DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

PubMed

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

2012-06-15

A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Web-Based Urban Metabolic Mapping for Bangalore, India

NASA Astrophysics Data System (ADS)

Mehta, V. K.; Kemp-Benedict, E.; Wang, G.; Malghan, D.

2012-12-01

Cities are like living entities, needing a continuous throughput of resources and energy for survival and growth, creating waste in the process. This paper documents the Bangalore Urban Mapping Project: an initiative that uses this metabolic concept [1],[2]. to inform comprehensive planning in the rapidly growing software capital of Bangalore city in India. Focusing on demographic growth, and water supply and consumption in its first phase, a web-based geo-portal has been developed for two purposes - interactive information communication and delivery, and online planning in the water supply sector. The application, titled Bangalore Urban Mapping Project (BUMP) is built on a free and open source web GIS stack consisting of a Postgis database, PHP, OpenLayers, and Apache Web Server deployed on a 64-bit Ubuntu Linux server platform. The interactive planning portion of the application allows BUMP users to build, run and visualize demographic growth, water supply, and growth scenarios on the browser. Application logic is written in PHP to connect the many components of the interactive application, which is available on the BUMP website (http://www.seimapping.org/bump/index.php). It relies on AJAX to fetch layer data from the server and render the layer using OpenLayers on the fly. This allows users to view multiple layers at the same time without refreshing the page. Data is packed in GeoJSON format and is compressed to reduce traffic. The information communication portion of the application provides thematic representation of each of twenty different map layers, graphical and tabular summaries of demographic and water data that are presented dynamically using Javascript libraries including the Google Chart API. The application also uses other common Javascript libraries/plug-ins, like jQuery, jQuery UI, qTip, to ease the development and to ensure cross-browser compatibility. The planning portion of the platform allows the user to interact with a scenario explorer through which key aspects of the city's growth, water demand, and supply infrastructure can be entered. This drives a water resources model built on the Water Evaluation And Planning (www.weap21.org) software platform [3] running on a server, that returns key results to the browser. The paper concludes with plans for future development of BUMP, which include crowd-sourcing of water demand and groundwater information, in the face of a critical knowledge gap on both the demand and supply side of the water sector in Indian cities. [1] Newman, P.W.G., 1999. Sustainability and cities: extending the metabolism model. Landscape and urban planning 44, 219-226. [2] Sieferle, R.P., 2011. Cultural Evolution and Social Metabolism. Geografiska Annaler: Series B, Human Geography [3] 93, 315-324. Yates, D., Sieber, J., Purkey, D., Huber-Lee, A., 2005. WEAP21—A Demand-, Priority-, and Preference-Driven Water Planning Model. Water International 30, 487-500.

WEB-server for search of a periodicity in amino acid and nucleotide sequences

NASA Astrophysics Data System (ADS)

E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

2017-12-01

A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

PubMed Central

Karpievitch, Yuliya V; Almeida, Jonas S

2006-01-01

Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet. PMID:16539707

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

PubMed

Karpievitch, Yuliya V; Almeida, Jonas S

2006-03-15

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

PubMed

Wang, Lin; Zhang, Min; Alexov, Emil

2016-02-15

A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Black Sea GIS developed in MHI

NASA Astrophysics Data System (ADS)

Zhuk, E.; Khaliulin, A.; Zodiatis, G.; Nikolaidis, A.; Isaeva, E.

2016-08-01

The work aims at creating the Black Sea geoinformation system (GIS) and complementing it with a model bank. The software for data access and visualization was developed using client server architecture. A map service based on MapServer and MySQL data management system were chosen for the Black Sea GIS. Php-modules and python-scripts are used to provide data access, processing, and exchange between the client application and the server. According to the basic data types, the module structure of GIS was developed. Each type of data is matched to a module which allows selection and visualization of the data. At present, a GIS complement with a model bank (the models build in to the GIS) and users' models (programs launched on users' PCs but receiving and displaying data via GIS) is developed.

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

Client-Side Image Maps: Achieving Accessibility and Section 508 Compliance

ERIC Educational Resources Information Center

Beasley, William; Jarvis, Moana

2004-01-01

Image maps are a means of making a picture "clickable", so that different portions of the image can be hyperlinked to different URLS. There are two basic types of image maps: server-side and client-side. Besides requiring access to a CGI on the server, server-side image maps are undesirable from the standpoint of accessibility--creating…

Developing Server-Side Infrastructure for Large-Scale E-Learning of Web Technology

ERIC Educational Resources Information Center

Simpkins, Neil

2010-01-01

The growth of E-business has made experience in server-side technology an increasingly important area for educators. Server-side skills are in increasing demand and recognised to be of relatively greater value than comparable client-side aspects (Ehie, 2002). In response to this, many educational organisations have developed E-business courses,…

Implementation of an interactive database interface utilizing HTML, PHP, JavaScript, and MySQL in support of water quality assessments in the Northeastern North Carolina Pasquotank Watershed

NASA Astrophysics Data System (ADS)

Guion, A., Jr.; Hodgkins, H.

2015-12-01

The Center of Excellence in Remote Sensing Education and Research (CERSER) has implemented three research projects during the summer Research Experience for Undergraduates (REU) program gathering water quality data for local waterways. The data has been compiled manually utilizing pen and paper and then entered into a spreadsheet. With the spread of electronic devices capable of interacting with databases, the development of an electronic method of entering and manipulating the water quality data was pursued during this project. This project focused on the development of an interactive database to gather, display, and analyze data collected from local waterways. The database and entry form was built in MySQL on a PHP server allowing participants to enter data from anywhere Internet access is available. This project then researched applying this data to the Google Maps site to provide labeling and information to users. The NIA server at http://nia.ecsu.edu is used to host the application for download and for storage of the databases. Water Quality Database Team members included the authors plus Derek Morris Jr., Kathryne Burton and Mr. Jeff Wood as mentor.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

PubMed

Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

2007-07-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

Selection of Server-Side Technologies for an E-Business Curriculum

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2007-01-01

The rapid growth of e-business and e-commerce has made server-side programming an increasingly important topic in information systems (IS) and computer science (CS) curricula. This article presents an overview of the major features of several popular server-side programming technologies and discusses the factors that influence the selection of…

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

Since April 2004 the EarthScope USArray seismic network has grown to over 850 broadband stations that stream multi-channel data in near real-time to the Array Network Facility in San Diego. Providing secure, yet open, access to real-time and archived data for a broad range of audiences is best served by a series of platform agnostic low-latency web-based applications. We present a framework of tools that mediate between the world wide web and Boulder Real Time Technologies Antelope Environmental Monitoring System data acquisition and archival software. These tools provide comprehensive information to audiences ranging from network operators and geoscience researchers, to funding agencies and the general public. This ranges from network-wide to station-specific metadata, state-of-health metrics, event detection rates, archival data and dynamic report generation over a station's two year life span. Leveraging open source web-site development frameworks for both the server side (Perl, Python and PHP) and client-side (Flickr, Google Maps/Earth and jQuery) facilitates the development of a robust extensible architecture that can be tailored on a per-user basis, with rapid prototyping and development that adheres to web-standards. Typical seismic data warehouses allow online users to query and download data collected from regional networks, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have recently developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running the Antelope Real Time System. The software is freely available from the Antelope contributed code Git repository (http://www.antelopeusersgroup.org).

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

PubMed

Pinciroli, Francesco; Masseroli, Marco; Acerbo, Livio A; Bonacina, Stefano; Ferrari, Roberto; Marchente, Mario

2004-01-01

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

Design and Delivery of Multiple Server-Side Computer Languages Course

ERIC Educational Resources Information Center

Wang, Shouhong; Wang, Hai

2011-01-01

Given the emergence of service-oriented architecture, IS students need to be knowledgeable of multiple server-side computer programming languages to be able to meet the needs of the job market. This paper outlines the pedagogy of an innovative course of multiple server-side computer languages for the undergraduate IS majors. The paper discusses…

ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

PubMed

Li, Guipeng; Li, Ming; Zhang, Yiwei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q

2014-01-01

Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide" in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request.

Integration of gel-based proteome data with pProRep.

PubMed

Laukens, Kris; Matthiesen, Rune; Lemière, Filip; Esmans, Eddy; Onckelen, Harry Van; Jensen, Ole Nørregaard; Witters, Erwin

2006-11-15

pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

Development of Innovative Design Processor

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

Park, Y.S.; Park, C.O.

2004-07-01

The nuclear design analysis requires time-consuming and erroneous model-input preparation, code run, output analysis and quality assurance process. To reduce human effort and improve design quality and productivity, Innovative Design Processor (IDP) is being developed. Two basic principles of IDP are the document-oriented design and the web-based design. The document-oriented design is that, if the designer writes a design document called active document and feeds it to a special program, the final document with complete analysis, table and plots is made automatically. The active documents can be written with ordinary HTML editors or created automatically on the web, which ismore » another framework of IDP. Using the proper mix-up of server side and client side programming under the LAMP (Linux/Apache/MySQL/PHP) environment, the design process on the web is modeled as a design wizard style so that even a novice designer makes the design document easily. This automation using the IDP is now being implemented for all the reload design of Korea Standard Nuclear Power Plant (KSNP) type PWRs. The introduction of this process will allow large reduction in all reload design efforts of KSNP and provide a platform for design and R and D tasks of KNFC. (authors)« less

For and from Cyberspace: Conceptualizing Cyber Intelligence, Surveillance, and Reconnaissance

DTIC Science & Technology

2012-12-01

intelligence. Cyber ISR, there- fore, “requires the development of algorithms and visualizations capa- bilities to make activities in the cyber domain... Pentagon , 19 January 2012), https://www.intelink.gov/inteldocs/action.php?kt_path_info=ktcore.actions.docu- ment.view&fDocumentId=1517681, defines...selected proxy servers, with successive levels of encryption and then de- cryption, before delivery to their final destination as plain text. W. Earl

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

PubMed

Tubiana, Luca; Polles, Guido; Orlandini, Enzo; Micheletti, Cristian

2018-06-07

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PREDICT: Privacy and Security Enhancing Dynamic Information Monitoring

DTIC Science & Technology

2015-08-03

consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided local...12], consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided...these methods achieve high sensing coverage with low cost using cloaked locations [3]. In follow-on work, the issue of mobility is addressed. Task

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

PubMed

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

2007-12-11

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

An Internet supported workflow for the publication process in UMVF (French Virtual Medical University).

PubMed

Renard, Jean-Marie; Bourde, Annabel; Cuggia, Marc; Garcelon, Nicolas; Souf, Nathalie; Darmoni, Stephan; Beuscart, Régis; Brunetaud, Jean-Marc

2007-01-01

The " Université Médicale Virtuelle Francophone" (UMVF) is a federation of French medical schools. Its main goal is to share the production and use of pedagogic medical resources generated by academic medical teachers. We developed an Open-Source application based upon a workflow system, which provides an improved publication process for the UMVF. For teachers, the tool permits easy and efficient upload of new educational resources. For web masters it provides a mechanism to easily locate and validate the resources. For librarian it provide a way to improve the efficiency of indexation. For all, the utility provides a workflow system to control the publication process. On the students side, the application improves the value of the UMVF repository by facilitating the publication of new resources and by providing an easy way to find a detailed description of a resource and to check any resource from the UMVF to ascertain its quality and integrity, even if the resource is an old deprecated version. The server tier of the application is used to implement the main workflow functionalities and is deployed on certified UMVF servers using the PHP language, an LDAP directory and an SQL database. The client tier of the application provides both the workflow and the search and check functionalities. A unique signature for each resource, was needed to provide security functionality and is implemented using a Digest algorithm. The testing performed by Rennes and Lille verified the functionality and conformity with our specifications.

CPU Performance Counter-Based Problem Diagnosis for Software Systems

DTIC Science & Technology

2009-09-01

application servers and implementation techniques), this thesis only used the Enterprise Java Bean (EJB) SessionBean version of RUBiS. The PHP and Servlet ...collection statistics at the Java Virtual Machine (JVM) level can be reused for any Java application. Other examples of gray-box instrumentation include path...used gray-box approaches. For example, PinPoint [11, 14] and [29] use request tracing to diagnose Java exceptions, endless calls, and null calls in

Developing a Philippine Cancer Grid. Part 1: Building a Prototype for a Data Retrieval System for Breast Cancer Research Using Medical Ontologies

NASA Astrophysics Data System (ADS)

Coronel, Andrei D.; Saldana, Rafael P.

Cancer is a leading cause of morbidity and mortality in the Philippines. Developed within the context of a Philippine Cancer Grid, the present study used web development technologies such as PHP, MySQL, and Apache server to build a prototype data retrieval system for breast cancer research that incorporates medical ontologies from the Unified Medical Language System (UMLS).

Lowering the Barrier for Standards-Compliant and Discoverable Hydrological Data Publication

NASA Astrophysics Data System (ADS)

Kadlec, J.

2013-12-01

The growing need for sharing and integration of hydrological and climate data across multiple organizations has resulted in the development of distributed, services-based, standards-compliant hydrological data management and data hosting systems. The problem with these systems is complicated set-up and deployment. Many existing systems assume that the data publisher has remote-desktop access to a locally managed server and experience with computer network setup. For corporate websites, shared web hosting services with limited root access provide an inexpensive, dynamic web presence solution using the Linux, Apache, MySQL and PHP (LAMP) software stack. In this paper, we hypothesize that a webhosting service provides an optimal, low-cost solution for hydrological data hosting. We propose a software architecture of a standards-compliant, lightweight and easy-to-deploy hydrological data management system that can be deployed on the majority of existing shared internet webhosting services. The architecture and design is validated by developing Hydroserver Lite: a PHP and MySQL-based hydrological data hosting package that is fully standards-compliant and compatible with the Consortium of Universities for Advancement of Hydrologic Sciences (CUAHSI) hydrologic information system. It is already being used for management of field data collection by students of the McCall Outdoor Science School in Idaho. For testing, the Hydroserver Lite software has been installed on multiple different free and low-cost webhosting sites including Godaddy, Bluehost and 000webhost. The number of steps required to set-up the server is compared with the number of steps required to set-up other standards-compliant hydrologic data hosting systems including THREDDS, IstSOS and MapServer SOS.

Server-Side Includes Made Simple.

ERIC Educational Resources Information Center

Fagan, Jody Condit

2002-01-01

Describes server-side include (SSI) codes which allow Webmasters to insert content into Web pages without programming knowledge. Explains how to enable the codes on a Web server, provides a step-by-step process for implementing them, discusses tags and syntax errors, and includes examples of their use on the Web site for Southern Illinois…

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

[Development of quality assurance/quality control web system in radiotherapy].

PubMed

Okamoto, Hiroyuki; Mochizuki, Toshihiko; Yokoyama, Kazutoshi; Wakita, Akihisa; Nakamura, Satoshi; Ueki, Heihachi; Shiozawa, Keiko; Sasaki, Koji; Fuse, Masashi; Abe, Yoshihisa; Itami, Jun

2013-12-01

Our purpose is to develop a QA/QC (quality assurance/quality control) web system using a server-side script language such as HTML (HyperText Markup Language) and PHP (Hypertext Preprocessor), which can be useful as a tool to share information about QA/QC in radiotherapy. The system proposed in this study can be easily built in one's own institute, because HTML can be easily handled. There are two desired functions in a QA/QC web system: (i) To review the results of QA/QC for a radiotherapy machine, manuals, and reports necessary for routinely performing radiotherapy through this system. By disclosing the results, transparency can be maintained, (ii) To reveal a protocol for QA/QC in one's own institute using pictures and movies relating to QA/QC for simplicity's sake, which can also be used as an educational tool for junior radiation technologists and medical physicists. By using this system, not only administrators, but also all staff involved in radiotherapy, can obtain information about the conditions and accuracy of treatment machines through the QA/QC web system.

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

36 CFR 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

36 CFR 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2014 CFR

2014-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

36 CFR § 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.

PubMed

Garcia-Garcia, Javier; Schleker, Sylvia; Klein-Seetharaman, Judith; Oliva, Baldo

2012-07-01

Protein-protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased the coverage of known interactions. Still, identification of complete inter- and intraspecies interactomes is far from being complete. Experimental data can be complemented by the prediction of PPIs within an organism or between two organisms based on the known interactions of the orthologous genes of other organisms (interologs). Here, we present the BIANA (Biologic Interactions and Network Analysis) Interolog Prediction Server (BIPS), which offers a web-based interface to facilitate PPI predictions based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related databases. Additional metadata can be used to improve the reliability of the predicted interactions. Sensitivity and specificity of the server have been calculated using known PPIs from different interactomes using a leave-one-out approach. The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php.

Computers in Small Libraries: Learning Server-Side Scripting

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

In this column, the author compares and contrasts the most popular scripting languages that are used to create truly dynamic service-oriented Web sites, building a conceptual framework that be can used as a starting point for specific server-side library projects.

Building a Snow Data Management System using Open Source Software (and IDL)

NASA Astrophysics Data System (ADS)

Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

2012-12-01

At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version 3.01

Partitioned key-value store with atomic memory operations

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

Bent, John M.; Faibish, Sorin; Grider, Gary

A partitioned key-value store is provided that supports atomic memory operations. A server performs a memory operation in a partitioned key-value store by receiving a request from an application for at least one atomic memory operation, the atomic memory operation comprising a memory address identifier; and, in response to the atomic memory operation, performing one or more of (i) reading a client-side memory location identified by the memory address identifier and storing one or more key-value pairs from the client-side memory location in a local key-value store of the server; and (ii) obtaining one or more key-value pairs from themore » local key-value store of the server and writing the obtained one or more key-value pairs into the client-side memory location identified by the memory address identifier. The server can perform functions obtained from a client-side memory location and return a result to the client using one or more of the atomic memory operations.« less

Assessment of feasibility of running RSNA's MIRC on a Raspberry Pi: a cost-effective solution for teaching files in radiology.

PubMed

Pereira, Andre; Atri, Mostafa; Rogalla, Patrik; Huynh, Thien; O'Malley, Martin E

2015-11-01

The value of a teaching case repository in radiology training programs is immense. The allocation of resources for putting one together is a complex issue, given the factors that have to be coordinated: hardware, software, infrastructure, administration, and ethics. Costs may be significant and cost-effective solutions are desirable. We chose Medical Imaging Resource Center (MIRC) to build our teaching file. It is offered by RSNA for free. For the hardware, we chose the Raspberry Pi, developed by the Raspberry Foundation: a small control board developed as a low cost computer for schools also used in alternative projects such as robotics and environmental data collection. Its performance and reliability as a file server were unknown to us. For the operational system, we chose Raspbian, a variant of Debian Linux, along with Apache (web server), MySql (database server) and PHP, which enhance the functionality of the server. A USB hub and an external hard drive completed the setup. Installation of software was smooth. The Raspberry Pi was able to handle very well the task of hosting the teaching file repository for our division. Uptime was logged at 100 %, and loading times were similar to other MIRC sites available online. We setup two servers (one for backup), each costing just below $200.00 including external storage and USB hub. It is feasible to run RSNA's MIRC off a low-cost control board (Raspberry Pi). Performance and reliability are comparable to full-size servers for the intended purpose of hosting a teaching file within an intranet environment.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

The establishment and use of the point source catalog database of the 2MASS near infrared survey

NASA Astrophysics Data System (ADS)

Gao, Y. F.; Shan, H. G.; Cheng, D.

2003-02-01

The 2MASS near infrared survey project is introduced briefly. The 2MASS point sources catalog (2MASS PSC) database and the network query system are established by using the PHP Hypertext Preprocessor and MySQL database server. By using the system, one can not only query information of sources listed in the catalog, but also draw the plots related. Moreover, after the 2MASS data are diagnosed , some research fields which can be benefited from this database are suggested.

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

Development of Web-Based Menu Planning Support System and its Solution Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Kashima, Tomoko; Matsumoto, Shimpei; Ishii, Hiroaki

2009-10-01

Recently lifestyle-related diseases have become an object of public concern, while at the same time people are being more health conscious. As an essential factor for causing the lifestyle-related diseases, we assume that the knowledge circulation on dietary habits is still insufficient. This paper focuses on everyday meals close to our life and proposes a well-balanced menu planning system as a preventive measure of lifestyle-related diseases. The system is developed by using a Web-based frontend and it provides multi-user services and menu information sharing capabilities like social networking services (SNS). The system is implemented on a Web server running Apache (HTTP server software), MySQL (database management system), and PHP (scripting language for dynamic Web pages). For the menu planning, a genetic algorithm is applied by understanding this problem as multidimensional 0-1 integer programming.

ASPEN--A Web-Based Application for Managing Student Server Accounts

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2004-01-01

The growth of the Internet has greatly increased the demand for server-side programming courses at colleges and universities. Students enrolled in such courses must be provided with server-based accounts that support the technologies that they are learning. The process of creating, managing and removing large numbers of student server accounts is…

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

Advancing the Power and Utility of Server-Side Aggregation

NASA Technical Reports Server (NTRS)

Fulker, Dave; Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters.Topics 2 through 7 will be relevant to data consumers, data providers andnotably, due to the open-source nature of all OPeNDAP softwareto developers wishing to extend Hyrax, to build compatible clients and servers, andor to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

Weng, Y. H.; Sun, F. S.

2014-12-01

A web-based field data management system has been designed and developed to allow field geologists to store, organize, manage, and share field data online. System requirements were analyzed and clearly defined first regarding what data are to be stored, who the potential users are, and what system functions are needed in order to deliver the right data in the right way to the right user. A 3-tiered architecture was adopted to create this secure, scalable system that consists of a web browser at the front end while a database at the back end and a functional logic server in the middle. Specifically, HTML, CSS, and JavaScript were used to implement the user interface in the front-end tier, the Apache web server runs PHP scripts, and MySQL to server is used for the back-end database. The system accepts various types of field information, including image, audio, video, numeric, and text. It allows users to select data and populate them on either Google Earth or Google Maps for the examination of the spatial relations. It also makes the sharing of field data easy by converting them into XML format that is both human-readable and machine-readable, and thus ready for reuse.

Hybrid Rendering with Scheduling under Uncertainty

PubMed Central

Tamm, Georg; Krüger, Jens

2014-01-01

As scientific data of increasing size is generated by today’s simulations and measurements, utilizing dedicated server resources to process the visualization pipeline becomes necessary. In a purely server-based approach, requirements on the client-side are minimal as the client only displays results received from the server. However, the client may have a considerable amount of hardware available, which is left idle. Further, the visualization is put at the whim of possibly unreliable server and network conditions. Server load, bandwidth and latency may substantially affect the response time on the client. In this paper, we describe a hybrid method, where visualization workload is assigned to server and client. A capable client can produce images independently. The goal is to determine a workload schedule that enables a synergy between the two sides to provide rendering results to the user as fast as possible. The schedule is determined based on processing and transfer timings obtained at runtime. Our probabilistic scheduler adapts to changing conditions by shifting workload between server and client, and accounts for the performance variability in the dynamic system. PMID:25309115

Remotely accessible laboratory for MEMS testing

NASA Astrophysics Data System (ADS)

Sivakumar, Ganapathy; Mulsow, Matthew; Melinger, Aaron; Lacouture, Shelby; Dallas, Tim E.

2010-02-01

We report on the construction of a remotely accessible and interactive laboratory for testing microdevices (aka: MicroElectroMechancial Systems - MEMS). Enabling expanded utilization of microdevices for research, commercial, and educational purposes is very important for driving the creation of future MEMS devices and applications. Unfortunately, the relatively high costs associated with MEMS devices and testing infrastructure makes widespread access to the world of MEMS difficult. The creation of a virtual lab to control and actuate MEMS devices over the internet helps spread knowledge to a larger audience. A host laboratory has been established that contains a digital microscope, microdevices, controllers, and computers that can be logged into through the internet. The overall layout of the tele-operated MEMS laboratory system can be divided into two major parts: the server side and the client side. The server-side is present at Texas Tech University, and hosts a server machine that runs the Linux operating system and is used for interfacing the MEMS lab with the outside world via internet. The controls from the clients are transferred to the lab side through the server interface. The server interacts with the electronics required to drive the MEMS devices using a range of National Instruments hardware and LabView Virtual Instruments. An optical microscope (100 ×) with a CCD video camera is used to capture images of the operating MEMS. The server broadcasts the live video stream over the internet to the clients through the website. When the button is pressed on the website, the MEMS device responds and the video stream shows the movement in close to real time.

Asynchronous data change notification between database server and accelerator controls system

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

Fu, W.; Morris, J.; Nemesure, S.

2011-10-10

Database data change notification (DCN) is a commonly used feature. Not all database management systems (DBMS) provide an explicit DCN mechanism. Even for those DBMS's which support DCN (such as Oracle and MS SQL server), some server side and/or client side programming may be required to make the DCN system work. This makes the setup of DCN between database server and interested clients tedious and time consuming. In accelerator control systems, there are many well established software client/server architectures (such as CDEV, EPICS, and ADO) that can be used to implement data reflection servers that transfer data asynchronously to anymore » client using the standard SET/GET API. This paper describes a method for using such a data reflection server to set up asynchronous DCN (ADCN) between a DBMS and clients. This method works well for all DBMS systems which provide database trigger functionality. Asynchronous data change notification (ADCN) between database server and clients can be realized by combining the use of a database trigger mechanism, which is supported by major DBMS systems, with server processes that use client/server software architectures that are familiar in the accelerator controls community (such as EPICS, CDEV or ADO). This approach makes the ADCN system easy to set up and integrate into an accelerator controls system. Several ADCN systems have been set up and used in the RHIC-AGS controls system.« less

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

This paper introduces the design and implementation of a Multimedia Data Repository served as a multimedia information system, which provides users a Web accessible, platform independent interface to query, browse, and retrieve multimedia data such as images, graphics, audio, video from a large multimedia data repository. By integrating the multimedia DBMS, in which the textual information and samples of the multimedia data is organized and stored, and Web server together into the Microsoft ActiveX Server Framework, users can access the DBMS and query the information by simply using a Web browser at the client-side. The original multimedia data can then be located and transmitted through the Internet from the tertiary storage device, a 400 CDROM optical jukebox at the server-side, to the client-side for further use.

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

PubMed Central

Nadzirin, Nurul; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

2013-01-01

We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/. PMID:23716645

Mars @ ASDC

NASA Astrophysics Data System (ADS)

Carraro, Francesco

"Mars @ ASDC" is a project born with the goal of using the new web technologies to assist researches involved in the study of Mars. This project employs Mars map and javascript APIs provided by Google to visualize data acquired by space missions on the planet. So far, visualization of tracks acquired by MARSIS and regions observed by VIRTIS-Rosetta has been implemented. The main reason for the creation of this kind of tool is the difficulty in handling hundreds or thousands of acquisitions, like the ones from MARSIS, and the consequent difficulty in finding observations related to a particular region. This led to the development of a tool which allows to search for acquisitions either by defining the region of interest through a set of geometrical parameters or by manually selecting the region on the map through a few mouse clicks The system allows the visualization of tracks (acquired by MARSIS) or regions (acquired by VIRTIS-Rosetta) which intersect the user defined region. MARSIS tracks can be visualized both in Mercator and polar projections while the regions observed by VIRTIS can presently be visualized only in Mercator projection. The Mercator projection is the standard map provided by Google. The polar projections are provided by NASA and have been developed to be used in combination with APIs provided by Google The whole project has been developed following the "open source" philosophy: the client-side code which handles the functioning of the web page is written in javascript; the server-side code which executes the searches for tracks or regions is written in PHP and the DB which undergoes the system is MySQL.

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

PubMed

Poitevin, Frédéric; Orland, Henri; Doniach, Sebastian; Koehl, Patrice; Delarue, Marc

2011-07-01

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).

Design of a Golf Swing Injury Detection and Evaluation open service platform with Ontology-oriented clustering case-based reasoning mechanism.

PubMed

Ku, Hao-Hsiang

2015-01-01

Nowadays, people can easily use a smartphone to get wanted information and requested services. Hence, this study designs and proposes a Golf Swing Injury Detection and Evaluation open service platform with Ontology-oritened clustering case-based reasoning mechanism, which is called GoSIDE, based on Arduino and Open Service Gateway initative (OSGi). GoSIDE is a three-tier architecture, which is composed of Mobile Users, Application Servers and a Cloud-based Digital Convergence Server. A mobile user is with a smartphone and Kinect sensors to detect the user's Golf swing actions and to interact with iDTV. An application server is with Intelligent Golf Swing Posture Analysis Model (iGoSPAM) to check a user's Golf swing actions and to alter this user when he is with error actions. Cloud-based Digital Convergence Server is with Ontology-oriented Clustering Case-based Reasoning (CBR) for Quality of Experiences (OCC4QoE), which is designed to provide QoE services by QoE-based Ontology strategies, rules and events for this user. Furthermore, GoSIDE will automatically trigger OCC4QoE and deliver popular rules for a new user. Experiment results illustrate that GoSIDE can provide appropriate detections for Golfers. Finally, GoSIDE can be a reference model for researchers and engineers.

Development of informational-communicative system, created to improve medical help for family medicine doctors.

PubMed

Smiianov, Vladyslav A; Dryha, Natalia O; Smiianova, Olha I; Obodyak, Victor K; Zudina, Tatyana O

2018-01-01

Introduction: Today mobile health`s protection service has no concrete meaning. As an research object it was called mHealth and named by Global observatory of electronic health`s protection as "Doctor and social health practice that can be supported by any mobile units (mobile phones or smartphones), units for patient`s health control, personal computers and other units of non-wired communication". An active usage of SMS in programs for patients` cure regimen keeping was quiet predictable. Mobile and electronic units only begin their development in medical sphere. Thus, to solve all health`s protection system reformation problems a special memorandum about cooperation in creating E-Health system in Ukraine was signed. The aim: Development of ICS for monitoring and non-infection ill patients` informing system optimization as a first level of medical help. Materials and methods: During research, we used systematical approach, meta-analysis, informational-analytical systems` schemes projection, expositive modeling. Developing the backend (server part of the site), we used next technologies: 1) the Apache web server; 2) programming language PHP; 3) Yii 2 PHP Framework. In the frontend developing were used the following technologies (client part of the site): 1) Bootstrap 3; 2) Vue JS Framework. Results and conclusions: Created duo-channel system "doctor-patient" and "patient-doctor" will allow usual doctors of family medicine (DFM) take the interactive dispensary cure and avoid uncontrolled illness progress. Doctor will monitor basic physical data of patient`s health and curing process. The main goal is to create automatic system to allow doctor regularly write periodical or non-periodical notifications, get patients` questioning answers and spread information between doctor and patient; that will optimize work of DFMs.

Research of GIS-services applicability for solution of spatial analysis tasks.

NASA Astrophysics Data System (ADS)

Terekhin, D. A.; Botygin, I. A.; Sherstneva, A. I.; Sherstnev, V. S.

2017-01-01

Experiments for working out the areas of applying various gis-services in the tasks of spatial analysis are discussed in this paper. Google Maps, Yandex Maps, Microsoft SQL Server are used as services of spatial analysis. All services have shown a comparable speed of analyzing the spatial data when carrying out elemental spatial requests (building up the buffer zone of a point object) as well as the preferences of Microsoft SQL Server in operating with more complicated spatial requests. When building up elemental spatial requests, internet-services show higher efficiency due to cliental data handling with JavaScript-subprograms. A weak point of public internet-services is an impossibility to handle data on a server side and a barren variety of spatial analysis functions. Microsoft SQL Server offers a large variety of functions needed for spatial analysis on the server side. The authors conclude that when solving practical problems, the capabilities of internet-services used in building up routes and completing other functions with spatial analysis with Microsoft SQL Server should be involved.

Percutaneous Hepatic Perfusion (PHP) with Melphalan as a Treatment for Unresectable Metastases Confined to the Liver.

PubMed

de Leede, Eleonora M; Burgmans, Mark C; Martini, Christian H; Tijl, Fred G J; van Erkel, Arian R; Vuyk, Jaap; Kapiteijn, Ellen; Verhoef, Cornelis; van de Velde, Cornelis J H; Vahrmeijer, Alexander L

2016-07-31

Unresectable liver metastases of colorectal cancer can be treated with systemic chemotherapy, aiming to limit the disease, extend survival or turn unresectable metastases into resectable ones. Some patients however, suffer from side effects or progression under systemic treatment. For patients with metastasized uveal melanoma there are no standard systemic therapy options. For patients without extrahepatic disease, isolated liver perfusion (IHP) may enable local disease control with limited systemic side effects. Previously, this was performed during open surgery with satisfying results, but morbidity and mortality related to the open procedure, prohibited a widespread application. Therefore, percutaneous hepatic perfusion (PHP) with simultaneous chemofiltration was developed. Besides decreasing morbidity and mortality, this procedure can be repeated, hopefully leading to a higher response rate and improved survival (by local control of disease). During PHP, catheters are placed in the proper hepatic artery, to infuse the chemotherapeutic agent, and in the inferior caval vein to aspirate the chemosaturated blood returning through the hepatic veins. The caval vein catheter is a double balloon catheter that prohibits leakage into the systemic circulation. The blood returning from the hepatic veins is aspirated through the catheter fenestrations and then perfused through an extra-corporeal filtration system. After filtration, the blood is returned to the patient by a third catheter in the right internal jugular vein. During PHP a high dose of melphalan is infused into the liver, which is toxic and would lead to life threatening complications when administered systemically. Because of the significant hemodynamic instability resulting from the combination of caval vein occlusion and chemofiltration, hemodynamic monitoring and hemodynamic support is of paramount importance during this complex procedure.

Web-based health services and clinical decision support.

PubMed

Jegelevicius, Darius; Marozas, Vaidotas; Lukosevicius, Arunas; Patasius, Martynas

2004-01-01

The purpose of this study was the development of a Web-based e-health service for comprehensive assistance and clinical decision support. The service structure consists of a Web server, a PHP-based Web interface linked to a clinical SQL database, Java applets for interactive manipulation and visualization of signals and a Matlab server linked with signal and data processing algorithms implemented by Matlab programs. The service ensures diagnostic signal- and image analysis-sbased clinical decision support. By using the discussed methodology, a pilot service for pathology specialists for automatic calculation of the proliferation index has been developed. Physicians use a simple Web interface for uploading the pictures under investigation to the server; subsequently a Java applet interface is used for outlining the region of interest and, after processing on the server, the requested proliferation index value is calculated. There is also an "expert corner", where experts can submit their index estimates and comments on particular images, which is especially important for system developers. These expert evaluations are used for optimization and verification of automatic analysis algorithms. Decision support trials have been conducted for ECG and ophthalmology ultrasonic investigations of intraocular tumor differentiation. Data mining algorithms have been applied and decision support trees constructed. These services are under implementation by a Web-based system too. The study has shown that the Web-based structure ensures more effective, flexible and accessible services compared with standalone programs and is very convenient for biomedical engineers and physicians, especially in the development phase.

Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

NASA Astrophysics Data System (ADS)

Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition, we can obtain temporal dynamics (mpeg- files) of the main oscillation characteristics: amplitude, power and phase as a spatial-temporal coordinates. For periodogram mapping of data cubes as a method for the pre-analysis, we developed preparation of the color maps where the pixel's colour corresponds to the frequency of the power spectrum maximum. The computer system based on applications ION-scripts, algorithmic languages IDL and PHP, and Apache WEB server. The IDL ION-scripts use for preparation and configuration of network requests at the central data server with subsequent connection to IDL run-unit software and graphic output on FTP-server and screen. Web page is constructed using PHP language.

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

WebGLORE: a web service for Grid LOgistic REgression.

PubMed

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-12-15

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation.

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

POOL server: machine learning application for functional site prediction in proteins.

PubMed

Somarowthu, Srinivas; Ondrechen, Mary Jo

2012-08-01

We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information for high-performance prediction of catalytic residues from 3D structures. Input features consist of THEMATICS electrostatics data and pocket information from ConCavity. THEMATICS measures deviation from typical, sigmoidal titration behavior to identify functionally important residues and ConCavity identifies binding pockets by analyzing the surface geometry of protein structures. Both THEMATICS and ConCavity (structure only) do not require the query protein to have any sequence or structure similarity to other proteins. Hence, POOL is applicable to proteins with novel folds and engineered proteins. As an additional option for cases where sequence homologues are available, users can include evolutionary information from INTREPID for enhanced accuracy in site prediction. The web site is free and open to all users with no login requirements at http://www.pool.neu.edu. m.ondrechen@neu.edu Supplementary data are available at Bioinformatics online.

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A web accessible scientific workflow system for vadoze zone performance monitoring: design and implementation examples

NASA Astrophysics Data System (ADS)

Mattson, E.; Versteeg, R.; Ankeny, M.; Stormberg, G.

2005-12-01

Long term performance monitoring has been identified by DOE, DOD and EPA as one of the most challenging and costly elements of contaminated site remedial efforts. Such monitoring should provide timely and actionable information relevant to a multitude of stakeholder needs. This information should be obtained in a manner which is auditable, cost effective and transparent. Over the last several years INL staff has designed and implemented a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition from diverse sensors (geophysical, geochemical and hydrological) with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic javascript and html/css) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This system has been implemented and is operational for several sites, including the Ruby Gulch Waste Rock Repository (a capped mine waste rock dump on the Gilt Edge Mine Superfund Site), the INL Vadoze Zone Research Park and an alternative cover landfill. Implementations for other vadoze zone sites are currently in progress. These systems allow for autonomous performance monitoring through automated data analysis and report generation. This performance monitoring has allowed users to obtain insights into system dynamics, regulatory compliance and residence times of water. Our system uses modular components for data selection and graphing and WSDL compliant webservices for external functions such as statistical analyses and model invocations. Thus, implementing this system for novel sites and extending functionality (e.g. adding novel models) is relatively straightforward. As system access requires a standard webbrowser and uses intuitive functionality, stakeholders with diverse degrees of technical insight can use this system with little or no training.

User-driven Cloud Implementation of environmental models and data for all

NASA Astrophysics Data System (ADS)

Gurney, R. J.; Percy, B. J.; Elkhatib, Y.; Blair, G. S.

2014-12-01

Environmental data and models come from disparate sources over a variety of geographical and temporal scales with different resolutions and data standards, often including terabytes of data and model simulations. Unfortunately, these data and models tend to remain solely within the custody of the private and public organisations which create the data, and the scientists who build models and generate results. Although many models and datasets are theoretically available to others, the lack of ease of access tends to keep them out of reach of many. We have developed an intuitive web-based tool that utilises environmental models and datasets located in a cloud to produce results that are appropriate to the user. Storyboards showing the interfaces and visualisations have been created for each of several exemplars. A library of virtual machine images has been prepared to serve these exemplars. Each virtual machine image has been tailored to run computer models appropriate to the end user. Two approaches have been used; first as RESTful web services conforming to the Open Geospatial Consortium (OGC) Web Processing Service (WPS) interface standard using the Python-based PyWPS; second, a MySQL database interrogated using PHP code. In all cases, the web client sends the server an HTTP GET request to execute the process with a number of parameter values and, once execution terminates, an XML or JSON response is sent back and parsed at the client side to extract the results. All web services are stateless, i.e. application state is not maintained by the server, reducing its operational overheads and simplifying infrastructure management tasks such as load balancing and failure recovery. A hybrid cloud solution has been used with models and data sited on both private and public clouds. The storyboards have been transformed into intuitive web interfaces at the client side using HTML, CSS and JavaScript, utilising plug-ins such as jQuery and Flot (for graphics), and Google Maps APIs. We have demonstrated that a cloud infrastructure can be used to assemble a virtual research environment that, coupled with a user-driven development approach, is able to cater to the needs of a wide range of user groups, from domain experts to concerned members of the general public.

An object-oriented approach to deploying highly configurable Web interfaces for the ATLAS experiment

NASA Astrophysics Data System (ADS)

Lange, Bruno; Maidantchik, Carmen; Pommes, Kathy; Pavani, Varlen; Arosa, Breno; Abreu, Igor

2015-12-01

The ATLAS Technical Coordination disposes of 17 Web systems to support its operation. These applications, whilst ranging from managing the process of publishing scientific papers to monitoring radiation levels in the equipment in the experimental cavern, are constantly prone to changes in requirements due to the collaborative nature of the experiment and its management. In this context, a Web framework is proposed to unify the generation of the supporting interfaces. FENCE assembles classes to build applications by making extensive use of JSON configuration files. It relies heavily on Glance, a technology that was set forth in 2003 to create an abstraction layer on top of the heterogeneous sources that store the technical coordination data. Once Glance maps out the database modeling, records can be referenced in the configuration files by wrapping unique identifiers around double enclosing brackets. The deployed content can be individually secured by attaching clearance attributes to their description thus ensuring that view/edit privileges are granted to eligible users only. The framework also provides tools for securely writing into a database. Fully HTML5-compliant multi-step forms can be generated from their JSON description to assure that the submitted data comply with a series of constraints. Input validation is carried out primarily on the server- side but, following progressive enhancement guidelines, verification might also be performed on the client-side by enabling specific markup data attributes which are then handed over to the jQuery validation plug-in. User monitoring is accomplished by thoroughly logging user requests along with any POST data. Documentation is built from the source code using the phpDocumentor tool and made readily available for developers online. Fence, therefore, speeds up the implementation of Web interfaces and reduces the response time to requirement changes by minimizing maintenance overhead.

A Remote Health Monitoring System for the Elderly Based on Smart Home Gateway

PubMed Central

Shao, Minggang

2017-01-01

This paper proposed a remote health monitoring system for the elderly based on smart home gateway. The proposed system consists of three parts: the smart clothing, the smart home gateway, and the health care server. The smart clothing collects the elderly's electrocardiogram (ECG) and motion signals. The home gateway is used for data transmission. The health care server provides services of data storage and user information management; it is constructed on the Windows-Apache-MySQL-PHP (WAMP) platform and is tested on the Ali Cloud platform. To resolve the issues of data overload and network congestion of the home gateway, an ECG compression algorithm is applied. System demonstration shows that the ECG signals and motion signals of the elderly can be monitored. Evaluation of the compression algorithm shows that it has a high compression ratio and low distortion and consumes little time, which is suitable for home gateways. The proposed system has good scalability, and it is simple to operate. It has the potential to provide long-term and continuous home health monitoring services for the elderly. PMID:29204258

A Remote Health Monitoring System for the Elderly Based on Smart Home Gateway.

PubMed

Guan, Kai; Shao, Minggang; Wu, Shuicai

2017-01-01

This paper proposed a remote health monitoring system for the elderly based on smart home gateway. The proposed system consists of three parts: the smart clothing, the smart home gateway, and the health care server. The smart clothing collects the elderly's electrocardiogram (ECG) and motion signals. The home gateway is used for data transmission. The health care server provides services of data storage and user information management; it is constructed on the Windows-Apache-MySQL-PHP (WAMP) platform and is tested on the Ali Cloud platform. To resolve the issues of data overload and network congestion of the home gateway, an ECG compression algorithm is applied. System demonstration shows that the ECG signals and motion signals of the elderly can be monitored. Evaluation of the compression algorithm shows that it has a high compression ratio and low distortion and consumes little time, which is suitable for home gateways. The proposed system has good scalability, and it is simple to operate. It has the potential to provide long-term and continuous home health monitoring services for the elderly.

SciServer Compute brings Analysis to Big Data in the Cloud

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Medvedev, Dmitry; Lemson, Gerard; Souter, Barbara

2016-06-01

SciServer Compute uses Jupyter Notebooks running within server-side Docker containers attached to big data collections to bring advanced analysis to big data "in the cloud." SciServer Compute is a component in the SciServer Big-Data ecosystem under development at JHU, which will provide a stable, reproducible, sharable virtual research environment.SciServer builds on the popular CasJobs and SkyServer systems that made the Sloan Digital Sky Survey (SDSS) archive one of the most-used astronomical instruments. SciServer extends those systems with server-side computational capabilities and very large scratch storage space, and further extends their functions to a range of other scientific disciplines.Although big datasets like SDSS have revolutionized astronomy research, for further analysis, users are still restricted to downloading the selected data sets locally - but increasing data sizes make this local approach impractical. Instead, researchers need online tools that are co-located with data in a virtual research environment, enabling them to bring their analysis to the data.SciServer supports this using the popular Jupyter notebooks, which allow users to write their own Python and R scripts and execute them on the server with the data (extensions to Matlab and other languages are planned). We have written special-purpose libraries that enable querying the databases and other persistent datasets. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files. Communication between the various components of the SciServer system is managed through SciServer‘s new Single Sign-on Portal.We have created a number of demos to illustrate the capabilities of SciServer Compute, including Python and R scripts accessing a range of datasets and showing the data flow between storage and compute components.Demos, documentation, and more information can be found at www.sciserver.org.SciServer is funded by the National Science Foundation Award ACI-1261715.

Graph and Network for Model Elicitation (GNOME Phase 2)

DTIC Science & Technology

2013-02-01

10 3.3 GNOME UI Components for NOEM Web Client...20 Figure 17: Sampling in Web -client...the web -client). The server-side service can run and generate data asynchronously, allowing a cluster of servers to run the sampling. Also, a

WebGLORE: a Web service for Grid LOgistic REgression

PubMed Central

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-01-01

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. Availability and implementation: http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation. Contact: x1jiang@ucsd.edu PMID:24072732

Development of Applications about Hazards and Preventions of Drug Based On Android

NASA Astrophysics Data System (ADS)

Hartatik; Febriyanto, F.; Munawaroh, H.

2018-03-01

The number of drug abuse was increase among the younger generation, it caused younger generation fall into drug abuse, and it will lead to physical and mental damage. The lack of knowledge of drugs danger is one of the most potential problems, so in this study we made an application about the types, dangers, and how to avoid its abusement. The application built using PHP programming language with codeiniter framework on admin part, while the parsing data between mobile application server using Javascript Object Notation (JSON). This application has been tested and 85% respondents stated that this application provides positive benefits especially for the socialization of drug abuse.

Menu-driven cloud computing and resource sharing for R and Bioconductor.

PubMed

Bolouri, Hamid; Dulepet, Rajiv; Angerman, Michael

2011-08-15

We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. hbolouri@fhcrc.org.

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

On-demand server-side image processing for web-based DICOM image display

NASA Astrophysics Data System (ADS)

Sakusabe, Takaya; Kimura, Michio; Onogi, Yuzo

2000-04-01

Low cost image delivery is needed in modern networked hospitals. If a hospital has hundreds of clients, cost of client systems is a big problem. Naturally, a Web-based system is the most effective solution. But a Web browser could not display medical images with certain image processing such as a lookup table transformation. We developed a Web-based medical image display system using Web browser and on-demand server-side image processing. All images displayed on a Web page are generated from DICOM files on a server, delivered on-demand. User interaction on the Web page is handled by a client-side scripting technology such as JavaScript. This combination makes a look-and-feel of an imaging workstation not only for its functionality but also for its speed. Real time update of images with tracing mouse motion is achieved on Web browser without any client-side image processing which may be done by client-side plug-in technology such as Java Applets or ActiveX. We tested performance of the system in three cases. Single client, small number of clients in a fast speed network, and large number of clients in a normal speed network. The result shows that there are very slight overhead for communication and very scalable in number of clients.

Sirocco Storage Server v. pre-alpha 0.1

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

Curry, Matthew L.; Danielson, Geoffrey; Ward, H. Lee

Sirocco is a parallel storage system under development, designed for write-intensive workloads on large-scale HPC platforms. It implements a keyvalue object store on top of a set of loosely federated storage servers that cooperate to ensure data integrity and performance. It includes support for a range of different types of storage transactions. This software release constitutes a conformant storage server, along with the client-side libraries to access the storage over a network.

Automatic Thermal Infrared Panoramic Imaging Sensor

DTIC Science & Technology

2006-11-01

hibernation, in which power supply to the server computer , the wireless network hardware, the GPS receiver, and the electronic compass / tilt sensor...prototype. At the operator’s command on the client laptop, the receiver wakeup device on the server side will switch on the ATX power supply at the...server, to resume the power supply to all the APTIS components. The embedded computer will resume all of the functions it was performing when put

GrayStarServer: Server-side Spectrum Synthesis with a Browser-based Client-side User Interface

NASA Astrophysics Data System (ADS)

Short, C. Ian

2016-10-01

We present GrayStarServer (GSS), a stellar atmospheric modeling and spectrum synthesis code of pedagogical accuracy that is accessible in any web browser on commonplace computational devices and that runs on a timescale of a few seconds. The addition of spectrum synthesis annotated with line identifications extends the functionality and pedagogical applicability of GSS beyond that of its predecessor, GrayStar3 (GS3). The spectrum synthesis is based on a line list acquired from the NIST atomic spectra database, and the GSS post-processing and user interface client allows the user to inspect the plain text ASCII version of the line list, as well as to apply macroscopic broadening. Unlike GS3, GSS carries out the physical modeling on the server side in Java, and communicates with the JavaScript and HTML client via an asynchronous HTTP request. We also describe other improvements beyond GS3 such as a more physical treatment of background opacity and atmospheric physics, the comparison of key results with those of the Phoenix code, and the use of the HTML < {canvas}> element for higher quality plotting and rendering of results. We also present LineListServer, a Java code for converting custom ASCII line lists in NIST format to the byte data type file format required by GSS so that users can prepare their own custom line lists. We propose a standard for marking up and packaging model atmosphere and spectrum synthesis output for data transmission and storage that will facilitate a web-based approach to stellar atmospheric modeling and spectrum synthesis. We describe some pedagogical demonstrations and exercises enabled by easily accessible, on-demand, responsive spectrum synthesis. GSS may serve as a research support tool by providing quick spectroscopic reconnaissance. GSS may be found at www.ap.smu.ca/~ishort/OpenStars/GrayStarServer/grayStarServer.html, and source tarballs for local installations of both GSS and LineListServer may be found at www.ap.smu.ca/~ishort/OpenStars/.

The PhEDEx next-gen website

NASA Astrophysics Data System (ADS)

Egeland, R.; Huang, C.-H.; Rossman, P.; Sundarrajan, P.; Wildish, T.

2012-12-01

PhEDEx is the data-transfer management solution written by CMS. It consists of agents running at each site, a website for presentation of information, and a web-based data-service for scripted access to information. The website allows users to monitor the progress of data-transfers, the status of site agents and links between sites, and the overall status and behaviour of everything about PhEDEx. It also allows users to make and approve requests for data-transfers and for deletion of data. It is the main point-of-entry for all users wishing to interact with PhEDEx. For several years, the website has consisted of a single perl program with about 10K SLOC. This program has limited capabilities for exploring the data, with only coarse filtering capabilities and no context-sensitive awareness. Graphical information is presented as static images, generated on the server, with no interactivity. It is also not well connected to the rest of the PhEDEx codebase, since much of it was written before the data-service was developed. All this makes it hard to maintain and extend. We are re-implementing the website to address these issues. The UI is being rewritten in Javascript, replacing most of the server-side code. We are using the YUI toolkit to provide advanced features and context-sensitive interaction, and will adopt a Javascript charting library for generating graphical representations client-side. This relieves the server of much of its load, and automatically improves server-side security. The Javascript components can be re-used in many ways, allowing custom pages to be developed for specific uses. In particular, standalone test-cases using small numbers of components make it easier to debug the Javascript than it is to debug a large server program. Information about PhEDEx is accessed through the PhEDEx data-service, since direct SQL is not available from the clients’ browser. This provides consistent semantics with other, externally written monitoring tools, which already use the data-service. It also reduces redundancy in the code, yielding a simpler, consolidated codebase. In this talk we describe our experience of re-factoring this monolithic server-side program into a lighter client-side framework. We describe some of the techniques that worked well for us, and some of the mistakes we made along the way. We present the current state of the project, and its future direction.

Designing indonesian teacher engagement index (itei) applications based on android

NASA Astrophysics Data System (ADS)

Manalu, S. R.; Sasmoko; Permai, S. D.; Widhoyoko, S. A.; Indrianti, Y.

