lintang Timur Aji Pamungkas

    2014-11-01

    Full Text Available In this era of globalization and modernity, it is important to obtain information, and the role of Internet in providing information is indispensable. The existence of the World Wide Web technology makes it easy for people to surf various websites. The elements on the website are the code javascript, css, and HTML5

  16. Engineering Competencies in International Development Co-operation - the Case of Capacity Development in Environment (CDE)

    DEFF Research Database (Denmark)

    Wangel, Arne

    2001-01-01

    on the transfer of managerial models across cultures, on how to develop inter-cultural competence in management, and on the significance of differences in engineering and industrial culture. Second, the concepts of dynamic assimilation and local learning processes and their implications for the practicing...... assistance provide a wider perspective on the need for new competencies. Funded by the Danish Agency for Environment and Development (DANCED) of the Ministry of Environment and Energy, a consortium of five Danish universities has conducted a series of field courses in Thailand, Malaysia and South Africa...

  17. Intercity Variations in Returns to Migration. CDE Working Paper 84-22.

    Science.gov (United States)

    Wilson, Franklin D.

    This paper explores the following questions: Does the demand/supply allocation process affect the return migrants receive for their human capital attributes? Specifically, do returns to migration vary across places of destination, and does this variation reflect labor supply and demand differentials and/or other characteristics of places of…

  18. CDE Perspectives of Providing New-Onset Type 1 Diabetes Education Using Formal Vignettes and Simulation.

    Science.gov (United States)

    Ramchandani, Neesha; Johnson, Kim; Cullen, Karen; Hamm, Terri; Bisordi, Jean; Sullivan-Bolyai, Susan

    2017-02-01

    Purpose The purpose of this article is to describe the 4 Parent Education Through Simulation-Diabetes (PETS-D) nurse certified diabetes educators' (CDEs) perspectives of teaching parents of children with newly diagnosed type 1 diabetes mellitus (T1DM) early diabetes management skills using formal vignettes and a human patient simulator/human patient simulation (HPS) to augment/enhance the teaching-learning process. Methods A qualitative descriptive approach was used. Four CDEs were interviewed by phone about their teaching experiences. Meticulous notes were taken. Data were analyzed using qualitative content analysis. Results The vignettes (and use of HPS) provided structure, especially for parents who were struggling to learn. Certified diabetes educators described a short learning curve to master the use of the HPS manikin. Human patient simulation-enhanced education was described as helpful for teaching multiple caregivers about diabetes. Certified diabetes educators also described factors that affect parent learning, mechanical issues with the HPS, and additional space requirements for HPS-enhanced education. Conclusion Vignettes and HPS-enhanced education can successfully be used to educate parents of children with new-onset T1DM and were preferred by the CDEs when compared with previous teaching strategies. The results of this study support the use of both vignette-based and HPS-enhanced education when a child is newly diagnosed with T1DM. Further studies need to be done to see if these effects persist with different populations, during different stages of the disease, and for individuals with other chronic illnesses.

  19. 75 FR 44053 - Proposed Collection; Comment Request: CDFI/CDE Project Profiles Web Form

    Science.gov (United States)

    2010-07-27

    ... provide loans, investments, financial services and technical assistance to underserved populations and... DEPARTMENT OF THE TREASURY Community Development Financial Institutions Fund Proposed Collection.... 3506(c)(2)(A). Currently, the Community Development Financial Institutions (CDFI) Fund, Department of...

  20. Enzyme kinetics informatics: From instrument to browser

    OpenAIRE

    Swainston, Neil; Golebiewski, Martin; Messiha, Hanan L.; Malys, Naglis; Kania, Renate; Kengne, Sylvestre; Krebs, Olga; Mir, Saqib; Sauer-Danzwith, Heidrun; Smallbone, Kieran; Weidemann, Andreas; Wittig, Ulrike; Kell, Douglas B.; Mendes, Pedro; Müller, Wolfgang

    2010-01-01

    A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrume...

  1. Adinda : A knowledgeable, browser-based IDE

    NARCIS (Netherlands)

    Van Deursen, A.; Mesbah, A.; Cornelissen, B.; Zaidman, A.; Pinzger, M.; Guzzi, A.

    2010-01-01

    In practice, many people have to work together to develop and maintain a software system. However, the programmer’s key tool, the Integrated Development Environment (IDE), is a solo-tool, serving to help individual programmers understand and modify the system. Such an IDE does not leverage the

  2. Defending against Browser Based Data Exfiltration Attacks

    Science.gov (United States)

    Sood, Aditya

    2013-01-01

    The global nature of Internet has revolutionized cultural and commercial interactions while at the same time it has provided opportunities for cyber criminals. Crimeware services now exist that have transformed the nature of cyber crime by making it more automated and robust. Furthermore, these crimeware services are sold as a part of a growing…

  3. The GLOBE 3D Genome Browser

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); H.J.F.M.M. Eussen (Bert); M.J. Moorhouse (Michael)

    2007-01-01

    textabstractThe combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various

  4. Feicim: A browser for data and algorithms

    International Nuclear Information System (INIS)

    Lazar, Z I; McNulty, R; Kechadi, T

    2008-01-01

    As programming and programming environments become increasingly complex, more effort must be invested in presenting the user with a simple yet comprehensive interface. Feicim is a tool that unifies the representation of data and algorithms. It provides resource discovery of data-files, data-content and algorithm implementation through an intuitive graphical user interface. It allows local or remote data stored on Grid type platforms to be accessed by the users, the viewing and creation of user-defined or collaboration-defined algorithms, the implementation of algorithms, and the production of output data-files and/or histograms. An application of Feicim is illustrated using the LHCb data. It provides a graphical view of the Gaudi architecture, LHCb event data model, and interfaces to the file catalogue. Feicim is particularly suited to such frameworks as Gaudi which consider algorithms as objects [2]. Instant viewing of any LHCb data will be of particular value in the commissioning of the detector and for quickly familiarizing newcomers to the data and software environment

  5. A knowledge base browser using hypermedia

    Science.gov (United States)

    Pocklington, Tony; Wang, Lui

    1990-01-01

    A hypermedia system is being developed to browse CLIPS (C Language Integrated Production System) knowledge bases. This system will be used to help train flight controllers for the Mission Control Center. Browsing this knowledge base will be accomplished either by having navigating through the various collection nodes that have already been defined, or through the query languages.

  6. The Common Data Elements for Cancer Research: Remarks on Functions and Structure

    Science.gov (United States)

    Nadkarni, Prakash M.; Brandt, Cynthia A.

    2010-01-01

    Objectives The National Cancer Institute (NCI) has developed the Common Data Elements (CDE) to serve as a controlled vocabulary of data descriptors for cancer research, to facilitate data interchange and inter-operability between cancer research centers. We evaluated CDE’s structure to see whether it could represent the elements necessary to support its intended purpose, and whether it could prevent errors and inconsistencies from being accidentally introduced. We also performed automated checks for certain types of content errors that provided a rough measure of curation quality. Methods Evaluation was performed on CDE content downloaded via the NCI’s CDE Browser, and transformed into relational database form. Evaluation was performed under three categories: 1) compatibility with the ISO/IEC 11179 metadata model, on which CDE structure is based, 2) features necessary for controlled vocabulary support, and 3) support for a stated NCI goal, set up of data collection forms for cancer research. Results Various limitations were identified both with respect to content (inconsistency, insufficient definition of elements, redundancy) as well as structure – particularly the need for term and relationship support, as well as the need for metadata supporting the explicit representation of electronic forms that utilize sets of common data elements. Conclusions While there are numerous positive aspects to the CDE effort, there is considerable opportunity for improvement. Our recommendations include review of existing content by diverse experts in the cancer community; integration with the NCI thesaurus to take advantage of the latter’s links to nationally used controlled vocabularies, and various schema enhancements required for electronic form support. PMID:17149500

  7. /facet: A browser for heterogeneous semantic web repositories

    NARCIS (Netherlands)

    M. Hildebrand (Michiel); J.R. van Ossenbruggen (Jacco); L. Hardman (Lynda)

    2006-01-01

    textabstractFacet browsing has become popular as a user friendly interface to data repositories. We extend facet browsing of Semantic Web data in four ways. First, users are able to select and navigate through facets of resources of any type and to make selections based on properties of other,

  8. Cytoscape Web: an interactive web-based network browser.

    Science.gov (United States)

    Lopes, Christian T; Franz, Max; Kazi, Farzana; Donaldson, Sylva L; Morris, Quaid; Bader, Gary D

    2010-09-15

    Cytoscape Web is a web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/.

  9. /facet: A Browser for Heterogeneous Semantic Web Repositories

    NARCIS (Netherlands)

    M. Hildebrand (Michiel); J.R. van Ossenbruggen (Jacco); L. Hardman (Lynda)

    2006-01-01

    textabstractFacet browsing has become popular as a user friendly interface to data repositories. The Semantic Web raises new challenges due to the heterogeneous character of the data. First, users should be able to select and navigate through facets of resources of any type and to make selections

  10. The forms open differently in different browsers and in different ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC CRDI

    We challenge proponents to consider creative ways to self-monitor throughout the life of a project and we encourage evaluations that consider issues such as use and practice. e) Our third outcome area is concerned with learning and we encourage proponents to reflect on learning outside of your comfort zone. This does ...

  11. A virtual reality browser for Space Station models

    Science.gov (United States)

    Goldsby, Michael; Pandya, Abhilash; Aldridge, Ann; Maida, James

    1993-01-01

    The Graphics Analysis Facility at NASA/JSC has created a visualization and learning tool by merging its database of detailed geometric models with a virtual reality system. The system allows an interactive walk-through of models of the Space Station and other structures, providing detailed realistic stereo images. The user can activate audio messages describing the function and connectivity of selected components within his field of view. This paper presents the issues and trade-offs involved in the implementation of the VR system and discusses its suitability for its intended purposes.

  12. CS Circles: An In-Browser Python Course for Beginners

    OpenAIRE

    Pritchard, David; Vasiga, Troy

    2012-01-01

    Computer Science Circles is a free programming website for beginners that is designed to be fun, easy to use, and accessible to the broadest possible audience. We teach Python since it is simple yet powerful, and the course content is well-structured but written in plain language. The website has over one hundred exercises in thirty lesson pages, plus special features to help teachers support their students. It is available in both English and French. We discuss the philosophy behind the cour...

  13. OLSVis: an animated, interactive visual browser for bio-ontologies

    Directory of Open Access Journals (Sweden)

    Vercruysse Steven

    2012-07-01

    Full Text Available Abstract Background More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS. Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible. Results We created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.com Conclusions The OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method.

  14. Mouse Resource Browser-a database of mouse databases

    NARCIS (Netherlands)

    Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M.; Schofield, Paul N.; Kollias, George; Aidinis, Vassilis

    2010-01-01

    The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the

  15. Internet Browser for Ice, Weather and Ocean Information

    DEFF Research Database (Denmark)

    Pedersen, Leif Toudal; Saldo, Roberto

    2005-01-01

    Abstract An Internet based distribution system for ice, weather and ocean information has been set up. The system provides near real time access to a large variety of data about the polar environment in a standard user environment. The system is freely available at: http://www.seaice.dk Specific...

  16. Beyond the browser web 2.0 and librarianship

    CERN Document Server

    Bridges, Karl

    2012-01-01

    ""Offering concrete information on how librarians will need to respond to these rapid changes, the title first shares an overview of the history of libraries and the Internet. What follows is an easy-to-read investigation of the impact of second-generation web technologies on library organization and services."" - Library Media Connection

  17. Introgression Browser: High throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Aflitos, S.A.; Sanchez Perez, G.F.; Ridder, de D.; Fransz, P.; Schranz, M.E.; Jong, de J.H.S.G.M.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  18. Introgression browser: high-throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    Alves Aflitos, S.; Sanchez-Perez, G.; de Ridder, D.; Fransz, P.; Schranz, M.E.; de Jong, H.; Peters, S.A.

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  19. Dietary overlap between Boer goats and indigenous browsers in a ...

    African Journals Online (AJOL)

    Highly preferred species were Capparis sepiaria, Phyllanthus verrucosus and Scolopia zeyheri, while Rhoicissus tridentata, Calpurnia aurea, Acacia ataxacantha, Euclea natalensis, Clerodendrum glabrum, Zanthoxylum capense and Hippobromus paucifolia were strongly avoided. Goats fed between ground level and 1m, ...

  20. Now playing in a browser near you: TEDxCERN

    CERN Multimedia

    Katarina Anthony

    2013-01-01

    Earlier this month, CERN played host to one of the hottest, hippest and most educational parties around: TEDx. The event brought together thousands of viewers, speakers and participants from around the world.   The TEDxCERN event was the hottest ticket in town – and those who couldn’t make the event in person turned up online! More than 1,000 TEDxCERN fans watched the event via simulcast at viewing parties held in 27 institutions, but dominating the audience were the 10,870 unique viewers who tuned in to the live webcast, along with over 300 people who joined the webcast from CERN and another 300 watching it live from the Globe of Science and Innovation at CERN. But if you missed the excitement, never fear. Videos of the talks, as well as the clips presented during the talks themselves, are now available online. Just head to the TEDxCERN homepage and catch up! Watch as researcher Maya Tolstoy discusses seafloor earthquakes, Google Science Fair winner Brittany Wengler ...

  1. Anisoft 4.2. – Anisotropy data browser

    Czech Academy of Sciences Publication Activity Database

    Chadima, Martin; Jelínek, V.

    2008-01-01

    Roč. 38, special issue (2008), s. 41-41 ISSN 1335-2806. [Paleo, Rock and Environmental Magnetism. Castle Meeting /11./. 22.06.2008-28.06.2008, Bojnice] R&D Projects: GA AV ČR IAA300130612 Institutional research plan: CEZ:AV0Z30130516 Keywords : anisotropy of magnetic susceptibility * tensor statisticsntation * anisotropy of magnetic remanence Subject RIV: DE - Earth Magnetism, Geodesy, Geography http://gauss.savba.sk/GPIweb/conferences/nt2008/abstr/Chadima-2.pdf

  2. The Multi-Sector Sustainability Browser (MSSB): A Tool for ...

    Science.gov (United States)

    The MSSB is the first and only decision support tool containing information from scientific literature and technical reports that can be used to develop and implement sustainability initiatives. The MSSB is designed to assist individuals and communities in understanding the impacts that the four key dimensions of sustainability - Land Use, Buildings and Infrastructure, Transportation, and Materials Management - can have on human health, the economy, the built environment and natural environments. The MSSB has the following capabilities: a. Displays and describes linkages between the four major sustainability concepts (Land Use, Buildings and Infrastructure, Transportation, and Materials Management) and their subordinate concepts. b. Displays and lists literature sources and references (including weblinks where applicable) providing information about each major sustainability concept and its associated subordinate concepts. c. Displays and lists quantitative data related to each major sustainability concept and its associated subordinate concepts, with weblinks where applicable.The MSSB serves as a ‘visual database’, allowing users to: investigate one or more of the four key sustainability dimensions; explore available scientific literature references, and; assess potential impacts of sustainability activities. The MSSB reduces the amount of time and effort required to assess the state of sustainability science and engineering research pertaining

  3. A Comparative Performance Analysis of Popular Internet Browsers ...

    African Journals Online (AJOL)

    As more and more services become available on the Internet, the issue of fast and secured access to online resources gains more importance. The growth of the internet has encouraged a high number of people to explore and take advantage of the World Wide Web (www). The window to the World Wide Web is a web ...

  4. 4DGeoBrowser: A Web-Based Data Browser and Server for Accessing and Analyzing Multi-Disciplinary Data

    National Research Council Canada - National Science Library

    Lerner, Steven

    2001-01-01

    .... Once the information is loaded onto a Geobrowser server the investigator-user is able to login to the website and use a set of data access and analysis tools to search, plot, and display this information...

  5. Roles of MinC and MinD in the site-specific septation block mediated by the MinCDE system of Escherichia coli.

    OpenAIRE

    de Boer, P A; Crossley, R E; Rothfield, L I

    1992-01-01

    The proper placement of the cell division site in Escherichia coli requires the site-specific inactivation of potential division sites at the cell poles in a process that requires the coordinate action of the MinC, MinD, and MinE proteins. In the absence of MinE, the coordinate expression of MinC and MinD leads to a general inhibition of cell division. MinE gives topological specificity to the division inhibition process, so that the septation block is restricted to the cell poles. At normal ...

  6. There is no A in CD&E, Neither for Analysis nor for Anarchy - Ensuring Scientific Rigour and Analytical Structure while maintaining Military Relevance and Artistic Freedom

    Science.gov (United States)

    2010-04-01

    what constitutes the other extreme of the spectrum, but terms like anti-positivism, interpretivism and phenomenology are frequently used. Somewhere...of the positivist paradigm excludes other paradigms like interpretivism , scientific realism, and pragmatism. Hence, research approaches like...Conversely, it seems likely that paradigms from the social sciences, such as interpretivism , scientific realism, or pragmatism, should be better suited to

  7. Adaptation of the Yeast URA3 Selection System to Gram-Negative Bacteria and Generation of a ΔbetCDE Pseudomonas putida Strain

    OpenAIRE

    Galvão, Teca Calcagno; de Lorenzo, Víctor

    2005-01-01

    A general procedure for efficient generation of gene knockouts in gram-negative bacteria by the adaptation of the Saccharomyces cerevisiae URA3 selection system is described. A Pseudomonas putida strain lacking the URA3 homolog pyrF (encoding orotidine-5′-phosphate decarboxylase) was constructed, allowing the use of a plasmid-borne copy of the gene as the target of selection. The delivery vector pTEC contains the pyrF gene and promoter, a conditional origin of replication (oriR6K), an origin ...

  8. Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements.

    Science.gov (United States)

    Hudson, Cody L; Topaloglu, Umit; Bian, Jiang; Hogan, William; Kieber-Emmons, Thomas

    2014-01-01

    Clinical research data generated by a federation of collection mechanisms and systems often produces highly dissimilar data with varying quality. Poor data quality can result in the inefficient use of research data or can even require the repetition of the performed studies, a costly process. This work presents two tools for improving data quality of clinical research data relying on the National Cancer Institute's Common Data Elements as a standard representation of possible questions and data elements to A: automatically suggest CDE annotations for already collected data based on semantic and syntactic analysis utilizing the Unified Medical Language System (UMLS) Terminology Services' Metathesaurus and B: annotate and constrain new clinical research questions though a simple-to-use "CDE Browser." In this work, these tools are built and tested on the open-source LimeSurvey software and research data analyzed and identified to contain various data quality issues captured by the Comprehensive Research Informatics Suite (CRIS) at the University of Arkansas for Medical Sciences.

  9. Will this work for Susan? Challenges for Delivering Usable and Useful Generic Linked Data Browsers

    OpenAIRE

    schraefel, monica; Smith, Daniel Alexander; Popov, Igor; Van Kleek, Max; Shadbolt, Nigel

    2010-01-01

    While we witness an explosion of exploration tools for simple datasets on Web 2.0 designed for use by ordinary citizens, the goal of a usable interface for supporting navigation and sense-making over arbitrary linked data has remained elusive. The purpose of this paper is to analyse why - what makes exploring linked data so hard? Through a user-centered use case scenario, we work through requirements for sense making with data to extract functional requirements and to compare these against ou...

  10. Webvise: Browser and Proxy support for open hypermedia structuring mechanisms on the WWW

    DEFF Research Database (Denmark)

    Grønbæk, Kaj; Sloth, Lennard; Ørbæk, Peter

    1999-01-01

    This paper discusses how to augment the World Wide Web with an open hypermedia service (Webvise) that provides structures such as contexts, links, annotations, and guided tours stored in hypermedia databases external to the Web pages. This includes the ability for users collaboratively to create...... be manipulated and used via special Java applets and a pure proxy server solution is provided for users who only need to browse the structures. A user can create and use the external structures as ‘transparency' layers on top of arbitrary Web pages, the user can switch between viewing pages with one or more...

  11. Feicim: A browser and analysis tool for distributed data in particle physics

    CERN Document Server

    Mathe, Zoltan

    The Grid was developed to solve large-scale scientific problems by providing access to widearea distributed computing resources. The Grid is used by various communities: high-energy physics, earth observation, biology, etc. LHCb is one of the four Large Hadron Collider (LHC) experiments based at the European Organisation for Nuclear Research (CERN). The LHCb experiment produces a huge amount of data. As a single institution does not have the computing resources to handle this data, Grid computing is adopted to store and process the data. Managing PetaBytes of data in distributed environments provides a large scale of challenges related to performance, reliability and scalability. PetaBytes of data are spread over several Grid sites. The users and applications need an efficient mechanism to locate datasets based on their content, which can be achieved by associating descriptive attributes to these datasets and providing the associated information to the users. A Grid service, called the Metadata Catalogue was ...

  12. QuickGO: a user tutorial for the web-based Gene Ontology browser.

    Science.gov (United States)

    Huntley, Rachael P; Binns, David; Dimmer, Emily; Barrell, Daniel; O'Donovan, Claire; Apweiler, Rolf

    2009-01-01

    The Gene Ontology (GO) has proven to be a valuable resource for functional annotation of gene products. At well over 27 000 terms, the descriptiveness of GO has increased rapidly in line with the biological data it represents. Therefore, it is vital to be able to easily and quickly mine the functional information that has been made available through these GO terms being associated with gene products. QuickGO is a fast, web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. After undergoing a redevelopment, QuickGO is now able to offer many more features beyond simple browsing. Users have responded well to the new tool and given very positive feedback about its usefulness. This tutorial will demonstrate how some of these features could be useful to the researcher wanting to discover more about their dataset, particular areas of biology or to find new ways of directing their research.Database URL:http://www.ebi.ac.uk/QuickGO.

  13. Remote Mobile Health Monitoring System Based on Smart Phone and Browser/Server Structure

    Directory of Open Access Journals (Sweden)

    Yunzhou Zhang

    2015-01-01

    Full Text Available A remote mobile health monitoring system with mobile phone and web service capabilities is proposed in this paper. It provides an end-to-end solution; specifically, (1 physiologic parameters, including respiration rate and heart rate, are measured by wearable sensors and recorded by a mobile phone which presents the graphical interface for the user to observe his/her health status more easily; (2 it provides doctors and family members with necessary data through a web interface and enables authorized personnel to monitor the patient’s condition and to facilitate remote diagnosis; and (3 it supports real-time alarming and positioning services during an urgent situation, such as a tumble or a heart attack, so that unexpected events can be handled in a timely manner. Experimental results show that the proposed system can reliably monitor the physiologic parameters and conveniently report the user’s position.

  14. G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

    Science.gov (United States)

    Kawahara, Yoshihiro; Sakate, Ryuichi; Matsuya, Akihiro; Murakami, Katsuhiko; Sato, Yoshiharu; Zhang, Hao; Gojobori, Takashi; Itoh, Takeshi; Imanishi, Tadashi

    2009-12-15

    G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes. The current version of G-compass allows us to browse two corresponding genomic regions between human and another species in parallel. One-to-one evolutionarily conserved regions (i.e. orthologous regions) between species are highlighted along the genomes. Information such as locations of duplicated regions, copy number variations and mammalian ultra-conserved elements is also provided. These features of G-compass enable us to easily determine patterns of genomic rearrangements and changes in gene orders through evolutionary time. Since G-compass is a satellite database of H-InvDB, which is a comprehensive annotation resource for human genes and transcripts, users can easily refer to manually curated functional annotations and other abundant biological information for each human transcript. G-compass is expected to be a valuable tool for comparing human and model organisms and promoting the exchange of functional information. G-compass is freely available at http://www.h-invitational.jp/g-compass/. t.imanishi@aist.go.jp

  15. Translog, a web browser for studying the expression divergence of homologous genes.

    Science.gov (United States)

    Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris

    2010-01-18

    Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous studies have individually highlighted factors that contribute to the expression divergence of duplicate genes, e.g. promoter changes, exon structure heterogeneity, asymmetric histone modifications and genomic neighborhood conservation. However, there is a lack of a tool to integrate multiple factors and visualize their variety among homologous genes in a straightforward way. We introduce Translog (a web-based tool for Transcriptome comparison of homologous genes) that assists in the comparison of homologous genes by displaying the loci in three different views: promoter view for studying the sharing/turnover of transcription initiations, exon structure for displaying the exon-intron structure changes, and genomic neighborhood to show the macro-synteny conservation in a larger scale. CAGE data for transcription initiation are mapped for each transcript and can be used to study transcription turnover and expression changes. Alignment anchors between homologous loci can be used to define the precise homologous transcripts. We demonstrate how these views can be used to visualize the changes of homologous genes during evolution, particularly after the 2R and 3R whole genome duplication. We have developed a web-based tool for assisting in the transcriptome comparison of homologous genes, facilitating the study of expression divergence.

  16. Surfing the web using browser interface facilities: a performance evaluation approach

    OpenAIRE

    Peña Ortiz, Raúl; Gil Salinas, José Antonio; Sahuquillo Borrás, Julio; Pont Sanjuan, Ana

    2015-01-01

    The user interaction with the current web contents is a major concern when defining web workloads in order to precisely estimate system performance. However, the intrinsic difficulty to represent this dynamic behavior with a workload model has caused that many research studies are still using non representative workloads of the current web navigations. In contrast, in previous works we demonstrated that the use of an accurate workload model which considers user s dynamism when navigating the ...

  17. Gene Expression Browser: Large-Scale and Cross-Experiment Microarray Data Management, Search & Visualization

    Science.gov (United States)

    The amount of microarray gene expression data in public repositories has been increasing exponentially for the last couple of decades. High-throughput microarray data integration and analysis has become a critical step in exploring the large amount of expression data for biological discovery. Howeve...

