WorldWideScience

Sample records for ebis

  1. The EBI enzyme portal.

    Science.gov (United States)

    Alcántara, Rafael; Onwubiko, Joseph; Cao, Hong; Matos, Paula de; Cham, Jennifer A; Jacobsen, Jules; Holliday, Gemma L; Fischer, Julia D; Rahman, Syed Asad; Jassal, Bijay; Goujon, Mikael; Rowland, Francis; Velankar, Sameer; López, Rodrigo; Overington, John P; Kleywegt, Gerard J; Hermjakob, Henning; O'Donovan, Claire; Martín, María Jesús; Thornton, Janet M; Steinbeck, Christoph

    2013-01-01

    The availability of comprehensive information about enzymes plays an important role in answering questions relevant to interdisciplinary fields such as biochemistry, enzymology, biofuels, bioengineering and drug discovery. At the EMBL European Bioinformatics Institute, we have developed an enzyme portal (http://www.ebi.ac.uk/enzymeportal) to provide this wealth of information on enzymes from multiple in-house resources addressing particular data classes: protein sequence and structure, reactions, pathways and small molecules. The fact that these data reside in separate databases makes information discovery cumbersome. The main goal of the portal is to simplify this process for end users.

  2. libChEBI: an API for accessing the ChEBI database.

    Science.gov (United States)

    Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

    2016-01-01

    ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

  3. Progress on Test EBIS and the Design of an EBIS-Based RHIC Preinjector

    CERN Document Server

    Alessi, James; Gould, Omar; Kponou, Ahovi; Lockey, Robert; Pikin, Alexander I; Prelec, Krsto; Raparia, Deepak; Ritter, John; Snydstrup, Louis

    2005-01-01

    Following the successful development of the Test EBIS at BNL,* we now have a design for an EBIS-based heavy ion preinjector which would serve as an alternative to the Tandem Van de Graaffs in providing beams for RHIC and the NASA Space Radiation Laboratory. This baseline design includes an EBIS producing mA-level currents of heavy ions (ex. Au 32+) in ~ 10-20

  4. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.

    Science.gov (United States)

    Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Gur, Tamer; Cowley, Andrew; Li, Weizhong; Uludag, Mahmut; Pundir, Sangya; Cham, Jennifer A; McWilliam, Hamish; Lopez, Rodrigo

    2015-07-01

    The European Bioinformatics Institute (EMBL-EBI-https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.

  5. Design of the EBIS vacuum system

    Energy Technology Data Exchange (ETDEWEB)

    Mapes, M.; Smart, L.; Weiss, D.

    2011-03-28

    At Brookhaven National Laboratory the Electron Beam Ion Source (EBIS) is presently being commissioned. The EBIS will be a new heavy ion pre-injector for the Relativistic Heavy Ion Collider (RHIC). The new preinjector has the potential for significant future intensity increases and can produce heavy ion beams of all species including uranium. The background pressure in the ionization region of the EBIS required to be low enough that it does not produce a significant number of ions from background gas. The pressure in the regions of the electron gun and electron collector can be higher than in the ionization region provided there is efficient vacuum separation between the sections. For injection the ions must be accelerated to 100KV by pulsing the EBIS platform. All associated equipment including the vacuum equipment on the platform is at a 100KV potential. The vacuum system design and the vacuum controls for the EBIS platform and transport system will be presented as well as the interface with the Booster Ring which has a pressure 10-11 Torr.

  6. The CARIBU EBIS control and synchronization system

    Science.gov (United States)

    Dickerson, Clayton; Peters, Christopher

    2015-01-01

    The Californium Rare Isotope Breeder Upgrade (CARIBU) Electron Beam Ion Source (EBIS) charge breeder has been built and tested. The bases of the CARIBU EBIS electrical system are four voltage platforms on which both DC and pulsed high voltage outputs are controlled. The high voltage output pulses are created with either a combination of a function generator and a high voltage amplifier, or two high voltage DC power supplies and a high voltage solid state switch. Proper synchronization of the pulsed voltages, fundamental to optimizing the charge breeding performance, is achieved with triggering from a digital delay pulse generator. The control system is based on National Instruments realtime controllers and LabVIEW software implementing Functional Global Variables (FGV) to store and access instrument parameters. Fiber optic converters enable network communication and triggering across the platforms.

  7. The EMBL-EBI bioinformatics web and programmatic tools framework.

    Science.gov (United States)

    Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

    2015-07-01

    Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.

  8. Weighted (C)eby(s)ev-Ostrowski type inequalities

    Institute of Scientific and Technical Information of China (English)

    Arif Rafiq; Nazir Ahmad Mir; Farooq Ahmad

    2007-01-01

    In account of the famous (C)eby(s)ev inequality, a rich theory has appeared in the literature. We establish some new weighted (C)eby(s)ev type integral inequalities. Our proofs are of independent interest and provide new estimates on these types of inequalities.

  9. An EBIS-based heavy ion injector for the AGS

    Energy Technology Data Exchange (ETDEWEB)

    Kponou, A.; Alessi, J.; Beebe, E.; Brennan, J.M.; Hershcovitch, A.; Prelec, K.; Raparia, D.

    1994-09-01

    An electron beam ion source (EBIS), followed by a heavy ion RFQ and superconducting linac, can be considered as a heavy ion injector for high energy accelerators, such as the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. A test EBIS, on long term loan from Sandia National Laboratory, is presently being commissioned at BNL. Experiments on this source will be used in evaluating the parameters for an EBIS-based RHIC injector. Some results of this commissioning, as well as the conceptual designs of the RFQ and linac, are presented.

  10. Frankfurt EBIS development: Fundamental research and new applications

    Science.gov (United States)

    Kleinod, M.; Becker, R.; Kester, O.; Lakatos, A.; Thomae, H.; Zipfel, B.; Klein, H.

    1994-04-01

    Fundamental questions of electron beam ion sources (EBIS) are studied using three different setups. Cryogenic classical EBIS: The limit of ion-ion cooling in EBIS devices operating near the space-charge neutralization limit has been studied experimentally. To investigate different degrees of compensation of the electron beam by highly charged ions, a hemispherical analyzer has been constructed including a novel deceleration optic for high resolution. Using its energy definition we tested different modes of ion transportation in our multipassage magnetic spectrometer, which can be operated chromatically as well as extremely dispersively: up to 200 passages could be obtained. EBIS without magnetic field: First results on ion production in the short trap at the very dense crossover of an electron beam (XEBIS) confined only inertially without the use of magnetic fields are presented. Normal conducting short EBIS: Using a normal conducting field of 0.8 T of 25-cm length an EBIS is under construction to study extremely short ion extraction of approximately 4 μs for single turn injection into a medical synchrotron for cancer therapy (MEDEBIS).

  11. Status report on the Frankfurt EBIS research program

    Science.gov (United States)

    Kleinod, M.; Becker, R.; Kester, O.; Lakatos, A.; Mücke, M.; Pfisterer, B.; Rao, R.; Schneider, J.; Teske, L.; Thomae, H.; Zipfel, B.

    1997-01-01

    The Frankfurt superconducting EBIS has been run beyond the space-charge neutralization limit making use of the evaporative cooling technique showing a continuous transition between EBIS to EBIT operation. The experience gained on the performance of this more sophisticated source has been employed to develop simpler EBIS sources: The MEDEBIS using a warm solenoid will demonstrate rapid extraction of bare nuclei for single turn injection into a synchrotron for cancer therapy. The PPM-focused EBIS with permanent magnets and the XEBIS without any focusing magnetic field have been developed to demonstrate by its reduced power consumption and size to be more suitable to small laboratories. High emission current densities from a laser heated tip cathode offer the formation of a well-defined high current density beam. Several spectrometers have been built and installed to offer diagnostics for the EBIS operation as well as atomic physics research. Ionization measurements can be performed using the magnetic switchyard, an external electrostatic and magnetic spectrometer allows to study secondary electron emission by highly charged ions as well as to ionize and analyse sputtered atoms.

  12. Simulation of ion beam injection and extraction in an EBIS

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, L., E-mail: zhao@far-tech.com; Kim, J. S. [FAR-TECH, Inc., San Diego, California 92121 (United States)

    2016-02-15

    An example simulation of Au+ charge breeding using FAR-TECH’s integrated EBIS (electron beam ion source) modeling toolset is presented with the emphasis on ion beam injection and extraction. The trajectories of injected ions are calculated with PBGUNS (particle beam gun simulation) self-consistently by including the space charges from both ions and electrons. The ion beam, starting with initial conditions within the 100% acceptance of the electron beam, is then tracked by EBIS-PIC (particle-in-cell EBIS simulation code). In the trap, the evolution of the ion charge state distribution is estimated by charge state estimator. The extraction of charge bred ions is simulated with PBGUNS. The simulations of the ion injections show significant ion space charge effects on beam capture efficiency and the ionization efficiency.

  13. Simulation of ion beam injection and extraction in an EBIS

    Science.gov (United States)

    Zhao, L.; Kim, J. S.

    2016-02-01

    An example simulation of Au+ charge breeding using FAR-TECH's integrated EBIS (electron beam ion source) modeling toolset is presented with the emphasis on ion beam injection and extraction. The trajectories of injected ions are calculated with PBGUNS (particle beam gun simulation) self-consistently by including the space charges from both ions and electrons. The ion beam, starting with initial conditions within the 100% acceptance of the electron beam, is then tracked by EBIS-PIC (particle-in-cell EBIS simulation code). In the trap, the evolution of the ion charge state distribution is estimated by charge state estimator. The extraction of charge bred ions is simulated with PBGUNS. The simulations of the ion injections show significant ion space charge effects on beam capture efficiency and the ionization efficiency.

  14. submitter The TwinEBIS setup: Machine description

    CERN Document Server

    Breitenfeldt, M; Pitters, J; Shornikov, A; Wenander, F

    2017-01-01

    TwinEBIS is an Electron Beam Ion Source (EBIS) recently made operational at CERN. The device is similar in construction to the REXEBIS charge breeder operating at the ISOLDE facility. After relocation of the solenoid from the Manne Siegbahn Laboratory (MSL) Stockholm, TwinEBIS was commissioned at CERN and serves as a test bench dedicated to manipulation of low-energy highly charged ions. In this paper we give an overview of the setup and present advanced numerical simulations of the electron optics. In addition, the alignment procedure of the solenoid magnetic field is described and measurement results are presented. Results from cathode investigations, electron beam tests and ion extraction modulation are presented in a follow-up paper.

  15. ELECTRON BEAM ION SOURCE PREINJECTOR PROJECT (EBIS) CONCEPTUAL DESIGN REPORT.

    Energy Technology Data Exchange (ETDEWEB)

    ALESSI, J.; BARTON, D.; BEEBE, E.; GASSNER, D.; ET AL.

    2005-02-28

    This report describes a new heavy ion pre-injector for the Relativistic Heavy Ion Collider (RHIC) based on a high charge state Electron Beam Ion Source (EBIS), a Radio Frequency Quadrupole (RFQ) accelerator, and a short Linac. The highly successful development of an EBIS at BNL now makes it possible to replace the present pre-injector that is based on an electrostatic Tandem with a reliable, low maintenance Linac-based pre-injector. Linac-based pre-injectors are presently used at most accelerator and collider facilities with the exception of RHIC, where the required gold beam intensities could only be met with a Tandem until the recent EBIS development. EBIS produces high charge state ions directly, eliminating the need for the two stripping foils presently used with the Tandem. Unstable stripping efficiencies of these foils are a significant source of luminosity degradation in RHIC. The high reliability and flexibility of the new Linac-based pre-injector will lead to increased integrated luminosity at RHIC and is an essential component for the long-term success of the RHIC facility. This new pre-injector, based on an EBIS, also has the potential for significant future intensity increases and can produce heavy ion beams of all species including uranium beams and, as part of a future upgrade, might also be used to produce polarized {sup 3}He beams. These capabilities will be critical to the future luminosity upgrades and electron-ion collisions in RHIC. The new RFQ and Linac that are used to accelerate beams from the EBIS to an energy sufficient for injection into the Booster are both very similar to existing devices already in operation at other facilities. Injection into the Booster will occur at the same location as the existing injection from the Tandem.

  16. A database for chemical proteomics: ChEBI.

    Science.gov (United States)

    de Matos, Paula; Adams, Nico; Hastings, Janna; Moreno, Pablo; Steinbeck, Christoph

    2012-01-01

    Chemical proteomics is concerned with the identification of protein targets interacting with small molecules. Hence, the availability of a high quality and free resource storing small molecules is essential for the future development of the field. The Chemical Entities of Biological Interest (ChEBI) database is one such database. The scope of ChEBI includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. These entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small molecules with each other thereby making it easier for users to discover data. The ontology also describes the biological roles that the small molecules are active in. The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures.

  17. ELECTRON BEAM ION SOURCE PREINJECTOR PROJECT (EBIS) CONCEPTUAL DESIGN REPORT.

    Energy Technology Data Exchange (ETDEWEB)

    ALESSI, J.; BARTON, D.; BEEBE, E.; GASSNER, D.; GRANDINETTI, R.; HSEUH, H.; JAVIDFAR, A.; KPONOU, A.; LAMBIASE, R.; LESSARD, E.; LOCKEY, R.; LODESTRO, V.; MAPES, M.; MIRABELLA, D.; NEHRING, T.; OERTER, B.; PENDZICK, A.; PIKIN, A.; RAPARIA, D.; RITTER, J.; ROSER, T.; RUSSO, T.; SNYDSTRUP, L.; WILINSKI, M.; ZALTSMAN, A.; ZHANG, S.

    2005-09-01

    This report describes a new heavy ion pre-injector for the Relativistic Heavy Ion Collider (RHIC) based on a high charge state Electron Beam Ion Source (EBIS), a Radio Frequency Quadrupole (RFQ) accelerator, and a short Linear accelerator (Linac). The highly successful development of an EBIS at Brookhaven National Laboratory (BNL) now makes it possible to replace the present pre-injector that is based on an electrostatic Tandem with a reliable, low maintenance Linac-based pre-injector. Linac-based preinjectors are presently used at most accelerator and collider facilities with the exception of RHIC, where the required gold beam intensities could only be met with a Tandem until the recent EBIS development. EBIS produces high charge state ions directly, eliminating the need for the two stripping foils presently used with the Tandem. Unstable stripping efficiencies of these foils are a significant source of luminosity degradation in RHIC. The high reliability and flexibility of the new Linac-based pre-injector will lead to increased integrated luminosity at RHIC and is an essential component for the long-term success of the RHIC facility. This new pre-injector, based on an EBIS, also has the potential for significant future intensity increases and can produce heavy ion beams of all species including uranium beams and, as part of a future upgrade, might also be used to produce polarized {sup 3}He beams. These capabilities will be critical to the future luminosity upgrades and electron-ion collisions in RHIC. The proposed pre-injector system would also provide for a major enhancement in capability for the NASA Space Radiation Laboratory (NSRL), which utilizes heavy-ion beams from the RHIC complex. EBIS would allow for the acceleration of all important ion species for the NASA radiobiology program, such as, helium, argon, and neon which are unavailable with the present Tandem injector. In addition, the new system would allow for very rapid switching of ion species for

  18. An EBIS for charge state breeding in the SPES project

    Indian Academy of Sciences (India)

    V Variale; G Brautti; T Clauser; A Rainò; V Stagno; G Lamanna; V Valentino; A Boggia; Y Boimelshtein; P Logatchov; B Skarbo; M Tiunov

    2002-11-01

    The ‘charge state breeder’, BRIC (breeding ion charge) is in construction at the INFN section of Bari (Italy). It is based on EBIS scheme and it is designed to accept radioactive ion beam (RIB) with charge state +1 in a slow injection mode. This experiment can be considered as a first step towards the design and construction of a charge breeder for the SPES project. The new feature of BRIC, with respect to the classical EBIS, is given by the insertion, in the ion chamber, of a rf-quadrupole aiming at filtering the unwanted masses and then making a more efficient containment of the wanted ions. In this paper, the breeder design, the simulation results of the electron and ion beam propagation and the construction problems of the device will be reported.

  19. Analysis Tool Web Services from the EMBL-EBI.

    Science.gov (United States)

    McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

    2013-07-01

    Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

  20. On-line charge breeding using ECRIS and EBIS

    Science.gov (United States)

    Vondrasek, Richard

    2016-06-01

    The efficient and rapid production of a high-quality, pure beam of highly charged ions is at the heart of any radioactive ion beam facility. Whether an electron cyclotron resonance (ECR) ion source or an electron beam ion source (EBIS) is used to produce these highly charged ions, their operating characteristics will set the boundaries on the range of experiments which can be performed. In addition, time structure and duty cycle have to be considered when defining the operating parameters of the accelerator system as a whole. At Argonne National Laboratory (ANL), an ECR charge breeder was developed as part of the Californium Rare Ion Breeder Upgrade (CARIBU) program. The charge breeding efficiency and high charge state production of the source is at the forefront of ECR charge breeders, but its overall performance as part of the accelerator system is limited by pervasive background and relatively long breeding times. As such, an EBIS charge breeder has been developed and is running in an off-line configuration. It has already demonstrated good breeding efficiencies, shorter residence times, and reduced background and is scheduled to replace the ECR charge breeder in late 2015. The resultant change in duty cycle and time structure necessitates changes to the overall operation of the facility. The experiences with these breeders, as well as from several other facilities which already utilize an ECR or EBIS for charge breeding, help to define the operational characteristics of each technology - their strengths, their weaknesses, and the possible paths to improvement.

  1. EBI3 regulates the NK cell response to mouse cytomegalovirus infection

    DEFF Research Database (Denmark)

    Jensen, Helle; Chen, Shih-Yu; Folkersen, Lasse Westergaard

    2017-01-01

    . The induction of EBI3 protein expression in mouse NK cells is a late activation event. Thus, early activation events of NK cells, such as IFNγ production and CD69 expression, were not affected in EBI3-deficient (Ebi3-/-) C57BL/6 (B6) mice during MCMV infection. Furthermore, comparable levels of early viral...... replication in spleen and liver were observed in MCMV-infected Ebi3-/- and wild-type (WT) B6 mice. Interestingly, the viral load in salivary glands and oral lavage was strongly decreased in the MCMV-infected Ebi3-/- B6 mice, suggesting that EBI3 plays a role in the establishment of MCMV latency. We detected...

  2. Oxysterol-EBI2 signaling in immune regulation and viral infection

    DEFF Research Database (Denmark)

    Daugvilaite, Viktorija; Arfelt, Kristine Niss; Benned-Jensen, Tau

    2014-01-01

    The seven transmembrane G protein-coupled receptor Epstein-Barr virus (EBV) induced gene 2 (EBI2; also known as GPR183) was identified in 1993 on the basis of its substantial upregulation in EBV-infected cells. It is primarily expressed in lymphoid cells; most abundantly in B cells. EBI2 is central......), yet many structurally related oxysterols can bind to an EBI2 pocket that is defined by the upper parts of the transmembrane helices and extracellular receptor regions. EBI2 signals via Gαi, as well as via G protein-independent pathways like β-arrestin recruitment. The concerted action...

  3. Charge breeding of radioactive ions with EBIS and EBIT

    CERN Document Server

    Wenander, Fredrik

    2010-01-01

    A charge state breeder, which transforms externally injected singly charged ions to a higher charge state q+, is an important tool which has applications within atomic, nuclear and even particle physics. The charge breeding concept of radioactive ions has already been demonstrated at REX-ISOLDE/CERN with the use of an Electron beam Ion Source (EBIS) and at several facilities employing Electron Resonance Cyclotron Ion Sources (ECRIS). As will be demonstrated in this paper, EBIS and Electron Beam Ion Traps (EBIT), are well suited for the task as they are capable of delivering clean, highly charged beams within a short transformation time. The increasing demand for highly charged ions of all kind of elements and isotopes, stable and radioactive, to be used for low-energy experiments such as TITAN at TRIUMF and MATS at FAIR, but also for post-acceleration to higher energies, is now pushing the development of the breeders. The next challenge will be to satisfy the needs, for example space-charge capacity, of the s...

  4. Ligand Modulation of the Epstein-Barr Virus-induced Seven-transmembrane Receptor EBI2

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Smethurst, Christopher; Holst, Peter Johannes;

    2011-01-01

    The Epstein-Barr virus-induced receptor 2 (EBI2) is a constitutively active seven-transmembrane receptor, which was recently shown to orchestrate the positioning of B cells in the follicle. To date, no ligands, endogenously or synthetic, have been identified that modulate EBI2 activity. Here we...

  5. Molecular pharmacological phenotyping of EBI2. An orphan seven-transmembrane receptor with constitutive activity

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Benned-Jensen, Tau; Holst, Peter J

    2006-01-01

    Epstein-Barr virus (EBV)-induced receptor 2 (EBI2) is an orphan seven-transmembrane (7TM) receptor originally identified as the most up-regulated gene (>200-fold) in EBV-infected cells. Here we show that EBI2 signals with constitutive activity through Galpha(i) as determined by a receptor-mediate...

  6. Design and numerical characterization of a crossover EBIS

    Science.gov (United States)

    Geyer, Sabrina; Langbein, A.; Meusel, Oliver; Kester, Oliver

    2015-01-01

    For the investigation of highly charged ions, a crossover EBIS (XEBIS) was developed at the University of Frankfurt. In contrast to conventional EBIS/T devices the compression of the electron beam is achieved by electrostatic focusing to a crossover point in the interaction region. This concept allows a compact and simple design. Simulations performed with EGUN show a perveance of 2.1×10-7 A/V3/2 for the realized gun system. In the interaction region the electron beam has a density of around 10 A/cm2 and a minimum radius of 0.15 mm. The XEBIS has a total length of 112 mm with a trap length of 26 mm. It is designed for electron beam energies of up to 6 keV/q. The storage capacity of the trap region is in the order of 1×108 charges. Charge state breeding studies with CBSIM indicate for the noble gases as maximal achievable charge state Ar16+, Kr30+ and Xe35+. Thus ion beam currents of around 2.04 nA assuming 50 Hz repetition rate can be expected. The emittance of the extracted beam is approximated to 8 mm mrad. After completion of the construction phase, the XEBIS will be installed for first performance investigations at a dedicated test bench, equipped with a fast Faraday Cup (FC), a retarding field spectrometer, a luminescence screen and optical diagnostics. Subsequently the XEBIS will serve as source for highly charged ions at different experimental setups.

  7. Genetic characterization of ebi reveals its critical role in Drosophila wing growth

    Science.gov (United States)

    Walker, Cherryl D; Orme, Mariam H; Leevers, Sally J

    2011-01-01

    The ebi gene of Drosophila melanogaster has been implicated in diverse signaling pathways, cellular functions and developmental processes. However, a thorough genetic analysis of this gene has been lacking and the true extent of its biological roles is unclear. Here, we characterize eleven ebi mutations and find that ebi has a novel role in promoting growth of the wing imaginal disc: viable combinations of mutant alleles give rise to adults with small wings. Wing discs with reduced EBI levels are correspondingly small and exhibit downregulation of Notch target genes. Furthermore, we show that EBI colocalizes on polytene chromosomes with Smrter (SMR), a transcriptional corepressor, and Suppressor of Hairless (SU(H)), the primary transcription factor involved in Notch signaling. Interestingly, the mammalian orthologs of ebi, transducin β-like 1 (TBL1) and TBL-related 1 (TBLR1), function as corepressor/coactivator exchange factors and are required for transcriptional activation of Notch target genes. We hypothesize that EBI acts to activate (de-repress) transcription of Notch target genes important for Drosophila wing growth by functioning as a corepressor/coactivator exchange factor for SU(H). PMID:22041576

  8. Inequalities of Čebyšev Type for Lipschitzian Functions in Banach Algebras

    Directory of Open Access Journals (Sweden)

    Boldea Marius V.

    2016-12-01

    Full Text Available In this paper we give some Čebyšev type norm inequalities for two Lipschitzian functions on Banach algebras. Some examples for power function, exponential and the resolvent functions are also provided

  9. Electron-beam-ion-source (EBIS) modeling progress at FAR-TECH, Inc.

    Science.gov (United States)

    Kim, J. S.; Zhao, L.; Spencer, J. A.; Evstatiev, E. G.

    2015-01-01

    FAR-TECH, Inc. has been developing a numerical modeling tool for Electron-Beam-Ion-Sources (EBISs). The tool consists of two codes. One is the Particle-Beam-Gun-Simulation (PBGUNS) code to simulate a steady state electron beam and the other is the EBIS-Particle-In-Cell (EBIS-PIC) code to simulate ion charge breeding with the electron beam. PBGUNS, a 2D (r,z) electron gun and ion source simulation code, has been extended for efficient modeling of EBISs and the work was presented previously. EBIS-PIC is a space charge self-consistent PIC code and is written to simulate charge breeding in an axisymmetric 2D (r,z) device allowing for full three-dimensional ion dynamics. This 2D code has been successfully benchmarked with Test-EBIS measurements at Brookhaven National Laboratory. For long timescale (< tens of ms) ion charge breeding, the 2D EBIS-PIC simulations take a long computational time making the simulation less practical. Most of the EBIS charge breeding, however, may be modeled in 1D (r) as the axial dependence of the ion dynamics may be ignored in the trap. Where 1D approximations are valid, simulations of charge breeding in an EBIS over long time scales become possible, using EBIS-PIC together with PBGUNS. Initial 1D results are presented. The significance of the magnetic field to ion dynamics, ion cooling effects due to collisions with neutral gas, and the role of Coulomb collisions are presented.

  10. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  11. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

    Science.gov (United States)

    Hill, David P; Adams, Nico; Bada, Mike; Batchelor, Colin; Berardini, Tanya Z; Dietze, Heiko; Drabkin, Harold J; Ennis, Marcus; Foulger, Rebecca E; Harris, Midori A; Hastings, Janna; Kale, Namrata S; de Matos, Paula; Mungall, Christopher J; Owen, Gareth; Roncaglia, Paola; Steinbeck, Christoph; Turner, Steve; Lomax, Jane

    2013-07-29

    The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl.

  12. Reliable operation of the Brookhaven EBIS for highly charged ion production for RHIC and NSRL

    Energy Technology Data Exchange (ETDEWEB)

    Beebe, E., E-mail: beebe@bnl.gov; Alessi, J., E-mail: beebe@bnl.gov; Binello, S., E-mail: beebe@bnl.gov; Kanesue, T., E-mail: beebe@bnl.gov; McCafferty, D., E-mail: beebe@bnl.gov; Morris, J., E-mail: beebe@bnl.gov; Okamura, M., E-mail: beebe@bnl.gov; Pikin, A., E-mail: beebe@bnl.gov; Ritter, J., E-mail: beebe@bnl.gov; Schoepfer, R., E-mail: beebe@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2015-01-09

    An Electron Beam Ion Source for the Relativistic Heavy Ion Collider (RHIC EBIS) was commissioned at Brookhaven in September 2010 and since then it routinely supplies ions for RHIC and NASA Space Radiation Laboratory (NSRL) as the main source of highly charged ions from Helium to Uranium. Using three external primary ion sources for 1+ injection into the EBIS and an electrostatic injection beam line, ion species at the EBIS exit can be switched in 0.2 s. A total of 16 different ion species have been produced to date. The length and the capacity of the ion trap have been increased by 20% by extending the trap by two more drift tubes, compared with the original design. The fraction of Au{sup 32+} in the EBIS Au spectrum is approximately 12% for 70-80% electron beam neutralization and 8 pulses operation in a 5 Hertz train and 4-5 s super cycle. For single pulse per super cycle operation and 25% electron beam neutralization, the EBIS achieves the theoretical Au{sup 32+} fractional output of 18%. Long term stability has been very good with availability of the beam from RHIC EBIS during 2012 and 2014 RHIC runs approximately 99.8%.

  13. Reliable operation of the Brookhaven EBIS for highly charged ion production for RHIC and NSRL

    Science.gov (United States)

    Beebe, E.; Alessi, J.; Binello, S.; Kanesue, T.; McCafferty, D.; Morris, J.; Okamura, M.; Pikin, A.; Ritter, J.; Schoepfer, R.

    2015-01-01

    An Electron Beam Ion Source for the Relativistic Heavy Ion Collider (RHIC EBIS) was commissioned at Brookhaven in September 2010 and since then it routinely supplies ions for RHIC and NASA Space Radiation Laboratory (NSRL) as the main source of highly charged ions from Helium to Uranium. Using three external primary ion sources for 1+ injection into the EBIS and an electrostatic injection beam line, ion species at the EBIS exit can be switched in 0.2 s. A total of 16 different ion species have been produced to date. The length and the capacity of the ion trap have been increased by 20% by extending the trap by two more drift tubes, compared with the original design. The fraction of Au32+ in the EBIS Au spectrum is approximately 12% for 70-80% electron beam neutralization and 8 pulses operation in a 5 Hertz train and 4-5 s super cycle. For single pulse per super cycle operation and 25% electron beam neutralization, the EBIS achieves the theoretical Au32+ fractional output of 18%. Long term stability has been very good with availability of the beam from RHIC EBIS during 2012 and 2014 RHIC runs approximately 99.8%.

  14. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

    Science.gov (United States)

    MacArthur, Jacqueline; Bowler, Emily; Cerezo, Maria; Gil, Laurent; Hall, Peggy; Hastings, Emma; Junkins, Heather; McMahon, Aoife; Milano, Annalisa; Morales, Joannella; Pendlington, Zoe May; Welter, Danielle; Burdett, Tony; Hindorff, Lucia; Flicek, Paul; Cunningham, Fiona; Parkinson, Helen

    2017-01-01

    The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future. PMID:27899670

  15. Evaluation and cross-comparison of lexical entities of biological interest (LexEBI.

    Directory of Open Access Journals (Sweden)

    Dietrich Rebholz-Schuhmann

    Full Text Available MOTIVATION: Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical "term space" (the "Lexeome", forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness. RESULT: This study compiles a resource for lexical terms of biomedical interest in a standard format (called "LexEBI", determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their term variants and chemical entities amongst other terms. In addition, disease terms have been identified from Medline and PubmedCentral and added to LexEBI. Our analysis demonstrates that the baseforms of terms from the different semantic types show only little polysemous use. Nonetheless, the term variants of protein and gene names (PGNs frequently contain species mentions, which should have been avoided according to protein annotation guidelines. Furthermore, the protein and gene entities as well as the chemical entities, both do comprise enzymes leading to hierarchical polysemy, and a large portion of PGNs make reference to a chemical entity. Altogether, according to our analysis based on the Medline distribution, 401,869 unique PGNs in the documents contain a reference to 25,022 chemical entities, 3,125 disease terms or 1,576 species mentions. CONCLUSION: LexEBI delivers the complete biomedical and chemical Lexeome in a standardized representation (http://www.ebi.ac.uk/Rebholz-srv/LexEBI/. The resource provides the disease terms as

  16. Advanced Electron Beam Ion Sources (EBIS) for 2-nd generation carbon radiotherapy facilities

    CERN Document Server

    Shornikov, A.

    2016-01-01

    In this work we analyze how advanced Electron Beam Ion Sources (EBIS) can facilitate the progress of carbon therapy facilities. We will demonstrate that advanced ion sources enable operation of 2-nd generation ion beam therapy (IBT) accelerators. These new accelerator concepts with designs dedicated to IBT provide beams better suited for therapy and, are more cost efficient than contemporary IBT facilities. We will give a sort overview of the existing new IBT concepts and focus on those where ion source technology is the limiting factor. We will analyse whether this limitation can be overcome in the near future thanks to ongoing EBIS development.

  17. Respiration monitoring by Electrical Bioimpedance (EBI) Technique in a group of healthy males. Calibration equations.

    Science.gov (United States)

    Balleza, M.; Vargas, M.; Kashina, S.; Huerta, M. R.; Delgadillo, I.; Moreno, G.

    2017-01-01

    Several research groups have proposed the electrical impedance tomography (EIT) in order to analyse lung ventilation. With the use of 16 electrodes, the EIT is capable to obtain a set of transversal section images of thorax. In previous works, we have obtained an alternating signal in terms of impedance corresponding to respiration from EIT images. Then, in order to transform those impedance changes into a measurable volume signal a set of calibration equations has been obtained. However, EIT technique is still expensive to attend outpatients in basics hospitals. For that reason, we propose the use of electrical bioimpedance (EBI) technique to monitor respiration behaviour. The aim of this study was to obtain a set of calibration equations to transform EBI impedance changes determined at 4 different frequencies into a measurable volume signal. In this study a group of 8 healthy males was assessed. From obtained results, a high mathematical adjustment in the group calibrations equations was evidenced. Then, the volume determinations obtained by EBI were compared with those obtained by our gold standard. Therefore, despite EBI does not provide a complete information about impedance vectors of lung compared with EIT, it is possible to monitor the respiration.

  18. ChEBI in 2016: Improved services and an expanding collection of metabolites.

    Science.gov (United States)

    Hastings, Janna; Owen, Gareth; Dekker, Adriano; Ennis, Marcus; Kale, Namrata; Muthukrishnan, Venkatesh; Turner, Steve; Swainston, Neil; Mendes, Pedro; Steinbeck, Christoph

    2016-01-04

    ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46,000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

    Science.gov (United States)

    Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

  20. 7a, 25-dihydroxycholesterol-mediated activation of EBI2 in immune regulation and diseases

    Directory of Open Access Journals (Sweden)

    Siquan eSun

    2015-03-01

    Full Text Available EBI2, aka GPR183, is a G-couple receptor originally identified in 1993 as one of main genes induced in Burkitt’s lymphoma cell line BL41 by Epstein-Barr virus (EBV infection. After it was reported in 2009 that the receptor played a key role in regulating B cell migration and responses, we initiated an effort in looking for its endogenous ligand. In 2011 we and another group reported the identification of 7a, 25-dihydroxyxcholesterol (7a, 25-OHC, an oxysterol, as the likely physiological ligand of EBI2. A few subsequently published studies further elucidated how 7a, 25-OHC bound to EBI2, and how a gradient of 7a, 25-OHC could be generated in vivo and regulated migration, activation, and functions of B cells, T cells, dendritic cells (DC, monocytes/macrophages and astrocytes. The identification of 7a, 25-OHC as a GPCR ligand revealed a previously unknown signaling system of oxysterols, a class of molecules which exert profound biological functions. Dysregulation of the synthesis or functions of these molecules is believed to contribute to inflammation and autoimmune diseases, cardiovascular diseases, neurodegenerative diseases, cancer as well as metabolic diseases such as diabetes, obesity, and dyslipidemia. Therefore EBI2 may represent a promising target for therapeutic interventions for human diseases.

  1. Design of an EBIS charge breeder system for rare-isotope beams

    Science.gov (United States)

    Park, Young-Ho; Son, Hyock-Jun; Kim, Jongwon

    2016-09-01

    Rare-isotope beams will be produced by using the isotope separation on-line (ISOL) system at the Rare Isotope Science Project (RISP). A proton cyclotron is the driver accelerator for ISOL targets, and uranium carbide (UCx) will be a major target material. An isotope beam of interest extracted from the target will be ionized and selected by using a mass separator. The beam emittance will then be reduced by using a radio-frequency quadrupole (RFQ) cooler before the beam is injected into the electron-beam ion-source (EBIS) charge breeder (CB). The maximum electron beam current of the EBIS is 3 A from a cathode made of IrCe in an applied magnetic field of 0.2 T. The size of the electron beam is compressed by magnetic fields of up to 6 T caused in the charge-breeding region by a superconducting solenoid. The design of EBIS-CB was performed by using mechanics as well as beam optics. A test stand for the electron gun and its collector, which can take an electron-beam power of 20 kW, are under construction. The gun assembly was first tested by using a high-voltage pulse so as to measure its perveance. The design of the EBIS, along with its test stand, is described.

  2. Recent charge-breeding developments with EBIS/T devices (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, S., E-mail: schwarz@nscl.msu.edu; Lapierre, A. [National Superconducting Cyclotron Laboratory (NSCL), Michigan State University, East Lansing, Michigan 48824 (United States)

    2016-02-15

    Short breeding times, narrow charge state distributions, low background, high efficiency, and the flexible time structure of the ejected low-emittance ion pulses are among the most attractive features of electron beam ion source or trap (EBIS/T) based charge breeders. Significant progress has been made to further improve these properties: Several groups are working to increase current densities towards 10{sup 3} or even 10{sup 4} A/cm{sup 2}. These current densities will become necessary to deliver high charge states of heavy nuclei in a short time and/or provide sufficient space-charge capacity to handle high-current ion beams in next-generation rare-isotope beam (RIB) facilities. Efficient capture of continuous beams, attractive because of its potential of handling highest-current ion beams, has become possible with the development of high-density electron beams of >1 A. Requests for the time structure of the charge bred ion pulse range from ultra-short pulses to quasi-continuous beams. Progress is being made on both ends of this spectrum, by either dividing the extracted charge in many pulse-lets, adjusting the extraction potential for a near-uniform long pulse, or adding dedicated devices to spread the ion bunches delivered from the EBIS/T in time. Advances in EBIS/T charge state breeding are summarized, including recent results with NSCL’s ReA EBIS/T charge breeder.

  3. Charge Breeding and Production of Multiply Charged Ions in EBIS and ECRIS

    CERN Document Server

    Wenander, Frederik J C

    2001-01-01

    The REXEBIS is an Electron Beam Ion Source (EBIS) developed for charge breeding of the exotic and sometimes short-lived isotopes that are produced at ISOLDE for the REX-ISOLDE post accelerator. Bunches of singly charged radioactive ions are injected into the EBIS and charge bred to a charge-to-mass ratio of approximately ¼, and thereafter extracted and injected into a short 3-stage LINAC for acceleration to a few MeV/u. This novel concept, employing a Penning trap to bunch and cool the ions from an on-line mass separator in combination with a charge breeding EBIS, should result in an efficient and compact system. The REXEBIS is based on a 0.5 A electron beam produced in the fringe field of a magnetic solenoid, and compressed to a current density of >200 A/cm2. The 2 T magnetic field is provided by a warm-bore superconducting solenoid, thus giving easy accessibility but no cryogenic pumping. The EBIS is switched between 60 kV (ion injection) and ~20 kV (ion extraction). This thesis presents the design and con...

  4. Recent charge-breeding developments with EBIS/T devices (invited)

    Science.gov (United States)

    Schwarz, S.; Lapierre, A.

    2016-02-01

    Short breeding times, narrow charge state distributions, low background, high efficiency, and the flexible time structure of the ejected low-emittance ion pulses are among the most attractive features of electron beam ion source or trap (EBIS/T) based charge breeders. Significant progress has been made to further improve these properties: Several groups are working to increase current densities towards 103 or even 104 A/cm2. These current densities will become necessary to deliver high charge states of heavy nuclei in a short time and/or provide sufficient space-charge capacity to handle high-current ion beams in next-generation rare-isotope beam (RIB) facilities. Efficient capture of continuous beams, attractive because of its potential of handling highest-current ion beams, has become possible with the development of high-density electron beams of >1 A. Requests for the time structure of the charge bred ion pulse range from ultra-short pulses to quasi-continuous beams. Progress is being made on both ends of this spectrum, by either dividing the extracted charge in many pulse-lets, adjusting the extraction potential for a near-uniform long pulse, or adding dedicated devices to spread the ion bunches delivered from the EBIS/T in time. Advances in EBIS/T charge state breeding are summarized, including recent results with NSCL's ReA EBIS/T charge breeder.

  5. A multipassage spectrometer for the study of electron-ion interactions in the EBIS

    Science.gov (United States)

    Kleinod, M.; Dietrich, J.; Lakatos, A.; Langbein, I.; Becker, R.

    1992-04-01

    A multipassage magnetic spectrometer has been constructed which allows selection of a specific high charge state from the extracted ion pulse of our electron beam ion source (EBIS) and to reinject it in the emptied source, now using the electron beam of meanwhile changed energy as a target of free electrons for the study of ionization, dielectronic recombination (DR), or radiative electron capture (REC). The spectrometer consists of a H-magnet with round pole pieces and 4 identical arrangements of achromatic lenses and mirrors under 90° forming a versatile ion switchyard with the possibility of recirculation. The chromaticity of the recirculating transport system and the dispersion of this spectrometer are adjustable by electric potentials on suitably placed electrostatic deflectors inside of the magnetic field. For the injection of ions from an external ion source into the EBIS and to the beam lines, the mirror potentials are pulsed accordingly.

  6. Emittance Reduction between EBIS LINAC and Booster by Electron Beam Cooling; Is Single Pass Cooling Possible?

    Energy Technology Data Exchange (ETDEWEB)

    Hershcovitch,A.

    2008-04-01

    Electron beam cooling is examined as an option to reduce momentum of gold ions exiting the EBIS LINAC before injection into the booster. Electron beam parameters are based on experimental data (obtained at BNL) of electron beams extracted from a plasma cathode. Preliminary calculations indicate that single pass cooling is feasible; momentum spread can be reduced by more than an order of magnitude in less than one meter.

  7. cMapper: gene-centric connectivity mapper for EBI-RDF platform.

    Science.gov (United States)

    Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

    2017-01-15

    In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at

  8. Surface and material analytics based on Dresden-EBIS platform technology

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, M., E-mail: mike.schmidt@dreebit.com; König, J., E-mail: mike.schmidt@dreebit.com [DREEBIT GmbH, Grossroehrsdorf (Germany); Bischoff, L. [Helmholtz-Zentrum Dresden-Rossendorf, Dresden (Germany); Pilz, W. [Dresden University of Technology, Dresden (Germany); Zschornack, G. [Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany and Dresden University of Technology, Dresden (Germany)

    2015-01-09

    Nowadays widely used mass spectrometry systems utilize energetic ions hitting a sample and sputter material from the surface of a specimen. The generated secondary ions are separated and detected with high mass resolution to determine the target materials constitution. Based on this principle, we present an alternative approach implementing a compact Electron Beam Ion Source (EBIS) in combination with a Liquid Metal Ion Source (LMIS). An LMIS can deliver heavy elements which generate high sputter yields on a target surface. More than 90% of this sputtered material consists of mono- and polyatomic neutrals. These particles are able to penetrate the magnetic field of an EBIS and they will be ionized within the electron beam. A broad spectrum of singly up to highly charged ions can be extracted depending on the operation conditions. Polyatomic ions will decay during the charge-up process. A standard bending magnet or a Wien filter is used to separate the different ion species due to their mass-to-charge ratio. Using different charge states of ions as it is common with EBIS it is also possible to resolve interfering charge-to-mass ratios of only singly charged ions. Different setups for the realization of feeding the electron beam with sputtered atoms of solids will be presented and discussed. As an example the analysis of a copper surface is used to show high-resolution spectra with low background noise. Individual copper isotopes and clusters with different isotope compositions can be resolved at equal atomic numbers. These results are a first step for the development of a new compact low-cost and high-resolution mass spectrometry system. In a more general context, the described technique demonstrates an efficient method for feeding an EBIS with atoms of nearly all solid elements from various solid target materials. The new straightforward design of the presented setup should be of high interest for a broad range of applications in materials research as well as for

  9. Surface and material analytics based on Dresden-EBIS platform technology

    Science.gov (United States)

    Schmidt, M.; König, J.; Bischoff, L.; Pilz, W.; Zschornack, G.

    2015-01-01

    Nowadays widely used mass spectrometry systems utilize energetic ions hitting a sample and sputter material from the surface of a specimen. The generated secondary ions are separated and detected with high mass resolution to determine the target materials constitution. Based on this principle, we present an alternative approach implementing a compact Electron Beam Ion Source (EBIS) in combination with a Liquid Metal Ion Source (LMIS). An LMIS can deliver heavy elements which generate high sputter yields on a target surface. More than 90% of this sputtered material consists of mono- and polyatomic neutrals. These particles are able to penetrate the magnetic field of an EBIS and they will be ionized within the electron beam. A broad spectrum of singly up to highly charged ions can be extracted depending on the operation conditions. Polyatomic ions will decay during the charge-up process. A standard bending magnet or a Wien filter is used to separate the different ion species due to their mass-to-charge ratio. Using different charge states of ions as it is common with EBIS it is also possible to resolve interfering charge-to-mass ratios of only singly charged ions. Different setups for the realization of feeding the electron beam with sputtered atoms of solids will be presented and discussed. As an example the analysis of a copper surface is used to show high-resolution spectra with low background noise. Individual copper isotopes and clusters with different isotope compositions can be resolved at equal atomic numbers. These results are a first step for the development of a new compact low-cost and high-resolution mass spectrometry system. In a more general context, the described technique demonstrates an efficient method for feeding an EBIS with atoms of nearly all solid elements from various solid target materials. The new straightforward design of the presented setup should be of high interest for a broad range of applications in materials research as well as for

  10. EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

    Science.gov (United States)

    Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

    2014-01-01

    Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.

  11. Prediction of Drugs Target Groups Based on ChEBI Ontology

    Directory of Open Access Journals (Sweden)

    Yu-Fei Gao

    2013-01-01

    Full Text Available Most drugs have beneficial as well as adverse effects and exert their biological functions by adjusting and altering the functions of their target proteins. Thus, knowledge of drugs target proteins is essential for the improvement of therapeutic effects and mitigation of undesirable side effects. In the study, we proposed a novel prediction method based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the kind of functions of a drug may be deduced. By collecting data in KEGG, a benchmark dataset consisting of 876 drugs, categorized into four target groups, was constructed. To evaluate the method more thoroughly, the benchmark dataset was divided into a training dataset and an independent test dataset. It is observed by jackknife test that the overall prediction accuracy on the training dataset was 83.12%, while it was 87.50% on the test dataset—the predictor exhibited an excellent generalization. The good performance of the method indicates that the ontology information of the drugs contains rich information about their target groups, and the study may become an inspiration to solve the problems of this sort and bridge the gap between ChEBI ontology and drugs target groups.

  12. BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

    Science.gov (United States)

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-02-21

    Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

  13. Ebi/AP-1 suppresses pro-apoptotic genes expression and permits long-term survival of Drosophila sensory neurons.

    Directory of Open Access Journals (Sweden)

    Young-Mi Lim

    Full Text Available Sensory organs are constantly exposed to physical and chemical stresses that collectively threaten the survival of sensory neurons. Failure to protect stressed neurons leads to age-related loss of neurons and sensory dysfunction in organs in which the supply of new sensory neurons is limited, such as the human auditory system. Transducin β-like protein 1 (TBL1 is a candidate gene for ocular albinism with late-onset sensorineural deafness, a form of X-linked age-related hearing loss. TBL1 encodes an evolutionarily conserved F-box-like and WD40 repeats-containing subunit of the nuclear receptor co-repressor/silencing mediator for retinoid and thyroid hormone receptor and other transcriptional co-repressor complexes. Here we report that a Drosophila homologue of TBL1, Ebi, is required for maintenance of photoreceptor neurons. Loss of ebi function caused late-onset neuronal apoptosis in the retina and increased sensitivity to oxidative stress. Ebi formed a complex with activator protein 1 (AP-1 and was required for repression of Drosophila pro-apoptotic and anti-apoptotic genes expression. These results suggest that Ebi/AP-1 suppresses basal transcription levels of apoptotic genes and thereby protects sensory neurons from degeneration.

  14. Higher decidual EBI3 and HLA-G mRNA expression in preeclampsia : Cause or consequence of preeclampsia

    NARCIS (Netherlands)

    Prins, J.R.; van der Hoorn, M L P; Keijser, R; Ris-Stalpers, C; van Beelen, E; Afink, G B; Claas, F H J; van der Post, J A M; Scherjon, S A

    2016-01-01

    The maternal immune system must adapt to tolerate the invasion of the allogeneic feto-placental unit. It is generally accepted that improper adaptation causes pregnancy complications like preeclampsia. The Epstein-Barr virus-induced gene 3 (EBI3) protein is a subunit of immune-modulatory cytokines i

  15. Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience

    NARCIS (Netherlands)

    De Sousa, Paul A.; Steeg, Rachel; Wachter, Elisabeth; Bruce, Kevin; King, Jason; Hoeve, Marieke; Khadun, Shalinee; McConnachie, George; Holder, Julie; Kurtz, Andreas; Seltmann, Stefanie; Dewender, Johannes; Reimann, Sascha; Stacey, Glyn; O'Shea, Orla; Chapman, Charlotte; Healy, Lyn; Zimmermann, Heiko; Bolton, Bryan; Rawat, Trisha; Atkin, Isobel; Veiga, Anna; Kuebler, Bernd; Serano, Blanca Miranda; Saric, Tomo; Hescheler, Jürgen; Brüstle, Oliver; Peitz, Michael; Thiele, Cornelia; Geijsen, Niels; Holst, Bjørn; Clausen, Christian; Lako, Majlinda; Armstrong, Lyle; Gupta, Shailesh K.; Kvist, Alexander J.; Hicks, Ryan; Jonebring, Anna; Brolén, Gabriella; Ebneth, Andreas; Cabrera-Socorro, Alfredo; Foerch, Patrik; Geraerts, Martine; Stummann, Tina C.; Harmon, Shawn; George, Carol; Streeter, Ian; Clarke, Laura; Parkinson, Helen; Harrison, Peter W.; Faulconbridge, Adam; Cherubin, Luca; Burdett, Tony; Trigueros, Cesar; Patel, Minal J.; Lucas, Christa; Hardy, Barry; Predan, Rok; Dokler, Joh; Brajnik, Maja; Keminer, Oliver; Pless, Ole; Gribbon, Philip; Claussen, Carsten; Ringwald, Annette; Kreisel, Beate; Courtney, Aidan; Allsopp, Timothy E.

    2017-01-01

    A fast track “Hot Start” process was implemented to launch the European Bank for Induced Pluripotent Stem Cells (EBiSC) to provide early release of a range of established control and disease linked human induced pluripotent stem cell (hiPSC) lines. Established practice amongst consortium members was

  16. Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC - the Hot Start experience

    Directory of Open Access Journals (Sweden)

    Paul A. De Sousa

    2017-04-01

    eTOC: The report focuses on the EBiSC experience of rapidly establishing an operational capacity to procure, bank and distribute a foundational collection of established hiPSC lines. It validates the feasibility and defines the challenges of harnessing and integrating the capability and productivity of centres across Europe using commonly available resources currently in the field.

  17. Higher decidual EBI3 and HLA-G mRNA expression in preeclampsia : Cause or consequence of preeclampsia

    NARCIS (Netherlands)

    Prins, J. R.; van der Hoorn, M. L. P.; Keijser, R.; Ris-Stalpers, C.; van Beelen, E.; Afink, G. B.; Claas, F. H. J.; van der Post, J. A. M.; Scherjon, S. A.

    The maternal immune system must adapt to tolerate the invasion of the allogeneic feto-placental unit. It is generally accepted that improper adaptation causes pregnancy complications like preeclampsia. The Epstein-Barr virus-induced gene 3 (EBI3) protein is a subunit of immune-modulatory cytokines

  18. Development of the Oldenburg Epistemic Beliefs Questionnaire (OLEQ), a German Questionnaire Based on the Epistemic Belief Inventory (EBI)

    Science.gov (United States)

    Paechter, Manuela; Rebmann, Karin; Schloemer, Tobias; Mokwinski, Bjoern; Hanekamp, Yvonne; Arendasy, Martin

    2013-01-01

    The present research describes the development of a German questionnaire for measurement of domain-general epistemic beliefs. Pre-studies on the psychometric properties of a German version of the Epistemic Beliefs Inventory (EBI) had emphasized the necessity to develop an instrument that is especially constructed for German-speaking samples. The…

  19. EBI2 augments Tfh cell fate by promoting interaction with IL-2-quenching dendritic cells.

    Science.gov (United States)

    Li, Jianhua; Lu, Erick; Yi, Tangsheng; Cyster, Jason G

    2016-05-05

    T follicular helper (Tfh) cells are a subset of T cells carrying the CD4 antigen; they are important in supporting plasma cell and germinal centre responses. The initial induction of Tfh cell properties occurs within the first few days after activation by antigen recognition on dendritic cells, although how dendritic cells promote this cell-fate decision is not fully understood. Moreover, although Tfh cells are uniquely defined by expression of the follicle-homing receptor CXCR5 (refs 1, 2), the guidance receptor promoting the earlier localization of activated T cells at the interface of the B-cell follicle and T zone has been unclear. Here we show that the G-protein-coupled receptor EBI2 (GPR183) and its ligand 7α,25-dihydroxycholesterol mediate positioning of activated CD4 T cells at the interface of the follicle and T zone. In this location they interact with activated dendritic cells and are exposed to Tfh-cell-promoting inducible co-stimulator (ICOS) ligand. Interleukin-2 (IL-2) is a cytokine that has multiple influences on T-cell fate, including negative regulation of Tfh cell differentiation. We demonstrate that activated dendritic cells in the outer T zone further augment Tfh cell differentiation by producing membrane and soluble forms of CD25, the IL-2 receptor α-chain, and quenching T-cell-derived IL-2. Mice lacking EBI2 in T cells or CD25 in dendritic cells have reduced Tfh cells and mount defective T-cell-dependent plasma cell and germinal centre responses. These findings demonstrate that distinct niches within the lymphoid organ T zone support distinct cell fate decisions, and they establish a function for dendritic-cell-derived CD25 in controlling IL-2 availability and T-cell differentiation.

  20. EBI2 Is Highly Expressed in Multiple Sclerosis Lesions and Promotes Early CNS Migration of Encephalitogenic CD4 T Cells

    Directory of Open Access Journals (Sweden)

    Florian Wanke

    2017-01-01

    Full Text Available Arrival of encephalitogenic T cells at inflammatory foci represents a critical step in development of experimental autoimmune encephalomyelitis (EAE, the animal model for multiple sclerosis. EBI2 and its ligand, 7α,25-OHC, direct immune cell localization in secondary lymphoid organs. CH25H and CYP7B1 hydroxylate cholesterol to 7α,25-OHC. During EAE, we found increased expression of CH25H by microglia and CYP7B1 by CNS-infiltrating immune cells elevating the ligand concentration in the CNS. Two critical pro-inflammatory cytokines, interleukin-23 (IL-23 and interleukin-1 beta (IL-1β, maintained expression of EBI2 in differentiating Th17 cells. In line with this, EBI2 enhanced early migration of encephalitogenic T cells into the CNS in a transfer EAE model. Nonetheless, EBI2 was dispensable in active EAE. Human Th17 cells do also express EBI2, and EBI2 expressing cells are abundant within multiple sclerosis (MS white matter lesions. These findings implicate EBI2 as a mediator of CNS autoimmunity and describe mechanistically its contribution to the migration of autoreactive T cells into inflamed organs.

  1. Elevated serum IL-35 and increased expression of IL-35-p35 or -EBI3 in CD4+CD25+ T cells in patients with active tuberculosis

    Science.gov (United States)

    Kong, Bin; Liu, Gan-Bin; Zhang, Jun-Ai; Fu, Xiao-Xia; Xiang, Wen-Yu; Gao, Yu-Chi; Lu, Yuan-Bin; Wu, Xian-Jing; Qiu, Feng; Wang, Wan-Dang; Yi, Lai-Long; Zhong, Ji-Xin; Chen, Zheng W; Xu, Jun-Fa

    2016-01-01

    Despite the recent appreciation of interleukin 35 (IL-35) function in inflammatory diseases, little is known for IL-35 response in patients with active tuberculosis (ATB). In the current study, we demonstrated that ATB patients exhibited increases in serum IL-35 and in mRNA expression of both subunits of IL-35 (p35 and EBI3) in white blood cells and peripheral blood mononuclear cells. Consistently, anti-TB drug treatment led to reduction in serum IL-35 level and p35 or EBI3 expression. TB infection was associated with expression of p35 or EBI3 protein in CD4+ but not CD8+ T cells. Most p35+CD4+ T cells and EBI3+CD4+ T cells expressed Treg-associated marker CD25. Our findings may be important in understanding immune pathogenesis of TB. IL-35 in the blood may potentially serve as a biomarker for immune status and prognosis in TB. PMID:27158354

  2. Elevated serum IL-35 and increased expression of IL-35-p35 or -EBI3 in CD4(+)CD25(+) T cells in patients with active tuberculosis.

    Science.gov (United States)

    Kong, Bin; Liu, Gan-Bin; Zhang, Jun-Ai; Fu, Xiao-Xia; Xiang, Wen-Yu; Gao, Yu-Chi; Lu, Yuan-Bin; Wu, Xian-Jing; Qiu, Feng; Wang, Wan-Dang; Yi, Lai-Long; Zhong, Ji-Xin; Chen, Zheng W; Xu, Jun-Fa

    2016-01-01

    Despite the recent appreciation of interleukin 35 (IL-35) function in inflammatory diseases, little is known for IL-35 response in patients with active tuberculosis (ATB). In the current study, we demonstrated that ATB patients exhibited increases in serum IL-35 and in mRNA expression of both subunits of IL-35 (p35 and EBI3) in white blood cells and peripheral blood mononuclear cells. Consistently, anti-TB drug treatment led to reduction in serum IL-35 level and p35 or EBI3 expression. TB infection was associated with expression of p35 or EBI3 protein in CD4(+) but not CD8(+) T cells. Most p35(+)CD4(+) T cells and EBI3(+)CD4(+) T cells expressed Treg-associated marker CD25. Our findings may be important in understanding immune pathogenesis of TB. IL-35 in the blood may potentially serve as a biomarker for immune status and prognosis in TB.

  3. New Čebyšev Type Inequalities and Applications for Functions of Self-Adjoint Operators on Complex Hilbert Spaces

    Directory of Open Access Journals (Sweden)

    Mohammad W. Alomari

    2014-01-01

    Full Text Available Several new error bounds for the Čebyšev functional under various assumptions are proved. Applications for functions of self-adjoint operators on complex Hilbert spaces are provided as well.

  4. EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data.

    Science.gov (United States)

    Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; ten Hoopen, Petra; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert D

    2016-01-01

    EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans.

  5. EBIS-A facility for the studies of X-ray emission from solids bombarded by highly charged ions

    Energy Technology Data Exchange (ETDEWEB)

    Banaś, D., E-mail: d.banas@ujk.edu.pl [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Jabłoński, Ł. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Jagodziński, P. [Department of Physics, Kielce University of Technology, 25-314 Kielce (Poland); Kubala-Kukuś, A.; Sobota, D.; Pajek, M. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland)

    2015-07-01

    We report here on the progress in the X-ray spectroscopy program at the EBIS-A facility installed recently at the Institute of Physics of Jan Kochanowski University in Kielce. In this facility the beams of low-energy highly charged ions (HCI) produced by the Dresden EBIS-A ion source, after extraction and charge-state separation in the double focusing magnet, are directed to the experimental UHV chamber equipped with a 5-axis universal sample manipulator. The X-rays emitted in interaction of the highly charged ions with solids can be measured by an energy dispersive X-ray silicon drift detector (SDD) and/or a wavelength-dispersive X-ray spectrometer (WDS) mounted at the experimental chamber. The surface nanostructures formed by an impact of HCI will be studied by the grazing emission X-ray fluorescence (GEXRF) technique and using a multiprobe surface analysis system based on the X-ray photoelectron spectrometer (XPS) coupled to the UHV chamber of the EBIS-A facility. In this paper a brief description of the facility, X-ray instrumentation and the surface analysis system is given and the first results are presented.

  6. Modelling and design of high compression electron guns for EBIS/T charge breeders

    CERN Document Server

    AUTHOR|(CDS)2087190; Zschornack, G.; Lettry, J.; Wenander, F.

    In this thesis the optimization of the REXEBIS charge breeder at the ISOLDE facility is presented. REXEBIS in its current state provides a current density of 200A/cm² inside the trapping region at 2 T and will be optimized to the physical limit of its design. To overcome this limit a new electron gun, the HEC² gun, was designed in collaboration with the BNL and is in commission at TestEBIS. This electron gun promises a current density of >10 kA/cm², which decreases the charge breeding time significantly. This thesis presents novel simulation techniques supporting the commissioning phase by explaining the sources of occurring loss current and, in addition, evaluate the currently installed collector for compatibility with the HEC2 gun operating at its design limit. The experience gained from the commission of the HEC² gun and the established numerical techniques lead to the development of a smaller high-compression electron gun for medical purposes, the MEDeGUN. This electron gun should provide a high-quali...

  7. EBIS/T charge breeding for intense rare isotope beams at MSU

    CERN Document Server

    Schwarz, S; Marrs, R E; Kittimanapun, K; Lapierre, A; Mendez, A J; Ames, F; Beene, J R; Lindroos, M; Ahle, L E; Stracener, D W; Kester, O; Wenander, F; Lopez-Urrutia, J R Crespo; Dilling, J; Bollen, G

    2010-01-01

    Experiments with reaccelerated beams are an essential component of the science program of existing and future rare isotope beam facilities. NSCL is currently constructing ReA3, a reaccelerator for rare isotopes that have been produced by projectile fragmentation and in-flight fission and that have been thermalized in a gas stopper. The resulting low-energy beam will be brought to an Electron Beam Ion Source/Trap (EBIS/T) in order to obtain highly charged ions at an energy of 12 keV/u. This charge breeder is followed by a compact linear accelerator with a maximum beam energy of 3MeV/u for U-238 and higher energies for lighter isotopes. Next-generation rare isotope beam facilities like the Facility for Rare Isotope Beams FRIB, but also existing Isotope Separator On-line (ISOL) facilities are expected to provide rare-isotope beam rates in the order of 10(11) particles per second for reacceleration. At present the most promising scheme to efficiently start the reacceleration of these intense beams is the use of a...