2018-03-01

Teachers who have a good level of engagement will be able to produce students who engage and excel. Level of national teachers’ engagement needs to be a reference to the level of educational success and equity of national education. The spread of geographically inaccessible Indonesian teachers is a barrier to these measurements. ITEI Android application developed by analysing the geographical problem, so that each teacher can participate wherever they are. The ITEI app is designed by implementing Android on the client side and load balancer on the server side. Android ITEI will feature a number of questions questionnaire to teachers. Meanwhile, the load balancer will distribute the answers to each server for processing. Load Balancer ensures fast data processing and minimize server failure. The results of the processing on the server will be sent back to Android in the form of profiling themselves ITEI teachers. While the data obtained and stored in the server can be used to measure the level of national teachers’ engagement. The result of this research is the design of ITEI application ready to be implemented in order to support the data collection process of teacher national engagement level.

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

PubMed

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-01-01

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

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

PubMed Central

Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir

2016-01-01

The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree. PMID:27166375

Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

Caching Servers for ATLAS

NASA Astrophysics Data System (ADS)

Gardner, R. W.; Hanushevsky, A.; Vukotic, I.; Yang, W.

2017-10-01

As many LHC Tier-3 and some Tier-2 centers look toward streamlining operations, they are considering autonomously managed storage elements as part of the solution. These storage elements are essentially file caching servers. They can operate as whole file or data block level caches. Several implementations exist. In this paper we explore using XRootD caching servers that can operate in either mode. They can also operate autonomously (i.e. demand driven), be centrally managed (i.e. a Rucio managed cache), or operate in both modes. We explore the pros and cons of various configurations as well as practical requirements for caching to be effective. While we focus on XRootD caches, the analysis should apply to other kinds of caches as well.

A Brief Assessment of LC2IEDM, MIST and Web Services for use in Naval Tactical Data Management

DTIC Science & Technology

2004-07-01

server software, messaging between the client and server, and a database. The MIST database is implemented in an open source DBMS named PostGreSQL ... PostGreSQL had its beginnings at the University of California, Berkley, in 1986 [11]. The development of PostGreSQL has since evolved into a...contact history from the database. DRDC Atlantic TM 2004-148 9 Request Software Request Software Server Side Response from service

Dynamic Server-Based KML Code Generator Method for Level-of-Detail Traversal of Geospatial Data

NASA Technical Reports Server (NTRS)

Baxes, Gregory; Mixon, Brian; Linger, TIm

2013-01-01

Web-based geospatial client applications such as Google Earth and NASA World Wind must listen to data requests, access appropriate stored data, and compile a data response to the requesting client application. This process occurs repeatedly to support multiple client requests and application instances. Newer Web-based geospatial clients also provide user-interactive functionality that is dependent on fast and efficient server responses. With massively large datasets, server-client interaction can become severely impeded because the server must determine the best way to assemble data to meet the client applications request. In client applications such as Google Earth, the user interactively wanders through the data using visually guided panning and zooming actions. With these actions, the client application is continually issuing data requests to the server without knowledge of the server s data structure or extraction/assembly paradigm. A method for efficiently controlling the networked access of a Web-based geospatial browser to server-based datasets in particular, massively sized datasets has been developed. The method specifically uses the Keyhole Markup Language (KML), an Open Geospatial Consortium (OGS) standard used by Google Earth and other KML-compliant geospatial client applications. The innovation is based on establishing a dynamic cascading KML strategy that is initiated by a KML launch file provided by a data server host to a Google Earth or similar KMLcompliant geospatial client application user. Upon execution, the launch KML code issues a request for image data covering an initial geographic region. The server responds with the requested data along with subsequent dynamically generated KML code that directs the client application to make follow-on requests for higher level of detail (LOD) imagery to replace the initial imagery as the user navigates into the dataset. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics. The method yields significant improvements in userinteractive geospatial client and data server interaction and associated network bandwidth requirements. The innovation uses a C- or PHP-code-like grammar that provides a high degree of processing flexibility. A set of language lexer and parser elements is provided that offers a complete language grammar for writing and executing language directives. A script is wrapped and passed to the geospatial data server by a client application as a component of a standard KML-compliant statement. The approach provides an efficient means for a geospatial client application to request server preprocessing of data prior to client delivery. Data is structured in a quadtree format. As the user zooms into the dataset, geographic regions are subdivided into four child regions. Conversely, as the user zooms out, four child regions collapse into a single, lower-LOD region. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics.

Data-driven decision support for radiologists: re-using the National Lung Screening Trial dataset for pulmonary nodule management.

PubMed

Morrison, James J; Hostetter, Jason; Wang, Kenneth; Siegel, Eliot L

2015-02-01

Real-time mining of large research trial datasets enables development of case-based clinical decision support tools. Several applicable research datasets exist including the National Lung Screening Trial (NLST), a dataset unparalleled in size and scope for studying population-based lung cancer screening. Using these data, a clinical decision support tool was developed which matches patient demographics and lung nodule characteristics to a cohort of similar patients. The NLST dataset was converted into Structured Query Language (SQL) tables hosted on a web server, and a web-based JavaScript application was developed which performs real-time queries. JavaScript is used for both the server-side and client-side language, allowing for rapid development of a robust client interface and server-side data layer. Real-time data mining of user-specified patient cohorts achieved a rapid return of cohort cancer statistics and lung nodule distribution information. This system demonstrates the potential of individualized real-time data mining using large high-quality clinical trial datasets to drive evidence-based clinical decision-making.

Menu-driven cloud computing and resource sharing for R and Bioconductor

PubMed Central

Bolouri, Hamid; Angerman, Michael

2011-01-01

Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. Contact: hbolouri@fhcrc.org PMID:21685055

A teledentistry system for the second opinion.

PubMed

Gambino, Orazio; Lima, Fausto; Pirrone, Roberto; Ardizzone, Edoardo; Campisi, Giuseppina; di Fede, Olga

2014-01-01

In this paper we present a Teledentistry system aimed to the Second Opinion task. It make use of a particular camera called intra-oral camera, also called dental camera, in order to perform the photo shooting and real-time video of the inner part of the mouth. The pictures acquired by the Operator with such a device are sent to the Oral Medicine Expert (OME) by means of a current File Transfer Protocol (FTP) service and the real-time video is channeled into a video streaming thanks to the VideoLan client/server (VLC) application. It is composed by a HTML5 web-pages generated by PHP and allows to perform the Second Opinion both when Operator and OME are logged and when one of them is offline.

[Construction of DICOM-WWW gateway by open source, and application to PDAs using the high-speed mobile communications network].

PubMed

Yokohama, Noriya

2003-09-01

The author constructed a medical image network system using open source software that took security into consideration. This system was enabled for search and browse with a WWW browser, and images were stored in a DICOM server. In order to realize this function, software was developed to fill in the gap between the DICOM protocol and HTTP using PHP language. The transmission speed was evaluated by the difference in protocols between DICOM and HTTP. Furthermore, an attempt was made to evaluate the convenience of medical image access with a personal information terminal via the Internet through the high-speed mobile communication terminal. Results suggested the feasibility of remote diagnosis and application to emergency care.

Location based chat application for iPhone

NASA Astrophysics Data System (ADS)

Rana, Pradeep

With the increasing use of mobile devices everywhere in the world, there is a lack of social interaction between people. The objective of this thesis project is to create a location based chat application, which will help users to interact with other people around them. It will provide an opportunity to meet people when someone visits a new place. The app will use GPS coordinates of the user and will show him a list of other users based on his location. The user can then choose any of the other users from the list and start chatting with them. This app will consist of a frontend and backend. The frontend will be an iOS application and the backend will be a PHP/MYSQL server.

Promotion Assistance Tool for Mobile Phone Users

NASA Astrophysics Data System (ADS)

Intraprasert, P.; Jatikul, N.; Chantrapornchai, C.

In this paper, we propose an application tool to help analyze the usage of a mobile phone for a typical user. From the past usage, the tool can analyze the promotion that is suitable for the user which may save the total expense. The application consists of both client and server side. On the server side, the information for each promotion package for a phone operator is stored as well as the usage database for each client. The client side is a user interface for both phone operators and users to enter their information. The analysis engine are based on KNN, ANN, decision tree and Naïve Bayes models. For comparison, it is shown that KNN and decision outperforms the others.

Share Data with OPeNDAP Hyrax: New Features and Improvements

NASA Technical Reports Server (NTRS)

Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in 1. server installation, 2. server configuration, 3. Hyrax aggregation capabilities, 4. support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS), 5. support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

Accessing multimedia content from mobile applications using semantic web technologies

NASA Astrophysics Data System (ADS)

Kreutel, Jörn; Gerlach, Andrea; Klekamp, Stefanie; Schulz, Kristin

2014-02-01

We describe the ideas and results of an applied research project that aims at leveraging the expressive power of semantic web technologies as a server-side backend for mobile applications that provide access to location and multimedia data and allow for a rich user experience in mobile scenarios, ranging from city and museum guides to multimedia enhancements of any kind of narrative content, including e-book applications. In particular, we will outline a reusable software architecture for both server-side functionality and native mobile platforms that is aimed at significantly decreasing the effort required for developing particular applications of that kind.

Deploying Server-side File System Monitoring at NERSC

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

Uselton, Andrew

2009-05-01

The Franklin Cray XT4 at the NERSC center was equipped with the server-side I/O monitoring infrastructure Cerebro/LMT, which is described here in detail. Insights gained from the data produced include a better understanding of instantaneous data rates during file system testing, file system behavior during regular production time, and long-term average behaviors. Information and insights gleaned from this monitoring support efforts to proactively manage the I/O infrastructure on Franklin. A simple model for I/O transactions is introduced and compared with the 250 million observations sent to the LMT database from August 2008 to February 2009.

The PhEDEx next-gen website

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

Egeland, R.; Huang, C. H.; Rossman, P.

PhEDEx is the data-transfer management solution written by CMS. It consists of agents running at each site, a website for presentation of information, and a web-based data-service for scripted access to information. The website allows users to monitor the progress of data-transfers, the status of site agents and links between sites, and the overall status and behaviour of everything about PhEDEx. It also allows users to make and approve requests for data-transfers and for deletion of data. It is the main point-of-entry for all users wishing to interact with PhEDEx. For several years, the website has consisted of a singlemore » perl program with about 10K SLOC. This program has limited capabilities for exploring the data, with only coarse filtering capabilities and no context-sensitive awareness. Graphical information is presented as static images, generated on the server, with no interactivity. It is also not well connected to the rest of the PhEDEx codebase, since much of it was written before the data-service was developed. All this makes it hard to maintain and extend. We are re-implementing the website to address these issues. The UI is being rewritten in Javascript, replacing most of the server-side code. We are using the YUI toolkit to provide advanced features and context-sensitive interaction, and will adopt a Javascript charting library for generating graphical representations client-side. This relieves the server of much of its load, and automatically improves server-side security. The Javascript components can be re-used in many ways, allowing custom pages to be developed for specific uses. In particular, standalone test-cases using small numbers of components make it easier to debug the Javascript than it is to debug a large server program. Information about PhEDEx is accessed through the PhEDEx data-service, since direct SQL is not available from the clients browser. This provides consistent semantics with other, externally written monitoring tools, which already use the data-service. It also reduces redundancy in the code, yielding a simpler, consolidated codebase. In this talk we describe our experience of re-factoring this monolithic server-side program into a lighter client-side framework. We describe some of the techniques that worked well for us, and some of the mistakes we made along the way. We present the current state of the project, and its future direction.« less

Experiment Management System for the SND Detector

NASA Astrophysics Data System (ADS)

Pugachev, K.

2017-10-01

We present a new experiment management system for the SND detector at the VEPP-2000 collider (Novosibirsk). An important part to report about is access to experimental databases (configuration, conditions and metadata). The system is designed in client-server architecture. User interaction comes true using web-interface. The server side includes several logical layers: user interface templates; template variables description and initialization; implementation details. The templates are meant to involve as less IT knowledge as possible. Experiment configuration, conditions and metadata are stored in a database. To implement the server side Node.js, a modern JavaScript framework, has been chosen. A new template engine having an interesting feature is designed. A part of the system is put into production. It includes templates dealing with showing and editing first level trigger configuration and equipment configuration and also showing experiment metadata and experiment conditions data index.

OnlineTED.com--a novel web-based audience response system for higher education. A pilot study to evaluate user acceptance.

PubMed

Kühbeck, Felizian; Engelhardt, Stefan; Sarikas, Antonio

2014-01-01

Audience response (AR) systems are increasingly used in undergraduate medical education. However, high costs and complexity of conventional AR systems often limit their use. Here we present a novel AR system that is platform independent and does not require hardware clickers or additional software to be installed. "OnlineTED" was developed at Technische Universität München (TUM) based on Hypertext Preprocessor (PHP) with a My Structured Query Language (MySQL)-database as server- and Javascript as client-side programming languages. "OnlineTED" enables lecturers to create and manage question sets online and start polls in-class via a web-browser. Students can participate in the polls with any internet-enabled device (smartphones, tablet-PCs or laptops). A paper-based survey was conducted with undergraduate medical students and lecturers at TUM to compare "OnlineTED" with conventional AR systems using clickers. "OnlineTED" received above-average evaluation results by both students and lecturers at TUM and was seen on par or superior to conventional AR systems. The survey results indicated that up to 80% of students at TUM own an internet-enabled device (smartphone or tablet-PC) for participation in web-based AR technologies. "OnlineTED" is a novel web-based and platform-independent AR system for higher education that was well received by students and lecturers. As a non-commercial alternative to conventional AR systems it may foster interactive teaching in undergraduate education, in particular with large audiences.

Identification of phase I and II metabolites of the new designer drug α-pyrrolidinohexiophenone (α-PHP) in human urine by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS).

PubMed

Paul, Michael; Bleicher, Sergej; Guber, Susanne; Ippisch, Josef; Polettini, Aldo; Schultis, Wolfgang

2015-11-01

Pyrrolidinophenones represent one emerging class of newly encountered drugs of abuse, also known as 'new psychoactive substances', with stimulating psychoactive effects. In this work, we report on the detection of the new designer drug α-pyrrolidinohexiophenone (α-PHP) and its phase I and II metabolites in a human urine sample of a drug abuser. Determination and structural elucidation of these metabolites have been achieved by liquid chromatography electrospray ionisation quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS). By tentative identification, the exact and approximate structures of 19 phase I metabolites and nine phase II glucuronides were elucidated. Major metabolic pathways revealed the reduction of the ß-keto moieties to their corresponding alcohols, didesalkylation of the pyrrolidine ring, hydroxylation and oxidation of the aliphatic side chain leading to n-hydroxy, aldehyde and carboxylate metabolites, and oxidation of the pyrrolidine ring to its lactam followed by ring cleavage and additional hydroxylation, reduction and oxidation steps and combinations thereof. The most abundant phase II metabolites were glucuronidated ß-keto-reduced alcohols. Besides the great number of metabolites detected in this sample, α-PHP is still one of the most abundant ions together with its ß-keto-reduced alcoholic dihydro metabolite. Monitoring of these metabolites in clinical and forensic toxicology may unambiguously prove the abuse of the new designer drug α-PHP. Copyright © 2015 John Wiley & Sons, Ltd.

E-Valuation: Pricing E-Learning.

ERIC Educational Resources Information Center

Hartley, Darin E.

2001-01-01

Looks at the ways that electronic learning is priced in organizations and the factors that influence the pricing. Discusses pros and cons of several pricing options: price per seat, subscription, pay as you go, per server, free, and payment based on time. (JOW)

A client–server framework for 3D remote visualization of radiotherapy treatment space

PubMed Central

Santhanam, Anand P.; Min, Yugang; Dou, Tai H.; Kupelian, Patrick; Low, Daniel A.

2013-01-01

Radiotherapy is safely employed for treating wide variety of cancers. The radiotherapy workflow includes a precise positioning of the patient in the intended treatment position. While trained radiation therapists conduct patient positioning, consultation is occasionally required from other experts, including the radiation oncologist, dosimetrist, or medical physicist. In many circumstances, including rural clinics and developing countries, this expertise is not immediately available, so the patient positioning concerns of the treating therapists may not get addressed. In this paper, we present a framework to enable remotely located experts to virtually collaborate and be present inside the 3D treatment room when necessary. A multi-3D camera framework was used for acquiring the 3D treatment space. A client–server framework enabled the acquired 3D treatment room to be visualized in real-time. The computational tasks that would normally occur on the client side were offloaded to the server side to enable hardware flexibility on the client side. On the server side, a client specific real-time stereo rendering of the 3D treatment room was employed using a scalable multi graphics processing units (GPU) system. The rendered 3D images were then encoded using a GPU-based H.264 encoding for streaming. Results showed that for a stereo image size of 1280 × 960 pixels, experts with high-speed gigabit Ethernet connectivity were able to visualize the treatment space at approximately 81 frames per second. For experts remotely located and using a 100 Mbps network, the treatment space visualization occurred at 8–40 frames per second depending upon the network bandwidth. This work demonstrated the feasibility of remote real-time stereoscopic patient setup visualization, enabling expansion of high quality radiation therapy into challenging environments. PMID:23440605

Automatic Identification of Application I/O Signatures from Noisy Server-Side Traces

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

Liu, Yang; Gunasekaran, Raghul; Ma, Xiaosong

2014-01-01

Competing workloads on a shared storage system cause I/O resource contention and application performance vagaries. This problem is already evident in today s HPC storage systems and is likely to become acute at exascale. We need more interaction between application I/O requirements and system software tools to help alleviate the I/O bottleneck, moving towards I/O-aware job scheduling. However, this requires rich techniques to capture application I/O characteristics, which remain evasive in production systems. Traditionally, I/O characteristics have been obtained using client-side tracing tools, with drawbacks such as non-trivial instrumentation/development costs, large trace traffic, and inconsistent adoption. We present a novelmore » approach, I/O Signature Identifier (IOSI), to characterize the I/O behavior of data-intensive applications. IOSI extracts signatures from noisy, zero-overhead server-side I/O throughput logs that are already collected on today s supercomputers, without interfering with the compiling/execution of applications. We evaluated IOSI using the Spider storage system at Oak Ridge National Laboratory, the S3D turbulence application (running on 18,000 Titan nodes), and benchmark-based pseudo-applications. Through our ex- periments we confirmed that IOSI effectively extracts an application s I/O signature despite significant server-side noise. Compared to client-side tracing tools, IOSI is transparent, interface-agnostic, and incurs no overhead. Compared to alternative data alignment techniques (e.g., dynamic time warping), it offers higher signature accuracy and shorter processing time.« less

OceanNOMADS: Real-time and retrospective access to operational U.S. ocean prediction products

NASA Astrophysics Data System (ADS)

Harding, J. M.; Cross, S. L.; Bub, F.; Ji, M.

2011-12-01

The National Oceanic and Atmospheric Administration (NOAA) National Operational Model Archive and Distribution System (NOMADS) provides both real-time and archived atmospheric model output from servers at the National Centers for Environmental Prediction (NCEP) and National Climatic Data Center (NCDC) respectively (http://nomads.ncep.noaa.gov/txt_descriptions/marRutledge-1.pdf). The NOAA National Ocean Data Center (NODC) with NCEP is developing a complementary capability called OceanNOMADS for operational ocean prediction models. An NCEP ftp server currently provides real-time ocean forecast output (http://www.opc.ncep.noaa.gov/newNCOM/NCOM_currents.shtml) with retrospective access through NODC. A joint effort between the Northern Gulf Institute (NGI; a NOAA Cooperative Institute) and the NOAA National Coastal Data Development Center (NCDDC; a division of NODC) created the developmental version of the retrospective OceanNOMADS capability (http://www.northerngulfinstitute.org/edac/ocean_nomads.php) under the NGI Ecosystem Data Assembly Center (EDAC) project (http://www.northerngulfinstitute.org/edac/). Complementary funding support for the developmental OceanNOMADS from U.S. Integrated Ocean Observing System (IOOS) through the Southeastern University Research Association (SURA) Model Testbed (http://testbed.sura.org/) this past year provided NODC the analogue that facilitated the creation of an NCDDC production version of OceanNOMADS (http://www.ncddc.noaa.gov/ocean-nomads/). Access tool development and storage of initial archival data sets occur on the NGI/NCDDC developmental servers with transition to NODC/NCCDC production servers as the model archives mature and operational space and distribution capability grow. Navy operational global ocean forecast subsets for U.S waters comprise the initial ocean prediction fields resident on the NCDDC production server. The NGI/NCDDC developmental server currently includes the Naval Research Laboratory Inter-America Seas Nowcast/Forecast System over the Gulf of Mexico from 2004-Mar 2011, the operational Naval Oceanographic Office (NAVOCEANO) regional USEast ocean nowcast/forecast system from early 2009 to present, and the NAVOCEANO operational regional AMSEAS (Gulf of Mexico/Caribbean) ocean nowcast/forecast system from its inception 25 June 2010 to present. AMSEAS provided one of the real-time ocean forecast products accessed by NOAA's Office of Response and Restoration from the NGI/NCDDC developmental OceanNOMADS during the Deep Water Horizon oil spill last year. The developmental server also includes archived, real-time Navy coastal forecast products off coastal Japan in support of U.S./Japanese joint efforts following the 2011 tsunami. Real-time NAVOCEANO output from regional prediction systems off Southern California and around Hawaii, currently available on the NCEP ftp server, are scheduled for archival on the developmental OceanNOMADS by late 2011 along with the next generation Navy/NOAA global ocean prediction output. Accession and archival of additional regions is planned as server capacities increase.

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

Feeding People's Curiosity: Leveraging the Cloud for Automatic Dissemination of Mars Images

NASA Technical Reports Server (NTRS)

Knight, David; Powell, Mark

2013-01-01

Smartphones and tablets have made wireless computing ubiquitous, and users expect instant, on-demand access to information. The Mars Science Laboratory (MSL) operations software suite, MSL InterfaCE (MSLICE), employs a different back-end image processing architecture compared to that of the Mars Exploration Rovers (MER) in order to better satisfy modern consumer-driven usage patterns and to offer greater server-side flexibility. Cloud services are a centerpiece of the server-side architecture that allows new image data to be delivered automatically to both scientists using MSLICE and the general public through the MSL website (http://mars.jpl.nasa.gov/msl/).

An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

PubMed

Zhang, Zhe; Fenstermacher, David

2005-01-01

Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

Intro and Recent Advances: Remote Data Access via OPeNDAP Web Services

NASA Technical Reports Server (NTRS)

Fulker, David

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

Wireless access to a pharmaceutical database: a demonstrator for data driven Wireless Application Protocol (WAP) applications in medical information processing.

PubMed

Schacht Hansen, M; Dørup, J

2001-01-01

The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control.

Wireless access to a pharmaceutical database: A demonstrator for data driven Wireless Application Protocol applications in medical information processing

PubMed Central

Hansen, Michael Schacht

2001-01-01

Background The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. Objectives To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. Methods We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. Results A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. Conclusions We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control. PMID:11720946

Benchmark of Client and Server-Side Catchment Delineation Approaches on Web-Based Systems

NASA Astrophysics Data System (ADS)

Demir, I.; Sermet, M. Y.; Sit, M. A.

2016-12-01

Recent advances in internet and cyberinfrastructure technologies have provided the capability to acquire large scale spatial data from various gauges and sensor networks. The collection of environmental data increased demand for applications which are capable of managing and processing large-scale and high-resolution data sets. With the amount and resolution of data sets provided, one of the challenging tasks for organizing and customizing hydrological data sets is delineation of watersheds on demand. Watershed delineation is a process for creating a boundary that represents the contributing area for a specific control point or water outlet, with intent of characterization and analysis of portions of a study area. Although many GIS tools and software for watershed analysis are available on desktop systems, there is a need for web-based and client-side techniques for creating a dynamic and interactive environment for exploring hydrological data. In this project, we demonstrated several watershed delineation techniques on the web with various techniques implemented on the client-side using JavaScript and WebGL, and on the server-side using Python and C++. We also developed a client-side GPGPU (General Purpose Graphical Processing Unit) algorithm to analyze high-resolution terrain data for watershed delineation which allows parallelization using GPU. The web-based real-time analysis of watershed segmentation can be helpful for decision-makers and interested stakeholders while eliminating the need of installing complex software packages and dealing with large-scale data sets. Utilization of the client-side hardware resources also eliminates the need of servers due its crowdsourcing nature. Our goal for future work is to improve other hydrologic analysis methods such as rain flow tracking by adapting presented approaches.

The effect of eubiotic feed additives on the performance of growing pigs and the activity of intestinal microflora.

PubMed

Nowak, Piotr; Kasprowicz-Potocka, Małgorzata; Zaworska, Anita; Nowak, Włodzimierz; Stefańska, Barbara; Sip, Anna; Grajek, Włodzimierz; Juzwa, Wojciech; Taciak, Marcin; Barszcz, Marcin; Tuśnio, Anna; Grajek, Katarzyna; Foksowicz-Flaczyk, Joanna; Frankiewicz, Andrzej

2017-12-01

The aim of this study was to compare the effect of probiotic bacteria, prebiotics, phytobiotics and their combinations on performance and microbial activity in the digestive tract of growing pigs. The experiment was conducted over 28 d on 48 male pigs of about 12 kg body weight (BW), which were allocated to following treatments.: (1) Control Group (Con) without additive, (2) Group I, addition of a prebiotic (inulin), (3) Group Ph, a phytobiotic (herbal water extracts), (4) Group P, a probiotic composed of four strains of lactic acid bacteria, (5) Group PhP, phytobiotic and probiotic bacteria and (6) Group PhPI, a phytobiotic, probiotic bacteria and a prebiotic. Animal performance was recorded and at d 28 six pigs from each group were euthanised to collect digesta samples. In all groups except for Group I, diarrhoea incidents were observed. Groups Ph and P had significantly higher daily gains and final BW, and Group Ph utilised feed better than other groups. The pH of ileal digesta was significantly lower in Group PhPI. In the caecal digesta of Groups I, P and PhP, the pH level was lower than in the other groups but dry matter contents was significantly higher in Groups Con and I. The short-chain fatty acids and particular acid content differed significantly only in the colonic digesta. The yeast and mould numbers in caecal digesta was highest in Group Con. No treatment effects were observed for the number of lactic acid bacteria, coli group bacteria or Clostridium. However, the observed significantly higher number of total bacteria suggests that a multi-component eubiotic treatment changes the bacterial composition and distribution more effectively. Our findings indicated that all used additives changed the intestinal microflora, but the multi-component eubiotics were not beneficial as feed additives offered separately. Moreover, supplementation of phytobiotics and probiotic bacteria also improved the animal performance significantly.

Improvements to Autoplot's HAPI Support

NASA Astrophysics Data System (ADS)

Faden, J.; Vandegriff, J. D.; Weigel, R. S.

2017-12-01

Autoplot handles data from a variety of data servers. These servers communicate data in different forms, each somewhat different in capabilities and each needing new software to interface. The Heliophysics Application Programmer's Interface (HAPI) attempts to ease this by providing a standard target for clients and servers to meet. Autoplot fully supports reading data from HAPI servers, and support continues to improve as the HAPI server spec matures. This collaboration has already produced robust clients and documentation which would be expensive for groups creating their own protocol. For example, client-side data caching is introduced where Autoplot maintains a cache of data for performance and off-line use. This is a feature we considered for previous data systems, but we could never afford the time to study and implement this carefully. Also, Autoplot itself can be used as a server, making the data it can read and the results of its processing available to other data systems. Autoplot use with other data transmission systems is reviewed as well, outlining features of each system.

Development of new on-line statistical program for the Korean Society for Radiation Oncology

PubMed Central

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Choi, Eun Kyung; Cho, Kwan Ho

2015-01-01

Purpose To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. Materials and Methods The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Results Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. Conclusion The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology. PMID:26157684

Development of new on-line statistical program for the Korean Society for Radiation Oncology.

PubMed

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Shin, Kyung Hwan; Choi, Eun Kyung; Cho, Kwan Ho

2015-06-01

To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology.

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

PubMed

Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

2016-01-01

Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

PubMed

Geeleher, Paul; Morris, Dermot; Hinde, John P; Golden, Aaron

2009-06-01

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets. BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from (http://bioinf.nuigalway.ie).

De-MA: a web Database for electron Microprobe Analyses to assist EMP lab manager and users

NASA Astrophysics Data System (ADS)

Allaz, J. M.

2012-12-01

Lab managers and users of electron microprobe (EMP) facilities require comprehensive, yet flexible documentation structures, as well as an efficient scheduling mechanism. A single on-line database system for managing reservations, and providing information on standards, quantitative and qualitative setups (element mapping, etc.), and X-ray data has been developed for this purpose. This system is particularly useful in multi-user facilities where experience ranges from beginners to the highly experienced. New users and occasional facility users will find these tools extremely useful in developing and maintaining high quality, reproducible, and efficient analyses. This user-friendly database is available through the web, and uses MySQL as a database and PHP/HTML as script language (dynamic website). The database includes several tables for standards information, X-ray lines, X-ray element mapping, PHA, element setups, and agenda. It is configurable for up to five different EMPs in a single lab, each of them having up to five spectrometers and as many diffraction crystals as required. The installation should be done on a web server supporting PHP/MySQL, although installation on a personal computer is possible using third-party freeware to create a local Apache server, and to enable PHP/MySQL. Since it is web-based, any user outside the EMP lab can access this database anytime through any web browser and on any operating system. The access can be secured using a general password protection (e.g. htaccess). The web interface consists of 6 main menus. (1) "Standards" lists standards defined in the database, and displays detailed information on each (e.g. material type, name, reference, comments, and analyses). Images such as EDS spectra or BSE can be associated with a standard. (2) "Analyses" lists typical setups to use for quantitative analyses, allows calculation of mineral composition based on a mineral formula, or calculation of mineral formula based on a fixed amount of oxygen, or of cation (using an analysis in element or oxide weight-%); this latter includes re-calculation of H2O/CO2 based on stoichiometry, and oxygen correction for F and Cl. Another option offers a list of any available standards and possible peak or background interferences for a series of elements. (3) "X-ray maps" lists the different setups recommended for element mapping using WDS, and a map calculator to facilitate maps setups and to estimate the total mapping time. (4) "X-ray data" lists all x-ray lines for a specific element (K, L, M, absorption edges, and satellite peaks) in term of energy, wavelength and peak position. A check for possible interferences on peak or background is also possible. Theoretical x-ray peak positions for each crystal are calculated based on the 2d spacing of each crystal and the wavelength of each line. (5) "Agenda" menu displays the reservation dates for each month and for each EMP lab defined. It also offers a reservation request option, this request being sent by email to the EMP manager for approval. (6) Finally, "Admin" is password restricted, and contains all necessary options to manage the database through user-friendly forms. The installation of this database is made easy and knowledge of HTML, PHP, or MySQL is unnecessary to install, configure, manage, or use it. A working database is accessible at http://cub.geoloweb.ch.

A web-based solution for 3D medical image visualization

NASA Astrophysics Data System (ADS)

Hou, Xiaoshuai; Sun, Jianyong; Zhang, Jianguo

2015-03-01

In this presentation, we present a web-based 3D medical image visualization solution which enables interactive large medical image data processing and visualization over the web platform. To improve the efficiency of our solution, we adopt GPU accelerated techniques to process images on the server side while rapidly transferring images to the HTML5 supported web browser on the client side. Compared to traditional local visualization solution, our solution doesn't require the users to install extra software or download the whole volume dataset from PACS server. By designing this web-based solution, it is feasible for users to access the 3D medical image visualization service wherever the internet is available.

Template based protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Juyong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native-like structural aspects present in multiple templates. The LEE protocol is identical to the nns one except that CASP11-released server models are used as templates. The success of LEE in utilizing CASP11 server models indicates that proper template screening and template clustering assisted by appropriate cluster ranking promises a new direction to enhance protein 3D modeling. Proteins 2016; 84(Suppl 1):221-232. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design.

PubMed

Munteanu, Cristian R; Pedreira, Nieves; Dorado, Julián; Pazos, Alejandro; Pérez-Montoto, Lázaro G; Ubeira, Florencio M; González-Díaz, Humberto

2014-04-01

Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non-annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH-INSIDE software to calculate the Markov-Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure-Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this predictor in the web server named LECTINPred, freely available at http://bio-aims.udc.es/LECTINPred.php. This web server showed the following goodness-of-fit statistics: Sensitivity=96.7 % (for Ls), Specificity=87.6 % (non-active proteins), and Accuracy=92.5 % (for all proteins), considering altogether both the training and external prediction series. In mode 2, users can carry out an automatic retrieval of protein structures from PDB. We illustrated the use of this server, in operation mode 1, performing a data mining of PDB. We predicted Ls scores for +2000 proteins with unknown function and selected the top-scored ones as possible lectins. In operation mode 2, LECTINPred can also upload 3D structural models generated with structure-prediction tools like LOMETS or PHYRE2. The new Ls are expected to be of relevance as cancer biomarkers or useful in parasite vaccine design. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tripeptide amide L-pyroglutamyl-histidyl-L-prolineamide (L-PHP-thyrotropin-releasing hormone, TRH) promotes insulin-producing cell proliferation.

PubMed

Luo, LuGuang; Luo, John Z Q; Jackson, Ivor

2013-02-01

A very small tripeptide amide L-pyroglutamyl-L-histidyl-L-prolineamide (L-PHP, Thyrotropin-Releasing Hormone, TRH), was first identified in the brain hypothalamus area. Further studies found that L-PHP was expressed in pancreas. The biological role of pancreatic L-PHP is still not clear. Growing evidence indicates that L-PHP expression in the pancreas may play a pivotal role for pancreatic development in the early prenatal period. However, the role of L-PHP in adult pancreas still needs to be explored. L-PHP activation of pancreatic β cell Ca2+ flow and stimulation of β-cell insulin synthesis and release suggest that L-PHP involved in glucose metabolism may directly act on the β cell separate from any effects via the central nervous system (CNS). Knockout L-PHP animal models have shown that loss of L-PHP expression causes hyperglycemia, which cannot be reversed by administration of thyroid hormone, suggesting that the absence of L-PHP itself is the cause. L-PHP receptor type-1 has been identified in pancreas which provides a possibility for L-PHP autocrine and paracrine regulation in pancreatic function. During pancreatic damage in adult pancreas, L-PHP may protect beta cell from apoptosis and initiate its regeneration through signal pathways of growth hormone in β cells. L-PHP has recently been discovered to affect a broad array of gene expression in the pancreas including growth factor genes. Signal pathways linked between L-PHP and EGF receptor phosphorylation suggest that L-PHP may be an important factor for adult β-cell regeneration, which could involve adult stem cell differentiation. These effects suggest that L-PHP may benefit pancreatic β cells and diabetic therapy in clinic.

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

PubMed Central

Hackenberg, Michael; Rodríguez-Ezpeleta, Naiara; Aransay, Ana M.

2011-01-01

We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php. PMID:21515631

AIDE - Advanced Intrusion Detection Environment

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

Smith, Cathy L.

2013-04-28

Would you like to know when someone has dropped an undesirable executable binary on our system? What about something less malicious such as a software installation by a user? What about the user who decides to install a newer version of mod_perl or PHP on your web server without letting you know beforehand? Or even something as simple as when an undocumented config file change is made by another member of the admin group? Do you even want to know about all the changes that happen on a daily basis on your server? The purpose of an intrusion detection systemmore » (IDS) is to detect unauthorized, possibly malicious activity. The purpose of a host-based IDS, or file integrity checker, is check for unauthorized changes to key system files, binaries, libraries, and directories on the system. AIDE is an Open Source file and directory integrity checker. AIDE will let you know when a file or directory has been added, deleted, modified. It is included with the Red Hat Enterprise 6. It is available for other Linux distros. This is a case study describing the process of configuring AIDE on an out of the box RHEL6 installation. Its goal is to illustrate the thinking and the process by which a useful AIDE configuration is built.« less

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

PubMed

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

A web-based institutional DICOM distribution system with the integration of the Clinical Trial Processor (CTP).

PubMed

Aryanto, K Y E; Broekema, A; Langenhuysen, R G A; Oudkerk, M; van Ooijen, P M A

2015-05-01

To develop and test a fast and easy rule-based web-environment with optional de-identification of imaging data to facilitate data distribution within a hospital environment. A web interface was built using Hypertext Preprocessor (PHP), an open source scripting language for web development, and Java with SQL Server to handle the database. The system allows for the selection of patient data and for de-identifying these when necessary. Using the services provided by the RSNA Clinical Trial Processor (CTP), the selected images were pushed to the appropriate services using a protocol based on the module created for the associated task. Five pipelines, each performing a different task, were set up in the server. In a 75 month period, more than 2,000,000 images are transferred and de-identified in a proper manner while 20,000,000 images are moved from one node to another without de-identification. While maintaining a high level of security and stability, the proposed system is easy to setup, it integrate well with our clinical and research practice and it provides a fast and accurate vendor-neutral process of transferring, de-identifying, and storing DICOM images. Its ability to run different de-identification processes in parallel pipelines is a major advantage in both clinical and research setting.

Multi-resolution extension for transmission of geodata in a mobile context

NASA Astrophysics Data System (ADS)

Follin, Jean-Michel; Bouju, Alain; Bertrand, Frédéric; Boursier, Patrice

2005-03-01

A solution is proposed for the management of multi-resolution vector data in a mobile spatial information visualization system. The client-server architecture and the models of data and transfer of the system are presented first. The aim of this system is to reduce data exchanged between client and server by reusing data already present on the client side. Then, an extension of this system to multi-resolution data is proposed. Our solution is based on the use of increments in a multi-scale database. A database architecture where data sets for different predefined scales are precomputed and stored on the server side is adopted. In this model, each object representing the same real world entities at different levels of detail has to be linked beforehand. Increments correspond to the difference between two datasets with different levels of detail. They are transmitted in order to increase (or decrease) the detail to the client upon request. They include generalization and refinement operators allowing transitions between the different levels. Finally, a framework suited to the transfer of multi-resolution data in a mobile context is presented. This allows reuse of data locally available at different levels of detail and, in this way, reduces the amount of data transferred between client and server.

The Four Levels of Web Site Development Expertise.

ERIC Educational Resources Information Center

Ingram, Albert L.

2000-01-01

Discusses the design of Web pages and sites and proposes a four-level model of Web development expertise that can serve as a curriculum overview or as a plan for an individual's professional development. Highlights include page design, media use, client-side processing, server-side processing, and site structure. (LRW)

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

The Case for Adopting Server-side Analytics

NASA Astrophysics Data System (ADS)

Tino, C.; Holmes, C. P.; Feigelson, E.; Hurlburt, N. E.

2017-12-01

The standard method for accessing Earth and space science data relies on a scheme developed decades ago: data residing in one or many data stores must be parsed out and shipped via internet lines or physical transport to the researcher who in turn locally stores the data for analysis. The analyses tasks are varied and include visualization, parameterization, and comparison with or assimilation into physics models. In many cases this process is inefficient and unwieldy as the data sets become larger and demands on the analysis tasks become more sophisticated and complex. For about a decade, several groups have explored a new paradigm to this model. The names applied to the paradigm include "data analytics", "climate analytics", and "server-side analytics". The general concept is that in close network proximity to the data store there will be a tailored processing capability appropriate to the type and use of the data served. The user of the server-side analytics will operate on the data with numerical procedures. The procedures can be accessed via canned code, a scripting processor, or an analysis package such as Matlab, IDL or R. Results of the analytics processes will then be relayed via the internet to the user. In practice, these results will be at a much lower volume, easier to transport to and store locally by the user and easier for the user to interoperate with data sets from other remote data stores. The user can also iterate on the processing call to tailor the results as needed. A major component of server-side analytics could be to provide sets of tailored results to end users in order to eliminate the repetitive preconditioning that is both often required with these data sets and which drives much of the throughput challenges. NASA's Big Data Task Force studied this issue. This paper will present the results of this study including examples of SSAs that are being developed and demonstrated and suggestions for architectures that might be developed for future applications.

Clinical characterization and molecular classification of 12 Korean patients with pseudohypoparathyroidism and pseudopseudohypoparathyroidism.

PubMed

Cho, S Y; Yoon, Y A; Ki, C-S; Huh, H J; Yoo, H-W; Lee, B H; Kim, G-H; Yoo, J-H; Kim, S-Y; Kim, S J; Sohn, Y B; Park, S W; Huh, R; Chang, M S; Lee, J; Kwun, Y; Maeng, S H; Jin, D-K

2013-10-01

Pseudohypoparathyroidism (PHP) is defined as resistance toward parathyroid hormones. PHP and pseudopseudohypoparathyroidism (PPHP) are rare disorders resulting from genetic and epigenetic aberrations within or upstream of the GNAS locus. This study investigated the clinical characteristics and performed a molecular analysis of PHP and PPHP. A total of 12 patients with (P)PHP from 11 unrelated families (4 with PHP-Ia, 6 with PHP-Ib, and 2 with PPHP) were characterized using both clinical and molecular methods. Clinical features included the presenting symptoms, Albright hereditary osteodystrophy features, and resistance to hormones. Comprehensive analysis of the GNAS and STX16 loci was undertaken to investigate the molecular defects underlying (P)PHP. All PHP-Ib patients displayed hypocalcemic symptoms. All PHP-Ia patients showed resistance toward TSH, in addition to PTH. In most patients with PHP, when the diagnosis of PHP was first established, hypocalcemia and hyperphosphatemia were associated with a significant increase in serum PTH levels. One patient with PHP-Ia was diagnosed with growth hormone deficiency and showed a good response to human recombinant growth hormone therapy. 6 patients with PHP-Ia and PPHP showed 5 different mutations in the GNAS gene. 5 patients with PHP-Ib displayed a loss of differentially methylated region (DMR) imprints of the maternal GNAS. One PHP-Ib patient showed a de novo microdeletion in STX16 and a loss of methylation of exon A/B on the maternal allele. No patients revealed paternal disomy among 4 patients with PHP-Ib. Identification of the molecular causes of PHP and PPHP explains their distinctive clinical features and enables confirmation of the diagnosis and exact genetic counseling. © J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York.

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

OnlineTED.com − a novel web-based audience response system for higher education. A pilot study to evaluate user acceptance

PubMed Central

Kühbeck, Felizian; Engelhardt, Stefan; Sarikas, Antonio

2014-01-01

Background and aim: Audience response (AR) systems are increasingly used in undergraduate medical education. However, high costs and complexity of conventional AR systems often limit their use. Here we present a novel AR system that is platform independent and does not require hardware clickers or additional software to be installed. Methods and results: “OnlineTED” was developed at Technische Universität München (TUM) based on Hypertext Preprocessor (PHP) with a My Structured Query Language (MySQL)-database as server- and Javascript as client-side programming languages. “OnlineTED” enables lecturers to create and manage question sets online and start polls in-class via a web-browser. Students can participate in the polls with any internet-enabled device (smartphones, tablet-PCs or laptops). A paper-based survey was conducted with undergraduate medical students and lecturers at TUM to compare "OnlineTED" with conventional AR systems using clickers. "OnlineTED" received above-average evaluation results by both students and lecturers at TUM and was seen on par or superior to conventional AR systems. The survey results indicated that up to 80% of students at TUM own an internet-enabled device (smartphone or tablet-PC) for participation in web-based AR technologies. Summary and Conclusion: “OnlineTED” is a novel web-based and platform-independent AR system for higher education that was well received by students and lecturers. As a non-commercial alternative to conventional AR systems it may foster interactive teaching in undergraduate education, in particular with large audiences. PMID:24575156

A Functional Approach to Hyperspectral Image Analysis in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral image volumes are very large. A hyperspectral image analysis (HIA) may use 100TB of data, a huge barrier to their use. Hylatis is a new NASA project to create a toolset for HIA. Through web notebook and cloud technology, Hylatis will provide a more interactive experience for HIA by defining and implementing concepts and operations for HIA, identified and vetted by subject matter experts, and callable within a general purpose language, particularly Python. Hylatis leverages LaTiS, a data access framework developed at LASP. With an OPeNDAP compliant interface plus additional server side capabilities, the LaTiS API provides a uniform interface to virtually any data source, and has been applied to various storage systems, including: file systems, databases, remote servers, and in various domains including: space science, systems administration and stock quotes. In the LaTiS architecture, data `adapters' read data into a data model, where server-side computations occur. Data `writers' write data from the data model into the desired format. The Hylatis difference is the data model. In LaTiS, data are represented as mathematical functions of independent and dependent variables. Domain semantics are not present at this level, but are instead present in higher software layers. The benefit of a domain agnostic, mathematical representation is having the power of math, particularly functional algebra, unconstrained by domain semantics. This agnosticism supports reusable server side functionality applicable in any domain, such as statistical, filtering, or projection operations. Algorithms to aggregate or fuse data can be simpler because domain semantics are separated from the math. Hylatis will map the functional model onto the Spark relational interface, thereby adding a functional interface to that big data engine.This presentation will discuss Hylatis goals, strategies, and current state.

Design and evaluation of web-based image transmission and display with different protocols

NASA Astrophysics Data System (ADS)

Tan, Bin; Chen, Kuangyi; Zheng, Xichuan; Zhang, Jianguo

2011-03-01

There are many Web-based image accessing technologies used in medical imaging area, such as component-based (ActiveX Control) thick client Web display, Zerofootprint thin client Web viewer (or called server side processing Web viewer), Flash Rich Internet Application(RIA) ,or HTML5 based Web display. Different Web display methods have different peformance in different network environment. In this presenation, we give an evaluation on two developed Web based image display systems. The first one is used for thin client Web display. It works between a PACS Web server with WADO interface and thin client. The PACS Web server provides JPEG format images to HTML pages. The second one is for thick client Web display. It works between a PACS Web server with WADO interface and thick client running in browsers containing ActiveX control, Flash RIA program or HTML5 scripts. The PACS Web server provides native DICOM format images or JPIP stream for theses clients.

Developing an interactive teleradiology system for SARS diagnosis

NASA Astrophysics Data System (ADS)

Sun, Jianyong; Zhang, Jianguo; Zhuang, Jun; Chen, Xiaomeng; Yong, Yuanyuan; Tan, Yongqiang; Chen, Liu; Lian, Ping; Meng, Lili; Huang, H. K.

2004-04-01

Severe acute respiratory syndrome (SARS) is a respiratory illness that had been reported in Asia, North America, and Europe in last spring. Most of the China cases of SARS have occurred by infection in hospitals or among travelers. To protect the physicians, experts and nurses from the SARS during the diagnosis and treatment procedures, the infection control mechanisms were built in SARS hospitals. We built a Web-based interactive teleradiology system to assist the radiologists and physicians both in side and out side control area to make image diagnosis. The system consists of three major components: DICOM gateway (GW), Web-based image repository server (Server), and Web-based DICOM viewer (Viewer). This system was installed and integrated with CR, CT and the hospital information system (HIS) in Shanghai Xinhua hospital to provide image-based ePR functions for SARS consultation between the radiologists, physicians and experts inside and out side control area. The both users inside and out side the control area can use the system to process and manipulate the DICOM images interactively, and the system provide the remote control mechanism to synchronize their operations on images and display.

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework.

PubMed

Biermann, Martin

2014-04-01

Clinical trials aiming for regulatory approval of a therapeutic agent must be conducted according to Good Clinical Practice (GCP). Clinical Data Management Systems (CDMS) are specialized software solutions geared toward GCP-trials. They are however less suited for data management in small non-GCP research projects. For use in researcher-initiated non-GCP studies, we developed a client-server database application based on the public domain CakePHP framework. The underlying MySQL database uses a simple data model based on only five data tables. The graphical user interface can be run in any web browser inside the hospital network. Data are validated upon entry. Data contained in external database systems can be imported interactively. Data are automatically anonymized on import, and the key lists identifying the subjects being logged to a restricted part of the database. Data analysis is performed by separate statistics and analysis software connecting to the database via a generic Open Database Connectivity (ODBC) interface. Since its first pilot implementation in 2011, the solution has been applied to seven different clinical research projects covering different clinical problems in different organ systems such as cancer of the thyroid and the prostate glands. This paper shows how the adoption of a generic web application framework is a feasible, flexible, low-cost, and user-friendly way of managing multidimensional research data in researcher-initiated non-GCP clinical projects. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Hepatic Progression-free and Overall Survival After Regional Therapy to the Liver for Metastatic Melanoma.

PubMed

Abbott, Andrea M; Doepker, Matthew P; Kim, Youngchul; Perez, Matthew C; Gandle, Cassandra; Thomas, Kerry L; Choi, Junsung; Shridhar, Ravi; Zager, Jonathan S

2017-01-04

Regional therapy for metastatic melanoma to the liver represents an alternative to systemic therapy. Hepatic progression-free survival (HPFS), progression-free survival (PFS), and overall survival (OS) were evaluated. A retrospective review of patients with liver metastases from cutaneous or uveal melanoma treated with yttrium-90 (Y90), chemoembolization (CE), or percutaneous hepatic perfusion (PHP) was conducted. Thirty patients (6 Y90, 10 PHP, 12 CE, 1 PHP then Y90, 1 CE then PHP) were included. Multivariate analysis showed improved HPFS for PHP versus Y90 (P=0.004), PHP versus CE (P=0.02) but not for CE versus Y90. PFS was also significantly different: Y90 (54 d), CE (52 d), PHP (245 d), P=0.03. PHP treatment and lower tumor burden were significant predictors of prolonged PFS on multivariate analysis. Median OS from time of treatment was longest, but not significant, for PHP at 608 days versus Y90 (295 d) and CE (265 d), P=0.24. Only PHP treatment versus Y90 and lower tumor burden had improved OS on multivariate analysis (P=0.03, 0.03, respectively). HPFS and PFS were significantly prolonged in patients treated with PHP versus CE or Y90. Median OS in PHP patients was over double that seen in Y90 or CE patients but was significant only between PHP and Y90.

Data archiving and serving system implementation in CLEP's GRAS Core System

NASA Astrophysics Data System (ADS)

Zuo, Wei; Zeng, Xingguo; Zhang, Zhoubin; Geng, Liang; Li, Chunlai

2017-04-01

The Ground Research & Applications System(GRAS) is one of the five systems of China's Lunar Exploration Project(CLEP), it is responsible for data acquisition, processing, management and application, and it is also the operation control center during satellite in-orbit and payload operation management. Chang'E-1, Chang'E-2 and Chang'E-3 have collected abundant lunar exploration data. The aim of this work is to present the implementation of data archiving and Serving in CLEP's GRAS Core System software. This first approach provides a client side API and server side software allowing the creation of a simplified version of CLEPDB data archiving software, and implements all required elements to complete data archiving flow from data acquisition until its persistent storage technology. The client side includes all necessary components that run on devices that acquire or produce data, distributing and streaming to configure remote archiving servers. The server side comprises an archiving service that stores into PDS files all received data. The archiving solution aims at storing data coming for the Data Acquisition Subsystem, the Operation Management Subsystem, the Data Preprocessing Subsystem and the Scientific Application & Research Subsystem. The serving solution aims at serving data for the various business systems, scientific researchers and public users. The data-driven and component clustering methods was adopted in this system, the former is used to solve real-time data archiving and data persistence services; the latter is used to keep the continuous supporting ability of archive and service to new data from Chang'E Mission. Meanwhile, it can save software development cost as well.

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

Effects of Php Gene-Associated versus Induced Resistance to Tobacco Cyst Nematode in Flue-Cured Tobacco

PubMed Central

Johnson, Charles S.; Eisenback, Jon D.