  18. Nuun: A System for Developing Platform and Browser Independent Arabic Web Applications

    Science.gov (United States)

    2001-09-01

    trend in Arabic web publishing is the use of PDF files. This method may allow for beautifully typeset Arabic documents but is not useful for interactive...Translation systems, eBusiness and Web Mail. Already existing web applications using any standard Arabic encoding can be easily extended to use Nuun

  19. Grasses and browsers reinforce landscape heterogeneity by excluding trees from ecosystem hotspots.

    Science.gov (United States)

    Porensky, Lauren M; Veblen, Kari E

    2012-03-01

    Spatial heterogeneity in woody cover affects biodiversity and ecosystem function, and may be particularly influential in savanna ecosystems. Browsing and interactions with herbaceous plants can create and maintain heterogeneity in woody cover, but the relative importance of these drivers remains unclear, especially when considered across multiple edaphic contexts. In African savannas, abandoned temporary livestock corrals (bomas) develop into long-term, nutrient-rich ecosystem hotspots with unique vegetation. In central Kenya, abandoned corral sites persist for decades as treeless 'glades' in a wooded matrix. Though glades are treeless, areas between adjacent glades have higher tree densities than the background savanna or areas near isolated glades. The mechanisms maintaining these distinctive woody cover patterns remain unclear. We asked whether browsing or interactions with herbaceous plants help to maintain landscape heterogeneity by differentially impacting young trees in different locations. We planted the mono-dominant tree species (Acacia drepanolobium) in four locations: inside glades, far from glades, at edges of isolated glades and at edges between adjacent glades. Within each location, we assessed the separate and combined effects of herbivore exclusion (caging) and herbaceous plant removal (clearing) on tree survival and growth. Both caging and clearing improved tree survival and growth inside glades. When herbaceous plants were removed, trees inside glades grew more than trees in other locations, suggesting that glade soils were favorable for tree growth. Different types of glade edges (isolated vs. non-isolated) did not have significantly different impacts on tree performance. This represents one of the first field-based experiments testing the separate and interactive effects of browsing, grass competition and edaphic context on savanna tree performance. Our findings suggest that, by excluding trees from otherwise favorable sites, both herbaceous plants and herbivores help to maintain functionally important landscape heterogeneity in African savannas.

  20. Usability of Browser-Based Tools for Web-Search Privacy

    Science.gov (United States)

    2010-03-01

    favorite composer? — Ludwig Von Beethoven Who wrote “The Crucible”? — Arthur Miller Who wrote the book, “Dr. Jekyll and Mr. Hyde”? — Robert Louis Steven...presents the study design, and Section 6 presents the results. We draw conclusions in Section 7. 2 Related Work Clark, van Oorschot, and Adams [1...likely to be the easiest way for most people to get started on using TPTV. 5 User-Study Design Clark, van Oorschot, and Adams [1] identify the following

  1. The Use of Internet Resources and Browser-Based Virtual Worlds in Teaching Grammar

    Science.gov (United States)

    Kruk, Mariusz

    2014-01-01

    Online virtual worlds are becoming important tools in foreign/second language instruction in view of the fact that they enhance learner motivation, promote autonomy and social presence in a 3D environment. Virtual worlds are a type of reality in which students can meet and communicate with other learners in the target language using text, voice or…

  2. Nuun: A System for Developing Platform and Browser Independent Arabic Web Applications

    National Research Council Canada - National Science Library

    Habash, Nizar Y

    2001-01-01

    .... Arabic web applications are far from this state of ubiquitous support. Full support is available only under Arabic Windows, while little support is provided under other versions of Windows, and no support at all under UNIX systems...

  3. Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets.

    Directory of Open Access Journals (Sweden)

    Ilya Belevich

    2016-01-01

    Full Text Available Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.

  4. Ancillary Resistor Leads to Sparse Glitches: an Extra Approach to Avert Hacker Using Syndicate Browser Design

    OpenAIRE

    Pendlimarri, Devaki; Petlu, Paul Bharath Bhushan

    2012-01-01

    After the invention of internet most of the people all over the world have become a fan of it because of its vast exploitation for information exchange, e-mail, e-commerce etc. for their easy leading of life. On the other side, may be equally or less/more, many people are also using it for the purpose of hacking the information which is being communicated. Because, the data/information that is being communicated through the internet is via an unsecured networks. This gives breaches to the hac...

  5. BIOME: A scientific data archive search-and-order system using browser-aware, dynamic pages

    Science.gov (United States)

    Jennings, S. V.; Yow, T. G.; Ng, V. W.

    1997-01-01

    The Oak Ridge National Laboratory's (ORNL) Distributed Active Archive Center (DAAC) is a data archive and distribution center for the National Air and Space Administration's (NASA) Earth Observing System Data and Information System (EOSDIS). Both the Earth Observing System (EOS) and EOSDIS are components of NASA's contribution to the US Global Change Research Program through its Mission to Planet Earth Program. The ORNL DAAC provides access to data used in ecological and environmental research such as global change, global warming, and terrestrial ecology. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC has developed the Biogeochemical Information Ordering Management Environment (BIOME), a customized search and order system for the World Wide Web (WWW). BIOME is a public system located at http://www-eosdis. ornl.gov/BIOME/biome.html.

  6. BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

    Science.gov (United States)

    Di, Lia; Pagan, Pedro E; Packer, Daniel; Martin, Che L; Akther, Saymon; Ramrattan, Girish; Mongodin, Emmanuel F; Fraser, Claire M; Schutzer, Steven E; Luft, Benjamin J; Casjens, Sherwood R; Qiu, Wei-Gang

    2014-07-03

    The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes. We have developed BorreliaBase, an online database for comparative browsing of Borrelia genomes. The database is currently populated with sequences from 35 genomes of eight Lyme-borreliosis (LB) group Borrelia species and 7 Relapsing-fever (RF) group Borrelia species. Distinct from genome repositories and aggregator databases, BorreliaBase serves manually curated comparative-genomic data including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic spacers. With a genome phylogeny at its center, BorreliaBase allows online identification of hypervariable lipoprotein genes, potential regulatory elements, and recombination footprints by providing evolution-based expectations of sequence variability at each genomic locus. The phylo-centric design of BorreliaBase (http://borreliabase.org) is a novel model for interactive browsing and comparative analysis of bacterial genomes online.

  7. User-interactive sediment budgets in a browser: A web application for river science and management

    Science.gov (United States)

    Sibley, David M.; Topping, David; Hines, Megan K.; Garner, Bradley D.

    2015-01-01

    Decision-support tools providing accurate, near-real-time data and user-friendly interactive visualizations are of critical value to resource managers tasked with planning and carrying out management programs in their domain. Creating a system to continuously aggregate datasets and recompute derived values is difficult and error-prone when attempted by hand. To address this need for river managers in support of sediment budgeting, we have created a web-based, open source suite of tools and processes that 1) continually aggregate data of interest, 2) recompute derived values based upon latest available data, and 3) update visualizations on-demand, providing simple front-end tools available to resource managers and the public. For the first time, engineers and scientists can access these tools freely over the web to assist them with planning and adaptive management decisions.

  8. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser.

    Science.gov (United States)

    Walsh, Thomas P; Webber, Caleb; Searle, Stephen; Sturrock, Shane S; Barton, Geoffrey J

    2008-07-01

    SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance. This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks. Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases. A web server developed to run SCANPS searches is now available at http://www.compbio.dundee.ac.uk/www-scanps. The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains. The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly. For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.

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

    Science.gov (United States)

    2014-01-01

    casual web developer. Technically, this is the fifth-generation HTML specification, or HTML5 . But...there is often confusion when using this term (see page 8 of “Tracing the History of HTML5 ” in Jacob Seidelin’s book HTML5 Games). Here we simply...use HTML to refer to this latest version. 1Seidelin, J. HTML5 Games; John Wiley & Sons, Inc.: Hoboken, NJ, 2012. 2Parisi, T. WebGL Up and Running

  10. A Web Browser Interface to Manage the Searching and Organizing of Information on the Web by Learners

    Science.gov (United States)

    Li, Liang-Yi; Chen, Gwo-Dong

    2010-01-01

    Information Gathering is a knowledge construction process. Web learners make a plan for their Information Gathering task based on their prior knowledge. The plan is evolved with new information encountered and their mental model is constructed through continuously assimilating and accommodating new information gathered from different Web pages. In…

  11. Developing as new search engine and browser for libraries to search and organize the World Wide Web library resources

    OpenAIRE

    Sreenivasulu, V.

    2000-01-01

    Internet Granthalaya urges world wide advocates and targets at the task of creating a new search engine and dedicated browseer. Internet Granthalaya may be the ultimate search engine exclusively dedicated for every library use to search and organize the world wide web libary resources

  12. The Relative Concentrations of Nutrients and Toxins Dictate Feeding by a Vertebrate Browser, the Greater Glider Petauroides volans.

    Directory of Open Access Journals (Sweden)

    Lora M Jensen

    Full Text Available Although ecologists believe that vertebrate herbivores must select a diet that allows them to meet their nutritional requirements, while avoiding intoxication by plant secondary metabolites, this is remarkably difficult to show. A long series of field and laboratory experiments means that we have a good understanding of the factors that affect feeding by leaf-eating marsupials. This knowledge and the natural intraspecific variation in Eucalyptus chemistry allowed us to test the hypothesis that the feeding decisions of greater gliders (Petauroides volans depend on the concentrations of available nitrogen (incorporating total nitrogen, dry matter digestibility and tannins and of formylated phloroglucinol compounds (FPCs, potent antifeedants unique to Eucalyptus. We offered captive greater gliders foliage from two species of Eucalyptus, E. viminalis and E. melliodora, which vary naturally in their concentrations of available nitrogen and FPCs. We then measured the amount of foliage eaten by each glider and compared this with our laboratory analyses of foliar total nitrogen, available nitrogen and FPCs for each tree offered. The concentration of FPCs was the main factor that determined how much gliders ate of E. viminalis and E. melliodora, but in gliders fed E. viminalis the concentration of available nitrogen was also a significant influence. In other words, greater gliders ate E. viminalis leaves with a particular combination of FPCs and available nitrogen that maximised the nutritional gain but minimised their ingestion of toxins. In contrast, the concentration of total nitrogen was not correlated with feeding. This study is among the first to empirically show that browsing herbivores select a diet that balances the potential gain (available nutrients and the potential costs (plant secondary chemicals of eating leaves. The major implication of the study is that it is essential to identify the limiting nutrients and relevant toxins in a system in order to understand feeding behaviour.

  13. TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database

    OpenAIRE

    Lopez, Fabrice; Textoris, Julien; Bergon, Aurélie; Didier, Gilles; Remy, Elisabeth; Granjeaud, Samuel; Imbert, Jean; Nguyen, Catherine; Puthier, Denis

    2008-01-01

    BACKGROUND: As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. METHODOLOGY: We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested...

  14. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

    Directory of Open Access Journals (Sweden)

    Fabrice Lopez

    Full Text Available BACKGROUND: As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. METHODOLOGY: We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484. This approach led to the definition of 18,250 transcriptional signatures (TS that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%. We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/. User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs or associated with a set of functional terms. CONCLUSIONS/SIGNIFICANCE: As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.

  15. The Browser War: An Ethical Analysis of the Struggle between Microsoft and the U.S. Department of Justice.

    Science.gov (United States)

    Meier, Dennis

    1999-01-01

    Examines two ethical questions regarding the ongoing antitrust battle between the U.S. Department of Justice and Microsoft Corporation using traditional rights-based ethical theory, utilitarianism, and John Rawls's principles of justice. Concludes that it is neither good nor fair for a company having a near-monopoly over a market to sell products…

  16. The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

    Science.gov (United States)

    Vandervalk, Ben; McCarthy, E Luke; Cruz-Toledo, José; Klein, Artjom; Baker, Christopher J O; Dumontier, Michel; Wilkinson, Mark D

    2013-04-05

    The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies.

  17. Backboards and Browsers: A Qualitative Examination of Division I Student-Athlete Experiences in Online Learning Environments

    Science.gov (United States)

    Healy, Jonathan

    2013-01-01

    This research explored the experiences of student-athletes in online education. Interviews were conducted with scholarship student-athletes enrolled at a Bowl Championship Series level, Division I institution. Participants had completed at least one online course while actively participating in their sport. A conceptual framework was developed to…

  18. Browser App Approach: Can It Be an Answer to the Challenges in Cross-Platform App Development?

    Science.gov (United States)

    Huynh, Minh; Ghimire, Prashant

    2017-01-01

    Aim/Purpose: As smartphones proliferate, many different platforms begin to emerge. The challenge to developers as well as IS [Information Systems] educators and students is how to learn the skills to design and develop apps to run on cross-platforms. Background: For developers, the purpose of this paper is to describe an alternative to the complex…

  19. Detecting domestic violence: Showcasing a knowledge browser based on formal concept analysis and emergent self organizing maps

    NARCIS (Netherlands)

    Elzinga, P.; Poelmans, J.; Viaene, S.; Dedene, G.; Cordeiro, J.; Filipe, J.

    2009-01-01

    Over 90% of the case data from police inquiries is stored as unstructured text in police databases. We use the combination of Formal Concept Analysis and Emergent Self Organizing Maps for exploring a dataset of unstructured police reports out of the Amsterdam-Amstelland police region in the

  20. Design and Implementation of English for Academic Purpose Online Learning System Based on Browser/Server Framework

    Directory of Open Access Journals (Sweden)

    Yan Gong

    2018-03-01

    Full Text Available Today, with the rapid development of the information age, the education reform tends to be internationalized. The tertiary-level EFL education in colleges and universities has also changed its original model with focuses on cultivating gen-eral-purpose linguistic skills to one on students' English for Academic Purpose (EAP. EAP English instruction has been vigorously popularized in research-based universities. To achieve the informationized and standardized management for EAP English instruction work in the universities, in this paper, we design and develop a EAP English online learning system with B / S as the system develop-ment framework by which the system's overall functions are designed. MySQL is chosen as a database development tool used to implement the main object mod-ule, while JSP technology is used to support the cross-platform mechanism in order to access to diversified data sources. It is proved by the test on system op-eration that this system features operability, easy to use and maintain, and enables to meet the needs of university students for EAP English learning and teaching management, improves the students’ EAP English learning model and efficiency.

  1. Native and domestic browsers and grazers reduce fuels, fire temperatures, and acacia ant mortality in an African savanna.

    Science.gov (United States)

    Kimuyu, Duncan M; Sensenig, Ryan L; Riginos, Corinna; Veblen, Kari E; Young, Truman P

    2014-06-01

    Despite the importance of fire and herbivory in structuring savanna systems, few replicated experiments have examined the interactive effects of herbivory and fire on plant dynamics. In addition, the effects of fire on associated ant-tree mutualisms have been largely unexplored. We carried out small controlled burns in each of 18 herbivore treatment plots of the Kenya Long-term Exclosure Experiment (KLEE), where experimentally excluding elephants has resulted in 42% greater tree densities. The KLEE design includes six different herbivore treatments that allowed us to examine how different combinations of megaherbivore wildlife, mesoherbivore wildlife, and cattle affect fire temperatures and subsequent loss of ant symbionts from Acacia trees. Before burning, we quantified herbaceous fuel loads and plant community composition. We tagged all trees, measured their height and basal diameter, and identified the resident ant species on each. We recorded weather conditions during the burns and used ceramic tiles painted with fire-sensitive paints to estimate fire temperatures at different heights and in different microsites (under vs. between trees). Across all treatments, fire temperatures were highest at 0-50 cm off the ground and hotter in the grass under trees than in the grassy areas between trees. Plots with more trees burned hotter than plots with fewer trees, perhaps because of greater fine woody debris. Plots grazed by wildlife and by cattle prior to burning had lower herbaceous fuel loads and experienced lower burn temperatures than ungrazed plots. Many trees lost their ant colonies during the burns. Ant survivorship differed by ant species and at the plot level was positively associated with previous herbivory (and lower fire temperatures). Across all treatments, ant colonies on taller trees were more likely to survive, but even some of the tallest trees lost their ant colonies. Our study marks a significant step in understanding the mechanisms that underlie the interactions between fire and herbivory in savanna ecosystems.

  2. Beyond Continuous Delivery: An Empirical Investigation of Continuous Deployment Challenges

    DEFF Research Database (Denmark)

    Shahin, Mojtaba; Ali Babar, Muhammad; Zahedi, Mansooreh

    2017-01-01

    Context: A growing number of software organizations have been adopting Continuous DElivery (CDE) and Continuous Deployment (CD) practices. Researchers have started investing significant efforts in studying different aspects of CDE and CD. Many studies refer to CDE (i.e., where an application is p...

  3. SINGLE VERSUS MULTIPLE TRIAL VECTORS IN CLASSICAL DIFFERENTIAL EVOLUTION FOR OPTIMIZING THE QUANTIZATION TABLE IN JPEG BASELINE ALGORITHM

    Directory of Open Access Journals (Sweden)

    B Vinoth Kumar

    2017-07-01

    Full Text Available Quantization Table is responsible for compression / quality trade-off in baseline Joint Photographic Experts Group (JPEG algorithm and therefore it is viewed as an optimization problem. In the literature, it has been found that Classical Differential Evolution (CDE is a promising algorithm to generate the optimal quantization table. However, the searching capability of CDE could be limited due to generation of single trial vector in an iteration which in turn reduces the convergence speed. This paper studies the performance of CDE by employing multiple trial vectors in a single iteration. An extensive performance analysis has been made between CDE and CDE with multiple trial vectors in terms of Optimization process, accuracy, convergence speed and reliability. The analysis report reveals that CDE with multiple trial vectors improves the convergence speed of CDE and the same is confirmed using a statistical hypothesis test (t-test.

  4. Study of the K K{pi} meson resonances produced in antiproton proton annihilations at 750 MeV/c; Estudio de resonancias mesonicas en el sistema KK{pi} en aniquilaciones de antiprotones a 750 MeV/cde momento

    Energy Technology Data Exchange (ETDEWEB)

    Gil Lopez, E.

    1977-07-01

    In this work we present an analysis of the antiproton proton annihilations into strange particles at 700 and 750 MeV/c, restricted to the four and five body final states. We study in detail the resonances decaying into the K K{pi}; system, in particular the D and E mesons. For the D meson we present a determination of i ts mass, width, isospin, G-parity, C-parity and spin. For the E meson we present parametrizations of the complete final state which decrease its statistical significance in this type of production. (Author)

  5. A flow chart for the classification of igneous rocks in HTML — Is a web browser another way for teaching earth sciences?

    Science.gov (United States)

    Thum, Irmund

    1998-06-01

    The hypertext mark-up language (HTML) is a mark-up system used to create hypertext documents in use by the world-wide web (WWW). A flow chart for the classification of igneous rocks was written in HTML 3.2, a specification conforming to International Standard ISO 8879. HTML is ideal in teaching earth sciences on the Internet due to step by step nature of the classification of rocks because it is relatively straightforward to develop a series of graphically rich Web pages. The flow chart makes wide use of link techniques for references and terminology. As an essential result of the step by step technique, as proposed by the Recommendations of the International Union of Geological Sciences Subcommission on the Systematics of Igneous Rocks, the user should be able to classify any rock specimen with an appropriate nomenclature. Interested readers can download this software at the FTP-site from the server FTP.IAMG.ORG.

  6. The Kinzua Quality Deer Cooperative: can adaptive management and local stakeholder engagement sustain reduced impact of ungulate browsers in forest systems?

    Science.gov (United States)

    Susan L. Stout; Alejandro A. Royo; David S. deCalesta; Kevin McAleese; James C. Finley

    2013-01-01

    The Kinzua Quality Deer Cooperative (KQDC) was established in 2000 to test new approaches to stewardship of white-tailed deer and forest habitat on a 30 000 hectare landscape in northwest Pennsylvania, USA. Partners included land managers, scientists, educators, tourism promoters,and hunters. KQDC goals were adaptive management of the deer herd, improved habitat...

  7. Psychophysics in a Web browser? Comparing response times collected with JavaScript and Psychophysics Toolbox in a visual search task.

    Science.gov (United States)

    de Leeuw, Joshua R; Motz, Benjamin A

    2016-03-01

    Behavioral researchers are increasingly using Web-based software such as JavaScript to conduct response time experiments. Although there has been some research on the accuracy and reliability of response time measurements collected using JavaScript, it remains unclear how well this method performs relative to standard laboratory software in psychologically relevant experimental manipulations. Here we present results from a visual search experiment in which we measured response time distributions with both Psychophysics Toolbox (PTB) and JavaScript. We developed a methodology that allowed us to simultaneously run the visual search experiment with both systems, interleaving trials between two independent computers, thus minimizing the effects of factors other than the experimental software. The response times measured by JavaScript were approximately 25 ms longer than those measured by PTB. However, we found no reliable difference in the variability of the distributions related to the software, and both software packages were equally sensitive to changes in the response times as a result of the experimental manipulations. We concluded that JavaScript is a suitable tool for measuring response times in behavioral research.

  8. A simple method for estimating the convectiondispersion equation ...

    African Journals Online (AJOL)

    The convection-dispersion equation (CDE) is the classical approach for modeling solute transport in porous media. So, estimating parameters became a key problem in CDE. For statistical method, some problems such as parameter uniqueness are still unsolved because of more factors. Due to the advantage of clear ...

  9. Oxydative stress in rats caused by coal dust plus cigarette smoke

    Directory of Open Access Journals (Sweden)

    Nia Kania

    2016-02-01

    Full Text Available Coal dust and cigarette smoke are pollutants found in coal mines that are capable of inducing oxidative stress, the effects of which on blood malondialdehyde (MDA level and serum superoxide dismutase (SOD level are still unknown. The purpose of the present study was to evaluate the effect of coal dust and cigarette smoke on levels of MDA and SOD in rats. An experimental study was done on Wistar male rats divided into the following groups: control (C, coal dust exposure (14 days (CDE, cigarette smoke exposure (14 days (CSE, coal dust exposure (7 days followed by cigarette smoke exposure (7 days (CDE+CSE, cigarette smoke exposure (7 days followed by coal dust exposure (7 days (CSE+CDE. All exposures increased MDA levels and decreased SOD activity significantly between groups (p=0.000. All exposure groups had significantly increased blood MDA levels, compared to the control group, although there was no difference between CSE + CDE and CDE + CSE. For SOD levels, all exposure groups had significantly decreased the SOD levels compared to control. But there were no significant differences between CSE vs CDE and CDE + CSE vs CSE + CDE. We conclude that exposure to cigarette smoke significantly increases blood MDA level and decreases serum SOD activity, which was not found in exposure to coal dust. Combined exposures also increase blood MDA level and decrease serum SOD activity significantly.

  10. Oxydative stress in rats caused by coal dust plus cigarette smoke

    Directory of Open Access Journals (Sweden)

    Nia Kania

    2011-08-01

    Full Text Available Coal dust and cigarette smoke are pollutants found in coal mines that are capable of inducing oxidative stress, the effects of which on blood malondialdehyde (MDA level and serum superoxide dismutase (SOD level are still unknown. The purpose of the present study was to evaluate the effect of coal dust and cigarette smoke on levels of MDA and SOD in rats. An experimental study was done on Wistar male rats divided into the following groups: control (C, coal dust exposure (14 days (CDE, cigarette smoke exposure (14 days (CSE, coal dust exposure (7 days followed by cigarette smoke exposure (7 days (CDE+CSE, cigarette smoke exposure (7 days followed by coal dust exposure (7 days (CSE+CDE. All exposures increased MDA levels and decreased SOD activity significantly between groups (p=0.000. All exposure groups had significantly increased blood MDA levels, compared to the control group, although there was no difference between CSE + CDE and CDE + CSE. For SOD levels, all exposure groups had significantly decreased the SOD levels compared to control. But there were no significant differences between CSE vs CDE and CDE + CSE vs CSE + CDE. We conclude that exposure to cigarette smoke significantly increases blood MDA level and decreases serum SOD activity, which was not found in exposure to coal dust. Combined exposures also increase blood MDA level and decrease serum SOD activity significantly.

  11. An Observational Analysis of Coaching Behaviors for Career Development Event Teams: A Mixed Methods Study

    Science.gov (United States)

    Ball, Anna L.; Bowling, Amanda M.; Sharpless, Justin D.

    2016-01-01

    School Based Agricultural Education (SBAE) teachers can use coaching behaviors, along with their agricultural content knowledge to help their Career Development Event (CDE) teams succeed. This mixed methods, collective case study observed three SBAE teachers preparing multiple CDEs throughout the CDE season. The teachers observed had a previous…

  12. SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent.

    Science.gov (United States)

    Vignes, Matthieu; Blanchet, Juliette; Leroux, Damien; Forbes, Florence

    2011-03-15

    Among classical methods for module detection, SpaCEM(3) provides ad hoc algorithms that were shown to be particularly well adapted to specific features of biological data: high-dimensionality, interactions between components (genes) and integrated treatment of missingness in observations. The software, currently in its version 2.0, is developed in C++ and can be used either via command line or with the GUI under Linux and Windows environments. The SpaCEM(3) software, a documentation and datasets are available from http://spacem3.gforge.inria.fr/.