  8. TLR3 drives IRF6-dependent IL-23p19 expression and p19/EBI3 heterodimer formation in keratinocytes.

    Science.gov (United States)

    Ramnath, Divya; Tunny, Kathryn; Hohenhaus, Daniel M; Pitts, Claire M; Bergot, Anne-Sophie; Hogarth, P Mark; Hamilton, John A; Kapetanovic, Ronan; Sturm, Richard A; Scholz, Glen M; Sweet, Matthew J

    2015-10-01

    Interferon regulatory factor (IRF) family members impart cell-type specificity to toll-like receptor (TLR) signalling, and we recently identified a role for IRF6 in TLR2 signalling in epithelial cells. TLR3 has a well-characterized role in wound healing in the skin, and here, we examined TLR3-dependent IRF6 functions in human keratinocytes. Primary keratinocytes responded robustly to the TLR3 agonist poly(IC) with upregulation of mRNAs for interferon-β (IFN-β), the interleukin-12 (IL-12) family member IL-23p19 and the chemokines IL-8 and chemokine (C-C motif) ligand 5 (CCL5). Silencing of IRF6 expression enhanced poly(IC)-inducible IFN-β mRNA levels and inhibited poly(IC)-inducible IL-23p19 mRNA expression in primary keratinocytes. Consistent with these data, co-transfection of IRF6 increased poly(IC)-inducible IL-23p19 promoter activity, but inhibited poly(IC)-inducible IFN-β promoter activity in reporter assays. Surprisingly, poly(IC) did not regulate IL-12p40 expression in keratinocytes, suggesting that TLR3-inducible IL-23p19 may have an IL-23-independent function in these cells. The only other IL-12 family member that was strongly poly(IC) inducible was EBI3, which has not been shown to heterodimerize with IL-23p19. Both co-immunoprecipitation and proximity ligation assays revealed that IL-23p19 and EBI3 interact in cells. Co-expression of IL-23p19 and EBI3, as compared with IL-23p19 alone, resulted in increased levels of secreted IL-23p19, implying a functional role for this heterodimer. In summary, we report that IRF6 regulates a subset of TLR3 responses in human keratinocytes, including the production of a novel IL-12 family heterodimer (p19/EBI3). We propose that the TLR3-IRF6-p19/EBI3 axis may regulate keratinocyte and/or immune cell functions in the context of cell damage and wound healing in the skin.

  9. Effect of EBI3 on radiation-induced immunosuppression of cervical cancer HeLa cells by regulating Treg cells through PD-1/PD-L1 pathway.

    Science.gov (United States)

    Zhang, Song-An; Niyazi, Hu-Er-Xi-Dan; Hong, Wen; Tuluwengjiang, Gu-Li-Xian; Zhang, Lei; Zhang, Yang; Su, Wei-Peng; Bao, Yong-Xing

    2017-03-01

    This study aimed to investigate the effect of EBI3 on radiation-induced immunosuppression of cervical cancer HeLa cells by regulating Treg cells through PD-1/PD-L1 signaling pathway. A total of 43 adult female Wistar rats were selected and injected with HeLa cells in the caudal vein to construct a rat model of cervical cancer. All model rats were randomly divided into the radiotherapy group ( n = 31) and the control group ( n = 12). The immunophenotype of Treg cells was detected by the flow cytometry. The protein expressions of EBI3, PD-1, and PD-L1 in cervical cancer tissues were tested by the streptavidin-peroxidase method. HeLa cells in the logarithmic growth phase were divided into four groups: the blank, the negative control group, the EBI3 mimics group, and the EBI3 inhibitors group. Western blotting was used to detect PD-1 and PD-L1 protein expressions. MTT assay was performed to measure the proliferation of Treg cells. Flow cytometry was used to detect cell cycle and apoptosis, and CD4(+)/CD8(+) T cell ratio in each group. Compared with before and 1 week after radiotherapy, the percentages of CD4(+)T cells and CD8(+)T cells were significantly decreased in the radiotherapy group at 1 month after radiotherapy. Furthermore, down-regulation of EBI3 and up-regulation of PD-1 and PD-L1 were observed in cervical cancer tissues at 1 month after radiotherapy. In comparison to the blank and negative control groups, increased expression of EBI3 and decreased expressions of PD-1 and PD-L1 were found in the EBI3 mimics group. However, the EBI3 inhibitors group had a lower expression of EBI3 and higher expressions of PD-1 and PD-L1 than those in the blank and negative control groups. The EBI3 mimics group showed an increase in the optical density value (0.43 ± 0.05), while a decrease in the optical density value (0.31 ± 0.02) was found in the EBI3 inhibitors group. Moreover, compared with the blank and negative control groups, the apoptosis rates

  10. EBI-907, a novel BRAF(V600E) inhibitor, has potent oral anti-tumor activity and a broad kinase selectivity profile.

    Science.gov (United States)

    Zhang, Jiayin; Lu, Biao; Liu, Dong; Shen, Ru; Yan, Yinfa; Yang, Liuqing; Zhang, Minsheng; Zhang, Lei; Cao, Guoqing; Cao, Hu; Fu, Beibei; Gong, Aishen; Sun, Qiming; Wan, Hong; Zhang, Lianshan; Tao, Weikang; Cao, Jingsong

    2016-01-01

    The oncogenic mutation of BRAF(V600E) has been found in approximately 8% of all human cancers, including more than 60% of melanoma and 10% of colorectal cancers. The clinical proof of concept in treating BRAF(V600E)-driving melanoma patients with the BRAF inhibitors has been well established. We have sought to identify and develop novel BRAF(V600E) inhibitors with more favorable profiles. Our chemistry effort has led to the discovery of EBI-907 as a novel BRAF(V600E) inhibitor with potent anti-tumor activity in vitro and in vivo. In a LanthaScreen BRAF(V600E) kinase assay, EBI-907 showed an IC50 of 4.8 nM, which is >10 -fold more potent than Vemurafenib (IC50 = 58.5 nM). In addition, EBI-907 showed a broader kinase selectivity profile, with potent activity against a number of important oncogenic kinases including FGFR1-3, RET, c-Kit, and PDGFRb. Concomitant with such properties, EBI-907 exhibits potent and selective cytotoxicity against a broader range of BRAF(V600E)-dependent cell lines including certain colorectal cancer cell lines with innate resistance to Vemurafenib. In BRAF(V600E)-dependent human Colo-205 and A375 tumor xenograft mouse models, EBI-907 caused a marked tumor regression in a dose-dependent manner, with superior efficacy to Vemurafenib. Our results also showed that combination with EGFR or MEK inhibitor enhanced the potency of EBI-907 in cell lines with innate or acquired resistance to BRAF inhibition alone. Our findings present EBI-907 as a potent and promising BRAF inhibitor, which might be useful in broader indications.

  11. Possible application of an EBIS in preinjectors for large heavy ion colliders

    Energy Technology Data Exchange (ETDEWEB)

    Haseroth, H. [European Organization for Nuclear Research, Geneva (Switzerland); Prelec, K. [Brookhaven National Lab., Upton, NY (United States)

    1994-08-01

    High energy, heavy ion nuclear physics has so far been limited to experiments with a fixed target. Presently there are two projects that would greatly extend the available collision energy: the Relativistic Heavy Ion Collider (RHIC) under construction at Brookhaven National Laboratory (BNL), and the Large Hadron Collider (LHC) planned at CERN. While RHIC was from the very beginning designed for collisions of all heavy ions up to gold, LHC was initially considered as a p-p and, perhaps eventually, an e-p collider, with the heavy ion option added at a later stage; this option is now included in the planning right from the beginning. The present RHIC scenario for acceleration of gold ions starts with the BNL Tandem injecting Au{sup 14+} ions into the Booster; after acceleration ions are stripped to a charge state of 77+, injected into the AGS, stripped again to 79+ and injected into RHIC, with three bunches per cycle. The LHC scenario for acceleration of lead ions will use as the injector the CERN Heavy Ion Facility: production of ions in a charge state around 27+ in an ECR ion source, followed by an RFQ/linac combination, stripping to Pb{sup 53+} at 4.2 MeV/u, acceleration in the PSB and PS, stripping to the state 82+, and acceleration in the SPS. There would be 144 bunches injected into the LHC per SPS cycle. However, the resulting luminosity would be rather low and several accumulating schemes are being considered as well. In this paper we are considering a next-generation EBIS device as a possible substitution for ion sources in the preinjector stages of the two colliders with the objective of achieving an improved performance.

  12. EBI2 overexpression in mice leads to B1 B cell expansion and chronic lymphocytic leukemia-(CLL)-like B cell malignancies

    DEFF Research Database (Denmark)

    Niss Arfelt, Kristine; Barington, Line; Benned-Jensen, Tau

    2017-01-01

    Human and mouse chronic lymphocytic leukemia (CLL) develop from CD5+ B cells that in mice and macaques are known to define the distinct B1a B cell lineage. B1a cells are characterized by lack of germinal center development and the B1a cell population is increased in mice with reduced germinal...... center formation. As a major mediator of follicular B cell migration, the G protein-coupled receptor (GPCR) Epstein Barr virus-induced gene 2 (EBI2 or GPR183) directs B cell migration in the lymphoid follicles in response to its endogenous ligands, oxysterols. Thus, upregulation of EBI2 drives the B...... cells towards the extrafollicular area, whereas downregulation is essential for germinal center formation. We therefore speculated whether increased expression of EBI2 would lead to an expanded B1 cell subset and, ultimately, progression to chronic lymphocytic leukemia. Here we demonstrate that B cell...

  13. Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.

    Science.gov (United States)

    De Sousa, Paul A; Steeg, Rachel; Wachter, Elisabeth; Bruce, Kevin; King, Jason; Hoeve, Marieke; Khadun, Shalinee; McConnachie, George; Holder, Julie; Kurtz, Andreas; Seltmann, Stefanie; Dewender, Johannes; Reimann, Sascha; Stacey, Glyn; O'Shea, Orla; Chapman, Charlotte; Healy, Lyn; Zimmermann, Heiko; Bolton, Bryan; Rawat, Trisha; Atkin, Isobel; Veiga, Anna; Kuebler, Bernd; Serano, Blanca Miranda; Saric, Tomo; Hescheler, Jürgen; Brüstle, Oliver; Peitz, Michael; Thiele, Cornelia; Geijsen, Niels; Holst, Bjørn; Clausen, Christian; Lako, Majlinda; Armstrong, Lyle; Gupta, Shailesh K; Kvist, Alexander J; Hicks, Ryan; Jonebring, Anna; Brolén, Gabriella; Ebneth, Andreas; Cabrera-Socorro, Alfredo; Foerch, Patrik; Geraerts, Martine; Stummann, Tina C; Harmon, Shawn; George, Carol; Streeter, Ian; Clarke, Laura; Parkinson, Helen; Harrison, Peter W; Faulconbridge, Adam; Cherubin, Luca; Burdett, Tony; Trigueros, Cesar; Patel, Minal J; Lucas, Christa; Hardy, Barry; Predan, Rok; Dokler, Joh; Brajnik, Maja; Keminer, Oliver; Pless, Ole; Gribbon, Philip; Claussen, Carsten; Ringwald, Annette; Kreisel, Beate; Courtney, Aidan; Allsopp, Timothy E

    2017-04-01

    A fast track "Hot Start" process was implemented to launch the European Bank for Induced Pluripotent Stem Cells (EBiSC) to provide early release of a range of established control and disease linked human induced pluripotent stem cell (hiPSC) lines. Established practice amongst consortium members was surveyed to arrive at harmonised and publically accessible Standard Operations Procedures (SOPs) for tissue procurement, bio-sample tracking, iPSC expansion, cryopreservation, qualification and distribution to the research community. These were implemented to create a quality managed foundational collection of lines and associated data made available for distribution. Here we report on the successful outcome of this experience and work flow for banking and facilitating access to an otherwise disparate European resource, with lessons to benefit the international research community. ETOC: The report focuses on the EBiSC experience of rapidly establishing an operational capacity to procure, bank and distribute a foundational collection of established hiPSC lines. It validates the feasibility and defines the challenges of harnessing and integrating the capability and productivity of centres across Europe using commonly available resources currently in the field. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Structural motifs of importance for the constitutive activity of the orphan 7TM receptor EBI2: analysis of receptor activation in the absence of an agonist

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, Mette M

    2008-01-01

    ), in the conserved CW/FxP motif in TM 6, acted as negative regulators as Ala substitutions at these positions increased the constitutive activity 5.7- and 2.3-fold, respectively, compared with EBI2 wild type (wt). In contrast, ArgII:20 (Arg87) in TM-2 acted as a positive regulator, as substitution to Ala......, but not to Lys, decreased the constitutive activity more than 7-fold compared with wt EBI2. IleIII:03 (Ile106) is located only 4 A from ArgII:20, and a favorable electrostatic interaction with ArgII:20 was created by introduction of Glu in III:03, given that the activity increased to 4.4-fold of that wt EBI2....... It is noteworthy that swapping these charges by introduction of Glu in II:20 and Arg in III:03 resulted in a 2.7-fold increase compared with wt EBI2, thereby rescuing the two signaling-deficient single mutations, which exhibited a 3.8- to 4.5-fold decrease in constitutive activity. The uncovering...

  15. Parametric study of a high current–density EBIS Charge Breeder regarding Two Stream plasma Instability (TSI)

    Energy Technology Data Exchange (ETDEWEB)

    Shornikov, Andrey, E-mail: andrey.shornikov@cern.ch [CERN, AB Department, CH-1211 Geneva 23 (Switzerland); Mertzig, Robert; Breitenfeldt, Martin; Lombardi, Alessandra; Wenander, Fredrik [CERN, AB Department, CH-1211 Geneva 23 (Switzerland); Pikin, Alexander [BNL, Upton, NY (United States)

    2016-06-01

    In this paper we report on our results from the design study of an advanced Electron Beam Ion Source (EBIS) based Charge Breeder (ECB). The ECB should fulfill the requirements of the HIE-ISOLDE upgrade, and if possible be adapted for ion injection into TSR@ISOLDE, as well as serve as an early prototype of a future EURISOL ECB. Fulfilling the HIE-ISOLDE/TSR@ISOLDE specifications requires simultaneous increase in electron beam energy, current and current density in order to provide the requested beams with proper charge state, high intensity and with a specified pulse repetition rate. We have carried out a study on the technical requirements of the ECB. The obtained parameters were optimized to comply with technical limitations arising from the electron beam technology and plasma physics in an ECB.

  16. Epstein-Barr Virus-Induced Gene 3 (EBI3) Blocking Leads to Induce Antitumor Cytotoxic T Lymphocyte Response and Suppress Tumor Growth in Colorectal Cancer by Bidirectional Reciprocal-Regulation STAT3 Signaling Pathway

    Science.gov (United States)

    Liang, Yanfang; Chen, Qianqian; Du, Wenjing; Chen, Can; Li, Feifei; Yang, Jingying; Peng, Jianyu; Kang, Dongping; Lin, Bihua; Chai, Xingxing; Zhou, Keyuan; Zeng, Jincheng

    2016-01-01

    Epstein-Barr virus-induced gene 3 (EBI3) is a member of the interleukin-12 (IL-12) family structural subunit and can form a heterodimer with IL-27p28 and IL-12p35 subunit to build IL-27 and IL-35, respectively. However, IL-27 stimulates whereas IL-35 inhibits antitumor T cell responses. To date, little is known about the role of EBI3 in tumor microenvironment. In this study, firstly we assessed EBI3, IL-27p28, IL-12p35, gp130, and p-STAT3 expression with clinicopathological parameters of colorectal cancer (CRC) tissues; then we evaluated the antitumor T cell responses and tumor growth with a EBI3 blocking peptide. We found that elevated EBI3 may be associated with IL-12p35, gp130, and p-STAT3 to promote CRC progression. EBI3 blocking peptide promoted antitumor cytotoxic T lymphocyte (CTL) response by inducing Granzyme B, IFN-γ production, and p-STAT3 expression and inhibited CRC cell proliferation and tumor growth to associate with suppressing gp130 and p-STAT3 expression. Taken together, these results suggest that EBI3 may mediate a bidirectional reciprocal-regulation STAT3 signaling pathway to assist the tumor escape immune surveillance in CRC. PMID:27247488

  17. Seventh symposium on EBIS/T and their applications combined with a workshop on ion sources for hadron colliders, a satellite meeting to ICIS'97 (invited)

    Science.gov (United States)

    Becker, R.

    1998-02-01

    The 7th symposium on EBIS and EBIT and their applications has been organized by M. Kleinod and R. Becker in Gelnhausen, Germany the week before ICIS'97. It was combined with a workshop on ion sources for hadron colliders being reported on by J. Alessi. Former EBIS symposia which have taken place are: 1977 at GSI, Darmstadt, Germany; 1981 in Saclay and Orsay, France; 1985 at Cornell University, Ithaca, New York; 1988 at Brookhaven National Lab (BNL), Brookhaven, New York; 1991 at JINR, Dubna, Russia; and 1994 at MSI, Stockholm, Sweden. The next one will be organized in the year 2000 by Krsto Prelec, BNL and Martin Stöckli, Manhattan, Kansas.

  18. Cloning and Expression of EBI3 and p28 Subunits of Human Interleukin 27 in E. coli

    Directory of Open Access Journals (Sweden)

    Ameneh Koochaki

    2015-07-01

    Full Text Available Background: Interleukin-27 is a heterodimeric cytokine belonging to IL-12 and IL-23 families, secreted  by Antigen Presenting Cells(APCs .The IL-27 is composed of 2 subunits: Epstein-Barr virus induced gene 3 (EBI3 and p28. IL-27 is an anti-inflammatory cytokine which has an inhibitory effect on Th17 population and suppress the IL-17 expression. It is suggested that IL-27 could be a potent drug candidate for treating auto immune diseases.Methods: The IL-27 subunit genes were constructed into plasmid vectors, they sub-cloned into pETDeut-1an expression vector in restriction sites of BamHI, SacI and NotI. Subsequently the induction was done by IPTG and the recombinant proteins were confirmed by SDS-PAGE and Western Blot analysis using anti His-tag antibody.Results: The 28kDa and 25kDa protein bands were observed on SDS-PAGE and finally confirmed by Western blot technique.

  19. IORT and external beam irradiation (EBI) in clinical stage I-II NSCLC patients with severely compromised pulmonary function: an 52-patient single-institutional experience

    Energy Technology Data Exchange (ETDEWEB)

    Jakse, G.; Kapp, K.S.; Geyer, E.; Oechs, A. [Dept. of Therapeutic Radiology and Oncology, Dept. of Surgery, Medical Univ. of Graz (Austria); Maier, A.; Gabor, S.; Juettner, F.M. [Div. of Thoracic and Hyperbaric Surgery, Medical Univ. of Graz (Austria)

    2007-12-15

    In limited stage NSCLC surgery offers the best chance for cure. However, patients who would not tolerate a radical surgical procedure such as lobectomy on the basis of severely compromised pulmonary function or cardio respiratory impairment are also poor candidates for radical external beam irradiation. These patients may benefit from alternative procedures that allow maximum sparing of adjacent lung tissue such as brachytherapy, stereotactic radiotherapy or IORT. There is clear evidence that loco-regional control in lung cancer is dose related, but neighboring normal tissues such as ipsilateral or collateral lung, heart, spinal cord are limiting factors for delivering doses necessary to eradicate the primary or loco-regional metastases. The rational of IORT, builds on the observation that only patients in whom local control has been achieved had a prolonged survival. IORT permits to selectively deliver high single doses to the tumor or the tumor bed with maximum sparing of adjacent normal tissue and has been applied with curative and palliative intent in a variety of tumors. Experience with IORT in lung cancer is still very limited. The current study evaluates the outcome of combined IORT and EBI in a highly selected cohort of patients with clinical stage I-II NSCLC who were fit to undergo thoracotomy and lymph node sampling but unable to undergo lobectomy or conventional high dose EBI due to severely compromised pulmonary function. (orig.)

  20. Increased P-35, EBI3 Transcripts and Other Treg Markers in Peripheral Blood Mononuclear Cells of Breast Cancer Patients with Different clinical Stages

    Directory of Open Access Journals (Sweden)

    Maryam Hamidinia

    2015-06-01

    Full Text Available Purpose: Currently, cancer as a major problem around the world threatens human health and has a high incidence in developing countries. Many reports have indicated that patients suffering from cancer demonstrate decreased antitumor immune responses as well as a high prevalence of T regulatory population. It has been reported that Foxp3+Tregs exert suppression by cell contact-dependent mechanisms which are mediated by soluble factors such as immunosuppressive cytokines like IL-10, TGF-​B and IL-35. Consequently there is a great need to identify prognostic and diagnostic biomarkers of regulatory T cells for vaccine and drug development. Methods: In this study IL-10, TGF-B, IL-35 and Foxp3 mRNA gene expression has been measured in peripheral blood of 40 breast cancer patients and 40 normal age-matched women using quantitative real-time PCR (qRT-PCR method with Master Mix reaction containing SYBER Green. GAPDH gene was used as housekeeping gene. Results: Our data demonstrated a significant up-regulation of IL-10, TGF-​B, P35, EBI3 and Foxp3 gene expression in patients’ peripheral blood compared to normal healthy controls (p<0.05. Conclusion: The data suggests that the immune system is suppressed in breast cancer patients, which may be due to elevated Treg cells population. These results may be useful for diagnostic or therapeutic purposes. However it may require more investigations

  1. 支气管哮喘患儿外周血 IL-27、IL-35及 EBI3的表达变化及意义

    Institute of Scientific and Technical Information of China (English)

    周月朋; 李俊杰; 李晓东; 王伟; 陶开山; 钱钻好

    2014-01-01

    目的:探讨支气管哮喘患儿外周血白介素27(IL-27)、白介素35(IL-35)及 EBI3在不同阶段表达水平的变化及意义。方法采集2012年2月—2013年12月78例支气管哮喘患儿未控制期、部分控制后1周、控制后1周及对照组75例健康儿童外周血,利用酶联免疫吸附试验检测血清中 IL-27及 IL-35的表达水平,并利用实时荧光定量 RT-PCR 的方法检测外周血中单个核细胞中 IL-27、IL-35及 EBI3的 mRNA 的表达情况。结果未控制期、部分控制后1周、控制后1周血清 IL-27、IL-35均明显低于对照组(P <0.05)。在控制后1周单个核细胞 IL-27、IL-35的表达水平明显高于未控制期、部分控制后1周的表达水平,但是仍低于对照组(P <0.05);EBI3的表达水平在未控制期明显低于其他各组(P <0.05),而在部分控制后1周、控制后1周和对照组之间没有明显差异(P >0.05)。结论动态监测外周血中的 IL-27、IL-35 mRNA 及血清水平可以作为儿童哮喘控制水平的指标。

  2. Financování a účetnictví neziskových organizacích v konkrétních podmínkách Nadace Mezinárodní potřeby

    OpenAIRE

    Ptáčková, Kateřina

    2009-01-01

    This thesis deal with the concept of voluntary nonprofit organizations, especially foundantions. It describes the role and the function these organization in national economy. The thesis defines the finance management, the legal form of the accounting and the funding of foundantions. In the second part of the thesis there are applied the procured finding in the real-life situations. The existing organization, Nadace MEZINÁRODNÍ POTŘEBY, is introduced. One part of the revenue is mentioned as "...

  3. The Enriched Background Isotope Study (EBIS)

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Paul J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Trumbore, Susan [Univ. of California, Irvine, CA (United States); Swanston, Chris [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Torn, Margaret [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jastrow, Julie [Argonne National Lab. (ANL), Argonne, IL (United States); Parton, William A [Colorado State Univ., Fort Collins, CO (United States); Century Ecosystems, Inc. (United States); Post, Wilfred M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Froberg, Mats J [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hainsworth, Laura J [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kleber, Markus [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kramer, Christiane [Univ. of California, Irvine, CA (United States); Matamala-Paradeda, Roser [Argonne National Lab. (ANL), Argonne, IL (United States); Garten, Jr, Charles T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2007-02-05

    A unique, large release of radiocarbon occurred near the Oak Ridge Reservation (ORR), Oak Ridge, TN in July/August 1999. Measurements of 14C in tree ring cellulose throughout the ORR area demonstrate that the 1999 release was unprecedented in its uptake by vegetation. We are taking advantage of the whole-ecosystem isotopic label generated by this release to address five outstanding issues in the terrestrial carbon cycle: (1) partitioning of soil respiration between autotrophic and heterotrophic sources, and quantification of that partitioning seasonally and inter-annually, (2) partitioning of heterotrophic respiration sources between above-ground litter decomposition and below-ground root detritus decomposition, (3) identification of pathways leading from leaf and root detritus to long-term stabilization of soil organic matter, including the role of soil fauna, (4) the role of dissolved organic carbon (DOC) transport in distributing carbon within the soil profile, and, (5) the longevity and turnover time of fine roots. The first four issues are being addressed through a reciprocal litter transplant experiment set up at four sites on the ORR encompassing two soil types and two levels of 14C exposure in 1999. The fifth issue, longevity and turnover of fine roots, is being addressed by tracing the radiocarbon label through the fine root pool over time. With a combination of incubation, soil surface chamber and soil CO2 profiles, and continuous measurements of soil temperature and moisture controls, we are tracking changes in soil respiration partitioning over several years. The nature and source of organic matter pools that reside in soils for years to decades are being tracked with differently labeled root and surface litter, and experiments to exclude soil fauna have been initiated to elucidate their role in vertical transport. Periodic sampling of soils and soil solutions and the use of inert tracers, allow us to investigate the chemical nature and form of DOC and its transport in surface soil horizons. Results from these field observations will be used to parameterize and refine existing carbon dynamics models. Such models will then be used to quantitatively address the long-term fate of ecosystem carbon inputs and the potential for ecosystem carbon sequestration.

  4. Eliminating unwanted electrons in EBIS devices

    Science.gov (United States)

    Hershcovitch, Ady I.

    2016-02-01

    In electron beam ion sources, step-wise ionization to high charge states is accomplished by magnetically confined electron beam. Electron space charge and high voltage electrodes confine the ions. The relativistic heavy ion collider (RHIC) ion source Debye length meets requirements for instabilities with free source of energy to grow. Electrons stripped from ions provide energy for a variety of microinstabilities to grow. Possible solution is to remove these electrons from the trap to a drift tube biased to higher voltage than the other tubes between the gate and the collector. If needed, a split drift tube for bleeding these electrons to ground is added.

  5. Changes of Interleukin-27, Interleukin-35 and Epstein-Barr virus -induced Gene 3 Expressions in Peripheral Blood of Children with Bronchial Asthma and Its Significance%支气管哮喘患儿外周血 IL-27、IL-35及 EBI3的表达变化及意义

    Institute of Scientific and Technical Information of China (English)

    周月朋; 李俊杰; 李晓东; 王伟; 陶开山; 钱钻好

    2014-01-01

    Objective To investigate the changes of interleukin-27 (IL-27), interleukin-35 (IL-35) and Ep-stein-Barr virus -induced gene 3 (EBI3) expressions in different stages in children with bronchial asthma and its signifi-cance. Methods Seventy-eight children with bronchial asthma (observation group) and seventy-five healthy children (control group) during February 2012 and December 2013 were selected. The samples of peripheral blood were collected in the two groups in the stage of uncontrolled stage, 1 week after partly controlled stage and 1 week after controlled stage. Expression levels of serum IL-27, IL-35 and EBI3 were detected using enzyme-linked immunosorbent test, and the ex-pression levels of IL-27, IL-35 EBI3 and mRNA of mononuclearcell were also detected using real-time fluorescent quanti-tation RT-PCR (reverse transcription polymerase chain reaction) method. Results Levels of serum IL-27 and IL-35 in the stage of uncontrolled stage, 1 week after partly controlled stage and 1 week after controlled stage in observation group were significantly lower than those in control group (P 0. 05). Conclusion The dynamic monitoring of IL-27, IL-35 and mRNA in the peripheral blood and serum level may be used as indexes of control level of asthma in children.%目的:探讨支气管哮喘患儿外周血白介素27(IL-27)、白介素35(IL-35)及 EBI3在不同阶段表达水平的变化及意义。方法采集2012年2月—2013年12月78例支气管哮喘患儿未控制期、部分控制后1周、控制后1周及对照组75例健康儿童外周血,利用酶联免疫吸附试验检测血清中 IL-27及 IL-35的表达水平,并利用实时荧光定量 RT-PCR 的方法检测外周血中单个核细胞中 IL-27、IL-35及 EBI3的 mRNA 的表达情况。结果未控制期、部分控制后1周、控制后1周血清 IL-27、IL-35均明显低于对照组(P 0.05)。结论动态监测外周血中的 IL-27、IL-35 mRNA 及血清水平可以作为儿童哮喘控制水平的指标。

  6. Potřeby žen v klimakteriu

    OpenAIRE

    PERSANOVÁ, Eva

    2015-01-01

    The bachelor's work deals with the issues of menopause and changes, which take place in a woman's life in connection with it. The work is divided into a theoretical and a research part. At the beginning of the theoretical part there is a definition of the term "menopause", which is followed by the definition of the physiology of this period and hormonal changes which come up in the course of menopause. An integral part of the theoretical section is the description of climacteric syndrome, bot...

  7. Status report of the Dresden EBIS/EBIT developments.

    Science.gov (United States)

    Zschornack, G; Grossmann, F; Kentsch, U; Ovsyannikov, V P; Ritter, E; Schmidt, M; Thorn, A; Ullmann, F

    2010-02-01

    We give an overview about latest developments and measurements with the Dresden electron beam ion source family as compact and economically working table-top sources of highly charged ions. The ion sources are potential tools for various applications such as for use in combination with accelerators in medical particle therapy, as charge breeder or ion trap injector, as ion sources for a new generation of focused ion beam devices and for applications together with time-of-flight secondary mass spectrometers.

  8. Multiple column high-throughput e-beam inspection (EBI)

    Science.gov (United States)

    Lam, David K.; Monahan, Kevin M.; Liu, Enden D.; Tran, Cong; Prescop, Ted

    2012-03-01

    Single-column e-beam systems are used in production for the detection of electrical defects, but are too slow to be used for the detection of small physical defects, and can't meet future inspection requirements. This paper presents a multiplecolumn e-beam technology for high throughput wafer inspection. Multibeam has developed all-electrostatic columns for high-resolution imaging. The elimination of magnetic coils enables the columns to be small; e-beam deflection is faster in the absence of magnetic hysteresis. Multiple miniaturecolumns are assembled in an array. An array of 100 columns covers the entire surface of a 300mm wafer, affording simultaneous cross-wafer sampling. Column performance simulations and system architecture are presented. Also provided are examples of high throughput, more efficient, multiple-column wafer inspection.

  9. REGIONAL ECONOMIC DISPARITIES IN PAN-YANGTZE RIVER DELTA— BASED ON EBI AND EBIi%泛长江三角洲区域经济空间差异分析——基于经验贝叶斯修正的空间自相关指数

    Institute of Scientific and Technical Information of China (English)

    杨杨; 吴次芳

    2011-01-01

    paper investigated the spatial dynamics of regional disparities at the municipal level in Pan-Yangtze River Delta by analyzing per capita GDP data, 1999~2008. The results indicated that the economy development showed obvious spatial cluster pattern in Pan-Yangtze River Delta.The value of EBI showed a trend of increased volatility; the spatial transfer of clusters and outliers showed definite rules; the economy development showed obvious local spatial disparity pattern. The study indicated the feature of the Yangtze River Delta region with high-value and the new expansion provinces with lowvalue.

  10. EBI2, GPR18 and GPR17--three structurally related, but biologically distinct 7TM receptors

    DEFF Research Database (Denmark)

    Nørregaard, Kristine; Benned-Jensen, Tau; Rosenkilde, Mette Marie

    2011-01-01

    7TM receptors constitute one of the largest superfamilies of proteins in the human genome. They are involved in a large number of physiological and pathological processes in the human body and thus represent major and important drug targets for the pharmaceutical industry. Although the majority...

  11. Operator Inequalities of the Jensen, _eby_ev and Grüss Type

    CERN Document Server

    Dragomir, Silvestru Sever

    2012-01-01

    The main aim of this book is to present recent results concerning inequalities of the Jensen, AiebyA!ev and Gruss type for continuous functions of bounded selfadjoint operators on complex Hilbert spaces. In the introductory chapter, the author portrays fundamental facts concerning bounded selfadjoint operators on complex Hilbert spaces. The generalized Schwarz's inequality for positive selfadjoint operators as well as some results for the spectrum of this class of operators are presented. This text introduces the reader to the fundamental results for polynomials in a linear operator, continuou

  12. Serum CYFRA 21-1 in Egyptian women with breast cancer | Ebied ...

    African Journals Online (AJOL)

    Serum CYFRA 21-1 in Egyptian women with breast cancer. ... in the diagnosis and management of lung cancer, particularly of squamous cell histotype. ... clinicopathological factors and prognosis in comparison with serum CA15.3 and CEA ...

  13. BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

    OpenAIRE

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-01-01

    Background Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology,...

  14. Charge breeding investigation in EBIS/T and collision study of ions with cold atoms for HITRAP

    Energy Technology Data Exchange (ETDEWEB)

    Sokolov, Alexey

    2010-01-29

    Highly charged ions (HCI) at low velocities or at rest are interesting systems for various atomic physics experiments. For investigations on HCI of heavy stable or radioactive nuclides the HITRAP (Highly charged Ion TRAP) decelerator facility has been set up at GSI to deliver cooled beams of HCI at an energy of 5 keV/q. The HCI are produced in a stripper foil at relativistic energies and are decelerated in several steps at ESR storage ring and HITRAP before they are delivered to experimental setups. One of the experiments is the investigation of multi-electron charge exchange in collisions of heavy HCI with cold atoms using novel MOTRIMS technique. Collision experiments on light ions from an ECR ion source colliding with cold atoms in a MOT have been performed and the results are described. An electron beam ion trap (EBIT) has been tested and optimized for commissioning of the HITRAP physics experiments. The process of charge breeding in the EBIT has been successfully studied with gaseous elements and with an alkaline element injected from an external ion source. (orig.)

  15. Růst spotřeby ropy v ČLR jako riziko pro její energetickou bezpečnost

    OpenAIRE

    Staněk, Jiří

    2013-01-01

    The aim of this thesis is to investigate the way that growing demand for oil in China will influence the nation's energy security in its various aspects until year 2035. It is shown, that growing oil consumption in China is an irreversible trend that significantly endangers energy security both in the long-term and the short-term aspect. Consequently, author recommends steps that could eliminate or moderate those threats. Recommendations are than compared to actual policies of the Chinese gov...

  16. Pinning down QCD-matter shear viscosity in A + A collisions via EbyE fluctuations using pQCD + saturation + hydrodynamics

    Science.gov (United States)

    Niemi, H.; Eskola, K. J.; Paatelainen, R.; Tuominen, K.

    2016-12-01

    We compute the initial energy densities produced in ultrarelativistic heavy-ion collisions from NLO perturbative QCD using a saturation conjecture to control soft particle production, and describe the subsequent space-time evolution of the system with hydrodynamics, event by event. The resulting centrality dependence of the low-pT observables from this pQCD + saturation + hydro ("EKRT") framework are then compared simultaneously to the LHC and RHIC measurements. With such an analysis we can test the initial state calculation, and constrain the temperature dependence of the shear viscosity-to-entropy ratio η / s of QCD matter. Using these constraints from the current RHIC and LHC measurements we then predict the charged hadron multiplicities and flow coefficients for the 5 TeV Pb + Pb collisions.

  17. Soubor projektů pro potřeby výuky objektově orientovaného programování

    OpenAIRE

    ROHÁČEK, Břetislav

    2013-01-01

    The goal of this thesis is to create an universal scenario for solving small problems in small-scale within object-oriented programming. Freely available tools will be used for the implementation of each phase. Part of the thesis will be a set of projects that will be developed by proposed scenario. The results of the thesis can be used for teaching object-oriented programming.

  18. Pinning down QCD-matter shear viscosity in A+A collisions via EbyE fluctuations using pQCD + saturation + hydrodynamics

    CERN Document Server

    Niemi, H; Paatelainen, R; Tuominen, K

    2015-01-01

    We compute the initial energy densities produced in ultrarelativistic heavy-ion collisions from NLO perturbative QCD using a saturation conjecture to control soft particle production, and describe the subsequent space-time evolution of the system with hydrodynamics, event by event. The resulting centrality dependence of the low-$p_T$ observables from this pQCD + saturation + hydro ("EKRT") framework are then compared simultaneously to the LHC and RHIC measurements. With such an analysis we can test the initial state calculation, and constrain the temperature dependence of the shear viscosity-to-entropy ratio $\\eta/s$ of QCD matter. Using these constraints from the current RHIC and LHC measurements we then predict the charged hadron multiplicities and flow coefficients for the 5.023 TeV Pb+Pb collisions.

  19. Zajištěné napájení vlastní spotřeby parní elektrárny

    OpenAIRE

    Tomášek, Petr

    2009-01-01

    Tato práce se zabývá problematikou zajištěného napájení. Pod pojmem zajištěného napájení se skrývá soubor technologických celků, které zajišťují napájení zařízení podílejících se na bezpečném odstavení elektrárny v případě výpadku napájení z běžného napájecího zdroje. Práce je členěna do dvou základních částí – teoretické a praktické. Teoretická část pojednává o možnostech realizace zajištěného napájení. Je zde proveden výčet jednotlivých zařízení, která mohou být v sekci zajištěného napájení...

  20. Origin and switch of different colors: Thermo-isomerism and crystal structure of (1E,2E)-bis[1-(4-nitrophenyl)ethylidene] hydrazine

    Indian Academy of Sciences (India)

    Said Tighadouini; Smaail Radi; Loic Toupet; Muhammad Sirajuddin; Taibi Ben Hadda; Mehmet Akkurt; Ismail Warad; Yahia N Mabkhot; Saqib Ali

    2015-12-01

    A new symmetric branched 4-nitrophenyl hydrazine compound has been prepared in one-step procedure by direct condensation of aromatic ketone with hydrazine in MeOH. The synthesized compound, red isomer, was characterized by IR, 1H and 13C NMR spectroscopy, Elemental analyses, Mass spectrometry and X-ray crystallography. Refluxing in MeOH solution led to thermo-isomerism offering a white isomer product that was characterized by X-ray crystallography. The red isomer crystallizes in the orthorhombic system having space group Pbcn, with a = 12.7612(4), b = 11.5197(3), c = 20.1586(7) Å, V = 2963.42(16)Å3, Z = 8 while the white isomer crystallizes in the triclinic system having space group P−1, with a = 7.8007(4), 8.5966(7), 12.224 (1) Å, = 71.133(7), = 81.281(5), = 74.895(5)°, V = 746.86(9)Å3, Z = 2. Molecules of both compounds are twisted at N2–N3 bond with the C7-N2-N3-C9 torsion angle of 155.23(12) and −113.36(18)°, respectively. The crystal structures of both compounds are stabilized by weak intramolecular C—H. . .N contacts and intermolecular C—H. . .O hydrogen bonding interactions. In addition, – stacking interactions are observed between the same aromatic rings of molecules.

  1. Cultural Exchange and the Implementation of Evidence-Based Practices: Two Case Studies

    Science.gov (United States)

    Palinkas, Lawrence A.; Aarons, Gregory A.; Chorpita, Bruce F.; Hoagwood, Kimberly; Landsverk, John; Weisz, John R.

    2009-01-01

    Objective: The dynamics of interactions between evidence-based intervention (EBI) developers and trainers and organizations and providers that deliver the EBI was examined in two case studies, a statewide randomized effectiveness trial of an EBI to reduce child neglect and a randomized trial of EBIs for depression, anxiety, and conduct problems in…

  2. Relevance účetních výkazů s ohledem na informační potřeby uživatelů účetní závěrky

    Directory of Open Access Journals (Sweden)

    Lenka Zemánková

    2013-11-01

    Full Text Available Purpose: Purpose of the article is to describe the information needs of individual users of financial statements. Individual users have different needs of information, but in one need they are agreed. Some information, requiring users of accounting information the financial statements does not. Shortcomings of financial statements result from incomplete harmonization of Czech financial statements to International Financial Reporting Standards. Scientific aim: The main aim of this article is evaluating how output accounting information company contained in company financial statements come up to the expectations person, who are ask for the information. This may point to the shortcomings of the financial statements. Methods: The article is based on studies published in theme of information needs users of financial statements. Studies will be confronted with information potential of financial statements focused of the equity. In this article is mainly used logical and empirical methods. From logical methods was selected base pair-methods: Induction-illiation, analysis-synthesis and abstraction- concretization. From empiric methods was selected method comparison. Findings: The user of accounting information are agreed in one need. They need infrormation about going concern company. Financial statements does not contain this information. The reproduction of the equity can ensure going concern. The equity can be viewed in two ways. Looking in the equity like to production capacity the company, is one way. This method brings the idea that company can continue, when the equity is reproduced. But this method needs valuating all balance and profit and loss sheet items in regular price. Assess value in historical price causes overvalued trading income (undervalued of costs and undervalued the equity. Conslusions: Reproduction of the equity must be ensured to going concern company. It can be ensured by assess valuation in regular prices instead historical. Stiffen up the condition for pay profit, it is the second solution.

  3. Relevance účetních výkazů s ohledem na informační potřeby uživatelů účetní závěrky

    OpenAIRE

    Zemánková, Lenka; Fedorová, Anna

    2010-01-01

    Purpose Purpose of the article is to describe the information needs of individual users of financial statements. Individual users have different needs of information, but in one need they are agreed. Some information, requiring users of accounting information the financial statements does not. Shortcomings of financial statements result from incomplete harmonization of Czech financial statements to International Financial Reporting Standards. Scientific aim The main aim of this...

  4. Relevance účetních výkazů s ohledem na informační potřeby uživatelů účetní závěrky

    OpenAIRE

    Lenka Zemánková; Anna Fedorová

    2013-01-01

    Purpose: Purpose of the article is to describe the information needs of individual users of financial statements. Individual users have different needs of information, but in one need they are agreed. Some information, requiring users of accounting information the financial statements does not. Shortcomings of financial statements result from incomplete harmonization of Czech financial statements to International Financial Reporting Standards. Scientific aim: The main aim of this article i...

  5. Rekondiční masáže spotřeby prováděné centrálními bankami – experimentální verifikace

    Directory of Open Access Journals (Sweden)

    David Martinčík

    2017-06-01

    Full Text Available The contribution verifies the mainstream economics lemma that inflation stimulates consumption expenditures and vice versa deflation results in giving up of present consumption. We suggested the experimental design suitable for consumption-saving decision-making under different inflation and relative prices variability. More than four hundreds of students took part in the experiment. In each round they received some income and they must decide whether to buy one of the three durable goods or to buy nothing. The prices of the goods were displayed as well the utility of money holdings. Money holdings at the end of the round became the initial endowment for the next round, where they received new income. The utility of each durable goods was known and the goal of experiment participants was to maximize the sum of utility in all played rounds. The total amount of rounds was randomly generated and the participants didn't know it before. Five different set-ups of the experiment were realized. First zero inflation with middle variability of relative prices and then four combinations of positive or negative inflation and high or low relative prices variability. The nominal income received at the beginning of each period follows the inflation or deflation so the real income was still the same. The results show that there is no difference between consumption behaviour under inflationary and deflationary framework. Experimental subject didn't feel the aggregate price index as significant for their decisions and focused only on relative prices. In set-ups where the changes in relative prices were easily to recognize (i.e. higher variability, the negative correlation between price and consumption of individual good was relatively significant. The experimental results cannot verify the mainstream economics lemma about different consumption-saving behaviour under inflation or deflation; they rather confirm the monetary business cycle theory supported by Austrian school.

  6. Developing Theory to Guide Building Practitioners' Capacity to Implement Evidence-Based Interventions

    Science.gov (United States)

    Leeman, Jennifer; Calancie, Larissa; Kegler, Michelle C.; Escoffery, Cam T.; Herrmann, Alison K.; Thatcher, Esther; Hartman, Marieke A.; Fernandez, Maria E.

    2017-01-01

    Public health and other community-based practitioners have access to a growing number of evidence-based interventions (EBIs), and yet EBIs continue to be underused. One reason for this underuse is that practitioners often lack the capacity (knowledge, skills, and motivation) to select, adapt, and implement EBIs. Training, technical assistance, and…

  7. A wireless, compact, and scalable bioimpedance measurement system for energy-efficient multichannel body sensor solutions

    Science.gov (United States)

    Ramos, J.; Ausín, J. L.; Lorido, A. M.; Redondo, F.; Duque-Carrillo, J. F.

    2013-04-01

    In this paper, we present the design, realization and evaluation of a multichannel measurement system based on a cost-effective high-performance integrated circuit for electrical bioimpedance (EBI) measurements in the frequency range from 1 kHz to 1 MHz, and a low-cost commercially available radio frequency transceiver device, which provides reliable wireless communication. The resulting on-chip spectrometer provides high measuring EBI capabilities and constitutes the basic node to built EBI wireless sensor networks (EBI-WSNs). The proposed EBI-WSN behaves as a high-performance wireless multichannel EBI spectrometer where the number of nodes, i.e., number of channels, is completely scalable to satisfy specific requirements of body sensor networks. One of its main advantages is its versatility, since each EBI node is independently configurable and capable of working simultaneously. A prototype of the EBI node leads to a very small printed circuit board of approximately 8 cm2 including chip-antenna, which can operate several years on one 3-V coin cell battery. A specifically tailored graphical user interface (GUI) for EBI-WSN has been also designed and implemented in order to configure the operation of EBI nodes and the network topology. EBI analysis parameters, e.g., single-frequency or spectroscopy, time interval, analysis by EBI events, frequency and amplitude ranges of the excitation current, etc., are defined by the GUI.

  8. Developing Theory to Guide Building Practitioners' Capacity to Implement Evidence-Based Interventions

    Science.gov (United States)

    Leeman, Jennifer; Calancie, Larissa; Kegler, Michelle C.; Escoffery, Cam T.; Herrmann, Alison K.; Thatcher, Esther; Hartman, Marieke A.; Fernandez, Maria E.

    2017-01-01

    Public health and other community-based practitioners have access to a growing number of evidence-based interventions (EBIs), and yet EBIs continue to be underused. One reason for this underuse is that practitioners often lack the capacity (knowledge, skills, and motivation) to select, adapt, and implement EBIs. Training, technical assistance, and…

  9. Hairy mass bound in the Einstein-Born-Infeld black hole

    OpenAIRE

    Myung, Yun Soo; Moon, Taeyoon

    2012-01-01

    We study the Einstein-Born-Infeld (EBI) theory where the hairy black hole was found as the EBI black hole by using Hod's idea. The hair extends beyond the photon-sphere of the EBI black hole spacetimes. We show that the region beyond the photon-sphere involves more than half of the total hair's mass, which respects Hod's conjectured bound.

  10. Exploring Implementation and Fidelity of Evidence-Based Behavioral Interventions for HIV Prevention: Lessons Learned from the Focus on Kids Diffusion Case Study

    Science.gov (United States)

    Galbraith, Jennifer S.; Stanton, Bonita; Boekeloo, Bradley; King, Winifred; Desmond, Sharon; Howard, Donna; Black, Maureen M.; Carey, James W.

    2009-01-01

    Evidence-based interventions (EBIs) are used in public health to prevent HIV infection among youth and other groups. EBIs include core elements, features that are thought to be responsible for the efficacy of interventions. The authors evaluate experiences of organizations that adopted an HIV-prevention EBI, Focus on Kids (FOK), and their fidelity…

  11. Cultural Adaptation of a U.S. Evidence-Based Parenting Intervention for Rural Western Kenya: From Parents Matter! to Families Matter!

    Science.gov (United States)

    Poulsen, Melissa N.; Vandenhoudt, Hilde; Wyckoff, Sarah C.; Obong'o, Christopher O.; Ochura, Juliet; Njika, Gillian; Otwoma, Nelson Juma; Miller, Kim S.

    2010-01-01

    Evidence-based interventions (EBIs) are critical for effective HIV prevention, but time and resources required to develop and evaluate new interventions are limited. Alternatively, existing EBIs can be adapted for new settings if core elements remain intact. We describe the process of adapting the Parents Matter! Program, an EBI originally…

  12. A systematic review to identify challenges of demonstrating efficacy of HIV behavioral interventions for gay, bisexual, and other men who have sex with men (MSM).

    Science.gov (United States)

    Higa, Darrel H; Crepaz, Nicole; Marshall, Khiya J; Kay, Linda; Vosburgh, H Waverly; Spikes, Pilgrim; Lyles, Cynthia M; Purcell, David W

    2013-05-01

    Gay, bisexual, and other men who have sex with men (MSM) are disproportionately affected by HIV but few MSM-specific evidence-based interventions (EBIs) have been identified for this vulnerable group. We conducted a systematic review to identify reasons for the small number of EBIs for MSM. We also compared study, intervention and sample characteristics of EBIs versus non-EBIs to better understand the challenges of demonstrating efficacy evidence. Thirty-three MSM-specific studies were evaluated: Nine (27 %) were considered EBIs while 24 (73 %) were non-EBIs. Non-EBIs had multiple methodological limitations; the most common was not finding a significant positive effect. Compared to EBIs, non-EBIs were less likely to use peer intervention deliverers, include sexual communication in their interventions, and intervene at the community level. Incorporating characteristics associated with EBIs may strengthen behavioral interventions for MSM. More EBIs are needed for substance-using MSM, MSM of color, MSM residing in the south and MSM in couples.

  13. Developing Theory to Guide Building Practitioners’ Capacity to Implement Evidence-Based Interventions

    Science.gov (United States)

    Leeman, Jennifer; Calancie, Larissa; Kegler, Michelle C.; Escoffery, Cam T.; Herrmann, Alison K.; Thatcher, Esther; Hartman, Marieke A.; Fernandez, Maria

    2017-01-01

    Public health and other community-based practitioners have access to a growing number of evidence-based interventions (EBIs), and yet EBIs continue to be underused. One reason for this underuse is that practitioners often lack the capacity (knowledge, skills, and motivation) to select, adapt, and implement EBIs. Training, technical assistance, and other capacity-building strategies can be effective at increasing EBI adoption and implementation. However, little is known about how to design capacity-building strategies or tailor them to differences in capacity required across varying EBIs and practice contexts. To address this need, we conducted a scoping study of frameworks and theories detailing variations in EBIs or practice contexts and how to tailor capacity-building to address those variations. Using an iterative process, we consolidated constructs and propositions across 24 frameworks and developed a beginning theory to describe salient variations in EBIs (complexity and uncertainty) and practice contexts (decision-making structure, general capacity to innovate, resource and values fit with EBI, and unity vs. polarization of stakeholder support). The theory also includes propositions for tailoring capacity-building strategies to address salient variations. To have wide-reaching and lasting impact, the dissemination of EBIs needs to be coupled with strategies that build practitioners’ capacity to adopt and implement a variety of EBIs across diverse practice contexts. PMID:26500080

  14. Portfolio Management

    Science.gov (United States)

    Duncan, Sharon L.

    2011-01-01

    Enterprise Business Information Services Division (EBIS) supports the Laboratory and its functions through the implementation and support of business information systems on behalf of its business community. EBIS Five Strategic Focus Areas: (1) Improve project estimating, planning and delivery capability (2) Improve maintainability and sustainability of EBIS Application Portfolio (3) Leap forward in IT Leadership (4) Comprehensive Talent Management (5) Continuous IT Security Program. Portfolio Management is a strategy in which software applications are managed as assets

  15. Social functioning in children with brain insult

    Directory of Open Access Journals (Sweden)

    Mardee Greenham

    2010-03-01

    Full Text Available Social dysfunction is commonly reported by survivors of brain insult, and is often rated as the most debilitating of all sequelae, impacting on many areas of daily life, as well as overall quality of life. Within the early brain insult (EBI literature, physical and cognitive domains have been of primary interest and social skills have received scant attention. As a result it remains unclear how common these problems are, and whether factors predictive of recovery (insult severity, lesion location, age at insult, environment in other functional domains (motor, speech, cognition also contribute to social outcome. This study compared social outcomes for children sustaining EBI at different times from gestation to late childhood to determine whether EBI was associated with an increased risk of problems. Children with focal brain insults were categorized according to timing of brain insult: (i Congenital (n = 38: EBI: first–second trimester; (ii Perinatal (n = 33; EBI: third trimester to 1 month post-natal; (iii Infancy (n=23: EBI: 2 months–2 years post-birth; (iv Preschool (n = 19: EBI: 3–6 years; (v Middle Childhood (n = 31: EBI: 7–9 years; and (vi Late Childhood (n = 19: EBI: after age 10. Children’s teachers completed questionnaires measuring social function (Strengths and Difficulties Questionnaire, Walker McConnell Scale of Social Competence and School Adjustment. Results showed that children with EBI were at increased risk for social impairment compared to normative expectations. EBI before age 2 years was associated with most significant social impairment, while children with EBI in the preschool years and in late childhood recorded scores closer to normal. Lesion location and laterality were not predictive of social outcome, and nor was social risk. In contrast, presence of disability (seizures and family function were shown to contribute to aspects of social function.

  16. Contralateral hyperinflation: Computed tomography demonstration of an unusual complication of unrecognized endobronchial intubation

    Directory of Open Access Journals (Sweden)

    Jyotindu Debnath

    2011-01-01

    Full Text Available Endobronchial intubation (EBI is an important complication of endotracheal intubation. In a case of unrecognized EBI, usually, the intubated lung gets hyperinflated while the contralateral lung collapses. We report a case of unrecognized right main stem EBI with ipsilateral normal aeration and contralateral hyperinflation detected during computed tomography scan of the chest for trauma work up in a case of severe head injury.

  17. Portfolio Management

    Science.gov (United States)

    Duncan, Sharon L.

    2011-01-01

    Enterprise Business Information Services Division (EBIS) supports the Laboratory and its functions through the implementation and support of business information systems on behalf of its business community. EBIS Five Strategic Focus Areas: (1) Improve project estimating, planning and delivery capability (2) Improve maintainability and sustainability of EBIS Application Portfolio (3) Leap forward in IT Leadership (4) Comprehensive Talent Management (5) Continuous IT Security Program. Portfolio Management is a strategy in which software applications are managed as assets

  18. Clustal W and Clustal X version 2.0.

    Science.gov (United States)

    Larkin, M A; Blackshields, G; Brown, N P; Chenna, R; McGettigan, P A; McWilliam, H; Valentin, F; Wallace, I M; Wilm, A; Lopez, R; Thompson, J D; Gibson, T J; Higgins, D G

    2007-11-01

    The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

  19. Predication of Fhhh potential in PTA wastewater treatment

    Institute of Scientific and Technical Information of China (English)

    CHENG Shu-pei; SHI Lei; ZHANG Xu-xiang; YAN Jun; DING Zhong-hai; HAO Chun-bo

    2004-01-01

    Ebis is the intelligent environmental biotechnological informatics software developed for judging the effectiveness of the microorganism strain in the industrial wastewater treatment system(IWTS) at the optimal status. The parameter, as the objective function for the judgment, is the minimum reactor volume ( Vmin ) calculated by Ebis for microorganism required in wastewater treatment. The rationality and the universality of Ebis were demonstrated in the domestic sewage treatment system(DSTS) with the data published in USA and China at first, then Fhhh strain's potential for treating the purified terephthalic acid(PTA) was proved. It suggests that Ebis would be useful and universal for predicating the technique effectiveness in both DSTS and IWTS.

  20. IL-35 over-expression is associated with genesis of gastric cancer.

    Science.gov (United States)

    Fan, Yong-Gang; Zhai, Jing-Ming; Wang, Wei; Feng, Bing; Yao, Guo-Liang; An, Yan-Hui; Zeng, Chao

    2015-01-01

    Overexpression of interleukin (IL)-35 has been found in a variety of malignancies, but the expression status in gastric cancer has yet to be elucidated clearly. In the present study, positive expression of EBI3 and p35 was 63.3% and 70.0% of cases, respectively. EBI3 expression was strongly related with larger tumor size and invasion depth (PIL-35 might be involved in growth of gastric cancer. Interestingly, EBI3 and p35 expressions were positive correlated with Ki-67 expression. Moreover, EBI3 immunoreactivity was associated with Bcl-2 staining. Our data suggest IL-35 is correlated with genesis of gastric cancer by regulating growth and apoptosis.

  1. A method to detect heart rate based on electrical bio-impedance

    Directory of Open Access Journals (Sweden)

    Li Kun-Yang

    2016-01-01

    Full Text Available As a basic health indicator, heart rate has been widely used in clinical measurement and daily health care. Electrical bio-impedance (EBI measurement provides non-invasive method for heart rate detection. Therefore, this paper proposed a method to detect heart rate based on EBI. With the BIOPAC EBI module, the signal can be de-noised in real-time. Finally, the de-noised EBI signal is used to compute heart rate. Four electrodes are located at radial artery of left upper limb in this method. The result proves that this method has high accuracy on heart rate measurement.

  2. Hairy mass bound in the Einstein-Born-Infeld black hole

    CERN Document Server

    Myung, Yun Soo

    2012-01-01

    We study the Einstein-Born-Infeld (EBI) theory where hairy black hole was found as the EBI black hole by using Hod's idea. The hair extends beyond the photon-sphere of the EBI black hole spacetimes. We show that the region beyond the photon-sphere involves more than half of the total hair's mass. However, the hairy mass bound proposed by Hod is not suitable for accounting the hair (EBIon) distributed in the whole spacetimes. Hence, we propose a new hairy mass bound for the EBI black hole.

  3. Laser ion source with solenoid for Brookhaven National Laboratory-electron beam ion source.

    Science.gov (United States)

    Kondo, K; Yamamoto, T; Sekine, M; Okamura, M

    2012-02-01

    The electron beam ion source (EBIS) preinjector at Brookhaven National Laboratory (BNL) is a new heavy ion-preinjector for relativistic heavy ion collider (RHIC) and NASA Space Radiation Laboratory (NSRL). Laser ion source (LIS) is a primary ion source provider for the BNL-EBIS. LIS with solenoid at the plasma drift section can realize the low peak current (∼100 μA) with high charge (∼10 nC) which is the BNL-EBIS requirement. The gap between two solenoids does not cause serious plasma current decay, which helps us to make up the BNL-EBIS beamline.

  4. Laser ion source with solenoid for Brookhaven National Laboratory-electron beam ion sourcea)

    Science.gov (United States)

    Kondo, K.; Yamamoto, T.; Sekine, M.; Okamura, M.

    2012-02-01

    The electron beam ion source (EBIS) preinjector at Brookhaven National Laboratory (BNL) is a new heavy ion-preinjector for relativistic heavy ion collider (RHIC) and NASA Space Radiation Laboratory (NSRL). Laser ion source (LIS) is a primary ion source provider for the BNL-EBIS. LIS with solenoid at the plasma drift section can realize the low peak current (˜100 μA) with high charge (˜10 nC) which is the BNL-EBIS requirement. The gap between two solenoids does not cause serious plasma current decay, which helps us to make up the BNL-EBIS beamline.

  5. Disruptive innovations for designing and diffusing evidence-based interventions.

    Science.gov (United States)

    Rotheram-Borus, Mary Jane; Swendeman, Dallas; Chorpita, Bruce F

    2012-09-01

    Evidence-based therapeutic and preventive intervention programs (EBIs) have been growing exponentially. Yet EBIs have not been broadly adopted in the United States. In order for our EBI science to significantly reduce disease burden, we need to critically reexamine our scientific conventions and norms. Innovation may be spurred by reexamining the traditional biomedical model for validating, implementing, and diffusing EBI products and science. The model of disruptive innovations suggests that we reengineer EBIs on the basis of their most robust features in order to serve more people in less time and at lower cost. A disruptive innovation provides a simpler and less expensive alternative that meets the essential needs for the majority of consumers and is more accessible, scalable, replicable, and sustainable. Examples of disruptive innovations from other fields include minute clinics embedded in retail chain drug stores, $2 generic eyeglasses, automated teller machines, and telemedicine. Four new research approaches will be required to support disruptive innovations in EBI science: synthesize common elements across EBIs; experiment with new delivery formats (e.g., consumer controlled, self-directed, brief, paraprofessional, coaching, and technology and media strategies); adopt market strategies to promote and diffuse EBI science, knowledge, and products; and adopt continuous quality improvement as a research paradigm for systematically improving EBIs, based on ongoing monitoring data and feedback. EBI science can have more impact if it can better leverage what we know from existing EBIs in order to inspire, engage, inform, and support families and children to adopt and sustain healthy daily routines and lifestyles. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

  6. Areál bývalého šamotového závodu MŠLZ Mladějov na Moravě - funkční využití areálu pro potřeby Průmyslového muzea Mladějov

    OpenAIRE

    Racková, Eliška

    2010-01-01

    Předmětem projektu je využití rozsáhlého areálu obsahujícího nesourodou směsici výrobních, servisních a obytných objektů různého stáří a kvalit. Různý charakter má i území areálu – stará výrobní část, která je poměrně udržovaná a trvale osídlená, a nová část na severu – narychlo dobytá v šedesátých letech a rychle zarůstající sukcesním březovým lesem. Rozdíl se odráží nejen v urbanistickém řešení areálu (viz předchozí práce), ale i v architektonickém pojetí jednotlivých budov. Budovy ve stará...

  7. Beyond Evidence-Based Interventions for Teen Pregnancy Prevention

    Directory of Open Access Journals (Sweden)

    Emily Scribner-O'Pray

    2017-04-01

    Full Text Available This article examines how the field of adolescent sexual health came to embrace evidence-based interventions (EBIs; whether or not this approach is effective in meeting the needs of adolescents, especially those at high risk for teen pregnancy; concerns related to the scaling up of EBIs; and identifies issues which must be resolved as we move forward.