2009-01-01

Effects of the systemic acquired resistance (SAR)-inducing compound acibenzolar-S-methyl (ASM) and the plant-growth promoting rhizobacterial mixture Bacillus subtilis A13 and B. amyloliquefaciens IN937a (GB99+GB122) were assessed on the reproduction of a tobacco cyst nematode (TCN- Globodera tabacum solanacearum) under greenhouse conditions. Two sets of two independent experiments were conducted, each involving soil or root sampling. Soil sample experiments included flue-cured tobacco cultivars with (Php+: NC71 and NC102) and without (Php-: K326 and K346) a gene (Php) suppressing TCN parasitism. Root sample experiments examined TCN root parasitism of NC71 and K326. Cultivars possessing the Php gene (Php+) were compared with Php- cultivars to assess the effects of resistance mediated via Php gene vs. induced resistance to TCN. GB99+GB122 consistently reduced nematode reproductive ratio on both Php+ and Php- cultivars, but similar effects of ASM across Php- cultivars were less consistent. In addition, ASM application resulted in leaf yellowing and reduced root weight. GB99+GB122 consistently reduced nematode development in roots of both Php+ and Php- cultivars, while similar effects of ASM were frequently less consistent. The results of this study indicate that GB99+GB122 consistently reduced TCN reproduction in all flue-cured tobacco cultivars tested, while the effects of ASM were only consistent in Php+ cultivars. Under most circumstances, GB99+GB122 suppressed nematode reproduction more consistently than ASM compared to the untreated control. PMID:22736824

Development of mobile platform integrated with existing electronic medical records.

PubMed

Kim, YoungAh; Kim, Sung Soo; Kang, Simon; Kim, Kyungduk; Kim, Jun

2014-07-01

This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions.

Development of Mobile Platform Integrated with Existing Electronic Medical Records

PubMed Central

Kim, YoungAh; Kang, Simon; Kim, Kyungduk; Kim, Jun

2014-01-01

Objectives This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. Methods We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Results Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. Conclusions The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions. PMID:25152837

BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms.

PubMed

Lee, Preston V; Dinu, Valentin

2015-11-04

Our publication of the BitTorious portal [1] demonstrated the ability to create a privatized distributed data warehouse of sufficient magnitude for real-world bioinformatics studies using minimal changes to the standard BitTorrent tracker protocol. In this second phase, we release a new server-side specification to accept anonymous philantropic storage donations by the general public, wherein a small portion of each user's local disk may be used for archival of scientific data. We have implementated the server-side announcement and control portions of this BitTorrent extension into v3.0.0 of the BitTorious portal, upon which compatible clients may be built. Automated test cases for the BitTorious Volunteer extensions have been added to the portal's v3.0.0 release, supporting validation of the "peer affinity" concept and announcement protocol introduced by this specification. Additionally, a separate reference implementation of affinity calculation has been provided in C++ for informaticians wishing to integrate into libtorrent-based projects. The BitTorrent "affinity" extensions as provided in the BitTorious portal reference implementation allow data publishers to crowdsource the extreme storage prerequisites for research in "big data" fields. With sufficient awareness and adoption of BitTorious Volunteer-based clients by the general public, the BitTorious portal may be able to provide peta-scale storage resources to the scientific community at relatively insignificant financial cost.

Reference-frame-independent quantum-key-distribution server with a telecom tether for an on-chip client.

PubMed

Zhang, P; Aungskunsiri, K; Martín-López, E; Wabnig, J; Lobino, M; Nock, R W; Munns, J; Bonneau, D; Jiang, P; Li, H W; Laing, A; Rarity, J G; Niskanen, A O; Thompson, M G; O'Brien, J L

2014-04-04

We demonstrate a client-server quantum key distribution (QKD) scheme. Large resources such as laser and detectors are situated at the server side, which is accessible via telecom fiber to a client requiring only an on-chip polarization rotator, which may be integrated into a handheld device. The detrimental effects of unstable fiber birefringence are overcome by employing the reference-frame-independent QKD protocol for polarization qubits in polarization maintaining fiber, where standard QKD protocols fail, as we show for comparison. This opens the way for quantum enhanced secure communications between companies and members of the general public equipped with handheld mobile devices, via telecom-fiber tethering.

Optimizing the Replication of Multi-Quality Web Applications Using ACO and WoLF

DTIC Science & Technology

2006-09-14

bipartite graph in both directions as they construct solutions, pheromone is used for traversing from one side of the bipartite graph to the other and back...27 3.1.3 Transitioning From 〈d, q〉 pairs to Servers. . . . . 29 3.1.4 Pheromone Update Rule . . . . . . . . . . . . . . 30 vi Page 3.2 WoLFAntDA: A...35 3.2.6 Pheromone Update Rule . . . . . . . . . . . . . . 36 3.2.7 Policy Updates . . . . . . . . . . . . . . . . . . . 36 3.3 The Server-Filling

The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins

PubMed Central

Kozakov, Dima; Grove, Laurie E.; Hall, David R.; Bohnuud, Tanggis; Mottarella, Scott; Luo, Lingqi; Xia, Bing; Beglov, Dmitri; Vajda, Sandor

2016-01-01

FTMap is a computational mapping server that identifies binding hot spots of macromolecules, i.e., regions of the surface with major contributions to the ligand binding free energy. To use FTMap, users submit a protein, DNA, or RNA structure in PDB format. FTMap samples billions of positions of small organic molecules used as probes and scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots, in good agreement with experimental data. FTMap serves as basis for other servers, namely FTSite to predict ligand binding sites, FTFlex to account for side chain flexibility, FTMap/param to parameterize additional probes, and FTDyn to map ensembles of protein structures. Applications include determining druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures, and providing input for fragment based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and is much faster than the more recent approaches to protein mapping based on mixed molecular dynamics. Using 16 probe molecules, the FTMap server finds the hot spots of an average size protein in less than an hour. Since FTFlex performs mapping for all low energy conformers of side chains in the binding site, its completion time is proportionately longer. PMID:25855957

Clinical and genetic characteristics of Pseudohypoparathyroidism in the Chinese population.

PubMed

Chu, Xueying; Zhu, Yan; Wang, Ou; Nie, Min; Quan, Tingting; Xue, Yu; Wang, Wenbo; Jiang, Yan; Li, Mei; Xia, Weibo; Xing, Xiaoping

2018-02-01

Pseudohypoparathyroidism (PHP) is caused by mutations and epimutations in the GNAS locus, and characterized by the possibility of resistance to multiple hormones and Albright's hereditary osteodystrophy. PHP can be classified into the forms 1A/C, sporadic 1B and familial 1B. To obtain an overall view of the clinical and genetic characteristics of the Chinese PHP patient population. From 2000 to 2016, 120 patients were recruited and studied using Sanger sequencing, methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) and combined bisulfite restriction analysis (COBRA). Of these patients, 104 had positive molecular alterations indicative of certain forms of PHP and were included in data analysis. Clinical and laboratory features were compared between PHP1A/C and PHP1B patients. Ten PHP1A/C, 21 familial PHP1B and 73 sporadic PHP1B patients were identified. Four novel GNAS mutations were discovered in these patients, including c.1038+1G>T, c.530+2T>C, c.880_883delCAAG and c.311_312delAAG, insT. The most common symptoms in this series were recurrent tetany (89.4%) and epilepsy (47.1%). The prevalence of weight excess increased with age for PHP1B (10%-35%) and PHP1A/C (50%-75%). Intracranial calcification had a prevalence of 94.6% and correlated with seizures (r = .227, P = .029). Cataracts occurred in 56.2% PHP patients, and there was a trend towards longer disease duration in patients with cataracts (P = .051). Statistically significant differences (P < .05) were observed when comparing certain clinical characteristics between PHP1B and PHP1A/C patients, including age of onset (10 vs 7 year), short stature (21.3% vs 70%), rounded face (60.6% vs 100%), brachydactyly (25.5% vs 100%), ectopic ossification (1.1% vs 40%) and TSH resistance (44.6% vs 90%), respectively. This study is the largest single-centre series of PHP patients and summarizes the clinical and genetic features of the Chinese PHP population. While there was substantial clinical overlap between PHP1A/C and PHP1B, differences in disease progression were observed. © 2017 John Wiley & Sons Ltd.

Server-Side JavaScript Debugging: Viewing the Contents of an Object

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

Hampton, J.; Simons, R.

1999-04-21

JavaScript allows the definition and use of large, complex objects. Unlike some other object-oriented languages, it also allows run-time modifications not only of the values of object components, but also of the very structure of the object itself. This feature is powerful and sometimes very convenient, but it can be difficult to keep track of the object's structure and values throughout program execution. What's needed is a simple way to view the current state of an object at any point during execution. There is a debug function that is included in the Netscape server-side JavaScript environment. The function outputs themore » value(s) of the expression given as the argument to the function in the JavaScript Application Manager's debug window [SSJS].« less

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

BioPepDB: an integrated data platform for food-derived bioactive peptides.

PubMed

Li, Qilin; Zhang, Chao; Chen, Hongjun; Xue, Jitong; Guo, Xiaolei; Liang, Ming; Chen, Ming

2018-03-12

Food-derived bioactive peptides play critical roles in regulating most biological processes and have considerable biological, medical and industrial importance. However, a large number of active peptides data, including sequence, function, source, commercial product information, references and other information are poorly integrated. BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries. Moreover, BioPepDB provides modules of prediction and hydrolysis-simulation for discovering novel peptides. It can serve as a reference database to investigate the function of different bioactive peptides. BioPepDB is available at http://bis.zju.edu.cn/biopepdbr/ . The web page utilises Apache, PHP5 and MySQL to provide the user interface for accessing the database and predict novel peptides. The database itself is operated on a specialised server.

The Creative task Creator: a tool for the generation of customized, Web-based creativity tasks.

PubMed

Pretz, Jean E; Link, John A

2008-11-01

This article presents a Web-based tool for the creation of divergent-thinking and open-ended creativity tasks. A Java program generates HTML forms with PHP scripting that run an Alternate Uses Task and/or open-ended response items. Researchers may specify their own instructions, objects, and time limits, or use default settings. Participants can also be prompted to select their best responses to the Alternate Uses Task (Silvia et al., 2008). Minimal programming knowledge is required. The program runs on any server, and responses are recorded in a standard MySQL database. Responses can be scored using the consensual assessment technique (Amabile, 1996) or Torrance's (1998) traditional scoring method. Adoption of this Web-based tool should facilitate creativity research across cultures and access to eminent creators. The Creative Task Creator may be downloaded from the Psychonomic Society's Archive of Norms, Stimuli, and Data, www.psychonomic.org/archive.

Development of computer-assisted instruction application for statistical data analysis android platform as learning resource

NASA Astrophysics Data System (ADS)

Hendikawati, P.; Arifudin, R.; Zahid, M. Z.

2018-03-01

This study aims to design an android Statistics Data Analysis application that can be accessed through mobile devices to making it easier for users to access. The Statistics Data Analysis application includes various topics of basic statistical along with a parametric statistics data analysis application. The output of this application system is parametric statistics data analysis that can be used for students, lecturers, and users who need the results of statistical calculations quickly and easily understood. Android application development is created using Java programming language. The server programming language uses PHP with the Code Igniter framework, and the database used MySQL. The system development methodology used is the Waterfall methodology with the stages of analysis, design, coding, testing, and implementation and system maintenance. This statistical data analysis application is expected to support statistical lecturing activities and make students easier to understand the statistical analysis of mobile devices.

PKK-man: A System to Manage PKK Activities in Indonesia

NASA Astrophysics Data System (ADS)

Anggraini, R. N. E.; Rochimah, S.; Soedjono, A. R.

2016-01-01

PKK community is a well-known women community in Indonesia. PKK was formed from national level to neighbourhood association level and usually has a regular event and several activities. This is the reason why PKK is expected to play an active role in national development, started from PKK member family. This research intends to develop a system to manage PKK activities and prepares information sharing in PKK community. The application was built using client server architecture. The web version of PKK-man was developed using PHP framework and was prepared to be accessed by PKK board member. Since they will deal with more data so a wide interface in web version will be more suitable. While the ordinary PKK member can access PKK-man through mobile application. The mobile version was built using PhoneGap framework that supports different mobile operating systems.

BIRS - Bioterrorism Information Retrieval System.

PubMed

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

Insect barcode information system.

PubMed

Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

2014-01-01

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

Speed up of XML parsers with PHP language implementation

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2012-11-01

In this paper, authors introduce PHP5's XML implementation and show how to read, parse, and write a short and uncomplicated XML file using Simple XML in a PHP environment. The possibilities for mutual work of PHP5 language and XML standard are described. The details of parsing process with Simple XML are also cleared. A practical project PHP-XML-MySQL presents the advantages of XML implementation in PHP modules. This approach allows comparatively simple search of XML hierarchical data by means of PHP software tools. The proposed project includes database, which can be extended with new data and new XML parsing functions.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

An update on the clinical and molecular characteristics of pseudohypoparathyroidism

PubMed Central

Levine, Michael A.

2013-01-01

Purpose of review To provide the reader with a review of contemporary literature describing the evolving understanding of the molecular pathobiology of pseudohypoparathyroidism (PHP). Recent findings The features of PHP type 1 reflect imprinting of the GNAS gene, which encodes the α subunit of the heterotrimeric G protein (Gαs) that couples heptahelical receptors to activation of adenylyl cyclase. Transcription of Gαs is biallelic in most cells, but is primarily from the maternal allele in some tissues (e.g. proximal renal tubules, thyroid, pituitary somatotropes, gonads). Patients with PHP 1a have heterozygous mutations within the exons of the maternal GNAS allele that encode Gαs, whereas patients with PHP 1b have methylation defects in the GNAS locus that reduce transcription of Gαs from the maternal allele. In both PHP 1a and PHP 1b, paternal imprinting of Gαs leads to resistance to parathyroid hormone and TSH. Although brachydactyly is characteristic of PHP 1a, it is sometimes present in patients with PHP 1b. Summary Molecular studies enable a distinction between PHP 1a and PHP 1b, with different mechanisms accounting for Gαs deficiency. Clinical overlap between these two forms of PHP type 1 is likely due to the variable levels of Gαs activity expressed in specific cell types. PMID:23076042

Compound toxicity screening and structure-activity relationship modeling in Escherichia coli.

PubMed

Planson, Anne-Gaëlle; Carbonell, Pablo; Paillard, Elodie; Pollet, Nicolas; Faulon, Jean-Loup

2012-03-01

Synthetic biology and metabolic engineering are used to develop new strategies for producing valuable compounds ranging from therapeutics to biofuels in engineered microorganisms. When developing methods for high-titer production cells, toxicity is an important element to consider. Indeed the production rate can be limited due to toxic intermediates or accumulation of byproducts of the heterologous biosynthetic pathway of interest. Conversely, highly toxic molecules are desired when designing antimicrobials. Compound toxicity in bacteria plays a major role in metabolic engineering as well as in the development of new antibacterial agents. Here, we screened a diversified chemical library of 166 compounds for toxicity in Escherichia coli. The dataset was built using a clustering algorithm maximizing the chemical diversity in the library. The resulting assay data was used to develop a toxicity predictor that we used to assess the toxicity of metabolites throughout the metabolome. This new tool for predicting toxicity can thus be used for fine-tuning heterologous expression and can be integrated in a computational-framework for metabolic pathway design. Many structure-activity relationship tools have been developed for toxicology studies in eukaryotes [Valerio (2009), Toxicol Appl Pharmacol, 241(3): 356-370], however, to the best of our knowledge we present here the first E. coli toxicity prediction web server based on QSAR models (EcoliTox server: http://www.issb.genopole.fr/∼faulon/EcoliTox.php). Copyright © 2011 Wiley Periodicals, Inc.

m6ASNP: a tool for annotating genetic variants by m6A function.

PubMed

Jiang, Shuai; Xie, Yubin; He, Zhihao; Zhang, Ya; Zhao, Yuli; Chen, Li; Zheng, Yueyuan; Miao, Yanyan; Zuo, Zhixiang; Ren, Jian

2018-05-01

Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants that target m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants. We believe that m6ASNP is a very convenient tool that can be used to boost further functional studies investigating genetic variants. The web server "m6ASNP" is implemented in JAVA and PHP and is freely available at [60].

PHP14 regulates hepatic stellate cells migration in liver fibrosis via mediating TGF-β1 signaling to PI3Kγ/AKT/Rac1 pathway.

PubMed

Xu, Anjian; Li, Yanmeng; Zhao, Wenshan; Hou, Fei; Li, Xiaojin; Sun, Lan; Chen, Wei; Yang, Aiting; Wu, Shanna; Zhang, Bei; Yao, Jingyi; Wang, Huan; Huang, Jian

2018-02-01

Hepatic fibrosis is characterized by the activation of hepatic stellate cells (HSCs). Migration of the activated HSCs to the site of injury is one of the key characteristics during the wound healing process. We have previously demonstrated that 14 kDa phosphohistidine phosphatase (PHP14) is involved in migration and lamellipodia formation of HSCs. However, the role of PHP14 in liver fibrosis remains unknown. In this study, we first assessed PHP14 expression and distribution in liver fibrotic tissues using western blot, immunohistochemistry, and double immunofluorescence staining. Next, we investigated the role of PHP14 in liver fibrosis and, more specifically, the migration of HSCs by Transwell assay and 3D collagen matrices assay. Finally, we explored the possible molecular mechanisms of the effects of PHP14 on these processes. Our results show that the PHP14 expression is up-regulated in fibrotic liver and mainly in HSCs. Importantly, TGF-β1 can induce PHP14 expression in HSCs accompanied with the activation of HSCs. Consistent with the previous study, PHP14 promotes HSCs migration, especially, promotes 3D floating collagen matrices contraction but inhibits stressed-released matrices contraction. Mechanistically, the PI3Kγ/AKT/Rac1 pathway is involved in migration regulated by PHP14. Moreover, PHP14 specifically mediates the TGF-β1 signaling to PI3Kγ/AKT pathway and regulates HSC migration, and thus participates in liver fibrosis. Our study identified the role of PHP14 in liver fibrosis, particularly HSC migration, and suggested a novel mediator of transducting TGF-β1 signaling to PI3Kγ/AKT/Rac1 pathway. PHP14 is up-regulated in fibrotic liver and activated hepatic stellate cells. The expression of PHP14 is induced by TGF-β1. The migration of hepatic stellate cells is regulated by PHP14. PHP14 is a mediator of TGF-β1 signaling to PI3Kγ/AKT/Rac1 pathway in hepatic stellate cells.

Current Nomenclature of Pseudohypoparathyroidism: Inactivating Parathyroid Hormone/Parathyroid Hormone-Related Protein Signaling Disorder

PubMed Central

Turan, Serap

2017-01-01

Disorders related to parathyroid hormone (PTH) resistance and PTH signaling pathway impairment are historically classified under the term of pseudohypoparathyroidism (PHP). The disease was first described and named by Fuller Albright and colleagues in 1942. Albright hereditary osteodystrophy (AHO) is described as an associated clinical entity with PHP, characterized by brachydactyly, subcutaneous ossifications, round face, short stature and a stocky build. The classification of PHP is further divided into PHP-Ia, pseudo-PHP (pPHP), PHP-Ib, PHP-Ic and PHP-II according to the presence or absence of AHO, together with an in vivo response to exogenous PTH and the measurement of Gsα protein activity in peripheral erythrocyte membranes in vitro. However, PHP classification fails to differentiate all patients with different clinical and molecular findings for PHP subtypes and classification become more complicated with more recent molecular characterization and new forms having been identified. So far, new classifications have been established by the EuroPHP network to cover all disorders of the PTH receptor and its signaling pathway. Inactivating PTH/PTH-related protein signaling disorder (iPPSD) is the new name proposed for a group of these disorders and which can be further divided into subtypes - iPPSD1 to iPPSD6. These are termed, starting from PTH receptor inactivation mutation (Eiken and Blomstrand dysplasia) as iPPSD1, inactivating Gsα mutations (PHP-Ia, PHP-Ic and pPHP) as iPPSD2, loss of methylation of GNAS DMRs (PHP-Ib) as iPPSD3, PRKAR1A mutations (acrodysostosis type 1) as iPPSD4, PDE4D mutations (acrodysostosis type 2) as iPPSD5 and PDE3A mutations (autosomal dominant hypertension with brachydactyly) as iPPSD6. iPPSDx is reserved for unknown molecular defects and iPPSDn+1 for new molecular defects which are yet to be described. With these new classifications, the aim is to clarify the borders of each different subtype of disease and make the classification according to molecular pathology. The iPPSD group is designed to be expandable and new classifications will readily fit into it as necessary. PMID:29280743

Current Nomenclature of Pseudohypoparathyroidism: Inactivating Parathyroid Hormone/Parathyroid Hormone-Related Protein Signaling Disorder.

PubMed

Turan, Serap

2017-12-30

Disorders related to parathyroid hormone (PTH) resistance and PTH signaling pathway impairment are historically classified under the term of pseudohypoparathyroidism (PHP). The disease was first described and named by Fuller Albright and colleagues in 1942. Albright hereditary osteodystrophy (AHO) is described as an associated clinical entity with PHP, characterized by brachydactyly, subcutaneous ossifications, round face, short stature and a stocky build. The classification of PHP is further divided into PHP-Ia, pseudo-PHP (pPHP), PHP-Ib, PHP-Ic and PHP-II according to the presence or absence of AHO, together with an in vivo response to exogenous PTH and the measurement of Gsα protein activity in peripheral erythrocyte membranes in vitro. However, PHP classification fails to differentiate all patients with different clinical and molecular findings for PHP subtypes and classification become more complicated with more recent molecular characterization and new forms having been identified. So far, new classifications have been established by the EuroPHP network to cover all disorders of the PTH receptor and its signaling pathway. Inactivating PTH/PTH-related protein signaling disorder (iPPSD) is the new name proposed for a group of these disorders and which can be further divided into subtypes - iPPSD1 to iPPSD6. These are termed, starting from PTH receptor inactivation mutation (Eiken and Blomstrand dysplasia) as iPPSD1, inactivating Gsα mutations (PHP-Ia, PHP-Ic and pPHP) as iPPSD2, loss of methylation of GNAS DMRs (PHP-Ib) as iPPSD3, PRKAR1A mutations (acrodysostosis type 1) as iPPSD4, PDE4D mutations (acrodysostosis type 2) as iPPSD5 and PDE3A mutations (autosomal dominant hypertension with brachydactyly) as iPPSD6. iPPSDx is reserved for unknown molecular defects and iPPSDn+1 for new molecular defects which are yet to be described. With these new classifications, the aim is to clarify the borders of each different subtype of disease and make the classification according to molecular pathology. The iPPSD group is designed to be expandable and new classifications will readily fit into it as necessary.

Results of a Randomized Controlled Multicenter Phase III Trial of Percutaneous Hepatic Perfusion Compared with Best Available Care for Patients with Melanoma Liver Metastases.

PubMed

Hughes, Marybeth S; Zager, Jonathan; Faries, Mark; Alexander, H Richard; Royal, Richard E; Wood, Bradford; Choi, Junsung; McCluskey, Kevin; Whitman, Eric; Agarwala, Sanjiv; Siskin, Gary; Nutting, Charles; Toomey, Mary Ann; Webb, Carole; Beresnev, Tatiana; Pingpank, James F

2016-04-01

There is no consensus for the treatment of melanoma metastatic to the liver. Percutaneous hepatic perfusion with melphalan (PHP-Mel) is a method of delivering regional chemotherapy selectively to the liver. In this study, we report the results of a multicenter, randomized controlled trial comparing PHP-Mel with best alternative care (BAC) for patients with ocular or cutaneous melanoma metastatic to the liver. A total of 93 patients were randomized to PHP-Mel (n = 44) or BAC (n = 49). On the PHP-Mel arm, melphalan was delivered via the hepatic artery, and the hepatic effluent captured and filtered extracorporeally prior to return to the systemic circulation via a venovenous bypass circuit. PHP-Mel was repeatable every 4-8 weeks. The primary endpoint was hepatic progression-free survival (hPFS), and secondary endpoints included overall PFS (oPFS), overall survival (OS), hepatic objective response (hOR), and safety. hPFS was 7.0 months for PHP-Mel and 1.6 months for BAC (p < 0.0001), while oPFS was 5.4 months for PHP-Mel and 1.6 months for BAC (p < 0.0001). Median OS was not significantly different (PHP-Mel 10.6 months vs. BAC 10.0 months), likely due to crossover to PHP-Mel treatment (57.1 %) from the BAC arm, and the hOR was 36.4 % for PHP-Mel and 2.0 % for BAC (p < 0.001). The majority of adverse events were related to bone marrow suppression. Four deaths were attributed to PHP-Mel, three in the primary PHP-Mel group, and one post-crossover to PHP-Mel from BAC. This randomized, phase III study demonstrated the efficacy of the PHP-Mel procedure. hPFS, oPFS, and hOR were significantly improved with PHP-Mel. PHP with melphalan should provide a new treatment option for unresectable metastatic melanoma in the liver.

High-Fidelity Modeling of Computer Network Worms

DTIC Science & Technology

2004-06-22

plots the propagation of the TCP-based worm. This execution is among the largest TCP worm models simulated to date at packet-level. TCP vs . UDP Worm...the mapping of the virtual IP addresses to honeyd’s MAC address in the proxy’s ARP table. The proxy server listens for packets from both sides of...experimental setup, we used two ntium-4 ThinkPad , and an IBM Pentium-III ThinkPad ), running the proxy server and honeyd respectively. The Code Red II worm

Data Access Tools And Services At The Goddard Distributed Active Archive Center (GDAAC)

NASA Technical Reports Server (NTRS)

Pham, Long; Eng, Eunice; Sweatman, Paul

2003-01-01

As one of the largest providers of Earth Science data from the Earth Observing System, GDAAC provides the latest data from the Moderate Resolution Imaging Spectroradiometer (MODIS), Atmospheric Infrared Sounder (AIRS), Solar Radiation and Climate Experiment (SORCE) data products via GDAAC's data pool (50TB of disk cache). In order to make this huge volume of data more accessible to the public and science communities, the GDAAC offers multiple data access tools and services: Open Source Project for Network Data Access Protocol (OPeNDAP), Grid Analysis and Display System (GrADS/DODS) (GDS), Live Access Server (LAS), OpenGlS Web Map Server (WMS) and Near Archive Data Mining (NADM). The objective is to assist users in retrieving electronically a smaller, usable portion of data for further analysis. The OPeNDAP server, formerly known as the Distributed Oceanographic Data System (DODS), allows the user to retrieve data without worrying about the data format. OPeNDAP is capable of server-side subsetting of HDF, HDF-EOS, netCDF, JGOFS, ASCII, DSP, FITS and binary data formats. The GrADS/DODS server is capable of serving the same data formats as OPeNDAP. GDS has an additional feature of server-side analysis. Users can analyze the data on the server there by decreasing the computational load on their client's system. The LAS is a flexible server that allows user to graphically visualize data on the fly, to request different file formats and to compare variables from distributed locations. Users of LAS have options to use other available graphics viewers such as IDL, Matlab or GrADS. WMS is based on the OPeNDAP for serving geospatial information. WMS supports OpenGlS protocol to provide data in GIs-friendly formats for analysis and visualization. NADM is another access to the GDAAC's data pool. NADM gives users the capability to use a browser to upload their C, FORTRAN or IDL algorithms, test the algorithms, and mine data in the data pool. With NADM, the GDAAC provides an environment physically close to the data source. NADM will benefit users with mining or offer data reduction algorithms by reducing large volumes of data before transmission over the network to the user.

Acetylcholine content and viability of cholinergic neurons are influenced by the activity of protein histidine phosphatase

PubMed Central

2012-01-01

Background The first mammalian protein histidine phosphatase (PHP) was discovered in the late 90s of the last century. One of the known substrates of PHP is ATP-citrate lyase (ACL), which is responsible - amongst other functions - for providing acetyl-CoA for acetylcholine synthesis in neuronal tissues. It has been shown in previous studies that PHP downregulates the activity of ACL by dephosphorylation. According to this our present work focused on the influence of PHP activity on the acetylcholine level in cholinergic neurons. Results The amount of PHP in SN56 cholinergic neuroblastoma cells was increased after overexpression of PHP by using pIRES2-AcGFP1-PHP as a vector. We demonstrated that PHP overexpression reduced the acetylcholine level and induced cell death. The acetylcholine content of SN56 cells was measured by fast liquid chromatography-tandem mass spectrometry method. Overexpression of the inactive H53A-PHP mutant also induced cell damage, but in a significantly reduced manner. However, this overexpression of the inactive PHP mutant did not change the acetylcholine content of SN56 cells significantly. In contrast, PHP downregulation, performed by RNAi-technique, did not induce cell death, but significantly increased the acetylcholine content in SN56 cells. Conclusions We could show for the first time that PHP downregulation increased the acetylcholine level in SN56 cells. This might be a potential therapeutic strategy for diseases involving cholinergic deficits like Alzheimer's disease. PMID:22436051

Food Safety Impacts from Post-Harvest Processing Procedures of Molluscan Shellfish.

PubMed

Baker, George L

2016-04-18

Post-harvest Processing (PHP) methods are viable food processing methods employed to reduce human pathogens in molluscan shellfish that would normally be consumed raw, such as raw oysters on the half-shell. Efficacy of human pathogen reduction associated with PHP varies with respect to time, temperature, salinity, pressure, and process exposure. Regulatory requirements and PHP molluscan shellfish quality implications are major considerations for PHP usage. Food safety impacts associated with PHP of molluscan shellfish vary in their efficacy and may have synergistic outcomes when combined. Further research for many PHP methods are necessary and emerging PHP methods that result in minimal quality loss and effective human pathogen reduction should be explored.

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Fast lattice-based polynomial digital signature system for m-commerce

NASA Astrophysics Data System (ADS)

Wei, Xinzhou; Leung, Lin; Anshel, Michael

2003-01-01

The privacy and data integrity are not guaranteed in current wireless communications due to the security hole inside the Wireless Application Protocol (WAP) version 1.2 gateway. One of the remedies is to provide an end-to-end security in m-commerce by applying application level security on top of current WAP1.2. The traditional security technologies like RSA and ECC applied on enterprise's server are not practical for wireless devices because wireless devices have relatively weak computation power and limited memory compared with server. In this paper, we developed a lattice based polynomial digital signature system based on NTRU's Polynomial Authentication and Signature Scheme (PASS), which enabled the feasibility of applying high-level security on both server and wireless device sides.

Using a centralised database system and server in the European Union Framework Programme 7 project SEPServer

NASA Astrophysics Data System (ADS)

Heynderickx, Daniel

2012-07-01

The main objective of the SEPServer project (EU FP7 project 262773) is to produce a new tool, which greatly facilitates the investigation of solar energetic particles (SEPs) and their origin: a server providing SEP data, related electromagnetic (EM) observations and analysis methods, a comprehensive catalogue of the observed SEP events, and educational/outreach material on solar eruptions. The project is coordinated by the University of Helsinki. The project will combine data and knowledge from 11 European partners and several collaborating parties from Europe and US. The datasets provided by the consortium partners are collected in a MySQL database (using the ESA Open Data Interface under licence) on a server operated by DH Consultancy, which also hosts a web interface providing browsing, plotting and post-processing and analysis tools developed by the consortium, as well as a Solar Energetic Particle event catalogue. At this stage of the project, a prototype server has been established, which is presently undergoing testing by users inside the consortium. Using a centralized database has numerous advantages, including: homogeneous storage of the data, which eliminates the need for dataset specific file access routines once the data are ingested in the database; a homogeneous set of metadata describing the datasets on both a global and detailed level, allowing for automated access to and presentation of the various data products; standardised access to the data in different programming environments (e.g. php, IDL); elimination of the need to download data for individual data requests. SEPServer will, thus, add value to several space missions and Earth-based observations by facilitating the coordinated exploitation of and open access to SEP data and related EM observations, and promoting correct use of these data for the entire space research community. This will lead to new knowledge on the production and transport of SEPs during solar eruptions and facilitate the development of models for predicting solar radiation storms and calculation of expected fluxes/fluences of SEPs encountered by spacecraft in the interplanetary medium.

A public HTLV-1 molecular epidemiology database for sequence management and data mining.

PubMed

Araujo, Thessika Hialla Almeida; Souza-Brito, Leandro Inacio; Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

2012-01-01

It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

The Anatomy of a Grid portal

NASA Astrophysics Data System (ADS)

Licari, Daniele; Calzolari, Federico

2011-12-01

In this paper we introduce a new way to deal with Grid portals referring to our implementation. L-GRID is a light portal to access the EGEE/EGI Grid infrastructure via Web, allowing users to submit their jobs from a common Web browser in a few minutes, without any knowledge about the Grid infrastructure. It provides the control over the complete lifecycle of a Grid Job, from its submission and status monitoring, to the output retrieval. The system, implemented as client-server architecture, is based on the Globus Grid middleware. The client side application is based on a java applet; the server relies on a Globus User Interface. There is no need of user registration on the server side, and the user needs only his own X.509 personal certificate. The system is user-friendly, secure (it uses SSL protocol, mechanism for dynamic delegation and identity creation in public key infrastructures), highly customizable, open source, and easy to install. The X.509 personal certificate does not get out from the local machine. It allows to reduce the time spent for the job submission, granting at the same time a higher efficiency and a better security level in proxy delegation and management.

Pulmonary haptoglobin (pHp) is part of the surfactant system in the human lung.

PubMed

Abdullah, Mahdi; Goldmann, Torsten

2012-11-20

Since the existence of pHp was demonstrated, it has been shown that this molecule and its receptor CD163 are regulated by different stimuli. Furthermore, a comparably fast secretion of pHp was described as well as the immuno-stimulatory effects. The intention of this study was to elucidate the role of pHp in the human lungs further. Here we show, by means of confocal microscopy and immune-electron-microscopy, a clear co-localization of pHp with surfactant protein-B in lamellar bodies of alveolar epithelial cells type II. These results are underlined by immunohistochemical stainings in differently fixed human lung tissues, which show pHp in vesicular and released form. The images of the released form resemble the intended position of surfactant in the human alveolus. pHp is secreted by Alveolar epithelial cells type II as previously shown. Moreover, pHp is co-localized with Surfactant protein-B. We conclude that the presented data shows that pHp is a native part of the surfactant system in the human lung. http://www.diagnosticpathology.diagnomx.eu/vs/2563584738239912.

A Python object-oriented framework for the CMS alignment and calibration data

NASA Astrophysics Data System (ADS)

Dawes, Joshua H.; CMS Collaboration

2017-10-01

The Alignment, Calibrations and Databases group at the CMS Experiment delivers Alignment and Calibration Conditions Data to a large set of workflows which process recorded event data and produce simulated events. The current infrastructure for releasing and consuming Conditions Data was designed in the two years of the first LHC long shutdown to respond to use cases from the preceding data-taking period. During the second run of the LHC, new use cases were defined. For the consumption of Conditions Metadata, no common interface existed for the detector experts to use in Python-based custom scripts, resulting in many different querying and transaction management patterns. A new framework has been built to address such use cases: a simple object-oriented tool that detector experts can use to read and write Conditions Metadata when using Oracle and SQLite databases, that provides a homogeneous method of querying across all services. The tool provides mechanisms for segmenting large sets of conditions while releasing them to the production database, allows for uniform error reporting to the client-side from the server-side and optimizes the data transfer to the server. The architecture of the new service has been developed exploiting many of the features made available by the metadata consumption framework to implement the required improvements. This paper presents the details of the design and implementation of the new metadata consumption and data upload framework, as well as analyses of the new upload service’s performance as the server-side state varies.

A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

2014-12-01

Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

Bone Status Among Patients With Nonsurgical Hypoparathyroidism, Autosomal Dominant Hypocalcaemia, and Pseudohypoparathyroidism: A Cohort Study.

PubMed

Underbjerg, Line; Malmstroem, Sofie; Sikjaer, Tanja; Rejnmark, Lars

2018-03-01

Nonsurgical hypoparathyroidism (Ns-HypoPT) and pseudohypoparathyroidism (PHP) are both rare diseases, characterized by hypocalcemia. In Ns-HypoPT, PTH levels are low, whereas patients with PHP often have very high levels due to receptor-insensitivity to PTH (PTH-resistance). Accordingly, we hypothesized that indices of bone turnover and bone mineralization/architecture are similar in Ns-HypoPT and PHP despite marked differences in PTH levels. We studied 62 patients with Ns-HypoPT and 31 with PHP as well as a group of age- and sex-matched healthy controls. We found a significantly higher areal BMD (aBMD) by DXA among patients with Ns-HypoPT, both compared with PHP and the background population. Compared with Ns-HypoPT, PHP patients had significantly lower total and trabecular volumetric BMD (vBMD) assessed by quantitative computed tomography (QCT) scans at the spine and hip. High-resolution peripheral quantitative computed tomography (HRpQCT) scans showed a lower trabecular area and vBMD as well as a lower trabecular number at the tibia in PHP compared to Ns-HypoPT and matched controls. In PHP, PTH levels correlated with levels of markers of bone formation (osteocalcin, bone-specific alkaline phosphatase, P1NP), and bone resorption (CTx). In adult males, levels of bone markers were significantly higher in PHP compared with Ns-HypoPT. Levels of procalcitonin and calcitonin were significantly higher in PHP compared with Ns-HypoPT. In conclusion, indices of bone turnover, density, and microarchitecture differ between patients with Ns-HypoPT and PHP. Our data suggest that patients with PHP do not have a complete skeletal resistance to PTH and that the effects of chronically high PTH levels in PHP are mostly confined to the trabecular tissue. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

Testing theoretical relationships: factors influencing positive health practices (PHP) in Filipino college students.

PubMed

Ayres, Cynthia; Mahat, Ganga; Atkins, Robert

2013-01-01

To examine variables influencing the positive health practices (PHP) of Filipino college students to gain a better understanding of health practices in this ethnic/racial group. Cross-sectional study tested theoretical relationships postulated among (a) PHP, (b) social support (SS), (c) optimism, and (d) acculturation. A sample of Filipino college students (N = 226) aged 18 to 21 was obtained in June 2009. Participants completed 4 instruments. Statistical analyses were performed using SPSS 16.0. Positive correlations were found between PHP and SS (r = .39, p = .01) and optimism and PHP (r = .36, p = .01). No correlation was found between PHP and acculturation. Optimism and SS predicted performance of PHP (R (2) = .18, F[2, 221] = 24.927, p < .001). A difference was found in acculturation levels between participants who grew up in the United States (t[223] = 4.5, p < .001) and those who did not. Findings help health practitioners and educators to better understand the underlying factors that influence PHP in this population.

Reactions of R(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)]. A general and efficient entry to phosphanylphosphinidene complexes of platinum. Syntheses and structures of [(eta(2)-P=(i)Pr(2))Pt(p-Tol(3)P)(2)], [(eta(2)-P=(t)Bu(2))Pt(p-Tol(3)P)(2)], [{eta(2)-P=(N(i)Pr(2))(2)}Pt(p-Tol(3)P)(2)] and [{(Et(2)PhP)(2)Pt}(2)P(2)].

PubMed

Domańska-Babul, Wioleta; Chojnacki, Jaroslaw; Matern, Eberhard; Pikies, Jerzy

2009-01-07

The reactions of lithium derivatives of diphosphanes R(2)P-P(SiMe(3))Li (R = (t)Bu, (i)Pr, Et(2)N and (i)Pr(2)N) with [(R'(3)P)(2)PtCl(2)] (R'(3)P = Et(3)P, Et(2)PhP, EtPh(2)P and p-Tol(3)P) proceed in a facile manner to afford side-on bonded phosphanylphosphinidene complexes of platinum [(eta(2)-P=R(2))Pt(PR'(3))(2)]. The related reactions of Ph(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)] did not yield [(eta(2)-P=PPh(2))Pt(PR'(3))(2)] and resulted mainly in the formation of [{(R'(3)P)(2)Pt}(2)P(2)], Ph(2)P-PLi-PPh(2), (Me(3)Si)(2)PLi and (Me(3)Si)(3)P. Crystallographic data are reported for the compounds [(eta(2)-P=R(2))Pt(p-Tol(3)P)(2)] (R = (t)Bu, (i)Pr, ((i)Pr(2)N)(2)P) and for [{(Et(2)PhP)(2)Pt}(2)P(2)].

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures.

PubMed

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

PubMed Central

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/ PMID:18971256

Pulmonary haptoglobin (pHp) is part of the surfactant system in the human lung

PubMed Central

2012-01-01

Abstract Since the existence of pHp was demonstrated, it has been shown that this molecule and its receptor CD163 are regulated by different stimuli. Furthermore, a comparably fast secretion of pHp was described as well as the immuno-stimulatory effects. The intention of this study was to elucidate the role of pHp in the human lungs further. Here we show, by means of confocal microscopy and immune-electron-microscopy, a clear co-localization of pHp with Surfactant protein-B in lamellar bodies of Alveolar Epithelial Cells Type II. These results are underlined by immunohistochemical stainings in differently fixed human lung tissues, which show pHp in vesicular and released form. The images of the released form resemble the intended position of surfactant in the human alveolus. pHp is secreted by Alveolar epithelial cells type II as previously shown. Moreover, pHp is co-localized with Surfactant protein-B. We conclude that the presented data shows that pHp is a native part of the surfactant system in the human lung. Virtual slides http://www.diagnosticpathology.diagnomx.eu/vs/2563584738239912. PMID:23164167

Analysis of series resonant converter with series-parallel connection

NASA Astrophysics Data System (ADS)

Lin, Bor-Ren; Huang, Chien-Lan

2011-02-01

In this study, a parallel inductor-inductor-capacitor (LLC) resonant converter series-connected on the primary side and parallel-connected on the secondary side is presented for server power supply systems. Based on series resonant behaviour, the power metal-oxide-semiconductor field-effect transistors are turned on at zero voltage switching and the rectifier diodes are turned off at zero current switching. Thus, the switching losses on the power semiconductors are reduced. In the proposed converter, the primary windings of the two LLC converters are connected in series. Thus, the two converters have the same primary currents to ensure that they can supply the balance load current. On the output side, two LLC converters are connected in parallel to share the load current and to reduce the current stress on the secondary windings and the rectifier diodes. In this article, the principle of operation, steady-state analysis and design considerations of the proposed converter are provided and discussed. Experiments with a laboratory prototype with a 24 V/21 A output for server power supply were performed to verify the effectiveness of the proposed converter.

Low back pain and disability in individuals with plantar heel pain.

PubMed

McClinton, Shane; Weber, Carolyn F; Heiderscheit, Bryan

2018-03-01

Lack of response to plantar heel pain (PHP) treatment may be related to unmanaged low back pain (LBP) and low back dysfunction, but a relationship between LBP and PHP has not been established. The purpose of this investigation was to compare the prevalence of LBP among individuals with and without PHP and to assess the association between low back disability and foot/ankle function. A cross-sectional study compared the prevalence and likelihood of LBP in individuals with (n=27) and without (n=27) PHP matched to age, sex, BMI, foot posture, and foot mobility. In individuals with PHP, correlations were examined between foot/ankle function using the foot and ankle ability measure (FAAM), low back disability using the Oswestry low back disability questionnaire (OSW), duration of PHP symptoms, body mass index (BMI), and age. A greater percentage of individuals with PHP had LBP (74% versus 37% of controls, odds ratio=5.2, P=0.009) and higher levels of low back disability (17% higher OSW score than controls, P<0.001). In individuals with PHP, FAAM scores were correlated with OSW scores (ρ=-0.463, P=0.015), but not with duration of PHP symptoms, BMI, or age (P>0.150). Individuals with PHP had a greater prevalence of LBP and higher low back disability that was correlated to reduced foot and ankle function. Treatment to address both local and proximal impairments, including impairments related to LBP, may be warranted to improve the management of PHP. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automatic analysis of attack data from distributed honeypot network

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Voznak, MIroslav; Rezac, Filip; Partila, Pavol; Tomala, Karel

2013-05-01

There are many ways of getting real data about malicious activity in a network. One of them relies on masquerading monitoring servers as a production one. These servers are called honeypots and data about attacks on them brings us valuable information about actual attacks and techniques used by hackers. The article describes distributed topology of honeypots, which was developed with a strong orientation on monitoring of IP telephony traffic. IP telephony servers can be easily exposed to various types of attacks, and without protection, this situation can lead to loss of money and other unpleasant consequences. Using a distributed topology with honeypots placed in different geological locations and networks provides more valuable and independent results. With automatic system of gathering information from all honeypots, it is possible to work with all information on one centralized point. Communication between honeypots and centralized data store use secure SSH tunnels and server communicates only with authorized honeypots. The centralized server also automatically analyses data from each honeypot. Results of this analysis and also other statistical data about malicious activity are simply accessible through a built-in web server. All statistical and analysis reports serve as information basis for an algorithm which classifies different types of used VoIP attacks. The web interface then brings a tool for quick comparison and evaluation of actual attacks in all monitored networks. The article describes both, the honeypots nodes in distributed architecture, which monitor suspicious activity, and also methods and algorithms used on the server side for analysis of gathered data.

New implementation of OGC Web Processing Service in Python programming language. PyWPS-4 and issues we are facing with processing of large raster data using OGC WPS

NASA Astrophysics Data System (ADS)

Čepický, Jáchym; Moreira de Sousa, Luís

2016-06-01

The OGC® Web Processing Service (WPS) Interface Standard provides rules for standardizing inputs and outputs (requests and responses) for geospatial processing services, such as polygon overlay. The standard also defines how a client can request the execution of a process, and how the output from the process is handled. It defines an interface that facilitates publishing of geospatial processes and client discovery of processes and and binding to those processes into workflows. Data required by a WPS can be delivered across a network or they can be available at a server. PyWPS was one of the first implementations of OGC WPS on the server side. It is written in the Python programming language and it tries to connect to all existing tools for geospatial data analysis, available on the Python platform. During the last two years, the PyWPS development team has written a new version (called PyWPS-4) completely from scratch. The analysis of large raster datasets poses several technical issues in implementing the WPS standard. The data format has to be defined and validated on the server side and binary data have to be encoded using some numeric representation. Pulling raster data from remote servers introduces security risks, in addition, running several processes in parallel has to be possible, so that system resources are used efficiently while preserving security. Here we discuss these topics and illustrate some of the solutions adopted within the PyWPS implementation.

CBD: a biomarker database for colorectal cancer.

PubMed

Zhang, Xueli; Sun, Xiao-Feng; Cao, Yang; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD.Database URL: http://sysbio.suda.edu.cn/CBD/.

WordCluster: detecting clusters of DNA words and genomic elements

PubMed Central

2011-01-01

Background Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds. Results We introduce here an algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used WordCluster to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome. Conclusions WordCluster seems to predict biological meaningful clusters of DNA words (k-mers) and genomic entities. The implementation of the method into a web server is available at http://bioinfo2.ugr.es/wordCluster/wordCluster.php including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes. PMID:21261981

CBD: a biomarker database for colorectal cancer

PubMed Central

Zhang, Xueli; Sun, Xiao-Feng; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Abstract Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/ PMID:29846545

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.

PubMed

Hanson, Jack; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi

2017-03-01

Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction. The new method, named SPOT-Disorder, has steadily improved over a similar method using a traditional, window-based neural network (SPINE-D) in all datasets tested without separate training on short and long disordered regions. Independent tests on four other datasets including the datasets from critical assessment of structure prediction (CASP) techniques and >10 000 annotated proteins from MobiDB, confirmed SPOT-Disorder as one of the best methods in disorder prediction. Moreover, initial studies indicate that the method is more accurate in predicting functional sites in disordered regions. These results highlight the usefulness combining LSTM with deep bidirectional recurrent neural networks in capturing non-local, long-range interactions for bioinformatics applications. SPOT-disorder is available as a web server and as a standalone program at: http://sparks-lab.org/server/SPOT-disorder/index.php . j.hanson@griffith.edu.au or yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au. Supplementary data is available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

An Improved Publication Process for the UMVF.

PubMed

Renard, Jean-Marie; Brunetaud, Jean-Marc; Cuggia, Marc; Darmoni, Stephan; Lebeux, Pierre; Beuscart, Régis

2005-01-01

The "Université Médicale Virtuelle Francophone" (UMVF) is a federation of French medical schools. Its main goal is to share the production and use of pedagogic medical resources generated by academic medical teachers. We developed an Open-Source application based upon a workflow system which provides an improved publication process for the UMVF. For teachers, the tool permits easy and efficient upload of new educational resources. For web masters it provides a mechanism to easily locate and validate the resources. For both the teachers and the web masters, the utility provides the control and communication functions that define a workflow system.For all users, students in particular, the application improves the value of the UMVF repository by providing an easy way to find a detailed description of a resource and to check any resource from the UMVF to ascertain its quality and integrity, even if the resource is an old deprecated version. The server tier of the application is used to implement the main workflow functionalities and is deployed on certified UMVF servers using the PHP language, an LDAP directory and an SQL database. The client tier of the application provides both the workflow and the search and check functionalities and is implemented using a Java applet through a W3C compliant web browser. A unique signature for each resource, was needed to provide security functionality and is implemented using the MD5 Digest algorithm. The testing performed by Rennes and Lille verified the functionality and conformity with our specifications.

Analysing Student Programs in the PHP Intelligent Tutoring System

ERIC Educational Resources Information Center

Weragama, Dinesha; Reye, Jim

2014-01-01

Programming is a subject that many beginning students find difficult. The PHP Intelligent Tutoring System (PHP ITS) has been designed with the aim of making it easier for novices to learn the PHP language in order to develop dynamic web pages. Programming requires practice. This makes it necessary to include practical exercises in any ITS that…

HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.

PubMed

Ambroggio, Xavier I; Dommer, Jennifer; Gopalan, Vivek; Dunham, Eleca J; Taubenberger, Jeffery K; Hurt, Darrell E

2013-06-18

Influenza A viruses possess RNA genomes that mutate frequently in response to immune pressures. The mutations in the hemagglutinin genes are particularly significant, as the hemagglutinin proteins mediate attachment and fusion to host cells, thereby influencing viral pathogenicity and species specificity. Large-scale influenza A genome sequencing efforts have been ongoing to understand past epidemics and pandemics and anticipate future outbreaks. Sequencing efforts thus far have generated nearly 9,000 distinct hemagglutinin amino acid sequences. Comparative models for all publicly available influenza A hemagglutinin protein sequences (8,769 to date) were generated using the Rosetta modeling suite. The C-alpha root mean square deviations between a randomly chosen test set of models and their crystallographic templates were less than 2 Å, suggesting that the modeling protocols yielded high-quality results. The models were compiled into an online resource, the Hemagglutinin Structure Prediction (HASP) server. The HASP server was designed as a scientific tool for researchers to visualize hemagglutinin protein sequences of interest in a three-dimensional context. With a built-in molecular viewer, hemagglutinin models can be compared side-by-side and navigated by a corresponding sequence alignment. The models and alignments can be downloaded for offline use and further analysis. The modeling protocols used in the HASP server scale well for large amounts of sequences and will keep pace with expanded sequencing efforts. The conservative approach to modeling and the intuitive search and visualization interfaces allow researchers to quickly analyze hemagglutinin sequences of interest in the context of the most highly related experimental structures, and allow them to directly compare hemagglutinin sequences to each other simultaneously in their two- and three-dimensional contexts. The models and methodology have shown utility in current research efforts and the ongoing aim of the HASP server is to continue to accelerate influenza A research and have a positive impact on global public health.

An application for delivering field results to mobile devices

NASA Astrophysics Data System (ADS)

Kanta, A.; Hloupis, G.; Vallianatos, F.; Rust, D.

2009-04-01

Mobile devices (MD) such as personal digital assistants (PDAs) and Smartphones expand the ability of Internet communication between remote users. In particular these devices have the possibility to interact with data centres in order to request and receive information. For field surveys MDs used primarily for controlling instruments (in case of field measurements) or for entering data needed for later processing (e.g damage description after a natural hazard). It is not unusual in areas with high interest combined measurements took place. The results from these measurements usually stored in data servers and their publicity is driven mainly by web-based applications. Here we present a client / server application capable of displaying the results of several measurements for a specific area to a MD. More specific, we develop an application than can present to the screen of the MD the results of existing measurements according to the position of the user. The server side hosted at data centre and uses a relational data base (including the results), a SMS/MMS gateway and a receiver daemon application waiting for messages from MDs. The client side runs on MD and is a simple menu driven application which asks the user to enter the type of requested data and the geographical coordinates. In case of embedded GPS receiver, coordinates automatically derived from the receiver. Then a message is sent to server which responds with the results. In case of absence of Internet communication the application can switched to common Short/Multimedia Messaging Systems: the client request data using SMS and the server responds with MMS. We demonstrate the application using results from TEM, VES and HVSR measurements Acknowledgements Work of authors AK, GH and FV is partially supported by the EU-FP6-SSA in the frame of project "CYCLOPS: CYber-Infrastructure for CiviL protection Operative ProcedureS"

A structural role for the PHP domain in E. coli DNA polymerase III.