  13. Hygroscopicity of secondary organic aerosols formed by oxidation of cycloalkenes, monoterpenes, sesquiterpenes, and related compounds

    Directory of Open Access Journals (Sweden)

    V. Varutbangkul

    2006-01-01

    Full Text Available A series of experiments has been conducted in the Caltech indoor smog chamber facility to investigate the water uptake properties of aerosol formed by oxidation of various organic precursors. Secondary organic aerosol (SOA from simple and substituted cycloalkenes (C5-C8 is produced in dark ozonolysis experiments in a dry chamber (RH~5%. Biogenic SOA from monoterpenes, sesquiterpenes, and oxygenated terpenes is formed by photooxidation in a humid chamber (~50% RH. Using the hygroscopicity tandem differential mobility analyzer (HTDMA, we measure the diameter-based hygroscopic growth factor (GF of the SOA as a function of time and relative humidity. All SOA studied is found to be slightly hygroscopic, with smaller water uptake than that of typical inorganic aerosol substances. The aerosol water uptake increases with time early in the experiments for the cycloalkene SOA, but decreases with time for the sesquiterpene SOA. This behavior could indicate competing effects between the formation of more highly oxidized polar compounds (more hygroscopic, and formation of longer-chained oligomers (less hygroscopic. All SOA also exhibit a smooth water uptake with RH with no deliquescence or efflorescence. The water uptake curves are found to be fitted well with an empirical three-parameter functional form. The measured pure organic GF values at 85% RH are between 1.09–1.16 for SOA from ozonolysis of cycloalkenes, 1.01–1.04 for sesquiterpene photooxidation SOA, and 1.06–1.10 for the monoterpene and oxygenated terpene SOA. The GF of pure SOA (GForg in experiments in which inorganic seed aerosol is used is determined by assuming volume-weighted water uptake (Zdanovskii-Stokes-Robinson or 'ZSR' approach and using the size-resolved organic mass fraction measured by the Aerodyne Aerosol Mass Spectrometer. Knowing the water content associated with the inorganic fraction yields GForg values. However, for each precursor, the GForg values computed from different

  14. Chemical composition, antioxidant properties and hepatoprotective effects of chamomile (Matricaria recutita L.) decoction extract against alcohol-induced oxidative stress in rat.

    Science.gov (United States)

    Sebai, Hichem; Jabri, Mohamed-Amine; Souli, Abdelaziz; Hosni, Karim; Rtibi, Kais; Tebourbi, Olfa; El-Benna, Jamel; Sakly, Mohsen

    2015-07-01

    The present study assessed the chemical composition, antioxidant properties, and hepatoprotective effects of subacute pre-treatment with chamomile (Matricaria recutita L.) decoction extract (CDE) against ethanol (EtOH)-induced oxidative stress in rats. The colorimetric analysis demonstrated that the CDE is rich in total polyphenols, total flavonoids and condensed tannins, and exhibited an important in vitro antioxidant activity. The use of LC/MS technique allowed us to identify 10 phenolic compounds in CDE. We found that CDE pretreatment, in vivo, protected against EtOH-induced liver injury evident by plasma transaminases activity and preservation of the hepatic tissue structure. The CDE counteracted EtOH-induced liver lipoperoxidation, preserved thiol -SH groups and prevented the depletion of antioxidant enzyme activity of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx). We also showed that acute alcohol administration increased tissue and plasma hydrogen peroxide (H(2)O(2)), calcium and free iron levels. More importantly, CDE pre-treatment reversed all EtOH-induced disturbances in intracellular mediators. In conclusion, our data suggest that CDE exerted a potential hepatoprotective effect against EtOH-induced oxidative stress in rat, at least in part, by negatively regulating Fenton reaction components such as H(2)O(2) and free iron, which are known to lead to cytotoxicity mediated by intracellular calcium deregulation.

  15. A modified choline-deficient, ethionine-supplemented diet reduces morbidity and retains a liver progenitor cell response in mice

    Directory of Open Access Journals (Sweden)

    Adam M. Passman

    2015-12-01

    Full Text Available The choline-deficient, ethionine-supplemented (CDE dietary model induces chronic liver damage, and stimulates liver progenitor cell (LPC-mediated repair. Long-term CDE administration leads to hepatocellular carcinoma in rodents and lineage-tracing studies show that LPCs differentiate into functional hepatocytes in this model. The CDE diet was first modified for mice by our laboratory by separately administering choline-deficient chow and ethionine in the drinking water (CD+E diet. Although this CD+E diet is widely used, concerns with variability in weight loss, morbidity, mortality and LPC response have been raised by researchers who have adopted this model. We propose that these inconsistencies are due to differential consumption of chow and ethionine in the drinking water, and that incorporating ethionine in the choline-deficient chow, and altering the strength, will achieve better outcomes. Therefore, C57Bl/6 mice, 5 and 6 weeks of age, were fed an all-inclusive CDE diet of various strengths (67% to 100% for 3 weeks. The LPC response was quantitated and cell lines were derived. We found that animal survival, LPC response and liver damage are correlated with CDE diet strength. The 67% and 75% CDE diet administered to mice older than 5 weeks and greater than 18 g provides a consistent and acceptable level of animal welfare and induces a substantial LPC response, permitting their isolation and establishment of cell lines. This study shows that an all-inclusive CDE diet for mice reproducibly induces an LPC response conducive to in vivo studies and isolation, whilst minimizing morbidity and mortality.

  16. IDRC Login

    International Development Research Centre (IDRC) Digital Library (Canada)

    JavaScript required. JavaScript is required. This web browser does not support JavaScript or JavaScript in this web browser is not enabled. To find out if your web browser supports JavaScript or to enable JavaScript, see web browser help. IDRC. Sign in with your organizational account. Keep me signed in. Sign in.

  17. A pneumatic bellows-driven setup for controlled-distance electrochemical impedance measurements of Zircaloy-2 in simulated BWR conditions

    International Nuclear Information System (INIS)

    Arilahti, E.; Bojinov, M.; Hansson-Lyyra, L.

    2004-01-01

    This paper describes a novel pneumatic bellows-driven arrangement designed for controlled distance electrochemistry (CDE) measurements. The feasibility of the new arrangement has been verified by performing contact electric impedance measurements to study corrosion of Zircaloy-2 in a re-circulation loop simulating the BWR conditions. Until now, the measurements have been carried out using a step-motor driven controlled-distance electrochemistry (CDE) arrangement. The electrical and electrochemical properties of the pre transition oxide on Zircaloy-2 determined from these measurements were in good agreement with those estimated from measurements with a step-motor driven CDE. Furthermore, the results indicate that the bellows-driven CDE device is less sensitive to the contact pressure variation than the step-motor driven arrangement. This property combined with the bellows driven displacement mechanism provides a clear advantage for future in-core corrosion studies of fuel cladding materials. (Author)

  18. NIH Common Data Elements Repository

    Data.gov (United States)

    U.S. Department of Health & Human Services — The NIH Common Data Elements (CDE) Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have...

  19. A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer: PV: A genome browser-like tool, which includes MS data visualization and peptide identification parameters.

    Science.gov (United States)

    Kroll, José Eduardo; da Silva, Vandeclécio Lira; de Souza, Sandro José; de Souza, Gustavo Antonio

    2017-07-01

    In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry-based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non-coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation. Also see the video abstract here: http://youtu.be/5NzyRvuk4Ac. © 2017 WILEY Periodicals, Inc.

  20. Multi-Sector Sustainability Browser (MSSB) User Manual: A Decision Support Tool (DST) for Supporting Sustainability Efforts in Four Areas - Land Use, Transportation, Buildings and Infrastructure, and Materials Management

    Science.gov (United States)

    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 affecti...

  1. Proteolytic activity in cowshed dust extracts induces C5a release in murine bronchoalveolar lavage fluids which may account for its protective properties in allergic airway inflammation.

    Science.gov (United States)

    Stiehm, Matthias; Bufe, Albrecht; Peters, Marcus

    2013-01-01

    Intranasal application of cowshed dust extract (CDE) during sensitisation in a murine model of experimental asthma leads to a significant alleviation of the clinical parameters of the allergic immune response. However, neither the immunological mechanisms underlying this protective effect nor all of the protective substances included in CDE have yet been described. Recently, complement factor 5a (C5a) receptor signalling has been identified to play a regulatory role in allergic airway disease. Thus we investigated whether CDE can activate the complement system to release biologically active C5a in the lung. Proteins included in CDE were identified by mass spectrometry. Complement cleaving activity of a serine protease identified in CDE was validated with the purified enzyme, and the biological activity of the released C5a was determined. C5a was applied in a murine model of allergy to prove its protective impact on allergic airway disease. CDE induced the release of C5a in murine bronchoalveolar lavages (BAL). We identified a serine protease from the midgut of tenebrio molitor larvae in CDEs which was able to induce the release of biologically active C5a in murine BAL. We applied C5a in different doses to female Balb/c mice during the sensitisation phase and during the first antigen challenge and showed that C5a has the ability to dampen important parameters of allergic airway inflammation, such as infiltration of proinflammatory cells into lung tissue or Th2 cytokine secretion by lung cells. We conclude that the C5a generating enzyme included in CDE might account for some of the allergy protective effects of CDE by generation of C5a in murine lungs.

  2. Chamomile (Matricaria recutita L.) decoction extract inhibits in vitro intestinal glucose absorption and attenuates high fat diet-induced lipotoxicity and oxidative stress.

    Science.gov (United States)

    Jabri, Mohamed-Amine; Sakly, Mohsen; Marzouki, Lamjed; Sebai, Hichem

    2017-03-01

    The present study aimed to investigate the inhibitory effect of chamomile decoction extract (CDE) on intestinal glucose absorption as well as its protective role against high fat diet (HFD)-induced obesity and lipotoxicity in rats. We used the Ussing chamber system to investigate the effect of CDE on intestinal transport of glucose. Male Wistar rats were fed HFD for six weeks to provoke obesity. CDE (100mg/kg, b.w. p.o.) has been per orally administered to HFD fed rats. Ex vivo, we found that CDE significantly and dose-dependently increased intestinal absorption of glucose. In vivo, HFD increased the body, liver and kidney weights, while CDE treatment showed a significant protective effects. High fat diet induced also a lipid profiles disorder and a disturbances in kidney and liver function parameters. Moreover liver and kidney lipotoxicity is accompanied by an oxidative stress status characterized by increased lipoperoxidation, depletion of antioxidant enzymes activity and non-enzymatic antioxidant (-SH groups and GSH) levels as well as increased levels of free iron, hydrogen peroxide (H 2 O 2 ) and calcium. However, treatment with CDE alleviated all the deleterious effects of HFD feed. These findings suggest that chamomile decoction extract can be used as functional beverage against obesity, hyperglycemia and hyperlipidemia. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  3. Conditional density estimation with dimensionality reduction via squared-loss conditional entropy minimization.

    Science.gov (United States)

    Tangkaratt, Voot; Xie, Ning; Sugiyama, Masashi

    2015-01-01

    Regression aims at estimating the conditional mean of output given input. However, regression is not informative enough if the conditional density is multimodal, heteroskedastic, and asymmetric. In such a case, estimating the conditional density itself is preferable, but conditional density estimation (CDE) is challenging in high-dimensional space. A naive approach to coping with high dimensionality is to first perform dimensionality reduction (DR) and then execute CDE. However, a two-step process does not perform well in practice because the error incurred in the first DR step can be magnified in the second CDE step. In this letter, we propose a novel single-shot procedure that performs CDE and DR simultaneously in an integrated way. Our key idea is to formulate DR as the problem of minimizing a squared-loss variant of conditional entropy, and this is solved using CDE. Thus, an additional CDE step is not needed after DR. We demonstrate the usefulness of the proposed method through extensive experiments on various data sets, including humanoid robot transition and computer art.

  4. The Rh allele frequencies in Gaza city in Palestine

    Directory of Open Access Journals (Sweden)

    Skaik Younis

    2011-01-01

    Full Text Available Background: The Rh blood group system is the second most clinically significant blood group system. It includes 49 antigens, but only five (D, C, E, c and e are the most routinely identified due to their unique relation to hemolytic disease of the newborn (HDN and transfusion reactions. Frequency of the Rh alleles showed variation, with regard to race and ethnic. Objectives: The purpose of the study was to document the Rh alleles′ frequencies amongst males (M and females (F in Gaza city in Palestine. Materials and Methods: Two hundred and thirty-two blood samples (110 M and 122 F were tested against monoclonal IgM anti-C,anti-c, anti-E, anti-e and a blend of monoclonal/polyclonal IgM/IgG anti-D. The expected Rh phenotypes were calculated using gene counting method. Results: The most frequent Rh antigen in the total sample was e, while the least frequent was E.The order of the combined Rh allele frequencies in both M and F was CDe > cDe > cde > CdE > cDE > Cde > CDE. A significant difference was reported between M and F regarding the phenotypic frequencies (P < 0.05. However, no significance (P > 0.05 was reported with reference to the observed and expected Rh phenotypic frequencies in either M or F students. Conclusion: It was concluded that the Rh antigens, alleles and phenotypes in Gaza city have unique frequencies, which may be of importance to the Blood Transfusion Center in Gaza city and anthropology.

  5. Ladda

    DEFF Research Database (Denmark)

    Grall, Arnaud; Folz, Pauline; Montoya, Gabriela

    2017-01-01

    Clients of Triple Pattern Fragments (TPF) interfaces demonstrate how a SPARQL query engine can run within a browser and re-balance the load from the server to the clients. Imagine connecting these browsers using a browser-to-browser connection, sharing bandwidth and CPU. This builds a fog...... of browsers where end-user devices collaborate to process SPARQL queries over TPF servers. In this demo, we present Ladda: a framework for query execution in a fog of browsers. Thanks to client-side inter-query parallelism, Ladda reduces the makespan of the workload and improves the overall throughput...

  6. Sorting of bacterial lipoproteins to the outer membrane by the Lol system.

    Science.gov (United States)

    Narita, Shin-ichiro; Tokuda, Hajime

    2010-01-01

    Bacterial lipoproteins comprise a subset of membrane proteins with a lipid-modified cysteine residue at their amino termini through which they are anchored to the membrane. In Gram-negative bacteria, lipoproteins are localized on either the inner or the outer membrane. The Lol system is responsible for the transport of lipoproteins to the outer membrane.The Lol system comprises an inner-membrane ABC transporter LolCDE complex, a periplasmic carrier protein, LolA, and an outer membrane receptor protein, LolB. Lipoproteins are synthesized as precursors in the cytosol and then translocated across the inner membrane by the Sec translocon to the outer leaflet of the inner membrane, where lipoprotein precursors are processed to mature lipoproteins. The LolCDE complex then mediates the release of outer membrane-specific lipoproteins from the inner membrane while the inner membrane-specific lipoproteins possessing Asp at position 2 are not released by LolCDE because it functions as a LolCDE avoidance signal, causing the retention of these lipoproteins in the inner membrane. A water-soluble lipoprotein-LolA complex is formed as a result of the release reaction mediated by LolCDE. This complex traverses the hydrophilic periplasm to reach the outer membrane, where LolB accepts a lipoprotein from LolA and then catalyzes its incorporation into the inner leaflet of the outer membrane.

  7. Design of the CART data system for the US Department of Energy's ARM Program

    International Nuclear Information System (INIS)

    Melton, R.B.; Campbell, A.P.; Edwards, D.M.; Kanciruk, P.; Tichler, J.L.

    1991-01-01

    The Department of Energy (DOE) has initiated a major atmospheric research effort to reduce the uncertainties found in general circulation and other models due to the effects of clouds and radiation. The objective of the Atmospheric Radiation Measurement Program (ARM) is to provide an experimental testbed for the study of important atmospheric effects, particularly cloud and radiative processes, and testing parameterizations of the processes for use in atmospheric models. This experimental testbed, known as the Clouds and Radiation Testbed (CART), will include a complex data system, the CART Data Environment (CDE). The major functions of the CDE will be to: acquire environments from instruments and external data sources; perform quality assessments of the data streams; create data streams of known quality to be used as model input compared to model output; execute the models and capture their predictions; and make data streams associated with model tests available to ARM investigators in near real-time. The CDE will also be expected to capture ancillary information (''meta-data'') associated with the data streams, provide data management facilities for design of ARM experiments, and provide for archival data storage. The first section of this paper presents background information on CART. Next the process for the functional design of the system is described, the functional requirements summarized, and the conceptual architecture of the CDE is presented. Finally, the status of the CDE design activities is summarized, and major technical challenges are discussed

  8. Diminished agonist-stimulated inositol trisphosphate generation blocks stimulus-secretion coupling in mouse pancreatic acini during diet-induced experimental pancreatitis

    International Nuclear Information System (INIS)

    Powers, R.E.; Saluja, A.K.; Houlihan, M.J.; Steer, M.L.

    1986-01-01

    Young female mice fed a choline-deficient, ethionine-supplemented (CDE) diet rapidly develop acute hemorrhagic pancreatitis. We have observed that pancreatic acini prepared from these mice are unable to secrete amylase in response to addition of the cholinergic agonist carbachol, although they retain the ability to secrete amylase in response to the Ca2+ ionophore A23187. The CDE diet does not alter the binding characteristics (Kd or the maximal number of binding sites) for muscarinic cholinergic receptors as tested using the antagonist [ 3 H]N-methylscopolamine nor the competition for this binding by carbachol. Addition of carbachol to acini prepared from mice fed the CDE diet does not result in as marked an increase in cytosolic free Ca2+ levels as that noted in control samples (evaluated using quin2 fluorescence). These observations indicate that the CDE diet interferes with stimulus-secretion coupling in mouse pancreatic acini at a step subsequent to hormone-receptor binding and prior to Ca2+ release. This conclusion is confirmed by our finding that the hormone-stimulated generation of [ 3 H]inositol phosphates (inositol trisphosphate, inositol bisphosphate, and inositol monophosphate) from acini labeled with [ 3 H]myoinositol is markedly reduced in acini prepared from mice fed the CDE diet. This reduction is not due to a decrease in phosphatidylinositol-4,5-bisphosphate. This communication represents the first report of a system in which a blockade of inositol phosphate generation can be related to a physiologic defect and pathologic lesion

  9. Diabetes HealthSense: Resources for Living Well

    Medline Plus

    Full Text Available ... please copy the link from your browser's address bar, open your email program, and paste the link. ... and paste the link from your browser's address bar, then use your "Bookmarks" or "Favorites" menu to ...

  10. Evaluating Internet Health Information

    Science.gov (United States)

    ... content requires the Adobe Flash Player and a JavaScript-enabled browser. It seems JavaScript is disabled in your browser settings. Please enable JavaScript and reload this page, or use a different ...

  11. 78 FR 62788 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing...

    Science.gov (United States)

    2013-10-22

    ...\\ (2) clarify Level II Full Service Web Browser fee rates in light of the availability of additional... Historic TRACE Data for Rule 144A transactions, clarify Level II Full Service Web Browser fee rates in.... Level II Full Service Web Browser Fee FINRA proposes to clarify in FINRA Rule 7730(a)(1) applicable fees...

  12. Correlation transfer and diffusion of ultrasound-modulated multiply scattered light.

    Science.gov (United States)

    Sakadzić, Sava; Wang, Lihong V

    2006-04-28

    We develop a temporal correlation transfer equation (CTE) and a temporal correlation diffusion equation (CDE) for ultrasound-modulated multiply scattered light. These equations can be applied to an optically scattering medium with embedded optically scattering and absorbing objects to calculate the power spectrum of light modulated by a nonuniform ultrasound field. We present an analytical solution based on the CDE and Monte Carlo simulation results for light modulated by a cylinder of ultrasound in an optically scattering slab. We further validate with experimental measurements the numerical calculations for an actual ultrasound field. The CTE and CDE are valid for moderate ultrasound pressures and on a length scale comparable with the optical transport mean-free path. These equations should be applicable to a wide spectrum of conditions for ultrasound-modulated optical tomography of soft biological tissues.

  13. Role of bone marrow cells in the development of pancreatic fibrosis in a rat model of pancreatitis induced by a choline-deficient/ethionine-supplemented diet

    Energy Technology Data Exchange (ETDEWEB)

    Akita, Shingo; Kubota, Koji [Department of Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Kobayashi, Akira, E-mail: kbys@shinshu-u.ac.jp [Department of Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Misawa, Ryosuke; Shimizu, Akira; Nakata, Takenari; Yokoyama, Takahide [Department of Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Takahashi, Masafumi [Center for Molecular Medicine Division of Bioimaging Sciences, Jichi Medical University, 3311-1 Yakushiji, Shimono, Tochigi 329-0498 (Japan); Miyagawa, Shinichi [Department of Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan)

    2012-04-20

    Highlights: Black-Right-Pointing-Pointer BMC-derived PSCs play a role in a rat CDE diet-induced pancreatitis model. Black-Right-Pointing-Pointer BMC-derived PSCs contribute mainly to the early stage of pancreatic fibrosis. Black-Right-Pointing-Pointer BMC-derived activated PSCs can produce PDGF and TGF {beta}1. -- Abstract: Bone marrow cell (BMC)-derived myofibroblast-like cells have been reported in various organs, including the pancreas. However, the contribution of these cells to pancreatic fibrosis has not been fully discussed. The present study examined the possible involvement of pancreatic stellate cells (PSCs) originating from BMCs in the development of pancreatic fibrosis in a clinically relevant rat model of acute pancreatitis induced by a choline-deficient/ethionine-supplemented (CDE) diet. BMCs from female transgenic mice ubiquitously expressing green fluorescent protein (GFP) were transplanted into lethally irradiated male rats. Once chimerism was established, acute pancreatitis was induced by a CDE diet. Chronological changes in the number of PSCs originating from the donor BMCs were examined using double immunofluorescence for GFP and markers for PSCs, such as desmin and alpha smooth muscle actin ({alpha}SMA), 1, 3 and 8 weeks after the initiation of CDE feeding. We also used immunohistochemical staining to evaluate whether the PSCs from the BMCs produce growth factors, such as platelet-derived growth factor (PDGF) and transforming growth factor (TGF) {beta}1. The percentage of BMC-derived activated PSCs increased significantly, peaking after 1 week of CDE treatment (accounting for 23.3 {+-} 0.9% of the total population of activated PSCs) and then decreasing. These cells produced both PDGF and TGF{beta}1 during the early stage of pancreatic fibrosis. Our results suggest that PSCs originating from BMCs contribute mainly to the early stage of pancreatic injury, at least in part, by producing growth factors in a rat CDE diet-induced pancreatitis model.

  14. Large-scale preparation of the homogeneous LolA–lipoprotein complex and efficient in vitro transfer of lipoproteins to the outer membrane in a LolB-dependent manner

    OpenAIRE

    Watanabe, Shoji; Oguchi, Yuki; Yokota, Naoko; Tokuda, Hajime

    2007-01-01

    An ATP-binding cassette transporter LolCDE complex of Escherichia coli releases lipoproteins destined to the outer membrane from the inner membrane as a complex with a periplasmic chaperone, LolA. Interaction of the LolA–lipoprotein complex with an outer membrane receptor, LolB, then causes localization of lipoproteins to the outer membrane. As far as examined, formation of the LolA–lipoprotein complex strictly depends on ATP hydrolysis by the LolCDE complex in the presence of LolA. It has be...

  15. Genetic Analysis of the Mode of Interplay between an ATPase Subunit and Membrane Subunits of the Lipoprotein-Releasing ATP-Binding Cassette Transporter LolCDE†

    OpenAIRE

    Ito, Yasuko; Matsuzawa, Hitomi; Matsuyama, Shin-ichi; Narita, Shin-ichiro; Tokuda, Hajime

    2006-01-01

    The LolCDE complex, an ATP-binding cassette (ABC) transporter, releases lipoproteins from the inner membrane, thereby initiating lipoprotein sorting to the outer membrane of Escherichia coli. The LolCDE complex is composed of two copies of an ATPase subunit, LolD, and one copy each of integral membrane subunits LolC and LolE. LolD hydrolyzes ATP on the cytoplasmic side of the inner membrane, while LolC and/or LolE recognize and release lipoproteins anchored to the periplasmic leaflet of the i...

  16. Common data elements for spinal cord injury clinical research

    DEFF Research Database (Denmark)

    Biering-Sørensen, F; Alai, S; Anderson, K.

    2015-01-01

    OBJECTIVES: To develop a comprehensive set of common data elements (CDEs), data definitions, case report forms and guidelines for use in spinal cord injury (SCI) clinical research, as part of the CDE project at the National Institute of Neurological Disorders and Stroke (NINDS) of the US National...... with and cross-referenced to development of the International Spinal Cord Society (ISCoS) International SCI Data Sets. The recommendations were compiled, subjected to internal review and posted online for external public comment. The final version was reviewed by all working groups and the NINDS CDE team before...

  17. The CHR Promoter Element Controls Cell Cycle-Dependent Gene Transcription and Binds the DREAM and MMB Complexes

    OpenAIRE

    Müller, Gerd A.; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Fischer, Martin; Engeland, Kurt; Padi, Megha; Litovchick, Larisa; DeCaprio, James A.

    2011-01-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like \\(cyclin B, CDC2\\) and \\(CDC25C\\) are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in \\(G_0/G_1\\). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and...

  18. Unraveling a molecular determinant for clathrin-independent internalization of the M2 muscarinic acetylcholine receptor

    Science.gov (United States)

    Wan, Min; Zhang, Wenhua; Tian, Yangli; Xu, Chanjuan; Xu, Tao; Liu, Jianfeng; Zhang, Rongying

    2015-01-01

    Endocytosis and postendocytic sorting of G-protein-coupled receptors (GPCRs) is important for the regulation of both their cell surface density and signaling profile. Unlike the mechanisms of clathrin-dependent endocytosis (CDE), the mechanisms underlying the control of GPCR signaling by clathrin-independent endocytosis (CIE) remain largely unknown. Among the muscarinic acetylcholine receptors (mAChRs), the M4 mAChR undergoes CDE and recycling, whereas the M2 mAChR is internalized through CIE and targeted to lysosomes. Here we investigated the endocytosis and postendocytic trafficking of M2 mAChR based on a comparative analysis of the third cytoplasmic domain in M2 and M4 mAChRs. For the first time, we identified that the sequence 374KKKPPPS380 servers as a sorting signal for the clathrin-independent internalization of M2 mAChR. Switching 374KKKPPPS380 to the i3 loop of the M4 mAChR shifted the receptor into lysosomes through the CIE pathway; and therefore away from CDE and recycling. We also found another previously unidentified sequence that guides CDE of the M2 mAChR, 361VARKIVKMTKQPA373, which is normally masked in the presence of the downstream sequence 374KKKPPPS380. Taken together, our data indicate that endocytosis and postendocytic sorting of GPCRs that undergo CIE could be sequence-dependent. PMID:26094760

  19. semi-dwarf tef lines for high seed yield and lodging tolerance in ...