  8. Development of electron beam ion source charge breeder for rare isotopes at Californium Rare Isotope Breeder Upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Kondrashev, S.; Dickerson, C.; Levand, A.; Ostroumov, P. N.; Pardo, R. C.; Savard, G.; Vondrasek, R. [Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Alessi, J.; Beebe, E.; Pikin, A. [Collider-Accelerator Department, Brookhaven National Laboratory, Upton, New York 11973 (United States); Kuznetsov, G. I.; Batazova, M. A. [Budker Institute of Nuclear Physics, Novosibirsk 630090 (Russian Federation)

    2012-02-15

    Recently, the Californium Rare Isotope Breeder Upgrade (CARIBU) to the Argonne Tandem Linac Accelerator System (ATLAS) was commissioned and became available for production of rare isotopes. Currently, an electron cyclotron resonance ion source is used as a charge breeder for CARIBU beams. To further increase the intensity and improve the purity of neutron-rich ion beams accelerated by ATLAS, we are developing a high-efficiency charge breeder for CARIBU based on an electron beam ion source (EBIS). The CARIBU EBIS charge breeder will utilize the state-of-the-art EBIS technology recently developed at Brookhaven National Laboratory (BNL). The electron beam current density in the CARIBU EBIS trap will be significantly higher than that in existing operational charge-state breeders based on the EBIS concept. The design of the CARIBU EBIS charge breeder is nearly complete. Long-lead components of the EBIS such as a 6-T superconducting solenoid and an electron gun have been ordered with the delivery schedule in the fall of 2011. Measurements of expected breeding efficiency using the BNL Test EBIS have been performed using a Cs{sup +} surface ionization ion source for external injection in pulsed mode. In these experiments we have achieved {approx}70% injection/extraction efficiency and breeding efficiency into the most abundant charge state of {approx}17%.

  9. Development of electron beam ion source charge breeder for rare isotopes at Californium Rare Isotope Breeder Upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Kondrashev S.; Alessi J.; Dickerson, C.; Levand, A.; Ostroumov, P.N.; Pardo, R.C.; Savard, G.; Vondrasek, R.; Beebe, E.; Pikin, A.; Kuznetsov, G.I.; Batazova, M.A.

    2012-02-03

    Recently, the Californium Rare Isotope Breeder Upgrade (CARIBU) to the Argonne Tandem Linac Accelerator System (ATLAS) was commissioned and became available for production of rare isotopes. Currently, an electron cyclotron resonance ion source is used as a charge breeder for CARIBU beams. To further increase the intensity and improve the purity of neutron-rich ion beams accelerated by ATLAS, we are developing a high-efficiency charge breeder for CARIBU based on an electron beam ion source (EBIS). The CARIBU EBIS charge breeder will utilize the state-of-the-art EBIS technology recently developed at Brookhaven National Laboratory (BNL). The electron beam current density in the CARIBU EBIS trap will be significantly higher than that in existing operational charge-state breeders based on the EBIS concept. The design of the CARIBU EBIS charge breeder is nearly complete. Long-lead components of the EBIS such as a 6-T superconducting solenoid and an electron gun have been ordered with the delivery schedule in the fall of 2011. Measurements of expected breeding efficiency using the BNL Test EBIS have been performed using a Cs{sup +} surface ionization ion source for external injection in pulsed mode. In these experiments we have achieved {approx}70% injection/extraction efficiency and breeding efficiency into the most abundant charge state of {approx}17%.

  10. NCBI nr-aa BLAST: CBRC-TTRU-01-0045 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0045 ref|XP_001828037.1| hypothetical protein EBI_21926 [Enterocytozoon... bieneusi H348] gb|EDQ31003.1| hypothetical protein EBI_21926 [Enterocytozoon bieneusi H348] XP_001828037.1 0.084 22% ...

  11. NCBI nr-aa BLAST: CBRC-TTRU-01-0029 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0029 ref|XP_001827754.1| hypothetical protein EBI_26448 [Enterocytozoon... bieneusi H348] gb|EDQ31066.1| hypothetical protein EBI_26448 [Enterocytozoon bieneusi H348] XP_001827754.1 0.13 33% ...

  12. NCBI nr-aa BLAST: CBRC-OPRI-01-0328 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OPRI-01-0328 ref|XP_001827754.1| hypothetical protein EBI_26448 [Enterocytozoon... bieneusi H348] gb|EDQ31066.1| hypothetical protein EBI_26448 [Enterocytozoon bieneusi H348] XP_001827754.1 6e-04 28% ...

  13. NCBI nr-aa BLAST: CBRC-TTRU-01-0118 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0118 ref|XP_001828037.1| hypothetical protein EBI_21926 [Enterocytozoon... bieneusi H348] gb|EDQ31003.1| hypothetical protein EBI_21926 [Enterocytozoon bieneusi H348] XP_001828037.1 0.005 26% ...

  14. NCBI nr-aa BLAST: CBRC-TTRU-01-0600 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0600 ref|XP_001827754.1| hypothetical protein EBI_26448 [Enterocytozoon... bieneusi H348] gb|EDQ31066.1| hypothetical protein EBI_26448 [Enterocytozoon bieneusi H348] XP_001827754.1 0.075 32% ...

  15. 76 FR 6139 - Proposed Data Collections Submitted for Public Comment and Recommendations

    Science.gov (United States)

    2011-02-03

    ... implementation of Effective Behavioral Interventions (EBIs) for HIV prevention. CDC's EBIs have been shown to be... organizations interested in behavioral outcome monitoring of WILLOW or similar HIV prevention interventions can... positive HIV status for at least 6 months, and are enrolled in the WILLOW intervention to participate...

  16. Evidence-Based Practice: Promoting Evidence-Based Interventions in School Psychology. WCER Working Paper No. 2003-13

    Science.gov (United States)

    Kratochwill, Thomas R.; Shernoff, Elisa Steele

    2003-01-01

    The Evidence-Based Intervention (EBI) movement has gained tremendous momentum in the past few years with developments in psychology, medicine (e.g., psychiatry), education, and prevention science. The purpose of this paper is to present some of the issues relating to the adoption of EBIs in practice and, specifically, the multiple roles…

  17. Electrooculogram Signals Analysis for Process Control Operator Based on Fuzzy c-Means

    Directory of Open Access Journals (Sweden)

    Jiangwen Song

    2015-09-01

    Full Text Available Biomedical signals of human can reflect the body's task load, fatigue and other psychological information. Compared with other biomedical signals, electrooculogram (EOG has higher amplitude, less interference, and is easy to detect. In this paper, the EOG signals of operator’s were analyzed. Wavelet transform was used to remove the high-frequency artifacts. Then fuzzy c-means was adopted to detect the eye blink peak points of EOG. After that, eye blink interval (EBI of operator was calculated. Four EOG features (the average of EBI, variance of EBI, standard deviation of EBI and variation coefficient of EBI were extracted. Finally, the relationship between EOG features and operator’s fatigue, effort, anxiety and task load were analyzed. The experimental results illustrate that EOG features had some relation to the operator’s fatigue, effort, anxiety and task load respectively.

  18. A wireless multi-channel bioimpedance measurement system for personalized healthcare and lifestyle.

    Science.gov (United States)

    Ramos, Javier; Ausín, José Luis; Lorido, Antonio Manuel; Redondo, Francisco; Duque-Carrillo, Juan Francisco

    2013-01-01

    Miniaturized, noninvasive, wearable sensors constitute a fundamental prerequisite for pervasive, predictive, and preventive healthcare systems. In this sense, this paper presents the design, realization, and evaluation of a wireless multi-channel measurement system based on a cost-effective high-performance integrated circuit for electrical bioimpedance (EBI) measurements in the frequency range from 1 kHz to 1 MHz. The resulting on-chip spectrometer provides high measuring EBI capabilities and together with a low-cost, commercially available radio frequency transceiver device. It provides reliable wireless communication, constitutes the basic node to build EBI wireless sensor networks (EBI-WSNs). The proposed EBI-WSN behaves as a high-performance wireless multi-channel EBI spectrometer, where the number of channels is completely scalable and independently configurable to satisfy specific measurement requirements of each individual. A prototype of the EBI node leads to a very small printed circuit board of approximately 8 cm2 including chip-antenna, which can operate several years on one 3-V coin cell battery and make it suitable for long-term preventive healthcare monitoring.

  19. Assessment of training and technical assistance needs of Colorectal Cancer Control Program Grantees in the U.S.

    Science.gov (United States)

    Escoffery, Cam; Hannon, Peggy; Maxwell, Annette E; Vu, Thuy; Leeman, Jennifer; Dwyer, Andrea; Mason, Caitlin; Sowles, Shaina; Rice, Ketra; Gressard, Lindsay

    2015-01-31

    Practitioners often require training and technical assistance to build their capacity to select, adapt, and implement evidence-based interventions (EBIs). The CDC Colorectal Cancer Control Program (CRCCP) aims to promote CRC screening to increase population-level screening. This study identified the training and technical assistance (TA) needs and preferences for training related to the implementation of EBIs among CRCCP grantees. Twenty-nine CRCCP grantees completed an online survey about their screening activities, training and technical assistance in 2012. They rated desire for training on various evidence-based strategies to increase cancer screening, evidence-based competencies, and program management topics. They also reported preferences for training formats and facilitators and barriers to trainings. Many CRCCP grantees expressed the need for training with regards to specific EBIs, especially system-level and provider-directed EBIs to promote CRC screening. Grantees rated these EBIs as more difficult to implement than client-oriented EBIs. Grantees also reported a moderate need for training regarding finding EBIs, assessing organizational capacity, implementing selected EBIs, and conducting process and outcome evaluations. Other desired training topics reported with higher frequency were partnership development and data collection/evaluation. Grantees preferred training formats that were interactive such as on-site trainings, webinars or expert consultants. Public health organizations need greater supports for adopting evidence-based interventions, working with organizational-level change, partnership development and data management. Future capacity building efforts for the adoption of EBIs should focus on systems or provider level interventions and key processes for health promotion and should be delivered in a variety of ways to assist local organizations in cancer prevention and control.

  20. Human CD4+ CD25+ Foxp3+ regulatory T cells do not constitutively express IL-35.

    Science.gov (United States)

    Bardel, Emilie; Larousserie, Frédérique; Charlot-Rabiega, Pascaline; Coulomb-L'Herminé, Aurore; Devergne, Odile

    2008-11-15

    EBV-induced gene 3 (EBI3) can associate with p28 to form the heterodimeric cytokine IL-27, or with the p35 subunit of IL-12 to form the EBI3/p35 heterodimer, recently named IL-35. In mice, IL-35 has been shown to be constitutively expressed by CD4(+)CD25(+)Foxp3(+) regulatory T cells (Treg cells) and suggested to contribute to their suppressive activity. In this study, we investigated whether human Treg cells express IL-35. Double-staining analysis of human thymuses showed that neither Foxp3(+) nor CD25(+) cells coexpressed EBI3. Similarly, Foxp3(+) cells present in human lymph nodes, tonsils, spleens, and intestines did not express EBI3. Consistent with these in situ observations, Treg cells purified from blood or tonsils were negative for EBI3 by immunoblotting. Other human T cell subsets, including effector T cells, naive and memory CD4(+) T cells, CD8(+) and gammadelta T cells also did not constitutively express EBI3, which contrasts with IL-35 expression observed in murine CD8(+) and gammadelta T cells. Furthermore, although CD3/CD28 stimulation consistently induced low levels of EBI3 in various CD4(+) T cell subsets, no EBI3 could be detected in CD3/CD28-stimulated Treg cells. RT-PCR analysis showed that, whereas p35 transcripts were detected in both Teff and Treg cells, EBI3 transcripts were detected only in activated Teff cells, but not in resting or activated Treg cells. Thus, in contrast to their murine counterpart, human Treg cells do not express detectable amounts of IL-35.

  1. Synthesizing Marketing, Community Engagement, and Systems Science Approaches for Advancing Translational Research.

    Science.gov (United States)

    Kneipp, Shawn M; Leeman, Jennifer; McCall, Pamela; Hassmiller-Lich, Kristen; Bobashev, Georgiy; Schwartz, Todd A; Gilmore, Robert; Riggan, Scott; Gil, Benjamin

    2015-01-01

    The adoption and implementation of evidence-based interventions (EBIs) are the goals of translational research; however, potential end-users' perceptions of an EBI value have contributed to low rates of adoption. In this article, we describe our application of emerging dissemination and implementation science theoretical perspectives, community engagement, and systems science principles to develop a novel EBI dissemination approach. Using consumer-driven, graphics-rich simulation, the approach demonstrates predicted implementation effects on health and employment outcomes for socioeconomically disadvantaged women at the local level and is designed to increase adoption interest of county program managers accountable for improving these outcomes in their communities.

  2. Contracting and Procurement for Evidence-Based Interventions in Public-Sector Human Services: A Case Study.

    Science.gov (United States)

    Willging, Cathleen E; Aarons, Gregory A; Trott, Elise M; Green, Amy E; Finn, Natalie; Ehrhart, Mark G; Hecht, Debra B

    2016-09-01

    Sustainment of evidence-based interventions (EBIs) in human services depends on the inner context of community-based organizations (CBOs) that provide services and the outer context of their broader environment. Increasingly, public officials are experimenting with contracting models from for-profit industries to procure human services. In this case study, we conducted qualitative interviews with key government and CBO stakeholders to examine implementation of the Best Value-Performance Information Procurement System to contract for EBIs in a child welfare system. Findings suggest that stakeholder relationships may be compromised when procurement disregards local knowledge, communication, collaboration, and other factors supporting EBIs and public health initiatives.

  3. Environmental characteristics of Carza (Italy) freshwater stream in spring-summer 1991. Caratteristiche ambientali del torrente Carza (FI) nella primavera-estate 1991

    Energy Technology Data Exchange (ETDEWEB)

    Del Guasta, M.; Marcuzzi, N. (Consiglio Nazionale delle Ricerche, Florence (Italy). Ist. di Ricerca sulle Onde Elettromagnetiche)

    1993-09-01

    A map of biological quality of the Carza freshwater stream (FI) was produced using the E.B.I. (Extended Biotic Index) method, together with flow and oxygen analysis. Results are correlated with an ecological index of quality of tree vegetation of banks and with stream shading. An attempt was carried out to correlate the territory of the dipper bird (Cinclus cinclus) with E.B.I. and the other factors. Results show a good correlation between E.B.I. and dissolved oxygen but a scarce correlation with factors connected to the ecological quality of the banks. It is suggested to search new freshwater quality indexes, more sensitive to bank conditions. The authors suggest not to use the plecoptera Leuctra nigra as a quality indicator in the E.B.I. method.

  4. A compact electron beam ion source with integrated Wien filter providing mass and charge state separated beams of highly charged ions.

    Science.gov (United States)

    Schmidt, M; Peng, H; Zschornack, G; Sykora, S

    2009-06-01

    A Wien filter was designed for and tested with a room temperature electron beam ion source (EBIS). Xenon charge state spectra up to the charge state Xe46+ were resolved as well as the isotopes of krypton using apertures of different sizes. The complete setup consisting of an EBIS and a Wien filter has a length of less than 1 m substituting a complete classical beamline setup. The Wien filter is equipped with removable permanent magnets. Hence total beam current measurements are possible via simple removal of the permanent magnets. In dependence on the needs of resolution a weak (0.2 T) or a strong (0.5 T) magnets setup can be used. In this paper the principle of operation and the design of the Wien filter meeting the requirements of an EBIS are briefly discussed. The first ion beam extraction and separation experiments with a Dresden EBIS are presented.

  5. Energy Extraction from the Einstein-Born-Infeld Black Hole

    CERN Document Server

    Breton, Nora

    2016-01-01

    The energy extraction from a Einstein-Born-Infeld (EBI) black hole is addressed determining the extension of the ergosphere as well as the extractable energy using the irreducible mass concept. These results are compared with the Reissner-Nordstrom (RN) ones; RN is the linear electromagnetic counterpart of the BI black hole. It turns out that for a fixed charge Q, more energy can be extracted from the RN black hole than from the EBI one. The extreme case is investigated as well, presenting remarkable features, for instance that more energy can be extracted from extreme EBI black holes than from extreme RN, however, extreme EBI black holes lack of a linear electromagnetic black hole limit.

  6. Gene : CBRC-TNIG-02-0017 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TNIG-02-0017 2 A Orphan receptors EBI2_HUMAN 1e-108 57% emb|CAG07299.1| unname...d protein product [Tetraodon nigroviridis] 0.0 100% MAVTMVSSSTSNSSQNLTCTTLYDHREYASILMPLVYSVVFFVGLLGNCLALHVIR...LLNMSMSNEEADGYITCMEYPNFEIVDHIASVLIGAVIIGYVIPVMTILVCYSFLCYRLQFIAKNNRLTGKSGRNRKAIGV

  7. The European Bioinformatics Institute's data resources.

    Science.gov (United States)

    Brooksbank, Catherine; Cameron, Graham; Thornton, Janet

    2010-01-01

    The wide uptake of next-generation sequencing and other ultra-high throughput technologies by life scientists with a diverse range of interests, spanning fundamental biological research, medicine, agriculture and environmental science, has led to unprecedented growth in the amount of data generated. It has also put the need for unrestricted access to biological data at the centre of biology. The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two organisations worldwide providing access to a comprehensive, integrated set of these collections. Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope with increasing levels of submission, a growing and diversifying user base, and the demand for new types of data. All of the resources described here can be accessed from the EMBL-EBI website: http://www.ebi.ac.uk.

  8. Simulation and design of an electron beam ion source charge breeder for the californium rare isotope breeder upgrade

    Directory of Open Access Journals (Sweden)

    Clayton Dickerson

    2013-02-01

    Full Text Available An electron beam ion source (EBIS will be constructed and used to charge breed ions from the californium rare isotope breeder upgrade (CARIBU for postacceleration into the Argonne tandem linear accelerator system (ATLAS. Simulations of the EBIS charge breeder performance and the related ion transport systems are reported. Propagation of the electron beam through the EBIS was verified, and the anticipated incident power density within the electron collector was identified. The full normalized acceptance of the charge breeder with a 2 A electron beam, 0.024π  mm mrad for nominal operating parameters, was determined by simulating ion injection into the EBIS. The optics of the ion transport lines were carefully optimized to achieve well-matched ion injection, to minimize emittance growth of the injected and extracted ion beams, and to enable adequate testing of the charge bred ions prior to installation in ATLAS.

  9. First test of BNL electron beam ion source with high current density electron beam

    Science.gov (United States)

    Pikin, Alexander; Alessi, James G.; Beebe, Edward N.; Shornikov, Andrey; Mertzig, Robert; Wenander, Fredrik; Scrivens, Richard

    2015-01-01

    A new electron gun with electrostatic compression has been installed at the Electron Beam Ion Source (EBIS) Test Stand at BNL. This is a collaborative effort by BNL and CERN teams with a common goal to study an EBIS with electron beam current up to 10 A, current density up to 10,000 A/cm2 and energy more than 50 keV. Intensive and pure beams of heavy highly charged ions with mass-to-charge ratio heavy ion research facilities including NASA Space Radiation Laboratory (NSRL) at BNL and HIE-ISOLDE at CERN. With a multiampere electron gun, the EBIS should be capable of delivering highly charged ions for both RHIC facility applications at BNL and for ISOLDE experiments at CERN. Details of the electron gun simulations and design, and the Test EBIS electrostatic and magnetostatic structures with the new electron gun are presented. The experimental results of the electron beam transmission are given.

  10. Experiment list: ERX337095 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available .ebi.ac.uk/efo/EFO_0002356 || DISEASE_ONTOLOGY_URI=http://ncimeta.nci.nih.gov/ncimbrowser/ConceptReport.jsp?...dictionary=NCI%20MetaThesaurus&code=C1333295 http://dbarchive.biosciencedbc.jp/ky

  11. Changes in mechanical and chemical wood properties by electron beam irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Schnabel, Thomas, E-mail: thomas.schnabel@fh-salzburg.ac.at [Salzburg University of Applied Sciences, Department of Forest Products Technology and Wood Constructions, Marktstraße 136a, 5431 Kuchl (Austria); Huber, Hermann [Salzburg University of Applied Sciences, Department of Forest Products Technology and Wood Constructions, Marktstraße 136a, 5431 Kuchl (Austria); Grünewald, Tilman A. [BOKU University of Natural Resources and Life Sciences, Institute of Physics and Materials Science, Peter Jordan Straße 82, 1190 Vienna (Austria); Petutschnigg, Alexander [Salzburg University of Applied Sciences, Department of Forest Products Technology and Wood Constructions, Marktstraße 136a, 5431 Kuchl (Austria); BOKU University of Natural Resources and Life Sciences, Konrad Lorenzstraße 24, 3430 Tulln (Austria)

    2015-03-30

    Highlights: • Changes in wood due to electron beam irradiations (EBI) were evaluated. • Wood components undergo different altering mechanisms due to the irradiation. • Chemical reactions in wood lead to better surface hardness of low irradiated wood. - Abstract: This study deals with the influence of various electron beam irradiation (EBI) dosages on the Brinell hardness of Norway spruce. The results of the hardness measurements and the FT-IR spectroscopic analysis show different effects of the EBI at dosages of 25, 50, 100 and 200 kGy. It was assumed that the lignin and carbohydrates undergo different altering mechanisms due to the EBI treatment. New cleavage products and condensation reactions of lignin and carbohydrates lead to better surface hardness of low irradiated wood samples. These results provide a useful basis for further investigations on the changes in wood chemistry and material properties due to electron beam irradiations.

  12. General footage ISOLDE experimental hall

    CERN Multimedia

    2016-01-01

    Overview of the ISOLDE experimental hall. Equipment and experiments. Taken from the WITCH / EBIS platform: ISOLDE hall infrastructure, GHM line, LA1, LA2, LA0, central beamline, COLLAPS experiment, CRIS experiment, ISOLTRAP experiment, laser guidance from building 508 into the hall for laser spectroscopy COLLAPS and CRIS. Taken from the HIE ISOLDE shielding tunnel roof: ISOLDE hall infrastructure, WITCH experiment, VITO line, TAS experiment. General footage: High Tension room entrance and EBIS platform, staircases and passages in the experimental hall.

  13. General footage ISOLDE experimental hall HD

    CERN Multimedia

    2016-01-01

    Overview of the ISOLDE experimental hall. Equipment and experiments. Taken from the WITCH / EBIS platform: ISOLDE hall infrastructure, GHM line, LA1, LA2, LA0, central beamline, COLLAPS experiment, CRIS experiment, ISOLTRAP experiment, laser guidance from building 508 into the hall for laser spectroscopy COLLAPS and CRIS. Taken from the HIE ISOLDE shielding tunnel roof: ISOLDE hall infrastructure, WITCH experiment, VITO line, TAS experiment. General footage: High Tension room entrance and EBIS platform, staircases and passages in the experimental hall.

  14. EQUIVALENT BOUNDARY INTEGRAL EQUATIONS WITH INDIRECT VARIABLES FOR PLANE ELASTICITY PROBLEMS

    Institute of Scientific and Technical Information of China (English)

    张耀明; 温卫东; 张作泉; 孙焕纯; 吕和祥

    2003-01-01

    The exact form of the exterior problem for plane elasticity problems was produced and fully proved by the variational principle. Based on this, the equivalent boundary integral equations (EBIE) with direct variables, which are equivalent to the original boundary value problem, were deduced rigorously. The conventionally prevailing boundary integral equation with direct variables was discussed thoroughly by some examples and it is shown that the previous results are not EBIE.

  15. Spring 2007. Industry Study. Environment Industry

    Science.gov (United States)

    2007-01-01

    reports that the world’s population will increase to 7.5 billion by 2020 , and urban populations will almost double to over 4 billion in that same period...provided by Environmental Business International (EBI). 6 Environmental Business International Inc (2005). 2005.EBI Report 2020 B - The US...The Regional Office for the United Nations Environmental Program for Latin America, and the Caribbean. Pg. 5 ( México DF, México ) Retrieved March 20

  16. CDC’s dissemination of evidence-based behavioral HIV prevention interventions

    OpenAIRE

    Collins, Charles B; Wilson, Katherine M.

    2011-01-01

    The Division of HIV/AIDS Prevention at the National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention seeks to make evidence-based behavioral HIV prevention interventions (EBIs) accessible to HIV prevention providers through a systematic process of identification, packaging, and dissemination. This update synthesizes that process and describes recent efforts to expand the use of EBIs internationally through partnerships between the CDC's Global AIDS...

  17. Preparation and characterization of keratin-based biocomposite hydrogels prepared by electron beam irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Park, Mira; Kim, Byoung-Suhk [Department of Organic Materials and Fiber Engineering, Chonbuk National University, Jeonju 561-756 (Korea, Republic of); Shin, Hye Kyoung [Department of Chemistry, Inha University, 100 Inharo, Incheon 402-751 (Korea, Republic of); Park, Soo-Jin, E-mail: sjpark@inha.ac.kr [Department of Chemistry, Inha University, 100 Inharo, Incheon 402-751 (Korea, Republic of); Kim, Hak-Yong, E-mail: khy@jbnu.ac.kr [Department of Organic Materials and Fiber Engineering, Chonbuk National University, Jeonju 561-756 (Korea, Republic of)

    2013-12-01

    The biocompatible and highly porous keratin-based hydrogels were prepared using electron beam irradiation (EBI). The conditions for keratin-based hydrogel formation were investigated depending on several conditions, including the presence of poly(vinyl alcohol) (PVA), concentration of keratin solution, EBI dose, and poly(ethylene imine) (PEI) additives. The pure keratin (human hair and wool) aqueous solution was not gelled by EBI, while the aqueous keratin solutions blended with PVA were gelled at an EBI dose of more than 90 kGy. Furthermore, in the presence of PEI, the aqueous keratin solution blended with PVA could be gelled at a considerably lower EBI dose, even at 10 kGy. This finding suggests that the PEI additives significantly influence the rate of gelation and that PEIs function as an accelerator during gelation. The resulting keratin-based hydrogels were characterized using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), gel fraction, degree of swelling, gel strength, and kinetics of swelling analyses. - Highlights: • The biocompatible and highly porous keratin-based hydrogels were prepared using EBI. • The conditions for keratin-based hydrogel formation were examined. • PEI would play an accelerator role in the formation of keratin-based hydrogels. • The resulting keratin-based hydrogels are expected to be more environmentally friendly.

  18. AD5933-based spectrometer for electrical bioimpedance applications

    Science.gov (United States)

    Ferreira, J.; Seoane, F.; Ansede, A.; Bragos, R.

    2010-04-01

    To build an Electrical Bioimpedance (EBI) spectrometer using the Impedance Measurement System-On-Chip AD5933 together with a 4-Electrode Analog Front End (4E-AFE) has been proven practicable. Such small measurement devices can make possible several new applications of EBI technology, especially when combined with functional textiles, which can enable wearable applications for personal health and home monitoring. After the implementation and functional validation of the 4E-AFE-enabled spectrometer, the next natural step is to validate for which EBI applications the 4E-AFE-enabled system is suitable. To test the applicability of this novel spectrometer on several EBI applications, 2R1C equivalent models have been experimentally obtained and impedance spectroscopy measurements have been performed with the system under study and with the SFB7 EBI spectrometer manufactured by ImpediMed. The 2R1C circuit parameters have been estimated with the BioImp software from the spectra obtained with both EBI spectrometers and the estimated values have been compared with the original values used in each circuit model implementation. The obtained results indicated that the 4E-AFE-enabled system cannot beat the performance of the SFB7 in accuracy but it performs better in preciseness. In any case the overall performance indicates that the 4E-AFE-enabled system can perform spectroscopy measurements in the frequency range from 5 to 100 kHz.

  19. Balancing "fidelity" and community context in the adaptation of asthma evidence-based interventions in the "real world".

    Science.gov (United States)

    Lara, Marielena; Bryant-Stephens, Tyra; Damitz, Maureen; Findley, Sally; Gavillán, Jesús González; Mitchell, Herman; Ohadike, Yvonne U; Persky, Victoria W; Valencia, Gilberto Ramos; Smith, Lucia Rojas; Rosenthal, Michael; Thyne, Shannon; Uyeda, Kimberly; Viswanathan, Meera; Woodell, Carol

    2011-11-01

    The Merck Childhood Asthma Network (MCAN) initiative selected five sites (New York City, Puerto Rico, Chicago, Los Angeles, and Philadelphia) to engage in translational research to adapt evidence-based interventions (EBIs) to improve childhood asthma outcomes. The authors summarize the sites' experience by describing criteria defining the fidelity of translation, community contextual factors serving as barriers or enablers to fidelity, types of adaptation conducted, and strategies used to balance contextual factors and fidelity in developing a "best fit" for EBIs in the community. A conceptual model captures important structural and process-related factors and helps frame lessons learned. Site implementers and intervention developers reached consensus on qualitative rankings of the levels of fidelity of implementation for each of the EBI core components: low fidelity, adaptation (major vs. minor), or high fidelity. MCAN sites were successful in adapting core EBI components based on their understanding of structural and other contextual barriers and enhancers in their communities. Although the sites varied regarding both the EBI components they implemented and their respective levels of fidelity, all sites observed improvement in asthma outcomes. Our collective experiences of adapting and implementing asthma EBIs highlight many of the factors affecting translation of evidenced-based approaches to chronic disease management in real community settings.

  20. Capturing buried defects in metal interconnections with electron beam inspection system

    Science.gov (United States)

    Xiao, Hong; Jiang, Ximan; Trease, David; Van Riet, Mike; Ramprasad, Shishir; Bhatia, Anadi; Lefebvre, Pierre; Bastard, David; Moreau, Olivier; Maher, Chris; MacDonald, Paul; Campochiaro, Cecelia

    2013-04-01

    In this paper we present a novel mode of electron beam inspection (EBI), entitled super wide optics (SWO) mode, which can effectively detect buried defects in tungsten (W) plugs and copper (Cu) wires. These defects are defects of interest (DOI) to integrated circuit (IC) manufacturers because they are not detectable in optical inspection, voltage contrast (VC) mode EBI or physical mode EBI. We used engineering systems to study two samples, a tungsten chemical mechanical polish (CMP) wafer and a copper CMP wafer with a silicon carbon nitride (SiCN) cap layer. EBI with our novel SWO mode was found to capture many dark defects on these two wafers. Furthermore, defect review with all three EBI modes found some of these dark defects were unique to SWO mode. For verification, physical failure analysis was performed on some SWO-unique DOI. The cross-sectional scanning electron microscope (SEM) images and transmission electron microscope (TEM) images confirmed that the unique DOI were buried voids in W-plugs and copper wire thinning caused by either buried particles or buried particle induced metal trench under-etch. These DOI can significantly increase the resistance of metal interconnects of IC chip and affect the chip yield. This new EBI mode can provide an in-line monitoring solution for these DOI, which does not exist before this study.

  1. Moderate Effects of Same-Sex Legislation on Dependent Employer-Based Insurance Coverage Among Sexual Minorities.

    Science.gov (United States)

    Tran, Linda Diem

    2016-12-01

    A difference-in-difference approach was used to compare the effects of same-sex domestic partnership, civil union, and marriage policies on same- and different-sex partners who could have benefitted from their partners' employer-based insurance (EBI) coverage. Same-sex partners had 78% lower odds (Marginal Effect = -21%) of having EBI compared with different-sex partners, adjusting for socioeconomic and health-related factors. Same-sex partners living in states that recognized same-sex marriage or domestic partnership had 89% greater odds of having EBI compared with those in states that did not recognize same-sex unions (ME = 5%). The impact of same-sex legislation on increasing take-up of dependent EBI coverage among lesbians, gay men, and bisexual individuals was modest, and domestic partnership legislation was equally as effective as same-sex marriage in increasing same-sex partner EBI coverage. Extending dependent EBI coverage to same-sex partners can mitigate gaps in coverage for a segment of the lesbians, gay men, and bisexual population but will not eliminate them. © The Author(s) 2016.

  2. Interleukin 35 Polymorphisms Are Associated with Decreased Risk of Premature Coronary Artery Disease, Metabolic Parameters, and IL-35 Levels: The Genetics of Atherosclerotic Disease (GEA) Study

    Science.gov (United States)

    Posadas-Romero, Carlos

    2017-01-01

    Interleukin 35 (IL-35) is a heterodimeric cytokine involved in the development of atherosclerosis. The aim of the present study was to establish if the polymorphisms of IL-12A and EBI3 genes that encode the IL-35 subunits are associated with the development of premature coronary artery disease (CAD) in Mexican individuals. The IL-12A and EBI3 polymorphisms were determined in 1162 patients with premature CAD and 873 controls. Under different models, the EBI3 rs428253 (OR = 0.831, Padd = 0.036; OR = 0.614, Prec = 0.033; OR = 0.591, Pcod2 = 0.027) and IL-12A rs2243115 (OR = 0.674, Padd = 0.010; OR = 0.676, Pdom = 0.014; OR = 0.698, Phet = 0.027; OR = 0.694, Pcod1 = 0.024) polymorphisms were associated with decreased risk of developing premature CAD. Some polymorphisms were associated with clinical and metabolic parameters. Significant different levels of IL-35 were observed in EBI3 rs4740 and rs4905 genotypes only in the group of healthy controls. In summary, our study suggests that the EBI3 and IL-12A polymorphisms play an important role in decreasing the risk of developing premature CAD; it also demonstrates the relationship of the EBI3 rs4740 and rs4905 genotypes with IL-35 levels in healthy individuals. PMID:28321150

  3. Interleukin 35 Polymorphisms Are Associated with Decreased Risk of Premature Coronary Artery Disease, Metabolic Parameters, and IL-35 Levels: The Genetics of Atherosclerotic Disease (GEA Study

    Directory of Open Access Journals (Sweden)

    Rosalinda Posadas-Sánchez

    2017-01-01

    Full Text Available Interleukin 35 (IL-35 is a heterodimeric cytokine involved in the development of atherosclerosis. The aim of the present study was to establish if the polymorphisms of IL-12A and EBI3 genes that encode the IL-35 subunits are associated with the development of premature coronary artery disease (CAD in Mexican individuals. The IL-12A and EBI3 polymorphisms were determined in 1162 patients with premature CAD and 873 controls. Under different models, the EBI3 rs428253 (OR = 0.831, Padd = 0.036; OR = 0.614, Prec = 0.033; OR = 0.591, Pcod2 = 0.027 and IL-12A rs2243115 (OR = 0.674, Padd = 0.010; OR = 0.676, Pdom = 0.014; OR = 0.698, Phet = 0.027; OR = 0.694, Pcod1 = 0.024 polymorphisms were associated with decreased risk of developing premature CAD. Some polymorphisms were associated with clinical and metabolic parameters. Significant different levels of IL-35 were observed in EBI3 rs4740 and rs4905 genotypes only in the group of healthy controls. In summary, our study suggests that the EBI3 and IL-12A polymorphisms play an important role in decreasing the risk of developing premature CAD; it also demonstrates the relationship of the EBI3 rs4740 and rs4905 genotypes with IL-35 levels in healthy individuals.

  4. 小鼠 IL-35基因 shRNA 慢病毒载体构建与RNAi 效率的鉴定%Construction of shRNA Lentiviral Vector Targeting Mice IL-35 Gene and Identification of RNAi Efficiency

    Institute of Scientific and Technical Information of China (English)

    刘义帅; 王洪伟; 邸大琳; 付晓燕; 吴国庆; 王丽娜; 鞠吉雨

    2014-01-01

    目的:构建小鼠IL-35基因靶向shRNA干扰的慢病毒表达载体,抑制小鼠肝癌细胞Hepa1~6中IL-35的表达。方法设计合成IL-35EBI3亚基基因靶向shRNA序列,构建shRNA载体PLKO.1-IL-35 EBI3 shRNA-GFP,测序正确后,三质粒病毒包装系统(质粒载体+psPAX2+pMD2.G)包装成表达干扰IL-35 EBI3 shR-NA的慢病毒,慢病毒感染靶细胞Hepa1~6,荧光显微镜下观察感染效率,以实时定量RT-PCR分析对Hepa1~6细胞IL-35 EBI3基因表达的干扰效果。结果测序证实,成功构建了真核表达干扰载体PLKO.1-IL-35 EBI3 shRNA-GFP;并成功包装出表达干扰IL-35 EBI3 shRNA的慢病毒,以MOI值4.6pfu/细胞感染Hepa1~6细胞,镜下显示感染效率约90%;RT-PCR结果表明所构建的3个慢病毒载体PLKO.1-IL-35 EBI3 shRNA-GFP均可以有效干扰IL-35 EBI3的表达,其中E545干扰效率最高,为64%.结论成功构建IL-35EBI3亚基基因的shRNA慢病毒表达载体,该慢病毒表达载体能够在细胞水平有效沉默靶基因。%Objective To construct the shRNA lentiviral vectors targeting mice IL-35 gene and detect its effect of gene silence in Hepa1~6 cells.Methods The specific siRNA sequences targeting mice IL-35 gene were designed and cloned into eukaryotic expression vector PLKO.1-IL-35 EBI3 shRNA-GFP.After the correct sequencing identification ,the lentivirus particles targeting mice IL-35 gene were packaged with the three plasmid virus packaging system .The IL-35 gene specific shRNAs were infected into Hepa1~6 cells.Then,infection efficiency were observed by the fluorescence microscope .Real time reverse transcription PCR was performed to determine the expression level of IL-35 EBI3 mRNA.Results Sequencing results revealed that PLKO .1-IL-35 EBI3 shRNA-GFP plasmids were correctly constructed .The lentivirus particles targeting mice IL-35 gene were packaged successfully .The observed infection efficiency by the fluorescence

  5. Experimental validation of a method for removing the capacitive leakage artifact from electrical bioimpedance spectroscopy measurements

    Science.gov (United States)

    Buendia, R.; Seoane, F.; Gil-Pita, R.

    2010-11-01

    Often when performing electrical bioimpedance (EBI) spectroscopy measurements, the obtained EBI data present a hook-like deviation, which is most noticeable at high frequencies in the impedance plane. The deviation is due to a capacitive leakage effect caused by the presence of stray capacitances. In addition to the data deviation being remarkably noticeable at high frequencies in the phase and the reactance spectra, the measured EBI is also altered in the resistance and the modulus. If this EBI data deviation is not properly removed, it interferes with subsequent data analysis processes, especially with Cole model-based analyses. In other words, to perform any accurate analysis of the EBI spectroscopy data, the hook deviation must be properly removed. Td compensation is a method used to compensate the hook deviation present in EBI data; it consists of multiplying the obtained spectrum, Zmeas(ω), by a complex exponential in the form of exp(-jωTd). Although the method is well known and accepted, Td compensation cannot entirely correct the hook-like deviation; moreover, it lacks solid scientific grounds. In this work, the Td compensation method is revisited, and it is shown that it should not be used to correct the effect of a capacitive leakage; furthermore, a more developed approach for correcting the hook deviation caused by the capacitive leakage is proposed. The method includes a novel correcting expression and a process for selecting the proper values of expressions that are complex and frequency dependent. The correctness of the novel method is validated with the experimental data obtained from measurements from three different EBI applications. The obtained results confirm the sufficiency and feasibility of the correcting method.

  6. Stroke damage detection using classification trees on electrical bioimpedance cerebral spectroscopy measurements.

    Science.gov (United States)

    Atefi, Seyed Reza; Seoane, Fernando; Thorlin, Thorleif; Lindecrantz, Kaj

    2013-08-07

    After cancer and cardio-vascular disease, stroke is the third greatest cause of death worldwide. Given the limitations of the current imaging technologies used for stroke diagnosis, the need for portable non-invasive and less expensive diagnostic tools is crucial. Previous studies have suggested that electrical bioimpedance (EBI) measurements from the head might contain useful clinical information related to changes produced in the cerebral tissue after the onset of stroke. In this study, we recorded 720 EBI Spectroscopy (EBIS) measurements from two different head regions of 18 hemispheres of nine subjects. Three of these subjects had suffered a unilateral haemorrhagic stroke. A number of features based on structural and intrinsic frequency-dependent properties of the cerebral tissue were extracted. These features were then fed into a classification tree. The results show that a full classification of damaged and undamaged cerebral tissue was achieved after three hierarchical classification steps. Lastly, the performance of the classification tree was assessed using Leave-One-Out Cross Validation (LOO-CV). Despite the fact that the results of this study are limited to a small database, and the observations obtained must be verified further with a larger cohort of patients, these findings confirm that EBI measurements contain useful information for   assessing on the health of brain tissue after stroke and supports the hypothesis that classification features based on Cole parameters, spectral information and the geometry of EBIS measurements are useful to differentiate between healthy and stroke damaged brain tissue.

  7. Tuning of Schottky barrier height of Al/n-Si by electron beam irradiation

    Science.gov (United States)

    Vali, Indudhar Panduranga; Shetty, Pramoda Kumara; Mahesha, M. G.; Petwal, V. C.; Dwivedi, Jishnu; Choudhary, R. J.

    2017-06-01

    The effect of electron beam irradiation (EBI) on Al/n-Si Schottky diode has been studied by I-V characterization at room temperature. The behavior of the metal-semiconductor (MS) interface is analyzed by means of variations in the MS contact parameters such as, Schottky barrier height (ΦB), ideality factor (n) and series resistance (Rs). These parameters were found to depend on the EBI dose having a fixed incident beam of energy 7.5 MeV. At different doses (500, 1000, 1500 kGy) of EBI, the Schottky contacts were prepared and extracted their contact parameters by applying thermionic emission and Cheung models. Remarkably, the tuning of ΦB was observed as a function of EBI dose. The improved n with increased ΦB is seen for all the EBI doses. As a consequence of which the thermionic emission is more favored. However, the competing transport mechanisms such as space charge limited emission, tunneling and tunneling through the trap states were ascribed due to n > 1. The analysis of XPS spectra have shown the presence of native oxide and increased radiation induced defect states. The thickness variation in the MS interface contributing to Schottky contact behavior is discussed. This study explains a new technique to tune Schottky contact parameters by metal deposition on the electron beam irradiated n-Si wafers.

  8. Recombinant p35 from bacteria can form Interleukin (IL-)12, but Not IL-35.

    Science.gov (United States)

    Aparicio-Siegmund, Samadhi; Moll, Jens M; Lokau, Juliane; Grusdat, Melanie; Schröder, Jutta; Plöhn, Svenja; Rose-John, Stefan; Grötzinger, Joachim; Lang, Philipp A; Scheller, Jürgen; Garbers, Christoph

    2014-01-01

    The Interleukin (IL)-12 family contains several heterodimeric composite cytokines which share subunits among each other. IL-12 consists of the subunits p40 (shared with IL-23) and p35. p35 is shared with the composite cytokine IL-35 which comprises of the p35/EBI3 heterodimer (EBI3 shared with IL-27). IL-35 signals via homo- or heterodimers of IL-12Rβ2, gp130 and WSX-1, which are shared with IL-12 and IL-27 receptor complexes, respectively. p35 was efficiently secreted in complex with p40 as IL-12 but not with EBI3 as IL-35 in several transfected cell lines tested which complicates the analysis of IL-35 signal transduction. p35 and p40 but not p35 and EBI3 form an inter-chain disulfide bridge. Mutation of the responsible cysteine residue (p40C197A) reduced IL-12 formation and activity only slightly. Importantly, the p40C197A mutation prevented the formation of antagonistic p40 homodimers which enabled the in vitro reconstitution of biologically active IL-12 with p35 produced in bacteria (p35bac). Reconstitution of IL-35 with p35bac and EBI3 did, however, fail to induce signal transduction in Ba/F3 cells expressing IL-12Rβ2 and gp130. In summary, we describe the in vitro reconstitution of IL-12, but fail to produce recombinant IL-35 by this novel approach.

  9. Recombinant p35 from bacteria can form Interleukin (IL-12, but Not IL-35.

    Directory of Open Access Journals (Sweden)

    Samadhi Aparicio-Siegmund

    Full Text Available The Interleukin (IL-12 family contains several heterodimeric composite cytokines which share subunits among each other. IL-12 consists of the subunits p40 (shared with IL-23 and p35. p35 is shared with the composite cytokine IL-35 which comprises of the p35/EBI3 heterodimer (EBI3 shared with IL-27. IL-35 signals via homo- or heterodimers of IL-12Rβ2, gp130 and WSX-1, which are shared with IL-12 and IL-27 receptor complexes, respectively. p35 was efficiently secreted in complex with p40 as IL-12 but not with EBI3 as IL-35 in several transfected cell lines tested which complicates the analysis of IL-35 signal transduction. p35 and p40 but not p35 and EBI3 form an inter-chain disulfide bridge. Mutation of the responsible cysteine residue (p40C197A reduced IL-12 formation and activity only slightly. Importantly, the p40C197A mutation prevented the formation of antagonistic p40 homodimers which enabled the in vitro reconstitution of biologically active IL-12 with p35 produced in bacteria (p35bac. Reconstitution of IL-35 with p35bac and EBI3 did, however, fail to induce signal transduction in Ba/F3 cells expressing IL-12Rβ2 and gp130. In summary, we describe the in vitro reconstitution of IL-12, but fail to produce recombinant IL-35 by this novel approach.

  10. Evaluation of the Effectiveness and Implementation of an Adapted Evidence-Based Mammography Intervention for African American Women

    Directory of Open Access Journals (Sweden)

    Linda Highfield

    2015-01-01

    Full Text Available Breast cancer mortality disparities continue, particularly for uninsured and minority women. A number of effective evidence-based interventions (EBIs exist for addressing barriers to mammography screening; however, their uptake and use in community has been limited. Few cancer-specific studies have evaluated adapted EBIs in new contexts, and fewer still have considered implementation. This study sought to (1 evaluate the effectiveness of an adapted mammography EBI in improving appointment keeping in African American women and (2 describe processes of implementation in a new practice setting. We used the type 1 hybrid design to test effectiveness and implementation using a quasi-experimental design. Logistic regression and intent-to-treat analysis were used to evaluate mammography appointment attendance. The no-show rate was 44% (comparison versus 19% (intervention. The adjusted odds of a woman in the intervention group attending her appointment were 3.88 p<0.001. The adjusted odds of a woman attending her appointment in the intent-to-treat analysis were 2.31 p<0.05. Adapted EBI effectiveness was 3.88 (adjusted OR versus 2.10 (OR for the original program, indicating enhanced program effect. A number of implementation barriers and facilitators were identified. Our findings support previous studies noting that sequentially measuring EBI efficacy and effectiveness, followed by implementation, may be missing important contextual information.

  11. Characterization of pitch prepared from pyrolysis fuel oil via electron beam irradiation

    Science.gov (United States)

    Kim, Hong Gun; Park, Mira; Kim, Hak-Yong; Kwac, Lee Ku; Shin, Hye Kyoung

    2017-06-01

    Pitch samples were obtained from pyrolysis fuel oil by thermal treatment for 2 h at 300 °C after electron beam irradiation (EBI) treatment and by thermal treatment alone for different temperature of 250 °C, 300 °C, and 350 °C. EBI treatment was found to be an effective treatment for preparing pitch compare to the pitch obtained without EBI treatment. These results were confirmed by Fourier transform infrared spectroscopy (FT-IR) and Carbon-13 nuclear magnetic resonance (13C NMR) analyses, which showed the increase in the intensities of peaks corresponding to aromatic compounds. In the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectra, the amount of components with medium molecular weights in the pitch was found to increase with the temperature; likewise, in the case of the pitch obtained via EBI treatment, we found that the amount of components with higher molecular weight over 1000 (m/v) similarly increased. Further, the thermal stability and carbon yield at 850 °C of the pitch obtained by EBI were greater than those of samples subjected to thermal treatment at 250 and 300 °C.

  12. Project power: Adapting an evidence-based HIV/STI prevention intervention for incarcerated women.

    Science.gov (United States)

    Fasula, Amy M; Fogel, Catherine I; Gelaude, Deborah; Carry, Monique; Gaiter, Juarlyn; Parker, Sharon

    2013-06-01

    Incarcerated women are a critical population for targeted HIV/STI prevention programming; however, there is a dearth of evidence-based, genderspecific behavioral interventions for this population. Systematically adapting existing evidence-based interventions (EBIs) can help fill this gap. We illustrate the adaptation of the HIV/STI prevention EBI, Project Safe, for use among incarcerated women and delivery in prisons. Project POWER, the final adapted intervention, was developed using formative research with prison staff and administration, incarcerated and previously incarcerated women, and input of community advisory boards. Intervention delivery adaptations included: shorter, more frequent intervention sessions; booster sessions prior to and just after release; facilitator experience in prisons and counseling; and new videos. Intervention content adaptations addressed issues of empowerment, substance use, gender and power inequity in relationships, interpersonal violence, mental health, reentry, and social support. This illustration of the adaption process provides information to inform additional efforts to adapt EBIs for this underserved population.

  13. The European Bioinformatics Institute in 2016: Data growth and integration.

    Science.gov (United States)

    Cook, Charles E; Bergman, Mary Todd; Finn, Robert D; Cochrane, Guy; Birney, Ewan; Apweiler, Rolf

    2016-01-04

    New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources.

  14. REXEBTS, design and initial commissioning results

    CERN Document Server

    Wenander, F; Jonson, B; Liljeby, L; Nyman, G H; Rensfelt, K G; Skeppstedt, Ö; Wolf, B

    2001-01-01

    The REXEDIS is an Electron Beam Ion Source (EBIS) developed particularly for charge breeding of rare and short-lived isotopes produced at ISOLDE for the REX-ISOLDE post accelerator. Bunches of singly charged radioactive ions are injected into the EBIS and charge bred to a charge-to-mass ratio of approximately 1/4 and thereafter extracted and injected into a short LINAC. This novel concept, employing a Penning trap to bunch and cool the ions from an on-line mass separator prior to charge breeding in an EBIS, results in an efficient and compact system. In this article the final REXEBIS design is presented together with results from the first tests. (19 refs).

  15. The virial theorem in Eddington-Born-Infeld gravity

    CERN Document Server

    Santos, Noelia S

    2015-01-01

    We examine the possibility that the Eddington-Born-Infeld (EBI) modified gravity provides an alternative explanation for the mass discrepancy in clusters of galaxies. For this purpose we derive the modified Einstein field equations, finding an additional "geometrical mass" term which provides an effective contribution to the gravitational binding energy. Using some approximations and assumptions for week gravitational fields, and taking into account the collisionless relativistic Boltzmann equation, we derive a generalized version of the virial theorem in the framework of EBI gravity. We show that the "geometrical mass" term may account for the well known virial mass discrepancy in clusters of galaxies. We also derive the velocity dispersion relation for galaxies in the clusters, which could provide an efficient method for testing EBI gravity from astrophysical observations.

  16. The virial theorem in Eddington-Born-Infeld gravity

    Science.gov (United States)

    Santos, Noelia S.; Santos, Janilo

    2015-12-01

    We consider the possibility that the Eddington-Born-Infeld (EBI) modified gravity provides an alternative explanation for the mass discrepancy in clusters of galaxies. For this purpose we derive the modified Einstein field equations, finding an additional "geometrical mass" term which provides an effective contribution to the gravitational binding energy. Using some approximations and assumptions for weak gravitational fields, and taking into account the collisionless relativistic Boltzmann equation, we derive a generalized version of the virial theorem in the framework of EBI gravity. We show that the "geometrical mass" term may account for the well known virial mass discrepancy in clusters of galaxies. We also derive the velocity dispersion relation for galaxies in the clusters, which could provide an efficient method for testing EBI gravity from astrophysical observations.

  17. Physicochemical properties and volatile profile of chili shrimp paste as affected by irradiation and heat.

    Science.gov (United States)

    Cheok, Choon Yoong; Sobhi, Babak; Mohd Adzahan, Noranizan; Bakar, Jamilah; Abdul Rahman, Russly; Ab Karim, Muhammad Shahrim; Ghazali, Zulkafli

    2017-02-01

    Chili shrimp paste (CSP) is an exotic traditional Southeast Asian condiment prepared using mainly fresh chilies and fermented shrimp paste (belacan) which attributed to strong pungent fishy odor. This study aims to evaluate the effectiveness of electron beam irradiation (EBI) exposure on CSP for microorganisms decontamination, and its physicochemical qualities changes. Changes in capsaicinoid contents and volatile compounds were analyzed using HPLC and GC-MS. Mesophilic bacteria, yeast, mold and pathogenic Enterobacteriaceae decreased as irradiation dose increasing from 0 to 10kGy. EBI at 10kGy effectively decontaminated the samples with no significant effects on phenolic and capsaicinoids contents compared to the fresh samples. From 24 compounds, irradiated CSP retained 23 volatile compounds, while thermally treated CSP has only 19 compounds. EBI at 10kGy is effective for decontamination in CSP with lesser destructive effect on volatile compounds and texture compared to thermal treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. The Roles of System and Organizational Leadership in System-Wide Evidence-Based Intervention Sustainment: A Mixed-Method Study.

    Science.gov (United States)

    Aarons, Gregory A; Green, Amy E; Trott, Elise; Willging, Cathleen E; Torres, Elisa M; Ehrhart, Mark G; Roesch, Scott C

    2016-11-01

    If evidence-based interventions (EBIs) are not sustained, investments are wasted and public health impact is limited. Leadership has been suggested as a key determinant of implementation and sustainment; however, little empirical work has examined this factor. This mixed-methods study framed using the Exploration, Preparation, Implementation, Sustainment (EPIS) conceptual framework examines leadership in both the outer service system context and inner organizational context in eleven system-wide implementations of the same EBI across two U.S. states and 87 counties. Quantitative data at the outer context (i.e., system) and inner context (i.e., team) levels demonstrated that leadership predicted future sustainment and differentiated between sites with full, partial, or no sustainment. In the outer context positive sustainment leadership was characterized as establishing a project's mission and vision, early and continued planning for sustainment, realistic project plans, and having alternative strategies for project survival. Inner context frontline transformational leadership predicted sustainment while passive-avoidant leadership predicted non-sustainment. Qualitative results found that sustainment was associated with outer context leadership characterized by engagement in ongoing supportive EBI championing, marketing to stakeholders; persevering in these activities; taking action to institutionalize the EBI with funding, contracting, and system improvement plans; and fostering ongoing collaboration between stakeholders at state and county, and community stakeholder levels. For frontline leadership the most important activities included championing the EBI and providing practical support for service providers. There was both convergence and expansion that identified unique contributions of the quantitative and qualitative methods. Greater attention to leadership in both the outer system and inner organizational contexts is warranted to enhance EBI implementation

  19. Comparison of dry-textile electrodes for electrical bioimpedance spectroscopy measurements

    Science.gov (United States)

    Márquez, J. C.; Seoane, F.; Välimäki, E.; Lindecrantz, K.

    2010-04-01

    Textile Electrodes have been widely studied for biopotentials recordings, specially for monitoring the cardiac activity. Commercially available applications, such as Adistar T-shirt and Textronics Cardioshirt, have proved a good performance for heart rate monitoring and are available worldwide. Textile technology can also be used for Electrical Bioimpedance Spectroscopy measurements enabling home and personalized health monitoring applications however solid ground research about the measurement performance of the electrodes must be done prior to the development of any textile-enabled EBI application. In this work a comparison of the measurement performance of two different types of dry-textile electrodes and manufacturers has been performed against standardized RedDot 3M Ag/AgCl electrolytic electrodes. 4-Electrode, whole body, Ankle-to-Wrist EBI measurements have been taken with the Impedimed spectrometer SFB7 from healthy subjects in the frequency range of 3kHz to 500kHz. Measurements have been taken with dry electrodes at different times to study the influence of the interaction skin-electrode interface on the EBI measurements. The analysis of the obtained complex EBI spectra shows that the measurements performed with textile electrodes produce constant and reliable EBI spectra. Certain deviation can be observed at higher frequencies and the measurements obtained with Textronics and Ag/AgCl electrodes present a better resemblance. Textile technology, if successfully integrated it, may enable the performance of EBI measurements in new scenarios allowing the rising of novel wearable monitoring applications for home and personal care as well as car safety.

  20. Production of highly charged argon ions from a room temperature electron beam ion trap

    Institute of Scientific and Technical Information of China (English)

    WANG Tie-Shan; PENG Hai-Bo; Ovsyannikov V P; Kentsch U; Ullmann F; CHENG Rui; Zschornack G

    2008-01-01

    In this work.highly charged ions have been extracted from the advanced Electron Beam Ion Source (EBIS-A) developed in a scientific cooperation between the Dresden University of Technology and the DREEBIT GmbH Dresden.The charge state distributions of ions extracted from the EBIS-A are measured in and extracted in the leaky mode.3×105 Ar18+ ions per pulse are extracted in the pulse mode.The ion charge state distribution is a function of the ionization time.

  1. Electron beam ion source and electron beam ion trap (invited).

    Science.gov (United States)

    Becker, Reinard; Kester, Oliver

    2010-02-01

    The electron beam ion source (EBIS) and its trap variant [electron beam ion trap (EBIT)] celebrated their 40th and 20th anniversary, respectively, at the EBIS/T Symposium 2007 in Heidelberg. These technologically challenging sources of highly charged ions have seen a broad development in many countries over the last decades. In contrast to most other ion sources the recipe of improvement was not "sorcery" but a clear understanding of the physical laws and obeying the technological constraints. This review will report important achievements of the past as well as promising developments in the future.

  2. Electron beam ion source and electron beam ion trap (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Reinard [Scientific Software Service, Kapellenweg 2a, D-63571 Gelnhausen (Germany); Kester, Oliver [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States)

    2010-02-15

    The electron beam ion source (EBIS) and its trap variant [electron beam ion trap (EBIT)] celebrated their 40th and 20th anniversary, respectively, at the EBIS/T Symposium 2007 in Heidelberg. These technologically challenging sources of highly charged ions have seen a broad development in many countries over the last decades. In contrast to most other ion sources the recipe of improvement was not ''sorcery'' but a clear understanding of the physical laws and obeying the technological constraints. This review will report important achievements of the past as well as promising developments in the future.

  3. Electron beam ion source and electron beam ion trap (invited)a)

    Science.gov (United States)

    Becker, Reinard; Kester, Oliver

    2010-02-01

    The electron beam ion source (EBIS) and its trap variant [electron beam ion trap (EBIT)] celebrated their 40th and 20th anniversary, respectively, at the EBIS/T Symposium 2007 in Heidelberg. These technologically challenging sources of highly charged ions have seen a broad development in many countries over the last decades. In contrast to most other ion sources the recipe of improvement was not "sorcery" but a clear understanding of the physical laws and obeying the technological constraints. This review will report important achievements of the past as well as promising developments in the future.

  4. EBTS:DESIGN AND EXPERIMENTAL STUDY.

    Energy Technology Data Exchange (ETDEWEB)

    PIKIN,A.; ALESSI,J.; BEEBE,E.; KPONOU,A.; PRELEC,K.; KUZNETSOV,G.; TIUNOV,M.

    2000-11-06

    Experimental study of the BNL Electron Beam Test Stand (EBTS), which is a prototype of the Relativistic Heavy Ion Collider (RHIC) Electron Beam Ion Source (EBIS), is currently underway. The basic physics and engineering aspects of a high current EBIS implemented in EBTS are outlined and construction of its main systems is presented. Efficient transmission of a 10 A electron beam through the ion trap has been achieved. Experimental results on generation of multiply charged ions with both continuous gas and external ion injection confirm stable operation of the ion trap.

  5. Effects of electron beam irradiation on physicochemical properties of corn flour and improvement of the gelatinization inhibition.

    Science.gov (United States)

    Xue, Peiyu; Zhao, Yue; Wen, Chengrong; Cheng, Sheng; Lin, Songyi

    2017-10-15

    The properties and viscosity-reduction mechanism of corn flour irradiated by electron beam have not been understood properly. Here, we investigate the effects of electron beam irradiation (EBI) on the gelatinization and physicochemical properties of corn flour irradiated by 0-5.40kGy of electron beam. The total starch and crude fiber contents of corn flour decreased significantly (Pgelatinization of corn flour was completely inhibited. Thus, EBI can be used to inhibit the gelatinization of corn flour, which may be beneficial for industrial and food formulations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. FGFR1タンパク発現の低いFGFR1遺伝子増幅肺癌では他の活性型チロシンキナーゼ受容体がFGFR阻害剤の効果を軽減する

    OpenAIRE

    小谷, 浩

    2016-01-01

    博士論文要旨Abstract 以下に掲載:Oncogene Epub ahead of print Nature Publishing Group. 共著者:Hiroshi Kotani, Hiromichi Ebi, Hidenori Kitai, Shigeki Nanjo, Kenji Kita, Tiffany G. Huynh, Akishi Ooi, Anthony C. Faber, Mari Mino-Kenudson, Seiji Yano

  7. Characteristics and circumstances of injuries vary with ethnicity of different population groups living in the same country.

    Science.gov (United States)

    Tiruneh, Abebe; Siman-Tov, Maya; Radomislensky, Irina; Itg; Peleg, Kobi

    2017-02-01

    To examine whether characteristics and circumstances of injuries are related to ethnicity. The study was based on the Israeli National Trauma Registry data for patients hospitalized between 2008 and 2011. Data included demographics, injury, hospital resource utilization characteristics and outcome at discharge. Univariate analysis followed by logistic regression models were undertaken to examine the relationship between injury and ethnicity. The study included 116,946 subjects; 1% were Ethiopian Born Israelis (EBI), 11% Israelis born in the Former Soviet Union (FSUBI) and 88% the remaining Israelis (RI). EBI were injured more on street or at work place and had higher rates of penetrating and severe injuries. However, FSUBI were mostly injured at home, and had higher rates of fall injuries and hip fracture. Adjusted analysis showed that EBI and FSUBI were more likely to be hospitalized because of violence-related injuries compared with RI but less likely because of road traffic injuries. Undergoing surgery and referral for rehabilitation were greater among FSUBI, while admission to intensive care unit was greater among EBI. Targeted intervention programmes need to be developed for immigrants of different countries of origin in accordance with the identified characteristics.