PubMed

Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

2013-05-14

In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

The association between plantar heel pain and running surfaces in competitive long-distance male runners.

PubMed

Hotta, Takayuki; Nishiguchi, Shu; Fukutani, Naoto; Tashiro, Yuto; Adachi, Daiki; Morino, Saori; Aoyama, Tomoki

2016-09-01

Plantar heel pain (PHP) is a common complaint, and is most often caused by plantar fasciitis. Plantar fasciitis is reported to be associated with running surfaces, however the association between PHP and running surfaces has not previously been revealed in an epidemiological investigation. Therefore, the purpose of the current study was to examine the association between PHP and running surfaces. This is a cross-sectional study. A total of 347 competitive long-distance male runners participated in this study. The participants completed an original questionnaire, which included items assessing demographic characteristics, training characteristics focusing on running surfaces (soft surface, hard surface and tartan), and the prevalence of PHP during the previous 12 months. A logistic regression analysis was used to identify the effect of running surfaces on PHP. We found that 21.9% of participants had experienced PHP during the previous 12 months. The multivariate logistic regression analysis, after adjusting for demographic and training characteristics, revealed that running on tartan was associated with PHP (odds ratio 2.82, 95% confidence interval 1.42 to 5.61; P<0.01). Our findings suggest that running more than 25% on tartan is associated with PHP in competitive long-distance male runners.

High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.

PubMed

Baños-Mateos, Soledad; van Roon, Anne-Marie M; Lang, Ulla F; Maslen, Sarah L; Skehel, J Mark; Lamers, Meindert H

2017-10-11

High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs.The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.

Pretreating wheat straw by the concentrated phosphoric acid plus hydrogen peroxide (PHP): Investigations on pretreatment conditions and structure changes.

PubMed

Wang, Qing; Hu, Jinguang; Shen, Fei; Mei, Zili; Yang, Gang; Zhang, Yanzong; Hu, Yaodong; Zhang, Jing; Deng, Shihuai

2016-01-01

Wheat straw was pretreated by PHP (the concentrated H3PO4 plus H2O2) to clarify effects of temperature, time and H3PO4 proportion on hemicellulose removal, delignification, cellulose recovery and enzymatic digestibility. Overall, hemicellulose removal was intensified by PHP comparing to the concentrated H3PO4. Moreover, efficient delignification specially happened in PHP pretreatment. Hemicellulose removal and delignification by PHP positively responded to temperature and time. Increasing H3PO4 proportion in PHP can promote hemicellulose removal, however, decrease the delignification. Maximum hemicellulose removal and delignification were achieved at 100% and 83.7% by PHP. Enzymatic digestibility of PHP-pretreated wheat straw was greatly improved by increasing temperature, time and H3PO4 proportion, and complete hydrolysis can be achieved consequently. As temperature of 30-40°C, time of 2.0 h and H3PO4 proportion of 60% were employed, more than 92% cellulose was retained in the pretreated wheat straw, and 29.1-32.6g glucose can be harvested from 100g wheat straw. Copyright © 2015 Elsevier Ltd. All rights reserved.

Specification and Verification of Web Applications in Rewriting Logic

NASA Astrophysics Data System (ADS)

Alpuente, María; Ballis, Demis; Romero, Daniel

This paper presents a Rewriting Logic framework that formalizes the interactions between Web servers and Web browsers through a communicating protocol abstracting HTTP. The proposed framework includes a scripting language that is powerful enough to model the dynamics of complex Web applications by encompassing the main features of the most popular Web scripting languages (e.g. PHP, ASP, Java Servlets). We also provide a detailed characterization of browser actions (e.g. forward/backward navigation, page refresh, and new window/tab openings) via rewrite rules, and show how our models can be naturally model-checked by using the Linear Temporal Logic of Rewriting (LTLR), which is a Linear Temporal Logic specifically designed for model-checking rewrite theories. Our formalization is particularly suitable for verification purposes, since it allows one to perform in-depth analyses of many subtle aspects related to Web interaction. Finally, the framework has been completely implemented in Maude, and we report on some successful experiments that we conducted by using the Maude LTLR model-checker.

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.

PubMed

Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S; Honig, Barry

2014-01-01

We present OnTheFly (http://bhapp.c2b2.columbia.edu/OnTheFly/index.php), a database comprising a systematic collection of transcription factors (TFs) of Drosophila melanogaster and their DNA-binding sites. TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided. All known preferred TF DNA-binding sites obtained from the B1H, DNase I and SELEX methodologies are presented. DNA shape parameters predicted for these sites are obtained from a high throughput server or from crystal structures of protein-DNA complexes where available. An important feature of the database is that all DNA-binding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology. OnTheFly thus provides a comprehensive view of TFs and their binding sites that will be a valuable resource for deciphering non-coding regulatory DNA.

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

Development of a web application for water resources based on open source software

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

2014-01-01

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

MyLabStocks: a web-application to manage molecular biology materials

PubMed Central

Chuffart, Florent; Yvert, Gaël

2014-01-01

Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence. PMID:24643870

An open source, web based, simple solution for seismic data dissemination and collaborative research

NASA Astrophysics Data System (ADS)

Diviacco, Paolo

2005-06-01

Collaborative research and data dissemination in the field of geophysical exploration need network tools that can access large amounts of data from anywhere using any PC or workstation. Simple solutions based on a combination of Open Source software can be developed to address such requests, exploiting the possibilities offered by the web technologies, and at the same time avoiding the costs and inflexibility of commercial systems. A viable solution consists of MySQL for data storage and retrieval, CWP/SU and GMT for data visualisation and a scripting layer driven by PHP that allows users to access the system via an Apache web server. In the light of the experience building the on-line archive of seismic data of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), we describe the solutions and the methods adopted, with a view to stimulate both the attitude of network collaborative research of other institutions similar to ours, and the development of different applications.

BIRS – Bioterrorism Information Retrieval System

PubMed Central

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. Availability The database is freely available at http://www.bioterrorism.biowaves.org PMID:23390356

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

A simple and low-cost Internet-based teleconsultation system that could effectively solve the health care access problems in underserved areas of developing countries.

PubMed

Kuntalp, Mehmet; Akar, Orkun

2004-08-01

In many developing countries including Turkey, telemedicine systems are not in wide use due to the high cost and complexity of the required technology. Lack of these systems however has serious implications on patients who live in rural areas. The objective of this paper is to present a simple and economically affordable alternative to the current systems that would allow experts to easily access the medical data of their remote patients over the Internet. The system is developed in client-server architecture with a user-friendly graphical interface and various services are implemented as dynamic web pages based on PHP. The other key features of the system are its powerful security features and platform independency. An academic prototype is implemented and presented to the evaluation of a group of physicians. The results reveal that the system could find acceptance from the medical community and it could be an effective means of providing quality health care in developing countries.

Eating behaviors in obese children with pseudohypoparathyroidism type 1a: a cross-sectional study.

PubMed

Wang, Lulu; Shoemaker, Ashley H

2014-01-01

Children with pseudohypoparathyroidism type 1a (PHP-1a) develop early-onset obesity. These children have decreased resting energy expenditure but it is unknown if hyperphagia contributes to their obesity. We conducted a survey assessment of patients 2 to 12 years old with PHP-1a and matched controls using the Hyperphagia Questionnaire (HQ) and Children's Eating Behavior Questionnaire (CEBQ). Results of the PHP-1a group were also compared with an obese control group and normal weight sibling group. We enrolled 10 patients with PHP-1a and 9 matched controls. There was not a significant difference between the PHP-1a group and matched controls for total HQ score (p = 0.72), Behavior (p = 0.91), Drive (p = 0.48) or Severity (p = 0.73) subset scores. There was also no difference between the PHP-1a group and matched controls on the CEBQ. In a secondary analysis, the PHP-1a group was compared with obese controls (n = 30) and normal weight siblings (n = 6). Caregivers reported an increased interest in food before age 2 years in 6 of 10 PHP-1a patients (60%), 9 of 30 obese controls (30%) and none of the siblings (p = 0.04). The sibling group had a significantly lower Positive Eating Behavior score than the PHP-1a group (2.6 [2.4, 2.9] vs. 3.5 [3.1, 4.0], p < 0.01) and obese controls (2.6 [2.4, 2.9] vs. 3.4 [2.6, 3.8], p = 0.04), but there was not a significant difference between the PHP-1a and obese controls (p = 0.35). The sibling group had a lower Desire to Drink score than both the PHP-1a group (1.8 [1.6, 2.7] vs. 4.3 [3.3, 5.0], p < 0.01) and obese controls (1.8 [1.6, 2.7] vs. 3.3 [3.0, 4.0], p < 0.01) but there was not a significant difference between the PHP-1a and obese control Desire to Drink scores (p = 0.11). Patients with PHP-1a demonstrate hyperphagic symptoms similar to matched obese controls.

Eating behaviors in obese children with pseudohypoparathyroidism type 1a: a cross-sectional study

PubMed Central

2014-01-01

Background Children with pseudohypoparathyroidism type 1a (PHP-1a) develop early-onset obesity. These children have decreased resting energy expenditure but it is unknown if hyperphagia contributes to their obesity. Methods We conducted a survey assessment of patients 2 to 12 years old with PHP-1a and matched controls using the Hyperphagia Questionnaire (HQ) and Children’s Eating Behavior Questionnaire (CEBQ). Results of the PHP-1a group were also compared with an obese control group and normal weight sibling group. Results We enrolled 10 patients with PHP-1a and 9 matched controls. There was not a significant difference between the PHP-1a group and matched controls for total HQ score (p = 0.72), Behavior (p = 0.91), Drive (p = 0.48) or Severity (p = 0.73) subset scores. There was also no difference between the PHP-1a group and matched controls on the CEBQ. In a secondary analysis, the PHP-1a group was compared with obese controls (n = 30) and normal weight siblings (n = 6). Caregivers reported an increased interest in food before age 2 years in 6 of 10 PHP-1a patients (60%), 9 of 30 obese controls (30%) and none of the siblings (p = 0.04). The sibling group had a significantly lower Positive Eating Behavior score than the PHP-1a group (2.6 [2.4, 2.9] vs. 3.5 [3.1, 4.0], p < 0.01) and obese controls (2.6 [2.4, 2.9] vs. 3.4 [2.6, 3.8], p = 0.04), but there was not a significant difference between the PHP-1a and obese controls (p = 0.35). The sibling group had a lower Desire to Drink score than both the PHP-1a group (1.8 [1.6, 2.7] vs. 4.3 [3.3, 5.0], p < 0.01) and obese controls (1.8 [1.6, 2.7] vs. 3.3 [3.0, 4.0], p < 0.01) but there was not a significant difference between the PHP-1a and obese control Desire to Drink scores (p = 0.11). Conclusions Patients with PHP-1a demonstrate hyperphagic symptoms similar to matched obese controls. PMID:25337124

An application of second-order UV-derivative spectrophotometry for study of solvolysis of a novel fluocinolone acetonide ester

NASA Astrophysics Data System (ADS)

Markovic, Bojan; Vladimirov, Sote; Cudina, Olivera; Savic, Vladimir; Karljikovic-Rajic, Katarina

2010-02-01

A novel topical corticosteroid FA-21-PhP, 2-phenoxypropionate ester of fluocinolone acetonide, has been synthesized in order to investigate the possibility of decreasing systemic side effects. In this study model system for in vitro solvolytic reaction of FA-21-PhP has been analyzed in ethanol/water (90:10, v/v) with excess of sodium hydrogen carbonate. The selected conditions have been used as in vitro model for activation of corticosteroid C-21 ester prodrug. The second-order derivative spectrophotometric method (DS) using zero-crossing technique was developed for monitoring ternary mixture of solvolysis. Fluocinolone acetonide (FA) as a solvolyte was determined in the mixture in the concentration range 0.062-0.312 mM using amplitude 2D 274.96. Experimentally determined LOD value was 0.0295 mM. The accuracy of proposed DS method was confirmed with HPLC referent method. Peak area of parent ester FA-21-PhP was used for solvolysis monitoring to ensure the initial stage of changes. Linear relationship in HPLC assay for parent ester was obtained in the concentration range 0.054-0.54 mM, with experimentally determined LOD value of 0.0041 mM. Investigated solvolytic reaction in the presence of excess of NaHCO 3 proceeded via a pseudo-first-order kinetic with significant correlation coefficients 0.9891 and 0.9997 for DS and HPLC, respectively. The values of solvolysis rate constant calculated according to DS and HPLC methods are in good accordance 0.038 and 0.043 h -1, respectively.

DefEX: Hands-On Cyber Defense Exercise for Undergraduate Students

DTIC Science & Technology

2011-07-01

Injection, and 4) File Upload. Next, the students patched the associated flawed Perl and PHP Hypertext Preprocessor ( PHP ) code. Finally, students...underlying script. The Zora XSS vulnerability existed in a PHP file that echoed unfiltered user input back to the screen. To eliminate the...vulnerability, students filtered the input using the PHP htmlentities function and retested the code. The htmlentities function translates certain ambiguous

Health-related quality of life in patients with nonsurgical hypoparathyroidism and pseudohypoparathyroidism.

PubMed

Underbjerg, L; Sikjaer, T; Rejnmark, L

2018-03-09

Nonsurgical hypoparathyroidism (NS-HypoPT) and pseudohypoparathyroidism (PHP) are rare diseases, with a prevalence of 2/100.000 and 1/100.000, respectively. Only few studies on Quality of Life (QoL) among patients with Ns-HypoPT and PHP are available. We aimed to investigate the QoL among patients with Ns-HypoPT and PHP including information about education. A cohort study with patients identified from a previously epidemiological study. Fifty seven patients with Ns-HypoPT and 30 patients with PHP. The well-validated questionnaires SF-36v2 and WHO-5 Well Being Index. Results compared to norm-based material, disease-specific norm-based material and patients with postsurgical HypoPT RESULTS: SF36v2 showed a significantly reduced score in all eight subdomains in patients with NS-HypoPT compared with a norm-based population. PHP patients scored lower in five subdomains. Females were more affected than males. Compared with postsurgical HypoPT, Ns-HypoPT and PHP are compatible at most domains. At the domains Physical Function, Social Function and Mental Health, Ns-HypoPT and PHP patients scored significantly lower (P all  < .05). At the Mental Component Score, patients with Ns-HypoPT had a lower score compared with postsurgical HypoPT (P < .01). The overall WHO-5 Well Being Index score was comparable between groups (P = .45). No differences were seen comparing patients with postsurgical HypoPT and Ns-HypoPT (P = .68) or postsurgical HypoPT and PHP (P = .67). A WHO-5 score below 28 indicates depression (NS-HypoPT=7; PHP=3, P = .71), whereas a score between 28-50 suggesting poor emotional well-being (NS-HypoPT=19; PHP=5, P = .13). The remaining patients scored above 50 suggesting well-being. QoL is impaired equally among patients with Ns-HypoPT and PHP. © 2018 John Wiley & Sons Ltd.

On-demand rendering of an oblique slice through 3D volumetric data using JPEG2000 client-server framework

NASA Astrophysics Data System (ADS)

Joshi, Rajan L.

2006-03-01

In medical imaging, the popularity of image capture modalities such as multislice CT and MRI is resulting in an exponential increase in the amount of volumetric data that needs to be archived and transmitted. At the same time, the increased data is taxing the interpretation capabilities of radiologists. One of the workflow strategies recommended for radiologists to overcome the data overload is the use of volumetric navigation. This allows the radiologist to seek a series of oblique slices through the data. However, it might be inconvenient for a radiologist to wait until all the slices are transferred from the PACS server to a client, such as a diagnostic workstation. To overcome this problem, we propose a client-server architecture based on JPEG2000 and JPEG2000 Interactive Protocol (JPIP) for rendering oblique slices through 3D volumetric data stored remotely at a server. The client uses the JPIP protocol for obtaining JPEG2000 compressed data from the server on an as needed basis. In JPEG2000, the image pixels are wavelet-transformed and the wavelet coefficients are grouped into precincts. Based on the positioning of the oblique slice, compressed data from only certain precincts is needed to render the slice. The client communicates this information to the server so that the server can transmit only relevant compressed data. We also discuss the use of caching on the client side for further reduction in bandwidth requirements. Finally, we present simulation results to quantify the bandwidth savings for rendering a series of oblique slices.

A structural role for the PHP domain in E. coli DNA polymerase III

PubMed Central

2013-01-01

Background In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Results Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. Conclusions While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase. PMID:23672456

Chemosaturation with Percutaneous Hepatic Perfusion for Unresectable Isolated Hepatic Metastases from Sarcoma

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

Deneve, Jeremiah L., E-mail: Jeremiah.Deneve@Moffitt.org; Choi, Junsung; Gonzalez, Ricardo J.

Purpose: Treatment of patients with unresectable liver metastases is challenging. Regional therapies to the liver have been developed that maximize treatment of the localized disease process without systemic toxic adverse effects. We discuss the procedural aspects of liver chemosaturation with percutaneous hepatic perfusion (CS-PHP). Methods: We present as an illustration of this technique a case report of the treatment of unresectable metastatic leiomyosarcoma of the liver. Results: A randomized phase III trial for unresectable liver metastases from melanoma was recently completed comparing CS-PHP with melphalan vs. best alternative care (BAC). When compared with BAC, CS-PHP was associated with a significantmore » improvement in hepatic progression-free survival (8.0 months CS-PHP vs. 1.6 months BAC, p < 0.0001) and overall progression-free survival (6.7 months CS-PHP vs. 1.6 months BAC, p < 0.0001), respectively. On the basis of these results, and given our experience as one of the treating institutions for this phase III trial, we appealed for compassionate use of CS-PHP in a patient with isolated bilobar unresectable hepatic metastases from leiomyosarcoma. Four target lesions were identified and monitored to assess treatment response. A total of 4 CS-PHP procedures were performed, with a 25 % reduction in size of the largest lesion observed and 16 month hepatic progression-free survival. Toxicity was mild (neutropenia) and manageable on an outpatient basis. Conclusion: CS-PHP offers several advantages for unresectable hepatic sarcoma metastases. CS-PHP is minimally invasive and repeatable, and it has a predictable and manageable systemic toxicity profile. For appropriately selected patients, CS-PHP can delay tumor progression and could potentially improve survival.« less

Pseudohypoparathyroidism type Ib associated with novel duplications in the GNAS locus.

PubMed

Perez-Nanclares, Gustavo; Velayos, Teresa; Vela, Amaya; Muñoz-Torres, Manuel; Castaño, Luis

2015-01-01

Pseudohypoparathyroidism type 1b (PHP-Ib) is characterized by renal resistance to PTH (and, sometimes, a mild resistance to TSH) and absence of any features of Albright's hereditary osteodystrophy. Patients with PHP-Ib suffer of defects in the methylation pattern of the complex GNAS locus. PHP-Ib can be either sporadic or inherited in an autosomal dominant pattern. Whereas familial PHP-Ib is well characterized at the molecular level, the genetic cause of sporadic PHP-Ib cases remains elusive, although some molecular mechanisms have been associated with this subtype. The aim of the study was to investigate the molecular and imprinting defects in the GNAS locus in two unrelated patients with PHP-Ib. We have analyzed the GNAS locus by direct sequencing, Methylation-Specific Multiplex Ligation-dependent Probe Amplification, microsatellites, Quantitative Multiplex PCR of Short Fluorescent fragments and array-Comparative Genomic Hybridization studies in order to characterize two unrelated families with clinical features of PHP-Ib. We identified two duplications in the GNAS region in two patients with PHP-Ib: one of them, comprising ∼ 320 kb, occurred 'de novo' in the patient, whereas the other one, of ∼ 179 kb in length, was inherited from the maternal allele. In both cases, no other known genetic cause was observed. In this article, we describe the to-our-knowledge biggest duplications reported so far in the GNAS region. Both are associated to PHP-Ib, one of them occurring 'de novo' and the other one being maternally inherited.

Space Images for NASA JPL Android Version

NASA Technical Reports Server (NTRS)

Nelson, Jon D.; Gutheinz, Sandy C.; Strom, Joshua R.; Arca, Jeremy M.; Perez, Martin; Boggs, Karen; Stanboli, Alice

2013-01-01

This software addresses the demand for easily accessible NASA JPL images and videos by providing a user friendly and simple graphical user interface that can be run via the Android platform from any location where Internet connection is available. This app is complementary to the iPhone version of the application. A backend infrastructure stores, tracks, and retrieves space images from the JPL Photojournal and Institutional Communications Web server, and catalogs the information into a streamlined rating infrastructure. This system consists of four distinguishing components: image repository, database, server-side logic, and Android mobile application. The image repository contains images from various JPL flight projects. The database stores the image information as well as the user rating. The server-side logic retrieves the image information from the database and categorizes each image for display. The Android mobile application is an interfacing delivery system that retrieves the image information from the server for each Android mobile device user. Also created is a reporting and tracking system for charting and monitoring usage. Unlike other Android mobile image applications, this system uses the latest emerging technologies to produce image listings based directly on user input. This allows for countless combinations of images returned. The backend infrastructure uses industry-standard coding and database methods, enabling future software improvement and technology updates. The flexibility of the system design framework permits multiple levels of display possibilities and provides integration capabilities. Unique features of the software include image/video retrieval from a selected set of categories, image Web links that can be shared among e-mail users, sharing to Facebook/Twitter, marking as user's favorites, and image metadata searchable for instant results.

Implementation of the Algorithm for Congestion control in the Dynamic Circuit Network (DCN)

NASA Astrophysics Data System (ADS)

Nalamwar, H. S.; Ivanov, M. A.; Buddhawar, G. U.

2017-01-01

Transport Control Protocol (TCP) incast congestion happens when a number of senders work in parallel with the same server where the high bandwidth and low latency network problem occurs. For many data center network applications such as a search engine, heavy traffic is present on such a server. Incast congestion degrades the entire performance as packets are lost at a server side due to buffer overflow, and as a result, the response time becomes longer. In this work, we focus on TCP throughput, round-trip time (RTT), receive window and retransmission. Our method is based on the proactive adjust of the TCP receive window before the packet loss occurs. We aim to avoid the wastage of the bandwidth by adjusting its size as per the number of packets. To avoid the packet loss, the ICTCP algorithm has been implemented in the data center network (ToR).

MERRA/AS: The MERRA Analytic Services Project Interim Report

NASA Technical Reports Server (NTRS)

Schnase, John; Duffy, Dan; Tamkin, Glenn; Nadeau, Denis; Thompson, Hoot; Grieg, Cristina; Luczak, Ed; McInerney, Mark

2013-01-01

MERRA AS is a cyberinfrastructure resource that will combine iRODS-based Climate Data Server (CDS) capabilities with Coudera MapReduce to serve MERRA analytic products, store the MERRA reanalysis data collection in an HDFS to enable parallel, high-performance, storage-side data reductions, manage storage-side driver, mapper, reducer code sets and realized objects for users, and provide a library of commonly used spatiotemporal operations that can be composed to enable higher-order analyses.

Technology insertion of a COTS RAID server as an image buffer in the image chain of the Defense Mapping Agency's Digital Production System

NASA Astrophysics Data System (ADS)

Mehring, James W.; Thomas, Scott D.

1995-11-01

The Data Services Segment of the Defense Mapping Agency's Digital Production System provides a digital archive of imagery source data for use by DMA's cartographic user's. This system was developed in the mid-1980's and is currently undergoing modernization. This paper addresses the modernization of the imagery buffer function that was performed by custom hardware in the baseline system and is being replaced by a RAID Server based on commercial off the shelf (COTS) hardware. The paper briefly describes the baseline DMA image system and the modernization program, that is currently under way. Throughput benchmark measurements were made to make design configuration decisions for a commercial off the shelf (COTS) RAID Server to perform as system image buffer. The test program began with performance measurements of the RAID read and write operations between the RAID arrays and the server CPU for RAID levels 0, 5 and 0+1. Interface throughput measurements were made for the HiPPI interface between the RAID Server and the image archive and processing system as well as the client side interface between a custom interface board that provides the interface between the internal bus of the RAID Server and the Input- Output Processor (IOP) external wideband network currently in place in the DMA system to service client workstations. End to end measurements were taken from the HiPPI interface through the RAID write and read operations to the IOP output interface.

Reduced prokaryotic heterotrophic production at in situ pressure conditions in the dark ocean

NASA Astrophysics Data System (ADS)

Amano-Sato, Chie; Sintes, Eva; Reinthaler, Thomas; Utsumi, Motoo; Herndl, Gerhard J.

2017-04-01

Prokaryotic heterotrophic production (PHP) is a key process in the ocean's biological carbon cycle. About 50% of the oceanic PHP takes place in the dark ocean characterized by low temperature and high hydrostatic pressure, which increases by 1 MPa (10 atm) every 100 m depth. However, rate measurements of PHP are usually performed under atmospheric pressure conditions. Yet, the difference in pressure conditions and the handling of the samples on board may introduce biases in the PHP measurements. To determine PHP at in situ conditions, we developed an in situ microbial incubator (ISMI) designed to autonomously sample and incubate seawater down to a depth of 4000 m. Natural prokaryotic communities from the North Atlantic and Pacific Oceans were incubated in the ISMI with 5 nM 3H-leucine at different depths ranging between 10 and 3200 m. For comparison, atmospheric pressure incubations at in situ temperature were also conducted. PHP and single cell activity assessed by microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization (MICRO-CARD-FISH) were determined. PHP obtained under in situ pressure conditions was generally lower than under atmospheric pressure conditions, suggesting that incubation under atmospheric pressure on board stimulates activity of dark ocean prokaryotes. The ratio between the bulk PHP obtained under in situ and under atmospheric pressure conditions decreased with depth. Moreover, MICRO-CARD-FISH revealed that some specific prokaryotic groups are apparently more affected by the hydrostatic pressure condition than others. Our results suggest that PHP in the dark ocean might be lower than assumed based on measurements under surface pressure conditions.

Effectiveness of the polysaccharide hemostatic powder in non-variceal upper gastrointestinal bleeding: Using propensity score matching.

PubMed

Park, Jun Chul; Kim, Yeong Jin; Kim, Eun Hye; Lee, Jinae; Yang, Hyun Su; Kim, Eun Hwa; Hahn, Kyu Yeon; Shin, Sung Kwan; Lee, Sang Kil; Lee, Yong Chan

2018-02-07

Recently, the application of hemostatic powder to the bleeding site has been used to treat active upper gastrointestinal bleeding (UGIB). We aimed to assess the effectiveness of the polysaccharide hemostatic powder (PHP) in patients with non-variceal UGIB. We reviewed prospectively collected 40 patients with UGIB treated with PHP therapy between April 2016 and January 2017 (PHP group) and 303 patients with UGIB treated with conventional therapy between April 2012 and October 2014 (conventional therapy group). We compared the rate of successful hemostasis and the rebleeding between the two groups after as well as before propensity score matching using the Glasgow-Blatchford score and Forrest classification. Thirty patients treated with the PHP and 60 patients treated with conventional therapy were included in the matched groups. Baseline patient characteristics including comorbidities, vital signs, and bleeding scores were similar in the matched groups. The rate of immediate hemostasis and 7-day and 30-day rebleeding were also similar in the two groups before and after matching. In the subgroup analysis, no significant differences in immediate hemostasis or rebleeding rate were noted between PHP in monotherapy and PHP combined with a conventional hemostatic method. At 30 days after the therapy, there were no significant PHP-related complications or mortality. Given its safety, the PHP proved feasible for endoscopic treatment of UGIB, having similar effectiveness as that of conventional therapy. The PHP may become a promising hemostatic method for non-variceal UGIB. © 2018 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Is the risk of primary hyperparathyroidism increased in patients with untreated breast cancer?

PubMed

Belardi, V; Fiore, E; Giustarini, E; Muller, I; Sabatini, S; Rosellini, V; Seregni, E; Agresti, R; Marcocci, C; Vitti, P; Giani, C

2013-05-01

An increased frequency of primary hyperparathyroidism (PHP) has been reported in patients with treated breast cancer (BC). PHP has been found in about 7% of BC patients after surgery and radio-, chemio- or hormonal therapy. To evaluate the frequency of PHP in untreated BC patients. We evaluated 186 women with BC and 233 women with thyroid cancer (TC, no.=122) or benign thyroid diseases (BTD, no.=111). In all patients, serum calcium, albumin, PTH, and 25-hydroxyvitamin D (25-OH vitD) were measured before any treatment. Serum calcium concentrations were significantly higher in BC than in TC and BTD groups (median values 9.5 mg/dl, 9.3 mg/dl and 9.3 mg/dl, respectively) but, according to a logistic regression model, calcium was not significantly different between the 3 groups when age was taken into account. In all patients, serum calcium was in the normal range, indicating that no case of overt PHP was present. Five patients (1 in BC, 2 in TC, and 2 in BDT groups) had serum calcium close to the upper limit of normal range, high PTH and low 25-OH vitD, indicating a possible PHP with hypercalcemia masked by concomitant 25-OH vitD deficiency. In untreated BC group, no patient had overt PHP and 1/186 (0.5%) presented a possible PHP masked by 25-OH vitD deficiency, a PHP frequency much lower than that observed in treated BC patients. These data suggest that the treatments of BC may be responsible for the increased frequency of PHP reported in previous studies.

Exclusion of the GNAS Locus in PHP-Ib Patients With Broad GNAS Methylation Changes: Evidence for an Autosomal Recessive Form of PHP-Ib?

PubMed Central

Fernández-Rebollo, Eduardo; de Nanclares, Guiomar Pérez; Lecumberri, Beatriz; Turan, Serap; Anda, Emma; Pérez-Nanclares, Gustavo; Feig, Denice; Nik-Zainal, Serena; Bastepe, Murat; Jüppner, Harald

2013-01-01

Most patients with autosomal dominant pseudohypoparathyroidism type Ib (AD-PHP-Ib) carry maternally inherited microdeletions upstream of GNAS that are associated with loss of methylation restricted to GNAS exon A/B. Only few AD-PHP-Ib patients carry microdeletions within GNAS that are associated with loss of all maternal methylation imprints. These epigenetic changes are often indistinguishable from those observed in patients affected by an apparently sporadic PHP-Ib form that has not yet been defined genetically. We have now investigated six female patients affected by PHP-Ib (four unrelated and two sisters) with complete or almost complete loss of GNAS methylation, whose healthy children (11 in total) showed no epigenetic changes at this locus. Analysis of several microsatellite markers throughout the 20q13 region made it unlikely that PHP-Ib is caused in these patients by large deletions involving GNAS or by paternal uniparental isodisomy or heterodisomy of chromosome 20 (patUPD20). Microsatellite and single-nucleotide variation (SNV) data revealed that the two affected sisters share their maternally inherited GNAS alleles with unaffected relatives that lack evidence for abnormal GNAS methylation, thus excluding linkage to this locus. Consistent with these findings, healthy children of two unrelated sporadic PHP-Ib patients had inherited different maternal GNAS alleles, also arguing against linkage to this locus. Based on our data, it appears plausible that some forms of PHP-Ib are caused by homozygous or compound heterozygous mutation(s) in an unknown gene involved in establishing or maintaining GNAS methylation. PMID:21523828

[Comparison of Preferential Hyperacuity Perimeter (PHP) test and Amsler grid test in the diagnosis of different stages of age-related macular degeneration].

PubMed

Kampmeier, J; Zorn, M M; Lang, G K; Botros, Y T; Lang, G E

2006-09-01

Age-related macular degeneration (ARMD) is the leading cause of blindness in people over 65 years of age. A rapid loss of vision occurs especially in cases with choroidal neovascularisation. Early detection of ARMD and timely treatment are mandatory. We have prospectively studied the results of two diagnostic self tests for the early detection of metamorphopsia and scotoma, the PHP test and the Amsler grid test, in different stages of ARMD. Patients with ARMD and best corrected visual acuity of 6/30 or better (Snellen charts) were examined with a standardised protocol, including supervised Amsler grid examination and PHP, a new device for metamorphopsia or scotoma measurement, based on the hyperacuity phenomenon in the central 14 degrees of the visual field. The stages of ARMD were independently graded in a masked fashion by stereoscopic ophthalmoscopy, stereoscopic fundus colour photographs, fluorescein angiography, and OCT. The patients were subdivided into 3 non-neovascular groups [early, late (RPE atrophy > 175 microm) and geographic atrophy], a neovascular group (classic and occult CNV) and an age-matched control group (healthy volunteers). 140 patients, with ages ranging from 50 to 90 years (median 68 years), were included in the study. Best corrected visual acuity ranged from 6/30 to 6/6 with a median of 6/12. 95 patients were diagnosed as non-neovascular ARMD. Thirty eyes had early ARMD (9 were tested positive by the PHP test and 9 by the Amsler grid test), and 50 late ARMD (positive: PHP test 23, Amsler grid test 26). The group with geographic atrophy consisted of 15 eyes (positive: PHP test 13, Amsler grid test 10). Forty-five patients presented with neovascular ARMD (positive: PHP test 38, Amsler grid test 36), 34 volunteers served as control group (positive: PHP test 1, Amsler grid test 5). The PHP and Amsler grid tests revealed comparable results detecting metamorphopsia and scotoma in early ARMD (30 vs. 30 %) and late ARMD (46 vs. 52 %). However, the PHP test more often revealed disease-related functional changes in the groups of geographic atrophy (87 vs. 67 %) and neovascular ARMD (84 vs. 80 %). This implies that the PHP and Amsler grid self tests are useful tools for detection of ARMD and that the PHP test has a greater sensitivity in the groups of geographic atrophy and neovascular AMD.

Research on realization scheme of interactive voice response (IVR) system

NASA Astrophysics Data System (ADS)

Jin, Xin; Zhu, Guangxi

2003-12-01

In this paper, a novel interactive voice response (IVR) system is proposed, which is apparently different from the traditional. Using software operation and network control, the IVR system is presented which only depends on software in the server in which the system lies and the hardware in network terminals on user side, such as gateway (GW), personal gateway (PG), PC and so on. The system transmits the audio using real time protocol (RTP) protocol via internet to the network terminals and controls flow using finite state machine (FSM) stimulated by H.245 massages sent from user side and the system control factors. Being compared with other existing schemes, this IVR system results in several advantages, such as greatly saving the system cost, fully utilizing the existing network resources and enhancing the flexibility. The system is capable to be put in any service server anywhere in the Internet and even fits for the wireless applications based on packet switched communication. The IVR system has been put into reality and passed the system test.

A Functional Data Model Realized: LaTiS Deployments

NASA Astrophysics Data System (ADS)

Baltzer, T.; Lindholm, D. M.; Wilson, A.; Putnam, B.; Christofferson, R.; Flores, N.; Roughton, S.

2016-12-01

At prior AGU annual meetings, members of the University of Colorado Laboratory for Atmospheric and Space Physics (LASP) Web Team have described work being done on a functional data model and the software framework called LaTis, that implements it. This presentation describes the evolution of LaTiS and presents several instances of LaTiS in operation today that demonstrate its various capabilities. With LaTiS, serving a new dataset can be a simple as adding a small descriptor file. From providing access to spacecraft telemetry data in a variety of forms for the LASP missions operation group, to providing access to scientific data for the MMS and MAVEN science teams, to server-side functionality such as fusing satellite visible and infrared data along with forecast model data into a Geotiff image for situational awareness purposes, LaTiS has demonstrated itself as a highly flexible, standards-based framework that provides easy data access, dynamic reformatting, and customizable server side functionality.

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

A patient privacy protection scheme for medical information system.

PubMed

Lu, Chenglang; Wu, Zongda; Liu, Mingyong; Chen, Wei; Guo, Junfang

2013-12-01

In medical information systems, there are a lot of confidential information about patient privacy. It is therefore an important problem how to prevent patient's personal privacy information from being disclosed. Although traditional security protection strategies (such as identity authentication and authorization access control) can well ensure data integrity, they cannot prevent system's internal staff (such as administrators) from accessing and disclosing patient privacy information. In this paper, we present an effective scheme to protect patients' personal privacy for a medical information system. In the scheme, privacy data before being stored in the database of the server of a medical information system would be encrypted using traditional encryption algorithms, so that the data even if being disclosed are also difficult to be decrypted and understood. However, to execute various kinds of query operations over the encrypted data efficiently, we would also augment the encrypted data with additional index, so as to process as much of the query as possible at the server side, without the need to decrypt the data. Thus, in this paper, we mainly explore how the index of privacy data is constructed, and how a query operation over privacy data is translated into a new query over the corresponding index so that it can be executed at the server side immediately. Finally, both theoretical analysis and experimental evaluation validate the practicality and effectiveness of our proposed scheme.

Network oriented radiological and medical archive

NASA Astrophysics Data System (ADS)

Ferraris, M.; Frixione, P.; Squarcia, S.

2001-10-01

In this paper the basic ideas of NORMA (Network Oriented Radiological and Medical Archive) are discussed. NORMA is an original project built by a team of physicists in collaboration with radiologists in order to select the best Treatment Planning in radiotherapy. It allows physicians and health physicists, working in different places, to discuss on interesting clinical cases visualizing the same diagnostic images, at the same time, and highlighting zones of interest (tumors and organs at risk). NORMA has a client/server architecture in order to be platform independent. Applying World Wide Web technologies, it can be easily used by people with no specific computer knowledge providing a verbose help to guide the user through the right steps of execution. The client side is an applet while the server side is a Java application. In order to optimize execution the project also includes a proprietary protocol, lying over TCP/IP suite, that organizes data exchanges and control messages. Diagnostic images are retrieved from a relational database or from a standard DICOM (Digital Images and COmmunications in Medicine) PACS through the DICOM-WWW gateway allowing connection of the usual Web browsers, used by the NORMA system, to DICOM applications via the HTTP protocol. Browser requests are sent to the gateway from the Web server through CGI (Common Gateway Interface). DICOM software translates the requests in DICOM messages and organizes the communication with the remote DICOM Application.

Lsiviewer 2.0 - a Client-Oriented Online Visualization Tool for Geospatial Vector Data

NASA Astrophysics Data System (ADS)

Manikanta, K.; Rajan, K. S.

2017-09-01

Geospatial data visualization systems have been predominantly through applications that are installed and run in a desktop environment. Over the last decade, with the advent of web technologies and its adoption by Geospatial community, the server-client model for data handling, data rendering and visualization respectively has been the most prevalent approach in Web-GIS. While the client devices have become functionally more powerful over the recent years, the above model has largely ignored it and is still in a mode of serverdominant computing paradigm. In this paper, an attempt has been made to develop and demonstrate LSIViewer - a simple, easy-to-use and robust online geospatial data visualisation system for the user's own data that harness the client's capabilities for data rendering and user-interactive styling, with a reduced load on the server. The developed system can support multiple geospatial vector formats and can be integrated with other web-based systems like WMS, WFS, etc. The technology stack used to build this system is Node.js on the server side and HTML5 Canvas and JavaScript on the client side. Various tests run on a range of vector datasets, upto 35 MB, showed that the time taken to render the vector data using LSIViewer is comparable to a desktop GIS application, QGIS, over an identical system.

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pistachio hull water-soluble polysaccharides as a novel prebiotic agent.

PubMed

Akbari-Alavijeh, Safoura; Soleimanian-Zad, Sabihe; Sheikh-Zeinoddin, Mahmoud; Hashmi, Sarwar

2018-02-01

We isolated and characterized pistachio hull polysaccharides (PHP). The PHP was a heteropolysaccharide mainly contained 75.50% (w/w) total sugar and 9.51% (w/w) uronic acid. As determined by GPC analysis, the polysaccharide with a molecular weight of 3.71×10 6 D (83.2%) was the most dominant fraction. Moreover, HPLC analysis indicated that PHP was predominantly composed of xylose, glucose, arabinose, and fructose with a molar ratio of 1.00:2.50:19.67:28.81. FT-IR and NMR analysis also confirmed the results obtained by HPLC and characterized preliminary structure features of the PHP. Functional properties of the PHP including water holding capacity (WHC: 2.44±0.05g water/g DM), and oil holding capacity (OHC: 11.53±0.04g oil/g DM) were significant compared to inulin used as reference prebiotic (p<0.01). Furthermore, the PHP remained 94.37% undigested in the simulated digestion process and stimulated the growth of L. plantarum PTCC 1896 and L. rhamnosus GG and increased the acetate, propionate and butyrate production over inulin in vitro. Totally, the PHP showed a considerable prebiotic capability and high WHC, OHC suggesting that the PHP is a potent pharmaceutical with good technological properties which can be used in food and drug industries. Copyright © 2017 Elsevier B.V. All rights reserved.

Spinal cord compression in pseudohypoparathyroidism.

PubMed

Roberts, Timothy T; Khasnavis, Siddharth; Papaliodis, Dean N; Citone, Isabella; Carl, Allen L

2013-12-01

Spinal cord compression associated with pseudohypoparathyroidism (PHP) is an increasingly reported sequelae of the underlying metabolic syndrome. The association of neurologic dysfunction with PHP is not well appreciated. We believe this to be secondary to a combination of underlying congenital stenosis, manifest by short pedicles secondary to premature physeal closure, and hypertrophic ossification of the vertebral bony and ligamentous complexes. The purpose of this case report is to review the case of spinal stenosis in a child with PHP Type Ia. We are aware of only eight published reports of patients with PHP Type Ia and spinal stenosis-there are only two previously known cases of pediatric spinal stenosis secondary to PHP. This is a case report detailing the symptoms, diagnosis, interventions, complications, and ultimate outcomes of a pediatric patient undergoing spinal decompression and fusion for symptomatic stenosis secondary to PHP Type Ia. Literature search was reviewed regarding the reports of spinal stenosis and PHP, and the results are culminated and discussed. We report on a 14-year-old obese male with PHP and progressive lower extremity weakness secondary to congenital spinal stenosis. Examination revealed functional upper extremities with spastic paraplegia of bilateral lower extremities. The patient's neurologic function was cautiously monitored, but he deteriorated to a bed-bound state, preoperatively. The patient's chart was reviewed, summarized, and presented. Literature was searched using cross-reference of PHP and the terms "spinal stenosis," "myelopathy", "myelopathic," and "spinal cord compression." All relevant case reports were reviewed, and the results are discussed herein. The patient underwent decompression and instrumented fusion of T2-T11. He improved significantly with regard to lower extremity function, achieving unassisted ambulation function after extensive rehabilitation. Results from surgical decompression in previously reported cases are mixed, ranging from full recovery to iatrogenic paraplegia. The association of neurologic dysfunction with PHP is not well appreciated. It is important to highlight this rare association. Surgical decompression in patients with PHP yields mixed results but may be of greatest efficacy in younger patients who receive early intervention. Copyright © 2013 Elsevier Inc. All rights reserved.

SciServer: An Online Collaborative Environment for Big Data in Research and Education

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Souter, Barbara; Lemson, Gerard; Taghizadeh-Popp, Manuchehr

2017-01-01

For the past year, SciServer Compute (http://compute.sciserver.org) has offered access to big data resources running within server-side Docker containers. Compute has allowed thousands of researchers to bring advanced analysis to big datasets like the Sloan Digital Sky Survey and others, while keeping the analysis close to the data for better performance and easier read/write access. SciServer Compute is just one part of the SciServer system being developed at Johns Hopkins University, which provides an easy-to-use collaborative research environment for astronomy and many other sciences.SciServer enables these collaborative research strategies using Jupyter notebooks, in which users can write their own Python and R scripts and execute them on the same server as the data. We have written special-purpose libraries for querying, reading, and writing data. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files.SciServer Compute’s virtual research environment has grown with the addition of task management and access control functions, allowing collaborators to share both data and analysis scripts securely across the world. These features also open up new possibilities for education, allowing instructors to share datasets with students and students to write analysis scripts to share with their instructors. We are leveraging these features into a new system called “SciServer Courseware,” which will allow instructors to share assignments with their students, allowing students to engage with big data in new ways.SciServer has also expanded to include more datasets beyond the Sloan Digital Sky Survey. A part of that growth has been the addition of the SkyQuery component, which allows for simple, fast cross-matching between very large astronomical datasets.Demos, documentation, and more information about all these resources can be found at www.sciserver.org.

Coagulase-negative staphylococci isolated from ocular wound infections after laser refractive surgery: attachment to and accumulation on soft contact lenses.

PubMed

Faghri, Jamshid; Razavi, Mohamad Reza

2009-03-01

Disposable soft contact lenses that are commonly used after laser refractive surgery are known to be colonized by bacteria and play a key role in Bacterial Keraitis (BK) pathogenesis. Coagulase-negative staphylococci (CoNS) have been found to be the most common pathogen involved in this postoperative infection. In this study a rapid and a simple assay was developed for studying attachment and accumulation of CoNS on soft contact lenses in vitro using [3H] thymidine. Thirty-five isolates of CoNS were obtained from 27 laser refractive surgery patients. Twenty-five of these thirty-five CoNS were isolated in multiple cultures. Ten CoNS were isolated in cultures from patients who underwent reoperation. The assay was optimized using a biofilm-producing strain, S. epidermidis RP62A, which was subcultured overnight at 37 degrees C on blood agar medium. Quantitative determination of biofilm production was tested. Presence of the genes icaADB and icaD was determined in all isolates. All isolates were biochemically analyzed using the Phene Plate (PhP) system modified for typing of CoNS. The CoNS isolates were further characterized to species level using ID32Staph.Mann-Whitney rank sum test and chi-square test were used to identify statistical differences in adherence, index, antibiotic susceptibility patterns, and biofilm production or presence of the ica operon between clinically significant isolates and non-postoperative BK isolates. No differences in attachment and accumulation were found between isolates causing BK after laser refractive surgery and contaminant isolates. In addition, there were no differences in the distribution of the ica operon between the two groups, as determined by polymerase chain reaction. Nevertheless, the ability to produce biofilm was found to be present significantly more frequently among BK isolates than among non-postoperative BK isolates. This study shows that the method using radioactive thymidine to analyze adherence of CoNS to soft contact lenses enables detection of differences in the adherence patterns of individual isolates.

Performance evaluation of a distance learning program.

PubMed

Dailey, D J; Eno, K R; Brinkley, J F

1994-01-01

This paper presents a performance metric which uses a single number to characterize the response time for a non-deterministic client-server application operating over the Internet. When applied to a Macintosh-based distance learning application called the Digital Anatomist Browser, the metric allowed us to observe that "A typical student doing a typical mix of Browser commands on a typical data set will experience the same delay if they use a slow Macintosh on a local network or a fast Macintosh on the other side of the country accessing the data over the Internet." The methodology presented is applicable to other client-server applications that are rapidly appearing on the Internet.

Do Pneumococcal Conjugate Vaccines Represent Good Value for Money in a Lower-Middle Income Country? A Cost-Utility Analysis in the Philippines.

PubMed

Haasis, Manuel Alexander; Ceria, Joyce Anne; Kulpeng, Wantanee; Teerawattananon, Yot; Alejandria, Marissa

2015-01-01

The objective of this study is to assess the value for money of introducing pneumococcal conjugate vaccines as part of the immunization program in a lower-middle income country, the Philippines, which is not eligible for GAVI support and lower vaccine prices. It also includes the newest clinical evidence evaluating the efficacy of PCV10, which is lacking in other previous studies. A cost-utility analysis was conducted. A Markov simulation model was constructed to examine the costs and consequences of PCV10 and PCV13 against the current scenario of no PCV vaccination for a lifetime horizon. A health system perspective was employed to explore different funding schemes, which include universal or partial vaccination coverage subsidized by the government. Results were presented as incremental cost-effectiveness ratios (ICERs) in Philippine peso (Php) per QALY gained (1 USD = 44.20 Php). Probabilistic sensitivity analysis was performed to determine the impact of parameter uncertainty. With universal vaccination at a cost per dose of Php 624 for PCV10 and Php 700 for PCV13, both PCVs are cost-effective compared to no vaccination given the ceiling threshold of Php 120,000 per QALY gained, yielding ICERs of Php 68,182 and Php 54,510 for PCV10 and PCV13, respectively. Partial vaccination of 25% of the birth cohort resulted in significantly higher ICER values (Php 112,640 for PCV10 and Php 84,654 for PCV13) due to loss of herd protection. The budget impact analysis reveals that universal vaccination would cost Php 3.87 billion to 4.34 billion per annual, or 1.6 to 1.8 times the budget of the current national vaccination program. The inclusion of PCV in the national immunization program is recommended. PCV13 achieved better value for money compared to PCV10. However, the affordability and sustainability of PCV implementation over the long-term should be considered by decision makers.

Social support, acculturation, and optimism: understanding positive health practices in Asian American college students.

PubMed

Ayres, Cynthia G; Mahat, Ganga

2012-07-01

This study developed and tested a theory to better understand positive health practices (PHP) among Asian Americans aged 18 to 21 years. It tested theoretical relationships postulated between PHP and (a) social support (SS), (b) optimism, and (c) acculturation, and between SS and optimism and acculturation. Optimism and acculturation were also tested as possible mediators in the relationship between SS and PHP. A correlational study design was used. A convenience sample of 163 Asian college students in an urban setting completed four questionnaires assessing SS, PHP, optimism, and acculturation and one demographic questionnaire. There were statistically significant positive relationships between SS and optimism with PHP, between acculturation and PHP, and between optimism and SS. Optimism mediated the relationship between SS and PHP, whereas acculturation did not. Findings extend knowledge regarding these relationships to a defined population of Asian Americans aged 18 to 21 years. Findings contribute to a more comprehensive knowledge base regarding health practices among Asian Americans. The theoretical and empirical findings of this study provide the direction for future research as well. Further studies need to be conducted to identify and test other mediators in order to better understand the relationship between these two variables.

GLobal Integrated Design Environment

NASA Technical Reports Server (NTRS)

Kunkel, Matthew; McGuire, Melissa; Smith, David A.; Gefert, Leon P.

2011-01-01

The GLobal Integrated Design Environment (GLIDE) is a collaborative engineering application built to resolve the design session issues of real-time passing of data between multiple discipline experts in a collaborative environment. Utilizing Web protocols and multiple programming languages, GLIDE allows engineers to use the applications to which they are accustomed in this case, Excel to send and receive datasets via the Internet to a database-driven Web server. Traditionally, a collaborative design session consists of one or more engineers representing each discipline meeting together in a single location. The discipline leads exchange parameters and iterate through their respective processes to converge on an acceptable dataset. In cases in which the engineers are unable to meet, their parameters are passed via e-mail, telephone, facsimile, or even postal mail. The result of this slow process of data exchange would elongate a design session to weeks or even months. While the iterative process remains in place, software can now exchange parameters securely and efficiently, while at the same time allowing for much more information about a design session to be made available. GLIDE is written in a compilation of several programming languages, including REALbasic, PHP, and Microsoft Visual Basic. GLIDE client installers are available to download for both Microsoft Windows and Macintosh systems. The GLIDE client software is compatible with Microsoft Excel 2000 or later on Windows systems, and with Microsoft Excel X or later on Macintosh systems. GLIDE follows the Client-Server paradigm, transferring encrypted and compressed data via standard Web protocols. Currently, the engineers use Excel as a front end to the GLIDE Client, as many of their custom tools run in Excel.

Exclusion of the GNAS locus in PHP-Ib patients with broad GNAS methylation changes: evidence for an autosomal recessive form of PHP-Ib?