    African Journals Online (AJOL)

    ACSS

    4Center for Development and Environment (CDE), University of Bern, 3012 Bern, Switzerland. Corresponding author: Zerihun.tadele@ips.unibe.ch. (Received 2 July, 2016; accepted 4 October, 2017). ABSTRACT. Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in the Horn of Africa, especially in Ethiopia where it.

  20. Antibody-induced generation of reactive oxygen radicals by brain macrophages in canine distemper encephalitis: a mechanism for bystander demyelination.

    Science.gov (United States)

    Griot, C; Bürge, T; Vandevelde, M; Peterhans, E

    1989-01-01

    The mechanism of inflammatory demyelination in canine distemper encephalitis (CDE) is uncertain but macrophages are thought to play an important effector role in this lesion. Serum and cerebrospinal fluid (CSF), containing anti-canine distemper virus and anti-myelin antibodies from dogs with CDE were tested for their ability to generate reactive oxygen species (ROS) in macrophages in primary dog brain cell cultures using a chemiluminescence (CL) assay. The majority of serum samples and several CSF samples from animals with inflammatory demyelination elicited a CL signal in infected dog brain cell cultures. In contrast, none of these samples induced a positive response in uninfected cultures which contained large numbers of myelin antigen-presenting cells, although defined anti-myelin antibodies lead to a marked secretion of ROS in this system. It was concluded that antiviral antibody-induced secretion of ROS, known to be highly toxic for brain tissue, may play an important role in white matter damage in inflammatory lesions supporting a previous hypothesis of bystander demyelination in CDE. No evidence was found for a similar antibody-dependent cellular cytotoxicity-like mechanism mediated by anti-myelin antibodies in CDE, which does not support the concept of autoimmunity in this disease.

  1. ORiON - Vol 20, No 2 (2004)

    African Journals Online (AJOL)

    A single product perishing inventory model with demand interaction · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. VSS Yadavalli, CdeW van Schoor, JJ Strasheim, S Udayabaskaran, 109-124. http://dx.doi.org/10.5784/20-2-10 ...

  2. Remarkable heterogeneity displayed by oval cells in rat and mouse models of stem cell-mediated liver regeneration

    DEFF Research Database (Denmark)

    Jelnes, Peter; Santoni-Rugiu, Eric; Rasmussen, Morten

    2007-01-01

    the molecular phenotypes of oval cells in several of the most commonly used protocols of stem cell-mediated liver regeneration-namely, treatment with 2-acetylaminofluorene and partial (70%) hepatectomy (AAF/PHx); a choline-deficient, ethionine-supplemented (CDE) diet; a 3,5-diethoxycarbonyl-1,4-dihydro...

  3. Small-Molecule Inhibitors of Gram-Negative Lipoprotein Trafficking Discovered by Phenotypic Screening

    Science.gov (United States)

    Fleming, Paul R.; MacCormack, Kathleen; McLaughlin, Robert E.; Whiteaker, James D.; Narita, Shin-ichiro; Mori, Makiko; Tokuda, Hajime; Miller, Alita A.

    2015-01-01

    In Gram-negative bacteria, lipoproteins are transported to the outer membrane by the Lol system. In this process, lipoproteins are released from the inner membrane by the ABC transporter LolCDE and passed to LolA, a diffusible periplasmic molecular chaperone. Lipoproteins are then transferred to the outer membrane receptor protein, LolB, for insertion in the outer membrane. Here we describe the discovery and characterization of novel pyridineimidazole compounds that inhibit this process. Escherichia coli mutants resistant to the pyridineimidazoles show no cross-resistance to other classes of antibiotics and map to either the LolC or LolE protein of the LolCDE transporter complex. The pyridineimidazoles were shown to inhibit the LolA-dependent release of the lipoprotein Lpp from E. coli spheroplasts. These results combined with bacterial cytological profiling are consistent with LolCDE-mediated disruption of lipoprotein targeting to the outer membrane as the mode of action of these pyridineimidazoles. The pyridineimidazoles are the first reported inhibitors of the LolCDE complex, a target which has never been exploited for therapeutic intervention. These compounds open the door to further interrogation of the outer membrane lipoprotein transport pathway as a target for antimicrobial therapy. PMID:25583975

  4. Effect of nitrogen fertilizer on distribution of starch granules in different regions of wheat endosperm

    Directory of Open Access Journals (Sweden)

    Fei Xiong

    2014-02-01

    Full Text Available This study provided visual evidence of a nitrogen effect on starch granules (SGs in wheat endosperm. Winter wheat (Titicum aestivum L. cultivar Xumai 30 was cultured under no nitrogen (control and 240 kg ha− 1 of nitrogen applied at the booting stage. The number, morphology, and size of A- and B-type SGs in subaleurone of dorsal endosperm (SDE, center of dorsal endosperm (CDE, modified aleurone (MA, subaleurone of ventral endosperm (SVE, and center of ventral endosperm (CVE were observed under light and electron microscopes. (1 The distribution of SGs in SDE was similar to that in SVE, the distributions of SGs in CDE and CVE were similar, but the distribution of SGs in MA was different from those in the other four endosperm regions. The number of SGs in the five endosperm regions was in the order SDE > CDE > SVE > CVE > MA. (2 Nitrogen increased the number of A- and B-type SGs in SDE and SVE. Nitrogen also increased the number of B-type SGs but decreased the number of A-type SGs in CDE and CVE. Nitrogen decreased the numbers of A-type and B-type SGs in MA. The results suggest that increased N fertilizer application mainly increased the numbers of small SGs and decreased the numbers of large SGs, but that the results varied in different regions of the wheat endosperm.

  5. Transcriptional repressor role of PocR on the 1,3-propanediol biosynthetic pathway by Lactobacillus panis PM1.

    Science.gov (United States)

    Kang, Tae Sun; Korber, Darren R; Tanaka, Takuji

    2014-06-01

    The regulatory role of a transcriptional regulator (PocR) in the 1,3-propanediol biosynthetic pathway of Lactobacillus panis PM1 contributes to the optimization of 1,3-propanediol production by this strain, which potentially will lead to 1,3-propanediol manufacturing efficiencies. Lactobacillus panis PM1 can utilize a 1,3-propanediol (1,3-PDO) biosynthetic pathway, consisting of diol dehydratase (PduCDE) and 1,3-PDO dehydrogenase, as a NADH recycling system, to survive under various environmental conditions. In this study, we identified a key transcriptional repressor (PocR) which was annotated as a transcriptional factor of AraC family as part of the 1,3-PDO biosynthetic pathway of L. panis PM1. The over-expression of the PocR gene resulted in the significant repression (81 %) of pduC (PduCDE large subunit) transcription, and subsequently, the decreased activity of PduCDE by 22 %. As a result of the regulation of PduCDE, production of both 3-hydroxypropionaldehyde and 1,3-PDO in the PocR over-expressing strain were significantly decreased by 40 % relative to the control strain. These results clearly demonstrate the transcriptional repressor role of PocR in the 1,3-PDO biosynthetic pathway.

  6. Antidiarrheal and antioxidant activities of chamomile (Matricaria recutita L.) decoction extract in rats.

    Science.gov (United States)

    Sebai, Hichem; Jabri, Mohamed-Amine; Souli, Abdelaziz; Rtibi, Kais; Selmi, Slimen; Tebourbi, Olfa; El-Benna, Jamel; Sakly, Mohsen

    2014-03-14

    Matricaria recutita L. (Chamomile) has been widely used in the Tunisian traditional medicine for the treatment of digestive system disorders. The present work aims to investigate the protective effects of chamomile decoction extract (CDE) against castor oil-induced diarrhea and oxidative stress in rats. The antidiarrheal activity was evaluated using castor oil-induced diarrhea method. In this respect, rats were divided into six groups: Control, Castor oil, Castor oil+Loperamide (LOP) and Castor oil+various doses of CDE. Animals were per orally (p.o.) pre-treated with CDE during 1h and intoxicated for 2 or 4h by acute oral administration of castor oil. Our results showed that CDE produced a significant dose-dependent protection against castor oil-induced diarrhea and intestinal fluid accumulation. On the other hand, we showed that diarrhea was accompagned by an oxidative stress status assessed by an increase of malondialdehyde (MDA) level and depletion of antioxidant enzyme activities as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx). Castor oil also increased gastric and intestinal mucosa hydrogen peroxide (H2O2) and free iron levels. Importantly, we showed that chamomile pre-treatment abrogated all these biochemical alterations. These findings suggested that chamomile extract had a potent antidiarrheal and antioxidant properties in rats confirming their use in traditional medicine. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Common data elements for clinical research in mitochondrial disease: a National Institute for Neurological Disorders and Stroke project.

    Science.gov (United States)

    Karaa, Amel; Rahman, Shamima; Lombès, Anne; Yu-Wai-Man, Patrick; Sheikh, Muniza K; Alai-Hansen, Sherita; Cohen, Bruce H; Dimmock, David; Emrick, Lisa; Falk, Marni J; McCormack, Shana; Mirsky, David; Moore, Tony; Parikh, Sumit; Shoffner, John; Taivassalo, Tanja; Tarnopolsky, Mark; Tein, Ingrid; Odenkirchen, Joanne C; Goldstein, Amy

    2017-05-01

    The common data elements (CDE) project was developed by the National Institute of Neurological Disorders and Stroke (NINDS) to provide clinical researchers with tools to improve data quality and allow for harmonization of data collected in different research studies. CDEs have been created for several neurological diseases; the aim of this project was to develop CDEs specifically curated for mitochondrial disease (Mito) to enhance clinical research. Nine working groups (WGs), composed of international mitochondrial disease experts, provided recommendations for Mito clinical research. They initially reviewed existing NINDS CDEs and instruments, and developed new data elements or instruments when needed. Recommendations were organized, internally reviewed by the Mito WGs, and posted online for external public comment for a period of eight weeks. The final version was again reviewed by all WGs and the NINDS CDE team prior to posting for public use. The NINDS Mito CDEs and supporting documents are publicly available on the NINDS CDE website ( https://commondataelements.ninds.nih.gov/ ), organized into domain categories such as Participant/Subject Characteristics, Assessments, and Examinations. We developed a comprehensive set of CDE recommendations, data definitions, case report forms (CRFs), and guidelines for use in Mito clinical research. The widespread use of CDEs is intended to enhance Mito clinical research endeavors, including natural history studies, clinical trial design, and data sharing. Ongoing international collaboration will facilitate regular review, updates and online publication of Mito CDEs, and support improved consistency of data collection and reporting.

  8. High Angle-of-Attack Aerodynamics

    Science.gov (United States)

    1982-12-01

    poudre d’hostaflon ou Butres traceurs Idgera rdpandus &Is surface libre), dout l’emloi rests gindralesnt liaiti au courant plan 3-32 - peintures et huiles...rapages sans arrft de la soufflerie [28]J (fig. 7ab, fig.16g); -enduits visqueux (fig. 7cde ), peintures plastiques (fig.5b, 9j), psintures the

  9. Small-molecule inhibitors of gram-negative lipoprotein trafficking discovered by phenotypic screening.

    Science.gov (United States)

    McLeod, Sarah M; Fleming, Paul R; MacCormack, Kathleen; McLaughlin, Robert E; Whiteaker, James D; Narita, Shin-Ichiro; Mori, Makiko; Tokuda, Hajime; Miller, Alita A

    2015-03-01

    In Gram-negative bacteria, lipoproteins are transported to the outer membrane by the Lol system. In this process, lipoproteins are released from the inner membrane by the ABC transporter LolCDE and passed to LolA, a diffusible periplasmic molecular chaperone. Lipoproteins are then transferred to the outer membrane receptor protein, LolB, for insertion in the outer membrane. Here we describe the discovery and characterization of novel pyridineimidazole compounds that inhibit this process. Escherichia coli mutants resistant to the pyridineimidazoles show no cross-resistance to other classes of antibiotics and map to either the LolC or LolE protein of the LolCDE transporter complex. The pyridineimidazoles were shown to inhibit the LolA-dependent release of the lipoprotein Lpp from E. coli spheroplasts. These results combined with bacterial cytological profiling are consistent with LolCDE-mediated disruption of lipoprotein targeting to the outer membrane as the mode of action of these pyridineimidazoles. The pyridineimidazoles are the first reported inhibitors of the LolCDE complex, a target which has never been exploited for therapeutic intervention. These compounds open the door to further interrogation of the outer membrane lipoprotein transport pathway as a target for antimicrobial therapy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa

    NARCIS (Netherlands)

    Li, J.; Liu, B.; Cheng, F.; Wang, X.; Aarts, M.G.M.; Wu, J.

    2014-01-01

    Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of

  11. Ejercicio de los derechos y participación de las mujeres en los ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    19 juil. 2013 ... Le directeur. Gloria Bonder dirige le secteur Género, Sociedad y Políticas de la Facultad Latinoamericana de Ciencias Sociales en Argentine (FLACSO Argentina). Elle a coordonné la publication de ce volume avec Clyde Soto, chercheur au Centro de Documentación y Estudios (CDE), au Paraguay.

  12. Bistand til risikovurdering (evt. ændringer af tidligere risikovurdering). Zea mays (MON863; MON863x810). Supplerende materiale til ansøgningen. Modtaget 07-09-2004, deadline 19-09-2004, svar 17-09-2004

    DEFF Research Database (Denmark)

    Kjellsson, Gøsta; Strandberg, Morten Tune

    2012-01-01

    "DMU har modtaget og vurderet de supplerende oplysninger (mail fra Skov- og Naturstyrelsen d. 07-09-2004) til ansøgningen om tilladelse til markedsføring af genetisk modificeret majs C/DE/02/09 (MON863 og MON863 x MON810). Vi har gennemgået oplysningerne i det tilsendte materiale for at se om de ...

  13. An evaluation of a refresher training intervention for HIV lay ...

    African Journals Online (AJOL)

    Charles Msisuka a , Ikuma Nozaki b i-nozaki@it.ncgm.go.jpinozaki@hsph.harvard.edu, Kazuhiro Kakimoto c , Motoko Seko d & Mercy M S Ulaya e

    to evaluate the refresher training intervention for HIV lay counsellors in the rural district of Chongwe in Zambia. ..... Salaried employee. Homemaker. CDE in health facility. Other. Median educational level (Grade). Median experience as counsellor (years). Median number of ... The importance of refresher training courses.

  14. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes.

    Science.gov (United States)

    Müller, Gerd A; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Padi, Megha; Fischer, Martin; Litovchick, Larisa; DeCaprio, James A; Engeland, Kurt

    2012-02-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like cyclin B, CDC2 and CDC25C are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in G(0)/G(1). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and human cyclin B2 promoters in G(0). Association of DREAM and cell cycle-dependent regulation is abrogated when the CHR is mutated. Although E2f4 is part of the complex, a CDE is not essential but can enhance binding of DREAM. We show that the CHR element is not only necessary for repression of gene transcription in G(0)/G(1), but also for activation in S, G(2) and M phases. In proliferating cells, the B-myb-containing MMB complex binds the CHR of both promoters independently of the CDE. Bioinformatic analyses identify many genes which contain conserved CHR elements in promoters binding the DREAM complex. With Ube2c as an example from that screen, we show that inverse CHR sites are functional promoter elements that can bind DREAM and MMB. Our findings indicate that the CHR is central to DREAM/MMB-dependent transcriptional control during the cell cycle.

  15. 78 FR 45604 - Funding Opportunity Title: Notice of Allocation Availability (NOAA) Inviting Applications for the...

    Science.gov (United States)

    2013-07-29

    ... Investments that are evidenced by a written, signed document in which an investor: (i) commits to make a QEI..., but only a for-profit CDE is permitted to provide NMTCs to its investors. A non-profit applicant... raising capital, particularly from for-profit investors; the extent to which the applicant has secured...

  16. 77 FR 43418 - Funding Opportunity Title: Notice of Allocation Availability (NOAA) Inviting Applications for the...

    Science.gov (United States)

    2012-07-24

    ... evidenced by a written, signed document in which an investor: (i) Commits to make an investment in the... NMTC allocation authority, but only a for-profit CDE is permitted to provide NMTCs to its investors. A... raising capital, particularly from for-profit investors; the extent to which the applicant has secured...

  17. 76 FR 32880 - Encouraging New Markets Tax Credit Non-Real Estate Investments

    Science.gov (United States)

    2011-06-07

    ... proceeds is affiliated with the primary CDE or the qualified equity investment investors; and (iii) the... be a non-profit entity or the affiliate of a non-profit entity? B. Encouraging Equity Investments in... Encouraging New Markets Tax Credit Non-Real Estate Investments AGENCY: Internal Revenue Service (IRS...

  18. A general polynomial solution to convection–dispersion equation ...

    Indian Academy of Sciences (India)

    Jiao Wang

    A number of models have been established to simulate the behaviour of solute transport due to chemical pollution, both in croplands and groundwater systems. An approximate polynomial solution to convection–dispersion equation (CDE) based on boundary layer theory has been verified for the use to describe solute ...

  19. Development and characterization of genic SSR markers from low ...

    Indian Academy of Sciences (India)

    Abstract. Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde+4acde ver. 3.1 categories by the IUCN (2015) due to decreasing population trend. Microsatellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present ...

  20. Synthetic Study of Rubriflordilactone B: Highly Stereoselective Construction of the C-5-epi ABCDE Ring System.

    Science.gov (United States)

    Wang, Yong; Li, Zhongle; Lv, Liangbo; Xie, Zhixiang

    2016-02-19

    A highly stereocontrolled construction of the C-5-epi ABCDE-ring system of rubriflordilactone B has been developed. The present synthesis features a convergent strategy to construct the C-5-epi AB-ring utilizing Mukaiyama-Michael reaction and forge the CDE ring in one step using intramolecular [2 + 2 + 2] cycloaddition of triynes.

  1. [Reliability for detection of developmental problems using the semaphore from the Child Development Evaluation test: Is a yellow result different from a red result?

    Science.gov (United States)

    Rizzoli-Córdoba, Antonio; Ortega-Ríosvelasco, Fernando; Villasís-Keever, Miguel Ángel; Pizarro-Castellanos, Mariel; Buenrostro-Márquez, Guillermo; Aceves-Villagrán, Daniel; O'Shea-Cuevas, Gabriel; Muñoz-Hernández, Onofre

    The Child Development Evaluation (CDE) is a screening tool designed and validated in Mexico for detecting developmental problems. The result is expressed through a semaphore. In the CDE test, both yellow and red results are considered positive, although a different intervention is proposed for each. The aim of this work was to evaluate the reliability of the CDE test to discriminate between children with yellow/red result based on the developmental domain quotient (DDQ) obtained through the Battelle Development Inventory, 2nd edition (in Spanish) (BDI-2). The information was obtained for the study from the validation. Children with a normal (green) result in the CDE were excluded. Two different cut-off points of the DDQ were used (BDI-2): motor: 18.1% vs. 39.9%; personal-social: 20.1% vs. 28.9%; and adaptive: 6.9% vs. 20.4%. The semaphore result yellow/red allows identifying different magnitudes of delay in developmental domains or subdomains, supporting the recommendation of different interventions for each one. Copyright © 2014 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  2. Contaminant transport in soil with depth-dependent reaction coefficients and time-dependent boundary conditions.

    Science.gov (United States)

    Gao, Guangyao; Fu, Bojie; Zhan, Hongbin; Ma, Ying

    2013-05-01

    Predicting the fate and movement of contaminant in soils and groundwater is essential to assess and reduce the risk of soil contamination and groundwater pollution. Reaction processes of contaminant often decreased monotonously with depth. Time-dependent input sources usually occurred at the inlet of natural or human-made system such as radioactive waste disposal site. This study presented a one-dimensional convection-dispersion equation (CDE) for contaminant transport in soils with depth-dependent reaction coefficients and time-dependent inlet boundary conditions, and derived its analytical solution. The adsorption coefficient and degradation rate were represented as sigmoidal functions of soil depth. Solute breakthrough curves (BTCs) and concentration profiles obtained from CDE with depth-dependent and constant reaction coefficients were compared, and a constant effective reaction coefficient, which was calculated by arithmetically averaging the depth-dependent reaction coefficient, was proposed to reflect the lumped depth-dependent reaction effect. With the effective adsorption coefficient and degradation rate, CDE could produce similar BTCs and concentration profiles as those from CDE with depth-dependent reactions in soils with moderate chemical heterogeneity. In contrast, the predicted concentrations of CDE with fitted reaction coefficients at a certain depth departed significantly from those of CDE with depth-dependent reactions. Parametric analysis was performed to illustrate the effects of sinusoidally and exponentially decaying input functions on solute BTCs. The BTCs and concentration profiles obtained from the solutions for finite and semi-infinite domain were compared to investigate the effects of effluent boundary condition. The finite solution produced higher concentrations at the increasing limb of the BTCs and possessed a higher peak concentration than the semi-infinite solution which had a slightly long tail. Furthermore, the finite solution gave

  3. In vitro and in vivo siRNA delivery to hepatocyte utilizing ternary complexation of lactosylated dendrimer/cyclodextrin conjugates, siRNA and low-molecular-weight sacran.

    Science.gov (United States)

    Hayashi, Yuya; Higashi, Taishi; Motoyama, Keiichi; Jono, Hirofumi; Ando, Yukio; Arima, Hidetoshi

    2018-02-01

    In this study, we newly developed the ternary complexes consisting of lactosylated dendrimer (generation 3)/α-cyclodextrin conjugate (Lac-α-CDE), siRNA and the anionic polysaccharide sacrans, and evaluated their utility as siRNA transfer carriers. Three kinds of the low-molecular-weight sacrans, i.e. sacran (100) (Mw 44,889Da), sacran (1000) (Mw 943,692Da) and sacran (10,000) (Mw 1,488,281Da) were used. Lac-α-CDE/siRNA/sacran ternary complexes were prepared by adding the low-molecular-weight sacrans to the Lac-α-CDE/siRNA binary complex solution. Cellular uptake of the ternary complex with sacran (100) was higher than that of the binary complex or the other ternary complexes with sacran (1000) and sacran (10,000) in HepG2 cells. Additionally, the ternary complex possessed high serum resistance and endosomal escaping ability in HepG2 cells. High liver levels of siRNA and Lac-α-CDE were observed after the intravenous administration of the ternary complex rather than that of the binary complex. Moreover, intravenous administration of the ternary complex (siRNA 5mg/kg) induced the significant RNAi effect in the liver of mice with negligible change of blood chemistry values. Therefore, a ternary complexation of the Lac-α-CDE/siRNA binary complex with sacran is useful as a hepatocyte-specific siRNA delivery system. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Effects of cadmium, estradiol-17beta and their interaction on gonadal condition and metamorphosis of male and female African clawed frog, Xenopus laevis

    Science.gov (United States)

    Sharma, Bibek; Patino, Reynaldo

    2010-01-01

    To assess interaction effects between cadmium (Cd, a putative xenoestrogen) and estradiol-17beta (E(2)) on sex differentiation and metamorphosis, Xenopus laevis were exposed to solvent-control (0.005% ethanol), Cd (10microgL(-1)), E(2) (1microgL(-1)), or Cd and E(2) (Cd+E(2)) in FETAX medium from fertilization to 75d postfertilization. Each treatment was applied to four aquaria, each with 30 fertilized eggs. Mortality was recorded and animals were sampled as they completed metamorphosis (Nieuwkoop and Faber stage 66). Gonadal sex of individuals (including >or= tadpoles NF stage 55 at day 75) was determined gross-morphologically and used to compute sex ratios. Time course and percent completion of metamorphosis, snout-vent length (SVL), hindlimb length (HLL) and weight were analyzed for each gender separately. Survival rates did not differ among treatments. The E(2) and Cd+E(2) treatments significantly skewed sex ratios towards females; however, no sex-ratio differences were observed between the control and Cd treatments or between the E(2) and Cd+E(2) treatments. Time course of metamorphosis was generally delayed and percent completion of metamorphosis was generally reduced in males and females exposed to Cd, E(2) or their combination compared to control animals. In males, but not females, the effect of Cd+E(2) was greater than that of individual chemicals. Weight at completion of metamorphosis was reduced only in females and only by the Cd+E(2) treatment. In conclusion, although Cd at an environmentally relevant concentration did not exhibit direct or indirect feminizing effects in Xenopus tadpoles, the metal and E(2) both had similar inhibitory effects on metamorphosis that were of greater magnitude in males than females.

  5. Damage assessed by wavelet scale bands and b-value in dynamical tests of a reinforced concrete slab monitored with acoustic emission

    Science.gov (United States)

    Zitto, Miguel E.; Piotrkowski, Rosa; Gallego, Antolino; Sagasta, Francisco; Benavent-Climent, Amadeo

    2015-08-01

    The complex Morlet Continuous Wavelet Transform (CWT) was applied to acoustic emission (AE) signals from dynamic tests conducted on a reinforced concrete slab with a shaking table. The steel reinforcement bars did not yield during the tests, but a severe loss of bond between reinforcement bars and surrounding concrete was detected. Comparison of the evolution of the scale position of maximum values of CWT coefficients and the histories of response acceleration obtained in different seismic simulations allowed us to identify the (45-64 kHz) frequency band corresponding to the fracture of concrete. The Cumulative Acoustic Emission Energy (CAE) obtained by reconstructing the AE signals in this scale (frequency) band was compared with the Cumulative Dissipated Energy (CDE) of the tested structure. The CDE is accepted as a good parameter for characterizing the mechanical damage in structures. A reasonably good agreement was found between the normalized histories of CAE and CDE. This made it possible to categorize the cracking of concrete as the main source of damage in the reinforced concrete slab. Conversely, the differences between the CAE and CDE curves observed for high levels of peak acceleration applied to the shaking table can be attributed to the deformation of the steel that formed the columns. The AE coming from the plastic deformation of the steel is not detected by CAE due to the threshold amplitude (45 dB) used in the AE monitoring, but the strain energy dissipated by the steel through plastic deformations is included in the CDE. Further, a study of the evolution of the b-value in the successive seismic simulations revealed that the b-value can capture the inception of severe cracking in the concrete, which the tests described in this study attributed mainly to the loss of bond between reinforcing steel and surrounding concrete.