  8. Adaptation Guidance for Evidence-Based Teen Pregnancy and STI/HIV Prevention Curricula: From Development to Practice

    Science.gov (United States)

    Rolleri, Lori A.; Fuller, Taleria R.; Firpo-Triplett, Regina; Lesesne, Catherine A.; Moore, Claire; Leeks, Kimberly D.

    2014-01-01

    Evidence-based interventions (EBIs) are effective in preventing adolescent pregnancy and sexually transmitted infections; however, prevention practitioners are challenged when selecting and adapting the most appropriate programs. While there are existing adaptation frameworks, there is little practical guidance in applying research in the field.…

  9. Apigenin protects blood-brain barrier and ameliorates early brain injury by inhibiting TLR4-mediated inflammatory pathway in subarachnoid hemorrhage rats.

    Science.gov (United States)

    Zhang, Tingting; Su, Jingyuan; Guo, Bingyu; Wang, Kaiwen; Li, Xiaoming; Liang, Guobiao

    2015-09-01

    Early brain injury (EBI) following subarachnoid hemorrhage (SAH) is associated with high morbidity and mortality. Inflammation has been considered as the major contributor to brain damage after SAH. SAH induces a systemic increase in pro-inflammatory cytokines and chemokines. Disruption of blood-brain barrier (BBB) facilitates the influx of inflammatory cells. It has been reported that the activation of toll-like receptor 4 (TLR4)/NF-κB signaling pathway plays a vital role in the central nervous system diseases. Apigenin, a common plant flavonoid, possesses anti-inflammation effect. In this study, we focused on the effects of apigenin on EBI following SAH and its anti-inflammation mechanism. Our results showed that apigenin (20mg/kg) administration significantly attenuated EBI (including brain edema, BBB disruption, neurological deficient, severity of SAH, and cell apoptosis) after SAH in rats by suppressing the expression of TLR4, NF-κB and their downstream pro-inflammatory cytokines in the cortex and by up-regulating the expression of tight junction proteins of BBB. Double immunofluorescence staining demonstrated that TLR4 was activated following SAH in neurons, microglia cells, and endothelial cells but not in astrocytes. Apigenin could suppress the activation of TLR4 induced by SAH and inhibit apoptosis of cells in the cortex. These results suggested that apigenin could attenuate EBI after SAH in rats by suppressing TLR4-mediated inflammation and protecting against BBB disruption. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Preventing Prostate Cancer Metastasis by Targeting Exosome Secretion

    Science.gov (United States)

    2015-12-01

    taken from MEME Suite (http://meme.ebi.edu.au/ meme /db/sequences). The role in cancer formation was estimated based on Uniprot KB and OMIM (http...prediction of the MSI1 recognition motif in the 3’UTR of the mRNA was taken from MEME Suite REF. The role in cancer formation was estimated based on

  11. OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript

    NARCIS (Netherlands)

    Adamusiak, Tomasz; Burdett, Tony; Kurbatova, Natalja; van der Velde, K. Joeri; Abeygunawardena, Niran; Antonakaki, Despoina; Kapushesky, Misha; Parkinson, Helen; Swertz, Morris A.

    2011-01-01

    Background: Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontol

  12. Experimental Condition - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available phenotypes - Light condition etc. Plant Environment Ontology (EO) is used for standardization. - Existence .../togodb.biosciencedbc.jp/togodb/view/cpp_exp_condition#en Data acquisition method Plant Environment Ontolo...gy, ChEBI Data analysis method - Number of data entries 22 entries Data item Descri

  13. OntoQuery: easy-to-use web-based OWL querying.

    Science.gov (United States)

    Tudose, Ilinca; Hastings, Janna; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Dekker, Adriano; Kale, Namrata; Ennis, Marcus; Steinbeck, Christoph

    2013-11-15

    The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The Protégé-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the Protégé Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility.  The source code for this implementation together with instructions for installation is available at http://github.com/IlincaTudose/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. hastings@ebi.ac.uk.

  14. Derived Equivalence Relations of Geometry Skills in Students with Autism: An Application of the PEAK-E Curriculum

    Science.gov (United States)

    Dixon, Mark R.; Belisle, Jordan; Stanley, Caleb R.; Daar, Jacob H.; Williams, Leigh Anne

    2016-01-01

    The present study evaluated the efficacy of equivalence-based instruction (EBI) as described in the PEAK-E curriculum (Dixon, 2015) for promoting the emergence of derived geometry skills in two children with high-functioning autism. The results suggested that direct training of shape name (A) to shape property (B) (i.e., A-B relations) was…

  15. Adaptation Guidance for Evidence-Based Teen Pregnancy and STI/HIV Prevention Curricula: From Development to Practice

    Science.gov (United States)

    Rolleri, Lori A.; Fuller, Taleria R.; Firpo-Triplett, Regina; Lesesne, Catherine A.; Moore, Claire; Leeks, Kimberly D.

    2014-01-01

    Evidence-based interventions (EBIs) are effective in preventing adolescent pregnancy and sexually transmitted infections; however, prevention practitioners are challenged when selecting and adapting the most appropriate programs. While there are existing adaptation frameworks, there is little practical guidance in applying research in the field.…

  16. Lessons Learned From Dissemination of Evidence-Based Interventions for HIV Prevention.

    Science.gov (United States)

    Collins, Charles B; Sapiano, Tobey N

    2016-10-01

    In 1999, IOM issued a report that recommended that the Centers for Disease Control and Prevention should disseminate evidence-based HIV prevention interventions (EBIs) to be implemented by health departments, community-based organizations, drug treatment centers, and clinics. Based on these recommendations, the Diffusion of Effective Behavioral Interventions Project was initiated in 2000 and began disseminating interventions into public health practice. For 15 years, the Centers for Disease Control and Prevention has disseminated 29 EBIs to more than 11,300 agencies. Lessons were identified during the 15 years of implementation regarding successful methods of dissemination of EBIs. Lessons around selecting interventions for dissemination, developing a dissemination infrastructure including a resource website (https://effectiveinterventions.cdc.gov), and engagement with stakeholders are discussed. A continuous development approach ensured that intervention implementation materials, instructions, and technical assistance were all tailored to the needs of end users, focus populations, and agency capacities. Six follow-up studies demonstrated that adopters of EBIs were able to obtain comparable outcomes to those of the original efficacy research. The Diffusion of Effective Behavioral Interventions Project may offer guidance for other large, national, evidence-based public health dissemination projects.

  17. Effectiveness of an email-based intervention helping parents to enhance alcohol-related parenting skills and reduce their children's alcohol consumption: A randomised controlled trial

    NARCIS (Netherlands)

    Wurdak, M.; Kuntsche, E.N.; Wolstein, J.

    2017-01-01

    Aims: Developing and evaluating an email-based intervention (EBI) to enhance alcohol-related parenting skills and reduce alcohol consumption among adolescents. Methods: Over four weeks, participating parents received a weekly email containing scientific findings, practical advice and exercises in

  18. Transmission through Ferrite Samples at Submillimeter Frequencies

    Science.gov (United States)

    1986-05-01

    y Y In all the equations given above, c and 1’e are, in general, complex. Measurements are generally made on the power transmitted which is ITaI ? in...Frequency (cm-’) using measurements of2T 1 given eby Figure 8. Power transmission coeffi- equation( 2),Tp1 = ITaI ~cient for 100-m-thick ferrite slab

  19. Evaluation of charge breeding options for EURISOL

    CERN Document Server

    Delahaye, P; Lamy, T; Marie-Jeanne, M; Kester, O; Wenander, F

    2010-01-01

    A comprehensive study of charge breeding techniques for the most ambitious ISOL-facility project, EURISOL, is presented here. It is based on results obtained during the past years at CERN-ISOLDE and LPSC Grenoble with charge breeders of both ECR and EBIS types.

  20. Software Tool for Analysis of Breathing-Related Errors in Transthoracic Electrical Bioimpedance Spectroscopy Measurements

    Science.gov (United States)

    Abtahi, F.; Gyllensten, I. C.; Lindecrantz, K.; Seoane, F.

    2012-12-01

    During the last decades, Electrical Bioimpedance Spectroscopy (EBIS) has been applied in a range of different applications and mainly using the frequency sweep-technique. Traditionally the tissue under study is considered to be timeinvariant and dynamic changes of tissue activity are ignored and instead treated as a noise source. This assumption has not been adequately tested and could have a negative impact and limit the accuracy for impedance monitoring systems. In order to successfully use frequency-sweeping EBIS for monitoring time-variant systems, it is paramount to study the effect of frequency-sweep delay on Cole Model-based analysis. In this work, we present a software tool that can be used to simulate the influence of respiration activity in frequency-sweep EBIS measurements of the human thorax and analyse the effects of the different error sources. Preliminary results indicate that the deviation on the EBIS measurement might be significant at any frequency, and especially in the impedance plane. Therefore the impact on Cole-model analysis might be different depending on method applied for Cole parameter estimation.

  1. Simple voltage-controlled current source for wideband electrical bioimpedance spectroscopy: circuit dependences and limitations

    Science.gov (United States)

    Seoane, F.; Macías, R.; Bragós, R.; Lindecrantz, K.

    2011-11-01

    In this work, the single Op-Amp with load-in-the-loop topology as a current source is revisited. This circuit topology was already used as a voltage-controlled current source (VCCS) in the 1960s but was left unused when the requirements for higher frequency arose among the applications of electrical bioimpedance (EBI). The aim of the authors is not only limited to show that with the currently available electronic devices it is perfectly viable to use this simple VCCS topology as a working current source for wideband spectroscopy applications of EBI, but also to identify the limitations and the role of each of the circuit components in the most important parameter of a current for wideband applications: the output impedance. The study includes the eventual presence of a stray capacitance and also an original enhancement, driving with current the VCCS. Based on the theoretical analysis and experimental measurements, an accurate model of the output impedance is provided, explaining the role of the main constitutive elements of the circuit in the source's output impedance. Using the topologies presented in this work and the proposed model, any electronic designer can easily implement a simple and efficient current source for wideband EBI spectroscopy applications, e.g. in this study, values above 150 kΩ at 1 MHz have been obtained, which to the knowledge of the authors are the largest values experimentally measured and reported for a current source in EBI at this frequency.

  2. Conformational Temperature-Dependent Behavior of a Histone H2AX: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials

    Science.gov (United States)

    2012-03-19

    chemical approximation. Macromolecules 18: 534–552. 20. Eby DM, Johnson GR, Farmer BL, Pandey RB (2011) Supramolecular assembly of a biomineralizing ...soft epitaxy observed for peptides on metal surfaces. Soft Matter 7: 2113–2120. 22. Pandey RB, Farmer BL (2008) Phys Rev E 77: 031902–031910. 23

  3. Incidence of urinary tract infection (UTI) among pregnant women in ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-12-01

    Dec 1, 2009 ... the vagina makes it liable to trauma during sexual inter- course as well ... into the bladder during pregnancy/child birth (Duerden et al.,. 1990; Ebie et ... tion in use of diagnostic tests, interpretation of signs or ..... SENS Project.

  4. Environmental biophysical indicators at detailed scale for land management in Milpa Alta, Central Mexico

    Directory of Open Access Journals (Sweden)

    María de Lourdes Rodríguez Gamiño

    2013-04-01

    Full Text Available In order to evaluate the present condition of natural resources of the Milpa Alta area (Central Mexico Environmental Biophysical Indicators (EBI of state at detailed scale were determined. Environmental Biophysical Units (EBU from morphogenetic characteristics of relief were obtained, which served as base as synthetic-unit of reference. EBI indicators of relief, land use/cover, climate and soil, factors were determined. The dominant EBU are from endogenous accumulative volcanic origin of upper, medium and lower mountain slopes of andesite-basalte lava flows of Pleistocene-Holocene. The dominant land use is of rain-feed agriculture of annual and semi permanent prickly pear, crops. There are forest areas with Abies religiosa, Pinus spp and grassland areas which are used for sheep production. Climate influences the spatial distribution of land use-cover. Soils presented high organic matter contents, slightly acid, loamy-sand texture, and a complex of change dominated by Ca2+. The EBI indicators of state analyzed of EBU groups do not show deterioration for the study area. The statistical analyses from the EBI clustering using the EBU represent a spatial reference that will allow proposing strategies for handling and conservation of natural resources.

  5. EMBL rescue package keeps bioinformatics centre running

    CERN Multimedia

    Abott, A

    1999-01-01

    The threat to the EBI arising from the EC refusal to fund its running costs seems to have been temporarily lifted. At a meeting in EMBL, Heidelberg, delegates agreed in principle to make up the shortfall of 5 million euros. A final decision will be taken at a special meeting of the EMBL council in March (1 page).

  6. Study of program defects of 22nm nanoimprint template with an advanced e-beam inspection system

    Science.gov (United States)

    Hiraka, Takaaki; Mizuochi, Jun; Nakanishi, Yuko; Yusa, Satoshi; Sasaki, Shiho; Kurihara, Masaaki; Toyama, Nobuhito; Morikawa, Yasutaka; Mohri, Hiroshi; Hayashi, Naoya; Xiao, Hong; Kuan, Chiyan; Wang, Fei; Ma, Long; Zhao, Yan; Jau, Jack

    2009-10-01

    Nanoimprint lithography (NIL) is a candidate of alternative, low cost of ownership lithography solution for deep nano-meter device manufacturing12. For the NIL template pattern making, we have been developing the processes with 100keV SB EB writer and 50keV VSB EB writer to achieve the fine resolution of near 20nm1-7. However, inspection of nanoimprint template posed a big challenge to inspection system due to the small geometry, 1x comparing to 4x of Optical mask and EUV mask. Previous studies of nanoimprint template inspection were performed indirectly on a stamped wafer and/or on a round quartz wafer13. Electron beam inspection (EBI) systems have been widely used in semiconductor fabs in nanometer technology nodes. Most commonly EBI applications are electrical defects, or voltage contrast (VC) defects detection and monitoring8-11. In this study, we used a mask EBI system developed by Hermes Microvision, Inc. (HMI) to directly inspect a NIL template with line/space and hole patterns half pitched from 22nm to 90nm and with program defects sized from 4nm to 92nm. Capability of inspection with 10nm pixel size has been demonstrated and capability of capturing program defects sized 12nm and smaller has been shown. This study proved the feasibility of EBI as inspection solution of nanoimprint template for 22nmHP and beyond.

  7. First test of BNL electron beam ion source with high current density electron beam

    Energy Technology Data Exchange (ETDEWEB)

    Pikin, Alexander, E-mail: pikin@bnl.gov; Alessi, James G., E-mail: pikin@bnl.gov; Beebe, Edward N., E-mail: pikin@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States); Shornikov, Andrey; Mertzig, Robert; Wenander, Fredrik; Scrivens, Richard [CERN, CH-1211 Geneva 23 (Switzerland)

    2015-01-09

    A new electron gun with electrostatic compression has been installed at the Electron Beam Ion Source (EBIS) Test Stand at BNL. This is a collaborative effort by BNL and CERN teams with a common goal to study an EBIS with electron beam current up to 10 A, current density up to 10,000 A/cm{sup 2} and energy more than 50 keV. Intensive and pure beams of heavy highly charged ions with mass-to-charge ratio < 4.5 are requested by many heavy ion research facilities including NASA Space Radiation Laboratory (NSRL) at BNL and HIE-ISOLDE at CERN. With a multiampere electron gun, the EBIS should be capable of delivering highly charged ions for both RHIC facility applications at BNL and for ISOLDE experiments at CERN. Details of the electron gun simulations and design, and the Test EBIS electrostatic and magnetostatic structures with the new electron gun are presented. The experimental results of the electron beam transmission are given.

  8. AcEST: BP918432 [AcEST

    Lifescience Database Archive (English)

    Full Text Available rocytozoon bieneusi H348 GN=EBI_26386 PE=4 SV=1 Length =... Sbjct: 584 HLDPMLDAYYEARGWDRSGIPTMEKLRSLGLEHVSRDLNRAREEAGAPATA 634 >tr|A9CRL7|A9CRL7_9MICR t-SNARE complex subunit, syntaxin OS=Ente

  9. Taxonomy for Strengthening the Identification of Core Elements for Evidence-Based Behavioral Interventions for HIV/AIDS Prevention

    Science.gov (United States)

    Galbraith, Jennifer S.; Herbst, Jeffrey H.; Whittier, David K.; Jones, Patricia L.; Smith, Bryce D.; Uhl, Gary; Fisher, Holly H.

    2011-01-01

    The concept of core elements was developed to denote characteristics of an intervention, such as activities or delivery methods, presumed to be responsible for the efficacy of evidence-based behavioral interventions (EBIs) for HIV/AIDS prevention. This paper describes the development of a taxonomy of core elements based on a literature review of…

  10. 76 FR 17869 - Agency Forms Undergoing Paperwork Reduction Act Review

    Science.gov (United States)

    2011-03-31

    ... epidemic, including the diffusion and implementation of Effective Behavioral Interventions (EBIs) for HIV... intervention) to assess their HIV and STD related attitudes and behavioral risks. CBOs will be expected to... delivering particular individual- or group-level behavioral interventions by monitoring changes in...

  11. Links to Other DBs (based on UniChem) - NBDC NikkajiRDF | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available s and chemical substances registered in other databases* by using skos:closeMatch. This is based on a work a...hemical substances in other databases which were acquired using UniChem FTP service ( ftp://ftp.ebi.ac.uk/pub/databases

  12. Potential Effects in the Interaction of Highly Charged Ions with Solid Surfaces

    National Research Council Canada - National Science Library

    Sakurai, Makotoi; Sasaki, Kouji; Miyamoto, Takahiro; Kato, Daiji; A. Sakaue, Hiroyuki

    2016-01-01

    .... It is known that the luminescence of Er2O3 provides information on its crystallinity. We observed luminescence of various samples including Er2O3 during the irradiation with highly charged ions produced by an electron beam ion source (EBIS...

  13. Recent progress in heavy ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Clark, D.J.

    1977-03-01

    A summary is given of the progress during the last several years in the technology of sources of high charge state positive heavy ions and negative heavy ions. Subjects covered include recent results in ECR and EBIS source development and comparison of various source types for high charge state heavy ions.

  14. Investigation of morphological changes in platinum-containing nanostructures created by electron-beam-induced deposition

    NARCIS (Netherlands)

    Botman, A.; Hesselberth, M.; Mulders, J.J.L.

    2008-01-01

    Focused electron-beam-induced deposition (EBID) allows the rapid fabrication of three-dimensional nanodevices and metallic wiring of nanostructures, and is a promising technique for many applications in nanoresearch. The authors present two topics on platinum-containing nanostructures created by EBI

  15. Radiocarbon challenges archaeo-historical time frameworks in the near East : The Early Bronze Age of Jericho in relation to Egypt

    NARCIS (Netherlands)

    Bruins, HJ; van der Plicht, J; Bruins, Hendrik J.; Boaretto, E.; Carmi, I.

    2001-01-01

    Our stratified radiocarbon dates from EB Jericho (Trench III) on short-lived material are significantly older than conventional archaeo-historical time frameworks. The calibrated (14)C date of Stage XV Phase li-lii (Early to Middle EB-I Kenyon) is 100-450 years older. Stage XVI Phase lxi-lxii (Early

  16. Isolating the benefits of fluid restriction in patients with heart failure: A pilot study.

    Science.gov (United States)

    Reilly, Carolyn Miller; Higgins, Melinda; Smith, Andrew; Culler, Steven D; Dunbar, Sandra B

    2015-12-01

    Fluid restriction (FR) in persons with heart failure (HF) is often prescribed, yet self-regulation and the troublesome symptom of thirst are difficult for patients to manage. The purpose of this pilot study was to test an educational and behavioral intervention (EBI) on adherence with prescribed FR and outcome measures of fluid congestion, symptom distress, and health related quality of life (HRQL). Secondary aims were to describe the relationships between self-reported and objectively measured determinants of fluid status and symptoms, and assess the psychometric properties of piloted instruments, and intervention effect sizes. NYHA Class II-IV (n=25, 44-83 years, 56% male, 20% minority, mean EF 23.0+11.7%) participants were randomized to the EBI or attention control (AC) and evaluated at baseline, 3 and 6 months. EBI patients trended toward decreasing fluid ingestion (p=0.08), experienced less HF symptom frequency (p=0.13) and severity (p=0.06), and increased symptoms of thirst (pfluid congestion between groups. These outcomes suggest that patients receiving the EBI drank slightly less fluid, experienced less typical HF symptoms, greater thirst distress and stable HRQOL. Moderate to large effect sizes for the measures used were observed, and outcomes suggest that a randomized trial of various levels of FR would not potentiate fluid congestion but should specifically address preservation of HRQOL and thirst symptoms. © The European Society of Cardiology 2014.

  17. Real-time detection of cofactor availability in genetically modified living Saccharomyces cerevisiae cells - Simultaneous probing of different geno- and phenotypes

    DEFF Research Database (Denmark)

    Kostesha, Natalie; Heiskanen, Arto; Spegel, C.

    2009-01-01

    This work describes a mediated amperometric method for simultaneous real-time probing of the NAD(P)H availability in two different phenotypes, fermentative and respiratory, of the phosphoglucose isomerase deletion mutant strain of S. cerevisiae. EBY44 [ENY.WA-1A pgi1-1D::URA3], and its parental s...

  18. Mediator-assisted Simultaneous probing of Cytosolic and Mitochondrial Redox activity in living cells

    DEFF Research Database (Denmark)

    Heiskanen, Arto; Spegel, Christer; Kostesha, Natalie

    2009-01-01

    This work describes an electron transfer mediator-assisted amperometric flow injection method for assessing redox enzyme activity in different subcellular compartments of the phosphoglucose isomerase deletion mutant strain of Saccharomyces cerevisiae, EBY44. The method is demonstrated using the f...

  19. Monitoring of Saccharomyces cerevisiae cell proliferation on thiol-modified planar gold microelectrodes using impedance spectroscopy

    DEFF Research Database (Denmark)

    Heiskanen, Arto; Spegel, Christer F; Kostesha, Natalie

    2008-01-01

    An impedance spectroscopic study of the interaction between thiol-modified Au electrodes and Saccharomyces cerevisiae of strain EBY44 revealed that the cells formed an integral part of the interface, modulating the capacitive properties until a complete monolayer was obtained, whereas the charge ...

  20. From the Laboratory to the Classroom: The Effects of Equivalence-Based Instruction on Neuroanatomy Competencies

    Science.gov (United States)

    Fienup, Daniel M.; Mylan, Sanaa E.; Brodsky, Julia; Pytte, Carolyn

    2016-01-01

    Equivalence-based instruction (EBI) has been used to successfully teach college-level concepts in research laboratories, but few studies have examined the results of such instruction on classroom performance. The current study answered a basic question about the ordering of training stimuli as well as an applied question regarding the effects of…

  1. The inhibitory cytokine IL-35 contributes to regulatory T-cell function.

    Science.gov (United States)

    Collison, Lauren W; Workman, Creg J; Kuo, Timothy T; Boyd, Kelli; Wang, Yao; Vignali, Kate M; Cross, Richard; Sehy, David; Blumberg, Richard S; Vignali, Dario A A

    2007-11-22

    Regulatory T (T(reg)) cells are a critical sub-population of CD4+ T cells that are essential for maintaining self tolerance and preventing autoimmunity, for limiting chronic inflammatory diseases, such as asthma and inflammatory bowel disease, and for regulating homeostatic lymphocyte expansion. However, they also suppress natural immune responses to parasites and viruses as well as anti-tumour immunity induced by therapeutic vaccines. Although the manipulation of T(reg) function is an important goal of immunotherapy, the molecules that mediate their suppressive activity remain largely unknown. Here we demonstrate that Epstein-Barr-virus-induced gene 3 (Ebi3, which encodes IL-27beta) and interleukin-12 alpha (Il12a, which encodes IL-12alpha/p35) are highly expressed by mouse Foxp3+ (forkhead box P3) T(reg) cells but not by resting or activated effector CD4+ T (T(eff)) cells, and that an Ebi3-IL-12alpha heterodimer is constitutively secreted by T(reg) but not T(eff) cells. Both Ebi3 and Il12a messenger RNA are markedly upregulated in T(reg) cells co-cultured with T(eff) cells, thereby boosting Ebi3 and IL-12alpha production in trans. T(reg)-cell restriction of this cytokine occurs because Ebi3 is a downstream target of Foxp3, a transcription factor that is required for T(reg)-cell development and function. Ebi3-/- and Il12a-/- T(reg) cells have significantly reduced regulatory activity in vitro and fail to control homeostatic proliferation and to cure inflammatory bowel disease in vivo. Because these phenotypic characteristics are distinct from those of other IL-12 family members, this novel Ebi3-IL-12alpha heterodimeric cytokine has been designated interleukin-35 (IL-35). Ectopic expression of IL-35 confers regulatory activity on naive T cells, whereas recombinant IL-35 suppresses T-cell proliferation. Taken together, these data identify IL-35 as a novel inhibitory cytokine that may be specifically produced by T(reg) cells and is required for maximal suppressive

  2. Cole Parameter Estimation from the Modulus of the Electrical Bioimpeadance for Assessment of Body Composition. A Full Spectroscopy Approach.

    Directory of Open Access Journals (Sweden)

    Ruben Buendia

    2011-10-01

    Full Text Available Activities around applications of Electrical Bioimpedance Spectroscopy (EBIS have proliferated in the past decade significantly. Most of these activities have been focused in the analysis of the EBIS measurements, which eventually might enable novel applications. In Body Composition Assessment (BCA the most common analysis approach currently used in EBIS is based on the Cole function, which most often requires curve fitting. One of the most implemented approaches for obtaining the Cole parameters is performed in the impedance plane through the geometrical properties that the Cole function exhibit in such domain as depressed semi-circle. To fit the measured impedance data to a semi-circle in the impedance plane, obtaining the Cole parameters in an indirect and sequential manner has several drawbacks. Applying a Non-Linear Least Square (NLLS iterative fitting on the spectroscopy measurement, obtains the Cole parameters considering the frequency information contained in the measurement. In this work, from experimental total right side EBIS measurements, the BCA parameters have been obtained to assess the amount and distribution of whole body fluids. The values for the BCA parameters have been obtained using values for the Cole parameters estimated with both approaches: circular fitting on the impedance plane and NLLS impedance-only fitting. The comparison of the values obtained for the BCA parameters with both methods confirms that the NLLS impedance-only is an effective alternative as Cole parameter estimation method in BCA from EBIS measurements. Using the modulus of the Cole function as the model for the fitting would eliminate the need for performing a phase detection in the acquisition process, simplifying the hardware specifications of the measurement instrumentation when implementing a bioimpedance spectrometer.doi:10.5617/jeb.197 J Electr Bioimp, vol. 2, pp. 72-78, 2011

  3. The role of collaborations in sustaining an evidence-based intervention to reduce child neglect.

    Science.gov (United States)

    Green, Amy E; Trott, Elise; Willging, Cathleen E; Finn, Natalie K; Ehrhart, Mark G; Aarons, Gregory A

    2016-03-01

    Child neglect is the most prevalent form of child maltreatment and represents 79.5% of open child-welfare cases. A recent study found the evidence-based intervention (EBI) SafeCare(®) (SC) to significantly reduce child neglect recidivism rates. To fully capitalize on the effectiveness of such EBIs, service systems must engage in successful implementation and sustainment; however, little is known regarding what factors influence EBI sustainment. Collaborations among stakeholders are suggested as a means for facilitating EBI implementation and sustainment. This study combines descriptive quantitative survey data with qualitative interview and focus group findings to examine the role of collaboration within the context of public-private partnerships in 11 child welfare systems implementing SC. Participants included administrators of government child welfare systems and community-based organizations, as well as supervisors, coaches, and home visitors of the SC program. Sites were classified as fully-, partially-, and non-sustaining based on implementation fidelity. One-way analysis of variance was used to examine differences in stakeholder reported Effective Collaboration scores across fully-sustaining, partially-sustaining, and non-sustaining sites. Qualitative transcripts were analyzed via open and focused coding to identify the commonality, diversity, and complexity of collaborations involved in implementing and sustaining SC. Fully-sustaining sites reported significantly greater levels of effective collaboration than non-sustaining sites. Key themes described by SC stakeholders included shared vision, building on existing relationships, academic support, problem solving and resource sharing, and maintaining collaborations over time. Both quantitative and qualitative results converge in highlighting the importance of effective collaboration in EBI sustainment in child welfare service systems.

  4. Rhea--a manually curated resource of biochemical reactions.

    Science.gov (United States)

    Alcántara, Rafael; Axelsen, Kristian B; Morgat, Anne; Belda, Eugeni; Coudert, Elisabeth; Bridge, Alan; Cao, Hong; de Matos, Paula; Ennis, Marcus; Turner, Steve; Owen, Gareth; Bougueleret, Lydie; Xenarios, Ioannis; Steinbeck, Christoph

    2012-01-01

    Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models.

  5. IL-35: a potential target for the treatment of atherosclerosis.

    Science.gov (United States)

    Huang, Ying; Lin, Ying-Zhong; Shi, Ying; Ji, Qing-Wei

    2013-10-01

    The imbalance of anti- inflammatory/pro-inflammatory cytokines plays an important role in the process of atherosclerosis. IL-35 is an anti-inflammatory cytokine comprising the p35 subunit of IL-12 and the subunit Epstein-Barr virus (EBV) -induced gene 3(EBI3). Accumulating evidence showed that IL-35 up-regulates the expression of anti-inflammatory cytokines, induces the generation of CD4 + regulatory T cells, inhibits CD4 + effector T cells response and other target cells activity, and reduces the progression of inflammatory and autoimmune diseases. In addition, it has been found that Ebi3 and p35 strongly coexpressed in human advanced lesions. Therefore, we hypothesize that IL-35 may become a novel target for the treatment of atherosclerosis. Further studies are required to investigate the precise effect and the signaling pathway of IL-35 in atherosclerosis process.

  6. Studying the Performance of Conductive Polymer Films as Textile Electrodes for Electrical Bioimpedance Measurements

    Science.gov (United States)

    Cunico, F. J.; Marquez, J. C.; Hilke, H.; Skrifvars, M.; Seoane, F.

    2013-04-01

    With the goal of finding novel biocompatible materials suitable to replace silver in the manufacturing of textile electrodes for medical applications of electrical bioimpedance spectroscopy, three different polymeric materials have been investigated. Films have been prepared from different polymeric materials and custom bracelets have been confectioned with them. Tetrapolar total right side electrical bioimpedance spectroscopy (EBIS) measurements have been performed with polymer and with standard gel electrodes. The performance of the polymer films was compared against the performance of the gel electrodes. The results indicated that only the polypropylene 1380 could produce EBIS measurements but remarkably tainted with high frequency artefacts. The influence of the electrode mismatch, stray capacitances and large electrode polarization impedance are unclear and they need to be clarified with further studies. If sensorized garments could be made with such biocompatible polymeric materials the burden of considering textrodes class III devices could be avoided.

  7. Evaluating and optimizing horticultural regimes in space plant growth facilities

    Science.gov (United States)

    Berkovich, Y. A.; Chetirkin, P. V.; Wheeler, R. M.; Sager, J. C.

    2004-01-01

    In designing innovative space plant growth facilities (SPGF) for long duration space flight, various limitations must be addressed including onboard resources: volume, energy consumption, heat transfer and crew labor expenditure. The required accuracy in evaluating onboard resources by using the equivalent mass methodology and applying it to the design of such facilities is not precise. This is due to the uncertainty of the structure and not completely understanding the properties of all associated hardware, including the technology in these systems. We present a simple criteria of optimization for horticultural regimes in SPGF: Qmax = max [ M · (EBI) 2/( V · E · T) ], where M is the crop harvest in terms of total dry biomass in the plant growth system; EBI is the edible biomass index (harvest index), V is volume occupied by the crop; E is the crop light energy supply during growth; T is the crop growth duration. The criterion reflects directly on the consumption of onboard resources for crop production.

  8. A high-compression electron gun for C6+ production: concept, simulations and mechanical design

    Science.gov (United States)

    Mertzig, Robert; Breitenfeldt, M.; Mathot, S.; Pitters, J.; Shornikov, A.; Wenander, F.

    2017-07-01

    In this paper we report on simulations and the mechanical design of a high-compression electron gun for an Electron Beam Ion Source (EBIS) dedicated for production of high intensity and high repetition rate pulses of bare carbon ions for injection into linac-based hadron therapy facilities. The gun is presently under construction at CERN to be retrofitted into the TwinEBIS test bench for experimental studies. We describe the design constraints, show results of numeric simulations and report on the mechanical design featuring several novel ideas. The reported design makes use of combined-function units with reduced number of mechanical joints that were carefully controlled and tuned during the manufacturing phase. The simulations addressed a wide range of topics including the influence of thermal effects, focusing optics, symmetry-breaking misalignments and injection into a full 5 T field.

  9. CrossRef Optimizing charge breeding techniques for ISOL facilities in Europe: Conclusions from the EMILIE project

    CERN Document Server

    Delahaye, P; Angot, J; Cam, J F; Traykov, E; Ban, G; Celona, L; Choinski, J; Gmaj, P; Jardin, P; Koivisto, H; Kolhinen, V; Lamy, T; Maunoury, L; Patti, G; Thuillier, T; Tarvainen, O; Vondrasek, R; Wenander, F

    2016-01-01

    The present paper summarizes the results obtained from the past few years in the framework of the Enhanced Multi-Ionization of short-Lived Isotopes for Eurisol (EMILIE) project. The EMILIE project aims at improving the charge breeding techniques with both Electron Cyclotron Resonance Ion Sources (ECRIS) and Electron Beam Ion Sources (EBISs) for European Radioactive Ion Beam (RIB) facilities. Within EMILIE, an original technique for debunching the beam from EBIS charge breeders is being developed, for making an optimal use of the capabilities of CW post-accelerators of the future facilities. Such a debunching technique should eventually resolve duty cycle and time structure issues which presently complicate the data-acquisition of experiments. The results of the first tests of this technique are reported here. In comparison with charge breeding with an EBIS, the ECRIS technique had lower performance in efficiency and attainable charge state for metallic ion beams and also suffered from issues related to beam c...

  10. Performance on the low charge state laser ion source in BNL

    Energy Technology Data Exchange (ETDEWEB)

    Okamura, M.; Alessi, J.; Beebe, E.; Costanzo, M.; DeSanto, L.; Jamilkowski, J.; Kanesue, T.; Lambiase, R.; Lehn, D.; Liaw, C. J.; McCafferty, D.; Morris, J.; Olsen, R.; Pikin, A.; Raparia, D.; Steszyn, A.; Ikeda, S.

    2015-09-07

    On March 2014, a Laser Ion Source (LIS) was commissioned which delivers high-brightness, low-charge-state heavy ions for the hadron accelerator complex in Brookhaven National Laboratory (BNL). Since then, the LIS has provided many heavy ion species successfully. The low-charge-state (mostly singly charged) beams are injected to the Electron Beam Ion Source (EBIS), where ions are then highly ionized to fit to the following accelerator’s Q/M acceptance, like Au32+. Recently we upgraded the LIS to be able to provide two different beams into EBIS on a pulse-to-pulse basis. Now the LIS is simultaneously providing beams for both the Relativistic Heavy Ion Collider (RHIC) and NASA Space Radiation Laboratory (NSRL).

  11. A parametric framework for modelling of bioelectrical signals

    CERN Document Server

    Mughal, Yar Muhammad

    2016-01-01

    This book examines non-invasive, electrical-based methods for disease diagnosis and assessment of heart function. In particular, a formalized signal model is proposed since this offers several advantages over methods that rely on measured data alone. By using a formalized representation, the parameters of the signal model can be easily manipulated and/or modified, thus providing mechanisms that allow researchers to reproduce and control such signals. In addition, having such a formalized signal model makes it possible to develop computer tools that can be used for manipulating and understanding how signal changes result from various heart conditions, as well as for generating input signals for experimenting with and evaluating the performance of e.g. signal extraction methods. The work focuses on bioelectrical information, particularly electrical bio-impedance (EBI). Once the EBI has been measured, the corresponding signals have to be modelled for analysis. This requires a structured approach in order to move...

  12. Design study of primary ion provider for relativistic heavy ion collider electron beam ion source.

    Science.gov (United States)

    Kondo, K; Kanesue, T; Tamura, J; Okamura, M

    2010-02-01

    Brookhaven National Laboratory has developed the new preinjector system, electron beam ion source (EBIS) for relativistic heavy ion collider (RHIC) and National Aeronautics and Space Administration Space Radiation Laboratory. Design of primary ion provider is an essential problem since it is required to supply beams with different ion species to multiple users simultaneously. The laser ion source with a defocused laser can provide a low charge state and low emittance ion beam, and is a candidate for the primary ion source for RHIC-EBIS. We show a suitable design with appropriate drift length and solenoid, which helps to keep sufficient total charge number with longer pulse length. The whole design of primary ion source, as well as optics arrangement, solid targets configuration and heating about target, is presented.

  13. Teaching Fluid Mechanics for Undergraduate Students in Applied Industrial Biology: from Theory to Atypical Experiments

    CERN Document Server

    Absi, Rafik; Dufour, Florence; Huet, Denis; Bennacer, Rachid; Absi, Tahar

    2011-01-01

    EBI is a further education establishment which provides education in applied industrial biology at level of MSc engineering degree. Fluid mechanics at EBI was considered by students as difficult who seemed somewhat unmotivated. In order to motivate them, we applied a new play-based pedagogy. Students were asked to draw inspiration from everyday life situations to find applications of fluid mechanics and to do experiments to verify and validate some theoretical results obtained in course. In this paper, we present an innovative teaching/learning pedagogy which includes the concept of learning through play and its implications in fluid mechanics for engineering. Examples of atypical experiments in fluid mechanics made by students are presented. Based on teaching evaluation by students, it is possible to know how students feel the course. The effectiveness of this approach to motivate students is presented through an analysis of students' teaching assessment. Learning through play proved a great success in fluid...

  14. Early brain injury and subarachnoid hemorrhage: Where are we at present?

    Directory of Open Access Journals (Sweden)

    Tumul Chowdhury

    2013-01-01

    Full Text Available The current era has adopted many new innovations in nearly every aspect of management of subarachnoid hemorrhage (SAH; however, the neurological outcome has still not changed significantly. These major therapeutic advances mainly addressed the two most important sequels of the SAH-vasospasm and re-bleed. Thus, there is a possibility of some different pathophysiological mechanism that would be responsible for causing poor outcome in these patients. In this article, we have tried to compile the current role of this different yet potentially treatable pathophysiological mechanism in post-SAH patients. The main pathophysiological mechanism for the development of early brain injury (EBI is the apoptotic pathways. The macro-mechanism includes increased intracranial pressure, disruption of the blood-brain barrier, and finally global ischemia. Most of the treatment strategies are still in the experimental phase. Although the role of EBI following SAH is now well established, the treatment modalities for human patients are yet to be testified.

  15. ChEMBL web services: streamlining access to drug discovery data and utilities.

    Science.gov (United States)

    Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P

    2015-07-01

    ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology.

  16. Status of the REX-ISOLDE project

    CERN Document Server

    Von Hahn, R; Podlech, H; Repnow, R; Schwalm, D; Bongers, H; Habs, D; Kester, O; Sieber, T; Rudolph, K; Thirolf, P G; Schempp, A; Smes, F; Bollen, G; Deloose, I; Ratzinger, U; Liljeby, L; Rensfelt, K G; Wenander, F; Van Duppen, P; Walter, G; Richter, A; Ostrowski, A N; Schotter, A; MacKay, W W

    1999-01-01

    The radioactive beam experiment REX-ISOLDE, a pilot experiment testing a new concept of post acceleration of radioactive ions at ISOLDE/CERN is in progress. Singly charged radioactive ions delivered by the online mass separator ISOLDE are accumulated in a Penning trap (REX trap), charge bred in an electron beam ion source (EBIS), separated from the residual gas in a mass separator and then accelerated in a linac with output energies between 0.8 and 2.2 MeV /u. The REX trap is in operation, a first test beam was already injected. The design phase of the EBIS is finished and the construction has been started. The superconducting magnet is delivered. The linac consists of a radiofrequency quadrupole (RFQ) accelerator, an interdigital IH-structure and 3 seven gap resonators to vary the final energy. (12 refs).

  17. Design study of an upgraded charge breeder for ISOLDE

    CERN Document Server

    Shornikov, A; Wenander, F; Pikin, A

    2013-01-01

    In this work we present our progress in the design study of a new Electron Beam Ion Source (EBIS) to be installed as a charge breeder for reacceleration of rare ions at ISOLDE. The work is triggered by the HIE-ISOLDE upgrade {[}1] and the planned TSR@ISOLDE project {[}2]. To fulfill the requests of the user community the new EBIS should reach an electron beam density of 10(4) A/cm(2) at electron energies up to 150 key and, provide UHV environment and ion cooling in the breeding region to ensure confinement of the ions long enough to reach the requested charge states. We report on the established design parameters and first prototyping steps towards production and testing of suitable equipment. (C) 2013 Elsevier B.V. All rights reserved.

  18. Validation and comparison of two computerized methods of obtaining a diet history.

    Science.gov (United States)

    Landig, J; Erhardt, J G; Bode, J C; Bode, C

    1998-06-01

    The aim of this study was to validate two computerized methods of obtaining a diet history (DH and EBIS). The food consumption of 12 men and eight women was calculated by weighing each food item over a period of 8 days. Thereafter the diet history was taken over this period by using both programs alternatively. The intake of energy, protein, fat and carbohydrates, and 10 further nutrients was evaluated and the percentage difference calculated. In general, the intake of nutrients calculated from the diet history tended to be underestimated by most of the people interviewed. The mean daily intake of the nutrients calculated from the DH program deviates from -34% to +20% (mean SD = 48.1) and -35% to +15% for EBIS (mean SD = 28.1). In conclusion, both computerized methods proved useful for epidemiological studies, but not for the determination of deficiencies in individuals.

  19. Hydrogen Sulfide Ameliorates Early Brain Injury Following Subarachnoid Hemorrhage in Rats.

    Science.gov (United States)

    Cui, Yonghua; Duan, Xiaochun; Li, Haiying; Dang, Baoqi; Yin, Jia; Wang, Yang; Gao, Anju; Yu, Zhengquan; Chen, Gang

    2016-08-01

    Increasing studies have demonstrated the neuroprotective effect of hydrogen sulfide (H2S) in central nervous system (CNS) diseases. However, the potential application value of H2S in the therapy of subarachnoid hemorrhage (SAH) is still not well known. This study was to investigate the potential effect of H2S on early brain injury (EBI) induced by SAH and explore the underlying mechanisms. The role of sodium hydrosulfide (NaHS), a donor of H2S, in SAH-induced EBI, was investigated in both in vivo and in vitro. A prechiasmatic cistern single injection model was used to produce experimental SAH in vivo. In vitro, cultured primary rat cortical neurons and human umbilical vein endothelial cells (HUVECs) were exposed to OxyHb at concentration of 10 μM to mimic SAH. Endogenous production of H2S in the brain was significantly inhibited by SAH. The protein levels of the predominant H2S-generating enzymes in the brain, including cystathionineb-synthase (CBS) and 3-mercaptopyruvate sulfur transferase (3MST), were also correspondingly reduced by SAH, while treatment with NaHS restored H2S production and the expressions of CBS and 3MST. More importantly, NaHS treatment could significantly attenuate EBI (including brain edema, blood-brain barrier disruption, brain cell apoptosis, inflammatory response, and cerebral vasospasm) after SAH. In vitro, H2S protects neurons and endothelial function by functioning as an antioxidant and antiapoptotic mediator. Our results suggest that NaSH as an exogenous H2S donor could significantly reduce EBI induced by SAH.

  20. Generalizations of Steffensen’s inequality via some Euler-type identities

    Directory of Open Access Journals (Sweden)

    Pečarić Josip

    2016-08-01

    Full Text Available Using Euler-type identities some new generalizations of Steffensen’s inequality for n–convex functions are obtained. Moreover, the Ostrowski-type inequalities related to obtained generalizations are given. Furthermore, using inequalities for the Čebyšev functional in terms of the first derivative some new bounds for the remainder in identities related to generalizations of Steffensen’s inequality are proven.

  1. Adult Pacific Lamprey Migration in the Lower Columbia River: 2011 Half-Duplex Pit Tag Studies

    Science.gov (United States)

    2012-01-01

    Kasey Welch, Miro Zyndol, Robert Cordie , Brad Eby, and Mark Plummer. iv Table of Contents Executive Summary...reaches upstream from Bonneville Dam included one reservoir and one dam. Median migration rates ranged from 5-18 km●d-1 in reservoir- plus -dam reaches...River radiotelemetry studies, tributary 26 detection has occurred primarily at the Deschutes, Klickitat, and John Day rivers plus Fifteenmile

  2. Scan direction induced charging dynamics and the application for detection of gate to S/D shorts in logic devices

    Science.gov (United States)

    Lei, Ming; Tian, Qing; Wu, Kevin; Zhao, Yan

    2016-03-01

    Gate to source/drain (S/D) short is the most common and detrimental failure mechanism for advanced process technology development in Metal-Oxide-Semiconductor-Field-Effect-Transistor (MOSFET) device manufacturing. Especially for sub-1Xnm nodes, MOSFET device is more vulnerable to gate-S/D shorts due to the aggressive scaling. The detection of this kind of electrical short defect is always challenging for in-line electron beam inspection (EBI), especially new shorting mechanisms on atomic scale due to new material/process flow implementation. The second challenge comes from the characterization of the shorts including identification of the exact shorting location. In this paper, we demonstrate unique scan direction induced charging dynamics (SDCD) phenomenon which stems from the transistor level response from EBI scan at post metal contact chemical-mechanical planarization (CMP) layers. We found that SDCD effect is exceptionally useful for gate-S/D short induced voltage contrast (VC) defect detection, especially for identification of shorting locations. The unique SDCD effect signatures of gate-S/D shorts can be used as fingerprint for ground true shorting defect detection. Correlation with other characterization methods on the same defective location from EBI scan shows consistent results from various shorting mechanism. A practical work flow to implement the application of SDCD effect for in-line EBI monitor of critical gate-S/D short defects is also proposed, together with examples of successful application use cases which mostly focus on static random-access memory (SRAM) array regions. Although the capability of gate-S/D short detection as well as expected device response is limited to passing transistors and pull-down transistors due to the design restriction from standard 6-cell SRAM structure, SDCD effect is proven to be very effective for gate-S/D short induced VC defect detection as well as yield learning for advanced technology development.

  3. Fusion Analytics: A Data Integration System for Public Health and Medical Disaster Response Decision Support

    OpenAIRE

    2013-01-01

    Objective The objective of this demonstration is to show conference attendees how they can integrate, analyze, and visualize diverse data type data from across a variety of systems by leveraging an off-the-shelf enterprise business intelligence (EBI) solution to support decision-making in disasters. Introduction Fusion Analytics is the data integration system developed by the Fusion Cell at the U.S. Department of Health and Human Services (HHS), Office of the Assistant Secretary for Preparedn...

  4. Physiological and Growth Characteristics of Shewanella Species

    Science.gov (United States)

    2016-05-01

    282–287. 29. Dawood B. 1998. Corrosion-enhancing potential of Shewanella putrefaciens isolated from industrial cooling waters. J Appl Microbiol. 84...AFCEC-CX-TY-TR-2016-0016 PHYSIOLOGICAL AND GROWTH CHARACTERISTICS OF SHEWANELLA SPECIES Karen Farrington, D. Matthew Eby, Susan Sizemore...Technical Report 01 March 2012 - 01 March 2014 Physiological and growth characteristics of Shewanella species FA4819-11-C-0003 Karen Farrington (1

  5. The student experience of applied equivalence-based instruction for neuroanatomy teaching

    Science.gov (United States)

    2016-01-01

    Purpose Esoteric jargon and technical language are potential barriers to the teaching of science and medicine. Effective teaching strategies which address these barriers are desirable. Here, we created and evaluated the effectiveness of stand-alone ‘equivalence-based instruction’ (EBI) learning resources wherein the teaching of a small number of direct relationships between stimuli (e.g., anatomical regions, their function, and pathology) results in the learning of higher numbers of untaught relationships. Methods We used a pre and post test design to assess students’ learning of the relations. Resources were evaluated by students for perceived usefulness and confidence in the topic. Three versions of the resources were designed, to explore learning parameters such as the number of stimulus classes and the number of relationships within these classes. Results We show that use of EBI resulted in demonstrable learning of material that had not been directly taught. The resources were well received by students, even when the quantity of material to be learned was high. There was a strong desire for more EBI-based teaching. The findings are discussed in the context of an ongoing debate surrounding ‘rote’ vs. ‘deep’ learning, and the need to balance this debate with considerations of cognitive load and esoteric jargon routinely encountered during the study of medicine. Conclusion These standalone EBI resources were an effective, efficient and well-received method for teaching neuroanatomy to medical students. The approach may be of benefit to other subjects with abundant technical jargon, science and other areas of medicine. PMID:27649900

  6. Human tolerogenic dendritic cells produce IL-35 in the absence of other IL-12 family members.

    Science.gov (United States)

    Dixon, Karen O; van der Kooij, Sandra W; Vignali, Dario A A; van Kooten, Cees

    2015-06-01

    IL-35 is a cytokine of the IL-12 family, existing as a heterodimer of IL-12p35 and Ebi3. IL-35 has anti-inflammatory properties and is produced by regulatory T cells in humans and mice, where it is required for optimal suppression of immune responses. Distinct from other IL-12 cytokines, the expression of IL-35 has not been described in antigen-presenting cells. In view of the immune-regulatory properties of IL-35, we investigated the expression, regulation, and function of IL-12p35 and Ebi3 in human monocyte-derived dendritic cells and tolerogenic DCs (tolDCs). These tolDCs do not produce IL-12p70 or the homodimer IL-12p40. We demonstrate that tolDCs completely lack transcriptional expression of IL-12p40. However, tolDCs maintain mRNA expression of IL-12p35 and Ebi3. Using intracellular flow cytometry and Western blot analysis, we show that tolDCs produce Ebi3 and IL-12p35, and both can be enhanced upon stimulation with IFN-γ, LPS, or CD40L. tolDCs supernatants have the capacity to suppress T-cell activation. Using IL12A silencing, we demonstrate that IL-12p35 is required for tolDCs to reach their full suppressive potential. Taken together, our results indicate that tolDCs produce IL-35, providing an additional novel mechanism by which tolDCs elicit their tolerogenic potential.

  7. Circulating low IL-23: IL-35 cytokine ratio promotes progression associated with poor prognosisin breast cancer.

    Science.gov (United States)

    Chen, Guanghui; Liang, Yanfang; Guan, Xin; Chen, Hui; Liu, Qiankun; Lin, Bihua; Chen, Can; Huang, Mingyuan; Chen, Jianan; Wu, Weiquan; Liang, Yi; Zhou, Keyuan; Zeng, Jincheng

    2016-01-01

    The interleukin (IL)-12 family, composed of heterodimeric cytokines including IL-12 (formed by IL-12p35 and IL-12p40 subunits), IL-23 (formed by IL-23p19 and IL-12p40 subunits), IL-27 (formed by IL-27p28 and EBI3 subunits) and IL-35 (formed by IL-12p35 and EBI3 subunits), establishes a link between innate and adaptive immunity that involves different immune effector cells and cytokines to tumors. However, the role of IL-12 family in breast cancer (BC) progression and prognosis remains unclear. In the present study, we demonstrated evidence indicating that EBI3, IL-12p35 and IL-12p40 but not IL-23p19 or IL-27p28 were highly expressed in BC tissues, suggested that tumor derived EBI3, IL-12p35 and IL-12p40 were associated with tumor progression. Circulating IL-12 and IL-23 low expressed, but IL-27 and IL-35 high expressed in BC patients, especially circulating IL-23 associated with IL-35 to mediate BC tumor resection. Ki-67, p53 and EGFR expression on BC tissues, as well as CA125, CA153 and CA199 levels on BC bloods increased when circulating IL-23: IL-35 ratio decreased. Together, for the first time, our data suggest that circulating IL-23: IL-35 ratio may be an important indicator association with BC progression and prognosis. However, further research should be carried out to assess the implications of circulating IL-23: IL-35 ratio in a larger sample size.

  8. Oral Escherichia coli colonization factor antigen I fimbriae ameliorate arthritis via IL-35, not IL-27.

    Science.gov (United States)

    Kochetkova, Irina; Thornburg, Theresa; Callis, Gayle; Holderness, Kathryn; Maddaloni, Massimo; Pascual, David W

    2014-01-15

    A Salmonella therapeutic expressing enterotoxigenic Escherichia coli colonization factor Ag I (CFA/I) fimbriae protects against collagen-induced arthritis (CIA) by eliciting two regulatory T cell (Treg) subsets: TGF-β-producing Foxp3(-)CD39(+)CD4(+) T cells and IL-10-producing Foxp3(+)CD39(+)CD4(+) T cells. However, it is unclear whether CFA/I fimbriae alone are protective and whether other regulatory cytokines are involved, especially in the context for the EBI3-sharing cytokines, Treg-derived IL-35 and APC-derived IL-27, both capable of suppressing Th17 cells and regulating autoimmune diseases. Subsequent evaluation revealed that a single oral dose of purified, soluble CFA/I fimbriae protected against CIA as effectively as did Salmonella-CFA/I and found that Foxp3(+)CD39(+)CD4(+) T cells were the source of secreted IL-35, whereas IL-27 production by CD11c(+) cells was inhibited. Inquiring into their relevance, CFA/I fimbriae-treated IL-27R-deficient (WSX-1(-/-)) mice were equally protected against CIA as were wild-type mice, suggesting a limited role for IL-27. In contrast, CFA/I fimbriae-mediated protection was abated in EBI3(-/-) mice, accompanied by the loss of TGF-β- and IL-10-producing Tregs. Adoptive transfer of C57BL/6 CD39(+)CD4(+) T cells to EBI3(-/-) mice with concurrent CFA/I plus IL-35 treatment effectively stimulated Tregs suppressing proinflammatory collagen II-specific Th cells. In contrast, recipients cotransferred with C57BL/6 and EBI3(-/-) CD39(+)CD4(+) T cells and treated with CFA/I plus IL-35 were not protected, implicating the importance of endogenous IL-35 for conferring CFA/I-mediated protection. Thus, CFA/I fimbriae stimulate IL-35 required for the coinduction of TGF-β and IL-10.

  9. Production of High-Intensity, Highly Charged Ions

    OpenAIRE

    S. GamminoINFN, LNS, Catania

    2014-01-01

    In the past three decades, the development of nuclear physics facilities for fundamental and applied science purposes has required an increasing current of multicharged ion beams. Multiple ionization implies the formation of dense and energetic plasmas, which, in turn, requires specific plasma trapping configurations. Two types of ion source have been able to produce very high charge states in a reliable and reproducible way: electron beam ion sources (EBIS) and electron cyc...

  10. European Bioinformatics Institute: Research Infrastructure needed for Life Science

    CERN Document Server

    CERN. Geneva

    2015-01-01

    The life science community is an ever increasing source of data from increasing diverse range of instruments and sources. EMBL-EBI has a remit to store and exploit this data, collected and made available openly across the world, for the benefit of the whole research community. The research infrastructure needed to support the big data analysis around this mission encompasses high performance networks, high-throughput computing, and a range of cloud and storage solutions - and will be described in the presentation.

  11. The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.

    Science.gov (United States)

    Petryszak, Robert; Fonseca, Nuno A; Füllgrabe, Anja; Huerta, Laura; Keays, Maria; Tang, Y Amy; Brazma, Alvis

    2017-07-15

    The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api . The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library . rnaseq@ebi.ac.uk ; rpetry@ebi.ac.uk. Supplementary data are available at Bioinformatics online.

  12. From Peptidome to PRIDE: Public proteomics data migration at a large scale

    OpenAIRE

    Csordas, Attila; Wang, Rui; Ríos, Daniel; Ríos, Daniel; Reisinger, Florian; Foster, Joseph M; Slotta, Douglas J.; Vizcaíno, Juan Antonio; Vizcaíno, Juan Antonio; Hermjakob, Henning

    2013-01-01

    The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not “lost” to the wider...

  13. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

    OpenAIRE

    Vizcaino, J. A.; Cote, R. G.; Csordas, A.; Dianes, J. A.; Fabregat, A; Foster, J. M.; Griss, J.; Alpi, E.; Birim, M.; Contell, J.; O'Kelly, G.; O'Kelly, G.; Schoenegger, A.; Ovelleiro, D.; Perez-Riverol, Y.

    2013-01-01

    The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We t...

  14. Clinical practice guideline dissemination and a new approach using Haddon matrix as a conceptual framework of evidence-based implementation strategies.

    Science.gov (United States)

    Pang, Peter

    2010-01-01

    To err is human. Clinical practice guidelines (CPGs) are often not followed and lead to adverse outcomes. The issue on implementation of CPG is complex. A review of CPG implementation is done to identify the barriers and enablers. For the first time, a fishbone diagram is used to delineate the root-causes. And Haddon matrix is applied to help understand the complexity of evidence-based implementation (EBI) strategies.

  15. The student experience of applied equivalence-based instruction for neuroanatomy teaching

    Directory of Open Access Journals (Sweden)

    W. James Greville

    2016-09-01

    Full Text Available Purpose Esoteric jargon and technical language are potential barriers to the teaching of science and medicine. Effective teaching strategies which address these barriers are desirable. Here, we created and evaluated the effectiveness of stand-alone ‘equivalence-based instruction’ (EBI learning resources wherein the teaching of a small number of direct relationships between stimuli (e.g., anatomical regions, their function, and pathology results in the learning of higher numbers of untaught relationships. Methods We used a pre and post test design to assess students’ learning of the relations. Resources were evaluated by students for perceived usefulness and confidence in the topic. Three versions of the resources were designed, to explore learning parameters such as the number of stimulus classes and the number of relationships within these classes. Results We show that use of EBI resulted in demonstrable learning of material that had not been directly taught. The resources were well received by students, even when the quantity of material to be learned was high. There was a strong desire for more EBI-based teaching. The findings are discussed in the context of an ongoing debate surrounding ‘rote’ vs. ‘deep’ learning, and the need to balance this debate with considerations of cognitive load and esoteric jargon routinely encountered during the study of medicine. Conclusion These standalone EBI resources were an effective, efficient and well-received method for teaching neuroanatomy to medical students. The approach may be of benefit to other subjects with abundant technical jargon, science and other areas of medicine.

  16. Lysozyme Catalyzes the Formation of Antimicrobial Silver Nanoparticles

    Science.gov (United States)

    2009-04-03

    biomineralization A RT IC LE VOL. 3 ▪ NO. 4 ▪ EBY ET AL. www.acsnano.org984 part of the innate immune system in higher organisms and primarily acts...cationic and am- phiphilic protein that will adsorb to ionic and hydro- phobic surfaces, including metal surfaces.2124 After synthesis in methanol...This result is significant, as the strong ionic interactions be- tween metal nanoparticles normally make it difficult to achieve high concentrations of

  17. Resveratrol Attenuates Acute Inflammatory Injury in Experimental Subarachnoid Hemorrhage in Rats via Inhibition of TLR4 Pathway.

    Science.gov (United States)

    Zhang, Xiang-Sheng; Li, Wei; Wu, Qi; Wu, Ling-Yun; Ye, Zhen-Nan; Liu, Jing-Peng; Zhuang, Zong; Zhou, Meng-Liang; Zhang, Xin; Hang, Chun-Hua

    2016-08-12

    Toll-like receptor 4 (TLR4) has been proven to play a critical role in neuroinflammation and to represent an important therapeutic target following subarachnoid hemorrhage (SAH). Resveratrol (RSV), a natural occurring polyphenolic compound, has a powerful anti-inflammatory property. However, the underlying molecular mechanisms of RSV in protecting against early brain injury (EBI) after SAH remain obscure. The purpose of this study was to investigate the effects of RSV on the TLR4-related inflammatory signaling pathway and EBI in rats after SAH. A prechiasmatic cistern SAH model was used in our experiment. The expressions of TLR4, high-mobility group box 1 (HMGB1), myeloid differentiation factor 88 (MyD88), and nuclear factor-κB (NF-κB) were evaluated by Western blot and immunohistochemistry. The expressions of Iba-1 and pro-inflammatory cytokines in brain cortex were determined by Western blot, immunofluorescence staining, or enzyme-linked immunosorbent assay. Neural apoptosis, brain edema, and neurological function were further evaluated to investigate the development of EBI. We found that post-SAH treatment with RSV could markedly inhibit the expressions of TLR4, HMGB1, MyD88, and NF-κB. Meanwhile, RSV significantly reduced microglia activation, as well as inflammatory cytokines leading to the amelioration of neural apoptosis, brain edema, and neurological behavior impairment at 24 h after SAH. However, RSV treatment failed to alleviate brain edema and neurological deficits at 72 h after SAH. These results indicated that RSV treatment could alleviate EBI after SAH, at least in part, via inhibition of TLR4-mediated inflammatory signaling pathway.

  18. Tert-butylhydroquinone alleviates early brain injury and cognitive dysfunction after experimental subarachnoid hemorrhage: role of Keap1/Nrf2/ARE pathway.