PubMed

Fernández-Rebollo, Eduardo; Pérez de Nanclares, Guiomar; Lecumberri, Beatriz; Turan, Serap; Anda, Emma; Pérez-Nanclares, Gustavo; Feig, Denice; Nik-Zainal, Serena; Bastepe, Murat; Jüppner, Harald

2011-08-01

Most patients with autosomal dominant pseudohypoparathyroidism type Ib (AD-PHP-Ib) carry maternally inherited microdeletions upstream of GNAS that are associated with loss of methylation restricted to GNAS exon A/B. Only few AD-PHP-Ib patients carry microdeletions within GNAS that are associated with loss of all maternal methylation imprints. These epigenetic changes are often indistinguishable from those observed in patients affected by an apparently sporadic PHP-Ib form that has not yet been defined genetically. We have now investigated six female patients affected by PHP-Ib (four unrelated and two sisters) with complete or almost complete loss of GNAS methylation, whose healthy children (11 in total) showed no epigenetic changes at this locus. Analysis of several microsatellite markers throughout the 20q13 region made it unlikely that PHP-Ib is caused in these patients by large deletions involving GNAS or by paternal uniparental isodisomy or heterodisomy of chromosome 20 (patUPD20). Microsatellite and single-nucleotide variation (SNV) data revealed that the two affected sisters share their maternally inherited GNAS alleles with unaffected relatives that lack evidence for abnormal GNAS methylation, thus excluding linkage to this locus. Consistent with these findings, healthy children of two unrelated sporadic PHP-Ib patients had inherited different maternal GNAS alleles, also arguing against linkage to this locus. Based on our data, it appears plausible that some forms of PHP-Ib are caused by homozygous or compound heterozygous mutation(s) in an unknown gene involved in establishing or maintaining GNAS methylation. Copyright © 2011 American Society for Bone and Mineral Research.

Evaluation of a novel electronic genetic screening and clinical decision support tool in prenatal clinical settings.

PubMed

Edelman, Emily A; Lin, Bruce K; Doksum, Teresa; Drohan, Brian; Edelson, Vaughn; Dolan, Siobhan M; Hughes, Kevin; O'Leary, James; Vasquez, Lisa; Copeland, Sara; Galvin, Shelley L; DeGroat, Nicole; Pardanani, Setul; Gregory Feero, W; Adams, Claire; Jones, Renee; Scott, Joan

2014-07-01

"The Pregnancy and Health Profile" (PHP) is a free prenatal genetic screening and clinical decision support (CDS) software tool for prenatal providers. PHP collects family health history (FHH) during intake and provides point-of-care risk assessment for providers and education for patients. This pilot study evaluated patient and provider responses to PHP and effects of using PHP in practice. PHP was implemented in four clinics. Surveys assessed provider confidence and knowledge and patient and provider satisfaction with PHP. Data on the implementation process were obtained through semi-structured interviews with administrators. Quantitative survey data were analyzed using Chi square test, Fisher's exact test, paired t tests, and multivariate logistic regression. Open-ended survey questions and interviews were analyzed using qualitative thematic analysis. Of the 83% (513/618) of patients that provided feedback, 97% felt PHP was easy to use and 98% easy to understand. Thirty percent (21/71) of participating physicians completed both pre- and post-implementation feedback surveys [13 obstetricians (OBs) and 8 family medicine physicians (FPs)]. Confidence in managing genetic risks significantly improved for OBs on 2/6 measures (p values ≤0.001) but not for FPs. Physician knowledge did not significantly change. Providers reported value in added patient engagement and reported mixed feedback about the CDS report. We identified key steps, resources, and staff support required to implement PHP in a clinical setting. To our knowledge, this study is the first to report on the integration of patient-completed, electronically captured and CDS-enabled FHH software into primary prenatal practice. PHP is acceptable to patients and providers. Key to successful implementation in the future will be customization options and interoperability with electronic health records.

A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity

PubMed Central

Wahba, Alexander S.; Esmaeili, Abbasali; Damha, Masad J.; Hudson, Robert H. E.

2010-01-01

6-Phenylpyrrolocytidine (PhpC), a structurally conservative and highly fluorescent cytidine analog, was incorporated into oligoribonucleotides. The PhpC-containing RNA formed native-like duplex structures with complementary DNA or RNA. The PhpC-modification was found to act as a sensitive reporter group being non-disruptive to structure and the enzymatic activity of RNase H. A RNA/DNA hybrid possessing a single PhpC insert was an excellent substrate for HIV-1 RT Ribonuclease H and rapidly reported cleavage of the RNA strand with a 14-fold increase in fluorescence intensity. The PhpC-based assay for RNase H was superior to the traditional molecular beacon approach in terms of responsiveness, rapidity and ease (single label versus dual). Furthermore, the PhpC-based assay is amenable to high-throughput microplate assay format and may form the basis for a new screen for inhibitors of HIV-RT RNase H. PMID:19933258

Theoretical research of helium pulsating heat pipe under steady state conditions

NASA Astrophysics Data System (ADS)

Xu, D.; Liu, H. M.; Li, L. F.; Huang, R. J.; Wang, W.

2015-12-01

As a new-type heat pipe, pulsating heat pipe (PHP) has several outstanding features, such as great heat transport ability, strong adjustability, small size and simple construction. PHP is a complex two-phase flow system associated with many physical subjects and parameters, which utilizes the pressure and temperature changes in volume expansion and contraction during phase changes to excite the pulsation motion of liquid plugs and vapor bubbles in the capillary tube between the evaporator and the condenser. At present time, some experimental investigation of helium PHP have been done. However, theoretical research of helium PHP is rare. In this paper, the physical and mathematical models of operating mechanism for helium PHP under steady state are established based on the conservation of mass, momentum, and energy. Several important parameters are correlated and solved, including the liquid filling ratio, flow velocity, heat power, temperature, etc. Based on the results, the operational driving force and flow resistances of helium PHP are analysed, and the flow and heat transfer is further studied.

77 FR 21103 - Changes in Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... Maricopa County, index.php/arizona/ Buckeye, 530 East 2801 West Durango maricopa-county/. Monroe Avenue...-09- Chairman, Maricopa Maricopa County, index.php/arizona/ 3299P). County Board of 2801 West Durango... Maricopa County, index.php/arizona/ 3216P). County, Board of 2801 West Durango maricopa-county...

OceanNOMADS: A New Distribution Node for Operational Ocean Model Output

NASA Astrophysics Data System (ADS)

Cross, S.; Vance, T.; Breckenridge, T.

2009-12-01

The NOAA National Operational Model Archive and Distribution System (NOMADS) is a distributed, web-services based project providing real-time and retrospective access to climate and weather model data and related datasets. OceanNOMADS is a new NOMADS node dedicated to ocean model and related data, with an initial focus on operational ocean models from NOAA and the U.S. Navy. The node offers data access through a Thematic Real-time Environmental Distributed Data Services (THREDDS) server via the commonly used OPeNDAP protocol. The primary server is operated by the National Coastal Data Development Center and hosted by the Northern Gulf Institute at Stennis Space Center, MS. In cooperation with the National Marine Fisheries Service and Mississippi State University (MSU), a duplicate server is being installed at MSU with a 1-gigabit connection to the National Lambda Rail. This setup will allow us to begin to quantify the benefit of high-speed data connections to scientists needing remote access to these large datasets. Work is also underway on the next generation of services from OceanNOMADS, including user-requested server-side data reformatting, regridding, and aggregation, as well as tools for model-data comparison.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

A web-based approach for electrocardiogram monitoring in the home.

PubMed

Magrabi, F; Lovell, N H; Celler, B G

1999-05-01

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

PubMed Central

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

2016-01-01

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

SMART Careplan System for Continuum of Care

PubMed Central

Kim, Young Ah; Jang, Seon Young; Ahn, Meejung; Kim, Kyung Duck

2015-01-01

Objectives This paper describes the integrated Careplan system, designed to manage and utilize the existing Electronic Medical Record (EMR) system; the system also defines key items for interdisciplinary communication and continuity of patient care. Methods We structured the Careplan system to provide effective interdisciplinary communication for healthcare services. The design of the Careplan system architecture proceeded in four steps-defining target datasets; construction of conceptual framework and architecture; screen layout and storyboard creation; screen user interface (UI) design and development, and pilot test and step-by-step deployment. This Careplan system architecture consists of two parts, a server-side and client-side area. On the server-side, it performs the roles of data retrieval and storage from target EMRs. Furthermore, it performs the role of sending push notifications to the client depending on the careplan series. Also, the Careplan system provides various convenient modules to easily enter an individual careplan. Results Currently, Severance Hospital operates the Careplan system and provides a stable service dealing with dynamic changes (e.g., domestic medical certification, the Joint Commission International guideline) of EMR. Conclusions The Careplan system should go hand in hand with key items for strengthening interdisciplinary communication and information sharing within the EMR environment. A well-designed Careplan system can enhance user satisfaction and completed performance. PMID:25705559

SMART Careplan System for Continuum of Care.

PubMed

Kim, Young Ah; Jang, Seon Young; Ahn, Meejung; Kim, Kyung Duck; Kim, Sung Soo

2015-01-01

This paper describes the integrated Careplan system, designed to manage and utilize the existing Electronic Medical Record (EMR) system; the system also defines key items for interdisciplinary communication and continuity of patient care. We structured the Careplan system to provide effective interdisciplinary communication for healthcare services. The design of the Careplan system architecture proceeded in four steps-defining target datasets; construction of conceptual framework and architecture; screen layout and storyboard creation; screen user interface (UI) design and development, and pilot test and step-by-step deployment. This Careplan system architecture consists of two parts, a server-side and client-side area. On the server-side, it performs the roles of data retrieval and storage from target EMRs. Furthermore, it performs the role of sending push notifications to the client depending on the careplan series. Also, the Careplan system provides various convenient modules to easily enter an individual careplan. Currently, Severance Hospital operates the Careplan system and provides a stable service dealing with dynamic changes (e.g., domestic medical certification, the Joint Commission International guideline) of EMR. The Careplan system should go hand in hand with key items for strengthening interdisciplinary communication and information sharing within the EMR environment. A well-designed Careplan system can enhance user satisfaction and completed performance.

Rhodium-Catalyzed Insertion Reaction of PhP Group of Pentaphenylcyclopentaphosphine with Acyclic and Cyclic Disulfides.

PubMed

Arisawa, Mieko; Sawahata, Kyosuke; Yamada, Tomoki; Sarkar, Debayan; Yamaguchi, Masahiko

2018-02-16

Organophosphorus compounds with a phosphorus atom attached to a phenyl group and two organothio/organoseleno groups were synthesized using the rhodium-catalyzed insertion reaction of the PhP group of pentaphenylcyclopentaphosphine (PhP) 5 with acyclic disulfides and diselenides. The method was applied to the synthesis of heterocyclic compounds containing the S-P-S group by the reaction of (PhP) 5 and cyclic disulfides such as 1,2-dithietes, 1,2-dithiocane, 1,4,5-dithiopane, and 1,2-dithiolanes.

Effect of Riblets on Pressure Recovery in a Straight-Walled Diffuser

DTIC Science & Technology

1990-12-01

in the boundary layer velocity pro - file. As the flow continues to oppose the adverse pressure gradient, the fluid near the wall begins to flow in the...and was 37 inches long. The floor and ceiling of the test section were con - 3 structed of wood and the side panels were made of plexiglass. Both side...the diffuser remained fairly con - stant at 52 percent. The riblet results seem to follow the same trend, providing an approximate 35 percent increase in

Motivation and Design of the Sirocco Storage System Version 1.0.

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

Curry, Matthew Leon; Ward, H. Lee; Danielson, Geoffrey Charles

Sirocco is a massively parallel, high performance storage system for the exascale era. It emphasizes client-to-client coordination, low server-side coupling, and free data movement to improve resilience and performance. Its architecture is inspired by peer-to-peer and victim- cache architectures. By leveraging these ideas, Sirocco natively supports several media types, including RAM, flash, disk, and archival storage, with automatic migration between levels. Sirocco also includes storage interfaces and support that are more advanced than typical block storage. Sirocco enables clients to efficiently use key-value storage or block-based storage with the same interface. It also provides several levels of transactional data updatesmore » within a single storage command, including full ACID-compliant updates. This transaction support extends to updating several objects within a single transaction. Further support is provided for con- currency control, enabling greater performance for workloads while providing safe concurrent modification. By pioneering these and other technologies and techniques in the storage system, Sirocco is poised to fulfill a need for a massively scalable, write-optimized storage system for exascale systems. This is version 1.0 of a document reflecting the current and planned state of Sirocco. Further versions of this document will be accessible at http://www.cs.sandia.gov/Scalable_IO/ sirocco .« less

When Will It Be... USNO Seasons and Apsides Calculator

NASA Astrophysics Data System (ADS)

Chizek Frouard, Malynda; Bartlett, Jennifer Lynn

2018-01-01

The turning of the Earth’s seasons (solstices and equinoxes) and apsides (perihelions and aphelions) are times often used in observational astronomy and also of interest to the public. To avoid tedious calculations, the U.S. Naval Observatory (USNO) has developed an on-line interactive calculator, Earth’s Seasons and Apsides to provide information about events between 1600 and 2200. The new data service uses an Application Programming Interface (API), which returns values in JavaScript Object Notation (JSON) that can be incorporated into third-party websites or applications. For a requested year, the Earth’s Seasons and Apsides API provides the Gregorian calendar date and time of the Vernal Equinox, Summer Solstice, Autumnal Equinox, Winter Solstice, Aphelion, and Perihelion. The user may specify the time zone for their results, including the optional addition of U.S. daylight saving time for years after 1966.On-line documentation for using the API-enabled Earth’s Seasons and Apsides is available, including sample calls (http://aa.usno.navy.mil/data/docs/api.php). A traditional forms-based interface is available as well (http://aa.usno.navy.mil/data/docs/EarthSeasons.php). This data service replaces the popular Earth's Seasons: Equinoxes, Solstices, Perihelion, and Aphelion page that provided a static list of events for 2000–2025. The USNO also provides API-enabled data services for Complete Sun and Moon Data for One Day (http://aa.usno.navy.mil/data/docs/RS_OneDay.php), Dates of the Primary Phases of the Moon (http://aa.usno.navy.mil/data/docs/MoonPhase.php), Selected Christian Observances (http://aa.usno.navy.mil/data/docs/easter.php), Selected Islamic Observances (http://aa.usno.navy.mil/data/docs/islamic.php), Selected Jewish Observances (http://aa.usno.navy.mil/data/docs/passover.php), Julian Date Conversion (http://aa.usno.navy.mil/data/docs/JulianDate.php), and Sidereal Time (http://aa.usno.navy.mil/data/docs/siderealtime.php) as well as its Solar Eclipse Computer (http://aa.usno.navy.mil/data/docs/SolarEclipses.php).

Do Pneumococcal Conjugate Vaccines Represent Good Value for Money in a Lower-Middle Income Country? A Cost-Utility Analysis in the Philippines

PubMed Central

Haasis, Manuel Alexander; Ceria, Joyce Anne; Kulpeng, Wantanee; Teerawattananon, Yot; Alejandria, Marissa

2015-01-01

Objectives The objective of this study is to assess the value for money of introducing pneumococcal conjugate vaccines as part of the immunization program in a lower-middle income country, the Philippines, which is not eligible for GAVI support and lower vaccine prices. It also includes the newest clinical evidence evaluating the efficacy of PCV10, which is lacking in other previous studies. Methods A cost-utility analysis was conducted. A Markov simulation model was constructed to examine the costs and consequences of PCV10 and PCV13 against the current scenario of no PCV vaccination for a lifetime horizon. A health system perspective was employed to explore different funding schemes, which include universal or partial vaccination coverage subsidized by the government. Results were presented as incremental cost-effectiveness ratios (ICERs) in Philippine peso (Php) per QALY gained (1 USD = 44.20 Php). Probabilistic sensitivity analysis was performed to determine the impact of parameter uncertainty. Results With universal vaccination at a cost per dose of Php 624 for PCV10 and Php 700 for PCV13, both PCVs are cost-effective compared to no vaccination given the ceiling threshold of Php 120,000 per QALY gained, yielding ICERs of Php 68,182 and Php 54,510 for PCV10 and PCV13, respectively. Partial vaccination of 25% of the birth cohort resulted in significantly higher ICER values (Php 112,640 for PCV10 and Php 84,654 for PCV13) due to loss of herd protection. The budget impact analysis reveals that universal vaccination would cost Php 3.87 billion to 4.34 billion per annual, or 1.6 to 1.8 times the budget of the current national vaccination program. Conclusion The inclusion of PCV in the national immunization program is recommended. PCV13 achieved better value for money compared to PCV10. However, the affordability and sustainability of PCV implementation over the long-term should be considered by decision makers. PMID:26131961

Ultrasound combined transcutaneous electrical nerve stimulation (UltraTENS) versus phonophoresis of piroxicam (PhP) in symptomatic knee osteoarthritis: A randomized double-blind, controlled trial.

PubMed

Boonhong, Jariya; Suntornpiyapan, Phitsanu; Piriyajarukul, Apatchanee

2018-02-02

Ultrasound combined with transcutaneous electrical nerve stimulation (UltraTENS) and phonophoresis of piroxicam (PhP) are combined modality therapy that frequently used in musculoskeletal pain including knee osteoarthritis (OA). But it is lack of a good clinical trial to prove and compare their effects. To compare the effects of UltraTENS with PhP on mild to moderate degree of symptomatic knee OA. Sixty-one patients (55 women), mean age of 63.4 ± 8.1 y, 50-90 mm VAS of knee pain and Kellgren-Lawrence score of grade I-III were randomly allocated into UltraTENS and PhP (N = 31 and 30, respectively). The UltraTENS group received a combined ultrasound with TENS program and a non-drug gel, whereas the PhP group got an ultrasound program with piroxicam gel and sham TENS. All patients were treated for a total of 10 sessions, consisting of five times per week and 10 min per session. Before and after treatment, patients were evaluated knee pain by using the 100-mm VAS and functional performance by Western Ontario and McMaster Universities Osteoarthritis (WOMAC) index. The UltraTENS and PhP groups experienced considerable improvement in both VAS and total WOMAC scores post-treatment (P< 0.001). The PhP had better VAS of pain and WOMAC scores but no statistical significance. Results show that UltraTENS and PhP were effective for relieving pain and improve functionality knee OA without significant differences between their effects.

Developing a Data Discovery Tool for Interdisciplinary Science: Leveraging a Web-based Mapping Application and Geosemantic Searching

NASA Astrophysics Data System (ADS)

Albeke, S. E.; Perkins, D. G.; Ewers, S. L.; Ewers, B. E.; Holbrook, W. S.; Miller, S. N.

2015-12-01

The sharing of data and results is paramount for advancing scientific research. The Wyoming Center for Environmental Hydrology and Geophysics (WyCEHG) is a multidisciplinary group that is driving scientific breakthroughs to help manage water resources in the Western United States. WyCEHG is mandated by the National Science Foundation (NSF) to share their data. However, the infrastructure from which to share such diverse, complex and massive amounts of data did not exist within the University of Wyoming. We developed an innovative framework to meet the data organization, sharing, and discovery requirements of WyCEHG by integrating both open and closed source software, embedded metadata tags, semantic web technologies, and a web-mapping application. The infrastructure uses a Relational Database Management System as the foundation, providing a versatile platform to store, organize, and query myriad datasets, taking advantage of both structured and unstructured formats. Detailed metadata are fundamental to the utility of datasets. We tag data with Uniform Resource Identifiers (URI's) to specify concepts with formal descriptions (i.e. semantic ontologies), thus allowing users the ability to search metadata based on the intended context rather than conventional keyword searches. Additionally, WyCEHG data are geographically referenced. Using the ArcGIS API for Javascript, we developed a web mapping application leveraging database-linked spatial data services, providing a means to visualize and spatially query available data in an intuitive map environment. Using server-side scripting (PHP), the mapping application, in conjunction with semantic search modules, dynamically communicates with the database and file system, providing access to available datasets. Our approach provides a flexible, comprehensive infrastructure from which to store and serve WyCEHG's highly diverse research-based data. This framework has not only allowed WyCEHG to meet its data stewardship requirements, but can provide a template for others to follow.

The Benefits of Parenting Self-Help Groups for Rural Latino Parents.

ERIC Educational Resources Information Center

Wituk, Scott; Commer, Amy; Lindstrom, Julie; Meisen, Greg

2001-01-01

A survey of 118 rural, mostly female, Latino participants in Parents Helping Parents (PHP)--a Kansas network of parenting self-help groups--found high satisfaction with PHP. PHP provided support and information concerning child rearing and child development, improved family communication, and increased the use of alternative means of discipline.…

Testing Theoretical Relationships: Factors Influencing Positive Health Practices (PHP) in Filipino College Students

ERIC Educational Resources Information Center

Ayres, Cynthia; Mahat, Ganga; Atkins, Robert

2013-01-01

Objective: To examine variables influencing the positive health practices (PHP) of Filipino college students to gain a better understanding of health practices in this ethnic/racial group. Cross-sectional study tested theoretical relationships postulated among (a) PHP, (b) social support (SS), (c) optimism, and (d) acculturation. Participants: A…

PHP-HT (VitaResc Biotech).

PubMed

Baldwin, A; Wiley, E

2001-04-01

VitaResc (formerly Apex) is developing PHP-HT, pyridoxalated hemoglobin polyoxyethylene conjugate, for the potential treatment of nitric oxide-induced shock (characterized by hypotension), associated with various etiologies, initially in septic shock. A phase I safety study and an initial phase I/II patient trial for NO-induced shock have been completed, and VitaResc has enrolled patients in three of five planned cohorts in a continuation of these trials to include a protocol of continuous infusion and dose escalation [330680,349187,390918]. The results from the dose escalation trials are expected to provide the basis for a randomized, controlled phase II/III pivotal trial of PHP-HT [390918]. VitaResc has licensed PHP-HT exclusively from Ajinomoto for all indications, worldwide, except Japan [275263]. Ajinomoto originally developed the human derived and chemically modified hemoglobin preparation as a blood substitute, but no development has been reported by the company since 1997 [275277,303577]. The other potential indications of PHP-HT include shock associated with burns, pancreatitis, hemodialysis and cytokine therapies [275277]. VitaResc expects the annual market potential of PHP-HT to exceed 1 billion dollars [330680].

Pretreating lignocellulosic biomass by the concentrated phosphoric acid plus hydrogen peroxide (PHP) for enzymatic hydrolysis: evaluating the pretreatment flexibility on feedstocks and particle sizes.

PubMed

Wang, Qing; Wang, Zhanghong; Shen, Fei; Hu, Jinguang; Sun, Fubao; Lin, Lili; Yang, Gang; Zhang, Yanzong; Deng, Shihuai

2014-08-01

In order to seek a high-efficient pretreatment path for converting lignocellulosic feedstocks to fermentable sugars by enzymatic hydrolysis, the concentrated H₃PO₄ plus H₂O₂ (PHP) was attempted to pretreat different lignocellulosic biomass for evaluating the pretreatment flexibility on feedstocks. Meanwhile, the responses of pretreatment to particle sizes were also evaluated. When the PHP-pretreatment was employed (final H₂O₂ and H₃PO₄ concentration of 1.77% and 80.0%), 71-96% lignin and more than 95% hemicellulose in various feedstocks (agricultural residues, hardwood, softwood, bamboo, and their mixture, and garden wastes mixture) can be removed. Consequently, more than 90% glucose conversion was uniformly achieved indicating PHP greatly improved the pretreatment flexibility to different feedstocks. Moreover, when wheat straw and oak chips were PHP-pretreated with different sizes, the average glucose conversion reached 94.9% and 100% with lower coefficient of variation (7.9% and 0.0%), which implied PHP-pretreatment can significantly weaken the negative effects of feedstock sizes on subsequent conversion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of 3D browsing and interactive web system

NASA Astrophysics Data System (ADS)

Shi, Xiaonan; Fu, Jian; Jin, Chaolin

2017-09-01

In the current market, users need to download specific software or plug-ins to browse the 3D model, and browsing the system may be unstable, and it cannot be 3D model interaction issues In order to solve this problem, this paper presents a solution to the interactive browsing of the model in the server-side parsing model, and when the system is applied, the user only needs to input the system URL and upload the 3D model file to operate the browsing The server real-time parsing 3D model, the interactive response speed, these completely follows the user to walk the minimalist idea, and solves the current market block 3D content development question.

Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network.

PubMed

Li, Xiang; Xu, Youjun; Lai, Luhua; Pei, Jianfeng

2018-05-30

Adverse side effects of drug-drug interactions induced by human cytochrome P450 (CYP450) inhibition is an important consideration in drug discovery. It is highly desirable to develop computational models that can predict the inhibitive effect of a compound against a specific CYP450 isoform. In this study, we developed a multitask model for concurrent inhibition prediction of five major CYP450 isoforms, namely, 1A2, 2C9, 2C19, 2D6, and 3A4. The model was built by training a multitask autoencoder deep neural network (DNN) on a large dataset containing more than 13 000 compounds, extracted from the PubChem BioAssay Database. We demonstrate that the multitask model gave better prediction results than that of single-task models, previous reported classifiers, and traditional machine learning methods on an average of five prediction tasks. Our multitask DNN model gave average prediction accuracies of 86.4% for the 10-fold cross-validation and 88.7% for the external test datasets. In addition, we built linear regression models to quantify how the other tasks contributed to the prediction difference of a given task between single-task and multitask models, and we explained under what conditions the multitask model will outperform the single-task model, which suggested how to use multitask DNN models more effectively. We applied sensitivity analysis to extract useful knowledge about CYP450 inhibition, which may shed light on the structural features of these isoforms and give hints about how to avoid side effects during drug development. Our models are freely available at http://repharma.pku.edu.cn/deepcyp/home.php or http://www.pkumdl.cn/deepcyp/home.php .

Unusual downhole and surface free-field records near the Carquinez Strait bridges during the 24 August 2014 Mw6.0 South Napa, California earthquake

USGS Publications Warehouse

Çelebi, Mehmet; Ghahari, S. Farid; Taciroglu, Ertugrul

2015-01-01

This paper reports the results of Part A of a study of the recorded strong-motion accelerations at the well-instrumented network of the two side-by-side parallel bridges over the Carquinez Strait during the 24 August 2014 (Mw6.0 ) South Napa, Calif. earthquake that occurred at 03:20:44 PDT with epicentral coordinates 38.22N, 122.31W. (http://earthquake.usgs.gov/earthquakes/eqarchives/poster/2014/20140824.php, last accessed on October 17, 2014). Both bridges and two boreholes were instrumented by the California Strong motion Instrumentation Program (CSMIP) of California Geological Survey (CGS) (Shakal et al., 2014). A comprehensive comparison of several ground motion prediction equations as they relate to recorded ground motions of the earthquake is provided by Baltay and Boatright (2015).

UAF: a generic OPC unified architecture framework

NASA Astrophysics Data System (ADS)

Pessemier, Wim; Deconinck, Geert; Raskin, Gert; Saey, Philippe; Van Winckel, Hans

2012-09-01

As an emerging Service Oriented Architecture (SOA) specically designed for industrial automation and process control, the OPC Unied Architecture specication should be regarded as an attractive candidate for controlling scientic instrumentation. Even though an industry-backed standard such as OPC UA can oer substantial added value to these projects, its inherent complexity poses an important obstacle for adopting the technology. Building OPC UA applications requires considerable eort, even when taking advantage of a COTS Software Development Kit (SDK). The OPC Unied Architecture Framework (UAF) attempts to reduce this burden by introducing an abstraction layer between the SDK and the application code in order to achieve a better separation of the technical and the functional concerns. True to its industrial origin, the primary requirement of the framework is to maintain interoperability by staying close to the standard specications, and by expecting the minimum compliance from other OPC UA servers and clients. UAF can therefore be regarded as a software framework to quickly and comfortably develop and deploy OPC UA-based applications, while remaining compatible to third party OPC UA-compliant toolkits, servers (such as PLCs) and clients (such as SCADA software). In the rst phase, as covered by this paper, only the client-side of UAF has been tackled in order to transparently handle discovery, session management, subscriptions, monitored items etc. We describe the design principles and internal architecture of our open-source software project, the rst results of the framework running at the Mercator Telescope, and we give a preview of the planned server-side implementation.

Quantitative analysis of methylation defects and correlation with clinical characteristics in patients with pseudohypoparathyroidism type I and GNAS epigenetic alterations.

PubMed

Elli, Francesca M; de Sanctis, Luisa; Bollati, Valentina; Tarantini, Letizia; Filopanti, Marcello; Barbieri, Anna Maria; Peverelli, Erika; Beck-Peccoz, Paolo; Spada, Anna; Mantovani, Giovanna

2014-03-01

Pseudohypoparathyroidism type I (PHP-I) includes two main subtypes, PHP-Ia and -Ib. About 70% of PHP-Ia patients, who show Albright hereditary osteodystrophy (AHO) associated with resistance toward multiple hormones (PTH/TSH/GHRH/gonadotropins), carry heterozygous mutations in the α-subunit of the stimulatory G protein (Gsα) exons 1-13, encoded by the guanine nucleotide binding-protein α-stimulating activity polypeptide 1 (GNAS), whereas the majority of PHP-Ib patients, who classically display hormone resistance limited to PTH and TSH with no AHO sign, have methylation defects in the imprinted GNAS cluster. Recently methylation defects have been detected also in patients with PHP and different degrees of AHO, indicating a molecular overlap between the two forms. The objectives of the study were to collect patients with the following characteristics: clinical PHP-I (with or without AHO), no mutation in Gsα coding sequence, but the presence of GNAS methylation alterations and to investigate the existence of correlations between the degree of the epigenetic defect and the severity of the disease. We quantified GNAS methylation alterations by both PCR-pyrosequencing and methylation specific-multiplex ligation-dependent probe amplification assay in genomic DNA from 63 patients with PHP-I and correlated these findings with clinical parameters (age at diagnosis; calcium, phosphorus, PTH, TSH levels; presence or absence of each AHO sign). By both approaches, the degree of the imprinting defect did not correlate with the onset of the disease, the severity of endocrine resistances, or with the presence/absence of specific AHO signs. Similar molecular alterations may lead to a broad spectrum of diseases, from isolated PTH resistance to complete PHP-Ia, and the degree of methylation alterations does not reflect or anticipate the severity and the type of different PHP/AHO manifestations.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

A study of kinematic cues and anticipatory performance in tennis using computational manipulation and computer graphics.

PubMed

Ida, Hirofumi; Fukuhara, Kazunobu; Kusubori, Seiji; Ishii, Motonobu

2011-09-01

Computer graphics of digital human models can be used to display human motions as visual stimuli. This study presents our technique for manipulating human motion with a forward kinematics calculation without violating anatomical constraints. A motion modulation of the upper extremity was conducted by proportionally modulating the anatomical joint angular velocity calculated by motion analysis. The effect of this manipulation was examined in a tennis situation--that is, the receiver's performance of predicting ball direction when viewing a digital model of the server's motion derived by modulating the angular velocities of the forearm or that of the elbow during the forward swing. The results showed that the faster the server's forearm pronated, the more the receiver's anticipation of the ball direction tended to the left side of the serve box. In contrast, the faster the server's elbow extended, the more the receiver's anticipation of the ball direction tended to the right. This suggests that tennis players are sensitive to the motion modulation of their opponent's racket-arm.

Design and implementation of a cloud based lithography illumination pupil processing application

NASA Astrophysics Data System (ADS)

Zhang, Youbao; Ma, Xinghua; Zhu, Jing; Zhang, Fang; Huang, Huijie

2017-02-01

Pupil parameters are important parameters to evaluate the quality of lithography illumination system. In this paper, a cloud based full-featured pupil processing application is implemented. A web browser is used for the UI (User Interface), the websocket protocol and JSON format are used for the communication between the client and the server, and the computing part is implemented in the server side, where the application integrated a variety of high quality professional libraries, such as image processing libraries libvips and ImageMagic, automatic reporting system latex, etc., to support the program. The cloud based framework takes advantage of server's superior computing power and rich software collections, and the program could run anywhere there is a modern browser due to its web UI design. Compared to the traditional way of software operation model: purchased, licensed, shipped, downloaded, installed, maintained, and upgraded, the new cloud based approach, which is no installation, easy to use and maintenance, opens up a new way. Cloud based application probably is the future of the software development.

MISS-Prot: web server for self/non-self discrimination of protein residue networks in parasites; theory and experiments in Fasciola peptides and Anisakis allergens.

PubMed

González-Díaz, Humberto; Muíño, Laura; Anadón, Ana M; Romaris, Fernanda; Prado-Prado, Francisco J; Munteanu, Cristian R; Dorado, Julián; Sierra, Alejandro Pazos; Mezo, Mercedes; González-Warleta, Marta; Gárate, Teresa; Ubeira, Florencio M

2011-06-01

Infections caused by human parasites (HPs) affect the poorest 500 million people worldwide but chemotherapy has become expensive, toxic, and/or less effective due to drug resistance. On the other hand, many 3D structures in Protein Data Bank (PDB) remain without function annotation. We need theoretical models to quickly predict biologically relevant Parasite Self Proteins (PSP), which are expressed differentially in a given parasite and are dissimilar to proteins expressed in other parasites and have a high probability to become new vaccines (unique sequence) or drug targets (unique 3D structure). We present herein a model for PSPs in eight different HPs (Ascaris, Entamoeba, Fasciola, Giardia, Leishmania, Plasmodium, Trypanosoma, and Toxoplasma) with 90% accuracy for 15 341 training and validation cases. The model combines protein residue networks, Markov Chain Models (MCM) and Artificial Neural Networks (ANN). The input parameters are the spectral moments of the Markov transition matrix for electrostatic interactions associated with the protein residue complex network calculated with the MARCH-INSIDE software. We implemented this model in a new web-server called MISS-Prot (MARCH-INSIDE Scores for Self-Proteins). MISS-Prot was programmed using PHP/HTML/Python and MARCH-INSIDE routines and is freely available at: . This server is easy to use by non-experts in Bioinformatics who can carry out automatic online upload and prediction with 3D structures deposited at PDB (mode 1). We can also study outcomes of Peptide Mass Fingerprinting (PMFs) and MS/MS for query proteins with unknown 3D structures (mode 2). We illustrated the use of MISS-Prot in experimental and/or theoretical studies of peptides from Fasciola hepatica cathepsin proteases or present on 10 Anisakis simplex allergens (Ani s 1 to Ani s 10). In doing so, we combined electrophoresis (1DE), MALDI-TOF Mass Spectroscopy, and MASCOT to seek sequences, Molecular Mechanics + Molecular Dynamics (MM/MD) to generate 3D structures and MISS-Prot to predict PSP scores. MISS-Prot also allows the prediction of PSP proteins in 16 additional species including parasite hosts, fungi pathogens, disease transmission vectors, and biotechnologically relevant organisms.

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

PubMed

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

Development and implementation of a web-based system to study children with malnutrition.

PubMed

Syed-Mohamad, Sharifah-Mastura

2009-01-01

To develop and implement a collective web-based system to monitor child growth in order to study children with malnutrition. The system was developed using prototyping system development methodology. The implementation was carried out using open-source technologies that include Apache Web Server, PHP scripting, and MySQL database management system. There were four datasets collected by the system: demographic data, measurement data, parent data, and food program data. The system was designed to be used by two groups of users, the clinics and the researchers. The Growth Monitor System was successfully developed and used for the study, "Geoinformation System (GIS) and Remote Sensing in Mapping of Children with Malnutrition." Data collection was implemented in public clinics from two districts in the state of Kelantan, Malaysia. The development of an integrated web-based system, Growth Monitor, for the study of children with malnutrition has been achieved. This system can be expanded to new partners who are involved in the study of children with malnutrition in other parts of Malaysia as well as other countries.

MyLabStocks: a web-application to manage molecular biology materials.

PubMed

Chuffart, Florent; Yvert, Gaël

2014-05-01

Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence. © 2014 Laboratoire de Biologie Moleculaire de la Cellule CNRS. Yeast published by John Wiley & Sons, Ltd.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

PubMed Central

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

An Open-Source and Java-Technologies Approach to Web Applications

DTIC Science & Technology

2003-09-01

program for any purpose (Freedom 0). • The freedom to study how the program works, and adapt it to individual needs (Freedom 1). Access to the source...manage information for many purposes. Today a key technology that allows developers to make Web applications is server-side programming to generate a

Extensible 3D (X3D) Earth Technical Requirements Workshop Summary Report

DTIC Science & Technology

2007-08-01

world in detail already, but rarely interconnect on to another • Most interesting part of “virtual reality” (VR) is reality – which means physics... Two Web-Enabled Modeling and Simulation (WebSim) symposia have demonstrated that large partnerships can work 9. Server-side 3D graphics • Our

Computational algorithm to evaluate product disassembly cost index

NASA Astrophysics Data System (ADS)

Zeid, Ibrahim; Gupta, Surendra M.

2002-02-01

Environmentally conscious manufacturing is an important paradigm in today's engineering practice. Disassembly is a crucial factor in implementing this paradigm. Disassembly allows the reuse and recycling of parts and products that reach their death after their life cycle ends. There are many questions that must be answered before a disassembly decision can be reached. The most important question is economical. The cost of disassembly versus the cost of scrapping a product is always considered. This paper develops a computational tool that allows decision-makers to calculate the disassembly cost of a product. The tool makes it simple to perform 'what if' scenarios fairly quickly. The tool is Web based and has two main parts. The front-end part is a Web page and runs on the client side in a Web browser, while the back-end part is a disassembly engine (servlet) that has disassembly knowledge and costing algorithms and runs on the server side. The tool is based on the client/server model that is pervasively utilized throughout the World Wide Web. An example is used to demonstrate the implementation and capabilities of the tool.

QoE collaborative evaluation method based on fuzzy clustering heuristic algorithm.

PubMed

Bao, Ying; Lei, Weimin; Zhang, Wei; Zhan, Yuzhuo

2016-01-01

At present, to realize or improve the quality of experience (QoE) is a major goal for network media transmission service, and QoE evaluation is the basis for adjusting the transmission control mechanism. Therefore, a kind of QoE collaborative evaluation method based on fuzzy clustering heuristic algorithm is proposed in this paper, which is concentrated on service score calculation at the server side. The server side collects network transmission quality of service (QoS) parameter, node location data, and user expectation value from client feedback information. Then it manages the historical data in database through the "big data" process mode, and predicts user score according to heuristic rules. On this basis, it completes fuzzy clustering analysis, and generates service QoE score and management message, which will be finally fed back to clients. Besides, this paper mainly discussed service evaluation generative rules, heuristic evaluation rules and fuzzy clustering analysis methods, and presents service-based QoE evaluation processes. The simulation experiments have verified the effectiveness of QoE collaborative evaluation method based on fuzzy clustering heuristic rules.

Testnodes: a Lightweight Node-Testing Infrastructure

NASA Astrophysics Data System (ADS)

Fay, R.; Bland, J.

2014-06-01

A key aspect of ensuring optimum cluster reliability and productivity lies in keeping worker nodes in a healthy state. Testnodes is a lightweight node testing solution developed at Liverpool. While Nagios has been used locally for general monitoring of hosts and services, Testnodes is optimised to answer one question: is there any reason this node should not be accepting jobs? This tight focus enables Testnodes to inspect nodes frequently with minimal impact and provide a comprehensive and easily extended check with each inspection. On the server side, Testnodes, implemented in python, interoperates with the Torque batch server to control the nodes production status. Testnodes remotely and in parallel executes client-side test scripts and processes the return codes and output, adjusting the node's online/offline status accordingly to preserve the integrity of the overall batch system. Testnodes reports via log, email and Nagios, allowing a quick overview of node status to be reviewed and specific node issues to be identified and resolved quickly. This presentation will cover testnodes design and implementation, together with the results of its use in production at Liverpool, and future development plans.

Heat transfer performance of a pulsating heat pipe charged with acetone-based mixtures

NASA Astrophysics Data System (ADS)

Wang, Wenqing; Cui, Xiaoyu; Zhu, Yue

2017-06-01

Pulsating heat pipes (PHPs) are used as high efficiency heat exchangers, and the selection of working fluids in PHPs has a great impact on the heat transfer performance. This study investigates the thermal resistance characteristics of the PHP charged with acetone-based binary mixtures, where deionized water, methanol and ethanol were added to and mixed with acetone, respectively. The volume mixing ratios were 2:1, 4:1 and 7:1, and the heating power ranged from 10 to 100 W with filling ratios of 45, 55, 62 and 70%. At a low filling ratio (45%), the zeotropic characteristics of the binary mixtures have an influence on the heat transfer performance of the PHP. Adding water, which has a substantially different boiling point compared with that of acetone, can significantly improve the anti-dry-out ability inside the PHP. At a medium filling ratio (55%), the heat transfer performance of the PHP is affected by both phase transition characteristics and physical properties of working fluids. At high heating power, the thermal resistance of the PHP with acetone-water mixture is between that with pure acetone and pure water, whereas the thermal resistance of the PHP with acetone-methanol and acetone-ethanol mixtures at mixing ratios of 2:1 and 4:1 is less than that with the corresponding pure fluids. At high filling ratios (62 and 70%), the heat transfer performance of the PHP is mainly determined by the properties of working fluids that affects the flow resistance. Thus, the PHP with acetone-methanol and acetone-ethanol mixtures that have a lower flow resistance shows better heat transfer performance than that with acetone-water mixture.

Intravenous administration of the adeno-associated virus-PHP.B capsid fails to upregulate transduction efficiency in the marmoset brain.

PubMed

Matsuzaki, Yasunori; Konno, Ayumu; Mochizuki, Ryuta; Shinohara, Yoichiro; Nitta, Keisuke; Okada, Yukihiro; Hirai, Hirokazu

2018-02-05

Intravenous administration of adeno-associated virus (AAV)-PHP.B, a capsid variant of AAV9 containing seven amino acid insertions, results in a greater permeability of the blood brain barrier (BBB) than standard AAV9 in mice, leading to highly efficient and global transduction of the central nervous system (CNS). The present study aimed to examine whether the enhanced BBB penetrance of AAV-PHP.B observed in mice also occurs in non-human primates. Thus, a young adult (age, 1.6 years) and an old adult (age, 7.2 years) marmoset received an intravenous injection of AAV-PHP.B expressing enhanced green fluorescent protein (EGFP) under the control of the constitutive CBh promoter (a hybrid of cytomegalovirus early enhancer and chicken β-actin promoter). Age-matched control marmosets were treated with standard AAV9-capsid vectors. The animals were sacrificed 6 weeks after the viral injection. Based on the results, only limited transduction of neurons (0-2%) and astrocytes (0.1-2.5%) was observed in both AAV-PHP.B- and AAV9-treated marmosets. One noticeable difference between AAV-PHP.B and AAV9 was the marked transduction of the peripheral dorsal root ganglia neurons. Indeed, the soma and axons in the projection from the spinal cord to the nucleus cuneatus in the medulla oblongata were strongly labeled with EGFP by AAV-PHP.B. Thus, except for the peripheral dorsal root ganglia neurons, the AAV-PHP.B transduction efficiency in the CNS of marmosets was comparable to that of AAV9 vectors. Copyright © 2017 Elsevier B.V. All rights reserved.

Energy Expenditure in Obese Children with Pseudohypoparathyroidism Type 1a

PubMed Central

Shoemaker, Ashley H.; Lomenick, Jefferson P.; Saville, Benjamin R.; Wang, Wenli; Buchowski, Maciej S.; Cone, Roger D.

2012-01-01

Context Patients with pseudohypoparathyroidism type 1a (PHP-1a) develop early-onset obesity. The abnormality in energy expenditure and/or energy intake responsible for this weight gain is unknown. Objective The aim of this study was to evaluate energy expenditure in children with PHP-1a compared with obese controls. Patients We studied 6 obese females with PHP-1a and 17 obese female controls. Patients were recruited from a single academic center. Measurements Resting energy expenditure and thermogenic effect of a high fat meal were measured using whole room indirect calorimetry. Body composition was assessed using whole body dual energy x-ray absorptiometry. Fasting glucose, insulin and hemoglobin A1C were measured. Results Children with PHP-1a had decreased resting energy expenditure compared with obese controls (P <0.01). After adjustment for fat free mass, the PHP-1a group’s resting energy expenditure was 346.4 kcals/day less than obese controls (95% CI [−585.5 to −106.9], P <0.01). The thermogenic effect of food, expressed as percent increase in postprandial energy expenditure over resting energy expenditure, was lower in PHP-1a patients than obese controls but did not reach statistical significance (absolute reduction of 5.9%, 95% CI [−12.2% to 0.3%], P = 0.06). Conclusions Our data indicate that children with PHP-1a have decreased resting energy expenditure compared with obese controls and that may contribute to the development of obesity in these children. These patients may also have abnormal diet-induced thermogenesis in response to a high fat meal. Understanding the causes of obesity in PHP-1a may allow for targeted nutritional or pharmacologic treatments in the future. PMID:23229731

Using PHP/MySQL to Manage Potential Mass Impacts

NASA Technical Reports Server (NTRS)

Hager, Benjamin I.

2010-01-01

This paper presents a new application using commercially available software to manage mass properties for spaceflight vehicles. PHP/MySQL(PHP: Hypertext Preprocessor and My Structured Query Language) are a web scripting language and a database language commonly used in concert with each other. They open up new opportunities to develop cutting edge mass properties tools, and in particular, tools for the management of potential mass impacts (threats and opportunities). The paper begins by providing an overview of the functions and capabilities of PHP/MySQL. The focus of this paper is on how PHP/MySQL are being used to develop an advanced "web accessible" database system for identifying and managing mass impacts on NASA's Ares I Upper Stage program, managed by the Marshall Space Flight Center. To fully describe this application, examples of the data, search functions, and views are provided to promote, not only the function, but the security, ease of use, simplicity, and eye-appeal of this new application. This paper concludes with an overview of the other potential mass properties applications and tools that could be developed using PHP/MySQL. The premise behind this paper is that PHP/MySQL are software tools that are easy to use and readily available for the development of cutting edge mass properties applications. These tools are capable of providing "real-time" searching and status of an active database, automated report generation, and other capabilities to streamline and enhance mass properties management application. By using PHP/MySQL, proven existing methods for managing mass properties can be adapted to present-day information technology to accelerate mass properties data gathering, analysis, and reporting, allowing mass property management to keep pace with today's fast-pace design and development processes.

Distributed control system for demand response by servers

NASA Astrophysics Data System (ADS)

Hall, Joseph Edward

Within the broad topical designation of smart grid, research in demand response, or demand-side management, focuses on investigating possibilities for electrically powered devices to adapt their power consumption patterns to better match generation and more efficiently integrate intermittent renewable energy sources, especially wind. Devices such as battery chargers, heating and cooling systems, and computers can be controlled to change the time, duration, and magnitude of their power consumption while still meeting workload constraints such as deadlines and rate of throughput. This thesis presents a system by which a computer server, or multiple servers in a data center, can estimate the power imbalance on the electrical grid and use that information to dynamically change the power consumption as a service to the grid. Implementation on a testbed demonstrates the system with a hypothetical but realistic usage case scenario of an online video streaming service in which there are workloads with deadlines (high-priority) and workloads without deadlines (low-priority). The testbed is implemented with real servers, estimates the power imbalance from the grid frequency with real-time measurements of the live outlet, and uses a distributed, real-time algorithm to dynamically adjust the power consumption of the servers based on the frequency estimate and the throughput of video transcoder workloads. Analysis of the system explains and justifies multiple design choices, compares the significance of the system in relation to similar publications in the literature, and explores the potential impact of the system.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

PubMed

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A; Ryu, Seong Eon; Kim, Deok-Soo

2016-07-08

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Heat transfer mechanisms in pulsating heat-pipes with nanofluid

NASA Astrophysics Data System (ADS)

Gonzalez, Miguel; Kelly, Brian; Hayashi, Yoshikazu; Kim, Yoon Jo

2015-01-01

In this study, the effect of silver nanofluid on a pulsating heat-pipe (PHP) thermal performance was experimentally investigated to figure out how nanofluid works with PHP. A closed loop PHP was built with 3 mm diameter tubes. Thermocouples and pressure transducers were installed for fluid and surface temperature and pressure measurements. The operating temperature of the PHP varied from 30-100 °C, with power rates of 61 W and 119 W. The fill ratio of 30%, 50%, and 70% were tested. The results showed that the evaporator heat transfer performance was degraded by the addition of nanoparticles due to increased viscosity at high power rate, while the positive effects of high thermal conductivity and enhanced nucleate boiling worked better at low power rate. In the condenser section, owing to the relatively high liquid content, nanofluid more effectively improved the heat transfer performance. However, since the PHP performance was dominantly affected by evaporator heat transfer performance, the overall benefit of enhanced condenser section performance was greatly limited. It was also observed that the poor heat transfer performance with nanofluid at the evaporator section led to lower operating pressure of PHP.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Broadband Photometry Of The Potentially Asteroid 277475 (2005 WK4) and Corrected 52762 (1998 MT24) Colors.

NASA Astrophysics Data System (ADS)

Hicks, M.; Buratt, B.; Carcione, A.; Borlase, R.

2013-08-01

The Near-Earth Object (NEO) 277475 (2005 WK4) was discovered by the Siding Spring Survey (MPEC 2005-W79) on November 27, 2005. With a Minimum Orbit Intersection Distance (MOID) of 0.004 AU and absolute magnitude H_V=20.1 mag, this object has been designated a Potentially Hazardous Asteroid (PHA) by the Minor Planet Center. The asteroid made an Earth close-approach of 0.021 AU on August 09.2, 2013 and was extensively imaged by the JPL Planetary Radar Team ( http://www.jpl.nasa.gov/news/news.php?release=2013-254 ).

History and structures of telecommunication in pathology, focusing on open access platforms.

PubMed

Kayser, Klaus; Borkenfeld, Stephan; Djenouni, Amina; Kayser, Gian

2011-11-07

Telecommunication has matured to a broadly applied tool in diagnostic pathology. Contemporary with the development of fast electronic communication lines (Integrated digital network services (ISDN), broad band connections, and fibre optics, as well as the digital imaging technology (digital camera), telecommunication in tissue--based diagnosis (telepathology) has matured. Open access (internet) and server--based communication have induced the development of specific medical information platforms, such as iPATH, UICC-TPCC (telepathology consultation centre of the Union International against Cancer), or the Armed Forces Institute of Pathology (AFIP) teleconsultation system. They have been closed, and are subject to be replaced by specific open access forums (Medical Electronic Expert Communication System (MECES) with embedded virtual slide (VS) technology). MECES uses php language, data base driven mySqL architecture, X/L-AMPP infrastructure, and browser friendly W3C conform standards. The server--based medical communication systems (AFIP, iPATH, UICC-TPCC) have been reported to be a useful and easy to handle tool for expert consultation. Correct sampling and evaluation of transmitted still images by experts reported revealed no or only minor differences to the original images and good practice of the involved experts. β tests with the new generation medical expert consultation systems (MECES) revealed superior results in terms of performance, still image viewing, and system handling, especially as this is closely related to the use of so--called social forums (facebook, youtube, etc.). In addition to the acknowledged advantages of the former established systems (assistance of pathologists working in developing countries, diagnosis confirmation, international information exchange, etc.), the new generation offers additional benefits such as acoustic information transfer, assistance in image screening, VS technology, and teaching in diagnostic sampling, judgement, and verification.

The Open Data Repositorys Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

2015-01-01

Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

Integrated multimodal human-computer interface and augmented reality for interactive display applications

NASA Astrophysics Data System (ADS)

Vassiliou, Marius S.; Sundareswaran, Venkataraman; Chen, S.; Behringer, Reinhold; Tam, Clement K.; Chan, M.; Bangayan, Phil T.; McGee, Joshua H.