  6. On the Dagan Model of Solute Transport in Groundwater: Foundational Aspects

    Science.gov (United States)

    Sposito, Garrison; Barry, D. A.

    1987-10-01

    The convection-dispersion equation (CDE) developed by Dagan [1984] to predict the ensemble-average concentration of a conservative solute in groundwater has been used successfully to interpret recent tracer experiments in a sand aquifer at the Borden site in Canada. This successful application encouraged further investigation of the Dagan model in respect to its physical basis and predictive characteristics. It is shown in the present paper, which deals with the first topic, that the Dagan model CDE can be derived through an extension of the cumulant expansion technique applied previously by Chu and Sposito [1980] to develop a mean CDE for solute transport in homogeneous porous media. This technique also leads directly to the mean CDE developed by Gelhar and Axness [1983] as an asymptotic (large time) limit and to model dispersion coefficients derived by Mather on and de Marsily [1980] and Güven and MoIz [1986]. The Dagan CDE then is considered in detail in respect to which conceptualization of the solute concentration, resident or flux, the model may utilize in predictive applications. General mathematical expressions relating the two conceptualizations are derived for an arbitrary solute transport problem and then are applied to the Dagan model for point and prism source inputs. Finally, the Dagan model is interpreted physically using data from the recent tracer experiments of Roberts and Mackay [1986] at the Borden site. It is shown that model predictions of resident and flux concentrations are numerically indistinguishable on any time scale over which field solute concentration measurements typically are made. The model prediction of dispersion coefficients, on the other hand, leads to dramatic differences in predicted plume behavior depending on whether finite time expressions or their asymptotic limits are used. According to the Dagan model, the asymptotic transverse dispersion coefficient cannot replace the time-dependent coefficient on any realistic time

  7. Data Exchange Inventory System for Telecommunications and Systems Operations (DEXI-OTSO)

    Data.gov (United States)

    Social Security Administration — This Data Exchange Inventory (DEXI) for the Office of Telecommunications and System Operations, (OTSO) Network Troubleshooting is a browser-based inventory database...

  8. Enabling remote access to projects in a large collaborative environment

    International Nuclear Information System (INIS)

    Pais, V.; Balme, S.; Iannonec, F.; Strand, P.

    2009-01-01

    In the context of the Integrated Tokamak Modeling Task Force, a large number of software projects are made available to the task force members, including developers and end-users. This has been achieved through a combination of tools and technologies. The front-end is represented by a Java based portal system exposing a PHP project management system, Gforge. These two applications are linked by a single sign-on mechanism, Shibboleth, and through secure HTTP request rewriting, where appropriate. Furthermore, the underlying storage facility is an OpenAFS distributed file system and the user base comes from both a network information server and an LDAP directory. Security mechanisms are those of a distributed system, with multiple access points and protocols used for reading and writing data. This document presents the challenges of integrating these different technologies and programming languages into a single, working, application presented to its users as a web portal. The chaining of the tools is explored through the user perspective, with an in-depth overview of the background transitions between the various systems involved with regard to security requirements for the front-end nodes and the policies as seen by the users. This document is composed of a poster and its abstract. (authors)

  9. Enabling remote access to projects in a large collaborative environment

    International Nuclear Information System (INIS)

    Pais, V.F.; Balme, S.; Akpangny, H.S.; Iannone, F.; Strand, P.

    2010-01-01

    In the context of the Integrated Tokamak Modelling Task Force, a large number of software projects are made available to the task force members, including developers and end-users. This has been achieved through a combination of tools and technologies. The front-end is represented by a Java based portal system exposing a PHP project management system, GForge. These two applications are linked by a single sign-on mechanism, Shibboleth , and through secure HTTP request rewriting, where appropriate. Furthermore, the underlying storage facility is an OpenAFS distributed file system and the user base comes from both a network information server and an LDAP directory. Security mechanisms are those of a distributed system, with multiple access points and protocols used for reading and writing data. The present paper presents the challenges of integrating these different technologies and programming languages into a single, working, application presented to its users as a web portal. Chaining of the tools is explored through the user perspective, with an in-depth overview of the background transitions between the various systems involved with regard to security requirements for the front-end nodes and the policies as seen by the users.

  10. Enabling remote access to projects in a large collaborative environment

    Energy Technology Data Exchange (ETDEWEB)

    Pais, V.F., E-mail: pvf2005@gmail.co [Laser Department, National Institute for Laser, Plasma and Radiation Physics, P.O. Box MG-36, Bucharest 077125, Association EURATOM/MEdC (Romania); Balme, S.; Akpangny, H.S. [Association EURATOM CEA/IRFM CEA-Cadarache (France); Iannone, F. [Associazione EURATOM-ENEA sulla Fusione, C.R.ENEA Frascati, via E.Fermi 45, 00044 Frascati, Rome (Italy); Strand, P. [Department of Radio and Space Science, Chalmers University of Technology, SE-412 96 Goteborg (Sweden)

    2010-07-15

    In the context of the Integrated Tokamak Modelling Task Force, a large number of software projects are made available to the task force members, including developers and end-users. This has been achieved through a combination of tools and technologies. The front-end is represented by a Java based portal system exposing a PHP project management system, GForge. These two applications are linked by a single sign-on mechanism, Shibboleth , and through secure HTTP request rewriting, where appropriate. Furthermore, the underlying storage facility is an OpenAFS distributed file system and the user base comes from both a network information server and an LDAP directory. Security mechanisms are those of a distributed system, with multiple access points and protocols used for reading and writing data. The present paper presents the challenges of integrating these different technologies and programming languages into a single, working, application presented to its users as a web portal. Chaining of the tools is explored through the user perspective, with an in-depth overview of the background transitions between the various systems involved with regard to security requirements for the front-end nodes and the policies as seen by the users.

  11. Enabling remote access to projects in a large collaborative environment

    Energy Technology Data Exchange (ETDEWEB)

    Pais, V. [INFLPR National Institute for Laser, Plasma and Radiation Physics, Magurele (Romania); Balme, S. [CEA Cadarache, IRFM, 13 - Saint-Paul-lez-Durance (France); Iannonec, F. [Associazione EURATOM-ENEA sulla Fusione, Frascati (Italy); Strand, P. [Department of Radio and Space Science, Chalmers University of Technology, Goteborg (Sweden)

    2009-07-01

    In the context of the Integrated Tokamak Modeling Task Force, a large number of software projects are made available to the task force members, including developers and end-users. This has been achieved through a combination of tools and technologies. The front-end is represented by a Java based portal system exposing a PHP project management system, Gforge. These two applications are linked by a single sign-on mechanism, Shibboleth, and through secure HTTP request rewriting, where appropriate. Furthermore, the underlying storage facility is an OpenAFS distributed file system and the user base comes from both a network information server and an LDAP directory. Security mechanisms are those of a distributed system, with multiple access points and protocols used for reading and writing data. This document presents the challenges of integrating these different technologies and programming languages into a single, working, application presented to its users as a web portal. The chaining of the tools is explored through the user perspective, with an in-depth overview of the background transitions between the various systems involved with regard to security requirements for the front-end nodes and the policies as seen by the users. This document is composed of a poster and its abstract. (authors)

  12. A novel mechanism of high-level, broad-spectrum antibiotic resistance caused by a single base pair change in Neisseria gonorrhoeae.

    Science.gov (United States)

    Ohneck, Elizabeth A; Zalucki, Yaramah M; Johnson, Paul J T; Dhulipala, Vijaya; Golparian, Daniel; Unemo, Magnus; Jerse, Ann E; Shafer, William M

    2011-01-01

    The MtrC-MtrD-MtrE multidrug efflux pump of Neisseria gonorrhoeae confers resistance to a diverse array of antimicrobial agents by transporting these toxic compounds out of the gonococcus. Frequently in gonococcal strains, the expression of the mtrCDE operon is differentially regulated by both a repressor, MtrR, and an activator, MtrA. The mtrR gene lies 250 bp upstream of and is transcribed divergently from the mtrCDE operon. Previous research has shown that mutations in the mtrR coding region and in the mtrR-mtrCDE intergenic region increase levels of gonococcal antibiotic resistance and in vivo fitness. Recently, a C-to-T transition mutation 120 bp upstream of the mtrC start codon, termed mtr₁₂₀, was identified in strain MS11 and shown to be sufficient to confer high levels of antimicrobial resistance when introduced into strain FA19. Here we report that this mutation results in a consensus -10 element and that its presence generates a novel promoter for mtrCDE transcription. This newly generated promoter was found to be stronger than the wild-type promoter and does not appear to be subject to MtrR repression or MtrA activation. Although rare, the mtr₁₂₀ mutation was identified in an additional clinical isolate during sequence analysis of antibiotic-resistant strains cultured from patients with gonococcal infections. We propose that cis-acting mutations can develop in gonococci that significantly alter the regulation of the mtrCDE operon and result in increased resistance to antimicrobials. Gonorrhea is the second most prevalent sexually transmitted bacterial infection and a worldwide public health concern. As there is currently no vaccine against Neisseria gonorrhoeae, appropriate diagnostics and subsequent antibiotic therapy remain the primary means of infection control. However, the effectiveness of antibiotic treatment is constantly challenged by the emergence of resistant strains, mandating a thorough understanding of resistance mechanisms to

  13. 78 FR 29369 - Information Collections Being Reviewed by the Federal Communications Commission

    Science.gov (United States)

    2013-05-20

    ... browsers on mobile phones) of the Communications Act of 1934 (the Act), as amended, and the Commission's... achievable. 47 U.S.C. 255. Section 718 of the Act requires web browsers included on mobile phones to be... FEDERAL COMMUNICATIONS COMMISSION Information Collections Being Reviewed by the Federal...

  14. 78 FR 44119 - Information Collections Being Submitted for Review and Approval to the Office of Management and...

    Science.gov (United States)

    2013-07-23

    ... browsers on mobile phones) of the Communications Act of 1934 (the Act), as amended, and the Commission's.... Section 718 of the Act requires web browsers included on mobile phones to be accessible to and usable by... FEDERAL COMMUNICATIONS COMMISSION Information Collections Being Submitted for Review and Approval...

  15. 78 FR 72120 - Tennessee Valley Authority Watts Bar Nuclear Plant Unit No. 2; Order Approving Extension of...

    Science.gov (United States)

    2013-12-02

    ... install a Web browser plug-in from the NRC's Web site. Further information on the Web-based submission form, including the installation of the Web browser plug-in, is available on the NRC's public Web site... digital ID certificate is available on the NRC's public Web site at http://www.nrc.gov/site-help/e...

  16. 77 FR 39270 - In the Matter of Mr. Timothy Goold; Order Prohibiting Involvement in NRC-Licensed Activities

    Science.gov (United States)

    2012-07-02

    ... required to install a web browser plug-in from the NRC's Web site. Further information on the web-based submission form, including the installation of the Web browser plug-in, is available on the NRC's public Web... about applying for a digital ID certificate is available on the NRC's public Web site at http://www.nrc...

  17. 76 FR 41532 - Yankee Atomic Electric Company, Yankee Nuclear Power Station (Yankee-Rowe); Notice of...

    Science.gov (United States)

    2011-07-14

    ... documents through EIE, users will be required to install a Web browser plug-in from the NRC Web site. Further information on the Web- based submission form, including the installation of the Web browser plug... writing or in electronic form will be posted on the NRC Web site and on the Federal rulemaking Web site...

  18. 76 FR 70766 - Notice of Application From FMRI for Consent to an Indirect Change of Control for Source Material...

    Science.gov (United States)

    2011-11-15

    ... Web browser plug-in from the NRC Web site. Further information on the Web-based submission form, including the installation of the Web browser plug-in, is available on the NRC's public Web site at http.... You may submit comments by any one of the following methods: Federal Rulemaking Web site: Go to http...

  19. Savanna browse production. 2: Prediction | Penderis | African ...

    African Journals Online (AJOL)

    ... land managers with valuable insight whether the browse component of the system is under stress, is maintaining, or is encroaching, as well as the impact of browsers on the system. Keywords: browser carrying capacity, growing season, multivariate adaptive regression splines, predictive models. African Journal of Range ...

  20. Know How to Use Your Asthma Inhaler

    Medline Plus

    Full Text Available ... Your browser does not support iframes Cómo usar un inhalador de dosis fija con espaciador [PDF – 343 ... Your browser does not support iframes Cómo usar un inhalador de dosis fija (inhalador de boca) [PDF – ...

  1. Herbivores shape woody plant communities in the Kruger National Park: Lessons from three long-term exclosures

    Directory of Open Access Journals (Sweden)

    Benjamin J. Wigley

    2014-03-01

    Full Text Available The role of grazers in determining vegetation community compositions and structuring plant communities is well recognised in grassy systems. The role of browsers in affecting savanna woody plant communities is less clear. We used three long-term exclosures in the Kruger National Park to determine the effect of browsers on species compositions and population structures of woody communities. Species assemblages, plant traits relating to browsing and soil nutrients were compared inside and outside of the exclosures. Our results showed that browsers directly impact plant species distributions, densities and population structures by actively selecting for species with traits which make them desirable to browsers. Species with high leaf nitrogen, low total phenolic content and low acid detergent lignin appeared to be favoured by herbivores and therefore tend to be rare outside of the exclosures. This study also suggested that browsers have important indirect effects on savanna functioning, as the reduction of woody cover can result in less litter of lower quality, which in turn can result in lower soil fertility. However, the magnitude of browser effects appeared to depend on inherent soil fertility and climate. Conservation implications: Browsers were shown to have significant impacts on plant communities. They have noticeable effects on local species diversity and population structure, as well as soil nutrients. These impacts are shown to be related to the underlying geology and climate. The effects of browsers on woody communities were shown to be greater in low rainfall, fertile areas compared to high rainfall, infertile soils.

  2. Vertical Protocol Composition

    DEFF Research Database (Denmark)

    Groß, Thomas; Mödersheim, Sebastian Alexander

    2011-01-01

    composition, and it is truly commonplace in today’s communication with the diversity of VPNs and secure browser sessions. In fact, it is normal that we have several layers of secure channels: For instance, on top of a VPN-connection, a browser may establish another secure channel (possibly with a different...

  3. JSXGraph--Dynamic Mathematics with JavaScript

    Science.gov (United States)

    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…

  4. Determining the signalling overhead of two common WebRTC methods:JSON via XMLHttpRequest and SIP over WebSocket

    CSIR Research Space (South Africa)

    Adeyeye, M

    2013-09-01

    Full Text Available Web Real-Time Communication (WebRTC) introduces real-time multimedia communication as native capabilities of Web browsers. With the adoption of WebRTC the Web browsers will be able to use WebRTC to communicate with one another (peer...

  5. 76 FR 6830 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

    Science.gov (United States)

    2011-02-08

    ... corresponding to a reactor pressure of 100 psig) consistent with the flow assumed in the Emergency Core Cooling... browser plug-in from the NRC Web site. Further information on the Web-based submission form, including the installation of the Web browser plug-in, is available on the NRC's public Web site at http://www.nrc.gov/site...

  6. Use of online sources of information by dental practitioners

    DEFF Research Database (Denmark)

    Funkhouser, Ellen; Agee, Bonita S; Gordan, Valeria V

    2014-01-01

    OBJECTIVE: Estimate the proportion of dental practitioners who use online sources of information for practice guidance. METHODS: From a survey of 657 dental practitioners in The Dental Practice-Based Research Network, four indicators of online use for practice guidance were calculated: read...... journals online, obtained continuing education (CDE) through online sources, rated an online source as most influential, and reported frequently using an online source for guidance. Demographics, journals read, and use of various sources of information for practice guidance in terms of frequency...... percent, n = 34) read journals online, fewer (3 percent, n = 17) obtained CDE through online sources. Use of online information sources varied considerably by region and practice characteristics. In general, the four indicators represented practitioners with as many differences as similarities to each...

  7. Les droits de l'enfant à l'épreuve du sens

    OpenAIRE

    Hirschi, Coraline; Hanson, Karl

    2013-01-01

    L’objectif de ce travail est de mettre en exergue la place et le rôle du « sens » pour l’enfant au sein des droits participatifs ancrés dans la Convention internationale relative aux droits de l’enfant de 1989 (CDE). Cette étude démontre l’importance de prendre en compte le sens que donne l’enfant dans une dimension temporelle large dans le cadre des droits participatifs et propose d’ajouter le sens comme but explicite à part entière dans l’exercice du droit d’être entendu (art. 12 CDE). A ce...

  8. The rise of Chrome

    Directory of Open Access Journals (Sweden)

    Jonathan Tamary

    2015-10-01

    Full Text Available Since Chrome’s initial release in 2008 it has grown in market share, and now controls roughly half of the desktop browsers market. In contrast with Internet Explorer, the previous dominant browser, this was not achieved by marketing practices such as bundling the browser with a pre-loaded operating system. This raises the question of how Chrome achieved this remarkable feat, while other browsers such as Firefox and Opera were left behind. We show that both the performance of Chrome and its conformance with relevant standards are typically better than those of the two main contending browsers, Internet Explorer and Firefox. In addition, based on a survey of the importance of 25 major features, Chrome product managers seem to have made somewhat better decisions in selecting where to put effort. Thus the rise of Chrome is consistent with technical superiority over the competition.

  9. Model of mouth-to-mouth transfer of bacterial lipoproteins through inner membrane LolC, periplasmic LolA, and outer membrane LolB

    OpenAIRE

    Okuda, Suguru; Tokuda, Hajime

    2009-01-01

    Outer membrane-specific lipoproteins in Escherichia coli are released from the inner membrane by an ATP-binding cassette transporter, the LolCDE complex, which causes the formation of a soluble complex with a periplasmic molecular chaperone, LolA. LolA then transports lipoproteins to the outer membrane where an outer membrane receptor, LolB, incorporates lipoproteins into the outer membrane. The molecular mechanisms underlying the Lol-dependent lipoprotein sorting have been clarified in detai...

  10. Characterization of the Pseudomonas aeruginosa Lol system as a lipoprotein sorting mechanism.

    Science.gov (United States)

    Tanaka, Shin-Ya; Narita, Shin-Ichiro; Tokuda, Hajime

    2007-05-04

    Escherichia coli lipoproteins are localized to either the inner or the outer membrane depending on the residue that is present next to the N-terminal acylated Cys. Asp at position 2 causes the retention of lipoproteins in the inner membrane. In contrast, the accompanying study (9) revealed that the residues at positions 3 and 4 determine the membrane specificity of lipoproteins in Pseudomonas aeruginosa. Since the five Lol proteins involved in the sorting of E. coli lipoproteins are conserved in P. aeruginosa, we examined whether or not the Lol proteins of P. aeruginosa are also involved in lipoprotein sorting but utilize different signals. The genes encoding LolCDE, LolA, and LolB homologues were cloned and expressed. The LolCDE homologue thus purified was reconstituted into proteoliposomes with lipoproteins. When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. Lipoproteins were then incorporated into the outer membrane depending on a LolB homologue. As revealed in vivo, lipoproteins with Lys and Ser at positions 3 and 4, respectively, remained in proteoliposomes. On the other hand, E. coli LolCDE released lipoproteins with this signal and transferred them to LolA of not only E. coli but also P. aeruginosa. These results indicate that Lol proteins are responsible for the sorting of lipoproteins to the outer membrane of P. aeruginosa, as in the case of E. coli, but respond differently to inner membrane retention signals.

  11. iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency.

    Science.gov (United States)

    Chu, Pu; Yan, Gui Xia; Yang, Qing; Zhai, Li Na; Zhang, Cheng; Zhang, Feng Qi; Guan, Rong Zhan

    2015-01-15

    Photosynthesis, the primary source of plant biomass, is important for plant growth and crop yield. Chlorophyll is highly abundant in plant leaves and plays essential roles in photosynthesis. We recently isolated a chlorophyll-deficient mutant (cde1) from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Herein, quantitative proteomics analysis using the iTRAQ approach was conducted to investigate cde1-induced changes in the proteome. We identified 5069 proteins from B. napus leaves, of which 443 showed differential accumulations between the cde1 mutant and its corresponding wild-type. The differentially accumulated proteins were found to be involved in photosynthesis, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites, carbon fixation, spliceosome, mRNA surveillance and RNA degradation. Our results suggest that decreased abundance of chlorophyll biosynthetic enzymes and photosynthetic proteins, impaired carbon fixation efficiency and disturbed redox homeostasis might account for the reduced chlorophyll contents, impaired photosynthetic capacity and increased lipid peroxidation in this mutant. Epigenetics was implicated in the regulation of gene expression in cde1, as proteins involved in DNA/RNA/histone methylation and methylation-dependent chromatin silencing were up-accumulated in the mutant. Biological significance Photosynthesis produces more than 90% of plant biomass and is an important factor influencing potential crop yield. The pigment chlorophyll plays essential roles in light harvesting and energy transfer during photosynthesis. Mutants deficient in chlorophyll synthesis have been used extensively to investigate the chlorophyll metabolism, development and photosynthesis. However, limited information is available with regard to the changes of protein profiles upon chlorophyll deficiency. Here, a combined physiological, histological, proteomics and molecular analysis revealed several important pathways associated with

  12. Proximate Composition and Mineral Content in Different ,Types of

    African Journals Online (AJOL)

    The: concentration of protein in traditional and ... resuiis:in d;je~t types o[togwa wjth yariatiOl? in proximate comfX?sition, energy density and~mirieral content. " . ..... hi the preparation of simulated togwa l .,. "'.' .. IngredientS ,Dtj<: "\\C!~de P~o-.' Ct;ude fi-. Fat: --Ash. Caroo-. Energy matte; r tein (0/0) . ,; bee hydrate value .: (%).

  13. Role of Tellurite Resistance Operon in Filamentous Growth of Yersinia pestis in Macrophages.

    Science.gov (United States)

    Ponnusamy, Duraisamy; Clinkenbeard, Kenneth D

    2015-01-01

    Yersinia pestis initiates infection by parasitism of host macrophages. In response to macrophage infections, intracellular Y. pestis can assume a filamentous cellular morphology which may mediate resistance to host cell innate immune responses. We previously observed the expression of Y. pestis tellurite resistance proteins TerD and TerE from the terZABCDE operon during macrophage infections. Others have observed a filamentous response associated with expression of tellurite resistance operon in Escherichia coli exposed to tellurite. Therefore, in this study we examine the potential role of Y. pestis tellurite resistance operon in filamentous cellular morphology during macrophage infections. In vitro treatment of Y. pestis culture with sodium tellurite (Na2TeO3) caused the bacterial cells to assume a filamentous phenotype similar to the filamentous phenotype observed during macrophage infections. A deletion mutant for genes terZAB abolished the filamentous morphologic response to tellurite exposure or intracellular parasitism, but without affecting tellurite resistance. However, a terZABCDE deletion mutant abolished both filamentous morphologic response and tellurite resistance. Complementation of the terZABCDE deletion mutant with terCDE, but not terZAB, partially restored tellurite resistance. When the terZABCDE deletion mutant was complemented with terZAB or terCDE, Y. pestis exhibited filamentous morphology during macrophage infections as well as while these complemented genes were being expressed under an in vitro condition. Further in E. coli, expression of Y. pestis terZAB, but not terCDE, conferred a filamentous phenotype. These findings support the role of Y. pestis terZAB mediation of the filamentous response phenotype; whereas, terCDE confers tellurite resistance. Although the beneficial role of filamentous morphological responses by Y. pestis during macrophage infections is yet to be fully defined, it may be a bacterial adaptive strategy to macrophage

  14. The factors that limit activities of certified diabetes educators in Japan: a questionnaire survey

    OpenAIRE

    Kishimoto, Miyako; Noda, Mitsuhiko

    2014-01-01

    Background The certified diabetes educator (CDE) is a qualification awarded to health professionals with specialized knowledge, skills, and experiences in diabetes management and education. To clarify whether CDEs consider themselves to be working sufficiently, in other words, making sufficient use of their specialized skills or not, a questionnaire survey was conducted. The participants were persons involved in diabetes-related educational seminars and medical personnel engaged in diabetes c...

  15. JPRS Report, West Europe.

    Science.gov (United States)

    1987-06-29

    always be the subject of a good electoral victory. Jorge Sampaio. At the head of the list in Santarem, he became one of the most important figures...partisanship of the "chief," that is, Cavaco Silva. However, he had always been his supporter. Margarida Borges de Carvalho. PSD militant and... Luis Catarino. An attorney, former director of the MDP/CDE and instigator of the ID, he was a deputy for this party at the Constituent Assembly

  16. Testing - Smart strategy for safety and mission quality

    Science.gov (United States)

    Rodney, George A.

    The paper is concerned with the need for a comprehensive test plan for the Space Station Freedom (SST) that would fully verify specification compliance and be based on an error budget. In particular, attention is given to some lessons learned from other NASA programs and the principal challenges for SSF testing, including phase C/D/E agreements, testing parameters, phase testing, and the human element. The importance of close teamwork between the NASA/Contractor systems engineers and assurance engineers is emphasized.

  17. Effect of Lineage-Specific Metabolic Traits of Lactobacillus reuteri on Sourdough Microbial Ecology

    OpenAIRE

    Lin, Xiaoxi B.; Gänzle, Michael G.

    2014-01-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increas...

  18. Technical Evaluation Report 2: Selection of Collaborative Tools

    OpenAIRE

    Tom Kane; Jon Baggaley

    2002-01-01

    The previous report summarised the findings of an online survey concerning Master’s of Distance Education students’ attitudes to online collaborative tools. The respondents in the study were 135 graduate students and faculty members of Athabasca University’s Centre for Distance Education (CDE). They demonstrated particular interest in tools that offer the following features: file sharing; automatic synchronisation of documentation for the group; audio conferencing; text chat; and privacy. In ...