    Directory of Open Access Journals (Sweden)

    Zhong Wang

    Full Text Available Tert-butylhydroquinone (tBHQ, an Nrf2 activator, has demonstrated neuroprotection against brain trauma and ischemic stroke in vivo. However, little work has been done with respect to its effect on early brain injury (EBI after subarachnoid hemorrhage (SAH. At the same time, as an oral medication, it may have extensive clinical applications for the treatment of SAH-induced cognitive dysfunction. This study was undertaken to evaluate the influence of tBHQ on EBI, secondary deficits of learning and memory, and the Keap1/Nrf2/ARE pathway in a rat SAH model. SD rats were divided into four groups: (1 Control group (n=40; (2 SAH group (n=40; (3 SAH+vehicle group (n=40; and (4 SAH+tBHQ group (n=40. All SAH animals were subjected to injection of autologous blood into the prechiasmatic cistern once in 20 s. In SAH+tBHQ group, tBHQ was administered via oral gavage at a dose of 12.5 mg/kg at 2 h, 12 h, 24 h, and 36 h after SAH. In the first set of experiments, brain samples were extracted and evaluated 48 h after SAH. In the second set of experiments, changes in cognition and memory were investigated in a Morris water maze. Results shows that administration of tBHQ after SAH significantly ameliorated EBI-related problems, such as brain edema, blood-brain barrier (BBB impairment, clinical behavior deficits, cortical apoptosis, and neurodegeneration. Learning deficits induced by SAH was markedly alleviated after tBHQ therapy. Treatment with tBHQ markedly up-regulated the expression of Keap1, Nrf2, HO-1, NQO1, and GSTα1 after SAH. In conclusion, the administration of tBHQ abated the development of EBI and cognitive dysfunction in this SAH model. Its action was probably mediated by activation of the Keap1/Nrf2/ARE pathway.

  19. Workflows for fluxomics in the framework of PhenoMeNal project

    OpenAIRE

    2016-01-01

    In the framework of the PhenoMeNal project and e-infrastructures (www.phenomenal-h2020.eu/home/), two workflows were prepared using previously developed programs for analysis of intracellular fluxes from isotopologue distributions. Isotopologue distributions will be available on data repositories in MetaboLights (www.ebi.ac.uk/metabolights). With this aim, programs were adapted to the workflows, docker container dockerfiles for each program were uploaded to GitHub repositories, added to Jenki...

  20. Oral Escherichia coli Colonization Factor Antigen I (CFA/I) Fimbriae Ameliorate Arthritis via IL-35, not IL-27

    Science.gov (United States)

    Kochetkova, Irina; Thornburg, Theresa; Callis, Gayle; Holderness, Kathryn; Maddaloni, Massimo; Pascual, David W.

    2014-01-01

    A Salmonella therapeutic expressing enterotoxigenic E. coli colonization factor antigen I (CFA/I) fimbriae protects against collagen-induced arthritis (CIA) by eliciting two regulatory T cell (Treg) subsets: TGF-β-producing Foxp3−CD39+CD4+ and IL-10-producing Foxp3+CD39+CD4+ T cells. However, it is unclear if CFA/I fimbriae alone are protective, and if other regulatory cytokines are involved especially in the context for the EBI3-sharing cytokines, Treg-derived IL-35 and APC-derived IL-27, both capable of suppressing Th17 cells and regulating autoimmune diseases. Subsequent evaluation revealed that a single oral dose of purified, soluble CFA/I fimbriae protected against CIA as effectively as Salmonella-CFA/I, and found Foxp3+CD39+CD4+ T cells as the source of secreted IL-35, whereas IL-27 production by CD11c+ cells was inhibited. Inquiring into their relevance, CFA/I fimbriae-treated IL-27 receptor-deficient (WSX-1−/−) mice were equally protected against CIA as wild-type mice suggesting a limited role for IL-27. In contrast, CFA/I fimbriae-mediated protection was abated in EBI3−/− mice accompanied by the loss of TGF-β- and IL-10-producing Tregs. Adoptive transfer of B6 CD39+CD4+ T cells to EBI3−/− mice with concurrent CFA/I plus IL-35 treatment effectively stimulated Tregs suppressing proinflammatory CII-specific Th cells. Opposingly, recipients co-transferred with B6 and EBI3−/− CD39+CD4+ T cells and treated with CFA/I plus IL-35 failed in protecting mice implicating the importance for endogenous IL-35 to confer CFA/I-mediated protection. Thus, CFA/I fimbriae stimulate IL-35 required for the co-induction of TGF-β and IL-10. PMID:24337375

  1. Clinical practice guideline dissemination and a new approach using Haddon matrix as a conceptual framework of evidence-based implementation strategies

    Science.gov (United States)

    Pang, Peter

    2010-01-01

    To err is human. Clinical practice guidelines (CPGs) are often not followed and lead to adverse outcomes. The issue on implementation of CPG is complex. A review of CPG implementation is done to identify the barriers and enablers. For the first time, a fishbone diagram is used to delineate the root-causes. And Haddon matrix is applied to help understand the complexity of evidence-based implementation (EBI) strategies. PMID:25214934

  2. AcEST: BP920823 [AcEST

    Lifescience Database Archive (English)

    Full Text Available |B7XKX3|B7XKX3_9MICR HrpE OS=Enterocytozoon bieneusi H348 GN=E... 33 9.2 >tr|B5MGQ7|B5MGQ7_CARAU Alkaline ph...ARLADRYRL 283 >tr|B7XKX3|B7XKX3_9MICR HrpE OS=Enterocytozoon bieneusi H348 GN=EBI

  3. Fisetin alleviates early brain injury following experimental subarachnoid hemorrhage in rats possibly by suppressing TLR 4/NF-κB signaling pathway.

    Science.gov (United States)

    Zhou, Chen-hui; Wang, Chun-xi; Xie, Guang-bin; Wu, Ling-yun; Wei, Yong-xiang; Wang, Qiang; Zhang, Hua-sheng; Hang, Chun-hua; Zhou, Meng-liang; Shi, Ji-xin

    2015-12-10

    Early brain injury (EBI) determines the unfavorable outcomes after subarachnoid hemorrhage (SAH). Fisetin, a natural flavonoid, has anti-inflammatory and neuroprotection properties in several brain injury models, but the role of fisetin on EBI following SAH remains unknown. Our study aimed to explore the effects of fisetin on EBI after SAH in rats. Adult male Sprague-Dawley rats were randomly divided into the sham and SAH groups, fisetin (25mg/kg or 50mg/kg) or equal volume of vehicle was given at 30min after SAH. Neurological scores and brain edema were assayed. The protein expression of toll-like receptor 4 (TLR 4), p65, ZO-1 and bcl-2 was examined by Western blot. TLR 4 and p65 were also assessed by immunohistochemistry (IHC). Enzyme-linked immunosorbent assay (ELISA) was performed to detect the production of pro-inflammatory cytokines. Terminal deoxynucleotidyl transferase-mediated uridine 5'-triphosphate-biotin nick end-labeling (TUNEL) was perform to assess neural cell apoptosis. High-dose (50mg/kg) fisetin significantly improved neurological function and reduced brain edema at both 24h and 72h after SAH. Remarkable reductions of TLR 4 expression and nuclear factor κB (NF-κB) translocation to nucleus were detected after fisetin treatment. In addition, fisetin significantly reduced the productions of pro-inflammatory cytokines, decreased neural cell apoptosis and increased the protein expression of ZO-1 and bcl-2. Our data provides the evidence for the first time that fisetin plays a protective role in EBI following SAH possibly by suppressing TLR 4/NF-κB mediated inflammatory pathway. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry

    Directory of Open Access Journals (Sweden)

    Amulya Nidhi Shrivastava

    2016-06-01

    Full Text Available α-Synuclein (α-syn is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD. This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively (doi: 10.15252/embj.201591397 [1]. α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively. For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002263 and doi: 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002263.

  5. Advancing Behavioral HIV Prevention: Adapting an Evidence-Based Intervention for People Living with HIV and Alcohol Use Disorders

    OpenAIRE

    2015-01-01

    Alcohol use disorders (AUDs) are highly prevalent among people living with HIV/AIDS (PLWHA) and are associated with increased HIV risk behaviors, suboptimal treatment adherence, and greater risk for disease progression. We used the ADAPT-ITT strategy to adapt an evidence-based intervention (EBI), the Holistic Health Recovery Program (HHRP+), that focuses on secondary HIV prevention and antiretroviral therapy (ART) adherence and apply it to PLWHA with problematic drinking. Focus groups (FGs) w...

  6. Resveratrol Attenuates Acute Inflammatory Injury in Experimental Subarachnoid Hemorrhage in Rats via Inhibition of TLR4 Pathway

    Directory of Open Access Journals (Sweden)

    Xiang-Sheng Zhang

    2016-08-01

    Full Text Available Toll-like receptor 4 (TLR4 has been proven to play a critical role in neuroinflammation and to represent an important therapeutic target following subarachnoid hemorrhage (SAH. Resveratrol (RSV, a natural occurring polyphenolic compound, has a powerful anti-inflammatory property. However, the underlying molecular mechanisms of RSV in protecting against early brain injury (EBI after SAH remain obscure. The purpose of this study was to investigate the effects of RSV on the TLR4-related inflammatory signaling pathway and EBI in rats after SAH. A prechiasmatic cistern SAH model was used in our experiment. The expressions of TLR4, high-mobility group box 1 (HMGB1, myeloid differentiation factor 88 (MyD88, and nuclear factor-κB (NF-κB were evaluated by Western blot and immunohistochemistry. The expressions of Iba-1 and pro-inflammatory cytokines in brain cortex were determined by Western blot, immunofluorescence staining, or enzyme-linked immunosorbent assay. Neural apoptosis, brain edema, and neurological function were further evaluated to investigate the development of EBI. We found that post-SAH treatment with RSV could markedly inhibit the expressions of TLR4, HMGB1, MyD88, and NF-κB. Meanwhile, RSV significantly reduced microglia activation, as well as inflammatory cytokines leading to the amelioration of neural apoptosis, brain edema, and neurological behavior impairment at 24 h after SAH. However, RSV treatment failed to alleviate brain edema and neurological deficits at 72 h after SAH. These results indicated that RSV treatment could alleviate EBI after SAH, at least in part, via inhibition of TLR4-mediated inflammatory signaling pathway.

  7. Desired attributes and skills of program managers in translation of evidence-based interventions.

    Science.gov (United States)

    Williams, Rhonda; Woodell, Carol; McCarville, Erin; Damitz, Maureen; Banks, Tinesha; Montoya, Jorge; Lesch, Julie Kennedy; Peretz, Patricia; Lara, Marielena

    2011-11-01

    Successful chronic disease project management, especially of multiyear initiatives using evidence-based interventions (EBIs), is of great importance to funders, health care decision makers, and researchers, particularly in light of limited funding. However, a gap in knowledge may exist regarding which attributes and skills are most desirable in a program manager to help him or her ensure successful implementation of EBIs. Although some literature examines the dynamics contributing to the success of community coalitions, public health leadership, and community health education, there is minimal literature exploring the significance of a program manager's role in the conceptualization, implementation, and sustainability of initiatives to improve patient and community health. The authors present their experiences as participants in a large-scale asthma initiative implemented in priority communities, as well as results of a survey distributed among all personnel of the program sites. The survey aimed to assess the key skills and attributes, in addition to contextual factors, that contribute to the strength of a program manager overseeing EBIs in asthma initiatives. The results suggest that certain attributes and skills are desirable in recruiting and hiring of a program manager, especially when augmented by ongoing skill-building training, and can help ensure program and research success.

  8. Adapting an Evidence-Based Intervention Targeting HIV-Infected Prisoners in Malaysia

    Science.gov (United States)

    Copenhaver, Michael M.; Tunku, Noor; Ezeabogu, Ifeoma; Potrepka, Jessica; Zahari, Muhammad Muhsin A.; Kamarulzaman, Adeeba; Altice, Frederick L.

    2011-01-01

    HIV-infected prisoners in Malaysia represent a critical target population for secondary HIV risk reduction interventions and care. We report on the process and outcome of our formative research aimed at systematically selecting and adapting an EBI designed to reduce secondary HIV risk and improve adherence to antiretroviral therapy among soon-to-be-released HIV-infected prisoners. Our formative work involved a critical examination of established EBIs and associated published reports complemented by data elicited through structured interviews and focus groups with key stakeholders, members of the target population, and their family members. Based on all information, we adapted the Holistic Health Recovery Program targeting people living with HIV (HHRP+), an EBI, to consist of eight 2-hour sessions that cover a range of specified topics so that participants may individually apply intervention content as needed to accommodate their particular substance abuse, HIV risk, and antiretroviral adherence issues. This study provides a complete example of the process of selecting and adapting an EBI—taking into account both empirical evidence and input from target organization stakeholders and target population members and their families—for use in real world prison settings where high-risk populations are concentrated. PMID:21860786

  9. Updates in Rhea—a manually curated resource of biochemical reactions

    Science.gov (United States)

    Morgat, Anne; Axelsen, Kristian B.; Lombardot, Thierry; Alcántara, Rafael; Aimo, Lucila; Zerara, Mohamed; Niknejad, Anne; Belda, Eugeni; Hyka-Nouspikel, Nevila; Coudert, Elisabeth; Redaschi, Nicole; Bougueleret, Lydie; Steinbeck, Christoph; Xenarios, Ioannis; Bridge, Alan

    2015-01-01

    Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models. PMID:25332395

  10. Updates in Rhea--a manually curated resource of biochemical reactions.

    Science.gov (United States)

    Morgat, Anne; Axelsen, Kristian B; Lombardot, Thierry; Alcántara, Rafael; Aimo, Lucila; Zerara, Mohamed; Niknejad, Anne; Belda, Eugeni; Hyka-Nouspikel, Nevila; Coudert, Elisabeth; Redaschi, Nicole; Bougueleret, Lydie; Steinbeck, Christoph; Xenarios, Ioannis; Bridge, Alan

    2015-01-01

    Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Nrf2/HO-1 mediates the neuroprotective effect of mangiferin on early brain injury after subarachnoid hemorrhage by attenuating mitochondria-related apoptosis and neuroinflammation.

    Science.gov (United States)

    Wang, Zefeng; Guo, Songxue; Wang, Junxing; Shen, Yuanyuan; Zhang, Jianmin; Wu, Qun

    2017-09-19

    Early brain injury (EBI) is involved in the process of cerebral tissue damage caused by subarachnoid hemorrhage (SAH), and multiple mechanisms, such as apoptosis and inflammation, participate in its development. Mangiferin (MF), a natural C-glucoside xanthone, has been reported to exert beneficial effects against several types of organ injury by influencing various biological progresses. The current study aimed to investigate the potential of MF to protect against EBI following SAH via histological and biological assessments. A rat perforation model of SAH was established, and MF was subsequently administered via intraperitoneal injection at a low and a high dose. High-dose MF significantly lowered the mortality of SAH animals and ameliorated their neurological deficits and brain edema. MF also dose-relatedly attenuated SAH-induced oxidative stress and decreased cortical cell apoptosis by influencing mitochondria-apoptotic proteins. In addition, MF downregulated the activation of the NLRP3 inflammasome and NF-κB as well as the production of inflammatory cytokines, and the expression of Nrf2 and HO-1 was upregulated by MF. The abovementioned findings indicate that MF is neuroprotective against EBI after SAH and Nrf2/HO-1 cascade may play a key role in mediating its effect through regulation of the mitochondrial apoptosis pathway and activation of the NLRP3 inflammasome and NF-κB.

  12. Chemical substructure search in SQL.

    Science.gov (United States)

    Golovin, Adel; Henrick, Kim

    2009-01-01

    We present a novel technique for a fast chemical substructure search on a relational database by use of a standard SQL query. The symmetry of a query graph is analyzed to give additional constraints. Our method is based on breadth-first search (BFS) algorithms implementation using Relational Database Management Systems (RDBMS). In addition to the chemical search we apply our technique to the field of intermolecular interactions which involves nonplanar graphs and describe how to achieve linear time performance along with the suggestion on how to sufficiently reduce the linear coefficient. From the algorithms theory perspective these results mean that subgraph isomorphism is a polynomial time problem, hence equal problems have the same complexity. The application to subgraph isomorphism in chemical search is available at http://www.ebi.ac.uk/msd-srv/chemsearch and http://www.ebi.ac.uk/msd-srv/msdmotif/chem . The application to the network of molecule interactions is available at http://www.ebi.ac.uk/msd-srv/msdmotif .

  13. REXEBIS the Electron Beam Ion Source for the REX-ISOLDE project

    CERN Document Server

    Wenander, F; Liljeby, L; Nyman, G H

    1998-01-01

    The REXEBIS is an Electron Beam Ion Source (EBIS) developed especially to trap and further ionise the sometimes rare and short-lived isotopes that are produced in the ISOLDE separator for the Radioactive beam EXperiment at ISOLDE (REX-ISOLDE). By promoting the single-charged ions to a high charge-state the ions are more efficiently accelerated in the following linear accelerator. The EBIS uses an electron gun capable of producing a 0.5 A electron beam. The electron gun is immersed in a magnetic field of 0.2 T, and the electron beam is compressed to a current density of >200 A/cm2 inside a 2 T superconducting solenoid. The EBIS is situated on a high voltage (HV) platform with an initial electric potential of 60 kV allowing cooled and bunched 60 keV ions extracted from a Penning trap to be captured. After a period of confinement in the electron beam (<20 ms), the single-charged ions have been ionised to a charge-to-mass ratio of approximately ¼. During this confinement period, the platform potential is decr...

  14. Study of the Dynamics of Transcephalic Cerebral Impedance Data during Cardio-Vascular Surgery

    Science.gov (United States)

    Atefi, S. R.; Seoane, F.; Lindecrantz, K.

    2013-04-01

    Postoperative neurological deficits are one of the risks associated with cardio vascular surgery, necessitating development of new techniques for cerebral monitoring. In this study an experimental observation regarding the dynamics of transcephalic Electrical Bioimpedance (EBI) in patients undergoing cardiac surgery with and without extracorporeal circulation (ECC) was conducted to investigate the potential use of electrical Bioimpedance for cerebral monitoring in cardio vascular surgery. Tetrapolar transcephalic EBI measurements at single frequency of 50 kHz were recorded prior to and during cardio vascular surgery. The obtained results show that the transcephalic impedance decreases in both groups of patients as operation starts, however slight differences in these two groups were also observed with the cerebral impedance reduction in patients having no ECC being less common and not as pronounced as in the ECC group. Changes in the cerebral impedance were in agreement with changes of haematocrit and temperature. The origin of EBI changes is still unexplained however these results encourage us to continue investigating the application of electrical bioimpedance cerebral monitoring clinically.

  15. Effect of discarded keratin-based biocomposite hydrogels on the wound healing process in vivo.

    Science.gov (United States)

    Park, Mira; Shin, Hye Kyoung; Kim, Byoung-Suhk; Kim, Myung Jin; Kim, In-Shik; Park, Byung-Yong; Kim, Hak-Yong

    2015-10-01

    Biocompatible keratin-based hydrogels prepared by electron beam irradiation (EBI) were examined in wound healing. As the EBI dose increased to 60 kGy, the tensile strength of the hydrogels increased, while the percentage of elongation of the hydrogels decreased. After 7 days, the dehydrated wool-based hydrogels show the highest mechanical properties (the % elongation of 1341 and the tensile strength of 6030 g/cm(2) at an EBI dose of 30 kGy). Excision wound models were used to evaluate the effects of human hair-based hydrogels and wool-based hydrogels on various phases of healing. On post-wounding days 7 and 14, wounds treated with either human hair-based or wool-based hydrogels were greatly reduced in size compared to wounds that received other treatments, although the hydrocolloid wound dressing-treated wound also showed a pronounced reduction in size compared to an open wound as measured by a histological assay. On the 14th postoperative day, the cellular appearances were similar in the hydrocolloid wound dressing and wool-based hydrogel-treated wounds, and collagen fibers were substituted with fibroblasts and mixed with fibroblasts in the dermis. Furthermore, the wound treated with a human hair-based hydrogel showed almost complete epithelial regeneration, with the maturation of immature connective tissue and hair follicles and formation of a sebaceous gland. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Adaptation of a U.S. evidence-based Positive Prevention intervention for youth living with HIV/AIDS in Kinshasa, Democratic Republic of the Congo.

    Science.gov (United States)

    Parker, L; Maman, S; Pettifor, A; Chalachala, J L; Edmonds, A; Golin, C E; Moracco, K; Behets, F

    2013-02-01

    Effective HIV prevention programs for people living with HIV/AIDS (PLWH) are important to reduce new infections and to ensure PLWH remain healthy. This paper describes the systematic adaptation of a U.S.-developed Evidence Based Intervention (EBI) using the Centers for Disease Control and Prevention (CDC) Map of Adaption Process for use at a Pediatric Hospital in Kinshasa, Democratic Republic of the Congo (DRC). The adapted intervention, Supporting Youth and Motivating Positive Action or SYMPA, a six-session risk reduction intervention targeted for youth living with HIV/AIDS (YLWH) in Kinshasa was adapted from the Healthy Living Project and guided by the Social Action Theory. This paper describes the process of implementing the first four steps of the ADAPT framework (Assess, Select, Prepare, and Pilot). Our study has shown that an EBI developed and implemented in the U.S. can be adapted successfully for a different target population in a low-resource context through an iterative process following the CDC ADAPT framework. This process included reviewing existing literature, adapting and adding components, and focusing on increasing staff capacity. This paper provides a rare, detailed description of the adaptation process and may aid organizations seeking to adapt and implement HIV prevention EBIs in sub-Saharan Africa and beyond.

  17. Melatonin attenuated early brain injury induced by subarachnoid hemorrhage via regulating NLRP3 inflammasome and apoptosis signaling.

    Science.gov (United States)

    Dong, Yushu; Fan, Chongxi; Hu, Wei; Jiang, Shuai; Ma, Zhiqiang; Yan, Xiaolong; Deng, Chao; Di, Shouyin; Xin, Zhenlong; Wu, Guiling; Yang, Yang; Reiter, Russel J; Liang, Guobiao

    2016-04-01

    Subarachnoid hemorrhage (SAH) is a devastating condition with high morbidity and mortality rates due to the lack of effective therapy. Nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome activation associated with the upregulation of apoptotic signaling pathway has been implicated in various inflammatory diseases including hemorrhagic insults. Melatonin is reported to possess substantial anti-inflammatory properties, which is beneficial for early brain injury (EBI) after SAH. However, the molecular mechanisms have not been clearly identified. This study was designed to investigate the protective effects of melatonin against EBI induced by SAH and to elucidate the potential mechanisms. The adult mice were subjected to SAH. Melatonin or vehicle was injected intraperitoneally 2 hr after SAH. Melatonin was neuroprotective, as shown by increased survival rate, as well as elevated neurological score, greater survival of neurons, preserved brain glutathione levels, and reduced brain edema, malondialdehyde concentrations, apoptotic ratio, and blood-brain barrier (BBB) disruption. Melatonin also attenuated the expressions of NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), cleaved caspase-1, interleukin-1β (IL-1β), and interleukin-6 (IL-6); these changes were also associated with an increase in the anti-apoptotic factor (Bcl2) and reduction in the pro-apoptotic factor (Bim). In summary, our results demonstrate that melatonin treatment attenuates the EBI following SAH by inhibiting NLRP3 inflammasome-associated apoptosis.

  18. Melatonin Attenuates Early Brain Injury via the Melatonin Receptor/Sirt1/NF-κB Signaling Pathway Following Subarachnoid Hemorrhage in Mice.

    Science.gov (United States)

    Zhao, Lei; Liu, Haixiao; Yue, Liang; Zhang, Jingbo; Li, Xia; Wang, Bodong; Lin, Yan; Qu, Yan

    2017-04-01

    Melatonin (Mel) has been reported to alleviate early brain injury (EBI) following subarachnoid hemorrhage (SAH). The activation of silent information regulator 1 (Sirt1), a histone deacetylase, has been suggested to be beneficial in SAH. However, the precise role of Sirt1 in Mel-mediated protection against EBI following SAH has not been elucidated. The present study aims to evaluate the role of melatonin receptor/Sirt1/nuclear factor-kappa B (NF-κB) in this process. The endovascular perforation SAH model was used in male C57BL/6J mice, and melatonin was administrated intraperitoneally (150 mg/kg). The mortality, SAH grade, neurological score, brain water content, and neuronal apoptosis were evaluated. The expression of Sirt1, acetylated-NF-κB (Ac-NF-κB), Bcl-2, and Bax were detected by western blot. To study the underlying mechanisms, melatonin receptor (MR) antagonist luzindole and Sirt1 small interfering RNA (siRNA) were administrated to different groups. The results suggest that Mel improved the neurological deficits and reduced the brain water content and neuronal apoptosis. In addition, Mel enhanced the expression of Sirt1 and Bcl-2 and decreased the expression of Ac-NF-κB and Bax. However, the protective effects of Mel were abolished by luzindole or Sirt1 siRNA. In conclusion, our results demonstrate that Mel attenuates EBI following SAH via the MR/Sirt1/NF-κB signaling pathway.

  19. Quick and Simple Detection Technique to Assess the Binding of Antimicrotubule Agents to the Colchicine-Binding Site

    Directory of Open Access Journals (Sweden)

    Fortin Sébastien

    2010-04-01

    Full Text Available Abstract Development of antimitotic binding to the colchicine-binding site for the treatment of cancer is rapidly expanding. Numerous antimicrotubule agents are prepared every year, and the determination of their binding affinity to tubulin requires the use of purified tubulins and radiolabeled ligands. Such a procedure is costly and time-consuming and therefore is limited to the most promising candidates. Here, we report a quick and inexpensive method that requires only usual laboratory resources to assess the binding of antimicrotubules to colchicine-binding site. The method is based on the ability of N,N'-ethylene-bis(iodoacetamide (EBI to crosslink in living cells the cysteine residues at position 239 and 354 of β-tubulin, residues which are involved in the colchicine-binding site. The β-tubulin adduct formed by EBI is easily detectable by Western blot as a second immunoreacting band of β-tubulin that migrates faster than β-tubulin. The occupancy of colchicine-binding site by pertinent antimitotics inhibits the formation of the EBI: β-tubulin adduct, resulting in an assay that allows the screening of new molecules targeting this binding site.

  20. Quick and Simple Detection Technique to Assess the Binding of Antimicrotubule Agents to the Colchicine-Binding Site

    Directory of Open Access Journals (Sweden)

    Moreau Emmanuel

    2010-01-01

    Full Text Available Abstract Development of antimitotic binding to the colchicine-binding site for the treatment of cancer is rapidly expanding. Numerous antimicrotubule agents are prepared every year, and the determination of their binding affinity to tubulin requires the use of purified tubulins and radiolabeled ligands. Such a procedure is costly and time-consuming and therefore is limited to the most promising candidates. Here, we report a quick and inexpensive method that requires only usual laboratory resources to assess the binding of antimicrotubules to colchicine-binding site. The method is based on the ability of N,N'-ethylene-bis(iodoacetamide (EBI to crosslink in living cells the cysteine residues at position 239 and 354 of β-tubulin, residues which are involved in the colchicine-binding site. The β-tubulin adduct formed by EBI is easily detectable by Western blot as a second immunoreacting band of β-tubulin that migrates faster than β-tubulin. The occupancy of colchicine-binding site by pertinent antimitotics inhibits the formation of the EBI: β-tubulin adduct, resulting in an assay that allows the screening of new molecules targeting this binding site.

  1. Identification of bacterial endophytes associated with traditional medicinal plant Tridax procumbens Linn.

    Science.gov (United States)

    Preveena, Jagadesan; Bhore, Subhash J

    2013-01-01

    In traditional medicine, Tridax procumbens Linn. is used in the treatment of injuries and wounds. The bacterial endophytes (BEs) of medicinal plants could produce medicinally important metabolites found in their hosts; and hence, the involvement of BEs in conferring wound healing properties to T. Procumbens cannot be ruled out. But, we do not know which types of BEs are associated with T. Procumbens. The objective of this study was to investigate the fast growing and cultivable BEs associated with T. procumbens. Leaves and stems of healthy T. Procumbens plants were collected and cultivable BEs were isolated from surface-sterilized leaf and stem tissue samples using Luria-Bertani (LB) agar (medium) at standard conditions. A polymerase chain reaction was employed to amplify 16S rRNA coding gene fragments from the isolates. Cultivable endophytic bacterial isolates (EBIs) were identified using 16S rRNA gene nucleotide sequence similarity based method of bacterial identification. Altogether, 50 culturable EBIs were isolated. 16S rRNA gene nucleotide sequences analysis using the Basic Local Alignment Search Tool (BLAST) revealed identities of the EBIs. Analysis reveals that cultivable Bacillus spp., Cronobacter sakazakii, Enterobacter spp., Lysinibacillus sphaericus, Pantoea spp., Pseudomonas spp. and Terribacillus saccharophilus are associated with T. Procumbens. Based on the results, we conclude that 24 different types of culturable BEs are associated with traditionally used medicinal plant, T. Procumbens, and require further study.

  2. Contribution of IL-12/IL-35 common subunit p35 to maintaining the testicular immune privilege.

    Science.gov (United States)

    Terayama, Hayato; Yoshimoto, Takayuki; Hirai, Shuichi; Naito, Munekazu; Qu, Ning; Hatayama, Naoyuki; Hayashi, Shogo; Mitobe, Kana; Furusawa, Jun-Ichi; Mizoguchi, Izuru; Kezuka, Takeshi; Goto, Hiroshi; Suyama, Kaori; Moriyama, Hiroshi; Sakabe, Kou; Itoh, Masahiro

    2014-01-01

    The testis is an organ with immune privilege. The comprehensive blood-testis barrier formed by Sertoli cells protects autoimmunogenic spermatozoa and spermatids from attack by the body's immune system. The interleukin (IL)-6/IL-12 family cytokines IL-12 (p35/p40), IL-23 (p19/p40), IL-27 (p28/Epstein-Barr virus-induced gene 3 [EBI3]), and IL-35 (p35/EBI3) play critical roles in the regulation of various immune responses, but their roles in testicular immune privilege are not well understood. In the present study, we investigated whether these cytokines are expressed in the testes and whether they function in the testicular immune privilege by using mice deficient in their subunits. Expression of EBI3 was markedly increased at both mRNA and protein levels in the testes of 10- or 12-week-old wild-type mice as compared with levels in 2-week-old mice, whereas the mRNA expression of p40 was markedly decreased and that of p35 was conserved between these two groups. Lack of EBI3, p35, and IL-12 receptor β2 caused enhanced infiltration of lymphocytes into the testicular interstitium, with increased interferon-γ expression in the testes and autoantibody production against mainly acrosomal regions of spermatids. Spermatogenic disturbance was more frequently observed in the seminiferous tubules, especially when surrounded by infiltrating lymphocytes, of these deficient mice than in those of wild-type mice. In particular, p35-deficient mice showed the most severe spermatogenic disturbance. Immunohistochemical analyses revealed that endothelial cells and peritubular cells in the interstitium were highly positive for p35 at both ages, and CD163+ resident macrophages positive for p35 and EBI3, possibly producing IL-35, were also detected in the interstitium of 12-week-old mice but not those of 2-week-old mice. These results suggest that p35 helps in maintaining the testicular immune privilege, in part in an IL-35-dependent manner.

  3. Measurement properties of a novel survey to assess stages of organizational readiness for evidence-based interventions in community chronic disease prevention settings

    Directory of Open Access Journals (Sweden)

    Stamatakis Katherine A

    2012-07-01

    Full Text Available Abstract Background There is a great deal of variation in the existing capacity of primary prevention programs and policies addressing chronic disease to deliver evidence-based interventions (EBIs. In order to develop and evaluate implementation strategies that are tailored to the appropriate level of capacity, there is a need for an easy-to-administer tool to stage organizational readiness for EBIs. Methods Based on theoretical frameworks, including Rogers’ Diffusion of Innovations, we developed a survey instrument to measure four domains representing stages of readiness for EBI: awareness, adoption, implementation, and maintenance. A separate scale representing organizational climate as a potential mediator of readiness for EBIs was also included in the survey. Twenty-three questions comprised the four domains, with four to nine items each, using a seven-point response scale. Representatives from obesity, asthma, diabetes, and tobacco prevention programs serving diverse populations in the United States were surveyed (N = 243; test-retest reliability was assessed with 92 respondents. Results Confirmatory factor analysis (CFA was used to test and refine readiness scales. Test-retest reliability of the readiness scales, as measured by intraclass correlation, ranged from 0.47–0.71. CFA found good fit for the five-item adoption and implementation scales and resulted in revisions of the awareness and maintenance scales. The awareness scale was split into two two-item scales, representing community and agency awareness. The maintenance scale was split into five- and four-item scales, representing infrastructural maintenance and evaluation maintenance, respectively. Internal reliability of scales (Cronbach’s α ranged from 0.66–0.78. The model for the final revised scales approached good fit, with most factor loadings >0.6 and all >0.4. Conclusions The lack of adequate measurement tools hinders progress in dissemination and implementation

  4. Ethyl Pyruvate Attenuates Early Brain Injury Following Subarachnoid Hemorrhage in the Endovascular Perforation Rabbit Model Possibly Via Anti-inflammation and Inhibition of JNK Signaling Pathway.

    Science.gov (United States)

    Lv, Tao; Miao, Yi-Feng; Jin, Yi-Chao; Yang, Shao-Feng; Wu, Hui; Dai, Jiong; Zhang, Xiao-Hua

    2017-02-25

    Early brain injury (EBI) following subarachnoid hemorrhage (SAH) is the main cause to poor outcomes of SAH patients, and early inflammation plays an important role in the acute pathophysiological events. It has been demonstrated that ethyl pyruvate (EP) has anti-inflammatory and neuroprotective effects in various critical diseases, however, the role of EP on EBI following SAH remains to be elucidated. Our study aimed to evaluate the effects of EP on EBI following SAH in the endovascular perforation rabbit model. All rabbits were randomly divided into three groups: sham, SAH + Vehicle (equal volume) and SAH + EP (30 mg/kg/day). MRI was performed to estimate the reliability of the EBI at 24 and 72 h after SAH. Neurological scores were recorded to evaluate the neurological deficit, ELISA kit was used to measure the level of tumor necrosis factor-α (TNF-α), and western blot was used to detect the expression of TNF-α, tJNK, pJNK, bax and bcl-2 at 24 and 72 h after SAH. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and Fluoro-jade B (FJB) staining were used to detect neuronal apoptosis and neurodegeneration respectively, meanwhile hematoxylin and eosin (H&E) staining was used to assess the degree of vasospasm. Our results demonstrated that EP alleviated brain tissue injury (characterized by diffusion weighted imaging and T2 sequence in MRI scan), and significantly improved neurological scores at 72 h after SAH. EP decreased the level of TNF-α and downregulated pJNK/tJNK and bax/bcl-2 in cerebral cortex and hippocampus effectively both at 24 and 72 h after SAH. Furthermore, EP reduced TUNEL and FJB positive cells significantly. In conclusion, the present study supported that EP afforded neuroprotective effects possibly via reducing TNF-α expression and inhibition of the JNK signaling pathway. Therefore, EP may be a potent therapeutic agent to attenuate EBI following SAH.

  5. Inhibitory effects of omega-3 fatty acids on early brain injury after subarachnoid hemorrhage in rats: Possible involvement of G protein-coupled receptor 120/β-arrestin2/TGF-β activated kinase-1 binding protein-1 signaling pathway.

    Science.gov (United States)

    Yin, Jia; Li, Haiying; Meng, Chengjie; Chen, Dongdong; Chen, Zhouqing; Wang, Yibin; Wang, Zhong; Chen, Gang

    2016-06-01

    Omega-3 fatty acids have been reported to improve neuron functions during aging and in patients affected by mild cognitive impairment, and mediate potent anti-inflammatory via G protein-coupled receptor 120 (GPR120) signal pathway. Neuron dysfunction and inflammatory response also contributed to the progression of subarachnoid hemorrhage (SAH)-induced early brain injury (EBI). This study was to examine the effects of omega-3 fatty acids on SAH-induced EBI. Two weeks before SAH, 30% Omega-3 fatty acids was administered by oral gavage at 1g/kg body weight once every 24h. Specific siRNA for GPR120 was exploited. Terminal deoxynucleotidyl transferase dUTP nick end labeling, fluoro-Jade B staining, and neurobehavioral scores and brain water content test showed that omega-3 fatty acids effectively suppressed SAH-induced brain cell apoptosis and neuronal degradation, behavioral impairment, and brain edema. Western blot, immunoprecipitation, and electrophoretic mobility shift assays results showed that omega-3 fatty acids effectively suppressed SAH-induced elevation of inflammatory factors, including cyclooxygenase-2, monocyte chemoattractant protein-1, and inducible nitric oxide synthase. In addition, omega-3 fatty acids could inhibit phosphorylation of transforming growth factor β activated kinase-1 (TAK1), MEK4, c-Jun N-terminal kinase, and IkappaB kinase as well as activation of nuclear factor kappa B through regulating GPR120/β-arrestin2/TAK1 binding protein-1 pathway. Furthermore, siRNA-induced GPR120 silencing blocked the protective effects of omega-3 fatty acids. Here, we show that stimulation of GPR120 with omega-3 fatty acids pretreatment causes anti-apoptosis and anti-inflammatory effects via β-arrestin2/TAK1 binding protein-1/TAK1 pathway in the brains of SAH rats. Fish omega-3 fatty acids as part of a daily diet may reduce EBI in an experimental rat model of SAH.

  6. Acetylcholinesterases from entomopathogenic nematode Heterorhabditid bacteriophora: Susceptibility to insecticides and immunological characteristics.

    Science.gov (United States)

    Mohamed, Magda A; M E Mahdy, El-Sayed; Ghazy, Abd-El-Hady M; Ibrahim, Nihal M; El-Mezayen, Hatem A; Ghanem, Manal M E

    2017-01-01

    Acetylcholinesterases (AChEs) from the infective juveniles (IJs) of entomopathogenic nematode (EPN) have been investigated with respect to their susceptibility to insecticides and immunological characteristics, aiming at nominating the most compatible insecticide(s) to be used in conjunction with the most insecticide-tolerant EPN strain before incorporation in integrated pest management (IPM) programs. The inhibition kinetics of two purified AChE isoenzymes, AChEAII and AChEBI isolated from Heterorhabditid bacteriophora EM2 strain, by different insecticides revealed that the insensitivity to inhibition by such insecticides could be arranged in a descending order as; methomyl>carbofuran>acetamiprid>oxamyl>malathion. Except for malathion, the insecticides competitively inhibited AChEs with Ki values ranging from 0.1 to 15mM and IC50 values from 1.25 to 23mM. The two AChE isoforms are several folds less sensitive to inhibition by methomyl and carbofuran compared to those previously reported for other insect species. AChEBI was used as an immunogen to raise anti-AChEBI antisera in rabbits. The prepared antisera cross-reacted with AChEs of five different heterorhabditid nematode strains implying the presence of common epitopes shared along all the examined strains. Such studies could aid in the rational selection of the compatible insecticide(s) and the prepared polyclonal anti-AChE antisera would be a valuable immunodiagnostic tool for evaluating the most insecticide-tolerant EPN strain(s) in IPM programs. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Effect of discarded keratin-based biocomposite hydrogels on the wound healing process in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Park, Mira [Department of Organic Materials & Fiber Engineering, Chonbuk National University, Jeonju 561–756 (Korea, Republic of); Shin, Hye Kyoung [Department of Chemistry, Inha University, 100 Inharo, Incheon 402–751 (Korea, Republic of); Kim, Byoung-Suhk [Department of BIN fusion technology, Chonbuk National University, Jeonju 561–756 (Korea, Republic of); Kim, Myung Jin; Kim, In-Shik [Department of Veterinary Anatomy, College of Veterinary Medicine and Bio-safety Research institute, Chonbuk National University, Jeonju 561–756 (Korea, Republic of); Park, Byung-Yong, E-mail: parkb@jbnu.ac.kr [Department of Veterinary Anatomy, College of Veterinary Medicine and Bio-safety Research institute, Chonbuk National University, Jeonju 561–756 (Korea, Republic of); Kim, Hak-Yong, E-mail: khy@jbnu.ac.kr [Department of BIN fusion technology, Chonbuk National University, Jeonju 561–756 (Korea, Republic of)

    2015-10-01

    Biocompatible keratin-based hydrogels prepared by electron beam irradiation (EBI) were examined in wound healing. As the EBI dose increased to 60 kGy, the tensile strength of the hydrogels increased, while the percentage of elongation of the hydrogels decreased. After 7 days, the dehydrated wool-based hydrogels show the highest mechanical properties (the % elongation of 1341 and the tensile strength of 6030 g/cm{sup 2} at an EBI dose of 30 kGy). Excision wound models were used to evaluate the effects of human hair-based hydrogels and wool-based hydrogels on various phases of healing. On post-wounding days 7 and 14, wounds treated with either human hair-based or wool-based hydrogels were greatly reduced in size compared to wounds that received other treatments, although the hydrocolloid wound dressing-treated wound also showed a pronounced reduction in size compared to an open wound as measured by a histological assay. On the 14th postoperative day, the cellular appearances were similar in the hydrocolloid wound dressing and wool-based hydrogel-treated wounds, and collagen fibers were substituted with fibroblasts and mixed with fibroblasts in the dermis. Furthermore, the wound treated with a human hair-based hydrogel showed almost complete epithelial regeneration, with the maturation of immature connective tissue and hair follicles and formation of a sebaceous gland. - Highlights: • Biocompatible keratin-based hydrogels were examined for wound healing process. • Human hair-based hydrogel is superior to wool-based hydrogel in wound healing. • Discarded keratin-based hydrogels are expected more eco-friendly therapeutic agents.

  8. Cannabinoid type 2 receptor stimulation attenuates brain edema by reducing cerebral leukocyte infiltration following subarachnoid hemorrhage in rats.

    Science.gov (United States)

    Fujii, Mutsumi; Sherchan, Prativa; Krafft, Paul R; Rolland, William B; Soejima, Yoshiteru; Zhang, John H

    2014-07-15

    Early brain injury (EBI), following subarachnoid hemorrhage (SAH), comprises blood-brain barrier (BBB) disruption and consequent edema formation. Peripheral leukocytes can infiltrate the injured brain, thereby aggravating BBB leakage and neuroinflammation. Thus, anti-inflammatory pharmacotherapies may ameliorate EBI and provide neuroprotection after SAH. Cannabinoid type 2 receptor (CB2R) agonism has been shown to reduce neuroinflammation; however, the precise protective mechanisms remain to be elucidated. This study aimed to evaluate whether the selective CB2R agonist, JWH133 can ameliorate EBI by reducing brain-infiltrated leukocytes after SAH. Adult male Sprague-Dawley rats were randomly assigned to the following groups: sham-operated, SAH with vehicle, SAH with JWH133 (1.0mg/kg), or SAH with a co-administration of JWH133 and selective CB2R antagonist SR144528 (3.0mg/kg). SAH was induced by endovascular perforation, and JWH133 was administered 1h after surgery. Neurological deficits, brain water content, Evans blue dye extravasation, and Western blot assays were evaluated at 24h after surgery. JWH133 improved neurological scores and reduced brain water content; however, SR144528 reversed these treatment effects. JWH133 reduced Evans blue dye extravasation after SAH. Furthermore, JWH133 treatment significantly increased TGF-β1 expression and prevented an SAH-induced increase in E-selectin and myeloperoxidase. Lastly, SAH resulted in a decreased expression of the tight junction protein zonula occludens-1 (ZO-1); however, JWH133 treatment increased the ZO-1 expression. We suggest that CB2R stimulation attenuates neurological outcome and brain edema, by suppressing leukocyte infiltration into the brain through TGF-β1 up-regulation and E-selectin reduction, resulting in protection of the BBB after SAH.

  9. Stimulated human peripheral T cells produce high amounts of IL-35 protein in a proliferation-dependent manner.

    Science.gov (United States)

    Guttek, Karina; Reinhold, Dirk

    2013-10-01

    The p35 subunit of IL-12 and the Epstein-Barr virus-induced gene 3 (EBI3) have been shown to form a heterodimeric cytokine, named interleukin-35 (IL-35). Recently, mRNA expression of both IL-12p35 and EBI3 was clearly shown in stimulated human T effector cells. Here, we investigated the production of IL-35 protein in human anti-CD3/CD28-stimulated pan T cells as well as T cell subpopulations using a specific human IL-35 ELISA system. We measured high concentrations of IL-35 (up to 3 ng/ml) in cell culture supernatants of stimulated pan T cells as well as CD4(+), CD8(+) and CD4(+)CD25(-) T cell subpopulations at 72 h after stimulation. Very low amounts of IL-35, in the range of 100pg/ml, were detectable in supernatants of resting T cells. These observations could be confirmed using a dot-blot assay for IL-12p35 and EBI3. High concentrations of IL-35 could be also measured in cell culture supernatants of both, resting and stimulated CD4(+)CD25(+) T cells. In order to learn more about the regulation of IL-35 production, we studied the effect of dexamethasone, cyclosporine A and rapamycin on IL-35 production of anti-CD3/CD28-stimulated human pan T cells as well as CD4(+) and CD8(+) T cell subpopulations. All three drugs significantly suppressed IL-35 production of these cells in a proliferation-dependent manner. In summary, we could show that stimulated human peripheral blood T cells of healthy donors produce high amounts of IL-35 protein. However, the biological function of this cytokine remains to be elucidated.

  10. Combination of electron beam irradiation and thermal treatment to enhance the shelf-life of traditional Indian fermented food (Idli)

    Science.gov (United States)

    Mulmule, Manoj D.; Shimmy, Shankar M.; Bambole, Vaishali; Jamdar, Sahayog N.; Rawat, K. P.; Sarma, K. S. S.

    2017-02-01

    Idli, a steam-cooked breakfast food item consumed in India, is famous as a staple food for its spongy texture and unique fermented taste. Idli preparation is a time consuming process; although instant Idli pre-mixes as powder or batter are available in the market, they do not have the distinctive taste and aroma similar to the Idli prepared at home. Hence ready-to-eat (RTE) form of this food is in demand. Therefore, an attempt was made to prepare RTE Idli bearing similar taste as home-cooked Idli with an extended shelf-life of up to two months at an ambient temperature using Electron Beam Irradiation (EBI) at dosages 2.5 kGy, 5 kGy and 7.5 kGy and combination processing comprised of EBI dosage at 2.5 kGy and thermal treatment (80 °C for 20 min). The treated Idli's were microbiologically and sensorially evaluated at storage periods of zero day, 14 days, 30 days and 60 days. Idli's irradiated at 7.5 kGy and subjected to combination processing at 2.5 kGy and thermal treatment were shelf-stable for 60 days. 2.5 kGy and 5 kGy radiation dosages alone were not sufficient to preserve Idli samples for more than 14 days. Undesirable change in sensory properties of Idli was observed at an EBI dosage of 7.5 kGy. Sensory properties of combination processed Idli's were found to undergo minor change over the storage period. The present work suggests that lowest radiation dosage in combination with thermal treatment could be useful to achieve the extended shelf-life without considerably impairing the organoleptic quality of Ready-to-Eat Idli.

  11. Electron string phenomenon: physics and use

    Science.gov (United States)

    Donets, Evgeny D.

    2004-01-01

    Electron string phenomenon arises as a result of phase transition of a state of multiply reflected electron beam to this new discovered state of one component electron plasma and can be easily observed in the reflex mode of EBIS operation. The transition goes via a strong instability, which causes considerable electron energy spread, which in its turn suppresses the instability. Electron string state is a stationary state of hot pure electron plasma, which is heated by injected electron beam and cooled because of electron loses. Electron string is quiet in broad regions of experimental parameters, so that it is used for confinement and ionization of positive ions by electron impact to highly charge states similar to electron beams in EBIS. Application of electron strings instead of electron beams for ion production allows to save about 99% of electric power of electron beam and simultaneously to improve reliability of an ion source considerably. The JINR EBIS `Krion-2' in the string mode of operation is used for production of N7+, Ar16+ and Fe24+ ion beams and their acceleration to relativistic energies on the facility of the JINR super conducting one turn injection synchrotron `Nuklotron'. The tubular electron string possibly can exist and it is under study now theoretically and experiments are prepared now. Estimations show that a Tubular Electron String Ion Source (TESIS) could have up to three orders of magnitude higher ion output then a Linear one (LESIS). In frames of nuclear astrophysics electron strings can be used for research of fusion nuclear reactions at low energies in conditions when both beam and target nuclei do not carry orbital electrons. The project NARITA — Nuclear Astrophysics Researches in an Ion Trap Apparatus is proposed. Polarization effects also can be studied.

  12. Use of Evidence-Based Interventions to Address Disparities in Colorectal Cancer Screening.

    Science.gov (United States)

    Joseph, Djenaba A; Redwood, Diana; DeGroff, Amy; Butler, Emily L

    2016-02-12

    Colorectal cancer (CRC) is the second leading cause of cancer death among cancers that affect both men and women. Despite strong evidence of their effectiveness, CRC screening tests are underused. Racial/ethnic minority groups, persons without insurance, those with lower educational attainment, and those with lower household income levels have lower rates of CRC screening. Since 2009, CDC's Colorectal Cancer Control Program (CRCCP) has supported state health departments and tribal organizations in implementing evidence-based interventions (EBIs) to increase use of CRC screening tests among their populations. This report highlights the successful implementation of EBIs to address disparities by two CRCCP grantees: the Alaska Native Tribal Health Consortium (ANTHC) and Washington State's Breast, Cervical, and Colon Health Program (BCCHP). ANTHC partnered with regional tribal health organizations in the Alaska Tribal Health System to implement provider and client reminders and use patient navigators to increase CRC screening rates among Alaska Native populations. BCCHP identified patient care coordinators in each clinic who coordinated staff training on CRC screening and integrated client and provider reminder systems. In both the Alaska and Washington programs, instituting provider reminder systems, client reminder systems, or both was facilitated by use of electronic health record systems. Using multicomponent interventions in a single clinical site or facility can support more organized screening programs and potentially result in greater increases in screening rates than relying on a single strategy. Organized screening systems have an explicit policy for screening, a defined target population, a team responsible for implementation of the screening program, and a quality assurance structure. Although CRC screening rates in the United States have increased steadily over the past decade, this increase has not been seen equally across all populations. Increasing the

  13. A novel approach for removing the hook effect artefact from Electrical Bioimpedance spectroscopy measurements

    Science.gov (United States)

    Buendia, R.; Seoane, F.; Gil-Pita, R.

    2010-04-01

    Very often in Electrical Bioimpedance (EBI) spectroscopy measurements the presence of stray capacitances creates a measurement artefact commonly known as Hook Effect. Such an artefact creates a hook-alike deviation of the EBI data noticeable when representing the measurement on the impedance plane. Such Hook Effect is noticeable at high frequencies but it also causes a data deviation at lower measurement frequencies. In order to perform any accurate analysis of the EBI spectroscopy data, the influence of the Hook Effect must be removed. An established method to compensate the hook effect is the well known Td compensation, which consists on multiplying the obtained spectrum, Zmeas(ω) by a complex exponential in the form of exp[jωTd]. Such a method cannot correct entirely the Hook Effect since the hook-alike deviation occurs a broad frequency range in both magnitude and phase of the measured impedance, and by using a scalar value for Td. First a scalar only modifies the phase of the measured impedance and second, a single value can truly corrects the Hook Effect only at a single frequency. In addition, the process to select a value for the scalar Td by an iterative process with the aim to obtain the best Cole fitting lacks solid scientific grounds. In this work the Td compensation method is revisited and a modified approach for correcting the Hook Effect including a novel method for selecting the correcting values is proposed. The initial validation results confirm that the proposed method entirely corrects the Hook Effect at all frequencies.

  14. Textrode-enabled transthoracic electrical bioimpedance measurements - towards wearable applications of impedance cardiography

    Directory of Open Access Journals (Sweden)

    Juan Carlos Márquez Ruiz

    2013-10-01

    Full Text Available During the last decades the use of Electrical Bioimpedance (EBI in the medical field has been subject of extensive research, especially since it is an affordable, harmless and non-invasive technology. In some specific applications such as body composition assessment where EBI has proven a good degree of effectiveness and reliability, the use of textile electrodes and measurement garments have shown a good performance and reproducible results. Impedance Cardiography (ICG is another modality of EBI that can benefit from the implementation and use of wearable sensors. ICG technique is based on continuous impedance measurements of a longitudinal segment across the thorax taken at a single frequency. The need for specific electrode placement on the thorax and neck can be easily ensured with the use of a garment with embedded textile electrodes, textrodes. The first step towards the implementation of ICG technology into a garment is to find out if ICG measurements with textile sensors give a good enough quality of the signal to allow the estimation of the fundamental ICG parameters. In this work, the measurement performance of a 2-belt set with incorporated textrodes for thorax and neck was compared against ICG measurements obtained with Ag/AgCl electrodes. The analysis was based on the quality of the fundamental ICG signals (∆Z, dZ/dt and ECG, systolic time intervals and other ICG parameters. The obtained results indicate the feasibility of using textrodes for ICG measurements with consistent measurements and relatively low data dispersion. Thus, enabling the development of measuring garments for ICG measurements.

  15. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    Science.gov (United States)

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-04

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.

  16. Electron string phenomenon: physics and use

    Energy Technology Data Exchange (ETDEWEB)

    Donets, Evgeny D [Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation)

    2004-01-01

    Electron string phenomenon arises as a result of phase transition of a state of multiply reflected electron beam to this new discovered state of one component electron plasma and can be easily observed in the reflex mode of EBIS operation. The transition goes via a strong instability, which causes considerable electron energy spread, which in its turn suppresses the instability. Electron string state is a stationary state of hot pure electron plasma, which is heated by injected electron beam and cooled because of electron loses. Electron string is quiet in broad regions of experimental parameters, so that it is used for confinement and ionization of positive ions by electron impact to highly charge states similar to electron beams in EBIS. Application of electron strings instead of electron beams for ion production allows to save about 99% of electric power of electron beam and simultaneously to improve reliability of an ion source considerably. The JINR EBIS 'Krion-2' in the string mode of operation is used for production of N{sup 7+}, Ar{sup 16+} and Fe{sup 24+} ion beams and their acceleration to relativistic energies on the facility of the JINR super conducting one turn injection synchrotron 'Nuklotron'. The tubular electron string possibly can exist and it is under study now theoretically and experiments are prepared now. Estimations show that a Tubular Electron String Ion Source (TESIS) could have up to three orders of magnitude higher ion output then a Linear one (LESIS). In frames of nuclear astrophysics electron strings can be used for research of fusion nuclear reactions at low energies in conditions when both beam and target nuclei do not carry orbital electrons. The project NARITA - Nuclear Astrophysics Researches in an Ion Trap Apparatus is proposed. Polarization effects also can be studied.

  17. Topiramate attenuates early brain injury following subarachnoid haemorrhage in rats via duplex protection against inflammation and neuronal cell death.

    Science.gov (United States)

    Tian, Yong; Guo, Song-Xue; Li, Jian-Ru; Du, Hang-Gen; Wang, Chao-Hui; Zhang, Jian-Min; Wu, Qun

    2015-10-05

    Early brain injury (EBI) following aneurysmal subarachnoid haemorrhage (SAH) insults contributes to the poor prognosis and high mortality observed in SAH patients. Topiramate (TPM) is a novel, broad-spectrum, antiepileptic drug with a reported protective effect against several brain injuries. The current study aimed to investigate the potential of TPM for neuroprotection against EBI after SAH and the possible dose-dependency of this effect. An endovascular perforation SAH model was established in rats, and TPM was administered by intraperitoneal injection after surgery at three different doses (20mg/kg, 40mg/kg, and 80mg/kg). The animals' neurological scores and brain water content were evaluated, and ELISA, Western blotting and immunostaining assays were conducted to assess the effect of TPM. The results revealed that TPM lowers the elevated levels of myeloperoxidase and proinflammatory mediators observed after SAH in a dose-related fashion, and the nuclear factor-kappa B (NF-κB) signalling pathway is the target of neuroinflammation regulation. In addition, TPM ameliorated SAH-induced cortical neuronal apoptosis by influencing Bax, Bcl-2 and cleaved caspase-3 protein expression, and the effect of TPM was enhanced in a dose-dependent manner. Various dosages of TPM also upregulated the protein expression of the γ-aminobutyric acid (GABA)-ergic signalling molecules, GABAA receptor (GABAAR) α1, GABAAR γ2, and K(+)-Cl(-) co-transporter 2 (KCC2) together and downregulated Na(+)-K(+)-Cl(-) co-transporter 1 (NKCC1) expression. Thus, TPM may be an effective neuroprotectant in EBI after SAH by regulating neuroinflammation and neuronal cell death.

  18. Lentiviral Mediating Genetic Engineered Mesenchymal Stem Cells for Releasing IL-27 as a Gene Therapy Approach for Autoimmune Diseases

    Directory of Open Access Journals (Sweden)

    Shohreh Hajizadeh-Sikaroodi

    2014-04-01

    Full Text Available Objective: Autoimmune diseases precede a complex dysregulation of the immune system. T helper17 (Th17 and interleukin (IL-17 have central roles in initiation of inflammation and subsequent autoimmune diseases. IL-27 significantly controls autoimmune diseases by Th17 and IL-17 suppression. In the present study we have created genetic engineered mesenchymal stem cells (MSCs that mediate with lentiviral vectors to release IL-27 as an adequate vehicle for ex vivo gene therapy in the reduction of inflammation and autoimmune diseases. Materials and Methods: In this experimental study, we isolated adipose-derived MSCs (AD-MSCs from lipoaspirate and subsequently characterized them by differentiation. Two subunits of IL-27 (p28 and EBI3 were cloned in a pCDH-513B-1 lentiviral vector. Expressions of p28 and EBI3 (Epstein-Barr virus induced gene 3 were determined by real time polymerase chain reaction (PCR. MSCs were transduced by a pCDH-CMV-p28-IRESEBI3- EF-copGFP-Pur lentiviral vector and the bioassay of IL-27 was evaluated by IL-10 expression. Results: Cell differentiation confirmed true isolation of MSCs from lipoaspirate. Restriction enzyme digestion and sequencing verified successful cloning of both p28 and EBI3 in the pCDH-513B-1 lentiviral vector. Real time PCR showed high expressions level of IL-27 and IL-10 as well as accurate activity of IL-27. Conclusion: The results showed transduction of functional IL-27 to AD-MSCs by means of a lentiviral vector. The lentiviral vector did not impact MSC characteristics.

  19. Highly specific ''sensing'' of tryptophan by a luminescent europium(III) complex

    Energy Technology Data Exchange (ETDEWEB)

    Stubenrauch, Jan A.; Mevissen, Christian; Schulte, Marie F.; Bochenek, Steffen; Albrecht, Markus [RWTH Univ. Aachen (Germany). Inst. fuer Organische Chemie; Subramanian, Palani S. [Central Salt and Marine Chemicals, Research Institute (CSRI), Gujarat (India)

    2016-07-01

    The europium(III) complex 1-Cl{sub 3} (S,S-2,2{sup '}-(((1,10-phenanthroline-2,9-diyl)bis(methanylylidene))bis (azanylyliden e))bis(3-methylbutanamide)europiumtrichloride) undergoes, only in the presence of the amino acid tryptophan, a change of emission at 615 nm. In the presence of few equivalents of tryptophan, emission of the europium complex is enhanced while it disappears upon addition of large amounts. This behavior can be assigned to displacement of the sensitizing phenanthroline ligand of 1-Cl{sub 2} x Trp in the latter case.

  20. [Substrate specificity of carotenoid 3',4'-desaturase from Deinococcus radiodurans].

    Science.gov (United States)

    Sun, Zongtao; Tian, Bing; Shen, Shaochuan; Hu, Yuejin

    2010-10-01

    To examine the substrate specificity of carotenoid 3',4'-desaturase (DR2250) from Deinococcus radiodurans, we amplified the dr2250 gene by using PCR methods. The PCR products were digested by Hind III-BamH I and ligated into the vector pUC19, yielding recombinant vector pUC-CRTD. We analyzed the carotenoids of E. coli transformants containing pACCRT-EBI(Eu) and (or) pRK-CRTC and (or) pUC-CRTD. Our results demonstrated that DR2250 had substrate specificity on the carotenoids with hydroxyl group at C1 (1').

  1. Accessing and using chemical property databases.

    Science.gov (United States)

    Hastings, Janna; Josephs, Zara; Steinbeck, Christoph

    2012-01-01

    Chemical compounds participate in all the processes of life. Understanding the complex interactions of small molecules such as metabolites and drugs and the biological macromolecules that consume and produce them is key to gaining a wider understanding in a systemic context. Chemical property databases collect information on the biological effects and physicochemical properties of chemical entities. Accessing and using such databases is key to understanding the chemistry of toxic molecules. In this chapter, we present methods to search, understand, download, and manipulate the wealth of information available in public chemical property databases, with particular focus on the database of Chemical Entities of Biological Interest (ChEBI).