2000-08-01

We describe new systems for improved integrated multimodal human-computer interaction and augmented reality for a diverse array of applications, including future advanced cockpits, tactical operations centers, and others. We have developed an integrated display system featuring: speech recognition of multiple concurrent users equipped with both standard air- coupled microphones and novel throat-coupled sensors (developed at Army Research Labs for increased noise immunity); lip reading for improving speech recognition accuracy in noisy environments, three-dimensional spatialized audio for improved display of warnings, alerts, and other information; wireless, coordinated handheld-PC control of a large display; real-time display of data and inferences from wireless integrated networked sensors with on-board signal processing and discrimination; gesture control with disambiguated point-and-speak capability; head- and eye- tracking coupled with speech recognition for 'look-and-speak' interaction; and integrated tetherless augmented reality on a wearable computer. The various interaction modalities (speech recognition, 3D audio, eyetracking, etc.) are implemented a 'modality servers' in an Internet-based client-server architecture. Each modality server encapsulates and exposes commercial and research software packages, presenting a socket network interface that is abstracted to a high-level interface, minimizing both vendor dependencies and required changes on the client side as the server's technology improves.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Growth hormone deficiency in monozygotic twins with autosomal dominant pseudohypoparathyroidism type Ib.

PubMed

Sano, Shinichiro; Iwata, Hiromi; Matsubara, Keiko; Fukami, Maki; Kagami, Masayo; Ogata, Tsutomu

2015-01-01

Pseudohypoparathyroidism (PHP) is associated with compromised signal transductions via PTH receptor (PTH-R) and other G-protein-coupled receptors including GHRH-R. To date, while GH deficiency (GHD) has been reported in multiple patients with PHP-Ia caused by mutations on the maternally expressed GNAS coding regions and in two patients with sporadic form of PHP-Ib accompanied by broad methylation defects of maternally derived GNAS differentially methylated regions (DMRs), it has not been identified in a patient with an autosomal dominant form of PHP-Ib (AD-PHP-Ib) accompanied by an STX16 microdeletion and an isolated loss of methylation (LOM) at exon A/B-DMR. We studied 5 4/12-year-old monozygotic twins with short stature (both -3.4 SD) and GHD (peak GH values, <6.0 μg/L after arginine and clonidine stimulations). Molecular studies revealed maternally derived STX16 microdeletions and isolated LOMs at exon A/B-DMR in the twins, confirming the diagnosis of AD-PHP-Ib. GNAS mutation was not identified, and neither mutation nor copy number variation was detected in GH1, POU1F1, PROP1, GHRHR, LHX3, LHX4, and HESX1 in the twins. The results, in conjunction with the previous finding that GNAS shows maternal expression in the pituitary, suggest that GHD of the twins is primarily ascribed to compromised GHRH-R signaling caused by AD-PTH-Ib. Thus, resistance to multiple hormones including GHRH should be considered in AD-PHP-Ib.

The isokinetic rotator cuff strength ratios in overhead athletes: Assessment and exercise effect.

PubMed

Berckmans, Kelly; Maenhout, Annelies G; Matthijs, Lien; Pieters, Louise; Castelein, Birgit; Cools, Ann M

2017-09-01

Muscle strength imbalance in the shoulder region can be considered as a predisposing factor in the development of movement dysfunctions, possibly leading to overuse injuries. Repetitive overhead throwing, performed in sports, may result in muscle imbalance between the external (ER) and internal (IR) rotators. Muscle strength measured with an isokinetic device, is reported as a concentric (CON) or eccentric (ECC) force. The balance between an agonist and an antagonist is mentioned as a ratio (CON/CON or ECC/CON). The aim of this systematic literature review is to provide an overview of the existing evidence considering the isokinetic muscle strength ratios of ER and IR of the shoulder in healthy overhead athletes. In addition, the effect of exercise programs on these ratios was investigated. Two online databases (Web of Science and PubMed) were consulted using different search strategies. Articles were selected based on inclusion and exclusion criteria. All included articles were assessed on their methodological quality. There is moderate evidence for a lower functional deceleration ratio (ECC ER/CON IR) at the dominant side. This lower ratio is due to a large overweight of CON IR strength on that side. There is no consensus about which exercise program is the most effective in altering the shoulder isokinetic strength ratios. Copyright © 2017 Elsevier Ltd. All rights reserved.

Immunocontraception for Managing Feral Cattle in Hong Kong

PubMed Central

Massei, Giovanna; Koon, Ka-Kei; Benton, Steven; Brown, Richard; Gomm, Matt; Orahood, Darcy S.; Pietravalle, Stéphane; Eckery, Douglas C.

2015-01-01

Conflicts between human interests and feral cattle in Hong Kong derive from growing numbers of free-roaming cattle. Public antipathy towards lethal population control led the local authorities to consider fertility control to reduce cattle numbers. This study assessed the potential side effects of the immunocontraceptive GonaCon on individual female cattle and established the effectiveness of GonaCon to induce infertility. We evaluated GonaCon in 34 captive cattle assigned to four groups: Control administered a sham solution; Webbed (surgically sterilized through removal of the oviducts), administered one dose of GonaCon; Webbed, administered one dose of GonaCon and a booster dose three months later, and Treated, administered one dose of GonaCon. The side effects of GonaCon were assessed by monitoring injection site, body weight, body condition, size of lymph nodes, body temperature, and feeding behaviour 1 week and 1, 3, 6, 9 and 12 months after vaccination and by haematological and biochemical variables at vaccination and three months post-vaccination. The effectiveness of GonaCon to cause infertility was monitored by quantifying anti-GnRH antibody titres and by using kits to detect cycling and pregnancy. GonaCon-treated cattle showed no injection site reaction, limping, or abnormal behaviour. No differences were observed in all physiological and welfare indicators between control and vaccinated cattle. All control cattle and 4 of the 12 cattle in the Treated group became pregnant. Cattle administered a booster dose had higher anti-GnRH antibody titres than cattle that received one dose. We concluded that GonaCon does not compromise the animals’ welfare and is effective in reducing fertility in cattle. A booster dose is likely to increase the duration of infertility. Further studies are required to assess the feasibility and costs of immunocontraception for controlling free-roaming cattle populations. PMID:25856283

Immunocontraception for managing feral cattle in Hong Kong.

PubMed

Massei, Giovanna; Koon, Ka-Kei; Benton, Steven; Brown, Richard; Gomm, Matt; Orahood, Darcy S; Pietravalle, Stéphane; Eckery, Douglas C

2015-01-01

Conflicts between human interests and feral cattle in Hong Kong derive from growing numbers of free-roaming cattle. Public antipathy towards lethal population control led the local authorities to consider fertility control to reduce cattle numbers. This study assessed the potential side effects of the immunocontraceptive GonaCon on individual female cattle and established the effectiveness of GonaCon to induce infertility. We evaluated GonaCon in 34 captive cattle assigned to four groups: Control administered a sham solution; Webbed (surgically sterilized through removal of the oviducts), administered one dose of GonaCon; Webbed, administered one dose of GonaCon and a booster dose three months later, and Treated, administered one dose of GonaCon. The side effects of GonaCon were assessed by monitoring injection site, body weight, body condition, size of lymph nodes, body temperature, and feeding behaviour 1 week and 1, 3, 6, 9 and 12 months after vaccination and by haematological and biochemical variables at vaccination and three months post-vaccination. The effectiveness of GonaCon to cause infertility was monitored by quantifying anti-GnRH antibody titres and by using kits to detect cycling and pregnancy. GonaCon-treated cattle showed no injection site reaction, limping, or abnormal behaviour. No differences were observed in all physiological and welfare indicators between control and vaccinated cattle. All control cattle and 4 of the 12 cattle in the Treated group became pregnant. Cattle administered a booster dose had higher anti-GnRH antibody titres than cattle that received one dose. We concluded that GonaCon does not compromise the animals' welfare and is effective in reducing fertility in cattle. A booster dose is likely to increase the duration of infertility. Further studies are required to assess the feasibility and costs of immunocontraception for controlling free-roaming cattle populations.

Spatial decision supporting for winter wheat irrigation and fertilizer optimizing in North China Plain

NASA Astrophysics Data System (ADS)

Yang, Xiaodong; Yang, Hao; Dong, Yansheng; Yu, Haiyang

2014-11-01

Production management of winter wheat is more complicated than other crops since its growth period is covered all four seasons and growth environment is very complex with frozen injury, drought, insect or disease injury and others. In traditional irrigation and fertilizer management, agricultural technicians or farmers mainly make decision based on phenology, planting experience to carry out artificial fertilizer and irrigation management. For example, wheat needs more nitrogen fertilizer in jointing and booting stage by experience, then when the wheat grow to the two growth periods, the farmer will fertilize to the wheat whether it needs or not. We developed a spatial decision support system for optimizing irrigation and fertilizer measures based on WebGIS, which monitoring winter wheat growth and soil moisture content by combining a crop model, remote sensing data and wireless sensors data, then reasoning professional management schedule from expert knowledge warehouse. This system is developed by ArcIMS, IDL in server-side and JQuery, Google Maps API, ASP.NET in client-side. All computing tasks are run on server-side, such as computing 11 normal vegetable indexes (NDVI/ NDWI/ NDWI2/ NRI/ NSI/ WI/ G_SWIR/ G_SWIR2/ SPSI/ TVDI/ VSWI) and custom VI of remote sensing image by IDL; while real-time building map configuration file and generating thematic map by ArcIMS.

Building an FTP guard

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

Sands, P.D.

1998-08-01

Classified designs usually include lesser classified (including unclassified) components. An engineer working on such a design needs access to the various sub-designs at lower classification levels. For simplicity, the problem is presented with only two levels: high and low. If the low-classification component designs are stored in the high network, they become inaccessible to persons working on a low network. In order to keep the networks separate, the component designs may be duplicated in all networks, resulting in a synchronization problem. Alternatively, they may be stored in the low network and brought into the high network when needed. The lattermore » solution results in the use of sneaker-net (copying the files from the low system to a tape and carrying the tape to a high system) or a file transfer guard. This paper shows how an FTP Guard was constructed and implemented without degrading the security of the underlying B3 platform. The paper then shows how the guard can be extended to an FTP proxy server or an HTTP proxy server. The extension is accomplished by allowing the high-side user to select among items that already exist on the low-side. No high-side data can be directly compromised by the extension, but a mechanism must be developed to handle the low-bandwidth covert channel that would be introduced by the application.« less

The EarthServer project: Exploiting Identity Federations, Science Gateways and Social and Mobile Clients for Big Earth Data Analysis

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Messina, Antonio; Pappalardo, Marco; Passaro, Gianluca

2013-04-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. Six Lighthouse Applications are being established in EarthServer, each of which poses distinct challenges on Earth Data Analytics: Cryospheric Science, Airborne Science, Atmospheric Science, Geology, Oceanography, and Planetary Science. Altogether, they cover all Earth Science domains; the Planetary Science use case has been added to challenge concepts and standards in non-standard environments. In addition, EarthLook (maintained by Jacobs University) showcases use of OGC standards in 1D through 5D use cases. In this contribution we will report on the first applications integrated in the EarthServer Science Gateway and on the clients for mobile appliances developed to access them. We will also show how federated and social identity services can allow Big Earth Data Providers to expose their data in a distributed environment keeping a strict and fine-grained control on user authentication and authorisation. The degree of fulfilment of the EarthServer implementation with the recommendations made in the recent TERENA Study on AAA Platforms For Scientific Resources in Europe (https://confluence.terena.org/display/aaastudy/AAA+Study+Home+Page) will also be assessed.

nStudy: A System for Researching Information Problem Solving

ERIC Educational Resources Information Center

Winne, Philip H.; Nesbit, John C.; Popowich, Fred

2017-01-01

A bottleneck in gathering big data about learning is instrumentation designed to record data about processes students use to learn and information on which those processes operate. The software system nStudy fills this gap. nStudy is an extension to the Chrome web browser plus a server side database for logged trace data plus peripheral modules…

Map-IT! A Web-Based GIS Tool for Watershed Science Education.

ERIC Educational Resources Information Center

Curtis, David H.; Hewes, Christopher M.; Lossau, Matthew J.

This paper describes the development of a prototypic, Web-accessible GIS solution for K-12 science education and citizen-based watershed monitoring. The server side consists of ArcView IMS running on an NT workstation. The client is built around MapCafe. The client interface, which runs through a standard Web browser, supports standard MapCafe…

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

PubMed

Kaur, Paramjit; Krishan, Kewal; Sharma, Suresh K

2018-06-01

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

Paternal uniparental isodisomy of the entire chromosome 20 as a molecular cause of pseudohypoparathyroidism type Ib (PHP-Ib).

PubMed

Bastepe, Murat; Altug-Teber, Ozge; Agarwal, Chhavi; Oberfield, Sharon E; Bonin, Michael; Jüppner, Harald

2011-03-01

Pseudohypoparathyoridism type Ib (PHP-Ib) typically defines the presence of end-organ resistance to parathyroid hormone in the absence of Albright's hereditary osteodystrophy. Patients affected by this disorder present with imprinting defects in the complex GNAS locus. Microdeletions within STX16 or GNAS have been identified in familial cases with PHP-Ib, but the molecular cause of the GNAS imprinting defects in sporadic PHP-Ib cases remains poorly defined. We now report a case with sporadic PHP-Ib for whom a SNPlex analysis revealed loss of the maternal GNAS allele. Further analysis of the entire genome with a 100K SNP chip identified a paternal uniparental isodisomy affecting the entire chromosome 20 without evidence for another chromosomal abnormality. Our findings explain the observed GNAS methylation changes and the patient's hormone resistance, and furthermore suggest that chromosome 20 harbors, besides GNAS, no additional imprinted region that contributes to the clinical and laboratory phenotype. Copyright © 2010 Elsevier Inc. All rights reserved.

Determination of the concentration of potential efflux pump inhibitors, pheophorbide a and pyropheophorbide a, in the feces of animals by fluorescence spectroscopy.

PubMed

Barnes, Charles A; Rasmussen, Sharon L; Petrich, Jacob W; Rasmussen, Mark A

2012-10-24

Efflux pumps are vital bacterial components, and research has demonstrated that some plant compounds such as pheophorbide a (php) possess efflux pump inhibitor (EPI) activity. This study determined the quantity of php present in feces as an indicator of EPI activity. Feces were collected from different species of animals fed a variety of feeds. The chlorophyll metabolites php and pyropheophorbide a (pyp) were determined using fluorescense spectroscopy. The average concentrations [μg/g dry matter (DM) feces] of pyp/php in feces were as follows: guinea pig, 180; goat, 150; rabbit, 150; dairy cow, 120; feedlot cattle, 60; rat, <1; pig, <1; chicken, <1. These data indicate that animals consuming "green" diets will excrete feces with concentrations of php/pyp that exceed levels demonstrated to be inhibitory to bacterial efflux pumps (0.5 μg/mL). The natural presence EPIs in the gastrointestinal tract may modulate the activity of microbial efflux pumps and exert selection pressure upon resident microbial populations.

MCTP is an ER-resident calcium sensor that stabilizes synaptic transmission and homeostatic plasticity

PubMed Central

Genç, Özgür; Dickman, Dion K; Ma, Wenpei; Tong, Amy; Fetter, Richard D; Davis, Graeme W

2017-01-01

Presynaptic homeostatic plasticity (PHP) controls synaptic transmission in organisms from Drosophila to human and is hypothesized to be relevant to the cause of human disease. However, the underlying molecular mechanisms of PHP are just emerging and direct disease associations remain obscure. In a forward genetic screen for mutations that block PHP we identified mctp (Multiple C2 Domain Proteins with Two Transmembrane Regions). Here we show that MCTP localizes to the membranes of the endoplasmic reticulum (ER) that elaborate throughout the soma, dendrites, axon and presynaptic terminal. Then, we demonstrate that MCTP functions downstream of presynaptic calcium influx with separable activities to stabilize baseline transmission, short-term release dynamics and PHP. Notably, PHP specifically requires the calcium coordinating residues in each of the three C2 domains of MCTP. Thus, we propose MCTP as a novel, ER-localized calcium sensor and a source of calcium-dependent feedback for the homeostatic stabilization of neurotransmission. DOI: http://dx.doi.org/10.7554/eLife.22904.001 PMID:28485711

[Left-sided native valve endocarditis by coagulase-negative staphylococci: an emerging disease].

PubMed

Haro, Juan Luis; Lomas, José M; Plata, Antonio; Ruiz, Josefa; Gálvez, Juan; de la Torre, Javier; Hidalgo-Tenorio, Carmen; Reguera, José M; Márquez, Manuel; Martínez-Marcos, Francisco; de Alarcón, Arístides

2008-05-01

To describe the epidemiological, clinical, and prognostic characteristics of patients with left-sided native valve endocarditis (LNVE) caused by coagulase-negative staphylococci (CoNS). Prospective multicenter study of endocarditis cases reported in the Andalusian Cohort for the Study of Cardiovascular Infections between 1984 and 2005. Among 470 cases of LNVE, 39 (8.3%) were caused by CoNS, a number indicating a 30% increase in the incidence of this infection over the last decade. The mean age of affected patients was 58.32 +/- 15 years and 27 (69.2%) were men. Twenty-one patients (53.8%) had previous known valve disease and half the episodes were considered nosocomial (90% of them from vascular procedures). Median time interval from the onset of symptoms to diagnosis was 14 days (range: 1-120). Renal failure (21 cases, 53.8%), intracardiac damage (11 cases, 28.2%), and central nervous system involvement (10 cases, 25.6%) were the most frequent complications. There were only 3 cases (7.7%) of septic shock. Surgery was performed in 18 patients (46.2%). Nine patients (23.1%) died, overall. Factors associated with higher mortality in the univariate analysis were acute renal failure (P = 0.023), left-sided ventricular failure (P = 0.047), and time prior to diagnosis less than 21 days (P = 0.018). As compared to LNVE due to other microorganisms, the patients were older (P = 0.018), had experienced previous nosocomial manipulation as the source of bacteremia (P < 0.001), and developed acute renal failure more frequently (P = 0.001). Mortality of LNVE due to CoNS was lower than mortality in Staphylococcus aureus infection, but higher than in Streptococcus viridans infection. Left-sided native valve endocarditis due to CoNS is now increasing because of the ageing of the population. This implies more frequent invasive procedures (mainly vascular) as a consequence of the concomitant disease. Nonetheless, the mortality associated with LNVE due to CoNS does not seem to be greater than infection caused by other pathogens.

U-PHOS Project: Development of a Large Diameter Pulsating Heat Pipe Experiment on board REXUS 22

NASA Astrophysics Data System (ADS)

Nannipieri, P.; Anichini, M.; Barsocchi, L.; Becatti, G.; Buoni, L.; Celi, F.; Catarsi, A.; Di Giorgio, P.; Fattibene, P.; Ferrato, E.; Guardati, P.; Mancini, E.; Meoni, G.; Nesti, F.; Piacquadio, S.; Pratelli, E.; Quadrelli, L.; Viglione, A. S.; Zanaboni, F.; Mameli, M.; Baronti, F.; Fanucci, L.; Marcuccio, S.; Bartoli, C.; Di Marco, P.; Bianco, N.; Marengo, M.; Filippeschi, S.

2017-01-01

U-PHOS Project aims at analysing and characterising the behaviour of a large diameter Pulsating Heat Pipe (PHP) on board REXUS 22 sounding rocket. A PHP is a passive thermal control device where the heat is efficiently transported by means of the self-sustained oscillatory fluid motion driven by the phase change phenomena. Since, in milli-gravity conditions, buoyancy forces become less intense, the PHP diameter may be increased still maintaining the slug/plug typical flow pattern. Consequently, the PHP heat power capability may be increased too. U-PHOS aims at proving that a large diameter PHP effectively works in milli-g conditions by characterizing its thermal response during a sounding rocket flight. The actual PHP tube is made of aluminum (3 mm inner diameter, filled with FC-72), heated at the evaporator by a compact electrical resistance, cooled at the condenser by a Phase Change Material (PCM) embedded in a metallic foam. The tube wall temperatures are recorded by means of Fibre Bragg Grating (FBG) sensors; the local fluid pressure is acquired by means of a pressure transducer. The present work intends to report the actual status of the project, focusing in particular on the experiment improvements with respect to the previous campaign.

The NH2-terminal php domain of the alpha subunit of the Escherichia coli replicase binds the epsilon proofreading subunit.

PubMed

Wieczorek, Anna; McHenry, Charles S

2006-05-05

The alpha subunit of the replicase of all bacteria contains a php domain, initially identified by its similarity to histidinol phosphatase but of otherwise unknown function (Aravind, L., and Koonin, E. V. (1998) Nucleic Acids Res. 26, 3746-3752). Deletion of 60 residues from the NH2 terminus of the alpha php domain destroys epsilon binding. The minimal 255-residue php domain, estimated by sequence alignment with homolog YcdX, is insufficient for epsilon binding. However, a 320-residue segment including sequences that immediately precede the polymerase domain binds epsilon with the same affinity as the 1160-residue full-length alpha subunit. A subset of mutations of a conserved acidic residue (Asp43 in Escherichia coli alpha) present in the php domain of all bacterial replicases resulted in defects in epsilon binding. Using sequence alignments, we show that the prototypical gram+ Pol C, which contains the polymerase and proofreading activities within the same polypeptide chain, has an epsilon-like sequence inserted in a surface loop near the center of the homologous YcdX protein. These findings suggest that the php domain serves as a platform to enable coordination of proofreading and polymerase activities during chromosomal replication.

Endocrine profile and phenotype-(epi)genotype correlation in Spanish patients with pseudohypoparathyroidism.

PubMed

Fernández-Rebollo, Eduardo; Lecumberri, Beatriz; Gaztambide, Sonia; Martinez-Indart, Lorea; Perez de Nanclares, Guiomar; Castaño, Luis

2013-05-01

Recent advances in genetics and epigenetics have revealed an overlap between molecular and clinical features of pseudohypoparathyroidism (PHP) subtypes, broadening the previous spectrum of PHP genotype-phenotype correlations and indicating limitations of the current classification of the disease. The aim of the study was to screen patients with clinical diagnoses of PHP type I or pseudo-PHP for underlying molecular defects and explore possible correlations between molecular findings and clinical features. We investigated the GNAS locus at the molecular level in 72 affected patients (46 women and 26 men) from 56 nonrelated families. Clinical data were obtained for 63 of these patients (38 women and 25 men). The molecular analysis showed that 35 patients carried structural mutations, 32 had loss of methylation, and 2 had a 2q37 deletion but did not reveal any (epi)mutation for 3 patients. Comparing these results and the clinical data, we observed that a younger age at diagnosis was associated with structural defects at the GNAS gene and epigenetic defects with a diagnosis later in life (9.19 ± 1.64 vs 24.57 ± 2.28 years, P < .0001). This first global review of PHP in Spain highlights the importance of a detailed clinical and genetic study of each patient and the integrated analysis of the findings from the two approaches. It may also help geneticists and clinicians to raise the suspicion of PHP earlier, reach more accurate diagnoses, and provide patients with PHP and their families with useful genetic information and counseling, thereby improving outcomes and quality of life.

Correlations between M-CHARTS and PHP findings and subjective perception of metamorphopsia in patients with macular diseases.

PubMed

Arimura, Eiko; Matsumoto, Chota; Nomoto, Hiroki; Hashimoto, Shigeki; Takada, Sonoko; Okuyama, Sachiko; Shimomura, Yoshikazu

2011-01-05

To assess the correlations between a patient's subjective perception of metamorphopsia and the clinical measurements of metamorphopsia by M-CHARTS and PreView PHP (PHP). The authors designed a 10-item questionnaire focusing on the symptoms of metamorphopsia and verified its validity with a Rasch analysis. M-CHARTS measured the minimum visual angle of a dotted line needed to detect metamorphopsia, and PHP used the hyperacuity function for detection. Subjects were 39 patients with idiopathic epiretinal membrane (ERM), 22 patients with idiopathic macular hole (M-hole), 19 patients with age-related macular degeneration (AMD), and 51 healthy controls. Rasch analysis suggested the elimination of one question. The nine-item questionnaire score significantly correlated to the M-CHARTS score in ERM (r = 0.59; P = 0.0004) but not in M-hole and to the PHP result in AMD (r = -0.29; P = 0.04) but not in ERM. Eighty percent of ERM patients with greater horizontal M-CHARTS score subjectively perceived horizontal metamorphopsia more often. M-CHARTS showed better sensitivities than PHP in both ERM (89% vs. 42%) and AMD (74% vs. 68%) and better specificity (100% vs. 71%) in healthy controls. Rasch analysis indicated that the present form of the questionnaire is better suited for moderate to severe cases of metamorphopsia than for mild cases. The questionnaire appears to be a valid assessment of patient subjective perception of metamorphopsia and can be used to supplement the clinical measurements of metamorphopsia by M-CHARTS and PHP in patients with macular diseases.

Epidemiology of biopsy-proven glomerulonephritis in Queensland adults.

PubMed

Jegatheesan, Dev; Nath, Karthik; Reyaldeen, Reza; Sivasuthan, Goutham; John, George T; Francis, Leo; Rajmokan, Mohana; Ranganathan, Dwarakanathan

2016-01-01

There is a paucity of data pertaining to the incidence of biopsy-proven glomerulonephritis (GN) in Australia. This retrospective study aims to review the data from all adult native renal biopsies performed in the state of Queensland from 2002 to 2011--comparing results with centres from across the world. Pathology reports of 3697 adult native kidney biopsies were reviewed, of which 2048 had GN diagnoses. Age, gender, clinical indication and histopathology findings were compared. The average age at biopsy was 48 ± 17 years. Male preponderance was noted overall (∼60%), with lupus nephritis being the only individual GN with female predilection. The average rate of biopsy was 12.04 per hundred thousand people per year (php/yr). Nephrotic and nephritic syndromes comprised approximately 75% of all clinical indications that lead to GN diagnoses. IgA nephropathy (1.41 php/yr) was the most common primary GN followed by focal segmental glomerulosclerosis (1.02 php/yr) and crescentic GN (0.73 php/yr). Diabetic nephropathy (0.84 php/yr), lupus nephritis (0.69 php/yr) and amyloidosis (0.19 php/yr) were the most commonly identified secondary GN. IgA nephropathy is the predominant primary GN in Queensland, and nephrotic syndrome the most common indication for a renal biopsy. While crescentic GN incidence has significantly increased with time, focal segmental glomerulosclerosis incidence has not shown any trend. Incidence of GN overall appears to increase with age. The annual rate of biopsy in this study appears lower than previously published in an Australian population. © 2015 Asian Pacific Society of Nephrology.

In vitro activity of ceftazidime/avibactam against Gram-negative pathogens isolated from pneumonia in hospitalised patients, including ventilated patients.

PubMed

Flamm, Robert K; Nichols, Wright W; Sader, Helio S; Farrell, David J; Jones, Ronald N

2016-03-01

The activities of the novel β-lactam/non-β-lactam β-lactamase inhibitor combination ceftazidime/avibactam and comparators were evaluated against isolates from pneumonia in hospitalised patients including ventilated patients (PHP, pneumonia not designated as VABP; VABP, pneumonia in ventilated patients). Isolates were from the European-Mediterranean region (EuM), China and the USA collected in the SENTRY Antimicrobial Surveillance Program between 2009 and 2011 inclusive. A total of 2393 organisms from PHP were from the EuM, 888 from China and 3213 from the USA; from VABP patients there were 918, 97 and 692 organisms collected, respectively. Among Enterobacteriaceae from PHP, ceftazidime/avibactam MIC90 values against Escherichia coli ranged from 0.25-0.5mg/L and Klebsiella spp. MIC90 values were 0.5mg/L in each region. Among VABP isolates, MIC90 values for ceftazidime/avibactam against E. coli were 0.25mg/L; for Klebsiella spp. from VABP patients, MIC90 values were similar to those obtained against PHP isolates. The MIC of ceftazidime/avibactam was ≤8mg/L against 92-96% of Pseudomonas aeruginosa isolated from PHP patients. Isolates of P. aeruginosa from VABP patients were of lower susceptibility to all antibacterial agents (e.g. depending on region, meropenem susceptibilities were 51.2-69.4% in contrast to 68.3-76.7% among PHP patients). However, ceftazidime/avibactam inhibited 79.2-95.4% of VABP isolates at an MIC of ≤8mg/L. Acinetobacter spp. were resistant to many agents and only rates of susceptibility to colistin were >90% across all regions both for PHP and VABP isolates. Ceftazidime/avibactam was generally active against a high proportion of isolates resistant to ceftazidime from PHP and VAPB patients. Copyright © 2016 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Preferential Hyperacuity Perimeter (PreView PHP) for detecting choroidal neovascularization study.

PubMed

Alster, Yair; Bressler, Neil M; Bressler, Susan B; Brimacombe, Judith A; Crompton, R Michael; Duh, Yi-Jing; Gabel, Veit-Peter; Heier, Jeffrey S; Ip, Michael S; Loewenstein, Anat; Packo, Kirk H; Stur, Michael; Toaff, Techiya

2005-10-01

To assess the ability of the Preferential Hyperacuity Perimeter (PreView PHP; Carl Zeiss Meditec, Dublin, CA) to detect recent-onset choroidal neovascularization (CNV) resulting from age-related macular degeneration (AMD) and to differentiate it from an intermediate stage of AMD. Prospective, comparative, concurrent, nonrandomized, multicenter study. Eligible participants' study eyes had a corrected visual acuity of 20/160 or better and either untreated CNV from AMD diagnosed within the last 60 days or an intermediate stage of AMD. After obtaining consent, visual acuity with habitual correction, masked PHP testing, stereoscopic color fundus photography, and fluorescein angiography were performed. Photographs and angiograms were evaluated by graders masked to diagnosis and PHP results. The reading center's diagnosis determined if the patient was categorized as having intermediate AMD or neovascular AMD. A successful study outcome was defined a priori as a sensitivity of at least 80% and a specificity of at least 80%. Of 185 patients who gave consent to be enrolled, 11 (6%) had PHP results judged to be unreliable. An additional 52 were not included because they did not meet all eligibility criteria. Of the remaining 122 patients, 57 had an intermediate stage of AMD and 65 had neovascular AMD. The sensitivity to detect newly diagnosed CNV using PHP testing was 82% (95% confidence interval [CI], 70%-90%). The specificity to differentiate newly diagnosed CNV from the intermediate stage of AMD using PHP testing was 88% (95% CI, 76%-95%). Preferential Hyperacuity Perimeter testing can detect recent-onset CNV resulting from AMD and can differentiate it from an intermediate stage of AMD with high sensitivity and specificity. These data suggest that monitoring with PHP should detect most cases of CNV of recent onset with few false-positive results at a stage when treatment usually would be beneficial. Thus, this monitoring should be considered in the management of the intermediate stage of AMD.

Web-client based distributed generalization and geoprocessing

USGS Publications Warehouse

Wolf, E.B.; Howe, K.

2009-01-01

Generalization and geoprocessing operations on geospatial information were once the domain of complex software running on high-performance workstations. Currently, these computationally intensive processes are the domain of desktop applications. Recent efforts have been made to move geoprocessing operations server-side in a distributed, web accessible environment. This paper initiates research into portable client-side generalization and geoprocessing operations as part of a larger effort in user-centered design for the US Geological Survey's The National Map. An implementation of the Ramer-Douglas-Peucker (RDP) line simplification algorithm was created in the open source OpenLayers geoweb client. This algorithm implementation was benchmarked using differing data structures and browser platforms. The implementation and results of the benchmarks are discussed in the general context of client-side geoprocessing. (Abstract).

Java-based browsing, visualization and processing of heterogeneous medical data from remote repositories.

PubMed

Masseroli, M; Bonacina, S; Pinciroli, F

2004-01-01

The actual development of distributed information technologies and Java programming enables employing them also in the medical arena to support the retrieval, integration and evaluation of heterogeneous data and multimodal images in a web browser environment. With this aim, we used them to implement a client-server architecture based on software agents. The client side is a Java applet running in a web browser and providing a friendly medical user interface to browse and visualize different patient and medical test data, integrating them properly. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. Based on the Java Advanced Imaging API, processing and analysis tools were developed to support the evaluation of remotely retrieved bioimages through the quantification of their features in different regions of interest. The Java platform-independence allows the centralized management of the implemented prototype and its deployment to each site where an intranet or internet connection is available. Giving healthcare providers effective support for comprehensively browsing, visualizing and evaluating medical images and records located in different remote repositories, the developed prototype can represent an important aid in providing more efficient diagnoses and medical treatments.

An Inverse Modeling Plugin for HydroDesktop using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio, C.; Over, M. W.; Rubin, Y.

2011-12-01

The CUAHSI Hydrologic Information System (HIS) software stack is based on an open and extensible architecture that facilitates the addition of new functions and capabilities at both the server side (using HydroServer) and the client side (using HydroDesktop). The HydroDesktop client plugin architecture is used here to expose a new scripting based plugin that makes use of the R statistics software as a means for conducting inverse modeling using the Method of Anchored Distributions (MAD). MAD is a Bayesian inversion technique for conditioning computational model parameters on relevant field observations yielding probabilistic distributions of the model parameters, related to the spatial random variable of interest, by assimilating multi-type and multi-scale data. The implementation of a desktop software tool for using the MAD technique is expected to significantly lower the barrier to use of inverse modeling in education, research, and resource management. The HydroDesktop MAD plugin is being developed following a community-based, open-source approach that will help both its adoption and long term sustainability as a user tool. This presentation will briefly introduce MAD, HydroDesktop, and the MAD plugin and software development effort.

Effect of treatment with depot somatostatin analogue octreotide on primary hyperparathyroidism (PHP) in multiple endocrine neoplasia type 1 (MEN1) patients.

PubMed

Faggiano, Antongiulio; Tavares, Lidice Brandao; Tauchmanova, Libuse; Milone, Francesco; Mansueto, Gelsomina; Ramundo, Valeria; De Caro, Maria Laura Del Basso; Lombardi, Gaetano; De Rosa, Gaetano; Colao, Annamaria

2008-11-01

In patients with multiple endocrine neoplasia type 1 (MEN1), expression of somatostatin receptor (SST) in parathyroid adenomas and effectiveness of therapy with somatostatin analogues on primary hyperparathyroidism (PHP) have been scarcely investigated. To evaluate the effects of depot long acting octreotide (OCT-LAR) in patients with MEN1-related PHP. Eight patients with a genetically confirmed MEN1, presenting both PHP and duodeno-pancreatic neuroendocrine tumours (NET), were enrolled. The initial treatment was OCT-LAR 30 mg every 4 weeks. This therapy was established to stabilize the duodeno-pancreatic NET before to perform parathyroidectomy for PHP. Before OCT-LAR therapy, a SST scintigraphy was performed in all patients. SST subtype 2A immunohistochemistry was performed on parathyroid tumour samples from three patients undergone parathyroidectomy after OCT-LAR therapy. Serum concentrations of PTH, calcium and phosphorus as well as the 24-h urine calcium : creatinine ratio and the renal threshold phosphate concentration were evaluated before and after OCT-LAR. After OCT-LAR therapy, hypercalcaemia and hypercalciuria normalized in 75% and 62.5% of patients, respectively, and serum phosphorus and renal threshold phosphate significantly increased. Serum PTH concentrations significantly decreased in all patients and normalized in two of them. SST subtype 2A immunostaining was found in all parathyroid adenomas investigated, while SST scintigraphy showed a positive parathyroid tumour uptake in three of eight patients (37.5%). Six months of OCT-LAR therapy controlled hypercalcaemia and hypercalciuria in two-thirds of patients with MEN1-related PHP. Direct OCT-LAR effects mediated by binding to SST expression on parathyroid tumour cells are likely the main mechanism to explain the activity of this compound on calcium and phosphorus abnormalities in MEN1 PHP.

Phene Plate (PhP) biochemical fingerprinting. A screening method for epidemiological typing of enterococcal isolates.

PubMed

Saeedi, B; Tärnberg, M; Gill, H; Hällgren, A; Jonasson, J; Nilsson, L E; Isaksson, B; Kühn, I; Hanberger, H

2005-09-01

Pulsed-field gel electrophoresis (PFGE) is currently considered the gold standard for genotyping of enterococci. However, PFGE is both expensive and time-consuming. The purpose of this study was to investigate whether the PhP system can be used as a reliable clinical screening method for detection of genetically related isolates of enterococci. If so, it should be possible to minimize the number of isolates subjected to PFGE typing, which would save time and money. Ninety-nine clinical enterococcal isolates were analysed by PhP (similarity levels 0.90-0.975) and PFGE (similarity levels < or =3 and < or =6 bands) and all possible pairs of isolates were cross-classified as matched or mismatched. We found that the probability that a pair of isolates (A and B) belonging to the same type according to PhP also belong to the same cluster according to PFGE, i.e. p(A(PFGE)=B(PFGE) * A(PhP)=B(PhP)), and the probability that a pair of isolates of different types according to PhP also belong to different clusters according to PFGE, i.e. p(A(PFGE) not equalB(PFGE) * A(PhP) not equalB(PhP)), was relatively high for E. faecalis (0.86 and 0.96, respectively), but was lower for E. faecium (0.51 and 0.77, respectively). The concordance which shows the probability that PhP and PFGE agree on match or mismatch was 86%-93% for E. faecalis and 54%-66% for E. faecium, which indicates that the PhP method may be useful for epidemiological typing of E. faecalis in the current settings but not for E. faecium.

Evaluation of a pyridoxylated hemoglobin polyoxyethylene conjugate solution as a perfusate for small intestine preservation.

PubMed

Liu, H; Agishi, T; Kawai, T; Hayashi, T; Fujita, S; Fuchinoue, S; Takahashi, K; Teraoka, S; Ota, K

1992-01-01

A new type of artificial blood, pyridoxylated hemoglobin-polyoxyethylene conjugate (PHP) solution, (developed by PHP research group of the department of health and welfare of Japan, and produced by Ajinomoto Co., Inc. Tokyo) as an oxygen-carrying component, has been recently devised using hemoglobin obtained from hemolyzed human erythrocytes. Recently, the studies using this solution as a preservation solution were performed in some instances. To examine the mechanism of improved viability using this solution as a preservation solution, we developed a model of orthotopic small intestine transplantation (OIT) in the rat. As a baseline study, we compared parameters of viability of the grafts preserved in Collins and UW solution to those preserved in PHP solution including a survival rate, a serum level total protein and albumin, and a change in body weight after transplantation. In our study, the simple hypothermia storage together with intestinal perfusion preservation with PHP solution was performed. Animals were divided into 6, 12, and 24 hr preservation groups. All of the rats survived after 6 hr preservation following transplantation. However, in 12 hr storage, five of six rats in PHP solution preservation survived and recovery in body weight after grafting was better than those with Collins and UW solution. We conclude that the PHP solution is, therefore, considered to possibly be a more suitable perfusate for small intestine preservation than Collins and UW solution.

Better Targeting, Better Efficiency for Wide-Scale Neuronal Transduction with the Synapsin Promoter and AAV-PHP.B

PubMed Central

Jackson, Kasey L.; Dayton, Robert D.; Deverman, Benjamin E.; Klein, Ronald L.

2016-01-01

Widespread genetic modification of cells in the central nervous system (CNS) with a viral vector has become possible and increasingly more efficient. We previously applied an AAV9 vector with the cytomegalovirus/chicken beta-actin (CBA) hybrid promoter and achieved wide-scale CNS transduction in neonatal and adult rats. However, this method transduces a variety of tissues in addition to the CNS. Thus we studied intravenous AAV9 gene transfer with a synapsin promoter to better target the neurons. We noted in systematic comparisons that the synapsin promoter drives lower level expression than does the CBA promoter. The engineered adeno-associated virus (AAV)-PHP.B serotype was compared with AAV9, and AAV-PHP.B did enhance the efficiency of expression. Combining the synapsin promoter with AAV-PHP.B could therefore be advantageous in terms of combining two refinements of targeting and efficiency. Wide-scale expression was used to model a disease with widespread pathology. Vectors encoding the amyotrophic lateral sclerosis (ALS)-related protein transactive response DNA-binding protein, 43 kDa (TDP-43) with the synapsin promoter and AAV-PHP.B were used for efficient CNS-targeted TDP-43 expression. Intracerebroventricular injections were also explored to limit TDP-43 expression to the CNS. The neuron-selective promoter and the AAV-PHP.B enhanced gene transfer and ALS disease modeling in adult rats. PMID:27867348

Better Targeting, Better Efficiency for Wide-Scale Neuronal Transduction with the Synapsin Promoter and AAV-PHP.B.

PubMed

Jackson, Kasey L; Dayton, Robert D; Deverman, Benjamin E; Klein, Ronald L

2016-01-01

Widespread genetic modification of cells in the central nervous system (CNS) with a viral vector has become possible and increasingly more efficient. We previously applied an AAV9 vector with the cytomegalovirus/chicken beta-actin (CBA) hybrid promoter and achieved wide-scale CNS transduction in neonatal and adult rats. However, this method transduces a variety of tissues in addition to the CNS. Thus we studied intravenous AAV9 gene transfer with a synapsin promoter to better target the neurons. We noted in systematic comparisons that the synapsin promoter drives lower level expression than does the CBA promoter. The engineered adeno-associated virus (AAV)-PHP.B serotype was compared with AAV9, and AAV-PHP.B did enhance the efficiency of expression. Combining the synapsin promoter with AAV-PHP.B could therefore be advantageous in terms of combining two refinements of targeting and efficiency. Wide-scale expression was used to model a disease with widespread pathology. Vectors encoding the amyotrophic lateral sclerosis (ALS)-related protein transactive response DNA-binding protein, 43 kDa (TDP-43) with the synapsin promoter and AAV-PHP.B were used for efficient CNS-targeted TDP-43 expression. Intracerebroventricular injections were also explored to limit TDP-43 expression to the CNS. The neuron-selective promoter and the AAV-PHP.B enhanced gene transfer and ALS disease modeling in adult rats.

Mobile object retrieval in server-based image databases

NASA Astrophysics Data System (ADS)

Manger, D.; Pagel, F.; Widak, H.

2013-05-01

The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

Follow-up Findings in a Turkish Girl with Pseudohypoparathyroidism Type Ia Caused by a Novel Heterozygous Mutation in the GNAS Gene.

PubMed

Şahin, Sezgin; Hiort, Olaf; Thiele, Susanne; Evliyaoğlu, Olcay; Tüysüz, Beyhan

2017-03-01

Pseudohypoparathyroidism type Ia (PHP-Ia) is characterized by multihormone resistance and an Albright hereditary osteodystrophy (AHO) phenotype. It is caused by heterozygous mutations in GNAS gene. Clinical and biochemical findings of a female PHP-Ia patient were evaluated from age of diagnosis (6.5 years) to 14.5 years of age. The patient had short stature, brachydactyly, and subcutaneous heterotopic ossifications. Serum calcium and phosphorus levels were normal, but parathyroid hormone levels were high. Based on the typical clinical findings of AHO phenotype and biochemical findings, she was diagnosed as having PHP-Ia. A novel heterozygous mutation (c.128T>C) was found in the GNAS gene. Follow-up examinations revealed resistance to thyroid-stimulating hormone and a bioinactive growth hormone. Clinicians should take into consideration PHP-Ia in patients referred with short stature, and patients with an AHO phenotype must be further evaluated for hormone resistance, GNAS gene mutation, Gsα activity. To our knowledge, this is the first case report describing bioinactive growth hormone in PHP-Ia.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis.

PubMed

Zhang, Liang; Chen, Ruyi; Dong, Zhe; Li, Xin

2013-01-01

Organophosphates (OPs) are extremely toxic compounds that are used as insecticides or even as chemical warfare agents. Phosphotriesterases (PHPs) are responsible for the detoxification of OPs by catalysing their degradation. Almost 100 PHP structures have been solved to date, yet the crystal structure of the phosphotriesterase from Mycobacterium tuberculosis (mPHP) remains unavailable. This study reports the first crystallization of mPHP. The crystal belonged to space group C222(1), with unit-cell parameters a = 68.03, b = 149.60, c = 74.23 Å, α = β = γ = 90°. An analytical ultracentrifugation experiment suggested that mPHP exists as a dimer in solution, even though one molecule is calculated to be present in the asymmetric unit according to the structural data.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis

PubMed Central

Zhang, Liang; Chen, Ruyi; Dong, Zhe; Li, Xin

2013-01-01

Organophosphates (OPs) are extremely toxic compounds that are used as insecticides or even as chemical warfare agents. Phosphotriesterases (PHPs) are responsible for the detoxification of OPs by catalysing their degradation. Almost 100 PHP structures have been solved to date, yet the crystal structure of the phosphotriesterase from Mycobacterium tuberculosis (mPHP) remains unavailable. This study reports the first crystallization of mPHP. The crystal belonged to space group C2221, with unit-cell parameters a = 68.03, b = 149.60, c = 74.23 Å, α = β = γ = 90°. An analytical ultracentrifugation experiment suggested that mPHP exists as a dimer in solution, even though one molecule is calculated to be present in the asymmetric unit according to the structural data. PMID:23295488

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

PubMed

Bernal-Rusiel, Jorge L; Rannou, Nicolas; Gollub, Randy L; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView , a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

Large scale and cloud-based multi-model analytics experiments on climate change data in the Earth System Grid Federation

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Płóciennik, Marcin; Doutriaux, Charles; Blanquer, Ignacio; Barbera, Roberto; Donvito, Giacinto; Williams, Dean N.; Anantharaj, Valentine; Salomoni, Davide D.; Aloisio, Giovanni

2017-04-01

In many scientific domains such as climate, data is often n-dimensional and requires tools that support specialized data types and primitives to be properly stored, accessed, analysed and visualized. Moreover, new challenges arise in large-scale scenarios and eco-systems where petabytes (PB) of data can be available and data can be distributed and/or replicated, such as the Earth System Grid Federation (ESGF) serving the Coupled Model Intercomparison Project, Phase 5 (CMIP5) experiment, providing access to 2.5PB of data for the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5). A case study on climate models intercomparison data analysis addressing several classes of multi-model experiments is being implemented in the context of the EU H2020 INDIGO-DataCloud project. Such experiments require the availability of large amount of data (multi-terabyte order) related to the output of several climate models simulations as well as the exploitation of scientific data management tools for large-scale data analytics. More specifically, the talk discusses in detail a use case on precipitation trend analysis in terms of requirements, architectural design solution, and infrastructural implementation. The experiment has been tested and validated on CMIP5 datasets, in the context of a large scale distributed testbed across EU and US involving three ESGF sites (LLNL, ORNL, and CMCC) and one central orchestrator site (PSNC). The general "environment" of the case study relates to: (i) multi-model data analysis inter-comparison challenges; (ii) addressed on CMIP5 data; and (iii) which are made available through the IS-ENES/ESGF infrastructure. The added value of the solution proposed in the INDIGO-DataCloud project are summarized in the following: (i) it implements a different paradigm (from client- to server-side); (ii) it intrinsically reduces data movement; (iii) it makes lightweight the end-user setup; (iv) it fosters re-usability (of data, final/intermediate products, workflows, sessions, etc.) since everything is managed on the server-side; (v) it complements, extends and interoperates with the ESGF stack; (vi) it provides a "tool" for scientists to run multi-model experiments, and finally; and (vii) it can drastically reduce the time-to-solution for these experiments from weeks to hours. At the time the contribution is being written, the proposed testbed represents the first concrete implementation of a distributed multi-model experiment in the ESGF/CMIP context joining server-side and parallel processing, end-to-end workflow management and cloud computing. As opposed to the current scenario based on search & discovery, data download, and client-based data analysis, the INDIGO-DataCloud architectural solution described in this contribution addresses the scientific computing & analytics requirements by providing a paradigm shift based on server-side and high performance big data frameworks jointly with two-level workflow management systems realized at the PaaS level via a cloud infrastructure.

Pseudohypoparathyroidism with diabetes mellitus and hypothyroidism.

PubMed

Saikia, Bedangshu; Arora, Sunaina; Puliyel, Jacob M

2012-12-01

We report a 12-year-old child with pseudohypoparathyroidism (PHP) whose mother had pseudopseudohypoparathyroidism. The child had low serum calcium, high phosphorous and high parathormone (PTH) levels. PHP occurs due to a defect in the guanine nucleotide binding protein (G protein). She also had hypothyroidism which is known to utilize the G protein pathway. She developed T 1 diabetes mellitus (T1DM) while under follow-up. This is arguably the first time T1DM has been reported associated with PHP.

Environmental Data Store (EDS): A multi-node Data Storage Facility for diverse sets of Geoscience Data

NASA Astrophysics Data System (ADS)

Piasecki, M.; Ji, P.

2014-12-01

Geoscience data comes in many flavors that are determined by type of data such as continous on a grid or mesh or discrete colelcted at point either as one time samples or a stream of data coming of sensors, but coudl also encompass digital files of any time type such text files, WORD or EXCEL documents, or audio and video files. We present a storage facility that is comprsed of 6 nodes each of speciaized to host a certain data type: grid based data (netCDF on a THREDDS server), GIS data (shapefiles using GeoServer), point time series data (CUAHSI ODM), sample data (EDBS), and any digital data (RAMADAA) plus a server fro Remote sensing data and its products. While there is overlap in data type storage capabilities (rasters can go into several of these nodes) we prefer to use dedicated storage facilities that are a) freeware, and b) have a good degree of maturity, and c) have shown their utility for stroing a cetain type. In addition it allows to place these commonly used software stacks and storage solutiosn side-by-side to develop interoprability strategies. We have used a DRUPAL based system to handle user regoistration and authentication, and also use the system for data submission and data search. In support for tis system we developed an extensive controlled vocabulary system that is an amalgamation of various CVs used in the geosciecne community in order to achieve as high a degree of recognition, such the CF conventions, CUAHSI Cvs, , NASA (GCMD), EPA and USGS taxonomies, GEMET, in addition to ontological representations such as SWEET.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination

PubMed Central

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-01-01

Abstract Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. PMID:29025122

Prototyping Tool for Web-Based Multiuser Online Role-Playing Game

NASA Astrophysics Data System (ADS)

Okamoto, Shusuke; Kamada, Masaru; Yonekura, Tatsuhiro

This letter proposes a prototyping tool for Web-based Multiuser Online Role-Playing Game (MORPG). The design goal is to make this tool simple and powerful. The tool is comprised of a GUI editor, a translator and a runtime environment. The GUI editor is used to edit state-transition diagrams, each of which defines the behavior of the fictional characters. The state-transition diagrams are translated into C program codes, which plays the role of a game engine in RPG system. The runtime environment includes PHP, JavaScript with Ajax and HTML. So the prototype system can be played on the usual Web browser, such as Fire-fox, Safari and IE. On a click or key press by a player, the Web browser sends it to the Web server to reflect its consequence on the screens which other players are looking at. Prospected users of this tool include programming novices and schoolchildren. The knowledge or skill of any specific programming languages is not required to create state-transition diagrams. Its structure is not only suitable for the definition of a character behavior but also intuitive to help novices understand. Therefore, the users can easily create Web-based MORPG system with the tool.

Real-time Geographic Information System (GIS) for Monitoring the Area of Potential Water Level Using Rule Based System

NASA Astrophysics Data System (ADS)

Anugrah, Wirdah; Suryono; Suseno, Jatmiko Endro

2018-02-01

Management of water resources based on Geographic Information System can provide substantial benefits to water availability settings. Monitoring the potential water level is needed in the development sector, agriculture, energy and others. In this research is developed water resource information system using real-time Geographic Information System concept for monitoring the potential water level of web based area by applying rule based system method. GIS consists of hardware, software, and database. Based on the web-based GIS architecture, this study uses a set of computer that are connected to the network, run on the Apache web server and PHP programming language using MySQL database. The Ultrasound Wireless Sensor System is used as a water level data input. It also includes time and geographic location information. This GIS maps the five sensor locations. GIS is processed through a rule based system to determine the level of potential water level of the area. Water level monitoring information result can be displayed on thematic maps by overlaying more than one layer, and also generating information in the form of tables from the database, as well as graphs are based on the timing of events and the water level values.

Electronic patient record and archive of records in Cardio.net system for telecardiology.