  19. Bistand til risikovurdering (evt. ændringer af konklusioner af tidligere risikovurdering) . Zea mays (MON863; MON863x810). Opdateret rammenotat samt supplerende oplysninger til sagen. Modtaget 28-10-2004, deadline: snarest muligt, svar 01-11-2004

    DEFF Research Database (Denmark)

    Strandberg, Morten Tune; Damgaard, Christian; Kjellsson, Gøsta

    2004-01-01

    "Vedr. C/DE/02/09: Om Monsantos svar på Pusztai’s kritik giver anledning til ændring af DMU’s kommentarer til GM-majs MON863. Uanset om effekterne er tilfældige elller ej, er størrelsen af de mulige effekter på rotternes sundhed uden betydning i relation til den økologiske risikovurdering. Dermed...

  20. Control of gdhR Expression in Neisseria gonorrhoeae via Autoregulation and a Master Repressor (MtrR of a Drug Efflux Pump Operon

    Directory of Open Access Journals (Sweden)

    Corinne E. Rouquette-Loughlin

    2017-04-01

    Full Text Available The MtrCDE efflux pump of Neisseria gonorrhoeae contributes to gonococcal resistance to a number of antibiotics used previously or currently in treatment of gonorrhea, as well as to host-derived antimicrobials that participate in innate defense. Overexpression of the MtrCDE efflux pump increases gonococcal survival and fitness during experimental lower genital tract infection of female mice. Transcription of mtrCDE can be repressed by the DNA-binding protein MtrR, which also acts as a global regulator of genes involved in important metabolic, physiologic, or regulatory processes. Here, we investigated whether a gene downstream of mtrCDE, previously annotated gdhR in Neisseria meningitidis, is a target for regulation by MtrR. In meningococci, GdhR serves as a regulator of genes involved in glucose catabolism, amino acid transport, and biosynthesis, including gdhA, which encodes an l-glutamate dehydrogenase and is located next to gdhR but is transcriptionally divergent. We report here that in N. gonorrhoeae, expression of gdhR is subject to autoregulation by GdhR and direct repression by MtrR. Importantly, loss of GdhR significantly increased gonococcal fitness compared to a complemented mutant strain during experimental murine infection. Interestingly, loss of GdhR did not influence expression of gdhA, as reported for meningococci. This variance is most likely due to differences in promoter localization and utilization between gonococci and meningococci. We propose that transcriptional control of gonococcal genes through the action of MtrR and GdhR contributes to fitness of N. gonorrhoeae during infection.

  1. The Sea Breeze Circulation during the Land Sea Breeze Experiment (LASBEX) in Central California

    Science.gov (United States)

    1988-09-01

    conditions, an offshore gradient wind will generate a frontal zone at tie leading cde of a sea breeze .\\tkin, on, 19 1). Estoque 1962) notes in his model...the sodar in the de - tection and mappin2 of sea breeze events and to compare its measured wrind field with that of the lidar. A case study on 16...lidar operated under computer control and had real-time data processing and color display capabiiites. Tile system could compute the zero, first and

  2. [Diagnostic evaluation of the developmental level in children identified at risk of delay through the Child Development Evaluation Test].

    Science.gov (United States)

    Rizzoli-Córdoba, Antonio; Campos-Maldonado, Martha Carmen; Vélez-Andrade, Víctor Hugo; Delgado-Ginebra, Ismael; Baqueiro-Hernández, César Iván; Villasís-Keever, Miguel Ángel; Reyes-Morales, Hortensia; Ojeda-Lara, Lucía; Davis-Martínez, Erika Berenice; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Sidonio-Aguayo, Beatriz; Palma-Tavera, Josuha Alexander; Muñoz-Hernández, Onofre

    The Child Development Evaluation (or CDE Test) was developed in Mexico as a screening tool for child developmental problems. It yields three possible results: normal, slow development or risk of delay. The modified version was elaborated using the information obtained during the validation study but its properties according to the base population are not known. The objective of this work was to establish diagnostic confirmation of developmental delay in children 16- to 59-months of age previously identified as having risk of delay through the CDE Test in primary care facilities. A population-based cross-sectional study was conducted in one Mexican state. CDE test was administered to 11,455 children 16- to 59-months of age from December/2013 to March/2014. The eligible population represented the 6.2% of the children (n=714) who were identified at risk of delay through the CDE Test. For inclusion in the study, a block randomization stratified by sex and age group was performed. Each participant included in the study had a diagnostic evaluation using the Battelle Development Inventory, 2 nd edition. From the 355 participants included with risk of delay, 65.9% were male and 80.2% were from rural areas; 6.5% were false positives (Total Development Quotient ˃90) and 6.8% did not have any domain with delay (Domain Developmental Quotient motor 55.5%; and adaptive 41.7%. There were significant differences in the percentages of delay both by age and by domain/subdomain evaluated. In 93.2% of the participants, developmental delay was corroborated in at least one domain evaluated. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  3. Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa.

    Science.gov (United States)

    Li, Jimeng; Liu, Bo; Cheng, Feng; Wang, Xiaowu; Aarts, Mark G M; Wu, Jian

    2014-07-01

    Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  4. Fundamental Understanding of Crack Growth in Structural Components of Generation IV Supercritical Light Water Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Iouri I. Balachov; Takao Kobayashi; Francis Tanzella; Indira Jayaweera; Palitha Jayaweera; Petri Kinnunen; Martin Bojinov; Timo Saario

    2004-11-17

    This work contributes to the design of safe and economical Generation-IV Super-Critical Water Reactors (SCWRs) by providing a basis for selecting structural materials to ensure the functionality of in-vessel components during the entire service life. During the second year of the project, we completed electrochemical characterization of the oxide film properties and investigation of crack initiation and propagation for candidate structural materials steels under supercritical conditions. We ranked candidate alloys against their susceptibility to environmentally assisted degradation based on the in situ data measure with an SRI-designed controlled distance electrochemistry (CDE) arrangement. A correlation between measurable oxide film properties and susceptibility of austenitic steels to environmentally assisted degradation was observed experimentally. One of the major practical results of the present work is the experimentally proven ability of the economical CDE technique to supply in situ data for ranking candidate structural materials for Generation-IV SCRs. A potential use of the CDE arrangement developed ar SRI for building in situ sensors monitoring water chemistry in the heat transport circuit of Generation-IV SCWRs was evaluated and proved to be feasible.

  5. HmsC Controls Yersinia pestis Biofilm Formation in Response to Redox Environment

    Directory of Open Access Journals (Sweden)

    Gai-Xian Ren

    2017-08-01

    Full Text Available Yersinia pestis biofilm formation, controlled by intracellular levels of the second messenger molecule cyclic diguanylate (c-di-GMP, is important for blockage-dependent plague transmission from fleas to mammals. HmsCDE is a tripartite signaling system that modulates intracellular c-di-GMP levels to regulate biofilm formation in Y. pestis. Previously, we found that Y. pestis biofilm formation is stimulated in reducing environments in an hmsCDE-dependent manner. However, the mechanism by which HmsCDE senses the redox state remains elusive. Using a dsbA mutant and the addition of Cu2+ to simulate reducing and oxidizing periplasmic environments, we found that HmsC protein levels are decreased and the HmsC-HmsD protein-protein interaction is weakened in a reducing environment. In addition, we revealed that intraprotein disulphide bonds are critical for HmsC since breakage lowers protein stability and diminishes the interaction with HmsD. Our results suggest that HmsC might play a major role in sensing the environmental changes.

  6. Common Data Elements for Spinal Cord Injury Clinical Research: A National Institute for Neurological Disorders and Stroke Project

    Science.gov (United States)

    Biering-Sørensen, Fin; Alai, Sherita; Anderson, Kim; Charlifue, Susan; Chen, Yuying; DeVivo, Michael; Flanders, Adam E.; Jones, Linda; Kleitman, Naomi; Lans, Aria; Noonan, Vanessa K.; Odenkirchen, Joanne; Steeves, John; Tansey, Keith; Widerström-Noga, Eva; Jakeman, Lyn B.

    2015-01-01

    Objective To develop a comprehensive set of common data elements (CDEs), data definitions, case report forms and guidelines for use in spinal cord injury (SCI) clinical research, as part of the CDE project at the National Institute of Neurological Disorders and Stroke (NINDS) of the USA National Institutes of Health. Setting International Working Groups Methods Nine working groups composed of international experts reviewed existing CDEs and instruments, created new elements when needed, and provided recommendations for SCI clinical research. The project was carried out in collaboration with and cross-referenced to development of the International Spinal Cord Society (ISCoS) International SCI Data Sets. The recommendations were compiled, subjected to internal review, and posted online for external public comment. The final version was reviewed by all working groups and the NINDS CDE team prior to release. Results The NINDS SCI CDEs and supporting documents are publically available on the NINDS CDE website and the ISCoS website. The CDEs span the continuum of SCI care and the full range of domains of the International Classification of Functioning, Disability and Health. Conclusions Widespread use of common data elements can facilitate SCI clinical research and trial design, data sharing, and retrospective analyses. Continued international collaboration will enable consistent data collection and reporting, and will help ensure that the data elements are updated, reviewed and broadcast as additional evidence is obtained. PMID:25665542

  7. Design and implementation of a computer based site operations log for the ARM Program

    International Nuclear Information System (INIS)

    Tichler, J.L.; Bernstein, H.J.; Bobrowski, S.F.; Melton, R.B.; Campbell, A.P.; Edwards, D.M.; Kanciruk, P.; Singley, P.T.

    1992-01-01

    The Atmospheric Radiation Measurement (ARM) Program is a Department of Energy (DOE) research effort to reduce the uncertainties found in general circulation and other models due to the effects of clouds and solar radiation. ARM will provide an experimental testbed for the study of important atmospheric effects, particularly cloud and radiative processes, and testing of parameterizations of the processes for use in atmospheric models. The design of the testbed known as the Clouds and Radiation Testbed (CART), calls for five, long-term field data collection sites. The first site, located in the Southern Great Plains (SGP) in Lamont, OK began operation in the spring of 1992. The CART Data Environment (CDE) is the element of the testbed which acquires the basic observations from the instruments and processes them to meet the ARM requirements. A formal design was used to develop a description of the logical requirements for the CDE. This paper discusses the design and prototype implementation of a part of the CDE known as the site operations log, which records metadata defining the environment within which the data produced by the instruments is collected

  8. Recommendations for the National Institute for Neurologic Disorders and Stroke spinal cord injury common data elements for children and youth with SCI.

    Science.gov (United States)

    Mulcahey, M J; Vogel, L C; Sheikh, M; Arango-Lasprilla, J C; Augutis, M; Garner, E; Hagen, E M; Jakeman, L B; Kelly, E; Martin, R; Odenkirchen, J; Scheel-Sailer, A; Schottler, J; Taylor, H; Thielen, C C; Zebracki, K

    2017-04-01

    In 2014, the adult spinal cord injury (SCI) common data element (CDE) recommendations were made available. This project was a review of the adult SCI CDE for relevance to children and youth with SCI. The objective of this study was to review the National Institute of Neurologic Disorders and Stroke (NINDS) adult SCI CDEs for relevance to children and youth with SCI. International. The pediatric working group consisted of international members with varied fields of expertise related to pediatric SCI. The group convened biweekly meetings for 6 months in 2015. All of the adult SCI CDEs were reviewed, evaluated and modified/created for four age groups: 0-5 years, 6-12 years, 13-15 years and 16-18 years. Whenever possible, results of published research studies were used to guide recommendations. In the absence of empirical support, grey literature and international content expert consensus were garnered. Existing pediatric NINDS CDEs and new CDEs were developed in areas where adult recommendations were not appropriate. After internal working group review of domain recommendations, these pediatric CDEs were vetted during a public review from November through December 2015. Version 1.0 of the pediatric SCI CDEs was posted in February 2016. The pediatric SCI CDEs are incorporated directly into the NINDS SCI CDE sets and can be found at https://commondataelements.ninds.nih.gov.

  9. [Population-based study of child developmental screening in Mexican PROSPERA beneficiaries younger than 5 years old].

    Science.gov (United States)

    Rizzoli-Córdoba, Antonio; Martell-Valdez, Liliana; Delgado-Ginebra, Ismael; Villasís-Keever, Miguel Ángel; Reyes-Morales, Hortensia; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Vargas-López, Guillermo; Muñoz-Hernández, Onofre

    Evaluación del Desarrollo Infantil or Child Development Evaluation (CDE) test, a screening tool designed and validated in Mexico, classifies child development as normal (green) or abnormal (developmental lag or yellow and risk of delay or red). Population-based results of child development level with this tool are not known. The objective of this work was to evaluate the developmental level of children aged 1-59 months living in poverty (PROSPERA program beneficiaries) through application of the CDE test. CDE tests were applied by specifically trained and standardized personnel to children motor and social areas were more affected in children from rural areas; fine motor skills, language and knowledge were more affected in males. The proportion of children with abnormal results is similar to other population-based studies. The highest rate in older children reinforces the need for an early-based intervention. The different pattern of areas affected between urban and rural areas suggests the need for a differentiated intervention. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  10. Combined 30-degree bevel up and down technique against 0-degree phaco tip for phacoemulsification surgery of hard cataracts

    Directory of Open Access Journals (Sweden)

    Joshi RS

    2017-06-01

    Full Text Available Rajesh Subhash Joshi, Sonal Jayant Muley Department of Ophthalmology, Vasantrao Naik Government Medical College, Yavatmal, Maharashtra, India Purpose: To evaluate the effective phaco time (EPT, cumulative dissipated energy (CDE and nucleus emulsification time (NET as phaco parameters with 0- and 30-degree phaco tip. Patients and methods: This prospective, interventional and observational case series included 294 patients scheduled for cataract removal by phacoemulsification technique. Patients with nuclear cataracts of grade 4 and 5 nuclear opalescence of Lens Opacities Classification System III were included in the study. Patients were consecutively allocated to phaco chop technique with 0-degree (0-degree group, n=147 and combined bevel up and down position using 30-degree phaco tip (combined bevel up/down group, n=147. The 0-degree group had phacoemulsification with 0-degree phaco tip, while the 30-degree group had chopping of the nucleus with bevel down phaco tip and emulsification of nuclear fragments was accomplished with bevel up tip. EPT, CDE, NET and intraoperative complications were noted and compared between the groups using analysis of variance. Results: Average EPT, CDE and NET were lower in the 30-degree group than in the 0-degree group. However, no statistically significant difference was found in EPT (P=0.0733, CDE (P=0.0663 and NET (P=0.0633 between the two groups. No serious intraoperative complications were noted. The anterior chamber was maintained throughout the procedure in both groups. No patients had wound burn and miosis during the procedure. None of the patients developed bullous keratopathy, uveitis and cystoid macular edema during the follow-up period. Conclusion: Combined bevel up and down 30-degree tip can yield effective hard nucleus phacoemulsification. Bevel down tip of 30-degree helps in effective chopping and bevel up tip assists in emulsification of the nuclear fragments. Although combined bevel up and down 30

  11. AN INSECURE WILD WEB: A LARGE-SCALE STUDY OF EFFECTIVENESS OF WEB SECURITY MECHANISMS

    Directory of Open Access Journals (Sweden)

    Kailas Patil

    2017-03-01

    Full Text Available This research work presents a large-scale study of the problems in real-world web applications and widely-used mobile browsers. Through a large-scale experiment, we find inconsistencies in Secure Socket Layer (SSL warnings among popular mobile web browsers (over a billion users download. The majority of popular mobile browsers on the Google Play Store either provide incomplete information in SSL warnings shown to users or failed to provide SSL warnings in the presence of security certificate errors, thus making it a difficult task even for a security savvy user to make an informed decision. In addition, we find that 28% of websites are using mixed content. Mixed content means a secure website (https loads a sub resource using insecure HTTP protocol. The mixed content weakens the security of entire website and vulnerable to man-in-the-middle (MITM attacks. Furthermore, we inspected the default behavior of mobile web browsers and report that majority of mobile web browsers allow execution of mixed content in web applications, which implies billions of mobile browser users are vulnerable to eavesdropping and MITM attacks. Based on our findings, we make recommendations for website developers, users and browser vendors.

  12. Enumeration of minimal stoichiometric precursor sets in metabolic networks.

    Science.gov (United States)

    Andrade, Ricardo; Wannagat, Martin; Klein, Cecilia C; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V; Stougie, Leen; Sagot, Marie-France

    2016-01-01

    What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.

  13. US NDC Modernization Iteration E2 Prototyping Report: User Interface Framework

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, Jennifer E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Palmer, Melanie A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Vickers, James Wallace [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Voegtli, Ellen M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    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).

  14. Releasing CSS

    CERN Document Server

    Schmitt, Christopher

    2006-01-01

    In an industry that communicates with terms such as "Browser Hell" and "browser wars," a web designer can be excused for having some anxiety over Microsoft's recent upgrade of Internet Explorer 6 (IE6) to Internet Explorer 7 (IE7). Web designers should ask the following questions: What problems does IE6 possess and what fixes does IE7 provide? What part of the Cascading Style Sheets (CSS) specification does IE7 for Windows support? How can web designers work around any problems that exist within IE7's support for CSS? While web designers are testing their designs on the latest browser, how f

  15. Pro HTML 5 programming powerful APIs for richer internet application development

    CERN Document Server

    Lubbers, Peter; Salim, Frank

    2010-01-01

    HTML5 is here, and with it, web applications take on a power, ease, scalability, and responsiveness like never before. In this book, developers will learn how to use the latest cutting-edge HTML5 web technology - available in the most recent versions of modern browsers - to build web applications with unparalleled functionality, speed, and responsiveness. * Explains how you can create real-time HTML5 applications that tap the full potential of modern browsers * Provides practical, real-world examples of HTML5 features in action * Shows which HTML5 features are supported in current browsers * C

  16. NASA PDS IMG: Accessing Your Planetary Image Data

    Science.gov (United States)

    Padams, J.; Grimes, K.; Hollins, G.; Lavoie, S.; Stanboli, A.

    2017-06-01

    PDS IMG continues to develop and improve tools, like the Image Atlas, to support both the wide variety of available data and the ease of access to that data both interactively, through a web browser, and programmatically through web services.

  17. Eros-based Confined Capability Client

    National Research Council Canada - National Science Library

    Shapiro, Jonathan S

    2006-01-01

    .... This was accomplished by constructing of a single exemplar application, a web browser using capability-based structuring techniques, and determining whether this application can defend itself against hostile content...

  18. Sesamoid Injuries in the Foot

    Science.gov (United States)

    ... Javascript in your browser. Sesamoid Injuries in the Foot What Is a Sesamoid? A sesamoid is a ... contributing factor. Types of Sesamoid Injuries in the Foot There are three types of sesamoid injuries in ...

  19. Malignant Melanoma of the Foot

    Science.gov (United States)

    ... Javascript in your browser. Malignant Melanoma of the Foot What Is Malignant Melanoma? Melanoma is a cancer ... age groups, even the young. Melanoma in the Foot Melanoma that occurs in the foot or ankle ...

  20. Population densities of eastern black rhinoceros : unravelling the controls

    NARCIS (Netherlands)

    Ouma, B.O.

    2014-01-01

    Key words: black rhinoceros, browser, corticosterone, diet, density dependence, minerals, moisture, physiological stress, savanna, soil nutrients, woody cover.   Understanding the forces that cause variability in population sizes is a central theme in ecology. The limiting factor in

  1. RxClass

    Data.gov (United States)

    U.S. Department of Health & Human Services — The RxClass Browser is a web application for exploring and navigating through the class hierarchies to find the RxNorm drug members associated with each class....

  2. An XML-Based Knowledge Management System of Port Information for U.S. Coast Guard Cutters

    National Research Council Canada - National Science Library

    Stewart, Jeffrey

    2003-01-01

    .... The system uses XML technologies in server/client and stand alone environments. With a web browser, the user views and navigates the system's content from a downloaded file collection or from a centralized data source via a network connection...

  3. A Web-Based Architecture for Interactive Electronic Technical Manuals (IETMs)

    National Research Council Canada - National Science Library

    Jorgensen, Eric L; Fuller, Joseph J

    2006-01-01

    ...) Interactive Electronic Technical Manuals (IETMs) so that an end user can view any DoD IETM, no matter what the source, using only one electronic display device and common set of browser software...

  4. Know How to Use Your Asthma Inhaler

    Medline Plus

    Full Text Available ... Profile Tables and Graphs Asthma Call-back Survey Technical Information Prevalence Tables BRFSS Prevalence Data NHIS Prevalence ... inhaler with a spacer Your browser does not support iframes Using a metered dose inhaler with a ...

  5. Home Health Compare: Find a Home Health Agency

    Science.gov (United States)

    ... page could not be loaded. The Medicare.gov Home page currently does not fully support browsers with " ... widget - Select to show Back to top Footer Home A federal government website managed and paid for ...

  6. The Effectiveness of Web-Based Instruction

    National Research Council Canada - National Science Library

    Wisher, Robert

    2003-01-01

    .... A search of the literature between 1996 and 2002 identified more than 500 reports concerning Web-based courses, that is courses delivered over the Internet or an intranet and conveyed through a browser...

  7. Intranet Implementation in a Context of Web Technology Discovery

    National Research Council Canada - National Science Library

    Asnawi, Amrullah

    1999-01-01

    This thesis presents a model of intranet implementation for a military facility within the context of an organization that is in the process of discovering Web technology and the browser as a central...

  8. Administration for Children and Families

    Science.gov (United States)

    ... browser with HTML5 support. Dad Jokes Rule! New fatherhood PSAs celebrate “dad jokes” as a means for ... the bonds between them and creating lasting memories. Fatherhood Involvement PSAs Visit the Office of Family Assistance ...

  9. The comparative analysis of selected interactive data presentation techniques on the example of the land use structure in the commune of Tomice

    Directory of Open Access Journals (Sweden)

    Król Karol

    2016-09-01

    Full Text Available The authors present the results of a comparative analysis of selected techniques and programming tools for building interactive data presentation in the form of diagrams and maps generated in the browser.

  10. ToxMystery

    Science.gov (United States)

    ... the browser is being used. The javascript is functional ToxMystery uses Adobe Flash Player. If you cannot install Flash Player, please use the TEXT VERSION of ToxMystery. If you can install the ...

  11. Eldercare Locator

    Science.gov (United States)

    ... content Skip Navigation Department of Health and Human Services Your Browser does not support javascript, so the search function on this page is disabled 1-800-677-1116 Home About Resources Welcome ...

  12. Know How to Use Your Asthma Inhaler

    Medline Plus

    Full Text Available ... Submit Search The CDC Asthma Note: Javascript is disabled or is not supported by your browser. For ... Email CDC-INFO U.S. Department of Health & Human Services HHS/Open USA.gov TOP

  13. Heads Up: Concussion in Youth Sports

    Medline Plus

    Full Text Available ... CDC Injury Prevention & Control: Concussion Note: Javascript is disabled or is not supported by your browser. For ... Email CDC-INFO U.S. Department of Health & Human Services HHS/Open USA.gov Top

  14. Adult Day Care

    Science.gov (United States)

    ... content Skip Navigation Department of Health and Human Services Your Browser does not support javascript, so the search function on this page is disabled 1-800-677-1116 Home > Resources > Factsheets > Adult ...

  15. Home Health Care

    Science.gov (United States)

    ... content Skip Navigation Department of Health and Human Services Your Browser does not support javascript, so the search function on this page is disabled 1-800-677-1116 Home > Resources > Factsheets > Home ...

  16. Home Modifications

    Science.gov (United States)

    ... content Skip Navigation Department of Health and Human Services Your Browser does not support javascript, so the search function on this page is disabled 1-800-677-1116 Home > Resources > Factsheets > Home ...

  17. Measuring Physical Activity Intensity

    Medline Plus

    Full Text Available ... Search The CDC Physical Activity Note: Javascript is disabled or is not supported by your browser. For ... Email CDC-INFO U.S. Department of Health & Human Services HHS/Open USA.gov Top

  18. History of Bioterrorism: Botulism

    Medline Plus

    Full Text Available ... CDC Emergency Preparedness and Response Note: Javascript is disabled or is not supported by your browser. For ... Email CDC-INFO U.S. Department of Health & Human Services HHS/Open USA.gov Top

  19. Face the Facts

    Science.gov (United States)

    ... content Skip Navigation Department of Health and Human Services Your Browser does not support javascript, so the search function on this page is disabled 1-800-677-1116 Home > Resources > Factsheets > Face ...

  20. Training Results and Information Network

    Data.gov (United States)

    US Agency for International Development — TraiNet is USAID's official training data management system that is accessed from a web browser and the entry point for data about training programs and participants...

  1. Private Web Browsing

    National Research Council Canada - National Science Library

    Syverson, Paul F; Reed, Michael G; Goldschlag, David M

    1997-01-01

    .... These are both kept confidential from network elements as well as external observers. Private Web browsing is achieved by unmodified Web browsers using anonymous connections by means of HTTP proxies...

  2. Toe and Metatarsal Fractures (Broken Toes)

    Science.gov (United States)

    ... enable Javascript in your browser. Toe and Metatarsal Fractures (Broken Toes) The structure of the foot is ... received in an emergency room. What Is a Fracture? A fracture is a break in the bone. ...

  3. Binge Drinking

    Medline Plus

    Full Text Available ... is not supported by your browser. For this reason, some items on this page will be unavailable. For more information about this ... Cancer Be Brave No Excuses No Excuses (:60) No ...

  4. Know How to Use Your Asthma Inhaler

    Medline Plus

    Full Text Available ... avoid an attack by taking your medicine exactly as your doctor or other medical professional tells you ... keep them with your Asthma Action Plan. Using a metered dose inhaler with a spacer Your browser ...

  5. Airborne Hazards and Open Burn Pit Registry

    Science.gov (United States)

    ... problem if you are in a high security environment where this is disabled by a network policy. The Registry will work in JavaScript-enabled browsers such as: Google Chrome 17+ Mozilla Firefox 12+ Internet Explorer 10+ ...