  2. Expression of IL-35 in the Bronchoalveolar Lavage Fluid Mononuclear Cells in Patients with Tuberculosis%IL-35在结核患者肺泡灌洗液中的表达

    Institute of Scientific and Technical Information of China (English)

    丁春梅; 张军; 胡成进

    2012-01-01

    Objective To detect the expression level of IL-35 in the bronchoalveolar lavage fluid mononuclear cells in patients with active pulmoanry tuberculosis. Methods 80 patients with active pulmonary tuberculosis were admitted to this study. All patients were examined by fiberoptic bronchoscopy. Bronchoalveolar lavage fluid and peripheral blood were collected,and mononuclear cells were separated with Hypaque-ficoll method. The separated mononuclear cells were stimulated with extracts from inactive mycobacteria for 36h. Secretions of IL-35 in the culture supernatant of mononuclear cells were detected by IL-35 ELISA kit. mRNA level of IL-35 subunit IL-12a and EBI3 were detected by real-time RT-PCR. EBI3 subunit of IL-35 was detected by Western blot and Treg cells were detected by multicolor flow cytometry. Results The concentration of IL-35 in the supernatant of bronchoalveolar lavage fluid mononuclear cells (BLFMC) was 76. 6 + 20. 1 pg/ml, which was significantly higher than the peripheral-blood mononuclear cells (PBMC) ,(£=23. 07,P<0. 01). IL-35 expression was only observed in the culture supernatant of BLFMC by Western blot. mRNA level of IL-12a in BLFMC was about 6 folds of PBMC (t=18. 02,P<0. 01) and EBI3 were about 9 folds(£=17. 85,P<0. 01). Percentage of Treg cells in BLFMC were 12. 6%± 3. 3%,which was higher than in peripheral blood (4. 2%±1. 8%) ,(t=12. 24,P<0. 01). Treg cells in bronchoalveolar lavage fluid expressed a relative higher level of EBI3. Conclusion IL-35 could be detected in BLFMC (mainly Treg) in patients with active pulmonary tuberculosis,which suggests that IL-35 play a regulatory role in the cellular immune reaction of My-cobactenum tuberculosis infection.%目的 检测IL-35在结核患者肺泡灌洗液中的表达.方法 80例诊断为进展期肺结核患者全部采用支气管镜检查,收集肺泡灌洗液和外周血,淋巴细胞分离液分离其中的单个核细胞,经50 μg灭活的结核杆菌提取物刺激36 h后,采用ELISA

  3. Study on effects of storm-water detention facilities in an urbanized watershed using a distributed model

    OpenAIRE

    賈, 仰文; 倪, 广恒; 木内, 豪; 吉谷, 純一; 河原, 能久; 末次, 忠司

    2001-01-01

    A distributed hydrological model - WEP (Water and Energy transfer Process) model is improved at first by adding overland flow and storm-water detention pond's components, as well as changing the kinematic wave method into the dynamic wave method for the flow routing of main rivers to consider tidal effects. The modified model is then utilized to evaluate the effects of storm-water detention ponds and infiltration trenches in the Ebi river watershed with a grid size of 50m and a time step of 1...

  4. A CORBA server for the Radiation Hybrid DataBase.

    Science.gov (United States)

    Rodriguez-Tomé, P; Helgesen, C; Lijnzaad, P; Jungfer, K

    1997-01-01

    Modern biology depends on a wide range of software interacting with a large number of data sources, varying both in size, complexity and structure. The range of important databases in molecular biology and genetics makes it crucial to overcome the problems which this multiplicity presents. At EMBL-EBI we have started to use CORBA technology to support interoperability between a variety of databases, as well as to facilitate the integration of tools that access these databases. Within the Radiation Hybrid DataBase project we are confronted daily with the interoperation and linking issues. In this paper we present a CORBA infrastructure implemented to access the Radiation Hybrid DataBase.

  5. Role of IL-35-producing regulatory B cells in immunopathogenesis of Hashimoto thyroiditis%IL-35+调节性B细胞在桥本甲状腺炎免疫发病机制中的作用

    Institute of Scientific and Technical Information of China (English)

    陈占玲; 李春华; 孙庆凯; 张秀薇; 陈伟坤

    2016-01-01

    目的 探讨IL-35+调节性B细胞(i35-Breg)在桥本甲状腺炎(HT)免疫发病机制中的作用.方法 采用流式细胞术检测36例HT患者及32例对照者外周血CD 19+IL-12p35+IL-27EBI3+细胞比例及PD-L1、CD169、PD-1、CD43、IL-12p35、IL-27EBI3、IL-12Rp2、IL-27Rα、pSTAT1、pSTAT3蛋白表达水平,实时荧光定量PCR检测CD19+细胞SHP-2、Vav mRNA表达,ELISA检测血浆中IL-35、TNF-α、IL-12水平.结果 HT患者外周血CD 19+IL-12p35+IL-27EBI3+细胞比例及IL-12p35、IL-27EBI3、IL-10表达明显低于对照组(P<0.01).HT患者血浆IL-35水平及CD19+B细胞IL-12Rβ2、IL-27Rα、pSTAT1、pSTAT3表达明显低于对照组(P<0.01),而血浆TNF-α、IL-12水平及CD14+细胞PD-L1、CD169表达明显高于对照组(P<0.01).结论 i35-Breg细胞数量及功能异常可能是导致HT患者免疫功能紊乱的重要因素之一.

  6. 12th International Symposium on Electron Beam Ion Sources and Traps and Their Applications

    CERN Document Server

    Schwarz, Stefan; Baumann, Thomas M

    2014-01-01

    The EBIST symposia date back to 1977 and have taken place every 3 to 4 years to specifically discuss progress and exchange ideas in the design, development, applications of electron beam ion sources and traps, and the physics with highly charged ions. The topics to be covered in 2014 are: - Progress and status of EBIS/T facilities, - Atomic spectroscopy of highly charged ions, - Charge-exchange and surface interaction with highly charged ions, - Charge breeding of stable and radioactive isotopes, - Nuclear physics with highly charged ions.

  7. GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.

    Science.gov (United States)

    Sangrador-Vegas, Amaia; Mitchell, Alex L; Chang, Hsin-Yu; Yong, Siew-Yit; Finn, Robert D

    2016-01-01

    The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation. As a corollary, annotation stability is considered to be a measure of reliability. However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used to help annotate them. Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator. Database URL: http://www.ebi.ac.uk/interpro.

  8. Albedo decline on Greenland's Mittivakkat Gletscher in a warming climate

    DEFF Research Database (Denmark)

    Mernild, Sebastian H.; Malmros, Jeppe K.; Yde, Jacob C.

    2015-01-01

    Albedo is one of the parameters that govern energy availability for snow and ice surface ablation, and subsequently the surface mass balance conditions of temperate glaciers and ice caps (GIC). Here, we document snow and ice albedo changes for Mittivakkat Gletscher (MG) in Southeast Greenland (20.......10. The greatest decline in albedo, of 0.25, occurred near the equilibrium line altitude (ELA), an important surface cover and albedo transitional zone. The EBY albedo correlates significantly with ELA and net winter and summer glacier mass balance records....

  9. Heavy Ion Injection Into Synchrotrons, Based On Electron String Ion Sources

    CERN Document Server

    Donets, E E; Syresin, E M

    2004-01-01

    A possibility of heavy ions injection into synchrotrons is discussed on the base of two novel ion sources, which are under development JINR during last decade: 1) the electron string ion source (ESIS), which is a modified version of a conventional electron beam ion source (EBIS), working in a reflex mode of operation, and 2) the tubular electron string ion source (TESIS). The Electron String Ion Source "Krion-2" (VBLHE, JINR, Dubna) with an applied confining magnetic field of 3 T was used for injection into the superconducting JINR synchrotron - Nuclotron and during this runs the source provided a high pulse intensity of the highly charged ion beams: Ar16+

  10. A randomised controlled trial of extended brief intervention for alcohol dependent patients in an acute hospital setting (ADPAC

    Directory of Open Access Journals (Sweden)

    Williamson Paula

    2011-07-01

    Full Text Available Abstract Background Alcohol dependence affects approximately 3% of the English population, and accounts for significant medical and psychiatric morbidity. Only 5.6% of alcohol-dependent individuals ever access specialist treatment and only a small percentage ever seek treatment. As people who are alcohol dependent are more likely to have experienced health problems leading to frequent attendance at acute hospitals it would seem both sensible and practical to ensure that this setting is utilised as a major access point for treatment, and to test the effectiveness of these treatments. Methods/Design This is a randomised controlled trial with a primary hypothesis that extended brief interventions (EBI delivered to alcohol-dependent patients in a hospital setting by an Alcohol Specialist Nurse (ASN will be effective when compared to usual care in reducing overall alcohol consumption and improving on the standard measures of alcohol dependence. Consecutive patients will be screened for alcohol misuse in the Emergency Department (ED of a district general hospital. On identification of an alcohol-related problem, following informed written consent, we aim to randomize 130 patients per group. The ASN will discharge to usual clinical care all control group patients, and plan a programme of EBI for treatment group patients. Follow-up interview will be undertaken by a researcher blinded to the intervention at 12 and 24 weeks. The primary outcome measure is level of alcohol dependence as determined by the Severity of Alcohol Dependence Questionnaire (SADQ score. Secondary outcome measures include; Alcohol Use Disorders Identification Test (AUDIT score, quantity and frequency of alcohol consumption, health-related quality of life measures, service utilisation, and patient experience. The trial will also allow an assessment of the cost-effectiveness of EBI in an acute hospital setting. In addition, patient experience will be assessed using qualitative methods

  11. European Nucleotide Archive in 2016

    Science.gov (United States)

    Toribio, Ana Luisa; Alako, Blaise; Amid, Clara; Cerdeño-Tarrága, Ana; Clarke, Laura; Cleland, Iain; Fairley, Susan; Gibson, Richard; Goodgame, Neil; ten Hoopen, Petra; Jayathilaka, Suran; Kay, Simon; Leinonen, Rasko; Liu, Xin; Martínez-Villacorta, Josué; Pakseresht, Nima; Rajan, Jeena; Reddy, Kethi; Rosello, Marc; Silvester, Nicole; Smirnov, Dmitriy; Vaughan, Daniel; Zalunin, Vadim; Cochrane, Guy

    2017-01-01

    The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA. PMID:27899630

  12. Study of Effect of Ion Source Energy Spread on RFQ Beam Dynamics at REX-ISOLDE

    CERN Document Server

    Fraser, M A

    2013-01-01

    With an upgrade to the Electron Beam Ion Source (EBIS) at REX under consideration a study was launched in order to understand the effect of an increased energy spread from the ion source on the beam dynamics of the RFQ. Due to the increased electron beam potential needed to achieve the upgrade’s charge breeding specification it is expected that the energy spread of the beam will increase from today’s estimated value of approximately +-0.1%. It is shown through beam dynamics simulations that the energy spread can be increased to +-1% without significant degradation of the beam quality output by the RFQ.

  13. Bioelectrochemical probing of intracellular redox processes in living yeast cells—application of redox polymer wiring in a microfluidic environment

    DEFF Research Database (Denmark)

    Heiskanen, Arto; Coman, Vasile; Kostesha, Natalie

    2013-01-01

    utilizing a new double mediator system to map redox metabolism and screen for genetic modifications in Saccharomyces cerevisiae cells. The function of this new double mediator system based on menadione and osmium redox polymer (PVI-Os) is demonstrated. “Wiring” of S. cerevisiae cells using PVI-Os shows...... mutant EBY44, which lacks the enzyme phosphoglucose isomerase. The cellular responses to introduced glucose and fructose were recorded for the two S. cerevisiae strains, and the obtained results are compared with previously published work when using an electrochemical batch cell, indicating...

  14. RHIC PLANS TOWARDS HIGHER LUMINOSITY

    Energy Technology Data Exchange (ETDEWEB)

    FEDOTOV,A.

    2007-06-25

    The Relativistic Heavy Ion Collider (RHIC) is designed to provide luminosity over a wide range of beam energies and species, including heavy ions, polarized protons, and tric beam collisions. In the first seven years of operation there has been a rapid increase in the achieved peak and average luminosity, substantially exceeding design values. Work is presently underway to achieve the Enhanced Design parameters. Planned major upgrades include the Electron Beam Ion Source (EBIS), RHIC-11, and construction of an electron-ion collider (eRHIC). We review the expected RHIC upgrade performance. Electron cooling and its impact on the luminosity both for heavy ions and protons are discussed in detail.

  15. 11. international conference on ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Leitner, D.; Lyneis, C.; Cheng, D.; Galloway, M.L.; Leitner, M.; Todd, D.S.; Ciavola, G.; Gammino, S.; Celona, L.; Ando, L.; Torrisi, L.; Cavenago, M.; Galata, A.; Spaedtke, P.; Tinschert, K.; Lang, R.; Iannucci, R.; Leroy, R.; Barue, C.; Hitz, D.; Koivisto, H.; Suominen, P.; Tarvainen, O.; Beijers, H.; Brandenburg, S.; Vanrooyen, D.; Hillo, C.; Kuchler, D.; Homeyer, H.; Rohrich, J.; Schachter, L.; Dobrescu, S.; Nakagawa, T.; Higurashi, Y.; Kidera, M.; Aihara, T.; Kase, M.; Goto, A.; Yang, Y.; Zhao, H.W.; Zhang, Z.M.; Zhang, X.Z.; Guo, X.H.; He, W.E.; Sun, L.T.; Yuan, P.; Song, M.T.; Xie, Z.Q.; Cao, Y.; Zhan, W.L.; Wei, B.W.; Bricault, P.; Lau, C.; Essabaa, S.; Cheikh Mhamed, M.; Bajeat, O.; Ducourtieux, M.; Lefort, H.; Panteleev, V.N.; Barzakh, A.E.; Fedorov, D.V.; Ionan, A.M.; Mezilev, K.A.; Moroz, F.V.; Orlov, S.Y.; Volkov, Y.M.; Andrighetto, A.; Lhersonneau, G.; Rizzi, V.; Tecchio, L.B.; Dubois, M.; Gaubert, G.; Jardins, P.; Lecesne, N.; Leroy, R.; Pacquet, J.Y.; Saint Laurent, M.G.; Villari, A.C.O.; Bajeat, O.; Essabaa, S.; Lau, C.; Menna, M.; Franberg, H.; Ammann, M.; Gdggeler, H.W.; Koster, U.; Allen, F.; Biedermann, C.; Radtke, R.; Ames, F.; Baartman, R.; Bricault, P.; Jayamanna, K.; Lamy, T.; McDonald, M.; Olivo, M.; Schmorl, P.; Yuan, D.H.L.; Asaji, T.; Sasaki, H.; Kato, Y.; Atabaev, B.; Radjabov, S.S.; Akhmadjanova, M.K.; Yuzikaeva, F.R.; Baoqun, Cui; Liqiang, Li; Yingjun, Ma; Shengyun, Zhu; Cong, Jiang

    2005-07-01

    This document gathers the summaries of the presentations made at ICIS05 (international conference on ion sources). It can be organized into 3 main topics: 1) 'fundamentals and theory' that deals with plasma, beam extraction, transport and emittance, diagnostics and simulation; 2) 'various types of ion sources' that include ECRIS, EBIS, microwave, negative, radioactive, polarized and laser ion sources, and charge breeders; and 3) 'ion sources and applications' in fields like accelerator injection, fusion energy, space propulsion, mass spectrometry, and neutron and cluster and rare nuclide production.

  16. Simulation of hydrological cycle in an urbanized catchment and effect evaluation of infiltration facilities

    OpenAIRE

    賈, 仰文; 倪, 广恒; 河原, 能久; 末次, 忠司

    2000-01-01

    A distributed hydrological model is applied to simulate water balance in the Ebi river catchment (27km2) with a grid size of 50m and a time step of 1 hour. The simulation of 5 years from 1992 to 1996 is performed. The model is verified through comparisons of simulated river discharges and groundwater levels with the observed values. The comparison of water balance at present (1993) with that in future (2035) is also conducted and it shows the impact of urbanization. To conserve hydrological c...

  17. High-Intensity, High Charge-State Heavy Ion Sources

    CERN Document Server

    Alessi, J

    2004-01-01

    There are many accelerator applications for high intensity heavy ion sources, with recent needs including dc beams for RIA, and pulsed beams for injection into synchrotrons such as RHIC and LHC. The present status of sources producing high currents of high charge state heavy ions will be reviewed. These sources include ECR, EBIS, and Laser ion sources. The benefits and limitations for these type sources will be described, for both dc and pulsed applications. Possible future improvements in these type sources will also be discussed.

  18. The physics of Electron Beam Ion Sources

    Energy Technology Data Exchange (ETDEWEB)

    Stockli, M.P.; Cocke, C.L.

    1990-01-01

    There are 13 Electron Beam Ion Sources in operation which produce highly charged ions, up to Th[sup 80+] and Xe[sup 53+]. Most of the sources are used to study these ions under electron impact or when recombining with gaseous or solid targets. That provides an insight into the atomic physics of these highly charged ions and into the physics of the plasma in which such ions can be found. This paper reviews the present knowledge of atomic processes, important in the production of such ions with an EBIS.

  19. The physics of Electron Beam Ion Sources

    Energy Technology Data Exchange (ETDEWEB)

    Stockli, M.P.; Cocke, C.L.

    1990-12-31

    There are 13 Electron Beam Ion Sources in operation which produce highly charged ions, up to Th{sup 80+} and Xe{sup 53+}. Most of the sources are used to study these ions under electron impact or when recombining with gaseous or solid targets. That provides an insight into the atomic physics of these highly charged ions and into the physics of the plasma in which such ions can be found. This paper reviews the present knowledge of atomic processes, important in the production of such ions with an EBIS.

  20. Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India

    Directory of Open Access Journals (Sweden)

    Anjana Ghelani

    2015-06-01

    Full Text Available A taxonomic description of bacteria was deduced from 5.78 Mb metagenomic sequence retrieved from Tulsi Shyam hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP. Metagenome contained 10,893 16S rDNA sequences that were analyzed by MG-RAST server to generate the comprehensive profile of bacteria. Metagenomic data are available at EBI under EBI Metagenomics database with accession no. ERP009559. Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome. Most abundant phyla were Firmicutes (65.38%, Proteobacteria (21.21% and unclassified bacteria (10.69%. Whereas, Peptostreptococcaceae (37.33%, Clostridiaceae (23.36%, and Enterobacteriaceae (16.37% were highest reported families in metagenome. Ubiquitous species were Clostridium bifermentans (17.47%, Clostridium lituseburense (13.93% and uncultured bacterium (10.15%. Our data provide new information on hot spring bacteria and shed light on their abundance, diversity, distribution and coexisting organisms.

  1. Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India.

    Science.gov (United States)

    Ghelani, Anjana; Patel, Rajesh; Mangrola, Amitsinh; Dudhagara, Pravin

    2015-06-01

    A taxonomic description of bacteria was deduced from 5.78 Mb metagenomic sequence retrieved from Tulsi Shyam hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome contained 10,893 16S rDNA sequences that were analyzed by MG-RAST server to generate the comprehensive profile of bacteria. Metagenomic data are available at EBI under EBI Metagenomics database with accession no. ERP009559. Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome. Most abundant phyla were Firmicutes (65.38%), Proteobacteria (21.21%) and unclassified bacteria (10.69%). Whereas, Peptostreptococcaceae (37.33%), Clostridiaceae (23.36%), and Enterobacteriaceae (16.37%) were highest reported families in metagenome. Ubiquitous species were Clostridium bifermentans (17.47%), Clostridium lituseburense (13.93%) and uncultured bacterium (10.15%). Our data provide new information on hot spring bacteria and shed light on their abundance, diversity, distribution and coexisting organisms.

  2. Status of the REX-ISOLDE project

    Science.gov (United States)

    Kester, O.; Habs, D.; Sieber, T.; Bongers, H.; Rudolph, K.; Kolbe, A.; Thirolf, P.; Bollen, G.; Deloose, I.; Evensen, A. H.; Ravn, H.; Ames, F.; Schmidt, P.; Huber, G.; von Hahn, R.; Podlech, H.; Repnow, R.; Schwalm, D.; Liljeby, L.; Rensfelt, K. G.; Wenander, F.; Jonsson, B.; Nyman, G.; Schempp, A.; Kühnel, K.-U.; Welsch, C.; Ratzinger, U.; van Duppen, P.; Huyse, M.; Weismann, L.; Shotter, A.; Ostrowski, A.; Davison, T.; Woods, P. J.

    1999-06-01

    The Radioactive beam Experiment (REX-ISOLDE)(1,2,3) at ISOLDE/CERN is under progress and first tests are carried out with some of the structures. The radioactive ions from the online mass separator ISOLDE will be cooled and bunched in a Penning trap, charge bred in an electron beam ion source (EBIS) and finally accelerated in a short LINAC to a target energy between 0.8 and 2.2 MeV/u. The LINAC consists of a radio frequency quadrupole (RFQ) accelerator, which accelerates the ions up to 0.3 MeV/u, an interdigital H-type (IH) structure with a final energy between 1.1 and 1.2 MeV/u and three seven gap resonators, which allow the variation of the final energy. All components of the experiment are now in production or undergo first test measurements. Such measurements are ion capture tests of the trap, electron beam tests of the EBIS, low level measurements and first power tests of the RFQ and the first 7-gap resonator. In this paper the status of the experiment, and the proposed schedule are presented.

  3. InterProScan: protein domains identifier.

    Science.gov (United States)

    Quevillon, E; Silventoinen, V; Pillai, S; Harte, N; Mulder, N; Apweiler, R; Lopez, R

    2005-07-01

    InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics, 17, 847-848] is a tool that combines different protein signature recognition methods from the InterPro [N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bradley, P. Bork, P. Bucher, L. Cerutti et al. (2005) Nucleic Acids Res., 33, D201-D205] consortium member databases into one resource. At the time of writing there are 10 distinct publicly available databases in the application. Protein as well as DNA sequences can be analysed. A web-based version is accessible for academic and commercial organizations from the EBI (http://www.ebi.ac.uk/InterProScan/). In addition, a standalone Perl version and a SOAP Web Service [J. Snell, D. Tidwell and P. Kulchenko (2001) Programming Web Services with SOAP, 1st edn. O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results.

  4. Advancing Behavioral HIV Prevention: Adapting an Evidence-Based Intervention for People Living with HIV and Alcohol Use Disorders

    Directory of Open Access Journals (Sweden)

    M. L. Armstrong

    2015-01-01

    Full Text Available Alcohol use disorders (AUDs are highly prevalent among people living with HIV/AIDS (PLWHA and are associated with increased HIV risk behaviors, suboptimal treatment adherence, and greater risk for disease progression. We used the ADAPT-ITT strategy to adapt an evidence-based intervention (EBI, the Holistic Health Recovery Program (HHRP+, that focuses on secondary HIV prevention and antiretroviral therapy (ART adherence and apply it to PLWHA with problematic drinking. Focus groups (FGs were conducted with PLWHA who consume alcohol and with treatment providers at the largest HIV primary care clinic in New Orleans, LA. Overall themes that emerged from the FGs included the following: (1 negative mood states contribute to heavy alcohol consumption in PLWHA; (2 high levels of psychosocial stress, paired with few adaptive coping strategies, perpetuate the use of harmful alcohol consumption in PLWHA; (3 local cultural norms are related to the permissiveness and pervasiveness of drinking and contribute to heavy alcohol use; (4 healthcare providers unanimously stated that outpatient options for AUD intervention are scarce, (5 misperceptions about the relationships between alcohol and HIV are common; (6 PLWHA are interested in learning about alcohol’s impact on ART and HIV disease progression. These data were used to design the adapted EBI.

  5. Simulation and optimization of a 10 A electron gun with electrostatic compression for the electron beam ion source.

    Science.gov (United States)

    Pikin, A; Beebe, E N; Raparia, D

    2013-03-01

    Increasing the current density of the electron beam in the ion trap of the Electron Beam Ion Source (EBIS) in BNL's Relativistic Heavy Ion Collider facility would confer several essential benefits. They include increasing the ions' charge states, and therefore, the ions' energy out of the Booster for NASA applications, reducing the influx of residual ions in the ion trap, lowering the average power load on the electron collector, and possibly also reducing the emittance of the extracted ion beam. Here, we discuss our findings from a computer simulation of an electron gun with electrostatic compression for electron current up to 10 A that can deliver a high-current-density electron beam for EBIS. The magnetic field in the cathode-anode gap is formed with a magnetic shield surrounding the gun electrodes and the residual magnetic field on the cathode is (5 ÷ 6) Gs. It was demonstrated that for optimized gun geometry within the electron beam current range of (0.5 ÷ 10) A the amplitude of radial beam oscillations can be maintained close to 4% of the beam radius by adjusting the injection magnetic field generated by a separate magnetic coil. Simulating the performance of the gun by varying geometrical parameters indicated that the original gun model is close to optimum and the requirements to the precision of positioning the gun elements can be easily met with conventional technology.

  6. Irradiated Graphene Loaded with SnO₂ Quantum Dots for Energy Storage.

    Science.gov (United States)

    Huang, Ruting; Wang, Lijun; Zhang, Qian; Chen, Zhiwen; Li, Zhen; Pan, Dengyu; Zhao, Bing; Wu, Minghong; Wu, C M Lawrence; Shek, Chan-Hung

    2015-11-24

    Tin dioxide (SnO2) and graphene are unique strategic functional materials with widespread technological applications, particularly in the areas of solar batteries, optoelectronic devices, and solid-state gas sensors owing to advances in optical and electronic properties. Versatile strategies for microstructural evolution and related performance of SnO2 and graphene composites are of fundamental importance in the development of electrode materials. Here we report that a novel composite, SnO2 quantum dots (QDs) supported by graphene nanosheets (GNSs), has been prepared successfully by a simple hydrothermal method and electron-beam irradiation (EBI) strategies. Microstructure analysis indicates that the EBI technique can induce the exfoliation of GNSs and increase their interlayer spacing, resulting in the increase of GNS amorphization, disorder, and defects and the removal of partial oxygen-containing functional groups on the surface of GNSs. The investigation of SnO2 nanoparticles supported by GNSs (SnO2/GNSs) reveals that the GNSs are loaded with SnO2 QDs, which are dispersed uniformly on both sides of GNSs. Interestingly, the electrochemical performance of SnO2/GNSs indicates that SnO2 QDs supported by a 210 kGy irradiated GNS shows excellent cycle response, high specific capacity, and high reversible capacity. This novel SnO2/GNS composite has potential practical applications in SnO2 electrode materials during Li(+) insertion/extraction.

  7. Effects of Mobility-Enhancing Nursing Intervention in Patients with MS and Stroke: Randomised Controlled Trial.

    Science.gov (United States)

    Imhof, Lorenz; Suter-Riederer, Susanne; Kesselring, Jürg

    2015-01-01

    Background. Multiple sclerosis (MS) or stroke causes functional impairment which can have a major impact on patients' life. Objectives. This RCT investigated the effect of a new nursing intervention (Mobility Enhancing Nursing Intervention-MFP) designed to improve rehabilitation outcomes. Method. The study took place in a rehabilitation clinic in Switzerland. One hundred forty participants diagnosed with MS, stroke, and brain injuries were randomly assigned to control group (CG = standard care) or intervention group (IG). The IG combined standard care with 30 days of MFB. MFP placed patients on a mattress on the floor and used tactile-kinaesthetic stimulation to increase spatial orientation and independency. Outcomes were functionality (Extended Barthel Index, EBI), quality of life (WHOQoL), and fall-related self-efficacy (FES-I). Results. There was a significant main effect of the intervention on functionality (EBI-diff/day mean = 0.30, versus mean = 0.16, P = 0.008). There was also a significant main effect on QoL (WHOQoL-diff mean = 13.8, versus mean = 5.4, P = 0.046). No significant effect was observed on fall-related self-efficacy. Conclusions. The positive effect of MFP on rehabilitation outcomes and quality of life suggests that this specialized nursing intervention could become an effective part of rehabilitation programs. The study was approved by the Ethics Committee of St. Gallen (KEK-SG Nr. 09/021) and registered at ClinicalTrial.gov NCT02198599.

  8. MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.

    Science.gov (United States)

    Haug, Kenneth; Salek, Reza M; Conesa, Pablo; Hastings, Janna; de Matos, Paula; Rijnbeek, Mark; Mahendraker, Tejasvi; Williams, Mark; Neumann, Steffen; Rocca-Serra, Philippe; Maguire, Eamonn; González-Beltrán, Alejandra; Sansone, Susanna-Assunta; Griffin, Julian L; Steinbeck, Christoph

    2013-01-01

    MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.

  9. MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

    Science.gov (United States)

    Haug, Kenneth; Salek, Reza M.; Conesa, Pablo; Hastings, Janna; de Matos, Paula; Rijnbeek, Mark; Mahendraker, Tejasvi; Williams, Mark; Neumann, Steffen; Rocca-Serra, Philippe; Maguire, Eamonn; González-Beltrán, Alejandra; Sansone, Susanna-Assunta; Griffin, Julian L.; Steinbeck, Christoph

    2013-01-01

    MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry. PMID:23109552

  10. [Protective effect of mitochondria-targeted antioxidant SS31 on early brain injury following subarachnoid hemorrhage in rats].

    Science.gov (United States)

    Zhou, Jian; Li, Zhengzheng; Chen, Zhenggang; Yang, Kun

    2017-09-28

    To evaluate protective effects of SS31 on early brain injury (EBI) induced by subarachnoid hemorrhage (SAH) in rats.
 Methods: A total of 96 Sprague-Dawley rats were randomly divided into 4 groups: A sham group, an SAH group, an SAH+vehicle group (SAH+V), and an SAH+SS31 group. The SAH-induced prechiasmatic cistern rat model was established in this study. Neurological deficit scores were evaluated at 24 h after SAH. The SS31 (5 mg/kg) as well as equal volume of vehicle were administrated intraperitoneally at 2 h after SAH. The neurological scores, brain edema, blood-brain barrier (BBB) permeability, apoptosis, malondialdehyde (MDA), glutathione peroxidase (GPx) activity, superoride dismutase (SOD) activity, and the expression of cytosolic cytochrome c (Cyt C) and Bax were analyzed at 24 h after SAH.
 Results: Treatment with SS31 could significantly reduce MDA levels, and restored the activities of GPx and SOD in the cortex following SAH when compared with the SAH+V group. In addition, Bax SS31 trearment increased or decreased the levels of mitochondrial Cyt C or Bax, respectively. Moreover, SS31 treatment ameliorated brain edema and Evans blue dye extravasation, improved neurological deficits, and decreased neuronal apoptosis at 24 h after SAH.
 Conclusion: SS31 could alleviate EBI after SAH through its antioxidant property and ability in inhibition of neuronal apoptosis.

  11. Interleukin 27 inhibits atherosclerosis via immunoregulation of macrophages in mice.

    Science.gov (United States)

    Hirase, Tetsuaki; Hara, Hiromitsu; Miyazaki, Yoshiyuki; Ide, Noriko; Nishimoto-Hazuku, Ai; Fujimoto, Hirokazu; Saris, Christiaan J M; Yoshida, Hiroki; Node, Koichi

    2013-08-01

    Chronic inflammation in arterial wall that is driven by immune cells and cytokines plays pivotal roles in the development of atherosclerosis. Interleukin 27 (IL-27) is a member of the IL-12 family of cytokines that consists of IL-27p28 and Epstein-Barr virus induced gene 3 (EBI3) and has anti-inflammatory properties that regulate T cell polarization and cytokine production. IL-27-deficient (Ldlr-/-Ebi3-/-) and IL-27 receptor-deficient (Ldlr-/-WSX-1-/-) Ldlr-/- mice were generated and fed with a high-cholesterol diet to induce atherosclerosis. Roles of bone marrow-derived cells in vivo and macrophages in vitro were studied using bone marrow reconstitution by transplantation and cultured peritoneal macrophages, respectively. We demonstrate that mice lacking IL-27 or IL-27 receptor are more susceptible to atherosclerosis compared with wild type due to enhanced accumulation and activation of macrophages in arterial walls. The number of circulating proinflammatory Ly6C(hi) monocytes showed no significant difference between wild-type mice and mice lacking IL-27 or IL-27 receptor. Administration of IL-27 suppressed the development of atherosclerosis in vivo and macrophage activation in vitro that was indicated by increased uptake of modified low-density lipoprotein and augmented production of proinflammatory cytokines. These findings define a novel inhibitory role for IL-27 in atherosclerosis that regulates macrophage activation in mice.

  12. DNA sequence chromatogram browsing using JAVA and CORBA.

    Science.gov (United States)

    Parsons, J D; Buehler, E; Hillier, L

    1999-03-01

    DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

  13. Development of a new RFQ beam cooler and buncher for the CANREB project at TRIUMF

    Energy Technology Data Exchange (ETDEWEB)

    Barquest, B.R. [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada); Bale, J.C.; Dilling, J. [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada); UBC Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver, BC V6T 1Z1 (Canada); Gwinner, G. [University of Manitoba, Department of Physics and Astronomy, Allen Building, Winnipeg, MB R3T 2N2 (Canada); Kanungo, R. [Saint Mary’s University, Astronomy and Physics Department, 923 Robie Street, Halifax, NS B3H 3C3 (Canada); Krücken, R. [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada); UBC Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver, BC V6T 1Z1 (Canada); Pearson, M.R. [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada)

    2016-06-01

    A new radiofrequency quadrupole (RFQ) based ion beam cooler and buncher is under development for the CANadian Rare-isotope facility with Electron Beam ion source (CANREB) project at TRIUMF. The CANREB project requires an RFQ buncher that will efficiently accept continuous beams of rare isotopes from either the Advanced Rare IsotopE Laboratory (ARIEL) or Isotope Separator and ACcelerator (ISAC) target by way of a high resolution magnetic spectrometer, with energies up to 60 keV and deliver bunched beams to an electron beam ion source (EBIS) for charge breeding. The energy of the bunched beam delivered to the EBIS will be adjustable to match the requirements of the existing post acceleration infrastructure. The CANREB RFQ incorporates design considerations to facilitate ease of use over a wide range of ion masses, and is intended to accommodate incident beam rates as high as 10{sup 8} pps, delivering beam bunches at 100 Hz. An overview of the CANREB RFQ design concept will be presented, informed by results from both ion optical simulations as well as commissioning efforts with other beam cooler and buncher devices. Simulation results indicate that the design is well suited to deliver high quality bunched beams with high efficiency with as many as 10{sup 6} ions per bunch.

  14. Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India

    Directory of Open Access Journals (Sweden)

    Amit V. Mangrola

    2015-06-01

    Full Text Available This is the first report on the metagenomic approach for unveiling the microbial diversity of Lasundra hot spring, Gujarat State, India. High-throughput sequencing of community DNA was performed on an Ion Torrent PGM platform. Metagenome consisted of 606,867 sequences represent 98,567,305 bps size with an average length of 162 bps and 46% G + C content. Metagenome sequence information is available at EBI under EBI Metagenomic database with accession no. ERP009313. MG-RAST assisted community analysis revealed that 99.21% sequences were bacterial origin, 0.43% was fit to eukaryotes and 0.11% belongs to archaea. A total of 29 bacterial, 20 eukaryotic and 4 archaeal phyla were detected. Abundant genera were Bacillus (86.7%, Geobacillus (2.4%, Paenibacillus (1.0%, Clostridium (0.7% and Listeria (0.5%, that represent 91.52% in metagenome. In functional analysis, Cluster of Orthologous Group (COG based annotation revealed that 45.4% was metabolism connected and 19.6% falls in poorly characterized group. Subsystem based annotation approach suggests that the 14.0% was carbohydrates, 7.0% was protein metabolism and 3.0% genes for various stress responses together with the versatile presence of commercially useful traits.

  15. Prostaglandin E2 EP4 Receptor Activation Attenuates Neuroinflammation and Early Brain Injury Induced by Subarachnoid Hemorrhage in Rats.

    Science.gov (United States)

    Xu, Jie; Xu, Zhen; Yan, Ai

    2017-02-27

    Activation of E prostanoid 4 receptor (EP4) shows neuroprotective effects in multiple central nervous system (CNS) lesions, but the roles of EP4 receptor in subarachnoid hemorrhage (SAH) are not explored. This study was designed to research the effects of EP4 modulation on early brain injury (EBI) after experimental SAH in rats. We found that the administration of EP4 selective agonist AE1-329 significantly improved neurological dysfunction, blood brain barrier (BBB) damage and brain edema at 24 h after SAH. Furthermore, AE1-329 obviously reduced the number of activated microglia and the mRNA and protein levels of pro-inflammatory cytokines, and increased Ser1177 phosphorylated endothelial nitric oxide synthase (Ser1177 p-eNOS). Moreover, AE1-329 significantly reduced the number of TUNEL-positive cells and active caspase-3 in cortex after SAH. The EP4 selective antagonist AE3-208 was also administrated and the opposite effects were achieved. Our results indicate that activation of EP4 protects brain from EBI through downregulating neuroinflammation reaction after SAH.

  16. IL-35 is a novel cytokine with therapeutic effects against collagen-induced arthritis through the expansion of regulatory T cells and suppression of Th17 cells.

    Science.gov (United States)

    Niedbala, Wanda; Wei, Xiao-Qing; Cai, Beilei; Hueber, Axel J; Leung, Bernard P; McInnes, Iain B; Liew, Foo Y

    2007-11-01

    Epstein-Barr virus-induced gene 3 (EBI3) and the p35 subunit of IL-12 have been reported to form a heterodimeric hematopoietin in human and mouse. We have constructed a heterodimeric protein covalently linking EBI3 and p35, to form a novel cytokine which we now call IL-35. The Fc fusion protein of IL-35 induced proliferation of murine CD4(+)CD25(+) and CD4(+)CD25(-) T cells when stimulated with immobilized anti-CD3 and anti-CD28 antibodies in vitro. The IL-35-expanded CD4(+)CD25(+) T cell population expressed Foxp3 and produced elevated levels of IL-10, whereas the IL-35-induced CD4(+)CD25(-) T cells produced IFN-gamma but not IL-4. The in vitro expanded CD4(+)CD25(+) T cells retained their suppressive functions against CD4(+)CD25(-) effector cells. Furthermore, when cultured with soluble anti-CD3 antibody and antigen-presenting cells, IL-35 suppressed the proliferation of CD4(+)CD25(-) effector cells. Moreover, IL-35 inhibited the differentiation of Th17 cells in vitro. In vivo, IL-35 effectively attenuated established collagen-induced arthritis in mice, with concomitant suppression of IL-17 production but enhanced IFN-gamma synthesis. Thus, IL-35 is a novel anti-inflammatory cytokine suppressing the immune response through the expansion of regulatory T cells and suppression of Th17 cell development.

  17. Decreased IL-35 levels in patients with immune thrombocytopenia.

    Science.gov (United States)

    Yang, Yanhui; Xuan, Min; Zhang, Xian; Zhang, Donglei; Fu, Rongfeng; Zhou, Fangfang; Ma, Li; Li, Huiyuan; Xue, Feng; Zhang, Lei; Yang, Renchi

    2014-08-01

    IL-35 is a novel heterodimeric anti-inflammatory cytokine consisting of Epstein-Barr virus-induced gene 3 (EBI3) and the p35 subunit of IL-12. IL-35 has been shown to possess the potency of inhibiting the CD4+ effector T cells and alleviating autoimmune diseases. In the study we investigated the levels of IL-35 as well as its prospective role in immune thrombocytopenia (ITP).ELISA was adopted to measure plasma IL-35, TGF-β and IL-10 levels. The mRNA expression levels of P35 and EBI3 in peripheral blood mononuclear cells (PBMCs) were studied based on real-time quantitative PCR. The correlation between plasma cytokine levels and clinical parameters was analyzed. Significantly lower plasma IL-35 levels were found in active ITP patients compared with those in remission (p = 0.017) and the healthy controls (p IL-35 levels displayed a significantly positive correlation with platelet counts (r = 0.5335, p IL-35 levels in ITP patients, suggesting that IL-35 may be involved in the pathogenesis of ITP.

  18. Retaining clients in an outcome monitoring evaluation study: HIV prevention efforts in community settings.

    Science.gov (United States)

    Smith, Bryce D; Kalayil, Elizabeth J; Patel-Larson, Alpa; Chen, Brenda; Vaughan, Marla

    2012-02-01

    The Centers for Disease Control and Prevention (CDC), Division of HIV/AIDS Prevention (DHAP) conducted outcome monitoring studies on evidence-based interventions (EBIs) provided by CDC-funded community-based organizations (CBOs). Critical to the success of outcome monitoring was the ability of CBOs to recruit and retain clients in evaluation studies. Two EBIs, Video Opportunities for Innovative Condom Education and Safer Sex (VOICES/VOCES) and Healthy Relationships, were evaluated using repeated measure studies, which require robust follow-up retention rates to increase the validity and usefulness of the findings. The retention rates were high for both VOICES/VOCES CBOs (95.8% at 30 days and 91.1% at 120 days), and Healthy Relationships CBOs (89.5% at 90 days and 83.5% at 180 days). This paper presents an overview of the retention of clients, challenges to follow-up, and strategies developed by CBOs to achieve high retention rates. These strategies and rates are discussed within the context of the CBOs' target populations and communities. Published by Elsevier Ltd.

  19. The human-induced pluripotent stem cell initiative—data resources for cellular genetics

    Science.gov (United States)

    Streeter, Ian; Harrison, Peter W.; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen; Clarke, Laura

    2017-01-01

    The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases. The project will make 500 cell lines from healthy individuals, and from 150 patients with rare genetic diseases; these will be available through the European Collection of Authenticated Cell Cultures (ECACC). As of August 2016, 238 cell lines are available for purchase. Project data is presented through the HipSci data portal (http://www.hipsci.org/lines) and is downloadable from the associated FTP site (ftp://ftp.hipsci.ebi.ac.uk/vol1/ftp). The data portal presents a summary matrix of the HipSci cell lines, showing available data types. Each line has its own page containing descriptive metadata, quality information, and links to archived assay data. Analysis results are also available in a Track Hub, allowing visualization in the context of public genomic annotations (http://www.hipsci.org/data/trackhubs). PMID:27733501

  20. The human-induced pluripotent stem cell initiative-data resources for cellular genetics.

    Science.gov (United States)

    Streeter, Ian; Harrison, Peter W; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen; Clarke, Laura

    2017-01-04

    The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases. The project will make 500 cell lines from healthy individuals, and from 150 patients with rare genetic diseases; these will be available through the European Collection of Authenticated Cell Cultures (ECACC). As of August 2016, 238 cell lines are available for purchase. Project data is presented through the HipSci data portal (http://www.hipsci.org/lines) and is downloadable from the associated FTP site (ftp://ftp.hipsci.ebi.ac.uk/vol1/ftp). The data portal presents a summary matrix of the HipSci cell lines, showing available data types. Each line has its own page containing descriptive metadata, quality information, and links to archived assay data. Analysis results are also available in a Track Hub, allowing visualization in the context of public genomic annotations (http://www.hipsci.org/data/trackhubs). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. "Boring" family routines reduce non-communicable diseases: a commentary and call for action.

    Science.gov (United States)

    Rotheram-Borus, Mary Jane; Tomlinson, Mark; Davis, Emily

    2015-01-01

    As global donors shift their efforts from infectious diseases to non-communicable diseases (NCD), it is critical to capitalize on our prior mistakes and successes. Policy makers and public health administrators are often looking for magic bullets: drugs or treatments to eradicate disease. Yet, each potential magic bullet requires consistent, daily implementation and adherence to a new set of habits to actually work. Families' and communities' daily, interlocking routines will be the battlefield on which scientific and technological breakthroughs will be implemented and succeed or not. Currently, there are many evidence-based interventions (EBI) which have been demonstrated to shift specific habits which account for most NCD (eating, drinking, moving, and smoking). Yet, securing sustained uptake of these programs is rare - suggesting different intervention strategies are needed. Structural changes, policy nudges, and partnerships with private enterprise may be able to shift the health behaviors of more citizens faster and at a lower cost than existing EBI. Addressing concurrent risk and protective factors at the community level and intervening to shape new cultural routines may be useful to reduce NCD.

  2. Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

    Science.gov (United States)

    Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

    2010-11-01

    Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

  3. Mean Expected Error in Prediction of Total Body Water: A True Accuracy Comparison between Bioimpedance Spectroscopy and Single Frequency Regression Equations.

    Science.gov (United States)

    Seoane, Fernando; Abtahi, Shirin; Abtahi, Farhad; Ellegård, Lars; Johannsson, Gudmundur; Bosaeus, Ingvar; Ward, Leigh C

    2015-01-01

    For several decades electrical bioimpedance (EBI) has been used to assess body fluid distribution and body composition. Despite the development of several different approaches for assessing total body water (TBW), it remains uncertain whether bioimpedance spectroscopic (BIS) approaches are more accurate than single frequency regression equations. The main objective of this study was to answer this question by calculating the expected accuracy of a single measurement for different EBI methods. The results of this study showed that all methods produced similarly high correlation and concordance coefficients, indicating good accuracy as a method. Even the limits of agreement produced from the Bland-Altman analysis indicated that the performance of single frequency, Sun's prediction equations, at population level was close to the performance of both BIS methods; however, when comparing the Mean Absolute Percentage Error value between the single frequency prediction equations and the BIS methods, a significant difference was obtained, indicating slightly better accuracy for the BIS methods. Despite the higher accuracy of BIS methods over 50 kHz prediction equations at both population and individual level, the magnitude of the improvement was small. Such slight improvement in accuracy of BIS methods is suggested insufficient to warrant their clinical use where the most accurate predictions of TBW are required, for example, when assessing over-fluidic status on dialysis. To reach expected errors below 4-5%, novel and individualized approaches must be developed to improve the accuracy of bioimpedance-based methods for the advent of innovative personalized health monitoring applications.

  4. Detection of (reversible) myocardial ischemic injury by means of electrical bioimpedance.

    Science.gov (United States)

    Mellert, Fritz; Winkler, Kai; Schneider, Christian; Dudykevych, Taras; Welz, Armin; Osypka, Markus; Gersing, Eberhard; Preusse, Claus J

    2011-06-01

    The scope of this paper was to determine whether ischemic and reperfusion damage in cardiac surgery can be detected by measurement of electrical bioimpedance (EBI). Conventional pacing wires were replaced by pacing wires with sputtered iridium coating in order to reduce polarization associated with two-electrode impedance measurements. A custom-built bioimpedance analyzer (Osypka Medical GmbH, Berlin, Germany) measured the real part of impedance Re(Z) and the phase (ϕ) at three frequencies (1, 10, and 1000 kHz) and determined an extracellular space index (EZRI) as the quotient of Re(Z) at 1000 kHz and Re(Z) at 1 kHz. Our study included six patients (conventional coronary artery bypass graft, age 68.1 ± 8.3 years) subject to routine cardioplegic ischemia and reperfusion. Preischemic bioimpedance measurements were not impaired by interference of the beating heart. Intraischemically, bioimpedance at 1 kHz and phase at 10 kHz increased until opening of a bypass graft, which is probably induced by closure of gap junctions and cell swelling processes. After cross clamping, EZRI slowly decreased as an effect of mild cell swelling. After ischemia, values returned almost to baseline measurements, indicating sufficient reperfusion processes. Measurement of EBI correlates with myocardial ischemic injury and is applicable in a two-electrode setup providing low-polarization pacing wires.

  5. easyDAS: Automatic creation of DAS servers

    Directory of Open Access Journals (Sweden)

    Jimenez Rafael C

    2011-01-01

    Full Text Available Abstract Background The Distributed Annotation System (DAS has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.

  6. Kinetic energy offsets for multicharged ions from an electron beam ion source.

    Science.gov (United States)

    Kulkarni, D D; Ahl, C D; Shore, A M; Miller, A J; Harriss, J E; Sosolik, C E; Marler, J P

    2017-08-01

    Using a retarding field analyzer, we have measured offsets between the nominal and measured kinetic energy of multicharged ions extracted from an electron beam ion source (EBIS). By varying source parameters, a shift in ion kinetic energy was attributed to the trapping potential produced by the space charge of the electron beam within the EBIS. The space charge of the electron beam depends on its charge density, which in turn depends on the amount of negative charge (electron beam current) and its velocity (electron beam energy). The electron beam current and electron beam energy were both varied to obtain electron beams of varying space charge and these were related to the observed kinetic energy offsets for Ar(4+) and Ar(8+) ion beams. Knowledge of these offsets is important for studies that seek to utilize slow, i.e., low kinetic energy, multicharged ions to exploit their high potential energies for processes such as surface modification. In addition, we show that these offsets can be utilized to estimate the effective radius of the electron beam inside the trap.

  7. Permanent magnet electron beam ion source/trap systems with bakeable magnets for improved operation conditions.

    Science.gov (United States)

    Schmidt, M; Zschornack, G; Kentsch, U; Ritter, E

    2014-02-01

    The magnetic system of a Dresden electron beam ion source (EBIS) generating the necessary magnetic field with a new type of permanent magnet made of high energy density NdFeB-type material operable at temperatures above 100 °C has been investigated and tested. The employment of such kind of magnets provides simplified operation without the time-consuming installation and de-installation procedures of the magnets for the necessary baking of the ion source after commissioning and maintenance work. Furthermore, with the use of a new magnetization technique the geometrical filling factor of the magnetic Dresden EBIS design could be increased to a filling factor of 100% leading to an axial magnetic field strength of approximately 0.5 T exceeding the old design by 20%. Simulations using the finite element method software Field Precision and their results compared with measurements are presented as well. It could be shown that several baking cycles at temperatures higher than 100 °C did not change the magnetic properties of the setup.

  8. Identifying Best Practices for Increasing Linkage to, Retention, and Re-engagement in HIV Medical Care: Findings from a Systematic Review, 1996-2014.

    Science.gov (United States)

    Higa, Darrel H; Crepaz, Nicole; Mullins, Mary M

    2016-05-01

    A systematic review was conducted to identify best practices for increasing linkage, retention and re-engagement in HIV care (LRC) for persons living with HIV (PLWH). Our search strategy consisted of automated searches of electronic databases and hand searches of journals, reference lists and listservs. We developed two sets of criteria: evidence-based to identify evidence-based interventions (EBIs) tested with a comparison group and evidence-informed to identify evidence-informed interventions (EIs) tested with a one-group design. Eligible interventions included being published between 1996 and 2014, U.S.-based studies with a comparison or one-group designs with pre-post data, international randomized controlled trials, and having objective measures of LRC-relevant outcomes. We identified 10 best practices: 5 EBIs and 5 EIs. None focused on re-engagement. Providers and prevention planners can use the review findings to identify best practices suitable for their clinics, agencies, or communities to increase engagement in care for PLWH, ultimately leading to viral suppression.

  9. A hollow cathode ion source for production of primary ions for the BNL electron beam ion source.

    Science.gov (United States)

    Alessi, James; Beebe, Edward; Carlson, Charles; McCafferty, Daniel; Pikin, Alexander; Ritter, John

    2014-02-01

    A hollow cathode ion source, based on one developed at Saclay, has been modified significantly and used for several years to produce all primary 1+ ions injected into the Relativistic Heavy Ion Collider Electron Beam Ion Source (EBIS) at Brookhaven. Currents of tens to hundreds of microamperes have been produced for 1+ ions of He, C, O, Ne, Si, Ar, Ti, Fe, Cu, Kr, Xe, Ta, Au, and U. The source is very simple, relying on a glow discharge using a noble gas, between anode and a solid cathode containing the desired species. Ions of both the working gas and ionized sputtered cathode material are extracted, and then the desired species is selected using an ExB filter before being transported into the EBIS trap for charge breeding. The source operates pulsed with long life and excellent stability for most species. Reliable ignition of the discharge at low gas pressure is facilitated by the use of capacitive coupling from a simple toy plasma globe. The source design, and operating experience for the various species, is presented.

  10. Non-redundant patent sequence databases with value-added annotations at two levels.

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.

  11. Charge state breeding experiences and plans at TRIUMF

    Energy Technology Data Exchange (ETDEWEB)

    Ames, F., E-mail: ames@triumf.ca; Marchetto, M.; Mjøs, A.; Morton, A. C. [TRIUMF, 4004 Wesbrook Mall, Vancouver, British Columbia V6T2A3 (Canada)

    2016-02-15

    At the Isotope Separation and ACceleration (ISAC) facility at TRIUMF, an electron cyclotron resonance ion source (ECRIS) has been set up for the charge state breeding of radioactive ions. In order to reduce background from stable ions generated in the ECRIS, several measures, including changing materials for the plasma chamber and the surrounding components, have been implemented. Further reduction has been achieved by using the post-accelerator chain as a mass filter. Since the implementation of those measures in 2013, physics experiments with accelerated radioactive isotopes of Rb, Sr, K, and Mg have been performed. In most cases, a charge breeding efficiency of several percent has been achieved. With the planned expansion of the isotope production capabilities at TRIUMF within the Advanced Rare IsotopE Laboratory project, two new target stations, one using photo-fission induced by a high-power electron beam at 50 MeV and the other one using 480 MeV protons as at ISAC, will be put into operation within the next 5 yr. Additionally, a new electron beam ion source (EBIS) based charge state breeding system will be installed. Background from such a source is expected to be much lower. The drawback is that for the efficient operation of such a system, pulsed beam operation is required, which makes the installation of an additional ion buncher in front of the EBIS necessary.

  12. Improved mortality of the Formosan subterranean termite by fungi, when amended with cuticle-degrading enzymes or eicosanoid biosynthesis inhibitors.

    Science.gov (United States)

    Wright, Maureen S; Lax, Alan R

    2016-01-01

    Formosan subterranean termites (FST) were exposed to strains of Beauveria pseudobassiana (Bpb) and Isaria fumosorosea (Ifr) to determine virulence of the fungi. Once lethality was determined, sublethal doses of Bpb were combined with enzymes capable of degrading the insect cuticle to measure the potential to enhance fungal infection. Bpb applied to FST in combination with proteinases and a chitinase caused increased mortality over the fungus alone. Mortality was enhanced when Ifr was applied to FST in combination with a chitinase isolated from Serratia marcesans. A lipase isolated from Pseudomonas cepacia, when combined with Ifr, also resulted in greater mortality than all control treatments. FST were also exposed to the eicosanoid biosynthesis inhibitors (EBIs) dexamethasone (DEX), ibuprofen (IBU), and ibuprofen sodium salt (IBUNA), in combination with Ifr. Combining Ifr with IBUNA caused significantly increased mortality on days 6, 7, and 9. Cuticle-degrading enzymes and EBIs may have potential to enhance the pathogenic effect of a fungal control agent against the Formosan subterranean termite.

  13. Role of Mitochondrial Calcium Uniporter in Early Brain Injury After Experimental Subarachnoid Hemorrhage.

    Science.gov (United States)

    Yan, Huiying; Zhang, Dingding; Hao, Shuangying; Li, Kuanyu; Hang, Chun-Hua

    2015-12-01

    Previous studies have shown that mitochondrial Ca(2+) is undertaken by mitochondrial calcium uniporter (MCU), and its accumulation is associated with the development of many diseases. However, little was known about the role of MCU in early brain injury (EBI) after subarachnoid hemorrhage (SAH). MCU can be opened by spermine under a physiological condition and inhibited by ruthenium red (RR). Herein, we investigated the effects of RR and spermine to reveal the role of MCU in SAH animal model. The data obtained with biochemical and histological assays showed that mitochondrial Ca(2+) concentration was significantly increased in the temporal cortex of rats 1, 2, and 3 days after SAH, consistent with constant high levels of cellular Ca(2+) concentration. In agreement with the observation in the acute phase, SAH rats showed an obvious increase of reactive oxygen species (ROS) level and decrease of ATP production. Blockage of MCU prevented Ca(2+) accumulation, abated the level of oxidative stress, and improved the energy supply. Translocation of cytochrome c, increased cleaved caspase-3, and a large amount of apoptotic cells after SAH were reversed by RR administration. Surprisingly, exogenous spermine did not increase cellular Ca(2+) concentration, but lessened the Ca(2+) accumulation after SAH to benefit the rats. Taken together, our results demonstrated that blockage of MCU or prevention of Ca(2+) accumulation after SAH is essential in EBI after SAH. These findings suggest that MCU is considered to be a therapeutic target for patients suffering from SAH.

  14. Respecting the circle of life: one year outcomes from a randomized controlled comparison of an HIV risk reduction intervention for American Indian adolescents.

    Science.gov (United States)

    Tingey, Lauren; Mullany, Britta; Chambers, Rachel; Hastings, Ranelda; Lee, Angelita; Parker, Anthony; Barlow, Allison; Rompalo, Anne

    2015-01-01

    Potential for widespread transmission of HIV/AIDS among American Indian (AI) adolescents exists, yet no evidence-based interventions (EBIs) have been adapted and evaluated with this population. Intensive psychoeducation may improve knowledge and decision-making which could potentially translate to reductions in HIV risk behaviors. A peer group randomized controlled comparison of an adapted EBI vs. control was delivered over an eight-day summer basketball camp in one reservation-based tribal community to adolescents ages 13-19. Outcome data were gathered immediately post-camp and at 6 and 12 months follow-up. Self-selected peer groups were randomized to intervention (n = 138) or control (n = 129) conditions for a total sample of 267 participants (56.2% female), mean age 15.1 years (SD = 1.7). Intervention participants had better condom use self-efficacy post-camp (Adjusted Mean Difference [AMD] = -0.75, p AMD = -0.44, p AMD = -0.23, p AMD = 0.07, p AMD = 0.06, p AMD = 0.37, p impacts on AI adolescent risk for HIV/AIDS, but attenuated at 12 months. Intervention delivery through a community-based camp is feasible and acceptable with strong retention. Additional study is needed to evaluate the adapted intervention's impact on sexual risk behaviors and if booster sessions and parent involvement translate to long-term impacts.

  15. Dendritic cell SIRPα regulates homeostasis of dendritic cells in lymphoid organs.

    Science.gov (United States)

    Washio, Ken; Kotani, Takenori; Saito, Yasuyuki; Respatika, Datu; Murata, Yoji; Kaneko, Yoriaki; Okazawa, Hideki; Ohnishi, Hiroshi; Fukunaga, Atsushi; Nishigori, Chikako; Matozaki, Takashi

    2015-06-01

    Signal regulatory protein α (SIRPα), an immunoglobulin superfamily protein that is expressed predominantly in myeloid lineage cells such as dendritic cells (DCs) or macrophages, mediates cell-cell signaling. In the immune system, SIRPα is thought to be important for homeostasis of DCs, but it remains unclear whether SIRPα intrinsic to DCs is indeed indispensable for such functional role. Thus, we here generated the mice, in which SIRPα was specifically ablated in CD11c(+) DCs (Sirpa(Δ) (DC) ). Sirpa(Δ) (DC) mice manifested a marked reduction of CD4(+) CD8α(-) conventional DCs (cDCs) in the secondary lymphoid organs, as well as of Langerhans cells in the epidermis. Such reduction of cDCs in Sirpa(Δ) (DC) mice was comparable to that apparent with the mice, in which SIRPα was systemically ablated. Expression of SIRPα in DCs was well correlated with that of either endothelial cell-selective adhesion molecule (ESAM) or Epstein-Barr virus-induced molecule 2 (EBI2), both of which were also implicated in the regulation of DC homeostasis. Indeed, ESAM(+) or EBI2(+) cDCs were markedly reduced in the spleen of Sirpa(Δ) (DC) mice. Thus, our results suggest that SIRPα intrinsic to CD11c(+) DCs is essential for homeostasis of cDCs in the secondary lymphoid organs and skin.

  16. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

    Science.gov (United States)

    Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

    2013-01-01

    Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

  17. Simulation and optimization of a 10 A electron gun with electrostatic compression for the electron beam ion source

    Energy Technology Data Exchange (ETDEWEB)

    Pikin, A.; Beebe, E. N.; Raparia, D. [Brookhaven National Laboratory, Upton, New York 11973 (United States)

    2013-03-15

    Increasing the current density of the electron beam in the ion trap of the Electron Beam Ion Source (EBIS) in BNL's Relativistic Heavy Ion Collider facility would confer several essential benefits. They include increasing the ions' charge states, and therefore, the ions' energy out of the Booster for NASA applications, reducing the influx of residual ions in the ion trap, lowering the average power load on the electron collector, and possibly also reducing the emittance of the extracted ion beam. Here, we discuss our findings from a computer simulation of an electron gun with electrostatic compression for electron current up to 10 A that can deliver a high-current-density electron beam for EBIS. The magnetic field in the cathode-anode gap is formed with a magnetic shield surrounding the gun electrodes and the residual magnetic field on the cathode is (5 Division-Sign 6) Gs. It was demonstrated that for optimized gun geometry within the electron beam current range of (0.5 Division-Sign 10) A the amplitude of radial beam oscillations can be maintained close to 4% of the beam radius by adjusting the injection magnetic field generated by a separate magnetic coil. Simulating the performance of the gun by varying geometrical parameters indicated that the original gun model is close to optimum and the requirements to the precision of positioning the gun elements can be easily met with conventional technology.

  18. vbyCaHbeta CCD Photometry of Clusters. VIII. The Super-Metal Rich, Old Open Cluster NGC 6791

    CERN Document Server

    Anthony-Twarog, B J; Mayer, L

    2006-01-01

    CCD photometry on the intermediate-band vbyCaHbeta system is presented for the metal-rich, old open cluster, NGC 6791. Preliminary analysis led to [Fe/H] above +0.4 with an anomalously high reddening and an age below 5 Gyr. A revised calibration between (b-y)_0 and [Fe/H] at a given temperature shows that the traditional color-metallicity relations underestimate the color of the turnoff stars at high metallicity. With the revised relation, the metallicity from hk and the reddening for NGC 6791 become [Fe/H] = +0.45 +/- 0.04 and E(b-y) = 0.113 +/- 0.012 or E(B-V) = 0.155 +/- 0.016. Using the same technique, reanalysis of the photometry for NGC 6253 produces [Fe/H] = +0.58 +/-0.04 and E(b-y) = 0.120 +/- 0.018 or E(B-V) = 0.160 +/- 0.025. The errors quoted include both the internal and external errors. For NGC 6791, the metallicity from m_1 is a factor of two below that from hk, a result that may be coupled to the consistently low metal abundance from DDO photometry of the cluster and the C-deficiency found from...