PubMed

Sierdziński, Janusz; Karpiński, Grzegorz

2003-01-01

In modern medicine the well structured patient data set, fast access to it and reporting capability become an important question. With the dynamic development of information technology (IT) such question is solved via building electronic patient record (EPR) archives. We then obtain fast access to patient data, diagnostic and treatment protocols etc. It results in more efficient, better and cheaper treatment. The aim of the work was to design a uniform Electronic Patient Record, implemented in cardio.net system for telecardiology allowing the co-operation among regional hospitals and reference centers. It includes questionnaires for demographic data and questionnaires supporting doctor's work (initial diagnosis, final diagnosis, history and physical, ECG at the discharge, applied treatment, additional tests, drugs, daily and periodical reports). The browser is implemented in EPR archive to facilitate data retrieval. Several tools for creating EPR and EPR archive were used such as: XML, PHP, Java Script and MySQL. The separate question is the security of data on WWW server. The security is ensured via Security Socket Layer (SSL) protocols and other tools. EPR in Cardio.net system is a module enabling the co-work of many physicians and the communication among different medical centers.

Implementation of electronic logbook for trainees of general surgery in Thailand.

PubMed

Aphinives, Potchavit

2013-01-01

All trainees are required to keep a record of their surgical skill and experiences throughout the trainingperiod in a logbook format. Paper-based logbook has several limitations. Therefore, an electronic logbook was introduced to replace the paper-based logbook. An electronic logbook program was developed in November 2005. This program was designed as web-based application based upon PHP scripts beneath Apache web server and MySQL database implementation. Only simpliJfied and essential data, such as hospital number diagnosis, surgical procedure, and pathological findings, etc. are recorded. The electronic logbook databases between Academic year 2006 and 2011 were analyzed. The annual recordedsurgical procedures gradually increasedfrom 41,214 procedures in 2006 to 66,643 procedures in 2011. Around one-third of all records were not verified by attending staffs, i.e. 27.59% (2006), 31.69% (2007), 18.06% (2008), 28.42% (2009), 30.18% (2010), and 31.41% (2011). On the Education year 2011, the three most common procedural groups included colon, rectum & anus group, appendix group, and vascular group, respectively. Advantages of the electronic logbook included more efficient data access, increased ability to monitor trainees and trainers, and analysis of procedural varieties among the training institutes.

Kin-Driver: a database of driver mutations in protein kinases.

PubMed

Simonetti, Franco L; Tornador, Cristian; Nabau-Moretó, Nuria; Molina-Vila, Miguel A; Marino-Buslje, Cristina

2014-01-01

Somatic mutations in protein kinases (PKs) are frequent driver events in many human tumors, while germ-line mutations are associated with hereditary diseases. Here we present Kin-driver, the first database that compiles driver mutations in PKs with experimental evidence demonstrating their functional role. Kin-driver is a manual expert-curated database that pays special attention to activating mutations (AMs) and can serve as a validation set to develop new generation tools focused on the prediction of gain-of-function driver mutations. It also offers an easy and intuitive environment to facilitate the visualization and analysis of mutations in PKs. Because all mutations are mapped onto a multiple sequence alignment, analogue positions between kinases can be identified and tentative new mutations can be proposed for studying by transferring annotation. Finally, our database can also be of use to clinical and translational laboratories, helping them to identify uncommon AMs that can correlate with response to new antitumor drugs. The website was developed using PHP and JavaScript, which are supported by all major browsers; the database was built using MySQL server. Kin-driver is available at: http://kin-driver.leloir.org.ar/ © The Author(s) 2014. Published by Oxford University Press.

CrisprGE: a central hub of CRISPR/Cas-based genome editing.

PubMed

Kaur, Karambir; Tandon, Himani; Gupta, Amit Kumar; Kumar, Manoj

2015-01-01

CRISPR system is a powerful defense mechanism in bacteria and archaea to provide immunity against viruses. Recently, this process found a new application in intended targeting of the genomes. CRISPR-mediated genome editing is performed by two main components namely single guide RNA and Cas9 protein. Despite the enormous data generated in this area, there is a dearth of high throughput resource. Therefore, we have developed CrisprGE, a central hub of CRISPR/Cas-based genome editing. Presently, this database holds a total of 4680 entries of 223 unique genes from 32 model and other organisms. It encompasses information about the organism, gene, target gene sequences, genetic modification, modifications length, genome editing efficiency, cell line, assay, etc. This depository is developed using the open source LAMP (Linux Apache MYSQL PHP) server. User-friendly browsing, searching facility is integrated for easy data retrieval. It also includes useful tools like BLAST CrisprGE, BLAST NTdb and CRISPR Mapper. Considering potential utilities of CRISPR in the vast area of biology and therapeutics, we foresee this platform as an assistance to accelerate research in the burgeoning field of genome engineering. © The Author(s) 2015. Published by Oxford University Press.

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

PubMed

Fokkema, Ivo F A C; den Dunnen, Johan T; Taschner, Peter E M

2005-08-01

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server. (c) 2005 Wiley-Liss, Inc.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

High Speed Oblivious Random Access Memory (HS-ORAM)

DTIC Science & Technology

2015-09-01

Bryan Parno, “Non-interactive verifiable computing: Outsourcing computation to untrusted workers”, 30th International Cryptology Conference, pp. 465...holder or any other person or corporation; or convey any rights or permission to manufacture , use, or sell any patented invention that may relate to...secure outsourced data access protocols. HS-ORAM deploys a number of server- side software components running inside tamper-proof secure coprocessors

Mobile Code: The Future of the Internet

DTIC Science & Technology

1999-01-01

code ( mobile agents) to multiple proxies or servers " Customization " (e.g., re-formatting, filtering, metasearch) Information overload Diversified... Mobile code is necessary, rather than client-side code, since many customization features (such as information monitoring) do not work if the...economic foundation for Web sites, many Web sites earn money solely from advertisements . If these sites allow mobile agents to easily access the content

The OPEN Migration Platform Architecture

NASA Astrophysics Data System (ADS)

Martin, Miquel

This chapter establishes a common understanding of the meaning of migration, and introduces the OPEN functionalities, which enable application migration. We start by discussing the various definitions of migration, before focusing on the OPEN take on the concept. The chapter then covers our proposed architecture , as well as the functionality required, both from the server and the client side (i.e. the applications) in order to enable application migration.

Allostatic load: single parents, stress-related health issues, and social care.

PubMed

Johner, Randy L

2007-05-01

This article explores the possible relationships between allostatic load (AL) and stress-related health issues in the low-income single-parent population, using both a population health perspective (PHP) and a biological framework. A PHP identifies associations among such factors as gender, income, employment, and social support and their potential effect on health outcomes. A PHP also recognizes physiological and pathological manifestations of the body such as stress (mental or somatic) and individual biological parameters (for example, glucose levels) as health determinants. AL uses an aggregate score of individual biological parameters as a health measure that is exacerbated through repetitive movement of physiologic systems under stress. The social work profession should incorporate knowledge of both PHP and AL into its theory and practice domains for effective care of vulnerable populations such as single-parent families.

Experimental study on heat transfer performance of pulsating heat pipe with refrigerants

NASA Astrophysics Data System (ADS)

Wang, Xingyu; Jia, Li

2016-10-01

The effects of different refrigerants on heat transfer performance of pulsating heat pipe (PHP) are investigated experimentally. The working temperature of pulsating heat pipe is kept in the range of 20°C-50°C. The startup time of the pulsating heat pipe with refrigerants can be shorter than 4 min, when heating power is in the range of 10W?100W. The startup time decreases with heating power. Thermal resistances of PHP with filling ratio 20.55% were obviously larger than those with other filling ratios. Thermal resistance of the PHP with R134a is much smaller than that with R404A and R600a. It indicates that the heat transfer ability of R134a is better. In addition, a correlation to predict thermal resistance of PHP with refrigerants was suggested.

Biogenic platinum and palladium nanoparticles as new catalysts for the removal of pharmaceutical compounds.

PubMed

Martins, Mónica; Mourato, Cláudia; Sanches, Sandra; Noronha, João Paulo; Crespo, M T Barreto; Pereira, Inês A C

2017-01-01

Pharmaceutical products (PhP) are one of the most alarming emergent pollutants in the environment. Therefore, it is of extreme importance to investigate efficient PhP removal processes. Biologic synthesis of platinum nanoparticles (Bio-Pt) has been reported, but their catalytic activity was never investigated. In this work, we explored the potential of cell-supported platinum (Bio-Pt) and palladium (Bio-Pd) nanoparticles synthesized with Desulfovibrio vulgaris as biocatalysts for removal of four PhP: ciprofloxacin, sulfamethoxazole, ibuprofen and 17β-estradiol. The catalytic activity of the biological nanoparticles was compared with the PhP removal efficiency of D. vulgaris whole-cells. In contrast with Bio-Pd, Bio-Pt has a high catalytic activity in PhP removal, with 94, 85 and 70% removal of 17β-estradiol, sulfamethoxazole and ciprofloxacin, respectively. In addition, the estrogenic activity of 17β-estradiol was strongly reduced after the reaction with Bio-Pt, showing that this biocatalyst produces less toxic effluents. Bio-Pt or Bio-Pd did not act on ibuprofen, but this could be completely removed by D. vulgaris whole-cells, demonstrating that sulfate-reducing bacteria are among the microorganisms capable of biotransformation of ibuprofen in anaerobic environments. This study demonstrates for the first time that Bio-Pt has a high catalytic activity, and is a promising catalyst to be used in water treatment processes for the removal of antibiotics and endocrine disrupting compounds, the most problematic PhP. Copyright © 2016 Elsevier Ltd. All rights reserved.

Widespread transduction of astrocytes and neurons in the mouse central nervous system after systemic delivery of a self-complementary AAV-PHP.B vector.

PubMed

Rincon, Melvin Y; de Vin, Filip; Duqué, Sandra I; Fripont, Shelly; Castaldo, Stephanie A; Bouhuijzen-Wenger, Jessica; Holt, Matthew G

2018-04-01

Until recently, adeno-associated virus 9 (AAV9) was considered the AAV serotype most effective in crossing the blood-brain barrier (BBB) and transducing cells of the central nervous system (CNS), following systemic injection. However, a newly engineered capsid, AAV-PHP.B, is reported to cross the BBB at even higher efficiency. We investigated how much we could boost CNS transgene expression by using AAV-PHP.B carrying a self-complementary (sc) genome. To allow comparison, 6 weeks old C57BL/6 mice received intravenous injections of scAAV2/9-GFP or scAAV2/PHP.B-GFP at equivalent doses. Three weeks postinjection, transgene expression was assessed in brain and spinal cord. We consistently observed more widespread CNS transduction and higher levels of transgene expression when using the scAAV2/PHP.B-GFP vector. In particular, we observed an unprecedented level of astrocyte transduction in the cortex, when using a ubiquitous CBA promoter. In comparison, neuronal transduction was much lower than previously reported. However, strong neuronal expression (including spinal motor neurons) was observed when the human synapsin promoter was used. These findings constitute the first reported use of an AAV-PHP.B capsid, encapsulating a scAAV genome, for gene transfer in adult mice. Our results underscore the potential of this AAV construct as a platform for safer and more efficacious gene therapy vectors for the CNS.

Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.

PubMed

Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

2009-04-01

The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.

[Attitudes of physicians and nurses towards health prevention and promotion activities in Primary Care].

PubMed

Ramos-Morcillo, Antonio Jesús; Ruzafa-Martínez, María; Fernández-Salazar, Serafín; del-Pino-Casado, Rafael; Armero Barranco, David

2014-11-01

To determine the attitudes of physicians and registered nurses in the Andalusian Public Health System towards preventive and health promotion (PHP) interventions in the context of Primary Health Care and the relationship with occupational variables and self-reported competence in PHP. Multicenter, observational, descriptive study. Primary Health Care (PHC), Andalusia, Spain. A total of 282 professionals (physicians and nurses) from 22 Healthcare centers of the Andalusian public health system and who participated in the validation of CAPPAP were included. The attitude of physicians and registered nurses towards PHP activities consisted of five dimensions: improvements necessary, perception of peers attitude, importance, obstacles, and improvement opportunities. The validated CAPPAP questionnaire was used. Occupational variables and questions about self-reported competence in PHP were also included. All dimensions of CAPPAP exceeded the midpoint of the scale (2.5), with their values varying between 3.06 (SD: 0.76) in "improvement necessary", and 4.39 (SD: 0.49) in "importance". The self-declared social, occupational, and competences variables have a statistically significant relationship with the dimensions of the attitude of the professionals except: job experience in PHC, training and implementation of scheduled PHP activities. The attitudes of physicians and registered nurses towards PHP activities are acceptable, and work must be done to sustain it. Healthcare organizations should implement interventions adapted to different professional profiles. They should also increase activities to improve professional skills in order to provide the appropriate care. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

YRE Program Guide.

ERIC Educational Resources Information Center

California State Dept. of Education, Sacramento. Div. of School Facilities Planning.

This report examines single- and multi-track educational programs as found in California's public school system, explores the pros and cons of using year-round education (YRE) programs, and how to implement these programs. Each year-round tracking system is detailed using each of their calendars in a side-by-side comparison along with the…

Comparative Analysis of Active and Passive Mapping Techniques in an Internet-Based Local Area Network

DTIC Science & Technology

2004-03-01

PIII/500 (K) 512 A11 3C905 Honeynet PIII/1000 (C) 512 A11 3C905 Generator PIII/800 (C) 256 A11 3C905 Each system is running Debian GNU / Linux “unstable...Network,” September 2000. http://www.issues.af.mil/notams/notam00-5.html; accessed January 16, 2004. 5. “Debian GNU / Linux 3.0 Released,” Debian News...interact with those servers. 1.5 Summary The remainder of this document is organized into four chapters. Chapter 2 con - tains the literature review where

Anti-social networking: crowdsourcing and the cyber defence of national critical infrastructures.

PubMed

Johnson, Chris W

2014-01-01

We identify four roles that social networking plays in the 'attribution problem', which obscures whether or not cyber-attacks were state-sponsored. First, social networks motivate individuals to participate in Distributed Denial of Service attacks by providing malware and identifying potential targets. Second, attackers use an individual's social network to focus attacks, through spear phishing. Recipients are more likely to open infected attachments when they come from a trusted source. Third, social networking infrastructures create disposable architectures to coordinate attacks through command and control servers. The ubiquitous nature of these architectures makes it difficult to determine who owns and operates the servers. Finally, governments recruit anti-social criminal networks to launch attacks on third-party infrastructures using botnets. The closing sections identify a roadmap to increase resilience against the 'dark side' of social networking.

Electron tunneling in proteins program.

PubMed

Hagras, Muhammad A; Stuchebrukhov, Alexei A

2016-06-05

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi-empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross-platform client-server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well-known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

High-resolution Imaging of the Philippine Sea Plate subducting beneath Central Japan

NASA Astrophysics Data System (ADS)

Padhy, S.; Furumura, T.

2016-12-01

Thermal models predict that the oceanic crust of the young (<20 Ma) and warmer Philippine-sea plate (PHP) is more prone to melting. Deriving a high-resolution image of the PHP, including slab melting and other features of the subduction zone, is a key to understand the basics of earthquake occurrence and origin of magma in complex subduction zone like central Japan, where both the PHP and Pacific (PAC) Plates subduct. To this purpose, we analyzed high-resolution waveforms of moderate sized (M 4-6), intermediate-to-deep (>150 km) PAC earthquakes occurring in central Japan and conducted numerical simulation to derive a fine-scale PHP model, which is not constrained in earlier studies. Observations show spindle-shaped seismograms with strong converted phases and extended coda with very slow decay from a group of PAC events occurring in northern part of central Japan and recorded by high-sensitivity seismograph network (Hi-net) stations in the region. We investigate the mechanism of propagation of these anomalous waveforms using the finite difference method (FDM) simulation of wave propagation through the subduction zone. We examine the effects on waveform changes of major subduction zone features, such as the melting of oceanic crust in PHP, serpentinized mantle wedge, hydrated layer on the PAC due to slab dehydration, and anomaly in upper mantle between the PAC and PHP. Simulation results show that the waveform anomaly is primarily explained by strong scattering and absorption of high-frequency energy by the low-velocity anomalous mantle structure, with a strong coda excitation yielding spindle-shaped waveforms. The data are secondarily explained by melting of PHP in the basaltic crust. The location of the mantle anomaly is tightly constrained by the observation and evidence of PAC thinning in the region; these localized low-velocity structures aid in ascending the slab-derived fluids around the slab thinning. We expect that the results of this study will enhance our present understanding on the mechanism of intermediate to deep earthquakes in the region.

A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).

PubMed

Grigelioniene, Giedre; Nevalainen, Pasi I; Reyes, Monica; Thiele, Susanne; Tafaj, Olta; Molinaro, Angelo; Takatani, Rieko; Ala-Houhala, Marja; Nilsson, Daniel; Eisfeldt, Jesper; Lindstrand, Anna; Kottler, Marie-Laure; Mäkitie, Outi; Jüppner, Harald

2017-04-01

Pseudohypoparathyroidism type Ib (PHP1B) is characterized primarily by resistance to parathyroid hormone (PTH) and thus hypocalcemia and hyperphosphatemia, in most cases without evidence for Albright hereditary osteodystrophy (AHO). PHP1B is associated with epigenetic changes at one or several differentially-methylated regions (DMRs) within GNAS, which encodes the α-subunit of the stimulatory G protein (Gsα) and splice variants thereof. Heterozygous, maternally inherited STX16 or GNAS deletions leading to isolated loss-of-methylation (LOM) at exon A/B alone or at all maternal DMRs are the cause of autosomal dominant PHP1B (AD-PHP1B). In this study, we analyzed three affected individuals, the female proband and her two sons. All three revealed isolated LOM at GNAS exon A/B, whereas the proband's healthy maternal grandmother and uncle showed normal methylation at this locus. Haplotype analysis was consistent with linkage to the STX16/GNAS region, yet no deletion could be identified. Whole-genome sequencing of one of the patients revealed a large heterozygous inversion (1,882,433 bp). The centromeric breakpoint of the inversion is located 7,225 bp downstream of GNAS exon XL, but its DMR showed no methylation abnormality, raising the possibility that the inversion disrupts a regulatory element required only for establishing or maintaining exon A/B methylation. Because our three patients presented phenotypes consistent with PHP1B, and not with PHP1A, the Gsα promoter is probably unaffected by the inversion. Our findings expand the spectrum of genetic mutations that lead to LOM at exon A/B alone and thus biallelic expression of the transcript derived from this alternative first GNAS exon. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

Synapse-specific and compartmentalized expression of presynaptic homeostatic potentiation

PubMed Central

Li, Xiling; Goel, Pragya; Chen, Catherine; Angajala, Varun; Chen, Xun

2018-01-01

Postsynaptic compartments can be specifically modulated during various forms of synaptic plasticity, but it is unclear whether this precision is shared at presynaptic terminals. Presynaptic homeostatic plasticity (PHP) stabilizes neurotransmission at the Drosophila neuromuscular junction, where a retrograde enhancement of presynaptic neurotransmitter release compensates for diminished postsynaptic receptor functionality. To test the specificity of PHP induction and expression, we have developed a genetic manipulation to reduce postsynaptic receptor expression at one of the two muscles innervated by a single motor neuron. We find that PHP can be induced and expressed at a subset of synapses, over both acute and chronic time scales, without influencing transmission at adjacent release sites. Further, homeostatic modulations to CaMKII, vesicle pools, and functional release sites are compartmentalized and do not spread to neighboring pre- or post-synaptic structures. Thus, both PHP induction and expression mechanisms are locally transmitted and restricted to specific synaptic compartments. PMID:29620520

Identification and characterization of new designer drug 4-fluoro-PV9 and α-PHP in the seized materials.

PubMed

Majchrzak, Milena; Rojkiewicz, Marcin; Celiński, Rafał; Kuś, Piotr; Sajewicz, Mieczysław

In this study, we present identification and physicochemical characterization of new cathinone derivatives, 4-fluoro-PV9 and already known α-PHP in seized materials. Although the disclosure of α-PHP from an illegal product had been reported and characterized to some extent, the data on α-PHP are also presented together with those of 4-fluoro-PV9. The data of characterization for the two compounds were obtained by high-performance liquid chromatography (HPLC)-mass spectrometry and HPLC-diode array detection, electrospray ionization/ion trap mass spectrometry in MS 2 and MS 3 modes, gas chromatography-mass spectrometry, thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, ultraviolet-visible spectroscopy, and nuclear magnetic resonance spectroscopy. To our knowledge, this is the first report for identification and detailed characterization of 4-fluoro-PV9 circulated on the illegal drug market.

jSPyDB, an open source database-independent tool for data management

NASA Astrophysics Data System (ADS)

Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

2011-12-01

Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

Launch Support Video Site

NASA Technical Reports Server (NTRS)

OFarrell, Zachary L.

2013-01-01

The goal of this project is to create a website that displays video, countdown clock, and event times to customers during launches, without needing to be connected to the internal operations network. The requirements of this project are to also minimize the delay in the clock and events to be less than two seconds. The two parts of this are the webpage, which will display the data and videos to the user, and a server to send clock and event data to the webpage. The webpage is written in HTML with CSS and JavaScript. The JavaScript is responsible for connecting to the server, receiving new clock data, and updating the webpage. JavaScript is used for this because it can send custom HTTP requests from the webpage, and provides the ability to update parts of the webpage without having to refresh the entire page. The server application will act as a relay between the operations network, and the open internet. On the operations network side, the application receives multicast packets that contain countdown clock and events data. It will then parse the data into current countdown times and events, and create a packet with that information that can be sent to webpages. The other part will accept HTTP requests from the webpage, and respond to them with current data. The server is written in C# with some C++ files used to define the structure of data packets. The videos for the webpage will be shown in an embedded player from UStream.

Impact of sensory integration training on balance among stroke patients: sensory integration training on balance among stroke patients.

PubMed

Jang, Sang Hun; Lee, Jung-Ho

2016-01-01

This study attempts to investigate the impact that the sensory integration training has on the recovery of balance among patients with stroke by examining the muscle activity and limit of stability (LOS). A total of 28 subjects participated. The subjects were randomly allocated by the computer program to one of two groups: control (CON) group (n=15), sensory integration training (SIT) group (n=13). The research subjects received intervention five days a week for a total of four weeks. The CON group additionally received 30-minute general balance training, while the SIT group additionally received 30-minute sensory integration training. In the muscle activity, the improvement of Erector spinae (ES) and Gluteus medius (GM) was more significant in the SIT group than in the CON group. In the LOS, the improvement of affected side and forward side was significantly higher in the SIT group compared to the CON group. Sensory integration training can improve balance ability of patients with stroke by increasing muscle activity of stance limb muscles such as GM and trunk extensor such as ES along with enhancement of the limit of stability.

Modeling of pulsating heat pipes.

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

Givler, Richard C.; Martinez, Mario J.

This report summarizes the results of a computer model that describes the behavior of pulsating heat pipes (PHP). The purpose of the project was to develop a highly efficient (as compared to the heat transfer capability of solid copper) thermal groundplane (TGP) using silicon carbide (SiC) as the substrate material and water as the working fluid. The objective of this project is to develop a multi-physics model for this complex phenomenon to assist with an understanding of how PHPs operate and to be able to understand how various parameters (geometry, fill ratio, materials, working fluid, etc.) affect its performance. Themore » physical processes describing a PHP are highly coupled. Understanding its operation is further complicated by the non-equilibrium nature of the interplay between evaporation/condensation, bubble growth and collapse or coalescence, and the coupled response of the multiphase fluid dynamics among the different channels. A comprehensive theory of operation and design tools for PHPs is still an unrealized task. In the following we first analyze, in some detail, a simple model that has been proposed to describe PHP behavior. Although it includes fundamental features of a PHP, it also makes some assumptions to keep the model tractable. In an effort to improve on current modeling practice, we constructed a model for a PHP using some unique features available in FLOW-3D, version 9.2-3 (Flow Science, 2007). We believe that this flow modeling software retains more of the salient features of a PHP and thus, provides a closer representation of its behavior.« less

OpenGL in Multi-User Web-Based Applications

NASA Astrophysics Data System (ADS)

Szostek, K.; Piórkowski, A.

In this article construction and potential of OpenGL multi-user web-based application are presented. The most common technologies like: .NET ASP, Java and Mono were used with specific OpenGL libraries to visualize tree-dimensional medical data. The most important conclusion of this work is that server side applications can easily take advantage of fast GPU and produce efficient results of advanced computation just like the visualization.

Specifying and Verifying the Correctness of Dynamic Software Updates

DTIC Science & Technology

2011-11-15

additional branching introduced by update points and the need to analyze the state transformer code. As tools become faster and more effective , our...It shows the effectiveness of merging-based verification on practical examples, including Redis [20], a widely deployed server program. 2 Defining...Gupta’s reachability while side -stepping the problem that reachability can leave behavior CS-TR-4997 under-constrained. For example, for the vsftpd update

A streaming-based solution for remote visualization of 3D graphics on mobile devices.

PubMed

Lamberti, Fabrizio; Sanna, Andrea

2007-01-01

Mobile devices such as Personal Digital Assistants, Tablet PCs, and cellular phones have greatly enhanced user capability to connect to remote resources. Although a large set of applications are now available bridging the gap between desktop and mobile devices, visualization of complex 3D models is still a task hard to accomplish without specialized hardware. This paper proposes a system where a cluster of PCs, equipped with accelerated graphics cards managed by the Chromium software, is able to handle remote visualization sessions based on MPEG video streaming involving complex 3D models. The proposed framework allows mobile devices such as smart phones, Personal Digital Assistants (PDAs), and Tablet PCs to visualize objects consisting of millions of textured polygons and voxels at a frame rate of 30 fps or more depending on hardware resources at the server side and on multimedia capabilities at the client side. The server is able to concurrently manage multiple clients computing a video stream for each one; resolution and quality of each stream is tailored according to screen resolution and bandwidth of the client. The paper investigates in depth issues related to latency time, bit rate and quality of the generated stream, screen resolutions, as well as frames per second displayed.

Web tools for effective retrieval, visualization, and evaluation of cardiology medical images and records

NASA Astrophysics Data System (ADS)

Masseroli, Marco; Pinciroli, Francesco

2000-12-01

To provide easy retrieval, integration and evaluation of multimodal cardiology images and data in a web browser environment, distributed application technologies and java programming were used to implement a client-server architecture based on software agents. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. The client side is a Java applet running in a web browser and providing a friendly medical user interface to perform queries on patient and medical test dat and integrate and visualize properly the various query results. A set of tools based on Java Advanced Imaging API enables to process and analyze the retrieved cardiology images, and quantify their features in different regions of interest. The platform-independence Java technology makes the developed prototype easy to be managed in a centralized form and provided in each site where an intranet or internet connection can be located. Giving the healthcare providers effective tools for querying, visualizing and evaluating comprehensively cardiology medical images and records in all locations where they can need them- i.e. emergency, operating theaters, ward, or even outpatient clinics- the developed prototype represents an important aid in providing more efficient diagnoses and medical treatments.

77 FR 15933 - Importation of Wooden Handicrafts From China

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-19

..., in the third column, in footnote 2, in the third line `` https://www.ippc.int/index.php?id=13399&tx...://www.ippc.int/index.php?id=13399&tx_publication_pi1 [showUid]=133703&frompage=13399&type=publication...

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

PubMed Central

Bernal-Rusiel, Jorge L.; Rannou, Nicolas; Gollub, Randy L.; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E.; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution. PMID:28507515

Health risks, travel preparation, and illness among public health professionals during international travel.

PubMed

Balaban, Victor; Warnock, Eli; Ramana Dhara, V; Jean-Louis, Lee Ann; Sotir, Mark J; Kozarsky, Phyllis

2014-01-01

Few data currently exist on health risks faced by public health professionals (PHP) during international travel. We conducted pre- and post-travel health surveys to assess knowledge, attitudes, and practices (KAP), and illnesses among PHP international travelers. Anonymous surveys were completed by PHP from a large American public health agency who sought a pre-travel medical consult from September 1, 2009, to September 30, 2010. Surveys were completed by 122 participants; travelers went to 163 countries. Of the 122 respondents, 97 (80%) reported at least one planned health risk activity (visiting rural areas, handling animals, contact with blood or body fluids, visiting malarious areas), and 50 (41%) reported exposure to unanticipated health risks. Of the 62 travelers who visited malarious areas, 14 (23%) reported inconsistent or no use of malaria prophylaxis. Illness during travel was reported by 33 (27%) respondents. Most of the PHP travelers in our study reported at least one planned health risk activity, and almost half reported exposure to unanticipated health risks, and one-quarter of travelers to malarious areas reported inconsistent or no use of malaria chemoprophylaxis. Our findings highlight that communication and education outreach for PHP to prevent travel-associated illnesses can be improved. Published by Elsevier Ltd.

Guanine nucleotide-binding protein α subunit hypofunction in children with short stature and disproportionate shortening of the 4th and 5th metacarpals.

PubMed

Inta, Ioana Monica; Choukair, Daniela; Bender, Sebastian; Kneppo, Carolin; Knauer-Fischer, Sabine; Meyenburg, Kahina; Ivandic, Boris; Pfister, Stefan M; Bettendorf, Markus

2014-01-01

GNAS encodes the α subunit of the stimulatory G protein (Gsα). Maternal inherited Gsα mutations cause pseudohypoparathyroidism type Ia (PHP-Ia), associated with shortening of the 4th and 5th metacarpals. Here we investigated the Gsα pathway in short patients with distinct shortening of the 4th and 5th metacarpals. In 571 children with short stature and 4 patients with PHP-Ia metacarpal bone lengths were measured. In identified patients we analysed the Gsα protein function in platelets, performed GNAS sequencing, and epigenetic analysis of four significant differentially methylated regions. In 51 patients (8.9%) shortening of the 4th and 5th metacarpals was more pronounced than their height deficit. No GNAS coding mutations were identified in 20 analysed patients, except in 2 PHP-Ia patients. Gsα activity was reduced in all PHP-Ia patients and in 25% of the analysed patients. No significant methylation changes were identified. Our findings suggest that patients with short stature and distinct metacarpal bone shortening could be part of the wide variety of PHP/PPHP, therefore it was worthwhile analysing the Gsα protein function and GNAS gene in these patients in order to further elucidate the phenotype and genotype of Gsα dysfunction.

Youpi: A Web-based Astronomical Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Monnerville, M.; Sémah, G.

2010-12-01

Youpi stands for “YOUpi is your processing PIpeline”. It is a portable, easy to use web application providing high level functionalities to perform data reduction on scientific FITS images. It is built on top of open source processing tools that are released to the community by Terapix, in order to organize your data on a computer cluster, to manage your processing jobs in real time and to facilitate teamwork by allowing fine-grain sharing of results and data. On the server side, Youpi is written in the Python programming language and uses the Django web framework. On the client side, Ajax techniques are used along with the Prototype and script.aculo.us Javascript librairies.

78 FR 1832 - Nez Perce-Clearwater National Forests; Id; Crooked River Valley Rehabilitation Project

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-09

... the thirty-fourth through thirty-sixth lines, `` http://www.fs.fed.usinepa/fs-usda-pop.php/?project=40648 '' should read `` http://www.fs.fed.us/nepa/fs-usda-pop.php/?project=40648 ''. [FR Doc. C1-2012...

Aquarius's Instrument Science Data System (ISDS) Automated to Acquire, Process, Trend Data and Produce Radiometric System Assessment Reports

NASA Technical Reports Server (NTRS)

2008-01-01

The Aquarius Radiometer, a subsystem of the Aquarius Instrument required a data acquisition ground system to support calibration and radiometer performance assessment. To support calibration and compose performance assessments, we developed an automated system which uploaded raw data to a ftp server and saved raw and processed data to a database. This paper details the overall functionalities of the Aquarius Instrument Science Data System (ISDS) and the individual electrical ground support equipment (EGSE) which produced data files that were infused into the ISDS. Real time EGSEs include an ICDS Simulator, Calibration GSE, Labview controlled power supply, and a chamber data acquisition system. ICDS Simulator serves as a test conductor primary workstation, collecting radiometer housekeeping (HK) and science data and passing commands and HK telemetry collection request to the radiometer. Calibration GSE (Radiometer Active Test Source) provides source choice from multiple targets for the radiometer external calibration. Power Supply GSE, controlled by labview, provides real time voltage and current monitoring of the radiometer. And finally the chamber data acquisition system produces data reflecting chamber vacuum pressure, thermistor temperatures, AVG and watts. Each GSE system produce text based data files every two to six minutes and automatically copies the data files to the Central Archiver PC. The Archiver PC stores the data files, schedules automated uploads of these files to an external FTP server, and accepts request to copy all data files to the ISDS for offline data processing and analysis. Aquarius Radiometer ISDS contains PHP and MATLab programs to parse, process and save all data to a MySQL database. Analysis tools (MATLab programs) in the ISDS system are capable of displaying radiometer science, telemetry and auxiliary data in near real time as well as performing data analysis and producing automated performance assessment reports of the Aquarius Radiometer.

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

PubMed

Hallin, Peter F; Ussery, David W

2004-12-12

Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

SU-E-T-220: A Web-Based Research System for Outcome Analysis of NSCLC Treated with SABR.

PubMed

Le, A; Yang, Y; Michalski, D; Heron, D; Huq, M

2012-06-01

To establish a web-based software system, an electronic patient record (ePR), to consolidate and evaluate clinical data, dose delivery and treatment outcomes for non small cell lung cancer (NSCLC) patients treated with hypofractionated stereotactic ablative radiation therapy (SABR) across institutions. The new trend of information technology in medical imaging and informatics is towards the development of an electronic patient record (ePR), in which all health and medical information of each patient are organized under the patient's name and identification number. The system has been developed using the Wamp Server, a package of Apache web server, PHP and MySQL database to facilitate patient data input and management, and evaluation of patient clinical data and dose delivery across institution using web technology. The data of each patient to be recorded in the database include pre-treatment clinical data, treatment plan in DICOM-RT format and follow-up data. The pre-treatment data include demographics data, pathology condition, cancer staging. The follow-up data include the survival status, local tumor control condition and toxicity. The clinical data are entered to the system through the web page while the treatment plan data will be imported from the treatment planning system (TPS) using DICOM communication. The collection of data of NSCLC patients treated with SABR stored in the ePR is always accessible and can be retrieved and processed in the future. The core of the ePR is the database which integrates all patient data in one location. The web-based DICOM RT ePR system utilizes the current state-of-the-art medical informatics approach to investigate the combination and consolidation of patient data and outcome results. This will allow clinically-driven data mining for dose distributions and resulting treatment outcome in connection with biological modeling of the treatment parameters to quantify the efficacy of SABR in treating NSCLC patients. © 2012 American Association of Physicists in Medicine.

The Open Data Repository's Data Publisher

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

2015-12-01

Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A, Mars Science Laboratory Investigations and University of Arizona Geosciences.

Risk Factors Analysis and Death Prediction in Some Life-Threatening Ailments Using Chi-Square Case-Based Reasoning (χ2 CBR) Model.

PubMed

Adeniyi, D A; Wei, Z; Yang, Y

2018-01-30

A wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ 2 CBR) model. The proposed predictive engine is capable of reducing runtime and speeds up execution process through the use of critical χ 2 distribution value. This work also showcases the development of a novel feature selection method referred to as frequent item based rule (FIBR) method. This FIBR method is used for selecting the best feature for the proposed χ 2 CBR model at the preprocessing stage of the predictive procedures. The implementation of the proposed risk calculator is achieved through the use of an in-house developed PHP program experimented with XAMP/Apache HTTP server as hosting server. The process of data acquisition and case-based development is implemented using the MySQL application. Performance comparison between our system, the NBY, the ED-KNN, the ANN, the SVM, the Random Forest and the traditional CBR techniques shows that the quality of predictions produced by our system outperformed the baseline methods studied. The result of our experiment shows that the precision rate and predictive quality of our system in most cases are equal to or greater than 70%. Our result also shows that the proposed system executes faster than the baseline methods studied. Therefore, the proposed risk calculator is capable of providing useful, consistent, faster, accurate and efficient risk level prediction to both the patients and the physicians at any time, online and on a real-time basis.

Integration of dye-sensitized solar cells, thermoelectric modules and electrical storage loop system to constitute a novel photothermoelectric generator.

PubMed

Chang, Ho; Yu, Zhi-Rong

2012-08-01

This study self-develops a novel type of photothermoelectric power generation modules. Dye-sensitized solar cells (DSSCs) serve as the photoelectric conversion system and a copper (Cu) heat-transfer nanofilm coating on both sides of the thermoelectric generator (TEG) acts as a thermoelectric conversion system. Thus module assembly absorbs light and generates electricity by DSSCs, and also recycles waste heat and generates power by the TEG. In addition, a set of pulsating heat pipes (PHP) filled with Cu nanofluid is placed on the cooling side to increase cooling effects and enhance the power generation efficiency. Results show that when the heat source of thermoelectric modules reaches 90 degrees C, TEG power output is increased by 85.7%. Besides, after thermoelectric modules are heated by additional heat source at 80 degrees C, the electrical energy generated by them can let a NiMH cell (1.25 V) be sufficiently charged in about 30 minutes. When photothermoelectric modules is illumined by simulated light, the temperature difference of two sides of TEG can reach 7 degrees C and the thermoelectric conversion efficiency is 2.17%. Furthermore, the power output of the thermoelectric modules is 11.48 mW/cm2, enhancing 1.4 % compared to merely using DSSCs module.

NOAA Operational Model Archive Distribution System (NOMADS): High Availability Applications for Reliable Real Time Access to Operational Model Data

NASA Astrophysics Data System (ADS)

Alpert, J. C.; Wang, J.

2009-12-01

To reduce the impact of natural hazards and environmental changes, the National Centers for Environmental Prediction (NCEP) provide first alert and a preferred partner for environmental prediction services, and represents a critical national resource to operational and research communities affected by climate, weather and water. NOMADS is now delivering high availability services as part of NOAA’s official real time data dissemination at its Web Operations Center (WOC) server. The WOC is a web service used by organizational units in and outside NOAA, and acts as a data repository where public information can be posted to a secure and scalable content server. A goal is to foster collaborations among the research and education communities, value added retailers, and public access for science and development efforts aimed at advancing modeling and GEO-related tasks. The user (client) executes what is efficient to execute on the client and the server efficiently provides format independent access services. Client applications can execute on the server, if it is desired, but the same program can be executed on the client side with no loss of efficiency. In this way this paradigm lends itself to aggregation servers that act as servers of servers listing, searching catalogs of holdings, data mining, and updating information from the metadata descriptions that enable collections of data in disparate places to be simultaneously accessed, with results processed on servers and clients to produce a needed answer. The services used to access the operational model data output are the Open-source Project for a Network Data Access Protocol (OPeNDAP), implemented with the Grid Analysis and Display System (GrADS) Data Server (GDS), and applications for slicing, dicing and area sub-setting the large matrix of real time model data holdings. This approach insures an efficient use of computer resources because users transmit/receive only the data necessary for their tasks including metadata. Data sets served in this way with a high availability server offer vast possibilities for the creation of new products for value added retailers and the scientific community. We demonstrate how users can use NOMADS services to select the values of Ensemble model runs over the ith Ensemble component, (forecast) time, vertical levels, global horizontal location, and by variable, virtually a 6-Dimensional data cube of access across the internet. The example application called the “Ensemble Probability Tool” make probability predictions of user defined weather events that can be used in remote areas for weather vulnerable circumstances. An application to access data for a verification pilot study is shown in detail in a companion paper (U06) collaboration with the World Bank and is an example of high value, usability and relevance of NCEP products and service capability over a wide spectrum of user and partner needs.

(Epi)genotype-Phenotype Analysis in 69 Japanese Patients With Pseudohypoparathyroidism Type I

PubMed Central

Sano, Shinichiro; Nakamura, Akie; Matsubara, Keiko; Nagasaki, Keisuke; Fukami, Maki; Kagami, Masayo

2018-01-01

Context: Pseudohypoparathyroidism type I (PHP-I) is divided into PHP-Ia with Albright hereditary osteodystrophy and PHP-Ib, which usually shows no Albright hereditary osteodystrophy features. Although PHP-Ia and PHP-Ib are typically caused by genetic defects involving α subunit of the stimulatory G protein (Gsα)–coding GNAS exons and methylation defects of the GNAS differentially methylated regions (DMRs) on the maternal allele, respectively, detailed phenotypic characteristics still remains to be examined. Objective: To clarify phenotypic characteristics according to underlying (epi)genetic causes. Patients and Methods: We performed (epi)genotype-phenotype analysis in 69 Japanese patients with PHP-I; that is, 28 patients with genetic defects involving Gsα-coding GNAS exons (group 1) consisting of 12 patients with missense variants (subgroup A) and 16 patients with null variants (subgroup B), as well as 41 patients with methylation defects (group 2) consisting of 21 patients with broad methylation defects of the GNAS-DMRs (subgroup C) and 20 patients with an isolated A/B-DMR methylation defect accompanied by the common STX16 microdeletion (subgroup D). Results: Although (epi)genotype-phenotype findings were grossly similar to those reported previously, several important findings were identified, including younger age at hypocalcemic symptoms and higher frequencies of hyperphosphatemia in subgroup C than in subgroup D, development of brachydactyly in four patients of subgroup C, predominant manifestation of subcutaneous ossification in subgroup B, higher frequency of thyrotropin resistance in group 1 than in group 2, and relatively low thyrotropin values in four patients with low T4 values and relatively low luteinizing hormone/follicle-stimulating hormone values in five adult females with ovarian dysfunction. Conclusion: The results imply the presence of clinical findings characteristic of each underlying cause and provide useful information on the imprinting status of Gsα. PMID:29379892

Pros and cons of healthcare information technology implementation: the pros win.

PubMed

Maffei, Roxana

2006-01-01

Countless studies and investigations have been performed siding either for or against the implementation of technology in the healthcare setting. This article presents both sides of this debate, with an obvious conclusion that the pros of this debate win. The practice of information technology in the medical domain lags behind its knowledge and discovery by at least 7 years. The key to closing this gap is to show, through various studies, how information technology systems provide decision support to users at the point in time when decisions are needed. What the reader will obtain from this article is that the pros for information technology implementation in healthcare settings weigh much more and have a greater effect than the cons.

Framework for ReSTful Web Services in OSGi

NASA Technical Reports Server (NTRS)

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

2009-01-01

Ensemble ReST is a software system that eases the development, deployment, and maintenance of server-side application programs to perform functions that would otherwise be performed by client software. Ensemble ReST takes advantage of the proven disciplines of ReST (Representational State Transfer. ReST leverages the standardized HTTP protocol to enable developers to offer services to a diverse variety of clients: from shell scripts to sophisticated Java application suites

Delayed Instantiation Bulk Operations for Management of Distributed, Object-Based Storage Systems

DTIC Science & Technology

2009-08-01

source and destination object sets, while they have attribute pages to indicate that history . Fourth, we allow for operations to occur on any objects...client dialogue to the PostgreSQL database where server-side functions implement the service logic for the requests. The translation is done...to satisfy client requests, and performs delayed instantiation bulk operations. It is built around a PostgreSQL database with tables for storing

Optimization of Photooxidative Removal of Phenazopyridine from Water

NASA Astrophysics Data System (ADS)

Saeid, Soudabeh; Behnajady, Mohammad A.; Tolvanen, Pasi; Salmi, Tapio

2018-05-01

The photooxidative removal of analgesic pharmaceutical compound phenazopyridine (PhP) from aqueous solutions by UV/H2O2 system with a re-circulated photoreactor was investigated. Response surface methodology (RSM) was employed to optimize the effect of operational parameters on the photooxidative removal efficiency. The investigated variables were: the initial PhP and H2O2 concentrations, irradiation time, volume of solution and pH. The analysis of variance (ANOVA) of quadratic model demonstrated that the described model was highly significant. The predicted values of the photooxidative removal efficiency were found to be in a fair agreement with experimental values ( R 2 = 0.9832, adjusted R 2 = 0.9716). The model predicted that the optimal reaction conditions for a maximum removal of PhP (>98%) were: initial PhP concentration less than 23 mg L-1, initial concentration of H2O2 higher than 470 mg L-1, solution volume less than 500 mL, pH close to 2 and irradiation time longer than 6 min.

Phosphorylation of the Streptococcus pneumoniae cell wall biosynthesis enzyme MurC by a eukaryotic-like Ser/Thr kinase.

PubMed

Falk, Shaun P; Weisblum, Bernard

2013-03-01

Streptococcus pneumoniae contains a single Ser/Thr kinase-phosphatase pair known as StkP-PhpP. Here, we report the interaction of StkP-PhpP with S. pneumoniae UDP-N-acetylmuramoyl:L-alanine ligase, MurC, an enzyme that synthesizes an essential intermediate of the cell wall peptidoglycan pathway. Combinatorial phage display using StkP as target selected the peptide sequence YEVCGSDTVGC as an interacting partner and subsequently confirmed by ELISA. The phage peptide sequence YEVCGSDTVGC aligns closely with the MurC motif spanning S. pneumoniae amino acid coordinates 31-37. We show that MurC is phosphorylated by StkP and that phosphoMurC is dephosphorylated by PhpP. These data suggest a link between StkP-PhpP with the coordinated regulation of cell wall biosynthesis via MurC. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

PubMed Central

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; Adebesin, Funmilayo; Qian, Yichun; Guo, Longyun; Jaini, Rohit; Lynch, Joseph H.; McCoy, Rachel M.; Shreve, Jacob T.; Thimmapuram, Jyothi; Rhodes, David; Morgan, John A.; Dudareva, Natalia

2015-01-01

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles, as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network. PMID:26356302

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

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

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

DOE PAGES

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; ...

2015-09-10

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Cyclotetraphosphinophosphonium ions: synthesis, structures, and pseudorotation.

PubMed

Dyker, C Adam; Riegel, Susanne D; Burford, Neil; Lumsden, Michael D; Decken, Andreas

2007-06-13

The first derivatives of catenated cyclotetraphosphinophosphonium cations, [(PhP)4PPhMe]+ (8a), [(MeP)4PMe2]+ (8b), [(CyP)4PPh2]+ (8d), [(CyP)4PMe2]+ (8e), [(PhP)4PPh2]+ (8f), [(PhP)4PMe2]+ (8g), are synthesized as trifluoromethanesulfonate (triflate, OSO2CF3-) salts through the reaction of cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b) with methyl triflate (MeOTf) or by a net phosphenium ion [PR2+, R = Ph, Me; from R2PCl and trimethylsilyltriflate (Me3SiOTf)] insertion into the P-P bond of either cyclotetraphosphine (CyP)4 (3c) or cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b). Although more conveniently prepared from 4a, compound 8a[OTf] can also be formed from (PhP)4 (3a) and MeOTf, and derivatives 8f[OTf] and 8g[OTf] are also accessible through reactions of 3a and R2PCl/Me3SiOTf with R = Ph or Me, respectively. A tetrachlorogallate salt of [(PhP)4PPhtBu]+ (8c) has been synthesized by alkylation of 4a with tBuCl/GaCl3. 31P[1H] NMR parameters for all derivatives of 8 have been determined by iterative simulation of experimental data. Derivatives 8a[OTf], 8b[OTf], 8c[GaCl4], 8e[OTf], 8f[OTf], and 8g[OTf] and have been characterized by X-ray crystallography, showing the most favorable all-trans configuration of substituents for the phosphine centers, thus minimizing steric interactions. Each derivative adopts a unique envelope or twist conformation of C1 symmetry. The effective C2 symmetry observed for 8b, d, e, f, and g in solution, signified by their 31P[1H] NMR AA'BB'X spin systems, implies a rapid conformational exchange for derivatives of 8. The core frameworks of the cations in the solid state are viewed as snapshots of different conformational isomers within the solution-phase pseudorotation process.

The Effects of Engine Speed and Mixture Temperature on the Knocking Characteristics of Several Fuels

DTIC Science & Technology

1940-07-01

only. NACA list dtd 28 Sep 1945; NASA TR Server website ‘ ,f. ; :,““’? ,. .--:- .— #..- “W!+ ‘ ‘:u:i’w W9SlFlCAT10#CAME1lEO~ . TilCH131CAL NOTES...A photograph of the engine ’”used.is shown in figure 1. The electric air heater is above the engine and the cathod.e- ray oscill”ograph used as a...indicated that increasing the con- “press,ion ratio fro@ 6 to 11 results in.’a decie~se in the ‘dbzisity correction fact-or of shout . “0.030 at 1,500

A Web-based Examination System Based on PHP+MySQL.

PubMed

Wen, Ji; Zhang, Yang; Yan, Yong; Xia, Shunren

2005-01-01

The design and implementation of web-based examination system constructed by PHP and MySQL is presented in this paper. Three primary parts, including students',teachers' and administrators', are introduced and analyzed in detail. Initial application has demonstrated the system's feasibility and reasonability.^*

Renal effects of multiple infusion of pyridoxalated-hemoglobin-polyoxyethylene conjugate (PHP) solution in dogs.

PubMed

Takahashi, T; Iwasaki, K; Malchesky, P S; Harasaki, H; Matsushita, M; Nosé, Y; Rolin, H; Hall, P M

1993-03-01

Pyridoxalated-hemoglobin-polyoxyethylene conjugate (PHP), which is made from out-dated human red blood cells by two major chemical modifications, namely pyridoxalation and conjugation with polyoxyethylene (POE), is currently under development as a physiological oxygen carrier. This study assessed the effects of PHP-88 solution, which contains 8% (wt/vol) each of hemoglobin (Hb) and maltose, on renal function when it was infused 3 times every other day into the intact circulation of 8 dogs (5 dogs for the PHP group and 3 for the control group; 20 ml/kg for the first infusion, and 10 ml/kg each for the second and third infusions, at the rate of 2.5 ml/h/kg). Serial determinations of glomerular filtration rate (GFR) and renal plasma flow (RPF) were carried out pre- and postinfusion for up to 3 months along with measurements of blood and urine analyses, urine output rate, fractional excretion of sodium (FES), and free water clearance (CH2O). The results showed that plasma colloid osmotic pressure (COP) elevated an average of 3.3 mm Hg (p = 0.0085), and GFR and RPF tended to increase by 13% (NS) and 38% (NS), respectively, immediately after the third infusion with PHP solution. Urine output rate increased during and after the infusion, and FES and CH2O also increased for 24 h after the infusion in both groups. Blood urea nitrogen, serum creatinine, and serum Na+ concentrations were not affected greatly by the infusions, but hematocrit was decreased by 8% in the PHP group, indicating approximately a 42% expansion of plasma volume. These changes were observed to return to their preinfusion levels by 1 week postinfusion. Renal histology of the PHP group obtained at 2 weeks postinfusion revealed vacuole formation in the proximal tubules which was not associated with any pathologic changes indicative of cell death or regeneration. In 4 out of 5 dogs at 3 months postinfusion (necropsy), the vacuoles were not present. Though urinary N-acetyl-beta-glucosaminidase (NAG) activity had significantly increased after infusion, it returned to the preinfusion level by 1 month postinfusion. No detrimental effect of vacuoles on the assessed renal tubular functions was confirmed in the present study. The results demonstrated that multiple infusions of PHP solutions were well tolerated in normal dogs, and the observed effects were conceived predominantly attributable to the physiological response of the kidneys to an oncotic load into the circulation, which produced plasma volume expansion.

Assessment of Template-Based Modeling of Protein Structure in CASP11

PubMed Central

Modi, Vivek; Xu, Qifang; Adhikari, Sam; Dunbrack, Roland L.