  6. Binge Drinking

    Medline Plus

    Full Text Available ... is not supported by your browser. For this reason, some items on this page will be unavailable. ... Violence Injury Prevention Research In the Swim of Things Safe Teen Drivers Life Stages & Populations A Killer ...

  7. Diabetes HealthSense: Resources for Living Well

    Medline Plus

    Full Text Available ... print this page, please use your browser's File menu and select print. To email this page, please ... address bar, then use your "Bookmarks" or "Favorites" menu to add the page to your favorites. To ...

  8. Contact Center Manager Administration (CCMA)

    Data.gov (United States)

    Social Security Administration — CCMA is the server that provides a browser-based tool for contact center administrators and supervisors. It is used to manage and configure contact center resources...

  9. Commercial Technology at the Tactical Edge

    Science.gov (United States)

    2013-06-01

    Free Communications WICKR, Speech-to-text, Siri Information Sharing, Access Dropbox, browsers, Splashtop Whiteboard Document and Media Exploitation...Other examples include wearable components such as a Personal Digital Assistant (PDA) worn on an arm, or a head-mounted display or sleeves that...Free Communications WICKR, Speech-to-text, Siri Information Sharing, Access Dropbox, browsers, Splashtop Whiteboard Document and Media Exploitation

  10. Didelio formato nuotraukų manipuliavimo naršyklėje realizavimas ir algoritmų tyrimas

    OpenAIRE

    Pocius, Deivydas

    2017-01-01

    Large format photo printing market is constantly growing. Companies which are offering large-scale printing usually only let you upload your images file - PDF, "Adobe Photoshop", "Adobe InDesing" and in other formats in their websites. HTML5 standard introduced new technologies that created more possibilities for browsers and more companies are investing in this area. That's why we can assume that this technology has enough functionality for creating browser editor, which is ab...

  11. Certificate Transparency with Privacy

    Directory of Open Access Journals (Sweden)

    Eskandarian Saba

    2017-10-01

    Full Text Available Certificate transparency (CT is an elegant mechanism designed to detect when a certificate authority (CA has issued a certificate incorrectly. Many CAs now support CT and it is being actively deployed in browsers. However, a number of privacy-related challenges remain. In this paper we propose practical solutions to two issues. First, we develop a mechanism that enables web browsers to audit a CT log without violating user privacy. Second, we extend CT to support non-public subdomains.

  12. Extensible 3D (X3D) Graphics Clouds for Geographic Information Systems

    Science.gov (United States)

    2008-03-01

    browser such as Microsoft Internet Explorer or Netscape using an X3D or VRML supporting plug-in. The benefits of diverse support can cause...the cloud and in turn presented to the browser as a VRML file. While the methods researched and developed within this thesis are mostly manual...it is possible to completely author either an X3D(XML) or VRML file to produce the same cloud structures. For long-term data-driven production

  13. GeoScope, a system to finger-print vibrations

    OpenAIRE

    Ziemann, Volker

    2017-01-01

    We describe a system that interfaces a SM-24 geophone to a NodeMCU micro-controller and allows to display spectrograms on any web browser. The independent sensor nodes can be very exibly placed anywhere because they are battery-powered and connected to the network by WIFI. The presentation software is based on Javascript and can be used in an Internet browser on any computer connected to the same network.

  14. Simulation of chloride transport based description soil structure

    International Nuclear Information System (INIS)

    Mahmood-ul-Hassan, M.; Akhtar, M.S.; Gill, S.M.; Nabi, G.

    2003-01-01

    There is a need of environmental implications of rapid appearance of surface by applying chemical at depths below the vadose zone (tile line or shallow groundwater) for developing better insight into solute flow mechanism through the arable lands. Transport of chloride, a representative non-adsorbing solute, through a moderately structured silty clay loam soil (Gujranwala series, Typic Ustochrepts) and an un-structured sandy loam soil (Nabipur series, Typic Camborthid) was characterized and two existing models viz. convection dispersion equation (CDE) and preferential flow models were tested. The flux average of solute concentration in the outflow as a function of cumulative drainage was fitted to the models. The CDE fitted, relatively, better in the non-structured soil than in the moderately structured soil. Dispersivity value determined by CDE was very high for the structured soil which is physically not possible. The preferential flow model fitted well in the Gujranwala soil, but not in the Nabipur soil. The breakthrough characteristics i.e. drainage to peak concentration (Dp), symmetry coefficient (SC), skewness, and kurtosis were compared. Chloride breakthrough was earlier than expected based on piston flow. It indicated preferential flow in both the soils, yet, immediate appearance of the tracer in the Gujranwala soil demonstrated even larger magnitude of the preferential flow. Breakthrough curves' parameters indicated a large amount of the solute movement through the preferred pathways by passing the soil matrix in the Gujranwala soil. The study suggests that some soil structure parameters (size/shape and degree of aggregation) should be incorporated in the solute transport models.(author)

  15. Disentangling interacting dark energy cosmologies with the three-point correlation function

    Science.gov (United States)

    Moresco, Michele; Marulli, Federico; Baldi, Marco; Moscardini, Lauro; Cimatti, Andrea

    2014-10-01

    We investigate the possibility of constraining coupled dark energy (cDE) cosmologies using the three-point correlation function (3PCF). Making use of the CODECS N-body simulations, we study the statistical properties of cold dark matter (CDM) haloes for a variety of models, including a fiducial ΛCDM scenario and five models in which dark energy (DE) and CDM mutually interact. We measure both the halo 3PCF, ζ(θ), and the reduced 3PCF, Q(θ), at different scales (2 appears flat at small scales (for all redshifts) and at low redshifts (for all scales), while it builds up the characteristic V-shape anisotropy at increasing redshifts and scales. With respect to the ΛCDM predictions, cDE models show lower (higher) values of the halo 3PCF for perpendicular (elongated) configurations. The effect is also scale-dependent, with differences between ΛCDM and cDE models that increase at large scales. We made use of these measurements to estimate the halo bias, that results in fair agreement with the one computed from the two-point correlation function (2PCF). The main advantage of using both the 2PCF and 3PCF is to break the bias-σ8 degeneracy. Moreover, we find that our bias estimates are approximately independent of the assumed strength of DE coupling. This study demonstrates the power of a higher order clustering analysis in discriminating between alternative cosmological scenarios, for both present and forthcoming galaxy surveys, such as e.g. Baryon Oscillation Spectroscopic Survey and Euclid.

  16. The development of common data elements for a multi-institute prostate cancer tissue bank: The Cooperative Prostate Cancer Tissue Resource (CPCTR experience

    Directory of Open Access Journals (Sweden)

    Melamed Jonathan

    2005-08-01

    Full Text Available Abstract Background The Cooperative Prostate Cancer Tissue Resource (CPCTR is a consortium of four geographically dispersed institutions that are funded by the U.S. National Cancer Institute (NCI to provide clinically annotated prostate cancer tissue samples to researchers. To facilitate this effort, it was critical to arrive at agreed upon common data elements (CDEs that could be used to collect demographic, pathologic, treatment and clinical outcome data. Methods The CPCTR investigators convened a CDE curation subcommittee to develop and implement CDEs for the annotation of collected prostate tissues. The draft CDEs were refined and progressively annotated to make them ISO 11179 compliant. The CDEs were implemented in the CPCTR database and tested using software query tools developed by the investigators. Results By collaborative consensus the CPCTR CDE subcommittee developed 145 data elements to annotate the tissue samples collected. These included for each case: 1 demographic data, 2 clinical history, 3 pathology specimen level elements to describe the staging, grading and other characteristics of individual surgical pathology cases, 4 tissue block level annotation critical to managing a virtual inventory of cases and facilitating case selection, and 5 clinical outcome data including treatment, recurrence and vital status. These elements have been used successfully to respond to over 60 requests by end-users for tissue, including paraffin blocks from cases with 5 to 10 years of follow up, tissue microarrays (TMAs, as well as frozen tissue collected prospectively for genomic profiling and genetic studies. The CPCTR CDEs have been fully implemented in two major tissue banks and have been shared with dozens of other tissue banking efforts. Conclusion The freely available CDEs developed by the CPCTR are robust, based on "best practices" for tissue resources, and are ISO 11179 compliant. The process for CDE development described in this

  17. Biogenesis and Membrane Targeting of Lipoproteins.

    Science.gov (United States)

    Narita, Shin-Ichiro; Tokuda, Hajime

    2010-09-01

    Bacterial lipoproteins represent a unique class of membrane proteins, which are anchored to membranes through triacyl chains attached to the amino-terminal cysteine. They are involved in various functions localized in cell envelope. Escherichia coli possesses more than 90 species of lipoproteins, most of which are localized in the outer membrane, with others being in the inner membrane. All lipoproteins are synthesized in the cytoplasm with an N-terminal signal peptide, translocated across the inner membrane by the Sec translocon to the periplasmic surface of the inner membrane, and converted to mature lipoproteins through sequential reactions catalyzed by three lipoprotein-processing enzymes: Lgt, LspA, and Lnt. The sorting of lipoproteins to the outer membrane requires a system comprising five Lol proteins. An ATP-binding cassette transporter, LolCDE, initiates the sorting by mediating the detachment of lipoproteins from the inner membrane. Formation of the LolA-lipoprotein complex is coupled to this LolCDE-dependent release reaction. LolA accommodates the amino-terminal acyl chain of lipoproteins in its hydrophobic cavity, thereby generating a hydrophilic complex that can traverse the periplasmic space by diffusion. Lipoproteins are then transferred to LolB on the outer membrane and anchored to the inner leaflet of the outer membrane by the action of LolB. In contrast, since LolCDE does not recognize lipoproteins possessing Asp at position +2, these lipoproteins remain anchored to the inner membrane. Genes for Lol proteins are widely conserved among gram-negative bacteria, and Lol-mediated outer membrane targeting of lipoproteins is considered to be the general lipoprotein localization mechanism.

  18. Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology.

    Science.gov (United States)

    Lin, Xiaoxi B; Gänzle, Michael G

    2014-09-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increases acid resistance by generating a proton motive force. Glycerol and glutamate metabolisms are lineage-specific traits in L. reuteri; therefore, this study employed glycerol dehydratase-positive sourdough isolates of human-adapted L. reuteri lineage I, glutamate decarboxylase-positive strains of rodent-adapted L. reuteri lineage II, as well as mutants with deletions in gadB or gupCDE. The competitivenesses of the strains were quantified by inoculation of wheat and sorghum sourdoughs with defined strains, followed by propagation of doughs with a 10% inoculum and 12-h or 72-h fermentation cycles. Lineage I L. reuteri strains dominated sourdoughs propagated with 12-h fermentation cycles; lineage II L. reuteri strains dominated sourdoughs propagated with 72-h fermentation cycles. L. reuteri 100-23ΔgadB was outcompeted by its wild-type strain in sourdoughs fermented with 72-h fermentation cycles; L. reuteri FUA3400ΔgupCDE was outcompeted by its wild-type strain in sourdoughs fermented with both 12-h and 72-h fermentation cycles. Competition experiments with isogenic pairs of strains resulted in a constant rate of strain displacement of the less competitive mutant strain. In conclusion, lineage-specific traits of L. reuteri determine the competitiveness of this species in sourdough fermentations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Phylodynamics of hepatitis C virus subtype 2c in the province of Córdoba, Argentina.

    Directory of Open Access Journals (Sweden)

    Viviana E Ré

    Full Text Available The Hepatitis C Virus Genotype 2 subtype 2c (HCV-2c is detected as a low prevalence subtype in many countries, except in Southern Europe and Western Africa. The current epidemiology of HCV in Argentina, a low-prevalence country, shows the expected low prevalence for this subtype. However, this subtype is the most prevalent in the central province of Córdoba. Cruz del Eje (CdE, a small rural city of this province, shows a prevalence for HCV infections of 5%, being 90% of the samples classified as HCV-2c. In other locations of Córdoba Province (OLC with lower prevalence for HCV, HCV-2c was recorded in about 50% of the samples. The phylogenetic analysis of samples from Córdoba Province consistently conformed a monophyletic group with HCV-2c sequences from all the countries where HCV-2c has been sequenced. The phylogeographic analysis showed an overall association between geographical traits and phylogeny, being these associations significant (α = 0.05 for Italy, France, Argentina (places other than Córdoba, Martinique, CdE and OLC. The coalescence analysis for samples from CdE, OLC and France yielded a Time for the Most Common Recent Ancestor of about 140 years, whereas its demographic reconstruction showed a "lag" phase in the viral population until 1880 and then an exponential growth until 1940. These results were also obtained when each geographical area was analyzed separately, suggesting that HCV-2c came into Córdoba province during the migration process, mainly from Europe, which is compatible with the history of Argentina of the early 20th century. This also suggests that the spread of HCV-2c occurred in Europe and South America almost simultaneously, possibly as a result of the advances in medicine technology of the first half of the 20th century.

  20. Phylodynamics of hepatitis C virus subtype 2c in the province of Córdoba, Argentina.

    Science.gov (United States)

    Ré, Viviana E; Culasso, Andrés C A; Mengarelli, Silvia; Farías, Adrián A; Fay, Fabián; Pisano, María B; Elbarcha, Osvaldo; Contigiani, Marta S; Campos, Rodolfo H

    2011-01-01

    The Hepatitis C Virus Genotype 2 subtype 2c (HCV-2c) is detected as a low prevalence subtype in many countries, except in Southern Europe and Western Africa. The current epidemiology of HCV in Argentina, a low-prevalence country, shows the expected low prevalence for this subtype. However, this subtype is the most prevalent in the central province of Córdoba. Cruz del Eje (CdE), a small rural city of this province, shows a prevalence for HCV infections of 5%, being 90% of the samples classified as HCV-2c. In other locations of Córdoba Province (OLC) with lower prevalence for HCV, HCV-2c was recorded in about 50% of the samples. The phylogenetic analysis of samples from Córdoba Province consistently conformed a monophyletic group with HCV-2c sequences from all the countries where HCV-2c has been sequenced. The phylogeographic analysis showed an overall association between geographical traits and phylogeny, being these associations significant (α = 0.05) for Italy, France, Argentina (places other than Córdoba), Martinique, CdE and OLC. The coalescence analysis for samples from CdE, OLC and France yielded a Time for the Most Common Recent Ancestor of about 140 years, whereas its demographic reconstruction showed a "lag" phase in the viral population until 1880 and then an exponential growth until 1940. These results were also obtained when each geographical area was analyzed separately, suggesting that HCV-2c came into Córdoba province during the migration process, mainly from Europe, which is compatible with the history of Argentina of the early 20th century. This also suggests that the spread of HCV-2c occurred in Europe and South America almost simultaneously, possibly as a result of the advances in medicine technology of the first half of the 20th century.

  1. Determination of Research Priorities and Documentation of Information Sources for Army Civilian Personnel Management

    Science.gov (United States)

    1988-12-01

    GRADUATION IDsO5M ( ]SPEP GRAD/LOSSIREASON CDE 1D-a!N E ]YEAR DEBREE AWARDED tD *396 C ]ACADEMIC DISCIPLINE ID-39H I )OROANIZATIONAL NAME IDu28C C...C IMAGE-AREAS-FM C IWABE-SAL-SCHED-FN r IWORK-HOURS-FN C IWORK-SCHED-CODE C IYR -DESREE-ATTAIN C 3YR-DEGREE-BACH C 3YR-Ma-PROF-TESTED C 3YRS-SVC C-10

  2. Construcción del Cuestionario de Desarrollo Emocional de Adultos (QDE-A)

    OpenAIRE

    Pérez Escoda, Núria; Bisquerra Alzina, Rafael; Filella Guiu, Gemma; Soldevila Benet, Anna

    2010-01-01

    El propósito de este trabajo es presentar la construcción y aplicación del Questionari de Desarrollo Emocional para Adultos (QDE-A). Se trata de la versión catalana del Cuestionario de Desarrollo Emocional para Adultos (CDE-A). Los instrumentos disponibles para la medición de la competencia emocional son escasos y todos ellos sujetos a criticas centradas fundamentalmente en la falta de un marco teórico claro y de fundamentos empíricos firmes (Pérez, Petrides y Furnham, 2005). El QDE-A, se ...

  3. Construcción del Cuestionario de Desarrollo Emocional de Adultos (QDE-A).

    OpenAIRE

    Pérez Escoda, Núria; Bisquerra Alzina, Rafael; Filella Guiu, Gemma, 1966-; Soldevila, A.

    2010-01-01

    El propósito de este trabajo es presentar la construcción y aplicación del Questionari de Desarrollo Emocional para Adultos (QDE-A). Se trata de la versión catalana del Cuestionario de Desarrollo Emocional para Adultos (CDE-A). Los instrumentos disponibles para la medición de la competencia emocional son escasos y todos ellos sujetos a criticas centradas fundamentalmente en la falta de un marco teórico claro y de fundamentos empíricos firmes (Pérez, Petrides y Furnham, 2005). El QDE-A, se enm...

  4. Defective Lipoprotein Sorting Induces lolA Expression through the Rcs Stress Response Phosphorelay System

    OpenAIRE

    Tao, Kazuyuki; Narita, Shin-ichiro; Tokuda, Hajime

    2012-01-01

    The Escherichia coli LolA protein is a lipoprotein-specific chaperone that carries lipoproteins from the inner to the outer membrane. A dominant negative LolA mutant, LolA(I93C/F140C), in which both 93Ile and 140Phe are replaced by Cys, binds tightly to the lipoprotein-dedicated ABC transporter LolCDE complex on the inner membrane and therefore inhibits the detachment of outer membrane-specific lipoproteins from the inner membrane. We found that the expression of this mutant strongly induced ...

  5. Redefining the essential trafficking pathway for outer membrane lipoproteins

    OpenAIRE

    Grabowicz, Marcin; Silhavy, Thomas J.

    2017-01-01

    In Gram-negative bacteria, most lipoproteins synthesized in the inner membrane (IM) are trafficked to the outer membrane (OM). The Lol pathway is the trafficking paradigm: LolCDE releases lipoproteins from the IM; LolA shuttles them between membranes to LolB in the OM. Several OM lipoproteins are essential for viability. In apparent concordance, the Lol proteins are each essential in wild-type cells. However, we show that Escherichia coli grows well without LolA and LolB in the absence of one...

  6. A Cultural Resources Survey of Steele, New Franklin, and Main Ditches, and National Register of Historic Places Significance Testing of Sites 2PM574, 575, 577, and 23PM578, Pemiscot County Missouri

    Science.gov (United States)

    1990-07-15

    important find was the enamel portion of a buman tooth . 45 N ’" " - / " "’".. ’ 1 . , - -. . " . . The tooth is a right maxillary second molar. Only the...deposits are present on the mesial and buccal surfaces. Morphologically , the tooth is characterized by a Ř" cusp pattern, the hypocone being quite...complete information. When a peort is prepared in more than one volumne,Blc12.DsrbtoCde -e.eatthe primary title, ad’d volume number, and

  7. Reciprocal regulation of Yersinia pestis biofilm formation and virulence by RovM and RovA

    OpenAIRE

    Liu, Lei; Fang, Haihong; Yang, Huiying; Zhang, Yiquan; Han, Yanping; Zhou, Dongsheng; Yang, Ruifu

    2016-01-01

    RovA is known to enhance Yersinia pestis virulence by directly upregulating the psa loci. This work presents a complex gene regulatory paradigm involving the reciprocal regulatory action of RovM and RovA on the expression of biofilm and virulence genes as well as on their own genes. RovM and RovA enhance and inhibit Y. pestis biofilm production, respectively, whereas RovM represses virulence in mice. RovM directly stimulates the transcription of hmsT, hmsCDE and rovM, while indirectly enhanci...

  8. Cerebral desaturation events in the beach chair position: correlation of noninvasive blood pressure and estimated temporal mean arterial pressure.

    Science.gov (United States)

    Triplet, Jacob J; Lonetta, Christopher M; Levy, Jonathan C; Everding, Nathan G; Moor, Molly A

    2015-01-01

    Cerebral oximetry (rSO2) has emerged as an important tool for monitoring of cerebral perfusion during surgery. High rates of cerebral desaturation events (CDEs) have been reported during surgery in the beach chair position. However, correlations have not been made with blood pressure measured at the cerebral level. The purpose of this study was to examine the correlations between brachial noninvasive blood pressure (NIBP) and estimated temporal mean arterial pressure (eTMAP) during CDEs in the beach chair position. Fifty-seven patients underwent elective shoulder surgery in the beach chair position. Values for eTMAP, NIBP, and rSO2 were recorded supine (0°) after induction and when a CDE occurred in the 70° beach chair position. Twenty-six patients experienced 45 CDEs, defined as a 20% drop in rSO2 from baseline. Median reduction in NIBP, eTMAP, and rSO2 from baseline to the CDE were 48.2%, 75.5%, and 33.3%, respectively. At baseline, there was a significant weak negative correlation between rSO2 and NIBP (rs = -0.300; P = .045) and no significant association between rSO2 and eTMAP (rs = -0.202; P = .183). During CDEs, there were no significant correlations between rSO2 and NIBP (rs = -0.240; P = .112) or between rSO2 and eTMAP (rs = -0.190; P = .212). No significant correlation between the decrease in rSO2 and NIBP (rs = 0.064; P = .675) or between rSO2 and eTMAP (rs = 0.121; P = .430) from baseline to CDE was found. NIBP and eTMAP are unreliable methods for identifying a CDE in the beach chair position. Cerebral oximetry provides additional information to the values obtained from NIBP and eTMAP, and all should be considered independently and collectively. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  9. Early life-stage mortalities of Japanese medaka (Oryzias latipes) exposed to polychlorinated diphenyl ethers

    Energy Technology Data Exchange (ETDEWEB)

    Metcalfe, C.D.; Metcalfe, T.L. [Trent Univ., Peterborough, Ontario (Canada). Environmental and Resource Studies Program; Cormier, J.A. [St. Francis Xavier Univ., Antigonish, Nova Scotia (Canada). Chemistry Dept.; Huestis, S.Y.; Niimi, A.J. [Canada Centre for Inland Waters, Burlington, Ontario (Canada). Fisheries and Oceans

    1997-08-01

    Polychlorinated diphenyl ethers (PCDEs) are a group of compounds that resemble polychlorinated dibenzofurans in structure that have been detected at ppb concentrations in fish from the Great Lakes. The objective of this project was to determine the toxicological significance of PCDE residues in fish. PCDE congener 77 (3,3{prime},4,4{prime}-tetrachlorodiphenyl ether), congener 71 (2,3{prime},4{prime},6-tetrachlorodiphenyl ether), congener 118 (2,3{prime}4,4{prime},5-pentachlorodiphenyl ether), and congener 105 (2,3,3{prime},4,4{prime}-pentachlorodiphenyl) were tested for toxicity with early life stages (ELS) of Japanese medaka, Oryzias latipes. These embryotoxicity data showed that the mono-ortho congeners 105 and 118 and the non-ortho congener 77 were embryotoxic to medaka. However, the toxic equivalency factors (TEFs) estimated for congeners 105, 77, and 118 relative to 2,3,7,8-TCDD were relatively low at 0.00056, 0.00003, and 0.00001, respectively. PCDE compounds were isolated in a fraction prepared from a bulk extract of Lake Ontario lake trout. In this fraction, congeners 99 (2,2{prime},4,4{prime},5-pentaCDE), 153 (2,2{prime},4,m4{prime},5,5{prime}-hexaCDE), 154 (2,2{prime},4,4{prime},5,6{prime}-hexaCDE), and 163 (2,3,3{prime},4{prime},5,6-hexaCDE) comprised 81.3% of total PCDEs, while congeners 77, 71, 118, and 105 comprised only 1.1% of total PCDEs. The LC50 for embryotoxicity of this fraction was equivalent to 15.5 ng/ml of total PCDEs. Toxicopathic lesions noted in medaka embryos exposed to either individual PCDEs or the lake trout extract included vascular hemorrhage but no edematous lesions. Medaka fry did not exhibit symptoms of hyperexcitability prior to death, as has been noted for ELS of lake trout exhibiting swim-up syndrome. These data indicate that PCDEs in Lake Ontario lake trout have the potential to induce toxic effects in early life stages of fish.

  10. Remote plasma processing of thin film materials

    Science.gov (United States)

    Kastenmeier, Bernd E. E.

    1999-09-01

    In this thesis, phenomena and mechanisms of remote plasma processes are investigated. The plasmas are spatially separated from the sample surface. Chemically reactive species are produced in the discharge region from rather inert feed gases. They exit the discharge region and travel in the afterglow towards the reaction chamber, where primarily neutral species arrive. The interaction with the sample surface is purely chemical. The absence of direct plasma surface interactions distinguishes remote plasma Chemical Dry Etching (CDE) from other etch processes like Reactive Ion Etching (RIE) or Inductively Coupled Plasma (ICP) etching. The etch reactions in CDE are isotropic, potentially offer great etch rate ratios and minimize substrate damage due to the absence of direct plasma-surface interactions. However, some materials like silicon dioxide (SiO2) or fluorocarbon deposits are difficult to remove because of the lack of activation energy otherwise provided by ion bombardment. In CDE, rates can be enhanced by the introduction of a new reaction pathway. Remote plasma CDE of silicon nitride (Si3N4) is an example for increasing the overall reaction rate by introducing a new reaction channel. Typically, the Si3N4 surface is exposed to the fluorine rich afterglow of a fluorocarbon, nitrogen trifluoride (NF 3) or sulfur hexafluoride (SF6) based discharge. We find that the Si3N4 etch rate is dramatically enhanced when Nitric Oxide (NO) is present in the afterglow as compared to the case in which only fluorine is present. Presented here are detailed analyses of the etching of Si3N 4 and SiO2 in different chemistries. Several experimental techniques are employed to investigate the composition of the plasma and the afterglow, the surface modifications and the etch rates for tetrafluoromethane (CF4) and NF3 based processes. These measurements establish the effect of NO on the Si3N4 etch rate. The dominant mechanism for the etch rate enhancement is shown by mass spectrometry

  11. An ancestral bacterial division system is widespread in eukaryotic mitochondria

    Czech Academy of Sciences Publication Activity Database

    Leger, M.M.; Petrů, M.; Žárský, V.; Eme, L.; Vlček, Čestmír; Harding, T.; Lang, B.F.; Eliáš, M.; Doležal, P.; Roger, A. J.