  19. A hollow cathode ion source for production of primary ions for the BNL electron beam ion source

    Energy Technology Data Exchange (ETDEWEB)

    Alessi, James, E-mail: alessi@bnl.gov; Beebe, Edward; Carlson, Charles; McCafferty, Daniel; Pikin, Alexander; Ritter, John [Collider-Accelerator Department, Brookhaven National Laboratory, Upton, New York 11973 (United States)

    2014-02-15

    A hollow cathode ion source, based on one developed at Saclay, has been modified significantly and used for several years to produce all primary 1+ ions injected into the Relativistic Heavy Ion Collider Electron Beam Ion Source (EBIS) at Brookhaven. Currents of tens to hundreds of microamperes have been produced for 1+ ions of He, C, O, Ne, Si, Ar, Ti, Fe, Cu, Kr, Xe, Ta, Au, and U. The source is very simple, relying on a glow discharge using a noble gas, between anode and a solid cathode containing the desired species. Ions of both the working gas and ionized sputtered cathode material are extracted, and then the desired species is selected using an ExB filter before being transported into the EBIS trap for charge breeding. The source operates pulsed with long life and excellent stability for most species. Reliable ignition of the discharge at low gas pressure is facilitated by the use of capacitive coupling from a simple toy plasma globe. The source design, and operating experience for the various species, is presented.

  20. Non-redundant patent sequence databases with value-added annotations at two levels

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/. PMID:19884134

  1. Technical Assistance to Enhance Prevention Capacity: a Research Synthesis of the Evidence Base.

    Science.gov (United States)

    Katz, Jason; Wandersman, Abraham

    2016-05-01

    Despite the availability of many evidence-based prevention interventions (EBIs), gaps exist in bringing these programs into widespread practice. Technical assistance (TA) is a strategy for enhancing the readiness of practitioners to implement EBIs. Although many millions of dollars are spent on TA each year, there is little consensus about what the essential features of TA are and how to provide TA with quality. A broad-based research synthesis methodology was used for analyzing the current evidence base for TA using three frames: (1) applying the Getting To Outcomes (GTO) model for categorizing evidence on TA that specifies tasks for planning, implementing, and evaluating TA; (2) understanding the relevance of a successful relationship between the TA provider and TA recipient; and (3) considering the extent to which TA fits the life cycle needs of the preventive intervention. Results indicated that an explicit model or organizing framework is rarely used to plan, implement, and/or evaluate TA; specific TA tasks performed vary widely across studies; TA is rarely delivered to recipients who are seeking to sustain innovations subsequent to adoption and implementation; however, there is systematic attention to relationships and relationship-building. Overall, this synthesis indicates that the extent to which TA is being delivered systematically is limited. We suggest that funders and other stakeholders develop and implement standards for TA quality in order to ensure that many of these limitations are addressed.

  2. Investigation of multi-charged heavy ion production in an electron beam ion source

    Energy Technology Data Exchange (ETDEWEB)

    Hamm, R.W.

    1977-12-01

    Measurements of multi-charged heavy ions produced in an Electron Beam Ion Source (EBIS) were carried out with a test model ion source 20 cm in length. This test model utilized an electron gun placed external to the bore of the focusing solenoid in order to achieve electrostatically focussed electron beams and isolation of the vacuum surrounding the electron gun from the vacuum in the ionization region within the solenoid bore. An ultrahigh vacuum system utilizing liquid nitrogen (77/sup 0/K) cryopumping was used to achieve the low pressures needed in the ionization region for the operation of this ion source. Several technical problems limited the operation of this test model and prevented a thorough investigation of the ionization processes in the ion source, but the experimental results have shown qualitative agreement with the theoretical calculations for the operation of this type of ion source. Even with the problems of an insufficient vacuum and electron beam focussing field, measurable currents of C/sup +5/ and A/sup +8/ ions were produced. The present experimental results suggest that the approach taken in this work of using an external electron gun and cryopumping in the EBIS to achieve the large electron beam current density and low vacuum necessary for successful operation is a viable one. Such an ion source can be used to create highly-charged heavy ions for injection into a cyclotron or other type of particle accelerator.

  3. Electron beam ion sources for use in second generation synchrotrons for medical particle therapy

    Science.gov (United States)

    Zschornack, G.; Ritter, E.; Schmidt, M.; Schwan, A.

    2014-02-01

    Cyclotrons and first generation synchrotrons are the commonly applied accelerators in medical particle therapy nowadays. Next generation accelerators such as Rapid Cycling Medical Synchrotrons (RCMS), direct drive accelerators, or dielectric wall accelerators have the potential to improve the existing accelerator techniques in this field. Innovative accelerator concepts for medical particle therapy can benefit from ion sources which meet their special requirements. In the present paper we report on measurements with a superconducting Electron Beam Ion Source, the Dresden EBIS-SC, under the aspect of application in combination with RCMS as a well proven technology. The measurements indicate that this ion source can offer significant advantages for medical particle therapy. We show that a superconducting EBIS can deliver ion pulses of medically relevant ions such as protons, C4 + and C6 + ions with intensities and frequencies required for RCMS [S. Peggs and T. Satogata, "A survey of Hadron therapy accelerator technology," in Proceedings of PAC07, BNL-79826- 2008-CP, Albuquerque, New Mexico, USA, 2007; A. Garonna, U. Amaldi et al., "Cyclinac medical accelerators using pulsed C6 +/H+_2 ion sources," in Proceedings of EBIST 2010, Stockholm, Sweden, July 2010]. Ion extraction spectra as well as individual ion pulses have been measured. For example, we report on the generation of proton pulses with up to 3 × 109 protons per pulse and with frequencies of up to 1000 Hz at electron beam currents of 600 mA.

  4. Advancing Behavioral HIV Prevention: Adapting an Evidence-Based Intervention for People Living with HIV and Alcohol Use Disorders.

    Science.gov (United States)

    Armstrong, M L; LaPlante, A M; Altice, F L; Copenhaver, M; Molina, P E

    2015-01-01

    Alcohol use disorders (AUDs) are highly prevalent among people living with HIV/AIDS (PLWHA) and are associated with increased HIV risk behaviors, suboptimal treatment adherence, and greater risk for disease progression. We used the ADAPT-ITT strategy to adapt an evidence-based intervention (EBI), the Holistic Health Recovery Program (HHRP+), that focuses on secondary HIV prevention and antiretroviral therapy (ART) adherence and apply it to PLWHA with problematic drinking. Focus groups (FGs) were conducted with PLWHA who consume alcohol and with treatment providers at the largest HIV primary care clinic in New Orleans, LA. Overall themes that emerged from the FGs included the following: (1) negative mood states contribute to heavy alcohol consumption in PLWHA; (2) high levels of psychosocial stress, paired with few adaptive coping strategies, perpetuate the use of harmful alcohol consumption in PLWHA; (3) local cultural norms are related to the permissiveness and pervasiveness of drinking and contribute to heavy alcohol use; (4) healthcare providers unanimously stated that outpatient options for AUD intervention are scarce, (5) misperceptions about the relationships between alcohol and HIV are common; (6) PLWHA are interested in learning about alcohol's impact on ART and HIV disease progression. These data were used to design the adapted EBI.

  5. Measurements of Ion Selective Containment on the RF Charge Breeder Device BRIC

    CERN Document Server

    Variale, Vincenzo; Batazova, Marina; Boggia, Antonio; Clauser, Tarcisio; Kuznetsov, Gennady I; Rainò, Antonio; Shiyankov, Sergey; Skarbo, Boris A; Valentino, Vincenzo; Verrone, Grazia

    2005-01-01

    The "charge state breeder" BRIC (BReeding Ion Charge) is based on an EBIS source and it is designed to accept Radioactive Ion Beam (RIB) with charge +1, in a slow injection mode, to increase their charge state up to +n. BRIC has been developed at the INFN section of Bari (Italy) during these last 3 years with very limited funds. Now, it has been assembled at the LNL (Italy) where are in progress the first tests as stand alone source. The new feature of BRIC, with respect to the classical EBIS, is given by the insertion, in the ion drift chamber, of a Radio Frequency (RF) Quadrupole aiming to filtering the unwanted elements and then making a more efficient containment of the wanted ions. In this contribution, the measurements of the selective effect on the ion charge state containement of the RF quadrupole field, applied on the ion chamber, will be reported and discussed. The ion charge state analisys of the ions trapped in BRIC seem confirm, as foreseen by simulation results carried out previously, that the s...

  6. Electron beam irradiation enhances the digestibility and fermentation yield of water-soaked lignocellulosic biomass

    Directory of Open Access Journals (Sweden)

    Jin Seop Bak

    2014-12-01

    Full Text Available In order to overcome the limitation of commercial electron beam irradiation (EBI, lignocellulosic rice straw (RS was pretreated using water soaking-based electron beam irradiation (WEBI. This environment-friendly pretreatment, without the formation (or release of inhibitory compounds (especially hydroxymethylfurfural and furfural, significantly increased the enzymatic hydrolysis and fermentation yields of RS. Specifically, when water-soaked RS (solid:liquid ratio of 100% was treated with WEBI doses of 1 MeV at 80 kGy, 0.12 mA, the glucose yield after 120 h of hydrolysis was 70.4% of the theoretical maximum. This value was predominantly higher than the 29.5% and 52.1% measured from untreated and EBI-treated RS, respectively. Furthermore, after simultaneous saccharification and fermentation for 48 h, the ethanol concentration, production yield, and productivity were 9.3 g/L, 57.0% of the theoretical maximum, and 0.19 g/L h, respectively. Finally, scanning electron microscopy images revealed that WEBI induced significant ultrastructural changes to the surface of lignocellulosic fibers.

  7. Optimizing charge breeding techniques for ISOL facilities in Europe: Conclusions from the EMILIE project

    Energy Technology Data Exchange (ETDEWEB)

    Delahaye, P., E-mail: delahaye@ganil.fr; Jardin, P.; Maunoury, L. [GANIL, CEA/DSM-CNRS/IN2P3, Blvd. Becquerel, BP 55027, 14076 Caen Cedex 05 (France); Galatà, A.; Patti, G. [INFN–Laboratori Nazionali di Legnaro, Viale dell’Università 2, 35020 Legnaro (Padova) (Italy); Angot, J.; Lamy, T.; Thuillier, T. [LPSC–Université Grenoble Alpes–CNRS/IN2P3, 53 rue des Martyrs, 38026 Grenoble Cedex (France); Cam, J. F.; Traykov, E.; Ban, G. [LPC Caen, 6 Blvd. Maréchal Juin, 14050 Caen Cedex (France); Celona, L. [INFN–Laboratori Nazionali del Sud, via S. Sofia 62, 95125 Catania (Italy); Choinski, J.; Gmaj, P. [Heavy Ion Laboratory, University of Warsaw, ul. Pasteura 5a, 02 093 Warsaw (Poland); Koivisto, H.; Kolhinen, V.; Tarvainen, O. [Department of Physics, University of Jyväskylä, PB 35 (YFL), 40351 Jyväskylä (Finland); Vondrasek, R. [Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439 (United States); Wenander, F. [ISOLDE, CERN, 1211 Geneva 23 (Switzerland)

    2016-02-15

    The present paper summarizes the results obtained from the past few years in the framework of the Enhanced Multi-Ionization of short-Lived Isotopes for Eurisol (EMILIE) project. The EMILIE project aims at improving the charge breeding techniques with both Electron Cyclotron Resonance Ion Sources (ECRIS) and Electron Beam Ion Sources (EBISs) for European Radioactive Ion Beam (RIB) facilities. Within EMILIE, an original technique for debunching the beam from EBIS charge breeders is being developed, for making an optimal use of the capabilities of CW post-accelerators of the future facilities. Such a debunching technique should eventually resolve duty cycle and time structure issues which presently complicate the data-acquisition of experiments. The results of the first tests of this technique are reported here. In comparison with charge breeding with an EBIS, the ECRIS technique had lower performance in efficiency and attainable charge state for metallic ion beams and also suffered from issues related to beam contamination. In recent years, improvements have been made which significantly reduce the differences between the two techniques, making ECRIS charge breeding more attractive especially for CW machines producing intense beams. Upgraded versions of the Phoenix charge breeder, originally developed by LPSC, will be used at SPES and GANIL/SPIRAL. These two charge breeders have benefited from studies undertaken within EMILIE, which are also briefly summarized here.

  8. Gastric epithelial expression of IL-12 cytokine family in Helicobacter pylori infection in human: is it head or tail of the coin?

    Directory of Open Access Journals (Sweden)

    Fadi Al-Sammak

    Full Text Available Recently, there has been a growing interest in an expanding group of cytokines known as "IL-12 family". The so far gained knowledge about these cytokines, as crucial playmakers in mucosal immunity, has not yet been sufficiently investigated in the context of Helicobacter pylori infection. All genes encoding the monomeric components of these cytokines and their corresponding receptors were examined in gastric epithelial cell lines (AGS and MKN-28 after being infected with 4 H. pylori strains: BCM-300, P1 wild-type, and P1-derived isogenic mutants lacking cytotoxin-associated gene A (cagA or virulence gene virB7 (multiplicity of infection=50. Both infected and uninfected samples were analyzed after 24h and 48h using real-time quantitative polymerase chain reaction (RT-qPCR. Gene expression analysis demonstrated a strong upregulation of IL23A (encodes p19 by infection, whereas IL23R, Epstein-Barr virus-induced gene 3 (EBI3, IL6ST, IL12A, and IL27RA were found to be expressed, but not regulated, or to a lesser extent. Transcripts of IL12RB2, IL12B, IL12RB1, and IL27A were not detected. Interestingly, P1 resulted in stronger alterations of expression than CagA mutant and BCM-300, particularly for IL23A (59.7-fold versus 32.4- and 6.7-fold, respectively in AGS after 48h, P<.05, whereas no changes were seen with VirB7 mutant. In a proof-of-principle experiment, we demonstrated epithelial-derived expression of IL-12, p19, and Ebi3 in gastric mucosa of gastritis patients using immunohistochemistry (IHC. Unlike IL-12 and Ebi3, increased immunostaining of p19 was observed in H. pylori gastritis. Herein, we highlight the potential role of gastric epithelial cells in mucosal immunity, not only because they are predominant cell type in mucosa and initial site of host-bacterial interaction, but also as a major contributor to molecules that are thought to be primarily expressed by immune cells so far. Of these molecules, p19 was the most relevant one to H

  9. Environmental quality assessment of a river by using biological monitoring and traditional analyses; Valutazione della qualita' ambientale di un corso d'acqua mediante monitoraggio biologico e indagini tradizionali

    Energy Technology Data Exchange (ETDEWEB)

    Casula, R.; Diliberto, M.L.; Sanna, C.; Sulas, N. [Hydrocontrol, Centro Ricerca e Formazione per il Controllo dei Sistemi Idrici, Cagliari (Italy)

    2000-10-01

    In the present work the integration of chemical-physical and bacteriological analyses with biological surveys was carried out in order to assess the water quality of a river. Benthonic macro invertebrates as biological quality indicators were used for the biological survey (extended biotic index - EBI). The EBI method allows to carry out a more complete evaluation of a river ecological condition and by now it's considered so important to be reported in the new 152/99 italian legislature. By using this methodology, pollution biological implication can be analysed; in fact macro invertebrates colonies change consequently with pollution phenomena allowing to determine the river environmental quality using conventional numerical values. This study was carried out in an italian river located in Sardinia. The chemical-physical and microbiological data showed their importance in identifying a particular problem but only the integration and comparison with the EBI values resulted to be basic for a global evaluation of the river water quality necessary to plan interventions aimed at the possible recovery of these ecosystems. [Italian] Nel presente lavoro viene valutata la qualita' di un corso d'acqua della Sardegna mediante l'integrazione delle comuni analisi chimico-fisiche e batteriologiche con indagini biologiche che si avvalgono dell'utilizzo di macroinvertebrati bentonici come indicatori biologici di qualita' (indice bentonico esteso - I.B.E.). Il monitoraggio biologico, tramite la metodologia I.B.E. ci permette di effettuare una valutazione piu' completa dello stato ecologico del corso d'acqua ed e' considerato ormai di fondamentale importanza tanto da essere riportato come prioritario nel nuovo D.L. 152/99. Con l'I.B.E. si possono analizzare le implicazioni biologiche dell'inquinamento, infatti le comunita0 di macroinvertebrati bentonici variano al variare della normale composizione dell'acqua e si

  10. Dietary intake, eating behaviors, and quality of life in women with polycystic ovary syndrome who are trying to conceive.

    Science.gov (United States)

    Turner-McGrievy, Gabrielle; Davidson, Charis R; Billings, Deborah L

    2015-03-01

    The Healthy Eating for Reproductive Health study was conducted among 18 (45% non-white) mostly obese (BMI 39.9 ± 6.1) women with polycystic ovary syndrome (PCOS) who were experiencing infertility and interested in losing weight. A variety of markers were measured at baseline: body mass index (BMI), diet, physical activity, eating behaviors (using an Eating Behavior Inventory, a questionnaire which assesses both positive and negative eating behaviors associated with weight status, with a higher score indicating adoption of eating behaviors which have been shown in prior weight-loss research to promote a healthy weight (EBI) and the Three-Factor Eating Questionnaire, which assesses cognitive and behavioral components of eating among overweight adults), and a quality of life (PCOS Health-Related Quality of Life (PCOSQ)) index, which assesses satisfaction around five 'domains': emotional health, presence of body hair, infertility, weight, and menstrual problems). A comparison group of overweight women without PCOS (n = 28) was used to examine differences in measured outcomes between women with and without PCOS. Participants' habitual diets were high in fat and saturated fat and low in fiber, folate, and iron and contained significantly lower amounts of carbohydrate, iron, and whole grains compared with women without PCOS who had enrolled in a behavioral weight loss programme. Participants had a low EBI (indicating that most were not adopting eating behaviors associated with achieving a healthy weight), disinhibition (indicating participants had a tendency to overeat in the presence of highly palatable foods or were susceptible to emotional cues for eating, such as stress), and hunger scores (indicating participants did not report being susceptible to hunger, prompting overeating) and moderate dietary restraint (indicating they were not consistently attempting to restrict food intake consciously). PCOSQ scores were lowest for infertility and weight domains (indicating

  11. SOX2 and SOX2-MYC Reprogramming Process of Fibroblasts to the Neural Stem Cells Compromised by Senescence.

    Directory of Open Access Journals (Sweden)

    Marta Winiecka-Klimek

    Full Text Available Tumorigenic potential of induced pluripotent stem cells (iPSCs infiltrating population of induced neural stem cells (iNSCs generated from iPSCs may limit their medical applications. To overcome such a difficulty, direct reprogramming of adult somatic cells into iNSCs was proposed. The aim of this study was the systematic comparison of induced neural cells (iNc obtained with different methods-direct reprogramming of human adult fibroblasts with either SOX2 (SiNSc-like or SOX2 and c-MYC (SMiNSc-like and induced pluripotent stem cells differentiation to ebiNSc-in terms of gene expression profile, differentiation potential as well as proliferation properties. Immunocytochemistry and real-time PCR analyses were used to evaluate gene expression profile and differentiation potential of various iNc types. Bromodeoxyuridine (BrdU incorporation and senescence-associated beta-galactosidase (SA-β-gal assays were used to estimate proliferation potential. All three types of iNc were capable of neuronal differentiation; however, astrocytic differentiation was possible only in case of ebiNSc. Contrary to ebiNSc generation, the direct reprogramming was rarely a propitious process, despite 100% transduction efficiency. The potency of direct iNSCs-like cells generation was lower as compared to iNSCs obtained by iPSCs differentiation, and only slightly improved when c-MYC was added. Directly reprogrammed iNSCs-like cells were lacking the ability to differentiate into astrocytic cells and characterized by poor efficiency of neuronal cells formation. Such features indicated that these cells could not be fully reprogrammed, as confirmed mainly with senescence detection. Importantly, SiNSc-like and SMiNSc-like cells were unable to achieve the long-term survival and became senescent, which limits their possible therapeutic applicability. Our results suggest that iNSCs-like cells, generated in the direct reprogramming attempts, were either not fully reprogrammed or

  12. Expanding Diversity in Molecular Structures and Functions of the IL-6/IL-12 Heterodimeric Cytokine Family

    Directory of Open Access Journals (Sweden)

    Hideaki Hasegawa

    2016-11-01

    Full Text Available The interleukin (IL-6/IL-12 family cytokines have pleiotropic functions and play critical roles in multiple immune responses. This cytokine family has very unique characteristics in that they are composed of two distinct subunits forming a heterodimer and each cytokine and receptor subunit shares with each other. The members of this cytokine family are increasing; currently, there are more than 6 cytokines, including the tentatively named cytokines IL-Y (p28/p40, IL-12 (p35/p40, IL-23 (p19/p40, IL-27 p28/Epstein-Barr virus-induced protein 3 (EBI3, IL-35 (p35/EBI3, and IL-39 (p19/EBI3. This family of cytokines covers a very broad range of immune responses, including pro-inflammatory responses such as helper T (Th1, Th2, and Th17 to anti-inflammatory responses such as regulatory T (Treg cells and IL-10-producing Treg cells. IL-12 is the first member of this family, and IL-12, IL-23, and IL-27 are mainly produced by activated antigen-presenting cells such as dendritic cells and macrophages. IL-12 plays a critical role in the promotion of Th1 immune responses by inducing interferon-γ production to combat pathogens and malignant tumors. IL-23 induces IL-17 production and is necessary to maintain pathogenic Th17 cells that cause inflammatory and autoimmune diseases. IL-27 was initially reported to play a critical role in promotion of Th1 differentiation; however, subsequent studies revealed that IL-27 has broader stimulatory and inhibitory roles by inducing IL-10-producing Treg cells. IL-35 is produced by forkhead box P3+ Treg cells and activated B cells and has immunosuppressive functions to maintain immune tolerance. The most recently identified cytokine, IL-39, is produced by activated B cells and has pro-inflammatory functions. The cytokine tentatively named IL-Y seems to have anti-inflammatory functions by inhibiting Th1 and Th17 differentiation. In addition, individual cytokine subunits were also shown to have self-standing activities. Thus

  13. Data from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with Withaferin A (WA

    Directory of Open Access Journals (Sweden)

    Malathi Narayan

    2016-06-01

    Full Text Available Mass spectrometry data collected in a study analyzing the effect of withaferin A (WA on a mouse microglial (N9 cell line is presented in this article. Data was collected from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with either WA or DMSO vehicle control. This article reports all the proteins that were identified in this analysis. The data presented here is related to the published research article on the effect of WA on the differential regulation of proteins in mouse microglial cells [1]. Mass spectrometry data has also been deposited in the ProteomeXchange with the identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003032.

  14. Water Quality Vocabulary Development and Deployment

    Science.gov (United States)

    Simons, B. A.; Yu, J.; Cox, S. J.

    2013-12-01

    IdentifiedObject individuals are linked to the ChEBI ontology for definitions of chemical substances.. Second, to allow compatibility with SKOS-based tools and to ensure the vocabulary does not violate the meta-modelling constraints of the OWL-DL profile, the relevant classes in QUDT are declared to be subclasses of SKOS Concept and a shadow SKOS view of ChEBI was generated (as ChEBI models all elements and substances as OWL classes). The provenance of each SKOS concept shadowing an OWL class is recorded using the PROV-O ontology. Some aspects of these processing steps can be automated through SPARQL queries, while other aspects must be done manually. For maintenance and provenance purposes, the complete vocabulary and ontologies are persisted in around 20 separate RDF files (in addition to the QUDT and ChEBI sources), each of which constitutes a separate RDF graph and reflects the various aspects of above steps. The vocabularies are published in multiple ways: - For download as files from the ontology URI - At a SPARQL endpoint - Through a URI-based SKOS API (SISSvoc) - Through search UIs built on top of the SPARQL endpoint or SISSvoc service

  15. The yeast noncoding RNA interaction network.

    Science.gov (United States)

    Panni, Simona; Prakash, Ananth; Bateman, Alex; Orchard, Sandra

    2017-10-01

    This article describes the creation of the first expert manually curated noncoding RNA interaction networks for S. cerevisiae The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains. We also see an enrichment of WD40 domains suggesting their direct involvement in ncRNA interactions. We discuss the challenges in collecting noncoding RNA interaction data and the opportunities for worldwide collaboration to fill the unmet need for this data. © 2017 Panni et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  16. The MetaboLights repository: curation challenges in metabolomics.

    Science.gov (United States)

    Salek, Reza M; Haug, Kenneth; Conesa, Pablo; Hastings, Janna; Williams, Mark; Mahendraker, Tejasvi; Maguire, Eamonn; González-Beltrán, Alejandra N; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Steinbeck, Christoph

    2013-01-01

    MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Increases in the number of depositions, number of samples per study and the file size of data submitted to MetaboLights present a challenge for the objective of ensuring high-quality and standardized data in the context of diverse metabolomic workflows and data representations. Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights.

  17. Reaction Decoder Tool (RDT): extracting features from chemical reactions

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W.; Holliday, Gemma L.; Steinbeck, Christoph; Thornton, Janet M.

    2016-01-01

    Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder Contact: asad@ebi.ac.uk or s9asad@gmail.com PMID:27153692

  18. Reaction Decoder Tool (RDT): extracting features from chemical reactions.

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

    2016-07-01

    Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

  19. The MetaboLights repository: curation challenges in metabolomics

    Science.gov (United States)

    Salek, Reza M.; Haug, Kenneth; Conesa, Pablo; Hastings, Janna; Williams, Mark; Mahendraker, Tejasvi; Maguire, Eamonn; González-Beltrán, Alejandra N.; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Steinbeck, Christoph

    2013-01-01

    MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Increases in the number of depositions, number of samples per study and the file size of data submitted to MetaboLights present a challenge for the objective of ensuring high-quality and standardized data in the context of diverse metabolomic workflows and data representations. Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights PMID:23630246

  20. 高电荷态离子束的应用%Applications of Highly Ionized Ion Beams

    Institute of Scientific and Technical Information of China (English)

    J.P.Briand

    2007-01-01

    The ECR ion sources have mainly been used until now for injection of cyclotrons and a large number of these sources are presently in operation through the world,Most cyclotrons are used today for nuclear physics researches but an increasing number of these accelerators are now devoted to medical applications.The ECR ion sources have also been extensively used for producing low energy beams for academic researches in atomic and surface physics.These studies led to very encouraging results opening the way to industrial applications.In this talk some of the most promising applications of HCI beams will be reviewed.The development of these applications will require some important improvements of the ECR sources which will be discussed.A special emphasis will be given to the respective roles of ECR and EBIS ion sources in these industrial applications,and some economic and market consideratioas discussed.

  1. PaperMaker: validation of biomedical scientific publications.

    Science.gov (United States)

    Rebholz-Schuhmann, D; Kavaliauskas, S; Pezik, P

    2010-04-01

    The automatic analysis of scientific literature can support authors in writing their manuscripts. PaperMaker is a novel IT solution that receives a scientific manuscript via a Web interface, automatically analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It analyses the proper use of acronyms and their definitions, and the use of specialized terminology. It provides Gene Ontology (GO) and Medline Subject Headings (MeSH) categorization of text passages, the retrieval of relevant publications from public scientific literature repositories, and the identification of missing or unused references. The author receives a summary of findings, the manuscript in its corrected form and a digital abstract containing the GO and MeSH annotations in the NLM/PubMed format. http://www.ebi.ac.uk/Rebholz-srv/PaperMaker.

  2. Dataset of the Botrytis cinerea phosphoproteome induced by different plant-based elicitors

    Directory of Open Access Journals (Sweden)

    Eva Liñeiro

    2016-06-01

    Full Text Available Phosphorylation is one of the main post-translational modification (PTM involved in signaling network in the ascomycete Botrytis cinerea, one of the most relevant phytopathogenic fungus. The data presented in this article provided a differential mass spectrometry-based analysis of the phosphoproteome of B. cinerea under two different phenotypical conditions induced by the use of two different elicitors: glucose and deproteinized Tomate Cell Walls (TCW. A total 1138 and 733 phosphoproteins were identified for glucose and TCW culture conditions respectively. Raw data are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier (PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD003099. Further interpretation and discussion of these data are provided in our research article entitled “Phosphoproteome analysis of B.cinerea in response to different plant-based elicitors” (Liñeiro et al., 2016 [1].

  3. Functional properties of Virus-Encoded and Virus-Regulated 7TM Receptors

    DEFF Research Database (Denmark)

    Spiess, Katja; Rosenkilde, Mette Marie

    2014-01-01

    During co-evolution with their hosts, viruses have developed several survival strategies that involve exploitation of 7TM receptors. These include virus-encoded 7TM receptors and ligands and viral regulation of endogenous receptors. Many functional properties have been ascribed to virus-exploited 7......-herpesvirus-encoded BILF1 receptors, the human cytomegalovirus (HCMV)-encoded US28 receptor and the Epstein-Barr virus (EBV)-regulated EBI2 (or GPR183), 2) the tissue tropism and virus-dissemination properties, exemplified by the murine CMV-encoded M33, and 3) the tumorigenic properties, exemplified...... by the human herpesvirus 8 (HHV8)-encoded ORF74, HCMV-US28 and EBV-BILF1. Given the general high “druggability” of 7TM receptors, and the recent progress in the understanding of in particular immune evasive functions of the virus-exploited 7TM receptors, we put a special emphasis on the progress of novel anti...

  4. Lecture 10: The European Bioinformatics Institute - "Big data" for biomedical sciences

    CERN Document Server

    CERN. Geneva; Dana, Jose

    2013-01-01

    Part 1: Big data for biomedical sciences (Tom Hancocks) Ten years ago witnessed the completion of the first international 'Big Biology' project that sequenced the human genome. In the years since biological sciences, have seen a vast growth in data. In the coming years advances will come from integration of experimental approaches and the translation into applied technologies is the hospital, clinic and even at home. This talk will examine the development of infrastructure, physical and virtual, that will allow millions of life scientists across Europe better access to biological data Tom studied Human Genetics at the University of Leeds and McMaster University, before completing an MSc in Analytical Genomics at the University of Birmingham. He has worked for the UK National Health Service in diagnostic genetics and in training healthcare scientists and clinicians in bioinformatics. Tom joined the EBI in 2012 and is responsible for the scientific development and delivery of training for the BioMedBridges pr...

  5. [Current Research of the Roles of IL-35 in Tumor Progression].

    Science.gov (United States)

    Huang, Chongbiao; Tian, Ye; Cui, Yan; Xu, Jie; Xin, Liang; Yang, Xueling; Qi, Daliang

    2016-04-20

    Interleukin(IL)-35 is a new member of the interleukin-12 superfamily. Since its first report in 2007, IL-35 rapidly became a research highlight in the field of immunology. Like other IL-12 superfamily members, IL-35 was a heterodimer which was composed of an α chain P35 and a β chain Epstein-Barr virus induced gene 3 (EBI3). Recent research work revealed two distinct roles of IL-35. Firstly, IL-35 is highly expressed in some kinds of inflammatory diseases and autoimmune diseases and plays import roles in the pathogenesis. Secondly, IL-35 is positively expressed in some cancers and plays some roles in the process of tumor progression. Here we demonstrate the structure and the signalling of IL-35. We reviewed the the roles of IL-35 in promoting tumor progression.

  6. Production of High-Intensity, Highly Charged Ions

    CERN Document Server

    Gammino, S

    2013-01-01

    In the past three decades, the development of nuclear physics facilities for fundamental and applied science purposes has required an increasing current of multicharged ion beams. Multiple ionization implies the formation of dense and energetic plasmas, which, in turn, requires specific plasma trapping configurations. Two types of ion source have been able to produce very high charge states in a reliable and reproducible way: electron beam ion sources (EBIS) and electron cyclotron resonance ion sources (ECRIS). Multiple ionization is also obtained in laser-generated plasmas (laser ion sources (LIS)), where the high-energy electrons and the extremely high electron density allow step-by-step ionization, but the reproducibility is poor. This chapter discusses the atomic physics background at the basis of the production of highly charged ions and describes the scientific and technological features of the most advanced ion sources. Particular attention is paid to ECRIS and the latest developments, since they now r...

  7. BioJS: an open source standard for biological visualisation – its status in 2014 [v1; ref status: indexed, http://f1000r.es/2yy

    Directory of Open Access Journals (Sweden)

    Manuel Corpas

    2014-02-01

    Full Text Available BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

  8. REX-ISOLDE post-accelerated radioactive BEAMS at CERN-ISOLDE

    CERN Document Server

    Nilsson, T; Forstner, O; Ravn, H L; Oinonen, M; Simon, H; Cederkäll, J; Weissman, L; Habs, D; Ames, F; Kester, O; Sieber, T; Bongers, H; Emhofer, S; Reiter, P; Thirolf, P G; Bollen, G; Schmidt, P; Huber, G; Liljeby, L; Rensfelt, K G; Skeppstedt, Ö; Wenander, F; Jonson, B; Nyman, G H; Von Hahn, R; Podlech, H; Repnow, R; Gund, C; Schwalm, D; Schempp, A; Kühnel, K U; Welsch, C P; Ratzinger, U; Walter, G; Huck, A; Kruglov, K; Huyse, M; Van den Bergh, P; Van Duppen, P; Shotter, A C; Ostrowski, A N; Davinson, T; Woods, P J; Moukha, I; Richter, A; Schrieder, G

    2001-01-01

    The ISOLDE RIB-facility at CERN has today been producing a vast range of radioactive beams since more than 30 years. The low-energy beams of ISOLDE will be complemented by a post-accelerator, REX-ISOLDE, currently being assembled. In order to convert the pseudo-DC, singly-charged beam from the ISOLDE mass separators into a cooled and bunched beam at higher charge states a novel scheme of trapping, cooling and charge-state breeding has been devised, using a linear Penning trap and an Electron Beam Ion Source (EBIS). This allows for subsequent acceleration by a short, cost-effective LINAC consisting of an RFQ, an IH-structure and three seven-gap resonators, reaching 0.8 - 2.2 MeV/u. The installation of REX-ISOLDE is well underway and the first post-accelerated radioactive beams are expected to be obtained during late 2000.

  9. Dataset of integrin-linked kinase protein: Protein interactions in cardiomyocytes identified by mass spectrometry

    Directory of Open Access Journals (Sweden)

    Alexandra Traister

    2016-06-01

    Full Text Available Using hearts from mice overexpressing integrin linked kinase (ILK behind the cardiac specific promoter αMHC, we have performed immunoprecipitation and mass spectrometry to identify novel ILK protein:protein interactions that regulate cardiomyocyte activity and calcium flux. Integrin linked kinase complexes were captured from mouse heart lysates using a commercial antibody, with subsequent liquid chromatography tandem mass spectral analysis. Interacting partners were identified using the MASCOT server, and important interactions verified using reverse immunoprecipitation and mass spectrometry. All ILK interacting proteins were identified in a non-biased manner, and are stored in the ProteomeXchange Consortium via the PRIDE partner repository (reference ID PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD001053. The functional role of identified ILK interactions in cardiomyocyte function and arrhythmia were subsequently confirmed in human iPSC-cardiomyocytes.

  10. Current Research of the Roles of IL-35 in Tumor Progression

    Directory of Open Access Journals (Sweden)

    Chongbiao HUANG

    2016-04-01

    Full Text Available Interleukin(IL-35 is a new member of the interleukin-12 superfamily. Since its first report in 2007, IL-35 rapidly became a research highlight in the field of immunology. Like other IL-12 superfamily members, IL-35 was a heterodimer which was composed of an α chain P35 and a β chain Epstein-Barr virus induced gene 3 (EBI3. Recent research work revealed two distinct roles of IL-35. Firstly, IL-35 is highly expressed in some kinds of inflammatory diseases and autoimmune diseases and plays import roles in the pathogenesis. Secondly, IL-35 is positively expressed in some cancers and plays some roles in the process of tumor progression. Here we demonstrate the structure and the signalling of IL-35. We reviewed the the roles of IL-35 in promoting tumor progression.

  11. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

    Science.gov (United States)

    Kersey, Paul; Bower, Lawrence; Morris, Lorna; Horne, Alan; Petryszak, Robert; Kanz, Carola; Kanapin, Alexander; Das, Ujjwal; Michoud, Karine; Phan, Isabelle; Gattiker, Alexandre; Kulikova, Tamara; Faruque, Nadeem; Duggan, Karyn; Mclaren, Peter; Reimholz, Britt; Duret, Laurent; Penel, Simon; Reuter, Ingmar; Apweiler, Rolf

    2005-01-01

    Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a detailed statistical overview of the genome and proteome of the organism. The preparation of this analysis is supported through Genome Reviews, a new database of bacterial and archaeal DNA sequences in which annotation has been upgraded (compared to the original submission) through the integration of data from many sources, including the EMBL Nucleotide Sequence Database, the UniProt Knowledgebase, InterPro, CluSTr, GOA and HOGENOM. Integr8 also allows the users to customize their own interactive analysis, and to download both customized and prepared datasets for their own use. Integr8 is available at http://www.ebi.ac.uk/integr8.

  12. A System for Information Management in BioMedical Studies—SIMBioMS

    Science.gov (United States)

    Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

    2009-01-01

    Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

  13. Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Bob [EMBL; Kaye, Jon [Gordon and Betty Moore Foundation

    2009-09-09

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  14. The ChEMBL database in 2017

    Science.gov (United States)

    Gaulton, Anna; Hersey, Anne; Nowotka, Michał; Bento, A. Patrícia; Chambers, Jon; Mendez, David; Mutowo, Prudence; Atkinson, Francis; Bellis, Louisa J.; Cibrián-Uhalte, Elena; Davies, Mark; Dedman, Nathan; Karlsson, Anneli; Magariños, María Paula; Overington, John P.; Papadatos, George; Smit, Ines; Leach, Andrew R.

    2017-01-01

    ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. These include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. A number of improvements and new features have also been incorporated. These include the annotation of assays and targets using ontologies, the inclusion of targets and indications for clinical candidates, addition of metabolic pathways for drugs and calculation of structural alerts. The ChEMBL data can be accessed via a web-interface, RDF distribution, data downloads and RESTful web-services. PMID:27899562

  15. Cloud Computing for Solving E-Learning Problems

    Directory of Open Access Journals (Sweden)

    N. S. Abu El-Ala

    2013-01-01

    Full Text Available The integration of information and communication technologies in education according to the global trend occupied a great interest in the Arab world through E-Learning techniques and put it into the form of services within Services Oriented Architecture Technique (SOA, and mixing its input and outputs within the components of the Education Business Intelligence (EBI and enhance it to simulate reality by educational virtual worlds.This paper presents a creative environment derived from both virtual and personal learning environments based on cloud computing which contains variety of tools and techniques to enhance the educational process. The proposed environment focuses on designing and monitoring educational environment based on reusing the existing web tools, techniques, and services to provide Browser-based-Application.

  16. Experiment list: SRX146460 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX146460 ce10 TFs and others efl-1 Larvae L1 NA 4285635,95.6,7.9,1670 GSM928334: Snyder Pefl1 EFL...1 GFP L1 rep1 extraction1 seq1 aliquote 1 source_name=Snyder_Pefl1_EFL1_GFP_L1_rep1 || strain...=YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype :...e_by : ) || developmental stage=fed L1 || genotype=unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR

  17. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

    Science.gov (United States)

    Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

    2014-08-15

    Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

  18. SAIL—a software system for sample and phenotype availability across biobanks and cohorts

    Science.gov (United States)

    Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I.; Brazma, Alvis; Krestyaninova, Maria

    2011-01-01

    Summary: The Sample avAILability system—SAIL—is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. Availability: SAIL is available under Aferro-GPL open source license: https://github.com/sail. Contact: gostev@ebi.ac.uk, support@simbioms.org Supplementary information: Supplementary data are available at Bioinformatics online and from http://www.simbioms.org. PMID:21169373

  19. Fabrication and durable antibacterial properties of electrospun chitosan nanofibers with silver nanoparticles.

    Science.gov (United States)

    Liu, Yanan; Liu, Yang; Liao, Nina; Cui, Fuhai; Park, Mira; Kim, Hak-Yong

    2015-08-01

    Non-precipitation chitosan/silver nanoparticles (AgNPs) in 1% acetic acid aqueous solution was prepared from chitosan colloidal gel with various contents of silver nitrate via electron beam irradiation (EBI). Electrospun chitosan-based nanofibers decorated with AgNPs were successfully performed by blending poly(vinyl alcohol). The morphology of as-prepared nanofibers and the size of AgNPs in the nanofibers were investigated by field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). The presence of AgNPs in as-obtained nanofibers was also confirmed by ultraviolet-visible spectroscopy (UV), Fourier transform infrared (FT-IR) spectroscopy, EDX spectrum and metal mapping. Silver ion release behavior indicated that these hybrid nanofibers continually release adequate silver to exhibit antibacterial activity over 16 days. These biocomposite nanofibers showed pronounced antibacterial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli).

  20. Update of the androgen receptor gene mutations database.

    Science.gov (United States)

    Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

    1999-01-01

    The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca).

  1. The Androgen Receptor Gene Mutations Database.

    Science.gov (United States)

    Gottlieb, B; Lehvaslaiho, H; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

    1998-01-01

    The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 272 to 309 in the past year. We have expanded the database: (i) by giving each entry an accession number; (ii) by adding information on the length of polymorphic polyglutamine (polyGln) and polyglycine (polyGly) tracts in exon 1; (iii) by adding information on large gene deletions; (iv) by providing a direct link with a completely searchable database (courtesy EMBL-European Bioinformatics Institute). The addition of the exon 1 polymorphisms is discussed in light of their possible relevance as markers for predisposition to prostate or breast cancer. The database is also available on the internet (http://www.mcgill. ca/androgendb/ ), from EMBL-European Bioinformatics Institute (ftp. ebi.ac.uk/pub/databases/androgen ), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca).

  2. Ion optics of RHIC electron beam ion source

    Energy Technology Data Exchange (ETDEWEB)

    Pikin, A.; Alessi, J.; Beebe, E.; Kponou, A.; Okamura, M.; Raparia, D.; Ritter, J.; Tan, Y. [Brookhaven National Laboratory, Upton, New York 11973 (United States); Kuznetsov, G. [Budker Institute of Nuclear Physics, Novosibirsk 630090 (Russian Federation)

    2012-02-15

    RHIC electron beam ion source has been commissioned to operate as a versatile ion source on RHIC injection facility supplying ion species from He to Au for Booster. Except for light gaseous elements RHIC EBIS employs ion injection from several external primary ion sources. With electrostatic optics fast switching from one ion species to another can be done on a pulse to pulse mode. The design of an ion optical structure and the results of simulations for different ion species are presented. In the choice of optical elements special attention was paid to spherical aberrations for high-current space charge dominated ion beams. The combination of a gridded lens and a magnet lens in LEBT provides flexibility of optical control for a wide range of ion species to satisfy acceptance parameters of RFQ. The results of ion transmission measurements are presented.

  3. An Energy Upgrade of REX-ISOLDE to 3.1 MeV/u and Acceleration of Heavier Masses up to $A$=150.

    CERN Multimedia

    Wenander, F J C

    2002-01-01

    With an additional 9-gap resonator, operated at 202.56 MHz, the maximum beam energy of REX-ISOLDE will be increased from 2.2 MeV/u to 3.1 MeV/u. This enlarges considerably the range of mass numbers of projectiles reaching the Coulomb barrier for nuclear reactions. Acceleration of heavier projectiles, however, requires longer charge breeding times leading to smaller pulse repetition rates. Thus EBIS developments aiming at shorter breeding times by using higher electron beam current densities are foreseen. Moreover, longer breeding times require longer accumulation times and larger ion storage capacities in REXTRAP to maintain the beam intensities, which will be reached by using new cooling techniques. Although various optimization steps can be performed with ion sources local to REX-ISOLDE, a commissioning of the modified REX-ISOLDE with ISOLDE beams of heavier masses with 15 shifts is requested.

  4. Congressional Briefing on Climate Change Impacts and Adaptation

    Science.gov (United States)

    Landau, Elizabeth

    2010-01-01

    During an 8 January 2010 congressional briefing on climate change cosponsored by AGU, speakers discussed the impacts of climate change in the United States and the ability of society to cope with these impacts. More than 200 congressional and federal agency staff attended the briefing, which featured Michael MacCracken, chief scientist for climate change programs at the Climate Institute; Kristie Ebi, executive director of the Intergovernmental Panel on Climate Change Working Group 2 Technical Support Unit; Katharine Jacobs, professor at the University of Arizona's Soil, Water and Environmental Science Department; and Susanne Moser, director and principal researcher at Susanne Moser Research and Consulting. The briefing was jointly sponsored by AGU, the American Association for the Advancement of Science, American Meteorological Society, Ecological Society of America, and Pew Center on Global Climate Change. For more information about AGU's science policy program, visit http://www.agu.org/sci_pol/.

  5. Microfibrillar Structure of Silks

    Science.gov (United States)

    Putthanarat, Sirina; Eby, Ronald K.; Adams, W. W.; Liu, G. F.

    1998-03-01

    We have previously observed the dragline silk of Nephila clavipes and the silk of Bombyx mori exhibit a range of morphological feature including microfibers (S. Putthanarat; R.K. Eby; W.W. Adams; G.F. Liu J.M.S.-Pure Appl. Chem. 1996, A33(7), 899) and a layered structure. In successive layers the microfibers appeared to be oriented at different small angles to the fiber axis. Further work with the Atomic Force Microscope (AFM) on the silk of B. mori has confirmed these observations and shown other features. One of the latter is a series of raised "steps" spaced somewhat regularly along the fiber. Investigation of peeled three-molted B. mori and Antheraea yamamai (Japanese Tussah) and other silks has shown features very similar to all those in the silk of B. mori. AFM images, characterization, and analyses will be shown for all the silks and their features

  6. Electron Beam Ion Sources

    CERN Document Server

    Zschornacka, G.; Thorn, A.

    2013-12-16

    Electron beam ion sources (EBISs) are ion sources that work based on the principle of electron impact ionization, allowing the production of very highly charged ions. The ions produced can be extracted as a DC ion beam as well as ion pulses of different time structures. In comparison to most of the other known ion sources, EBISs feature ion beams with very good beam emittances and a low energy spread. Furthermore, EBISs are excellent sources of photons (X-rays, ultraviolet, extreme ultraviolet, visible light) from highly charged ions. This chapter gives an overview of EBIS physics, the principle of operation, and the known technical solutions. Using examples, the performance of EBISs as well as their applications in various fields of basic research, technology and medicine are discussed.

  7. The ChEMBL bioactivity database: an update.

    Science.gov (United States)

    Bento, A Patrícia; Gaulton, Anna; Hersey, Anne; Bellis, Louisa J; Chambers, Jon; Davies, Mark; Krüger, Felix A; Light, Yvonne; Mak, Lora; McGlinchey, Shaun; Nowotka, Michal; Papadatos, George; Santos, Rita; Overington, John P

    2014-01-01

    ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 Nucleic Acids Research Database Issue. Since then, a variety of new data sources and improvements in functionality have contributed to the growth and utility of the resource. In particular, more comprehensive tracking of compounds from research stages through clinical development to market is provided through the inclusion of data from United States Adopted Name applications; a new richer data model for representing drug targets has been developed; and a number of methods have been put in place to allow users to more easily identify reliable data. Finally, access to ChEMBL is now available via a new Resource Description Framework format, in addition to the web-based interface, data downloads and web services.

  8. Surface modification of oxide layer on Si using highly charged ions

    Energy Technology Data Exchange (ETDEWEB)

    Sakurai, M., E-mail: msakurai@kobe-u.ac.jp [Department of Physics, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501 (Japan); Liu, S.; Sakai, S. [Department of Physics, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501 (Japan); Ohtani, S. [Institute for Laser Science, University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Terui, T. [National Institute of Information and Communications Technology, Iwaoka, Nishi-ku, Kobe 651-2492 (Japan); Sakaue, H.A. [National Institute for Fusion Science, Oroshi-cho, Toki 509-5292 (Japan)

    2013-11-15

    Surface modification using highly charged ions is presented. The surface of a Si wafer which is covered with a native oxide layer is used as a sample. The sample was irradiated with Ar{sup 11+} ions at a fluence of 10{sup 13}–10{sup 14}/cm{sup 2}. The Ar{sup 11+} ions were obtained from an electron beam ion source (Kobe EBIS). The surface was investigated using secondary electron microscopy, X-ray photoelectron spectroscopy and high-resolution electron energy loss spectroscopy. The obtained results suggest that the native oxide layer is sputtered by the irradiation of Ar{sup 11+} ions and that the structural modification makes the density of the oxide layer lower and the electric conductivity higher.

  9. The software architecture of climate models: a graphical comparison of CMIP5 and EMICAR5 configurations

    Science.gov (United States)

    Alexander, K.; Easterbrook, S. M.

    2015-04-01

    We analyze the source code of eight coupled climate models, selected from those that participated in the CMIP5 (Taylor et al., 2012) or EMICAR5 (Eby et al., 2013; Zickfeld et al., 2013) intercomparison projects. For each model, we sort the preprocessed code into components and subcomponents based on dependency structure. We then create software architecture diagrams that show the relative sizes of these components/subcomponents and the flow of data between them. The diagrams also illustrate several major classes of climate model design; the distribution of complexity between components, which depends on historical development paths as well as the conscious goals of each institution; and the sharing of components between different modeling groups. These diagrams offer insights into the similarities and differences in structure between climate models, and have the potential to be useful tools for communication between scientists, scientific institutions, and the public.

  10. ​ SAKIZ AĞACI (Pistacia lentiscus var. chia Duhamel)'NIN IN VITRO MİKROÇOĞALTIMI ÜZERİNE ARAŞTIRMALAR

    OpenAIRE

    TAŞKIN, Tuncer; İnal, Abdullah

    2005-01-01

    Bu çalışmada, ülkemizde sayısı giderek azalan Sakız ağacı (Pistacia lentiscus L. var. chia)’ nın apikal sürgün uçları in vitro koşullarda farklı hormon konsantrasyonları içeren MS (Murashige ve Skoog, 1962) ve B5 (Gamborg ve ark., 1968) DKW (Driver ve Kuniyuki, 1984) ortamları orijinal ya da modifikasyonlar yapılarak ve antioksidantlar ilave edilerek hazırlanan ortamlarda kültüre alınmışlardır. Yaşlı ağaçlar ve genç fidanlardan alınan materyalde fenolik bileşiklerin etkisinden dolayı gelişebi...

  11. Synthesis of End Functional Polymers via Atom Transfer Radical Polymerization in Immobilized Catalytic System

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Cross-linked polystyrene with azo-crown ether functional side chain (PSt-1, 10-dicarbonyl-3,6,9-trizaocylcodecane) was prepared under microwave irradiation and the structure was characterized through FT-IR and element analysis. The functionalized cross-linked polystyrene (cross-link degree, 3.5%) combining with immobilized catalyst system (CuBr and ethyl α-bromo-isobutyrate) can catalyze atom transfer radical polymerization of Styrene. Neat polymer products can be obtained then. Complex of La and the polymer end group (EBiB) was synthesized. The third order nonlinear optical property of the polymer-La complex was investigated and the structure was also characterized by FT-IR and XPS.

  12. InterPro in 2017—beyond protein family and domain annotations

    Science.gov (United States)

    Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C.; Bateman, Alex; Bork, Peer; Bridge, Alan J.; Chang, Hsin-Yu; Dosztányi, Zsuzsanna; El-Gebali, Sara; Fraser, Matthew; Gough, Julian; Haft, David; Holliday, Gemma L.; Huang, Hongzhan; Huang, Xiaosong; Letunic, Ivica; Lopez, Rodrigo; Lu, Shennan; Marchler-Bauer, Aron; Mi, Huaiyu; Mistry, Jaina; Natale, Darren A.; Necci, Marco; Nuka, Gift; Orengo, Christine A.; Park, Youngmi; Pesseat, Sebastien; Piovesan, Damiano; Potter, Simon C.; Rawlings, Neil D.; Redaschi, Nicole; Richardson, Lorna; Rivoire, Catherine; Sangrador-Vegas, Amaia; Sigrist, Christian; Sillitoe, Ian; Smithers, Ben; Squizzato, Silvano; Sutton, Granger; Thanki, Narmada; Thomas, Paul D; Tosatto, Silvio C. E.; Wu, Cathy H.; Xenarios, Ioannis; Yeh, Lai-Su; Young, Siew-Yit; Mitchell, Alex L.

    2017-01-01

    InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences. PMID:27899635

  13. Data on mass spectrometry based identification of allergens from sunflower (Helianthus annuus L. pollen proteome

    Directory of Open Access Journals (Sweden)

    Nandini Ghosh

    2016-06-01

    Full Text Available Allergy is a type of abnormal immune reactions, which is triggered by environmental antigens or allergens and mediated by IgE antibodies. Now-a-days mass spectrometry is the method of choice for allergen identification based on homology searching. Here, we provide the mass spectrometry dataset associated with our previously published research article on identification of sunflower pollen allergens (Ghosh et al., 2015 [1]. In this study allergenicity of sunflower (Helianthus annuus pollen grains were primarily investigated by clinical studies followed by detailed immunobiochemical and immunoproteomic analyses. The mass spectrometry data for the identification of allergens were deposited to ProteomeXchange Consortium via PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002397.

  14. Accelerated radioactive beams from REX-ISOLDE

    Energy Technology Data Exchange (ETDEWEB)

    Kester, O. E-mail: oliver.kester@physik.uni-muenchen.de; Sieber, T.; Emhofer, S.; Ames, F.; Reisinger, K.; Reiter, P.; Thirolf, P.G.; Lutter, R.; Habs, D.; Wolf, B.H.; Huber, G.; Schmidt, P.; Ostrowski, A.N.; Hahn, R. von; Repnow, R.; Fitting, J.; Lauer, M.; Scheit, H.; Schwalm, D.; Podlech, H.; Schempp, A.; Ratzinger, U.; Forstner, O.; Wenander, F.; Cederkaell, J.; Nilsson, T.; Lindroos, M.; Fynbo, H.; Franchoo, S.; Bergmann, U.; Oinonen, M.; Aeystoe, J.; Den Bergh, P. Van; Duppen, P. Van; Huyse, M.; Warr, N.; Weisshaar, D.; Eberth, J.; Jonson, B.; Nyman, G.; Pantea, M.; Simon, H.; Shrieder, G.; Richter, A.; Tengblad, O.; Davinson, T.; Woods, P.J.; Bollen, G.; Weissmann, L.; Liljeby, L.; Rensfelt, K.G

    2003-05-01

    In 2001 the linear accelerator of the Radioactive beam EXperiment (REX-ISOLDE) delivered for the first time accelerated radioactive ion beams, at a beam energy of 2 MeV/u. REX-ISOLDE uses the method of charge-state breeding, in order to enhance the charge state of the ions before injection into the LINAC. Radioactive singly-charged ions from the on-line mass separator ISOLDE are first accumulated in a Penning trap, then charge bred to an A/q<4.5 in an electron beam ion source (EBIS) and finally accelerated in a LINAC from 5 keV/u to energies between 0.8 and 2.2 MeV/u. Dedicated measurements with REXTRAP, the transfer line and the EBIS have been carried out in conjunction with the first commissioning of the accelerator. Thus the properties of the different elements could be determined for further optimization of the system. In two test beam times in 2001 stable and radioactive Na isotopes ({sup 23}Na-{sup 26}Na) have been accelerated and transmitted to a preliminary target station. There {sup 58}Ni- and {sup 9}Be- and {sup 2}H-targets have been used to study exited states via Coulomb excitation and neutron transfer reactions. One MINIBALL triple cluster detector was used together with a double sided silicon strip detector to detect scattered particles in coincidence with {gamma}-rays. The aim was to study the operation of the detector under realistic conditions with {gamma}-background from the {beta}-decay of the radioactive ions and from the cavities. Recently for efficient detection eight tripple Ge-detectors of MINIBALL and a double sided silicon strip detector have been installed. We will present the first results obtained in the commissioning experiments and will give an overview of realistic beam parameters for future experiments to be started in the spring 2002.

  15. Loss of GCN5 leads to increased neuronal apoptosis by upregulating E2F1- and Egr-1-dependent BH3-only protein Bim.

    Science.gov (United States)

    Wu, Yanna; Ma, Shanshan; Xia, Yong; Lu, Yangpeng; Xiao, Shiyin; Cao, Yali; Zhuang, Sidian; Tan, Xiangpeng; Fu, Qiang; Xie, Longchang; Li, Zhiming; Yuan, Zhongmin

    2017-01-26

    Cellular acetylation homeostasis is a kinetic balance precisely controlled by histone acetyl-transferase (HAT) and histone deacetylase (HDAC) activities. The loss of the counterbalancing function of basal HAT activity alters the precious HAT:HDAC balance towards enhanced histone deacetylation, resulting in a loss of acetylation homeostasis, which is closely associated with neuronal apoptosis. However, the critical HAT member whose activity loss contributes to neuronal apoptosis remains to be identified. In this study, we found that inactivation of GCN5 by either pharmacological inhibitors, such as CPTH2 and MB-3, or by inactivation with siRNAs leads to a typical apoptosis in cultured cerebellar granule neurons. Mechanistically, the BH3-only protein Bim is transcriptionally upregulated by activated Egr-1 and E2F1 and mediates apoptosis following GCN5 inhibition. Furthermore, in the activity withdrawal- or glutamate-evoked neuronal apoptosis models, GCN5 loses its activity, in contrast to Bim induction. Adenovirus-mediated overexpression of GCN5 suppresses Bim induction and apoptosis. Interestingly, the loss of GCN5 activity and the induction of Egr-1, E2F1 and Bim are involved in the early brain injury (EBI) following subarachnoid haemorrhage (SAH) in rats. HDAC inhibition not only significantly rescues Bim expression and apoptosis induced by either potassium deprivation or GCN5 inactivation but also ameliorates these events and EBI in SAH rats. Taken together, our results highlight a new mechanism by which the loss of GCN5 activity promotes neuronal apoptosis through the transcriptional upregulation of Bim, which is probably a critical event in triggering neuronal death when cellular acetylation homeostasis is impaired.

  16. Mean Expected Error in Prediction of Total Body Water: A True Accuracy Comparison between Bioimpedance Spectroscopy and Single Frequency Regression Equations

    Directory of Open Access Journals (Sweden)

    Fernando Seoane

    2015-01-01

    Full Text Available For several decades electrical bioimpedance (EBI has been used to assess body fluid distribution and body composition. Despite the development of several different approaches for assessing total body water (TBW, it remains uncertain whether bioimpedance spectroscopic (BIS approaches are more accurate than single frequency regression equations. The main objective of this study was to answer this question by calculating the expected accuracy of a single measurement for different EBI methods. The results of this study showed that all methods produced similarly high correlation and concordance coefficients, indicating good accuracy as a method. Even the limits of agreement produced from the Bland-Altman analysis indicated that the performance of single frequency, Sun’s prediction equations, at population level was close to the performance of both BIS methods; however, when comparing the Mean Absolute Percentage Error value between the single frequency prediction equations and the BIS methods, a significant difference was obtained, indicating slightly better accuracy for the BIS methods. Despite the higher accuracy of BIS methods over 50 kHz prediction equations at both population and individual level, the magnitude of the improvement was small. Such slight improvement in accuracy of BIS methods is suggested insufficient to warrant their clinical use where the most accurate predictions of TBW are required, for example, when assessing over-fluidic status on dialysis. To reach expected errors below 4-5%, novel and individualized approaches must be developed to improve the accuracy of bioimpedance-based methods for the advent of innovative personalized health monitoring applications.

  17. A Non-Inferiority Trial of an Evidence-Based Secondary HIV Prevention Behavioral Intervention Compared to an Adapted, Abbreviated Version: Rationale and Intervention Description

    Science.gov (United States)

    Shrestha, Roman; Krishnan, Archana; Altice, Frederick L.; Copenhaver, Michael

    2015-01-01

    Background Real-world clinical settings like addiction treatment programs are ill-equipped to deploy and sustain the existing-resource-demanding evidence-based interventions (EBIs) that target HIV-infected people who use drugs (PWUDs), and this has left a critical void in current HIV prevention efforts. In response to this unmet need, we have conducted formative research in addiction treatment settings that has resulted in Holistic Health for HIV (3H+) – an empirically adapted, substantially abbreviated version of Holistic Health Recovery Program (HHRP+), a CDC-recommended EBI targeting HIV-infected PWUDs. Methods Using a non-inferiority randomized controlled trial design, we will determine whether the abbreviated 3H+ intervention is comparable (i.e., within a 10% margin) and cost-effective relative to the original HHRP+ intervention in terms of reducing HIV risk behaviors and improving antiretroviral therapy (ART) adherence among HIV-infected PWUDs in addiction treatment who report drug- or sex-related HIV risk behaviors. Conclusions This article provides a description of the development and adaptation of the 3H+ intervention, the innovative non-inferiority comparative experimental design for testing the 3H+ to the HHRP+. Furthermore, it provides empirical evidence from a formal cost-effectiveness analysis justifying the cost-effectiveness of the 3H+ intervention when compared to the HHRP+ intervention. If confirmed to be comparable and more cost-effective, as hypothesized, the 3H+ intervention has the potential to be readily and immediately integrated within common clinical settings where large numbers of HIV-infected PWUDs receive clinical services. PMID:26253181

  18. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  19. Bioinformatics meets user-centred design: a perspective.

    Science.gov (United States)

    Pavelin, Katrina; Cham, Jennifer A; de Matos, Paula; Brooksbank, Cath; Cameron, Graham; Steinbeck, Christoph

    2012-01-01

    Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  20. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  1. Interleukin-35 Inhibits Endothelial Cell Activation by Suppressing MAPK-AP-1 Pathway.