2016-01-01

We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction). Model quality was judged on the basis of global and local measures of accuracy on all atoms including side chains. The top groups on 39 human-server targets based on model 1 predictions were LEER, Zhang, LEE, MULTICOM, and Zhang-Server. The top groups on 81 targets by server groups based on model 1 predictions were Zhang-Server, nns, BAKER-ROSETTASERVER, QUARK, and myprotein-me. In CASP11, the best models for most targets were equal to or better than the best template available in the Protein Data Bank, even for targets with poor templates. The overall performance in CASP11 is similar to the performance of predictors in CASP10 with slightly better performance on the hardest targets. For most targets, assessment measures exhibited bimodal probability density distributions. Multi-dimensional scaling of an RMSD matrix for each target typically revealed a single cluster with models similar to the target structure, with a mode in the GDT-TS density between 40 and 90, and a wide distribution of models highly divergent from each other and from the experimental structure, with density mode at a GDT-TS value of ~20. The models in this peak in the density were either compact models with entirely the wrong fold, or highly non-compact models. The results argue for a density-driven approach in future CASP TBM assessments that accounts for the bimodal nature of these distributions instead of Z-scores, which assume a unimodal, Gaussian distribution. PMID:27081927

Expitope: a web server for epitope expression.

PubMed

Haase, Kerstin; Raffegerst, Silke; Schendel, Dolores J; Frishman, Dmitrij

2015-06-01

Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy. The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Are public health physicians still needed in medically underserved rural areas in Korea?

PubMed

Na, Baeg Ju; Lee, Jin Yong; Kim, Hyun Joo

2017-05-01

Public health physicians (PHPs) are certified physicians who are serving in a public health center or subcenter in a rural village, instead of serving in the military. However, the PHP program has recently become the subject of a profound debate, over 30 years after its adoption. In this study, we attempted to ascertain physicians' perspectives on the PHP program, including: whether the PHP policy should continue; if they agree on changing the role of PHPs in healthcare; what would be the desired role of PHPs; and what resources would be required and what possible barriers would be anticipated under the changes. We selected 88 PHPs as our study sample using quota sampling. Over 60% of respondents were in support of continuing the PHP program. They believed some remote islands and mountainous areas are still in need of public healthcare doctors. However, some of them believed that the role of PHPs should be changed to take on community health promotion, because the problem of medically underserved rural areas has almost been resolved. However, people living in rural areas are ageing and suffering from a lack of education and health information. In particular, in order to successfully transition into new roles, PHPs must be provided with continuing education and professional development programs covering their new responsibilities. It is imperative to refurbish the PHP program to meet current needs and continue its central role in public healthcare.

Understanding patients' oral health information needs: Findings of a survey on use of patient portals in dentistry.

PubMed

Shimpi, Neel; Schwei, Kelsey; Cooper, Sara; Chyou, Po-Huang; Acharya, Amit

2018-03-01

Patient engagement through web-based patient health portals (PHP) can offer important benefits to patients and provider organizations by improving both quality and access to care. The authors studied the most relevant, patient-identified, oral health information available in the PHP to inform their assessment of patient-centered care. The authors distributed a 17-question, paper-based survey to patients aged 18 through 80 years in the waiting rooms of 8 dental centers in Wisconsin. Descriptive statistics, along with differences in percentages by sex, age group, and metropolitan status were reported using the χ 2 and Wilcoxon rank sum test. A 75% (813 of 1,090) response rate was achieved. More than one-third of patients selected access to previous dental procedures, dental history, routine dental appointment reminders, date of last dental visit, tooth chart, date of last full-mouth radiograph, and dental problem list via the PHP. Patients identified and recommended incorporation of different types of oral health data for access via the PHP as vital to strengthening the communication between patients and dental professionals. Incorporating patient-identified oral health information in the PHP will inform strategies for improving patient engagement, strengthen patient-provider communication, and offer a venue for increasing oral health literacy and awareness. Copyright © 2018 American Dental Association. Published by Elsevier Inc. All rights reserved.

Two-Photon Activation of p-Hydroxyphenacyl Phototriggers: Toward Spatially Controlled Release of Diethyl Phosphate and ATP.

PubMed

Houk, Amanda L; Givens, Richard S; Elles, Christopher G

2016-03-31

Two-photon activation of the p-hydroxyphenacyl (pHP) photoactivated protecting group is demonstrated for the first time using visible light at 550 nm from a pulsed laser. Broadband two-photon absorption measurements reveal a strong two-photon transition (>10 GM) near 4.5 eV that closely resembles the lowest-energy band at the same total excitation energy in the one-photon absorption spectrum of the pHP chromophore. The polarization dependence of the two-photon absorption band is consistent with excitation to the same S3 ((1)ππ*) excited state for both one- and two-photon activation. Monitoring the progress of the uncaging reaction under nonresonant excitation at 550 nm confirms a quadratic intensity dependence and that two-photon activation of the uncaging reaction is possible using visible light in the range 500-620 nm. Deprotonation of the pHP chromophore under mildly basic conditions shifts the absorption band to lower energy (3.8 eV) in both the one- and two-photon absorption spectra, suggesting that two-photon activation of the pHP chromophore may be possible using light in the range 550-720 nm. The results of these measurements open the possibility of spatially and temporally selective release of biologically active compounds from the pHP protecting group using visible light from a pulsed laser.

PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex and assists in regulating expression of genes within H3K27ME3-enriched chromatin.

PubMed

Park, Sunchung; Oh, Sookyung; Ek-Ramos, Julissa; van Nocker, Steven

2010-06-01

The human Paf1 complex (Paf1C) subunit Parafibromin assists in mediating output from the Wingless/Int signaling pathway, and dysfunction of the encoding gene HRPT2 conditions specific cancer-related disease phenotypes. Here, we characterize the organismal and molecular roles of PLANT HOMOLOGOUS TO PARAFIBROMIN (PHP), the Arabidopsis (Arabidopsis thaliana) homolog of Parafibromin. PHP resides in an approximately 670-kD protein complex in nuclear extracts, and physically interacts with other known Paf1C-related proteins in vivo. In striking contrast to the developmental pleiotropy conferred by mutation in other plant Paf1C component genes in Arabidopsis, loss of PHP specifically conditioned accelerated phase transition from vegetative growth to flowering and resulted in misregulation of a very limited subset of genes that included the flowering repressor FLOWERING LOCUS C. Those genes targeted by PHP were distinguished from the bulk of Arabidopsis genes and other plant Paf1C targets by strong enrichment for trimethylation of lysine-27 on histone H3 (H3K27me3) within chromatin. These findings suggest that PHP is a component of a plant Paf1C protein in Arabidopsis, but has a more specialized role in modulating expression of a subset of Paf1C targets.

Infectious Disease Information Collection System at the Scene of Disaster Relief Based on a Personal Digital Assistant.

PubMed

Li, Ya-Pin; Gao, Hong-Wei; Fan, Hao-Jun; Wei, Wei; Xu, Bo; Dong, Wen-Long; Li, Qing-Feng; Song, Wen-Jing; Hou, Shi-Ke

2017-12-01

The objective of this study was to build a database to collect infectious disease information at the scene of a disaster through the use of 128 epidemiological questionnaires and 47 types of options, with rapid acquisition of information regarding infectious disease and rapid questionnaire customization at the scene of disaster relief by use of a personal digital assistant (PDA). SQL Server 2005 (Microsoft Corp, Redmond, WA) was used to create the option database for the infectious disease investigation, to develop a client application for the PDA, and to deploy the application on the server side. The users accessed the server for data collection and questionnaire customization with the PDA. A database with a set of comprehensive options was created and an application system was developed for the Android operating system (Google Inc, Mountain View, CA). On this basis, an infectious disease information collection system was built for use at the scene of disaster relief. The creation of an infectious disease information collection system and rapid questionnaire customization through the use of a PDA was achieved. This system integrated computer technology and mobile communication technology to develop an infectious disease information collection system and to allow for rapid questionnaire customization at the scene of disaster relief. (Disaster Med Public Health Preparedness. 2017;11:668-673).

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

PubMed

Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

2012-07-01

The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

Systematic plan of building Web geographic information system based on ActiveX control

NASA Astrophysics Data System (ADS)

Zhang, Xia; Li, Deren; Zhu, Xinyan; Chen, Nengcheng

2003-03-01

A systematic plan of building Web Geographic Information System (WebGIS) using ActiveX technology is proposed in this paper. In the proposed plan, ActiveX control technology is adopted in building client-side application, and two different schemas are introduced to implement communication between controls in users¡ browser and middle application server. One is based on Distribute Component Object Model (DCOM), the other is based on socket. In the former schema, middle service application is developed as a DCOM object that communicates with ActiveX control through Object Remote Procedure Call (ORPC) and accesses data in GIS Data Server through Open Database Connectivity (ODBC). In the latter, middle service application is developed using Java language. It communicates with ActiveX control through socket based on TCP/IP and accesses data in GIS Data Server through Java Database Connectivity (JDBC). The first one is usually developed using C/C++, and it is difficult to develop and deploy. The second one is relatively easy to develop, but its performance of data transfer relies on Web bandwidth. A sample application is developed using the latter schema. It is proved that the performance of the sample application is better than that of some other WebGIS applications in some degree.

Indoor Navigation Design Integrated with Smart Phones and Rfid Devices

NASA Astrophysics Data System (ADS)

Ortakci, Y.; Demiral, E.; Atila, U.; Karas, I. R.

2015-10-01

High rise, complex and huge buildings in the cities are almost like a small city with their tens of floors, hundreds of corridors and rooms and passages. Due to size and complexity of these buildings, people need guidance to find their way to the destination in these buildings. In this study, a mobile application is developed to visualize pedestrian's indoor position as 3D in their smartphone and RFID Technology is used to detect the position of pedestrian. While the pedestrian is walking on his/her way on the route, smartphone will guide the pedestrian by displaying the photos of indoor environment on the route. Along the tour, an RFID (Radio-Frequency Identification) device is integrated to the system. The pedestrian will carry the RFID device during his/her tour in the building. The RFID device will send the position data to the server directly in every two seconds periodically. On the other side, the pedestrian will just select the destination point in the mobile application on smartphone and sent the destination point to the server. The shortest path from the pedestrian position to the destination point is found out by the script on the server. This script also sends the environment photo of the first node on the acquired shortest path to the client as an indoor navigation module.

ABCs of Being Smart: S Is for Supporting

ERIC Educational Resources Information Center

Foster, Joanne

2014-01-01

Joanne Foster's article "R We There Yet?" was first published in "Parenting for High Potential" ("PHP") in 2006, which became the springboard for the "ABCs of Being Smart" series of columns. At that time, Foster invited "PHP" readers to think about their own versions of the "ABCs of Being…

Toward server-side, high performance climate change data analytics in the Earth System Grid Federation (ESGF) eco-system

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Williams, Dean; Aloisio, Giovanni

2016-04-01

In many scientific domains such as climate, data is often n-dimensional and requires tools that support specialized data types and primitives to be properly stored, accessed, analysed and visualized. Moreover, new challenges arise in large-scale scenarios and eco-systems where petabytes (PB) of data can be available and data can be distributed and/or replicated (e.g., the Earth System Grid Federation (ESGF) serving the Coupled Model Intercomparison Project, Phase 5 (CMIP5) experiment, providing access to 2.5PB of data for the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5). Most of the tools currently available for scientific data analysis in the climate domain fail at large scale since they: (1) are desktop based and need the data locally; (2) are sequential, so do not benefit from available multicore/parallel machines; (3) do not provide declarative languages to express scientific data analysis tasks; (4) are domain-specific, which ties their adoption to a specific domain; and (5) do not provide a workflow support, to enable the definition of complex "experiments". The Ophidia project aims at facing most of the challenges highlighted above by providing a big data analytics framework for eScience. Ophidia provides declarative, server-side, and parallel data analysis, jointly with an internal storage model able to efficiently deal with multidimensional data and a hierarchical data organization to manage large data volumes ("datacubes"). The project relies on a strong background of high performance database management and OLAP systems to manage large scientific data sets. It also provides a native workflow management support, to define processing chains and workflows with tens to hundreds of data analytics operators to build real scientific use cases. With regard to interoperability aspects, the talk will present the contribution provided both to the RDA Working Group on Array Databases, and the Earth System Grid Federation (ESGF) Compute Working Team. Also highlighted will be the results of large scale climate model intercomparison data analysis experiments, for example: (1) defined in the context of the EU H2020 INDIGO-DataCloud project; (2) implemented in a real geographically distributed environment involving CMCC (Italy) and LLNL (US) sites; (3) exploiting Ophidia as server-side, parallel analytics engine; and (4) applied on real CMIP5 data sets available through ESGF.

The D3 Middleware Architecture

NASA Technical Reports Server (NTRS)

Walton, Joan; Filman, Robert E.; Korsmeyer, David J.; Lee, Diana D.; Mak, Ron; Patel, Tarang

2002-01-01

DARWIN is a NASA developed, Internet-based system for enabling aerospace researchers to securely and remotely access and collaborate on the analysis of aerospace vehicle design data, primarily the results of wind-tunnel testing and numeric (e.g., computational fluid-dynamics) model executions. DARWIN captures, stores and indexes data; manages derived knowledge (such as visualizations across multiple datasets); and provides an environment for designers to collaborate in the analysis of test results. DARWIN is an interesting application because it supports high-volumes of data. integrates multiple modalities of data display (e.g., images and data visualizations), and provides non-trivial access control mechanisms. DARWIN enables collaboration by allowing not only sharing visualizations of data, but also commentary about and views of data. Here we provide an overview of the architecture of D3, the third generation of DARWIN. Earlier versions of DARWIN were characterized by browser-based interfaces and a hodge-podge of server technologies: CGI scripts, applets, PERL, and so forth. But browsers proved difficult to control, and a proliferation of computational mechanisms proved inefficient and difficult to maintain. D3 substitutes a pure-Java approach for that medley: A Java client communicates (though RMI over HTTPS) with a Java-based application server. Code on the server accesses information from JDBC databases, distributed LDAP security services, and a collaborative information system. D3 is a three tier-architecture, but unlike 'E-commerce' applications, the data usage pattern suggests different strategies than traditional Enterprise Java Beans - we need to move volumes of related data together, considerable processing happens on the client, and the 'business logic' on the server-side is primarily data integration and collaboration. With D3, we are extending DARWIN to handle other data domains and to be a distributed system, where a single login allows a user transparent access to test results from multiple servers and authority domains.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.

PubMed

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-10-01

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

The development of a web-based assessment system to identify students’ misconception automatically on linear kinematics with a four-tier instrument test

NASA Astrophysics Data System (ADS)

Pujayanto, Pujayanto; Budiharti, Rini; Adhitama, Egy; Nuraini, Niken Rizky Amalia; Vernanda Putri, Hanung

2018-07-01

This research proposes the development of a web-based assessment system to identify students’ misconception. The system, named WAS (web-based assessment system), can identify students’ misconception profile on linear kinematics automatically after the student has finished the test. The test instrument was developed and validated. Items were constructed and arranged from the result of a focus group discussion (FGD), related to previous research. Fifty eight students (female  =  37, male  =  21) were used as samples. They were from different classes with 18 students from the gifted class and another 40 students from the normal class. WAS was designed specifically to support the teacher as an efficient replacement for a paper-based test system. In addition, WAS offers flexible timing functionally, stand-alone subject module, robustness and scalability. The entire WAS program and interface was developed with open source-based technologies such as the XAMP server, MySQL database, Javascript and PHP. It provides results immediately and provides diagrammatic questions as well as scientific symbols. It is feasible to apply this system to many students at once. Thus, it could be integrated in many schools as part of physics courses.

Prediction of Safety Stock Using Fuzzy Time Series (FTS) and Technology of Radio Frequency Identification (RFID) for Stock Control at Vendor Managed Inventory (VMI)

NASA Astrophysics Data System (ADS)

Mashuri, Chamdan; Suryono; Suseno, Jatmiko Endro

2018-02-01

This research was conducted by prediction of safety stock using Fuzzy Time Series (FTS) and technology of Radio Frequency Identification (RFID) for stock control at Vendor Managed Inventory (VMI). Well-controlled stock influenced company revenue and minimized cost. It discussed about information system of safety stock prediction developed through programming language of PHP. Input data consisted of demand got from automatic, online and real time acquisition using technology of RFID, then, sent to server and stored at online database. Furthermore, data of acquisition result was predicted by using algorithm of FTS applying universe of discourse defining and fuzzy sets determination. Fuzzy set result was continued to division process of universe of discourse in order to be to final step. Prediction result was displayed at information system dashboard developed. By using 60 data from demand data, prediction score was 450.331 and safety stock was 135.535. Prediction result was done by error deviation validation using Mean Square Percent Error of 15%. It proved that FTS was good enough in predicting demand and safety stock for stock control. For deeper analysis, researchers used data of demand and universe of discourse U varying at FTS to get various result based on test data used.

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

PubMed

Schad, Eva; Fichó, Erzsébet; Pancsa, Rita; Simon, István; Dosztányi, Zsuzsanna; Mészáros, Bálint

2018-02-01

Intrinsically Disordered Proteins (IDPs) mediate crucial protein-protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode. Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes. DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. dosztanyi@caesar.elte.hu or bmeszaros@caesar.elte.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

PubMed

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-12-12

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

siRNAmod: A database of experimentally validated chemically modified siRNAs.

PubMed

Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

2016-01-28

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

PubMed Central

Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

X-PAT: a multiplatform patient referral data management system for small healthcare institution requirements.

PubMed

Masseroli, Marco; Marchente, Mario

2008-07-01

We present X-PAT, a platform-independent software prototype that is able to manage patient referral multimedia data in an intranet network scenario according to the specific control procedures of a healthcare institution. It is a self-developed storage framework based on a file system, implemented in eXtensible Markup Language (XML) and PHP Hypertext Preprocessor Language, and addressed to the requirements of limited-dimension healthcare entities (small hospitals, private medical centers, outpatient clinics, and laboratories). In X-PAT, healthcare data descriptions, stored in a novel Referral Base Management System (RBMS) according to Health Level 7 Clinical Document Architecture Release 2 (CDA R2) standard, can be easily applied to the specific data and organizational procedures of a particular healthcare working environment thanks also to the use of standard clinical terminology. Managed data, centralized on a server, are structured in the RBMS schema using a flexible patient record and CDA healthcare referral document structures based on XML technology. A novel search engine allows defining and performing queries on stored data, whose rapid execution is ensured by expandable RBMS indexing structures. Healthcare personnel can interface the X-PAT system, according to applied state-of-the-art privacy and security measures, through friendly and intuitive Web pages that facilitate user acceptance.

Scalable Multi-Platform Distribution of Spatial 3d Contents

NASA Astrophysics Data System (ADS)

Klimke, J.; Hagedorn, B.; Döllner, J.

2013-09-01

Virtual 3D city models provide powerful user interfaces for communication of 2D and 3D geoinformation. Providing high quality visualization of massive 3D geoinformation in a scalable, fast, and cost efficient manner is still a challenging task. Especially for mobile and web-based system environments, software and hardware configurations of target systems differ significantly. This makes it hard to provide fast, visually appealing renderings of 3D data throughout a variety of platforms and devices. Current mobile or web-based solutions for 3D visualization usually require raw 3D scene data such as triangle meshes together with textures delivered from server to client, what makes them strongly limited in terms of size and complexity of the models they can handle. In this paper, we introduce a new approach for provisioning of massive, virtual 3D city models on different platforms namely web browsers, smartphones or tablets, by means of an interactive map assembled from artificial oblique image tiles. The key concept is to synthesize such images of a virtual 3D city model by a 3D rendering service in a preprocessing step. This service encapsulates model handling and 3D rendering techniques for high quality visualization of massive 3D models. By generating image tiles using this service, the 3D rendering process is shifted from the client side, which provides major advantages: (a) The complexity of the 3D city model data is decoupled from data transfer complexity (b) the implementation of client applications is simplified significantly as 3D rendering is encapsulated on server side (c) 3D city models can be easily deployed for and used by a large number of concurrent users, leading to a high degree of scalability of the overall approach. All core 3D rendering techniques are performed on a dedicated 3D rendering server, and thin-client applications can be compactly implemented for various devices and platforms.

Datacasting V3.0

NASA Technical Reports Server (NTRS)

Bingham, Andrew W.; McCleese, Sean W.; Deen, Robert G.; Chung, Nga T.; Stough, Timothy M.

2013-01-01

Datacasting V3.0 provides an RSSbased feed mechanism for publishing the availability of Earth science data records in real time. It also provides a utility for subscribing to these feeds and sifting through all the items in an automatic manner to identify and download the data records that are required for a specific application. Datacasting is a method by which multiple data providers can publish the availability of new Earth science data and users download those files that meet a predefined need; for example, to only download data files related to a specific earthquake or region on the globe. Datacasting is a server-client architecture. The server-side software is used by data providers to create and publish the metadata about recently available data according to the Datacasting RSS (Really Simple Syndication) specification. The client software subscribes to the Datacasting RSS and other RSS-based feeds. By configuring filters associated with feeds, data consumers can use the client to identify and automatically download files that meet a specific need. On the client side, a Datacasting feed reader monitors the server for new feeds. The feed reader will be tuned by the user, via a graphical user interface (GUI), to examine the content of the feeds and initiate a data pull after some criteria are satisfied. The criteria might be, for example, to download sea surface temperature data for a particular region that has cloud cover less than 50% and during daylight hours. After the granule is downloaded to the client, the user will have the ability to visualize the data in the GUI. Based on the popular concept of podcasting, which gives listeners the capability to download only those MP3 files that match their preference, Earth science Datacasting will give users a method to download only the Earth science data files that are required for a particular application.

Interactive client side data visualization with d3.js

NASA Astrophysics Data System (ADS)

Rodzianko, A.; Versteeg, R.; Johnson, D. V.; Soltanian, M. R.; Versteeg, O. J.; Girouard, M.

2015-12-01

Geoscience data associated with near surface research and operational sites is increasingly voluminous and heterogeneous (both in terms of providers and data types - e.g. geochemical, hydrological, geophysical, modeling data, of varying spatiotemporal characteristics). Such data allows scientists to investigate fundamental hydrological and geochemical processes relevant to agriculture, water resources and climate change. For scientists to easily share, model and interpret such data requires novel tools with capabilities for interactive data visualization. Under sponsorship of the US Department of Energy, Subsurface Insights is developing the Predictive Assimilative Framework (PAF): a cloud based subsurface monitoring platform which can manage, process and visualize large heterogeneous datasets. Over the last year we transitioned our visualization method from a server side approach (in which images and animations were generated using Jfreechart and Visit) to a client side one that utilizes the D3 Javascript library. Datasets are retrieved using web service calls to the server, returned as JSON objects and visualized within the browser. Users can interactively explore primary and secondary datasets from various field locations. Our current capabilities include interactive data contouring and heterogeneous time series data visualization. While this approach is very powerful and not necessarily unique, special attention needs to be paid to latency and responsiveness issues as well as to issues as cross browser code compatibility so that users have an identical, fluid and frustration-free experience across different computational platforms. We gratefully acknowledge support from the US Department of Energy under SBIR Award DOE DE-SC0009732, the use of data from the Lawrence Berkeley National Laboratory (LBNL) Sustainable Systems SFA Rifle field site and collaboration with LBNL SFA scientists.

Web Application Design Using Server-Side JavaScript

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

Hampton, J.; Simons, R.

1999-02-01

This document describes the application design philosophy for the Comprehensive Nuclear Test Ban Treaty Research & Development Web Site. This design incorporates object-oriented techniques to produce a flexible and maintainable system of applications that support the web site. These techniques will be discussed at length along with the issues they address. The overall structure of the applications and their relationships with one another will also be described. The current problems and future design changes will be discussed as well.

Trends in access of plant biodiversity data revealed by Google Analytics

PubMed Central

Baxter, David G.; Hagedorn, Gregor; Legler, Ben; Gilbert, Edward; Thiele, Kevin; Vargas-Rodriguez, Yalma; Urbatsch, Lowell E.

2014-01-01

Abstract The amount of plant biodiversity data available via the web has exploded in the last decade, but making these data available requires a considerable investment of time and work, both vital considerations for organizations and institutions looking to validate the impact factors of these online works. Here we used Google Analytics (GA), to measure the value of this digital presence. In this paper we examine usage trends using 15 different GA accounts, spread across 451 institutions or botanical projects that comprise over five percent of the world's herbaria. They were studied at both one year and total years. User data from the sample reveal: 1) over 17 million web sessions, 2) on five primary operating systems, 3) search and direct traffic dominates with minimal impact from social media, 4) mobile and new device types have doubled each year for the past three years, 5) and web browsers, the tools we use to interact with the web, are changing. Server-side analytics differ from site to site making the comparison of their data sets difficult. However, use of Google Analytics erases the reporting heterogeneity of unique server-side analytics, as they can now be examined with a standard that provides a clarity for data-driven decisions. The knowledge gained here empowers any collection-based environment regardless of size, with metrics about usability, design, and possible directions for future development. PMID:25425933

(a,k)-Anonymous Scheme for Privacy-Preserving Data Collection in IoT-based Healthcare Services Systems.

PubMed

Li, Hongtao; Guo, Feng; Zhang, Wenyin; Wang, Jie; Xing, Jinsheng

2018-02-14

The widely use of IoT technologies in healthcare services has pushed forward medical intelligence level of services. However, it also brings potential privacy threat to the data collection. In healthcare services system, health and medical data that contains privacy information are often transmitted among networks, and such privacy information should be protected. Therefore, there is a need for privacy-preserving data collection (PPDC) scheme to protect clients (patients) data. We adopt (a,k)-anonymity model as privacy pretection scheme for data collection, and propose a novel anonymity-based PPDC method for healthcare services in this paper. The threat model is analyzed in the client-server-to-user (CS2U) model. On client-side, we utilize (a,k)-anonymity notion to generate anonymous tuples which can resist possible attack, and adopt a bottom-up clustering method to create clusters that satisfy a base privacy level of (a 1 ,k 1 )-anonymity. On server-side, we reduce the communication cost through generalization technology, and compress (a 1 ,k 1 )-anonymous data through an UPGMA-based cluster combination method to make the data meet the deeper level of privacy (a 2 ,k 2 )-anonymity (a 1  ≥ a 2 , k 2  ≥ k 1 ). Theoretical analysis and experimental results prove that our scheme is effective in privacy-preserving and data quality.

Trends in access of plant biodiversity data revealed by Google Analytics.

PubMed

Jones, Timothy Mark; Baxter, David G; Hagedorn, Gregor; Legler, Ben; Gilbert, Edward; Thiele, Kevin; Vargas-Rodriguez, Yalma; Urbatsch, Lowell E

2014-01-01

The amount of plant biodiversity data available via the web has exploded in the last decade, but making these data available requires a considerable investment of time and work, both vital considerations for organizations and institutions looking to validate the impact factors of these online works. Here we used Google Analytics (GA), to measure the value of this digital presence. In this paper we examine usage trends using 15 different GA accounts, spread across 451 institutions or botanical projects that comprise over five percent of the world's herbaria. They were studied at both one year and total years. User data from the sample reveal: 1) over 17 million web sessions, 2) on five primary operating systems, 3) search and direct traffic dominates with minimal impact from social media, 4) mobile and new device types have doubled each year for the past three years, 5) and web browsers, the tools we use to interact with the web, are changing. Server-side analytics differ from site to site making the comparison of their data sets difficult. However, use of Google Analytics erases the reporting heterogeneity of unique server-side analytics, as they can now be examined with a standard that provides a clarity for data-driven decisions. The knowledge gained here empowers any collection-based environment regardless of size, with metrics about usability, design, and possible directions for future development.

Multiple intracranial calcifications and spinal compressions: rare complications of type la pseudohypoparathyroidism.

PubMed

Chen, H; Tseng, F; Su, D; Chen, H; Tsai, K

2005-01-01

Type la pseudohypoparathyroidism (PHP la) is an unusual inherited disease. PHP la often causes extraskeletal calcifications and even soft tissue ossifications. Patients may present neurologic symptoms and signs related to hypocalcemia and hyperphosphatemia. We report here a 38-yr-old woman with PHP la who had two uncommon neurologic complications. One was involuntary movements related to basal ganglia calcification, and the other was myelopathy owing to ossifications of the posterior longitudinal ligament and multiple herniated intervertebral disks. Aggressive body weight control and corrections of hypocalcemia, hyperphosphatemia, and elevated PTH may be important to prevent these unusual neurologic complications. Regular and careful neurologic examinations should be performed for early diagnosis and treatments of these spinal lesions.

77 FR 47591 - Notice of Request for Extension of Approval of an Information Collection; Plant Protection and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-09

... performance of its quality management system by monitoring information related to customer perception in relationship to customer requirements. PHP has determined that the best method for obtaining this information... by the Office of Management and Budget (OMB), PHP would allow stakeholders and customers to complete...

Allostatic Load: Single Parents, Stress-Related Health Issues, and Social Care

ERIC Educational Resources Information Center

Johner, Randy L.

2007-01-01

This article explores the possible relationships between allostatic load (AL) and stress-related health issues in the low-income single-parent population, using both a population health perspective (PHP) and a biological framework. A PHP identifies associations among such factors as gender, income, employment, and social support and their…

Polyester type polyHIPE scaffolds with an interconnected porous structure for cartilage regeneration

NASA Astrophysics Data System (ADS)

Naranda, Jakob; Sušec, Maja; Maver, Uroš; Gradišnik, Lidija; Gorenjak, Mario; Vukasović, Andreja; Ivković, Alan; Rupnik, Marjan Slak; Vogrin, Matjaž; Krajnc, Peter

2016-06-01

Development of artificial materials for the facilitation of cartilage regeneration remains an important challenge in orthopedic practice. Our study investigates the potential for neocartilage formation within a synthetic polyester scaffold based on the polymerization of high internal phase emulsions. The fabrication of polyHIPE polymer (PHP) was specifically tailored to produce a highly porous (85%) structure with the primary pore size in the range of 50-170 μm for cartilage tissue engineering. The resulting PHP scaffold was proven biocompatible with human articular chondrocytes and viable cells were observed within the materials as evaluated using the Live/Dead assay and histological analysis. Chondrocytes with round nuclei were organized into multicellular layers on the PHP surface and were observed to grow approximately 300 μm into the scaffold interior. The accumulation of collagen type 2 was detected using immunohistochemistry and chondrogenic specific genes were expressed with favorable collagen type 2 to 1 ratio. In addition, PHP samples are biodegradable and their baseline mechanical properties are similar to those of native cartilage, which enhance chondrocyte cell growth and proliferation.

Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems

PubMed Central

Chan, Ken Y; Jang, Min J; Yoo, Bryan B; Greenbaum, Alon; Ravi, Namita; Wu, Wei-Li; Sánchez-Guardado, Luis; Lois, Carlos; Mazmanian, Sarkis K; Deverman, Benjamin E; Gradinaru, Viviana

2017-01-01

Adeno-associated viruses (AAVs) are commonly used for in vivo gene transfer. Nevertheless, AAVs that provide efficient transduction across specific organs or cell populations are needed. Here, we describe AAV-PHP.eB and AAV-PHP.S, capsids that efficiently transduce the central and peripheral nervous systems, respectively. In the adult mouse, intravenous administration of 1×1011 vector genomes (vg) of AAV-PHP.eB transduced 69% of cortical and 55% of striatal neurons, while 1×1012 vg AAV-PHP.S transduced 82% of dorsal root ganglion neurons, as well as cardiac and enteric neurons. The efficiency of these vectors facilitates robust co-transduction and stochastic, multicolor labeling for individual cell morphology studies. To support such efforts, we provide methods for labeling a tunable fraction of cells without compromising color diversity. Furthermore, when used with cell type-specific promoters, these AAVs provide targeted gene expression across the nervous system and enable efficient and versatile gene manipulation throughout the nervous system of transgenic and non-transgenic animals. PMID:28671695

Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.

PubMed

Baños, Benito; Lázaro, José M; Villar, Laurentino; Salas, Margarita; de Vega, Miguel

2008-10-01

Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolX(Bs)), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolX(Bs) possesses an intrinsic 3'-5' exonuclease activity specialized in resecting unannealed 3'-termini in a gapped DNA substrate. Biochemical analysis of a PolX(Bs) deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3'-5' exonuclease activity of PolX(Bs) resides in its PHP domain. Furthermore, site-directed mutagenesis of PolX(Bs) His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3'-termini resection by the 3'-5' exonuclease activity of PolX(Bs) in the DNA repair context are discussed.

Polyester type polyHIPE scaffolds with an interconnected porous structure for cartilage regeneration

PubMed Central

Naranda, Jakob; Sušec, Maja; Maver, Uroš; Gradišnik, Lidija; Gorenjak, Mario; Vukasović, Andreja; Ivković, Alan; Rupnik, Marjan Slak; Vogrin, Matjaž; Krajnc, Peter

2016-01-01

Development of artificial materials for the facilitation of cartilage regeneration remains an important challenge in orthopedic practice. Our study investigates the potential for neocartilage formation within a synthetic polyester scaffold based on the polymerization of high internal phase emulsions. The fabrication of polyHIPE polymer (PHP) was specifically tailored to produce a highly porous (85%) structure with the primary pore size in the range of 50–170 μm for cartilage tissue engineering. The resulting PHP scaffold was proven biocompatible with human articular chondrocytes and viable cells were observed within the materials as evaluated using the Live/Dead assay and histological analysis. Chondrocytes with round nuclei were organized into multicellular layers on the PHP surface and were observed to grow approximately 300 μm into the scaffold interior. The accumulation of collagen type 2 was detected using immunohistochemistry and chondrogenic specific genes were expressed with favorable collagen type 2 to 1 ratio. In addition, PHP samples are biodegradable and their baseline mechanical properties are similar to those of native cartilage, which enhance chondrocyte cell growth and proliferation. PMID:27340110

Switching sliding mode force tracking control of piezoelectric-hydraulic pump-based friction element actuation systems for automotive transmissions

NASA Astrophysics Data System (ADS)

Kim, Gi-Woo; Wang, K. W.

2009-08-01

In this study, a nonlinear sliding-mode controller is designed for force tracking of a piezoelectric-hydraulic pump (PHP)-based actuation system, which is developed to replace the current electro-hydraulic actuation systems for automatic transmission (AT) friction elements, such as band brakes or clutches. By utilizing the PHP, one can eliminate the various hydraulic components (oil pump, regulating valve and control valve) in current ATs and achieve a simpler configuration with more efficient operation. With the derived governing equation of motion of the PHP-based actuation system integrated with the friction element (band brake), a switching control law is synthesized based on the sliding-mode theory. To evaluate the effectiveness of the proposed control law, its force tracking performance for the engagement of a friction element during an AT 1\\to 2 up-shift is examined experimentally. It is shown that one can successfully track the desired force trajectory for AT shift control with small tracking error. This study demonstrates the potential of the PHP as a new controllable actuation system for AT friction elements.

Are public health physicians still needed in medically underserved rural areas in Korea?

PubMed Central

Na, Baeg Ju; Lee, Jin Yong; Kim, Hyun Joo

2017-01-01

Abstract Public health physicians (PHPs) are certified physicians who are serving in a public health center or subcenter in a rural village, instead of serving in the military. However, the PHP program has recently become the subject of a profound debate, over 30 years after its adoption. In this study, we attempted to ascertain physicians’ perspectives on the PHP program, including: whether the PHP policy should continue; if they agree on changing the role of PHPs in healthcare; what would be the desired role of PHPs; and what resources would be required and what possible barriers would be anticipated under the changes. We selected 88 PHPs as our study sample using quota sampling. Over 60% of respondents were in support of continuing the PHP program. They believed some remote islands and mountainous areas are still in need of public healthcare doctors. However, some of them believed that the role of PHPs should be changed to take on community health promotion, because the problem of medically underserved rural areas has almost been resolved. However, people living in rural areas are ageing and suffering from a lack of education and health information. In particular, in order to successfully transition into new roles, PHPs must be provided with continuing education and professional development programs covering their new responsibilities. It is imperative to refurbish the PHP program to meet current needs and continue its central role in public healthcare. PMID:28489812

The effect of total blood exchange with PHP solution on cardiac xenotransplantation.

PubMed

Liu, H; Agishi, T; Suga, H; Hayasaka, Y; Teraoka, S; Ota, K

1995-04-01

Prevention of hyperacute rejection is a difficult and unsolved problem in xenotransplantation. Natural antibodies and complement activation have been known to play an important role in the xenotransplantation between discordant species pairs. In the present study, total blood exchange (TBE) was performed with pyridoxalated-hemoglobin-polyoxyethylene conjugate (PHP) solution (Ajinomoto Co., Inc., Kawasaki, Japan) before cardiac xenotransplantation in order to remove the immunoglobulins and prolong xenograft survival time. Guinea pigs and rats were used as the discordant species combination for donor and recipient. Two groups were established: Group 1, untreated control (n = 8) and Group 2, TBT with PHP solution (n = 8). The exchange blood transfusion was carried out at the rate of 15-20 ml/h utilizing PHP solution using a blood pump. After the blood exchange was processed, hematocrit (Ht) levels dropped to 4 or 5%, and a cardiac xenotransplantation was performed within 24 h. The levels of serum IgA, IgM, and IgG were decreased to less than 25, 25, and 10% of the base line, respectively, after blood exchange. A mean xenograft survival time in Group 2 was prolonged to 472 +/- 74 min and to 10.4 +/- 1.8 min in Group 1 (p < 0.01). A titer of the anti-guinea pig lymphocytotoxic antibody in rat serum was decreased to almost nil. The data from this study suggest that total blood exchange with PHP solution may be useful in preoperative removal of xenograft antibodies in xenotransplantation.

Detection of new-onset choroidal neovascularization using optical coherence tomography: the AMD DOC Study.

PubMed

Do, Diana V; Gower, Emily W; Cassard, Sandra D; Boyer, David; Bressler, Neil M; Bressler, Susan B; Heier, Jeffrey S; Jefferys, Joan L; Singerman, Lawrence J; Solomon, Sharon D

2012-04-01

To determine the sensitivity of time domain optical coherence tomography (OCT) in detecting conversion to neovascular age-related macular degeneration (AMD) in eyes at high risk for choroidal neovascularization (CNV), compared with detection using fluorescein angiography (FA) as the gold standard. Prospective, multicenter, observational study. Individuals aged ≥50 years with nonneovascular AMD at high risk of progressing to CNV in the study eye and evidence of neovascular AMD in the fellow eye. At study entry and every 3 months through 2 years, participants underwent best-corrected visual acuity, supervised Amsler grid testing, preferential hyperacuity perimetry (PHP) testing, stereoscopic digital fundus photographs with FA, and OCT imaging. A central Reading Center graded all images. The sensitivity of OCT in detecting conversion to neovascular AMD by 2 years, using FA as the reference standard. Secondary outcomes included comparison of sensitivity, specificity, positive predictive value, and negative predictive value of OCT, PHP, and supervised Amsler grid relative to FA for detecting incident CNV. A total of 98 participants were enrolled; 87 (89%) of these individuals either completed the 24-month visit or exited the study after developing CNV. Fifteen (17%) study eyes had incident CNV confirmed on FA by the Reading Center. The sensitivity of each modality for detecting CNV was: OCT 0.40 (95% confidence interval [CI], 0.16-0.68), supervised Amsler grid 0.42 (95% CI, 0.15-0.72), and PHP 0.50 (95% CI, 0.23-0.77). Treatment for incident CNV was recommended by the study investigator in 13 study eyes. Sensitivity of the testing modalities for detection of CNV in these 13 eyes was 0.69 (95% CI, 0.39-0.91) for OCT, 0.50 (95% CI, 0.19-0.81) for supervised Amsler grid, and 0.70 (95% CI, 0.35-0.93) for PHP. Specificity of the OCT was higher than that of the Amsler grid and PHP. Time-domain OCT, supervised Amsler grid, and PHP have low to moderate sensitivity for detection of new-onset CNV compared with FA. Optical coherence tomography has greater specificity than Amsler grid or PHP. Among fellow eyes of individuals with unilateral CNV, FA remains the best method to detect new-onset CNV. Copyright © 2012 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Evolution of the Data Access Protocol in Response to Community Needs

NASA Astrophysics Data System (ADS)

Gallagher, J.; Caron, J. L.; Davis, E.; Fulker, D.; Heimbigner, D.; Holloway, D.; Howe, B.; Moe, S.; Potter, N.

2012-12-01

Under the aegis of the OPULS (OPeNDAP-Unidata Linked Servers) Project, funded by NOAA, version 2 of OPeNDAP's Data Access Protocol (DAP2) is being updated to version 4. DAP4 is the first major upgrade in almost two decades and will embody three main areas of advancement. First, the data-model extensions developed by the OPULS team focus on three areas: Better support for coverages, access to HDF5 files and access to relational databases. DAP2 support for coverages (defined as a sampled functions) was limited to simple rectangular coverages that work well for (some) model outputs and processed satellite data but that cannot represent trajectories or satellite swath data, for example. We have extended the coverage concept in DAP4 to remove these limitations. These changes are informed by work at Unidata on the Common Data Model and also by the OGC's abstract coverages specification. In a similar vein, we have extended DAP2's support for relations by including the concept of foreign keys, so that tables can be explicitly related to one another. Second, the web interfaces - web services - that provides access to data using via DAP will be more clearly defined and use other (, orthogonal), standards where they are appropriate. An important case is the XML interface, which provides a cleaner way to build other response media types such as JSON and RDF (for metadata) and to build support for Atom, thus simplify the integration of DAP servers with tools that support OpenSearch. Input from the ESIP federation and work performed with IOOS have informed our choices here. Last, DAP4-compliant servers will support richer data-processing capabilities than DAP2, enabling a wider array of server functions that manipulate data before returning values. Two projects currently are exploring just what can be done even with DAP2's server-function model: The MIIC project at LARC and OPULS itself (with work performed at the University of Washington). Both projects have demonstrated that server functions can be used to perform operations on large volumes of data and return results that are far smaller than would be required to achieve the same outcomes via client-side processing. We are using information from these efforts to inform the design of server functions in DAP4. Each of the three areas of DAP4 advancement is being guided by input from a number of community members, including an OPULS Advisory Committee.

Privacy-preserving public auditing for data integrity in cloud

NASA Astrophysics Data System (ADS)

Shaik Saleem, M.; Murali, M.

2018-04-01

Cloud computing which has collected extent concentration from communities of research and with industry research development, a large pool of computing resources using virtualized sharing method like storage, processing power, applications and services. The users of cloud are vend with on demand resources as they want in the cloud computing. Outsourced file of the cloud user can easily tampered as it is stored at the third party service providers databases, so there is no integrity of cloud users data as it has no control on their data, therefore providing security assurance to the users data has become one of the primary concern for the cloud service providers. Cloud servers are not responsible for any data loss as it doesn’t provide the security assurance to the cloud user data. Remote data integrity checking (RDIC) licenses an information to data storage server, to determine that it is really storing an owners data truthfully. RDIC is composed of security model and ID-based RDIC where it is responsible for the security of every server and make sure the data privacy of cloud user against the third party verifier. Generally, by running a two-party Remote data integrity checking (RDIC) protocol the clients would themselves be able to check the information trustworthiness of their cloud. Within the two party scenario the verifying result is given either from the information holder or the cloud server may be considered as one-sided. Public verifiability feature of RDIC gives the privilege to all its users to verify whether the original data is modified or not. To ensure the transparency of the publicly verifiable RDIC protocols, Let’s figure out there exists a TPA who is having knowledge and efficiency to verify the work to provide the condition clearly by publicly verifiable RDIC protocols.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Efficient privacy-preserving string search and an application in genomics.

PubMed

Shimizu, Kana; Nuida, Koji; Rätsch, Gunnar

2016-06-01

Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database. We propose a novel approach that combines efficient string data structures such as the Burrows-Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows-Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries. We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within [Formula: see text] 4.6 s and [Formula: see text] 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm. https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Efficient privacy-preserving string search and an application in genomics

PubMed Central

Shimizu, Kana; Nuida, Koji; Rätsch, Gunnar

2016-01-01

Motivation: Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database. Approach: We propose a novel approach that combines efficient string data structures such as the Burrows–Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows–Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries. Results: We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within ≈ 4.6 s and ≈ 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm. Availability and implementation: https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec. Contacts: shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153731

RIMS: An Integrated Mapping and Analysis System with Applications to Earth Sciences and Hydrology

NASA Astrophysics Data System (ADS)

Proussevitch, A. A.; Glidden, S.; Shiklomanov, A. I.; Lammers, R. B.

2011-12-01

A web-based information and computational system for analysis of spatially distributed Earth system, climate, and hydrologic data have been developed. The System allows visualization, data exploration, querying, manipulation and arbitrary calculations with any loaded gridded or vector polygon dataset. The system's acronym, RIMS, stands for its core functionality as a Rapid Integrated Mapping System. The system can be deployed for a Global scale projects as well as for regional hydrology and climatology studies. In particular, the Water Systems Analysis Group of the University of New Hampshire developed the global and regional (Northern Eurasia, pan-Arctic) versions of the system with different map projections and specific data. The system has demonstrated its potential for applications in other fields of Earth sciences and education. The key Web server/client components of the framework include (a) a visualization engine built on Open Source libraries (GDAL, PROJ.4, etc.) that are utilized in a MapServer; (b) multi-level data querying tools built on XML server-client communication protocols that allow downloading map data on-the-fly to a client web browser; and (c) data manipulation and grid cell level calculation tools that mimic desktop GIS software functionality via a web interface. Server side data management of the system is designed around a simple database of dataset metadata facilitating mounting of new data to the system and maintaining existing data in an easy manner. RIMS contains "built-in" river network data that allows for query of upstream areas on-demand which can be used for spatial data aggregation and analysis of sub-basin areas. RIMS is an ongoing effort and currently being used to serve a number of websites hosting a suite of hydrologic, environmental and other GIS data.

Introducing the CUAHSI Hydrologic Information System Desktop Application (HydroDesktop) and Open Development Community

NASA Astrophysics Data System (ADS)

Ames, D.; Kadlec, J.; Horsburgh, J. S.; Maidment, D. R.

2009-12-01

The Consortium of Universities for the Advancement of Hydrologic Sciences (CUAHSI) Hydrologic Information System (HIS) project includes extensive development of data storage and delivery tools and standards including WaterML (a language for sharing hydrologic data sets via web services); and HIS Server (a software tool set for delivering WaterML from a server); These and other CUASHI HIS tools have been under development and deployment for several years and together, present a relatively complete software “stack” to support the consistent storage and delivery of hydrologic and other environmental observation data. This presentation describes the development of a new HIS software tool called “HydroDesktop” and the development of an online open source software development community to update and maintain the software. HydroDesktop is a local (i.e. not server-based) client side software tool that ultimately will run on multiple operating systems and will provide a highly usable level of access to HIS services. The software provides many key capabilities including data query, map-based visualization, data download, local data maintenance, editing, graphing, data export to selected model-specific data formats, linkage with integrated modeling systems such as OpenMI, and ultimately upload to HIS servers from the local desktop software. As the software is presently in the early stages of development, this presentation will focus on design approach and paradigm and is viewed as an opportunity to encourage participation in the open development community. Indeed, recognizing the value of community based code development as a means of ensuring end-user adoption, this project has adopted an “iterative” or “spiral” software development approach which will be described in this presentation.

An Improved Model for Operational Specification of the Electron Density Structure up to Geosynchronous Heights

DTIC Science & Technology

2010-07-01

http://www.iono.noa.gr/ElectronDensity/EDProfile.php The web service has been developed with the following open source tools: a) PHP , for the... MySQL for the database, which was based on the enhancement of the DIAS database. Below we present some screen shots to demonstrate the functionality

Pediatric Healthcare Professionals' Views on Autism Spectrum Disorder Screening at 12-18 Months

ERIC Educational Resources Information Center

Crais, Elizabeth R.; McComish, Cara S.; Humphreys, Betsy P.; Watson, Linda R.; Baranek, Grace T.; Reznick, J. Steven; Christian, Rob B.; Earls, Marian

2014-01-01

This study explored North Carolina pediatric healthcare professional's (PHP) perceptions of screening 12-18 month old infants for Autism Spectrum Disorder (ASD). Eight focus groups (66 PHPs) were conducted across practice settings. The purpose was to explore PHP's perspectives to: inform development of ASD screening tools and ultimately impact…

An Educational Program for Sub-Professional Personnel to be Employed in Health Maintenance Organizations. Final Report.

ERIC Educational Resources Information Center

HMO Management, Inc., Los Angeles, CA.

Through Medicaid, the Health Maintenance Organization Act (HMO), and Prepaid Health Programs (PHP) approaches were established whereby the government can help alleviate the medical problems of the needy. A program to educate and train students in California in the philosophy, administration, and development of PHP was developed in response to…

Analysis of the Appropriateness of the Use of Peltier Cells as Energy Sources.

PubMed

Hájovský, Radovan; Pieš, Martin; Richtár, Lukáš

2016-05-25

The article describes the possibilities of using Peltier cells as an energy source to power the telemetry units, which are used in large-scale monitoring systems as central units, ensuring the collection of data from sensors, processing, and sending to the database server. The article describes the various experiments that were carried out, their progress and results. Based on experiments evaluated, the paper also discusses the possibilities of using various types depending on the temperature difference of the cold and hot sides.

PedNavigator: a pedigree drawing servlet for large and inbred populations.

PubMed

Mancosu, Gianmaria; Ledda, Giuseppe; Melis, Paola M

2003-03-22

PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on person's symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.

The Naval Research Laboratory’s Ongoing Implementation of the Open Geospatial Consortium’s Catalogue Services Specification

DTIC Science & Technology

2010-06-01

then forwarded to Tomcat for processing. Tomcat receives these requests and sends them to the NRL-created CSW servlet (a servlet is a Java -based...server-side program) running inside it. The CSW servlet identifies which HTTP method is being used and whether KVP or XML is being used to send the...request data. Once the CSW servlet identifies the parameter passing scheme it can extract the parameters from the request. It then identifies and

TeleProbe: design and development of an efficient system for telepathology

NASA Astrophysics Data System (ADS)

Ahmed, Wamiq M.; Robinson, J. Paul; Ghafoor, Arif

2005-10-01

This paper describes an internet-based system for telepathology. This system provides support for multiple users and exploits the opportunities for optimization that arise in multi-user environment. Techniques for increasing system responsiveness by improving resource utilization and lowering network traffic are explored. Some of the proposed optimizations include an auto-focus module, client and server side caching, and request reordering. These systems can be an economic solution not only for remote pathology consultation but also for pathology and biology education.

Experimental investigation on a pulsating heat pipe with hydrogen

NASA Astrophysics Data System (ADS)

Deng, H. R.; Liu, Y. M.; Ma, R. F.; Han, D. Y.; Gan, Z. H.; Pfotenhauer, J. M.

2015-12-01

The pulsating heat pipe (PHP) has been increasingly studied in cryogenic application, for its high transfer coefficient and quick response. Compared with Nb3Sn and NbTi, MgB2 whose critical transformation temperature is 39 K, is expected to replace some high-temperature superconducting materials at 25 K. In order to cool MgB2, this paper designs a Hydrogen Pulsating Heat Pipe, which allows a study of applied heat, filling ratio, turn number, inclination angle and length of adiabatic section on the thermal performance of the PHP. The thermal performance of the hydrogen PHP is investigated for filling ratios of 35%, 51%, 70% at different heat inputs, and provides information regarding the starting process is received at three filling ratios.

MySQL/PHP web database applications for IPAC proposal submission

NASA Astrophysics Data System (ADS)

Crane, Megan K.; Storrie-Lombardi, Lisa J.; Silbermann, Nancy A.; Rebull, Luisa M.

2008-07-01

The Infrared Processing and Analysis Center (IPAC) is NASA's multi-mission center of expertise for long-wavelength astrophysics. Proposals for various IPAC missions and programs are ingested via MySQL/PHP web database applications. Proposers use web forms to enter coversheet information and upload PDF files related to the proposal. Upon proposal submission, a unique directory is created on the webserver into which all of the uploaded files are placed. The coversheet information is converted into a PDF file using a PHP extension called FPDF. The files are concatenated into one PDF file using the command-line tool pdftk and then forwarded to the review committee. This work was performed at the California Institute of Technology under contract to the National Aeronautics and Space Administration.