    2015-01-01

    Roč. 112, č. 33 (2015), s. 10239-10246 ISSN 0027-8424 R&D Projects: GA ČR GA13-24983S; GA MŠk(CZ) ED1.1.00/02.0109 Grant - others:GA ČR GA13-29423S; GA MŠk(CZ) CZ.1.05/1.1.00/02.0109 Institutional support: RVO:68378050 Keywords : mitochondria * Min proteins * MinCDE * mitochondrial fission * mitochondrial division Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.423, year: 2015

  12. Technical Evaluation Report 1: Online Learners’ Interest in Collaborative Tools

    Directory of Open Access Journals (Sweden)

    Jon Baggaley

    2002-01-01

    Full Text Available An online survey was conducted (June 2001 of attitudes of distance education (DE learners/teachers to online collaborative tools. The respondents in the study were 135 graduate students and faculty members of Athabasca University’s Centre for Distance Education (CDE. They demonstrated particular interest in tools that offer the following features: file sharing, automatic synchronisation of documentation for the group, audio conferencing, text chat, and privacy. They also expressed useful opinions on topics including their willingness to upgrade their computer systems, and to pay to avoid online product advertising. These results will be useful in the selection of appropriate new methods for online instruction.

  13. PPARγ2s A/B-domæne spiller en genspecifik rolle i transaktivering og co-faktor rekruttering

    DEFF Research Database (Denmark)

    Bugge, Anne Skovsø; Grøntved, Lars; M. Aagaard, Mads

    putative PPARγ target genes in murine fibroblasts and to determine the role of the A/B-domain in PPARγ2 mediated transactivation of genomic target genes. RNA isolated from three biological replicates of fibroblasts transduced with adenovirus encoding full length PPARγ2 or A/B-domain deleted PPARγ (PPARγ......CDE) in the presence of agonist were evaluated by expression array analysis. In total, 218 genes were found to be significantly induced by acute PPARγ expression and agonist as compared to the empty adenovirus. Interestingly, only 22 of these genes displayed A/B-domain dependency, i.e. significantly reduced induction...

  14. A local potential for the Weyl tensor in all dimensions

    International Nuclear Information System (INIS)

    Edgar, S Brian; Senovilla, Jose M M

    2004-01-01

    In all dimensions n ≥ 4 and arbitrary signature, we demonstrate the existence of a new local potential-a double (2, 3)-form, P ab cde -for the Weyl curvature tensor C abcd , and more generally for all tensors W abcd with the symmetry properties of the Weyl tensor. The classical four-dimensional Lanczos potential for a Weyl tensor-a double (2, 1)-form, H ab c -is proven to be a particular case of the new potential: its double dual. (letter to the editor)

  15. Quorum Sensing Regulation of Competence and Bacteriocins in Streptococcus pneumoniae and mutans

    Science.gov (United States)

    Shanker, Erin; Federle, Michael J.

    2017-01-01

    The human pathogens Streptococcus pneumoniae and Streptococcus mutans have both evolved complex quorum sensing (QS) systems that regulate the production of bacteriocins and the entry into the competent state, a requirement for natural transformation. Natural transformation provides bacteria with a mechanism to repair damaged genes or as a source of new advantageous traits. In S. pneumoniae, the competence pathway is controlled by the two-component signal transduction pathway ComCDE, which directly regulates SigX, the alternative sigma factor required for the initiation into competence. Over the past two decades, effectors of cellular killing (i.e., fratricides) have been recognized as important targets of the pneumococcal competence QS pathway. Recently, direct interactions between the ComCDE and the paralogous BlpRH pathway, regulating bacteriocin production, were identified, further strengthening the interconnections between these two QS systems. Interestingly, a similar theme is being revealed in S. mutans, the primary etiological agent of dental caries. This review compares the relationship between the bacteriocin and the competence QS pathways in both S. pneumoniae and S. mutans, and hopes to provide clues to regulatory pathways across the genus Streptococcus as a potential tool to efficiently investigate putative competence pathways in nontransformable streptococci. PMID:28067778

  16. Modelling of the Ni(II) removal from aqueous solutions onto grape stalk wastes in fixed-bed column.

    Science.gov (United States)

    Valderrama, César; Arévalo, Jaime A; Casas, Ignasi; Martínez, María; Miralles, Nuria; Florido, Antonio

    2010-02-15

    Grape stalk wastes generated in the wine production process were used for the removal of nickel (II) from aqueous solution. The experimental breakthrough curves were obtained in fixed-bed columns. Experiments we carry out in order to evaluate the influence of inlet metal concentration (30 and 70 mg L(-1)) and the regeneration process in a double sorption cycle. The CXTFIT code was used to fit the experimental data and to determine the transport and sorption parameters of the convective-dispersive equation (CDE) and the two-site deterministic non-equilibrium (TSM/CDE) model by adjusting the models to the experimental breakthrough curves (BTC). The results showed that bed capacity as well as transport and sorption parameters were affected by the initial metal concentration, at the highest Ni(II) concentration the grape stalks column saturated quickly leading to earlier breakthrough. The sorption capacity of the sorbent was slightly reduced in a double sorption cycle, while the recovery of the metal in the desorption step was ranging between 80% and 85% in both cycles.

  17. Effects of thermal blooming on systems comprised of tiled subapertures

    Science.gov (United States)

    Leakeas, Charles L.; Bartell, Richard J.; Krizo, Matthew J.; Fiorino, Steven T.; Cusumano, Salvatore J.; Whiteley, Matthew R.

    2010-04-01

    Laser weapon systems comprise of tiled subapertures are rapidly emerging in the directed energy community. The Air Force Institute of Technology Center for Directed Energy (AFIT/CDE), under sponsorship of the HEL Joint Technology Office has developed performance models of such laser weapon system configurations consisting of tiled arrays of both slab and fiber subapertures. These performance models are based on results of detailed waveoptics analyses conducted using WaveTrain. Previous performance model versions developed in this effort represent system characteristics such as subaperture shape, aperture fill factor, subaperture intensity profile, subaperture placement in the primary aperture, subaperture mutual coherence (piston), subaperture differential jitter (tilt), and beam quality wave-front error associated with each subaperture. The current work is a prerequisite for the development of robust performance models for turbulence and thermal blooming effects for tiled systems. Emphasis is placed on low altitude tactical scenarios. The enhanced performance model developed will be added to AFIT/CDE's HELEEOS parametric one-on-one engagement level model via the Scaling for High Energy Laser and Relay Engagement (SHaRE) toolbox.

  18. Information-Seeking Behaviors of Dental Practitioners in Three Practice-Based Research Networks

    Science.gov (United States)

    Botello-Harbaum, Maria T.; Demko, Catherine A.; Curro, Frederick A.; Rindal, D. Brad; Collie, Damon; Gilbert, Gregg H.; Hilton, Thomas J.; Craig, Ronald G.; Wu, Juliann; Funkhouser, Ellen; Lehman, Maryann; McBride, Ruth; Thompson, Van; Lindblad, Anne

    2013-01-01

    Research on the information-seeking behaviors of dental practitioners is scarce. Knowledge of dentists’ information-seeking behaviors should advance the translational gap between clinical dental research and dental practice. A cross-sectional survey was conducted to examine the self-reported information-seeking behaviors of dentists in three dental practice-based research networks (PBRNs). A total of 950 dentists (65 percent response rate) completed the survey. Dental journals and continuing dental education (CDE) sources used and their influence on practice guidance were assessed. PBRN participation level and years since dental degree were measured. Full-participant dentists reported reading the Journal of the American Dental Association and General Dentistry more frequently than did their reference counterparts. Printed journals were preferred by most dentists. A lower proportion of full participants obtained their CDE credits at dental meetings compared to partial participants. Experienced dentists read other dental information sources more frequently than did less experienced dentists. Practitioners involved in a PBRN differed in their approaches to accessing information sources. Peer-reviewed sources were more frequently used by full participants and dentists with fifteen years of experience or more. Dental PBRNs potentially play a significant role in the dissemination of evidence-based information. This study found that specific educational sources might increase and disseminate knowledge among dentists. PMID:23382524

  19. Estimation of Genetic and Phenotypic Parameters for Udder Morphology Traits in Different Dairy Sheep Genotypes

    Directory of Open Access Journals (Sweden)

    Pavol Makovický

    2017-01-01

    Full Text Available Knowledge of genetic parameters is the basis of sound livestock improvement programmes. Genetic parameters have been estimated for linear udder traits: Udder depth (UD, Cistern depth (CD, Teat position (TP, Teat size (TS and external udder measurements: Rear udder depth (RUD, Cistern depth (CDe, Teat length (TL and Teat angle (TA – 1275 linear assessments (381 ewes and 1185 external udder measurements (355 ewes were included in the analysis for each character of 9 genotypes. Nine breeds and genotypes were included in these experiments: purebred Improved Valachian (IV, Tsigai (T, Lacaune (LC ewes, and IV and T crosses with genetic portion of Lacaune and East Friesian (EF – 25 %, 50 % and 75 %. Primary data were processed using restricted maximum likelihood (REML methodology and the multiple‑trait animal model, using programs REMLF90 and VCE 4.0. High genetic correlations were found between UD and RUD (0.86, CD and CD(e (0.93, TP and TA (0.90, TS and TL (0.94. The highest heritabilities were estimated for exact measurements of TL and CD (0.35–0.39 and subjectively assessed TA and TS (0.32 – 0.33.

  20. Mechanism underlying the inner membrane retention of Escherichia coli lipoproteins caused by Lol avoidance signals.

    Science.gov (United States)

    Hara, Takashi; Matsuyama, Shin-ichi; Tokuda, Hajime

    2003-10-10

    Escherichia coli lipoproteins are localized to either the inner or outer membrane depending on the residue at position 2. The inner membrane retention signal, Asp at position 2 in combination with certain residues at position 3, functions as a Lol avoidance signal, i.e. the signal inhibits the recognition of lipoproteins by LolCDE that releases lipoproteins from the inner membrane. To understand the role of the residue at position 2, outer membrane-specific lipoproteins with Cys at position 2 were subjected to chemical modification followed by the release reaction in reconstituted proteoliposomes. Sulfhydryl-specific introduction of nonprotein molecules or a negative charge to Cys did not inhibit the LolCDE-dependent release. In contrast, oxidation of Cys to cysteic acid resulted in generation of the Lol avoidance signal, indicating that the Lol avoidance signal requires a critical length of negative charge at the second residue. Furthermore, not only modification of the carboxylic acid of Asp at position 2 but also that of the amine of phosphatidylethanolamine abolished the Lol avoidance function. Based on these results, the Lol avoidance mechanism is discussed.

  1. Endothelial Cell Loss after Phacoemulsification according to Different Anterior Chamber Depths.

    Science.gov (United States)

    Hwang, Hyung Bin; Lyu, Byul; Yim, Hye Bin; Lee, Na Young

    2015-01-01

    Purpose. To compare the loss of corneal endothelial cells after phacoemulsification according to different anterior chamber depths (ACDs). Methods. We conducted a prospective study on 135 eyes with senile cataracts. Eyes with nuclear density grades of 2 to 4 were divided into three groups according to ACD: ACD I, 1.5 ACD ≤ 2.5 mm; ACD II, 2.5 ACD ≤ 3.5 mm; or ACD III, 3.5 ACD ≤ 4.5 mm. Intraoperative mean cumulative dissipated energy (CDE) was measured. Clinical examinations included central corneal thickness (CCT) and endothelial cell count (ECC) preoperatively and 2 months postoperatively. Results. There were no significant differences in CDE among the ACD groups (P > 0.05). Endothelial cell loss was significantly higher in ACD I than in ACD III in grades 3 and 4 cataract density groups 2 months after phacoemulsification (P ACD I group compared to the ACD II and III groups 2 months postoperatively, but the difference was not statistically significant. Conclusions. Eyes with shallow ACDs, especially those with relatively hard cataract densities, can be vulnerable to more corneal endothelial cell loss in phacoemulsification surgery.

  2. A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.

    Science.gov (United States)

    Sinaci, A Anil; Laleci Erturkmen, Gokce B

    2013-10-01

    In order to enable secondary use of Electronic Health Records (EHRs) by bridging the interoperability gap between clinical care and research domains, in this paper, a unified methodology and the supporting framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies. We introduce a federated semantic metadata registry framework by extending the ISO/IEC 11179 standard, and enable integration of data element registries through Linked Open Data (LOD) principles where each Common Data Element (CDE) can be uniquely referenced, queried and processed to enable the syntactic and semantic interoperability. Each CDE and their components are maintained as LOD resources enabling semantic links with other CDEs, terminology systems and with implementation dependent content models; hence facilitating semantic search, much effective reuse and semantic interoperability across different application domains. There are several important efforts addressing the semantic interoperability in healthcare domain such as IHE DEX profile proposal, CDISC SHARE and CDISC2RDF. Our architecture complements these by providing a framework to interlink existing data element registries and repositories for multiplying their potential for semantic interoperability to a greater extent. Open source implementation of the federated semantic MDR framework presented in this paper is the core of the semantic interoperability layer of the SALUS project which enables the execution of the post marketing safety analysis studies on top of existing EHR systems. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Development of Anti-G, Anti-C and Anti-Jk(b) in a 22-Year-Old Mother during Her Fourth Pregnancy.

    Science.gov (United States)

    Schulze, Torsten J; Goebel, Meike; Scharberg, Erwin A; Bugert, Peter; Janetzko, Karin

    2013-06-01

    Anti-G antibodies are rarely found since anti-D, in combination with anti-C, are difficult to discriminate from anti-G antibodies in routine testing. A 22-year-old, gravida-3, para-1, woman with blood group A Rh D neg ccddee and known antibody anti-Jk(b), gave birth to her second child. While anti-Jk(b) could not be detected at birth, a new anti-C was found. Antibody screening tests (IAT) were performed using gel cards and rare G positive rGr erythrocytes. Genotyping for RHD and RHCE was performed using PCR-SSP. The child's blood group was A Rh D neg Ccddee. Genotyping revealed Cde/cde haplotypes. The erythrocytes of the new-born showed a positive direct antiglobulin test with IgG; anti-D and anti-C could be eluted. Erythrocytes with the rare phenotype rGr were reactive with the serum of the mother. The presence of anti-D and anti-C in the eluate from then newborn's Ccddee erythrocytes proved anti-G or anti-G in combination with anti-D. When anti-C and anti-D are seen during a pregnancy, possibly anti-G is present. This observation is of relevance since women with anti-G can still develop anti-D and require rhesus prophylaxis.

  4. One-loop matching and running with covariant derivative expansion

    Science.gov (United States)

    Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

    2018-01-01

    We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these "mixed" one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-known matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of "integrating out" heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.

  5. Microincision versus small-incision coaxial cataract surgery using different power modes for hard nuclear cataract.

    Science.gov (United States)

    Kim, Eun Chul; Byun, Yong Soo; Kim, Man Soo

    2011-10-01

    To compare the efficacy of microincision and small-incision coaxial phacoemulsification in treating hard cataracts using different ultrasound power modes. Department of Ophthalmology, Seoul St. Mary's Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea. Randomized clinical trial. Eyes with hard cataract were randomized to have an initial incision of 1.80 mm, 2.20 mm, or 2.75 mm. The eyes in each group were equally randomized to treatment with burst, pulse, or continuous mode. Ultrasound time (UST), mean cumulative dissipated energy (CDE), corrected distance visual acuity (CDVA), surgically induced corneal astigmatism, incisional and central corneal thickness (CCT), and endothelial cell counts were evaluated. The study enrolled 180 eyes, 60 in each group. Two months postoperatively, there were no statistically significant differences in UST, CDE, CDVA, CCT, or percentage endothelial cell loss between the 3 incision groups. The 2.75 mm incision induced more astigmatism at 2 months and less incisional corneal edema at 1 week than the 1.80 mm or 2.20 mm incision (Phard cataract. The intraoperative energy use and ocular damage was less with the pulse and burst modes than with the continuous mode. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2011 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  6. [Computer-assisted phacoemulsification for hard cataracts].

    Science.gov (United States)

    Zemba, M; Papadatu, Adriana-Camelia; Sîrbu, Laura-Nicoleta; Avram, Corina

    2012-01-01

    to evaluate the efficiency of new torsional phacoemulsification software (Ozil IP system) in hard nucleus cataract extraction. 45 eyes with hard senile cataract (degree III and IV) underwent phacoemulsification performed by the same surgeon, using the same technique (stop and chop). Infiniti (Alcon) platform was used, with Ozil IP software and Kelman phaco tip miniflared, 45 degrees. The nucleus was split into two and after that the first half was phacoemulsificated with IP-on (group 1) and the second half with IP-off (group 2). For every group we measured: cumulative dissipated energy (CDE), numbers of tip closure that needed manual desobstruction the amount of BSS used. The mean CDE was the same in group 1 and in group 2 (between 6.2 and 14.9). The incidence of occlusion that needed manual desobstruction was lower in group 1 (5 times) than in group 2 (13 times). Group 2 used more BSS compared to group 1. The new torsional software (IP system) significantly decreased occlusion time and balanced salt solution use over standard torsional software, particularly with denser cataracts.

  7. On the Dagan Model of solute transport in groundwater: Application to the Borden Site

    Science.gov (United States)

    Barry, D. A.; Coves, J.; Sposito, Garrison

    1988-10-01

    In the first part of this study, Sposito and Barry (1987) derived an ensemble-mean convection-dispersion equation (CDE) for tracer solute transport subject to a random velocity field. It was shown that the model dispersion coefficients originally presented by Dagan (1984) could be derived from the general expression for the dispersion coefficients in this mean CDE. Under the assumption of ergodicity, the Dagan model is used in this paper to predict chloride and bromide concentrations in the well-documented Borden aquifer experiment reported by Roberts and Mackay (1986). Because of a possible influence on the solute from the upper aquifer boundary, it was appropriate to apply the two-dimensional form of the model. A number of steps was necessary to reduce the three-dimensional raw data to a two-dimensional form, the main ones being integration over the vertical axis and the use of a gridding algorithm to form a two-dimensional solute concentration surface. Incomplete sampling of the solute plume during the early sampling sessions, as well as the assumptions made with respect to the data analysis, produce a rather large degree of uncertainty in the specification of the initial solute plume. These factors hinder a thorough experimental evaluation of the Dagan model. Data from some of the later sampling sessions were more complete, however, and the model predictions appeared to agree well with the field concentration data, especially in the preasymptotic region for the longitudinal dispersion coefficient.

  8. Spin and isospin modes

    International Nuclear Information System (INIS)

    Suzuki, T.; Sagawa, H.

    2000-01-01

    Complete text of publication follows. Spin and isospin modes in nuclei are investigated. We discuss some of the following topics. 1. Spin-dipole excitations in 12 C and 16 O are studied (1). Effects of tensor and spin-orbit interactions on the distribution of the strengths are investigated, and neutral current neutrino scattering cross sections in 16 O are obtained for heavy-flavor neutrinos from the supernovae. 2. Gamow-Teller (GT) and spin-dipole (SD) modes in 208 Bi are investigated. Quenching and fragmentation of the GT strength are discussed (2). SD excitations and electric dipole (E1) transitions between the GT and SD states are studied (3). Calculated E1 strengths are compared with the sum rule values obtained within the 1p-1h and 1p-1h + 2p-2h configuration spaces. 3. Coulomb displacement energy (CDE) of the IAS of 14 Be is calculated, and the effects of the halo on the CDE and the configuration of the halo state are investigated. 4. Spreading width of IAS and isospin dependence of the width are investigated (4). Our formula for the width explains very well the observed isospin dependence (5). (author)

  9. Metadata aided run selection at ATLAS

    International Nuclear Information System (INIS)

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

    2011-01-01

    Management of the large volume of data collected by any large scale scientific experiment requires the collection of coherent metadata quantities, which can be used by reconstruction or analysis programs and/or user interfaces, to pinpoint collections of data needed for specific purposes. In the ATLAS experiment at the LHC, we have collected metadata from systems storing non-event-wise data (Conditions) into a relational database. The Conditions metadata (COMA) database tables not only contain conditions known at the time of event recording, but also allow for the addition of conditions data collected as a result of later analysis of the data (such as improved measurements of beam conditions or assessments of data quality). A new web based interface called 'runBrowser' makes these Conditions Metadata available as a Run based selection service. runBrowser, based on PHP and JavaScript, uses jQuery to present selection criteria and report results. It not only facilitates data selection by conditions attributes, but also gives the user information at each stage about the relationship between the conditions chosen and the remaining conditions criteria available. When a set of COMA selections are complete, runBrowser produces a human readable report as well as an XML file in a standardized ATLAS format. This XML can be saved for later use or refinement in a future runBrowser session, shared with physics/detector groups, or used as input to ELSSI (event level Metadata browser) or other ATLAS run or event processing services.

  10. Toward Exposing Timing-Based Probing Attacks in Web Applications

    Directory of Open Access Journals (Sweden)

    Jian Mao

    2017-02-01

    Full Text Available 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.

  11. Toward Exposing Timing-Based Probing Attacks in Web Applications †

    Science.gov (United States)

    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

  12. EPIC-CoGe: Managing and Analyzing Genomic Data.

    Science.gov (United States)

    Nelson, Andrew D L; Haug-Baltzell, Asher K; Davey, Sean; Gregory, Brian D; Lyons, Eric

    2018-02-20

    The EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse genome browser with the extensive CoGe genome database (currently containing over 30,000 genomes). In addition, the EPIC-CoGe browser boasts many additional features over basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons and analyses between all types of functional and diversity genomics data. There is no installation required and data (genome, annotation, functional genomic, and diversity data) can be loaded by following a simple point and click wizard, or using a REST API, making the browser widely accessible and easy to use by researchers of all computational skill levels. In addition, EPIC-CoGe and data tracks are easily embedded in other websites and JBrowse instances. EPIC-CoGe Browser is freely available for use online through CoGe (https://genomevolution.org). Source code (MIT open source) is available: https://github.com/LyonsLab/coge. ericlyons@email.arizona.edu. Supplementary data are available at Bioinformatics online.

  13. SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.

    Science.gov (United States)

    Audoux, Jérôme; Salson, Mikaël; Grosset, Christophe F; Beaumeunier, Sacha; Holder, Jean-Marc; Commes, Thérèse; Philippe, Nicolas

    2017-09-29

    for comparing the performance of RNA-Seq bioinformatics pipelines in addressing a specific biological question. We would like to see the creation of a reference corpus of data-sets that would allow accurate comparison between benchmarks performed by different groups and the publication of more benchmarks based on this public corpus. SimBA software and data-set are available at http://cractools.gforge.inria.fr/softwares/simba/ .

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

    Science.gov (United States)

    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.

  15. Your Life in Web Apps

    CERN Document Server

    Turnbull, Giles

    2008-01-01

    What is a web app? It's software that you use right in your web browser. Rather than installing an application on your computer, you visit a web site and sign up as a new user of its software. Instead of storing your files on your own hard disk, the web app stores them for you, online. Is it possible to switch entirely to web apps? To run nothing but a browser for an entire day? In this PDF we'll take you through one day in the life of a web apps-only user and chronicle the pros and cons of living by browser. And if the idea of switching, fully or partially, to web apps sounds appealing to

  16. Rweb:Web-based Statistical Analysis

    Directory of Open Access Journals (Sweden)

    Jeff Banfield

    1999-03-01

    Full Text Available Rweb is a freely accessible statistical analysis environment that is delivered through the World Wide Web (WWW. It is based on R, a well known statistical analysis package. The only requirement to run the basic Rweb interface is a WWW browser that supports forms. If you want graphical output you must, of course, have a browser that supports graphics. The interface provides access to WWW accessible data sets, so you may run Rweb on your own data. Rweb can provide a four window statistical computing environment (code input, text output, graphical output, and error information through browsers that support Javascript. There is also a set of point and click modules under development for use in introductory statistics courses.

  17. Interactive Web Graphs with Fewer Restrictions

    Science.gov (United States)

    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.

  18. Digital Forensic Analysis Of Malware Infected Machine- Case Study

    Directory of Open Access Journals (Sweden)

    Amulya Podile

    2015-08-01

    Full Text Available Abstract Internet banking has created a convenient way for us to handle our business without leaving our home. Man-in-the-Browser is a special case of Man-in-the-middle attack targeted against customers of Internet banking. One of the capabilities of Man-in-the-Browser Trojan is modification of html referred to as html injection that allows the attacker to alter the html of a page before it is sent to the browser for interpretation. In this paper the authors discussed about forensic analysis of RAM Volatile data system logs and registry collected from bank customer computer infected with Trojan and confirmed the source of attack time-stamps and the behavior of the malware by using open source and commercial tools.

  19. The RNAsnp web server

    DEFF Research Database (Denmark)

    Radhakrishnan, Sabarinathan; Tafer, Hakim; Seemann, Ernst Stefan

    2013-01-01

    , are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected...... to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/....

  20. KAMG: A Tool for Converting Blood Ties and Affinity Ties into Adjacency Matrices

    Directory of Open Access Journals (Sweden)

    Hang Xiong

    2016-07-01

    Full Text Available Kinship Adjacency Matrix Generator (KAMG is a browser-based software for creating adjacency matrices using the information of kinship ties. Specifically, it is capable of converting the family trees in the format of GEDCOM files into adjacency matrices of blood relationship. With the data of intermarriages between different families, it can further create the adjacency matrix of affinity relationship for the families. The outcomes can be directly used to create networks. KAMG is written in JavaScript and implemented on web browsers. It is completely open source and the source code is publicly available on GitHub.