    Science.gov (United States)

    Sha, Xiaojin; Meng, Shu; Li, Xinyuan; Xi, Hang; Maddaloni, Massimo; Pascual, David W; Shan, Huimin; Jiang, Xiaohua; Wang, Hong; Yang, Xiao-feng

    2015-07-31

    Vascular response is an essential pathological mechanism underlying various inflammatory diseases. This study determines whether IL-35, a novel responsive anti-inflammatory cytokine, inhibits vascular response in acute inflammation. Using a mouse model of LPS-induced acute inflammation and plasma samples from sepsis patients, we found that IL-35 was induced in the plasma of mice after LPS injection as well as in the plasma of sepsis patients. In addition, IL-35 decreased LPS-induced proinflammatory cytokines and chemokines in the plasma of mice. Furthermore, IL-35 inhibited leukocyte adhesion to the endothelium in the vessels of lung and cremaster muscle and decreased the numbers of inflammatory cells in bronchoalveolar lavage fluid. Mechanistically, IL-35 inhibited the LPS-induced up-regulation of endothelial cell (EC) adhesion molecule VCAM-1 through IL-35 receptors gp130 and IL-12Rβ2 via inhibition of the MAPK-activator protein-1 (AP-1) signaling pathway. We also found that IL-27, which shares the EBI3 subunit with IL-35, promoted LPS-induced VCAM-1 in human aortic ECs and that EBI3-deficient mice had similar vascular response to LPS when compared with that of WT mice. These results demonstrated for the first time that inflammation-induced IL-35 inhibits LPS-induced EC activation by suppressing MAPK-AP1-mediated VCAM-1 expression and attenuates LPS-induced secretion of proinflammatory cytokines/chemokines. Our results provide insight into the control of vascular inflammation by IL-35 and suggest that IL-35 is an attractive novel therapeutic reagent for sepsis and cardiovascular diseases.

  2. The regular distribution and expression pattern of immunosuppressive cytokine IL-35 in mouse uterus during early pregnancy.

    Science.gov (United States)

    Jin, Erhui; Wang, Chenfang; Hu, Qianqian; Jin, Guangming; Li, Shenghe

    2014-01-01

    Cytokines within the uterus are critical in the maternal-fetal immune regulation. Immunosuppressive cytokine IL-35 was recently discovered inhibitory cytokine, which were pivotal in the establishment of immune tolerance against self-antigens and antigens encountered in foreign implantation. In order to analyze the role of IL-35 in maternal-fetal immune tolerance, the expression patterns of IL-35 in mouse endometrium were studied during early pregnancy by immunohistochemistry, ELISA and quantitative real-time PCR. As results, we found that IL-35 positive cells in the uterus showed significant distribution difference after fetal implantation, which mainly distributed in luminal epithelium and glandular epithelium of mouse uterus from gestational day 1 to 2, and glandular epithelium and stroma from gestational day 4 to 7. The number of positive cells, immunoreactive scores, protein and mRNA expression of IL-35 showed firstly increased and then decreased with the increase of pregnancy day. The largest contents of IL-35 in the uterus were detected on gestational day 4. Compared with non-pregnant mice, pregnant mice showed the significantly increased mRNA expression of Ebi3 (Epstein-Barr virus-induced gene 3, IL-35 subunit) in the endometrium on gestational day 2 and the highest level of expression on gestational day 4. The mRNA expression of p35 (IL-35 subunit) was significantly lower than that of Ebi3 gene and showed the inconsistent change from gestational day 5 to 7. However, the significant correlation existed between the immunohistochemical expression, contents and mRNA expression of IL-35. These results indicated that IL-35 contributed to the establishment and maintenance of maternal-fetal tolerance during early pregnancy.

  3. Effects of phased joint intervention on IL-35 and IL-17 expression levels in patients with portal hypertension.

    Science.gov (United States)

    Wang, Yugang; Dong, Jinbin; Meng, Wenying; Ma, Jiali; Wang, Na; Wei, Jue; Shi, Min

    2014-05-01

    The aim of the present study was to investigate the clinical efficacy of phased joint intervention [percutaneous transhepatic variceal embolization (PTVE) + phased partial splenic embolization (PSE)] in patients with portal hypertension complicated by esophageal variceal bleeding and hypersplenism and the effect of this intervention on interleukin-35 (IL-35)/IL-17 expression. A review of 53 patients with portal hypertension caused by liver cirrhosis and complicated by esophageal variceal bleeding and hypersplenism treated with phased joint intervention was conducted, and portal hemodynamics, routine blood examinations and liver function were determined. Quantitative polymerase chain reaction (qPCR) was used to evaluate EBI3, FOXP3 and IL-17 mRNA expression levels in peripheral blood mononuclear cells (PBMC) before and after the phased joint intervention, while western blot analysis was used to determine their protein expression. All 53 patients required emergency hemostasis resulting in an emergency hemostatic rate of 100%. Varicose veins disappeared, portal hemodynamics and liver function improved subsequent to the intervention. The expression levels of EBI3, FOXP3 and IL-17 mRNA in the postoperative group were significantly lower than the preoperative levels (PIL-35, IL-6 and IL-17 in peripheral blood were significantly reduced after the phased joint intervention (PIL-35, IL-6 and IL-17 levels were positively correlated with total bilirubin and international normalized ratio, and negatively correlated with albumin. The phased joint intervention can effectively treat esophageal variceal bleeding and hypersplenism, and improve liver function. The efficacy of this intervention may be associated with the regulation of immune function.

  4. IL-35 inhibits HBV antigen-specific IFN-γ-producing CTLs in vitro.

    Science.gov (United States)

    Li, Xuefen; Tian, Li; Dong, Yuejiao; Zhu, Qiaoyun; Wang, Yiyin; Han, Wenzheng; Liu, Xia; Ni, Qin; Chen, Yu; Li, Lanjuan

    2015-09-01

    Interleukin (IL)-35 is an inhibitory cytokine consisting of IL-12A and Epstein-Barr virus-induced gene 3 (Ebi3) and is required by regulatory T-cells (Tregs) for maximal activity. During chronic hepatitis B virus (HBV) infection, Tregs have immunosuppressive effects on HBV-specific T helper (Th) cells, yet little is known about the complex regulation of Tregs and their contribution to the inadequate immune system response to the virus. In the present study, we investigated whether IL-35 is involved in HBV-related cellular immune responses. Cluster of differentiation (CD)4(+) T-cells from peripheral blood were derived from healthy volunteers, resolved HBV individuals and chronic active hepatitis B patients and stimulated with CD3/28-conjugated beads. We analysed mRNA and protein levels of IL-35 and assessed the inhibitory effect of IL-35 on HBV core antigen-specific cytotoxic T lymphocytes (CTLs), dendritic cells (DCs) and effector T-cells (Teffs). Correlation analyses between liver inflammation and HBV DNA load were conducted. Results show that chronic HBV patients harbour significantly higher levels of Ebi3 mRNA and protein in CD4(+) T-cells compared with healthy volunteers and resolved HBV individuals. IL-35 suppressed the proliferation of HBV antigen-specific CTLs and interferon (IFN)-γ production in vitro. Ex vivo, IL-35 decreased the proliferation of CD4(+)CD45RA(+) naïve T-cells, especially in CD4(+)CD25(-)CD45RA(+) naïve Teffs. IL-35 inhibited the expansion of CD11c(+) DCs. Our data indicate that IL-35 is highly expressed in chronic HBV CD4(+) T-cells and plays an important role in the inhibition of the cellular immune response in chronic HBV.

  5. Invited commentary: broadening the evidence for adolescent sexual and reproductive health and education in the United States.

    Science.gov (United States)

    Schalet, Amy T; Santelli, John S; Russell, Stephen T; Halpern, Carolyn T; Miller, Sarah A; Pickering, Sarah S; Goldberg, Shoshana K; Hoenig, Jennifer M

    2014-10-01

    Scientific research has made major contributions to adolescent health by providing insights into factors that influence it and by defining ways to improve it. However, US adolescent sexual and reproductive health policies-particularly sexuality health education policies and programs-have not benefited from the full scope of scientific understanding. From 1998 to 2009, federal funding for sexuality education focused almost exclusively on ineffective and scientifically inaccurate abstinence-only-until-marriage (AOUM) programs. Since 2010, the largest source of federal funding for sexual health education has been the "tier 1" funding of the Office of Adolescent Health's Teen Pregnancy Prevention Initiative. To be eligible for such funds, public and private entities must choose from a list of 35 programs that have been designated as "evidence-based" interventions (EBIs), determined based on their effectiveness at preventing teen pregnancies, reducing sexually transmitted infections, or reducing rates of sexual risk behaviors (i.e., sexual activity, contraceptive use, or number of partners). Although the transition from primarily AOUM to EBI is important progress, this definition of evidence is narrow and ignores factors known to play key roles in adolescent sexual and reproductive health. Important bodies of evidence are not treated as part of the essential evidence base, including research on lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth; gender; and economic inequalities and health. These bodies of evidence underscore the need for sexual health education to approach adolescent sexuality holistically, to be inclusive of all youth, and to address and mitigate the impact of structural inequities. We provide recommendations to improve US sexual health education and to strengthen the translation of science into programs and policy.

  6. Detailed spatiotemporal albedo observations at Greenland's Mittivakkat Gletscher

    Science.gov (United States)

    Mernild, Sebastian H.; Knudsen, Niels T.; Yde, Jacob C.; Malmros, Jeppe K.

    2015-04-01

    Surface albedo is defined as the reflected fraction of incoming solar shortwave radiation at the surface. On Greenland's Mittivakkat Gletscher the mean glacier-wide MODIS-estimated albedo dropped by 0.10 (2000-2013) from 0.43 to 0.33 by the end of the mass balance year (EBY). Hand-held albedo measurements as low as 0.10 were observed over debris-covered ice at the glacier margin at the EBY: these values were slightly below observed values for proglacial bedrock (~0.2). The albedo is highly variable in space - a significant variability occurred within few meters at the glacier margin area ranging from 0.10 to 0.39 due to variability in debris-cover thickness and composition, microbial activity (including algae and cyanobacteria), snow grain crystal metamorphism, bare ice exposure, and meltwater ponding. Huge dark-red-brown-colored ice algae colonies were observed. Albedo measurements on snow patches and bare glacier ice changed significant with increasing elevations (180-600 m a.s.l.) by lapse rates of 0.04 and 0.03 per 100 m, respectively, indicating values as high as 0.82 and 0.40 on the upper part of the glacier. Over a period of two weeks from early August to late August 2014 the hand-held observed mean glacier-wide albedo changed from 0.40 to 0.30 indicating that on average 10% more incoming solar shortwave radiation became available for surface ablation at the end of the melt season.

  7. Proteome data from a host-pathogen interaction study with Staphylococcus aureus and human lung epithelial cells

    Directory of Open Access Journals (Sweden)

    Kristin Surmann

    2016-06-01

    Full Text Available To simultaneously obtain proteome data of host and pathogen from an internalization experiment, human alveolar epithelial A549 cells were infected with Staphylococcus aureus HG001 which carried a plasmid (pMV158GFP encoding a continuously expressed green fluorescent protein (GFP. Samples were taken hourly between 1.5 h and 6.5 h post infection. By fluorescence activated cell sorting GFP-expressing bacteria could be enriched from host cell debris, but also infected host cells could be separated from those which did not carry bacteria after contact (exposed. Additionally, proteome data of A549 cells which were not exposed to S. aureus but underwent the same sample processing steps are provided as a control. Time-resolved changes in bacterial protein abundance were quantified in a label-free approach. Proteome adaptations of host cells were monitored by comparative analysis to a stable isotope labeled cell culture (SILAC standard. Proteins were extracted from the cells, digested proteolytically, measured by nanoLC–MS/MS, and subsequently identified by database search and then quantified. The data presented here are related to a previously published research article describing the interplay of S. aureus HG001 and human epithelial cells (Surmann et al., 2015 [1]. They have been deposited to the ProteomeXchange platform with the identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002384 for the S. aureus HG001 proteome dataset and PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002388 for the A549 proteome dataset.

  8. Proteome data from a host-pathogen interaction study with Staphylococcus aureus and human lung epithelial cells.

    Science.gov (United States)

    Surmann, Kristin; Simon, Marjolaine; Hildebrandt, Petra; Pförtner, Henrike; Michalik, Stephan; Dhople, Vishnu M; Bröker, Barbara M; Schmidt, Frank; Völker, Uwe

    2016-06-01

    To simultaneously obtain proteome data of host and pathogen from an internalization experiment, human alveolar epithelial A549 cells were infected with Staphylococcus aureus HG001 which carried a plasmid (pMV158GFP) encoding a continuously expressed green fluorescent protein (GFP). Samples were taken hourly between 1.5 h and 6.5 h post infection. By fluorescence activated cell sorting GFP-expressing bacteria could be enriched from host cell debris, but also infected host cells could be separated from those which did not carry bacteria after contact (exposed). Additionally, proteome data of A549 cells which were not exposed to S. aureus but underwent the same sample processing steps are provided as a control. Time-resolved changes in bacterial protein abundance were quantified in a label-free approach. Proteome adaptations of host cells were monitored by comparative analysis to a stable isotope labeled cell culture (SILAC) standard. Proteins were extracted from the cells, digested proteolytically, measured by nanoLC-MS/MS, and subsequently identified by database search and then quantified. The data presented here are related to a previously published research article describing the interplay of S. aureus HG001 and human epithelial cells (Surmann et al., 2015 [1]). They have been deposited to the ProteomeXchange platform with the identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002384 for the S. aureus HG001 proteome dataset and PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002388 for the A549 proteome dataset.

  9. Tamoxifen as an effective neuroprotectant against early brain injury and learning deficits induced by subarachnoid hemorrhage: possible involvement of inflammatory signaling.

    Science.gov (United States)

    Sun, Xuebo; Ji, Chengyuan; Hu, Tong; Wang, Zhong; Chen, Gang

    2013-12-28

    Tamoxifen, a selective estrogen receptor modulator, has successfully been used to treat several animal models of brain injury, but the underlying mechanisms remain unclear. This study was undertaken to evaluate the effect of tamoxifen on the toll-like receptor 4 (TLR4)- and nuclear factor-κB (NF-κB)-related inflammatory signaling pathway and secondary brain injury in rats after subarachnoid hemorrhage (SAH). Adult male Sprague-Dawley rats were divided into four groups: (1) control group (n = 28); (2) SAH group (n = 28); (3) SAH + vehicle group (n = 28); and (4) SAH + tamoxifen group (n = 28). All SAH animals were subjected to injection of autologous blood into the prechiasmatic cistern once on day 0. In SAH + tamoxifen group, tamoxifen was administered intraperitoneally at a dose of 5 mg/kg at 2 h, 12 h, and 36 h after SAH. In the first set of experiments, brain samples were extracted and evaluated at 48 h after SAH. In the second set of experiments, the Morris water maze was used to investigate cognitive and memory changes. We found that treatment with tamoxifen markedly inhibited the protein expressions of TLR4, NF-κB and the downstream inflammatory agents, such as interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and intercellular adhesion molecule-1 (ICAM-1). Administration of tamoxifen following SAH significantly ameliorated the early brain injury (EBI), such as brain edema, blood-brain barrier (BBB) impairment, and clinical behavior scale. Learning deficits induced by SAH were markedly alleviated after tamoxifen treatment. Post-SAH tamoxifen administration may attenuate TLR4/NF-kappaB-mediated inflammatory response in the rat brain and result in abatement of the development of EBI and cognitive dysfunction after SAH.

  10. Relationship between dairy cow genetic merit and profit on commercial spring calving dairy farms.

    Science.gov (United States)

    Ramsbottom, G; Cromie, A R; Horan, B; Berry, D P

    2012-07-01

    Because not all animal factors influencing profitability can be included in total merit breeding indices for profitability, the association between animal total merit index and true profitability, taking cognisance of all factors associated with costs and revenues, is generally not known. One method to estimate such associations is at the herd level, associating herd average genetic merit with herd profitability. The objective of this study was to primarily relate herd average genetic merit for a range of traits, including the Irish total merit index, with indicators of performance, including profitability, using correlation and multiple regression analyses. Physical, genetic and financial performance data from 1131 Irish seasonal calving pasture-based dairy farms were available following edits; data on some herds were available for more than 1 year of the 3-year study period (2007 to 2009). Herd average economic breeding index (EBI) was associated with reduced herd average phenotypic milk yield but with greater milk composition, resulting in higher milk prices. Moderate positive correlations (0.26 to 0.61) existed between genetic merit for an individual trait and average herd performance for that trait (e.g. genetic merit for milk yield and average per cow milk yield). Following adjustment for year, stocking rate, herd size and quantity of purchased feed in the multiple regression analysis, average herd EBI was positively and linearly associated with net margin per cow and per litre as well as gross revenue output per cow and per litre. The change in net margin per cow per unit change in the total merit index was €1.94 (s.e. = 0.42), which was not different from the expectation of €2. This study, based on a large data set of commercial herds with accurate information on profitability and genetic merit, confirms that, after accounting for confounding factors, the change in herd profitability per unit change in herd genetic merit for the total merit index is

  11. Electron beam simulation from gun to collector: Towards a complete solution

    Energy Technology Data Exchange (ETDEWEB)

    Mertzig, R., E-mail: robert.mertzig@cern.ch; Shornikov, A., E-mail: robert.mertzig@cern.ch; Wenander, F. [CERN, Geneva 23, CH-1211 (Switzerland); Beebe, E.; Pikin, A. [Brookhaven National Lab, Upton, NY 11973 (United States)

    2015-01-09

    An electron-beam simulation technique for high-resolution complete EBIS/T modelling is presented. The technique was benchmarked on the high compression HEC{sup 2} test-stand with an electron beam current, current density and energy of 10 A, 10 kA/cm{sup 2} and 49.2 keV, and on the immersed electron beam at REXEBIS for electron beam characteristics of 0.4 A, 200 A/cm{sup 2} and 4.5 keV. In both Brillouin-like and immersed beams the electron-beam radius varies from several millimeters at the gun, through some hundreds of micrometers in the ionization region to a few centimeters at the collector over a total length of several meters. We report on our approach for finding optimal meshing parameters, based on the local beam properties such as magnetic field-strength, electron energy and beam radius. This approach combined with dividing the problem domain into sub-domains, and subsequent splicing of the local solutions allowed us to simulate the beam propagation in EBISes from the gun to the collector using a conventional PC in about 24–36 h. Brillouin-like electron beams propagated through the complete EBIS were used to analyze the beam behavior within the collector region. We checked whether elastically reflected paraxial electrons from a Brillouin-like beam will escape from the collector region and add to the loss current. We have also studied the power deposition profiles as function of applied potentials using two electrode geometries for a Brillouin-like beam including the effects of backscattered electrons.

  12. Vaginal-cuff control and toxicity results of a daily HDR brachytherapy schedule in endometrial cancer patients.

    Science.gov (United States)

    Ríos, I; Rovirosa, A; Ascaso, C; Valduvieco, I; Herreros, A; Castilla, L; Sabater, S; Holub, K; Pahisa, J; Biete, A; Arenas, M

    2016-09-01

    To analyze the vaginal-cuff local control (VCC) and toxicity in postoperative endometrial carcinoma patients (EC) underwent high-dose-rate brachytherapy (HDR-BT) administered daily. 154 consecutive patients received postoperative HDR-BT for EC from January 2007 to September 2011. FIGO-staging I-IIIC2 patients were divided into two groups according to risk classification: Group 1 (94/154) included high-risk or advanced disease patients and Group 2 (60/154) included intermediate-risk EC patients. Group 1 underwent external beam irradiation (EBI) plus HDR-BT (2 fractions of 5 Gy) and Group 2 underwent HDR-BT alone (4 fractions of 5 Gy). Toxicity evaluation was done with RTOG scores for bladder and rectum, and the objective criteria of LENT-SOMA for vagina. With a median follow-up of 46.7 months (36.6-61 months) only two patients developed vaginal-cuff recurrence in Group 1 (2.1 %) and none in group 2 (0 %). Early toxicity in Group 1 appeared 5.3 % in rectum, 7.5 % in bladder (G1-G2) and 2.1 % in vagina (G1); late toxicity was present in 7.3 % in rectum (all G1-G2 but 1 G3) and in 27.7 % in vagina (all G1-G2 but one G4). In Group 2, 6.7 % developed acute G1-G2 bladder and 6.6 % acute vaginal (G1-G2) toxicity. No late rectal or bladder toxicity was observed; 21.7 % of G1-G2 presented late problems in vagina. The present HDR-BT schedule of 2 fractions of 5 Gy after EBI and 4 fractions of 5 Gy administered daily showed excellent results in terms of VCC and toxicity.

  13. Application and development of ion-source technology for radiation-effects testing of electronics

    Science.gov (United States)

    Kalvas, T.; Javanainen, A.; Kettunen, H.; Koivisto, H.; Tarvainen, O.; Virtanen, A.

    2017-09-01

    Studies of heavy-ion induced single event effect (SEE) on space electronics are necessary to verify the operation of the components in the harsh radiation environment. These studies are conducted by using high-energy heavy-ion beams to simulate the radiation effects in space. The ion beams are accelerated as so-called ion cocktails, containing several ion beam species with similar mass-to-charge ratio, covering a wide range of linear energy transfer (LET) values also present in space. The use of cocktails enables fast switching between beam species during testing. Production of these high-energy ion cocktails poses challenging requirements to the ion sources because in most laboratories reaching the necessary beam energies requires very high charge state ions. There are two main technologies producing these beams: The electron beam ion source EBIS and the electron cyclotron resonance ion source ECRIS. The EBIS is most suitable for pulsed accelerators, while ECRIS is most suitable for use with cyclotrons, which are the most common accelerators used in these applications. At the Accelerator Laboratory of the University of Jyväskylä (JYFL), radiation effects testing is currently performed using a K130 cyclotron and a 14 GHz ECRIS at a beam energy of 9.3 MeV/u. A new 18 GHz ECRIS, pushing the limits of the normal conducting ECR technology is under development at JYFL. The performances of existing 18 GHz ion sources have been compared, and based on this analysis, a 16.2 MeV/u beam cocktail with 1999 MeV 126Xe44+ being the most challenging component to has been chosen for development at JYFL. The properties of the suggested beam cocktail are introduced and discussed.

  14. Effect of psychological stress on gastric motility assessed by electrical bio-impedance

    Institute of Scientific and Technical Information of China (English)

    María Raquel Huerta-Franco; Miquel Vargas-Luna; Juana Berenice Montes-Frausto; Ismael Morales-Mata; Lorena Ramirez-Padilla

    2012-01-01

    AIM:To evaluate gastric motility using electrical bioimpedance (EBI) and gastric changes as a result of stress induced by psychological tests.METHODS:A group of 57 healthy women,aged 40-60years,was recruited,and a clinical history and physical examination were performed.The women were free from severe anxiety,chronic or acute stress,severe depression,mental diseases and conditions that affect gastric activity.The women were evaluated under fasting conditions,and using a four-electrode configuration,the gastric signals were obtained through a BIOPAC MP-150system.The volunteers were evaluated using the following paradigm:basal state,recording during the Stroop Test,intermediate resting period,recording during the Raven Test,and a final resting period.We analyzed the relative areas of the frequency spectrum:A1 (1-2 cpm),A2 (2-4 cpm),A3 (4-8 cpm),and A4 (8-12 cpm),as well as the median of area A2 + A3.The data were analyzed by an autoregressive method using a Butterworth filter with MatLab and Origin.Analysis of variance (ANOVA)and Friedman ANOVA (for nonparametric variables) were performed; in addition,pairs of groups were compared using the Tdependent and Wilcoxon Ttests.RESULTS:The results of the main values of area A2 were not significantly different comparing the five steps of the experimental paradigm.Nevertheless,there was a tendency of this A2 region to decrease during the stress tests,with recuperation at the final resting step.When an extended gastric region was considered (1-4cpm),significant differences with the psychological stress tests were present (F =3.85,P =0.005).The A3 region also showed significant changes when the stress psychological tests were administered (F =7.25,P <0.001).These differences were influenced by the changes in the adjacent gastric region of A2.The parameter that we proposed in previous studies for the evaluation of gastric motility by electrical bio-impedance (EBI)was the median of the area under the region from 2 to 8 cpm (A2

  15. Ecological modelling: from the biosphere to the everyday data gathering; filling the gap.

    Science.gov (United States)

    Banchetti, Rosalba; Marsili, David; Galleni, Lodovico

    2004-01-01

    Biosphere, according to many authors, can be considered as a system characterised by control mechanisms, which allow the maintenance of its stability. If the Biosphere is a complex object, the coming out of the equilibrium will have as a result a rapid change which cannot be controlled and whose results cannot be foresighted. Modelling is, for this reason, desperately needed. A general mathematical modelling suggested that the Biosphere evolution be characterised by periods of stability and instability, which are related to the connections between its components. These components, both living and not living, are connected by feedback relationships maintaining stability. From this model a general ecosystem modelling was developed which was first applied to a very peculiar situation i.e. that of the hydro-thermal marine vents. The hydrothermal ecosystem is, anyway, a very peculiar one and it can be considered also a micro-biosphere with its own sources of energy not related to sun radiation. For this reason it was possible to make a correlation between these very peculiar ecosystems and the Biosphere. More difficult it is to relate the modelling of the light depending ecosystems, which are, on the contrary, of great interest because they are directly linked to the Biosphere and objects of quite everyday data gathering. Usually the description of ecosystems, which is proposed by the everyday operative task of collecting data, and which represents the widest source of data for modelling, is related to the quality of waters or air. In this way we have to find tools correlating the data routinely investigated and the general model proposed. Here we present the other side of the approach, a local investigation of the qualities of water, with the hope to make a proposal for the ecologists to carry on their job also taking into consideration the problem of ecosystems modelling. An evaluation study of the environmental condition of Fine River, based on the E.B.I. method

  16. Uterine disease and its effect on subsequent reproductive performance of dairy cattle: a comparison of two cow-side diagnostic methods.

    Science.gov (United States)

    Šavc, Miha; Duane, Mary; O'Grady, Luke E; Somers, Joris R; Beltman, Marijke E

    2016-11-01

    The aim of this study was to compare vaginal mucus scoring and ultrasonographic assessment of uterine content as predictors of future reproductive performance of dairy cows. Holstein-Friesian cows (n = 493) from seven commercial dairy farms were enrolled in this study. All cows received one prebreeding examination (PBE) between 21 and 38 days after parturition. During the PBE, vaginal mucus was scored (MS) and the transrectal ultrasonographic examination of the uterus to assess content (UTS) took place. The MS was scored on a scale of 0 to 3 using a Metricheck device and appearance of the uterus on transrectal ultrasound was scored on a scale of 0 to 4 based on the presence and consistency of intraluminal fluid. Other data collected from each cow included the farm ID (F_ID), conception rate to first service, length of breeding window, lactation number, calving month, body condition score (BCS) at calving, BCS loss after calving, BCS at PBE, days in milk at PBE, 305 day milk yield, economic breeding index (EBI), EBI fertility subindex and EBI health subindex. For each cow these parameters were analyzed using univariate Cox proportional hazard model to evaluate the effect of variables on the reproductive performance, measured as positive pregnancy status (PS) at the end of the breeding season. Receiver-operating characteristic analysis of the diagnostic tests compared with each other took place as well. Cows with positive UTS were 7.75 times more likely to have a positive MS as well (P < 0.01). The PS hazard ratios for cows with UTS0, 1, 2, 3, and 4 were 1; 0.84; 0.53; 0.78; 0.28, respectively (P < 0.001). For the cows with MS0, 1, 2, and 3, the PR hazard ratios were 1; 1.02; 0.51; 0.75; respectively (P = 0.01). Conception rate to first service, breeding window, and PS were significantly better for the cows with UTS0, 1 and 2 compared with the cows with UTS3-4 and MS2+3 (68%; 18%, [P = 0.020]; 29; 75 days, [P = 0.001]; 95%; 55%; [P = 0

  17. Re-use of standard ontologies in a water quality vocabulary (Invited)

    Science.gov (United States)

    Cox, S. J.; Simons, B.; Yu, J.

    2013-12-01

    Interest (ChEBI). ChEBI is an OWL-based dictionary of over 70 000 molecular entities, based on existing scientific work and linked through to International Union of Pure and Applied Chemistry (IUPAC) Nomenclature. Within the model the relevant classes, including those from QUDT, are declared to be subclasses of SKOS Concept, so the resulting vocabularies may be directly mapped to other SKOS-based vocabularies, such as from the NERC Vocabulary Service or the Marine Metadata Initiative, using SKOS predicates. Where the external vocabularies are not published with persistent URIs, such as CUAHSI, the mapping may be recorded more informally using annotations, or use proxy URIs for the external vocabulary. The resulting SKOS vocabularies demonstrate a separation of governance of key definitions such as units and quantities and chemical entities, ensuring reuse where possible and extending and adding detail where necessary.

  18. Dayside aurora and the role of IMF ∣By∣/∣Bz∣: detailed morphology and response to magnetopause reconnection

    Directory of Open Access Journals (Sweden)

    W. F. Denig

    2004-01-01

    Full Text Available We document the detailed spatio-temporal structure of the dayside aurora during intervals of ongoing dayside magnetopause reconnection, primarily during interplanetary magnetic field (IMF Bz≤0 conditions. The present study is based on ground auroral observations in combination with particle precipitation data from a DMSP spacecraft. We describe auroral forms corresponding to the following particle precipitation regimes identified by Newell and Meng (1994: (i central plasma sheet (CPS, (ii precipitation void, (iii dayside boundary plasma sheet (BPS, and (iv cusp (LLBL/cusp/mantle. Two distinctly different auroral configurations are observed, corresponding to different regimes of the IMF clock angle (θ and the ∣By∣/∣Bz∣ ratio. Two regimes are defined. In regime (I θ lies within ∼ 90–135° and ∣By∣/∣Bz∣>1 (By-dominated, while in regime (II θ is in the range 135°–180° and ∣By∣/∣Bz∣Bz-dominated. Within regime (I the auroral response to reconnection events typically progresses from lower to higher latitudes in stages as indicated below: (A equatorward boundary intensifications (EBIs: sequential brightenings of closely spaced, fragmented, rayed bands (BPS aurora within the ∼08:00–15:00 MLT sector, each of which are moving noonward/sunward, (B poleward moving auroral forms (PMAFs: forms expanding westward from the postnoon side (By>0 and later appearing as a poleward expanding form in the convection throat in the ∼09:00–12:00 MLT sector, with a fading phase in the regime of mantle precipitation. During strongly southward IMF conditions (regime II, the intense PMAF activity is replaced by a more latitudinally restricted, but longitudinally wide aurora of moderate intensity. The latter auroral state is accompanied by a 2-cell convection pattern which is rather symmetrical about noon. This state is very different from the convection/FAC configuration present during IMF regime (I, with its strong zonal flows

  19. Structure-based classification and ontology in chemistry

    Directory of Open Access Journals (Sweden)

    Hastings Janna

    2012-04-01

    Full Text Available Abstract Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures, while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational

  20. Structure-based classification and ontology in chemistry.

    Science.gov (United States)

    Hastings, Janna; Magka, Despoina; Batchelor, Colin; Duan, Lian; Stevens, Robert; Ennis, Marcus; Steinbeck, Christoph

    2012-04-05

    Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic

  1. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

    Directory of Open Access Journals (Sweden)

    Camon Evelyn B

    2005-05-01

    Full Text Available Abstract Background The Gene Ontology Annotation (GOA database http://www.ebi.ac.uk/GOA aims to provide high-quality supplementary GO annotation to proteins in the UniProt Knowledgebase. Like many other biological databases, GOA gathers much of its content from the careful manual curation of literature. However, as both the volume of literature and of proteins requiring characterization increases, the manual processing capability can become overloaded. Consequently, semi-automated aids are often employed to expedite the curation process. Traditionally, electronic techniques in GOA depend largely on exploiting the knowledge in existing resources such as InterPro. However, in recent years, text mining has been hailed as a potentially useful tool to aid the curation process. To encourage the development of such tools, the GOA team at EBI agreed to take part in the functional annotation task of the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology challenge. BioCreAtIvE task 2 was an experiment to test if automatically derived classification using information retrieval and extraction could assist expert biologists in the annotation of the GO vocabulary to the proteins in the UniProt Knowledgebase. GOA provided the training corpus of over 9000 manual GO annotations extracted from the literature. For the test set, we provided a corpus of 200 new Journal of Biological Chemistry articles used to annotate 286 human proteins with GO terms. A team of experts manually evaluated the results of 9 participating groups, each of which provided highlighted sentences to support their GO and protein annotation predictions. Here, we give a biological perspective on the evaluation, explain how we annotate GO using literature and offer some suggestions to improve the precision of future text-retrieval and extraction techniques. Finally, we provide the results of the first inter-annotator agreement study for manual GO curation, as well as an

  2. Current Research of the Roles of IL-35 in Tumor Progression%白细胞介素35的在肿瘤发展中的作用

    Institute of Scientific and Technical Information of China (English)

    黄崇标; 田野; 崔焱; 徐杰; 辛亮; 杨雪玲; 齐大亮

    2016-01-01

    白细胞介素(interleukin, IL)-35是IL-12细胞因子家族的新成员,自2007年发现以来IL-35很快成为了相关领域的研究热点。与IL-12家族的其他成员(IL-12、IL-23以及IL-27)相类似,IL-35也是由异源性的α链及β链组成,即p35和EBI3蛋白组成。目前的研究发现IL-35的功能主要表现在两个方面,一方面是IL-35在体内某些炎性疾病及自身免疫性疾病患者体内异常表达,IL-35在这些疾病的发生发展过程中起到重要作用。另一方面,IL-35在某些肿瘤中也表达异常,在肿瘤的发展过程中起到了重要作用。本文对IL-35的结构及信号通路进行了阐述,并总结了IL-35在肿瘤发展中的作用的最新研究进展。%Interleukin(IL)-35 is a new member of the interleukin-12 superfamily. Since its first report in 2007, IL-35 rapidly became a research highlight in the ifeld of immunology. Like other IL-12 superfamily members, IL-35 was a heterodimer which was composed of anαchain P35 and aβchain Epstein-Barr virus induced gene 3 (EBI3). Recent research work revealed two distinct roles of IL-35. Firstly, IL-35 is highly expressed in some kinds of inlfammatory diseases and autoim-mune diseases and plays import roles in the pathogenesis. Secondly, IL-35 is positively expressed in some cancers and plays some roles in the process of tumor progression. Here we demonstrate the structure and the signalling of IL-35. We reviewed the the roles of IL-35 in promoting tumor progression.

  3. Nutritional status of care-dependent people with dementia in shared-housing arrangements--a one-year follow-up.

    Science.gov (United States)

    Meyer, Saskia; Gräske, Johannes; Worch, Andreas; Wolf-Ostermann, Karin

    2015-12-01

    Malnutrition in the elderly is an important nursing challenge. Persons with dementia disease are often affected by malnutrition. During recent years, shared-housing arrangements (SHA) for older care-dependent people, frequently with dementia disease, have evolved in Germany. SHA can be an alternative to traditional residential care in nursing homes. The prevalence of malnutrition in SHA is compared to the prevalence in community dwellings and lower than the prevalence of malnutrition in nursing homes. There are no scientific data about the development of the nutritional status of older care-dependent people in SHA over one year. The aim of this study is to describe the nutritional status of care-dependent people with dementia disease living in SHA and to investigate changes over a period of one year. A longitudinal study with a one-year follow-up was performed. Standardised interviews with nurses were conducted concerning nutritional status (Mini Nutritional Assessment--MNA), cognitive capacities (Mini Mental State Examination--MMSE), activities of daily living (Extended Barthel-Index--EBI) and socio-demographic characteristics. Nutritional data were available for 45 residents at baseline and 36 residents at follow-up. At baseline, 45 residents with an average age of 78.4 years living in SHA in the state of Berlin, Germany, were included in the study. Predominantly, residents were female (73.3%) and diagnosed with dementia (88.9%), with a moderate to severe cognitive impairment (MMSE: 10.8) and low daily living abilities (EBI: 33.7). Most residents (80.6%) have a risk of malnutrition regarding the MNA. The average MNA score did decline slightly within one year (t0 = 20.8 vs. t1 = 19.7). Regular screenings for malnutrition using validated standardised assessments, which are easy to apply, should be implemented in SHA to avoid nutritional and health-related problems arising from malnutrition. Flexible structures for care, as in SHA, can facilitate coping with

  4. Heterologous expression of the Monilinia fructicola CYP51 (MfCYP51 gene in Pichia pastoris confirms the mode of action of the novel fungicide, SYP-Z048

    Directory of Open Access Journals (Sweden)

    Fengping eChen

    2015-05-01

    Full Text Available The novel agricultural fungicide 3-[5-(4-chlorophenyl-2,3-dimethyl-3-isoxazolidinyl] pyridine (SYP-Z048 developed by China Shenyang Research Institute of Chemical Industry has been confirmed to be an ergosterol biosynthesis inhibitor (EBI. Previous studies have shown that EBIs target the proteins from a range of genes, including CYP51, ERG2 and/or ERG24, and ERG27, which are involved in the ergosterol biosynthesis pathway. In the current study the ERG2, ERG24, and ERG27 genes were cloned from wild type and resistant mutants of Monilinia fructicola in an attempt to clarify the target site of SYP-Z048. Comparative analysis of the deduced aa sequence of these genes, as well as CYP51, revealed several point mutations that resulted in amino acid variation among the sensitive and resistant isolates. However, sensitivity assays indicated that only one, the substitution of phenylalanine (F for the tyrosine (Y at 136 in CYP51, was correlated with reduced sensitivity to SYP-Z048. Heterologous expression of MfCYP51-136Y (MfCYP136Y and MfCYP51-136F (MfCYP136F in Pichia pastoris revealed that MfCYP136F significantly reduced sensitivity to SYP-Z048, increasing the average EC50 of the transformants 11-fold relative to those carrying MfCYP136Y. However, neither the additional copy of MfCYP136Y nor multiple copies of MfCYP136F were found to reduce sensitivity relative to the empty vector control or single copy transformants, respectively. Molecular docking experiments using SYP-Z048 with HsCYP145Y and the mutated version HsCYP145F as substitutes for MfCYP136Y and MfCYP136F, respectively, indicated that the reduced affinity of HsCYP145F for SYP-Z048 resulted from the loss of a hydrogen bond between the fungicide and the active site. Taken together these results indicate that MfCYP51 is the major target site of SYP-Z048 in M. fructicola, which has important implications for the resistance management of this fungicide in the field.

  5. Online resources for genomic structural variation.

    Science.gov (United States)

    Sneddon, Tam P; Church, Deanna M

    2012-01-01

    Genomic structural variation (SV) can be thought of on a continuum from a single base pair insertion/deletion (INDEL) to large megabase-scale rearrangements involving insertions, deletions, duplications, inversions, or translocations of whole chromosomes or chromosome arms. These variants can occur in coding or noncoding DNA, they can be inherited or arise sporadically in the germline or somatic cells. Many of these events are segregating in the population and can be considered common alleles while others are new alleles and thus rare events. All species studied to date harbor structural variants and these may be benign, contributing to phenotypes such as sensory perception and immunity, or pathogenic resulting in genomic disorders including DiGeorge/velocardiofacial, Smith-Margenis, Williams-Beuren, and Prader-Willi syndromes. As structural variants are identified, validated, and their significance, origin, and prevalence are elucidated, it is of critical importance that these data be collected and collated in a way that can be easily accessed and analyzed. This chapter describes current structural variation online resources (see Fig. 1 and Table 1), highlights the challenges in capturing, storing, and displaying SV data, and discusses how dbVar and DGVa, the genomic structural variation databases developed at NCBI and EBI, respectively, were designed to address these issues.

  6. The REX-ISOLDE project

    Energy Technology Data Exchange (ETDEWEB)

    Habs, D.; Kester, O.; Sieber, T.; Bongers, H.; Emhofer, S.; Reiter, P.; Thirolf, P.G.; Bollen, G. [LMU Muenchen, Sektion Physik (Germany); Aystoe, J.; Forstner, O.; Ravn, H.; Nilsson, T.; Oinonen, M.; Simon, H.; Cederkall, J. [CERN (Switzerland); Ames, F.; Schmidt, P.; Huber, G. [Johannes-Gutenberg Universitaet (Germany); Liljeby, L.; Skeppstedt, O. [Manne Siegbahn Laboratory (Sweden)] (and others)

    2000-12-15

    The Radioactive Beam Experiment REX-ISOLDE [1-3] is a pilot experiment at ISOLDE (CERN) testing the new concept of post acceleration of radioactive ion beams by using charge breeding of the ions in a high charge state ion source and the efficient acceleration of the highly charged ions in a short LINAC using modern ion accelerator structures. In order to prepare the ions for the experiments singly charged radioactive ions from the on-line mass separator ISOLDE will be cooled and bunched in a Penning trap, charge bred in an electron beam ion source (EBIS) and finally accelerated in the LINAC. The LINAC consists of a radiofrequency quadrupole (RFQ) accelerator, which accelerates the ions up to 0.3 MeV/u, an interdigital H-type (IH) structure with a final energy between 1.1 and 1.2 MeV/u and three seven gap resonators, which allow the variation of the final energy. With an energy of the radioactive beams between 0.8 MeV/u and 2.2 MeV/u a wide range of experiments in the field of nuclear spectroscopy, astrophysics and solid state physics will be addressed by REX-ISOLDE.

  7. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

    This paper describes a frame-based integration of the three GO subontologies, the Chemicals of Biological Interest ontology (ChEBI), and the Cell Type Ontology (CTO) in which relationships between elements of the ontologies are modeled in a way that better captures the relational semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions of the form (subject, relationship, object) by identifying patterns in GO terms, mapping these patterns and subpatterns to relationships, matching concepts to these patterns and subpatterns, and integrating these assertions into the ontologies. Using this methodology, a large number of reliable assertions linking previously unlinked OBO terms using a wide variety of specific, hierarchically arranged relationships were created: A predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid; a further 429 assertions (corresponding to 6% of the matching terms) were manually created, resulting in an initial set of 4,497 assertions. Furthermore, this methodology programmatically integrates assertions into a base ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels. Such an integration is absent from previous compositional efforts, and we argue its necessity for the creation of coherent biological ontologies when linking previously unlinked terms. PMID:17011833

  8. UniEuk: Time to Speak a Common Language in Protistology!

    Science.gov (United States)

    Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

    2017-05-01

    Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

  9. Activation of liver X receptor suppresses the production of the IL-12 family of cytokines by blocking nuclear translocation of NF-κBp50.

    Science.gov (United States)

    Canavan, Mary; McCarthy, Ciara; Larbi, Nadia Ben; Dowling, Jennifer K; Collins, Laura; O'Sullivan, Finbarr; Hurley, Grainne; Murphy, Carola; Quinlan, Aoife; Moloney, Gerry; Darby, Trevor; MacSharry, John; Kagechika, Hiroyuki; Moynagh, Paul; Melgar, Silvia; Loscher, Christine E

    2014-10-01

    There is now convincing evidence that liver X receptor (LXR) is an important modulator of the inflammatory response; however, its mechanism of action remains unclear. This study aimed to examine the effect of LXR on the IL-12 family of cytokines and examined the mechanism by which LXR exerted this effect. We first demonstrated that activation of murine-derived dendritic cells (DC) with a specific agonist to LXR enhanced expression of LXR following activation with LPS, suggesting a role in inflammation. Furthermore, we showed LXR expression to be increased in vivo in dextrane sulphate sodium-induced colitis. LXR activation also suppressed production of IL-12p40, IL-12p70, IL-27 and IL-23 in murine-derived DC following stimulation with LPS, and specifically targeted the p35, p40 and EBI3 subunits of the IL-12 cytokine family, which are under the control of the NF-κB subunit p50 (NF-κBp50). Finally, we demonstrated that LXR can associate with NF-κBp50 in DC and that LXR activation prevents translocation of the p50 subunit into the nucleus. In summary, our study indicates that LXR can specifically suppress the IL-12 family of cytokines though its association with NF-κBp50 and highlights its potential as a therapeutic target for chronic inflammatory diseases. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  10. MAFF – The Munich accelerator for fission fragments

    Indian Academy of Sciences (India)

    L Beck; D Habs; P Reiter; P Thirolf; T Seiber; H Bongers; S Emhofer; H Maier

    2002-12-01

    At the new high flux reactor FRM-II in Munich the accelerator MAFF (Munich accelerator for fission fragments) is under design. In the high neutron flux of 1014 n/cm2 s up to 1014 neutron-rich fission fragments per second are produced in the 1 g U-235 target. Ions with an energy of 30 keV are extracted from the ion source. In the mass seperator two isotopes can be selected. One of the beams is used for low energy experiments, the other one is injected into an ECRIS (or EBIS) for charge breeding to a / ≥ 0.16. A gas filled RFQ cooler is used for emittance improvement. The subsequent LINAC delivers beams with an energy ranging from 3.7 MeV/u to 5.9 MeV/u. New IH structures are being developed at the Munich tandem laboratory. A small storage ring is planned in a further stage to recycle the fission fragments. A thin target foil can be placed into this ring, e.g., for synthesis of super-heavy elements. The through-going beam tube has been installed in the heavy water tank of the reactor. Tests of the target ion source in a special oven to test long term stability and safety tests were in progress.

  11. WIYN Open Cluster Study. LXXII. A uvbyCa Hbeta CCD Analysis of the Metal-Deficient Open Cluster, NGC 2506

    CERN Document Server

    Anthony-Twarog, B J; Twarog, B A

    2016-01-01

    Precision uvbyCa Hbeta photometry of the metal-deficient, old open cluster, NGC 2506, is presented. The survey covers an area 20 by 20 arcminutes, and extends to V~18 for b-y and Hbeta and to V~17.0 for c_1 and hk. For V < 16.0, photometric scatter among the indices leads to the recovery of 6 known variables within the cluster core and 5 new variables in the outer 5 arcmin of the survey field. Proper motions, radial velocities, and precise multicolor indices are used to isolate a highly probable sample of cluster members from the very rich color-magnitude diagram (CMD). From 257 highly probable members at the cluster turnoff, we derive a reddening estimate of E(b-y) = 0.042 +/- 0.001 (E(B-V) = 0.058 +/- 0.001), where the errors refer to the internal standard errors of the mean. [Fe/H] is derived from the A/F dwarf members using both m_1 and hk, leading to [Fe/H] = -0.296 +/- 0.011 (sem) and -0.317 +/- 0.004 (sem), respectively. The weighted average, heavily dominated by hk, is [Fe/H] = -0.316 +/- 0.033. Ba...

  12. A uvbyCaHbeta Analysis of the Old Open Cluster, NGC 6819

    CERN Document Server

    Anthony-Twarog, B J; Twarog, B A

    2014-01-01

    NGC 6819 is a richly populated, older open cluster situated within the Kepler field. A CCD survey of the cluster on the uvbyCaHbeta system, coupled with proper-motion membership, has been used to isolate 382 highly probable, single-star unevolved main-sequence members over a 20-arcminute field centered on the cluster. From 278 F dwarfs with high precision photometry in all indices, a mean reddening of E(b-y) = 0.117 +/- 0.005 or E(B-V) = 0.160 +/- 0.007 is derived, where the standard errors of the mean include both internal errors and the photometric zero-point uncertainty. With the reddening fixed, the metallicity derived from the same 278 stars is [Fe/H] = -0.116 +/- 0.101 from m_1 and -0.055 +/- 0.033 from hk, for a weighted average of [Fe/H] = -0.06 +/- 0.04, where the quoted standard errors of the mean values include the internal errors from the photometric scatter plus the uncertainty in the photometric zero points. If metallicity is derived using individual reddening values for each star to account for...

  13. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

    Science.gov (United States)

    Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-Marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frédérick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaëlle; Wessner, Mark; Acinas, Silvia G; Royo-Llonch, Marta; Cornejo-Castillo, Francisco M; Logares, Ramiro; Fernández-Gómez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Hoopen, Petra Ten; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-Lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E; Stepanauskas, Ramunas; Sullivan, Matthew B; Brum, Jennifer R; Duhaime, Melissa B; Poulos, Bonnie T; Hurwitz, Bonnie L; Pesant, Stéphane; Karsenti, Eric; Wincker, Patrick

    2017-08-01

    A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

  14. A new reference implementation of the PSICQUIC web service.

    Science.gov (United States)

    del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

    2013-07-01

    The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

  15. Improvements in the Protein Identifier Cross-Reference service.

    Science.gov (United States)

    Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

    2012-07-01

    The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

  16. Different Transcriptional Profiles of Human Monocyte-Derived Dendritic Cells Infected with Distinct Strains of Mycobacterium tuberculosis and Mycobacterium bovis Bacillus Calmette-Guérin

    Directory of Open Access Journals (Sweden)

    Nunzia Sanarico

    2011-01-01

    Full Text Available In order to analyze dendritic cells (DCs activation following infection with different mycobacterial strains, we studied the expression profiles of 165 genes of human monocyte-derived DCs infected with H37Rv, a virulent Mycobacterium tuberculosis (MTB laboratory strain, CMT97, a clinical MTB isolate, Mycobacterium bovis bacillus Calmette-Guérin (BCG, Aventis Pasteur, and BCG Japan, both employed as vaccine against tuberculosis. The analysis of the gene expression reveals that, despite a set of genes similarly modulated, DCs response resulted strain dependent. In particular, H37Rv significantly upregulated EBI3 expression compared with BCG Japan, while it was the only strain that failed to release a significant IL-10 amount. Of note, BCG Japan showed a marked increase in CCR7 and TNF-α expression regarding both MTB strains and it resulted the only strain failing in exponential intracellular growth. Our results suggest that DCs display the ability to elicit a tailored strain-specific immune response.

  17. Preparation of ansa-metallocenes for production of poly(α-olefin) lubricants.

    Science.gov (United States)

    Park, Ji Hae; Jang, Young Eun; Jeon, Jong Yeob; Go, Min Jeong; Lee, Junseong; Kim, Sung Kwan; Lee, Sang-Ick; Lee, Bun Yeoul

    2014-07-14

    An ansa-zirconocene bearing methyl substituents at all positions adjacent to the bridgehead [(-C(Ph)HC(Ph)H-)(η(5)-2,5-Me2C5H2)2ZrCl2] (4) was prepared in high yields (78%) through the reductive dimerization of 1,4-dimethyl-6-phenylfulvene utilizing ZrCl2·DME generated in situ. The structure of 4 was subsequently confirmed using X-ray crystallography. 4 exhibited excellent catalytic performance with regard to 1-decene oligomerization, which was carried out with the intention of preparing lubricant base stocks. High activities (21 × 10(6) g mol(-1) Zr h(-1) activity; TON = 150 000; TOF = 42 s(-1)) were observed at temperatures as high as 120 °C and the oligomer distribution was appropriate for lubricant application. The simulated distillation (SIMDIS) data confirmed that a wide range of oligomers were formed, ranging from the dimer (2-mer) to 20-mer. A minimal amount of the dimer and oligomers larger than the 10-mer was formed (13 and 25 wt%, respectively). Alternatively, a typical unbridged complex such as (η(5)-nBuC5H4)2ZrCl2 primarily produced dimers (54 wt%), whereas the ansa-zirconocene (EBI)ZrCl2 primarily produced oligomers larger than 10-mer (62 wt%). The methyl substituents at the positions adjacent to the bridgehead in 4 played a significant role in the catalytic performance.

  18. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    Full Text Available Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/ for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/, the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  19. LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

    Directory of Open Access Journals (Sweden)

    Joseph M Foster

    Full Text Available Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

  20. MetaboLights: towards a new COSMOS of metabolomics data management.

    Science.gov (United States)

    Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L

    2012-10-01

    Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

  1. The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.

    Science.gov (United States)

    de Matos, Paula; Cham, Jennifer A; Cao, Hong; Alcántara, Rafael; Rowland, Francis; Lopez, Rodrigo; Steinbeck, Christoph

    2013-03-20

    User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.

  2. MetaboLights: An Open-Access Database Repository for Metabolomics Data.

    Science.gov (United States)

    Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

    2016-03-24

    MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

  3. KNIME-CDK: Workflow-driven cheminformatics.

    Science.gov (United States)

    Beisken, Stephan; Meinl, Thorsten; Wiswedel, Bernd; de Figueiredo, Luis F; Berthold, Michael; Steinbeck, Christoph

    2013-08-22

    Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process. KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest. KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.

  4. Metingear: a development environment for annotating genome-scale metabolic models

    Science.gov (United States)

    May, John W.; James, A. Gordon; Steinbeck, Christoph

    2013-01-01

    Summary: Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Availability: Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X. Contact: johnmay@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23766418

  5. Production of multiply charge-state ions in a multicusp ion source

    Science.gov (United States)

    Williams, M. D.; deVries, G. J.; Gough, R. A.; Leung, K. N.; Monroy, M.

    1996-03-01

    High charge state ion beams are commonly used in atomic and nuclear physics experiments. Multiply charged ions are normally produced in an ECR or in an EBIS. Multicusp generators can confine primary electrons very efficiently. Therefore, the electrical and gas efficiencies of these devices are high. Since the magnetic cusp fields are localized near the chamber wall, large volumes of uniform and high density plasmas can be obtained at low pressure, conditions favorable for the formation of multiply charged state ions. Attempts have been made at LBNL to generate multiply charged ion beams by employing a 25-cm diam by 25-cm long multicusp source. Experimental results demonstrated that charge states as high as 7+ can be obtained with argon or xenon plasmas. Multiply charged metallic ions such as tungsten and titanium have also been successfully formed in the multicusp source by evaporation and sputtering processes. In order to extend the charge state to higher values, a novel technique of injecting high energy electrons into the source plasma is proposed. If this is successful, the multicusp source will become very useful for radioactive beam accelerators, ion implantation, and nuclear physics applications.

  6. Production of multiply charge-state ions in a multicusp ion source

    Energy Technology Data Exchange (ETDEWEB)

    Williams, M.D.; deVries, G.J.; Gough, R.A.; Leung, K.N.; Monroy, M. [Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1996-03-01

    High charge state ion beams are commonly used in atomic and nuclear physics experiments. Multiply charged ions are normally produced in an ECR or in an EBIS. Multicusp generators can confine primary electrons very efficiently. Therefore, the electrical and gas efficiencies of these devices are high. Since the magnetic cusp fields are localized near the chamber wall, large volumes of uniform and high density plasmas can be obtained at low pressure, conditions favorable for the formation of multiply charged state ions. Attempts have been made at LBNL to generate multiply charged ion beams by employing a 25-cm diam by 25-cm long multicusp source. Experimental results demonstrated that charge states as high as 7+ can be obtained with argon or xenon plasmas. Multiply charged metallic ions such as tungsten and titanium have also been successfully formed in the multicusp source by evaporation and sputtering processes. In order to extend the charge state to higher values, a novel technique of injecting high energy electrons into the source plasma is proposed. If this is successful, the multicusp source will become very useful for radioactive beam accelerators, ion implantation, and nuclear physics applications. {copyright} {ital 1996 American Institute of Physics.}

  7. The ISOLDE hall

    CERN Multimedia

    Maximilien Brice

    2002-01-01

    Since 1992, after its move from the 600 MeV SC, ISOLDE is a customer of the Booster (then 1 GeV, now 1.4 GeV). The intense Booster beam (some 3E13 protons per pulse) is directed onto a target, from which a mixture of isotopes emanates. After ionization and electrostatic acceleration to 60 keV, they enter one of the 2 spectrometers (General Purpose Separator: GPS, and High Resolution Separator: HRS) from which the selected ions are directed to the experiments. The photos show: the REX-ISOLDE post accelerator; the mini-ball experiment; an overview of the ISOLDE hall. In the picture (_12) of the hall, the separators are behind the wall. From either of them, beams can be directed into any of the many beamlines towards the experiments, some of which are visible in the foreground. The elevated cubicle at the left is EBIS (Electron Beam Ion Source), which acts as a charge-state multiplier for the REX facility. The ions are further mass analzyzed and passed on to the linac which accelerates them to higher energies. T...

  8. Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL

    Indian Academy of Sciences (India)

    Margaret Biswas; Alex Kanapin; Rolf Apweiler

    2001-06-01

    InterPro (http://www.ebi.ac.uk/interpro/) is an integrated documentation resource for protein families, domains and sites, developed initially as a means of rationalizing the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. It is a useful resource that aids the functional classification of proteins. Almost 90% of the actinopterygii protein sequences from SWISS-PROT and TrEMBL can be classified using InterPro. Over 30% of the actinopterygii protein sequences currently in SWISS-PROT and TrEMBL are of mitochondrial origin, the majority of which belong to the cytochrome b/b6 family. InterPro also gives insights into the domain composition of the classified proteins and has applications in the functional classification of newly determined sequences lacking biochemical characterization, and in comparative genome analysis. A comparison of the actinopterygii protein sequences against the sequences of other eukaryotes confirms the high representation of eukaryotic protein kinase in the organisms studied. The comparisons also show that, based on InterPro families, the trans-species evolution of MHC class I and II molecules in mammals and teleost fish can be recognized.

  9. DESM: portal for microbial knowledge exploration systems

    KAUST Repository

    Salhi, Adil

    2015-11-05

    Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.

  10. The herpesvirus 8-encoded chemokine vMIP-II, but not the poxvirus-encoded chemokine MC148, inhibits the CCR10 receptor

    DEFF Research Database (Denmark)

    Lüttichau, H R; Lewis, I C; Gerstoft, J;

    2001-01-01

    The viral chemokine antagonist vMIP-II encoded by human herpesvirus 8 (HHV8) and MC148 encoded by the poxvirus - Molluscum contagiosum - were tested against the newly identified chemokine receptor CCR10. As the CCR10 ligand ESkine / CCL27 had the highest identity to MC148 and because both...... chemokines are expressed in the skin we suspected MC148 to block CCR10. However, in calcium mobilization assays we found MC148 unable to block CCR10 in micromolar concentrations in contrast to vMIP-II. (125)I-MC148 was only able to bind to CCR8, but not to CCR10, CCR11, CXCR6 / BONZO, APJ, DARC or the orphan...... receptors BOB, EBI-II, GPR4, GPR17, HCR or RDC1. We conclude that MC148 is a highly selective CCR8 antagonist conceivably optimized to interfere with NK cell and monocyte invasion, whereas the broad-spectrum antagonist vMIP-II protects HHV8 by blocking multiple receptors....

  11. CALBC silver standard corpus.

    Science.gov (United States)

    Rebholz-Schuhmann, Dietrich; Jimeno Yepes, Antonio José; Van Mulligen, Erik M; Kang, Ning; Kors, Jan; Milward, David; Corbett, Peter; Buyko, Ekaterina; Beisswanger, Elena; Hahn, Udo

    2010-02-01

    The CALBC initiative aims to provide a large-scale biomedical text corpus that contains semantic annotations for named entities of different kinds. The generation of this corpus requires that the annotations from different automatic annotation systems be harmonized. In the first phase, the annotation systems from five participants (EMBL-EBI, EMC Rotterdam, NLM, JULIE Lab Jena, and Linguamatics) were gathered. All annotations were delivered in a common annotation format that included concept identifiers in the boundary assignments and that enabled comparison and alignment of the results. During the harmonization phase, the results produced from those different systems were integrated in a single harmonized corpus ("silver standard" corpus) by applying a voting scheme. We give an overview of the processed data and the principles of harmonization--formal boundary reconciliation and semantic matching of named entities. Finally, all submissions of the participants were evaluated against that silver standard corpus. We found that species and disease annotations are better standardized amongst the partners than the annotations of genes and proteins. The raw corpus is now available for additional named entity annotations. Parts of it will be made available later on for a public challenge. We expect that we can improve corpus building activities both in terms of the numbers of named entity classes being covered, as well as the size of the corpus in terms of annotated documents.

  12. Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

    Science.gov (United States)

    Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

    2015-09-15

    Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

  13. Massive Analysis of cDNA Ends (MACE for transcript-based marker design in pea (Pisum sativum L.

    Directory of Open Access Journals (Sweden)

    Aleksandr Zhernakov

    2017-03-01

    Full Text Available Aimed at gene-based markers design, we generated and analyzed transcriptome sequencing datasets for six pea (Pisum sativum L. genetic lines that have not previously been massively genotyped. Five cDNA libraries obtained from nodules or nodulated roots of genetic lines Finale, Frisson, Sparkle, Sprint-2 and NGB1238 were sequenced using a versatile 3′-RNA-seq protocol called MACE (Massive Analysis of cDNA Ends. MACE delivers a single next-generation sequence from the 3′-end of each individual cDNA molecule that precisely quantifies the respective transcripts. Since the contig generated from the 3′-end of the cDNA by assembling all sequences encompasses the highly polymorphic 3′-untranslated region (3′-UTR, MACE efficiently detects single nucleotide variants (SNVs. Mapping MACE reads to the reference nodule transcriptome assembly of the pea line SGE (Transcriptome Shotgun Assembly GDTM00000000.1 resulted in characterization of over 34,000 polymorphic sites in more than 9700 contigs. Several of these SNVs were located within recognition sequences of restriction endonucleases which allowed the design of co-dominant CAPS markers for the particular transcript. Cleaned reads of sequenced libraries are available from European Nucleotide Archive (http://www.ebi.ac.uk/ under accessions PRJEB18101, PRJEB18102, PRJEB18103, PRJEB18104, PRJEB17691.

  14. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Cameron Palmer

    2017-07-01

    Full Text Available Genome-wide association studies (GWAS have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14, even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16. We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94. In contrast, ancestry differences between replication and discovery (13 studies, 385 loci cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.

  15. PDBe: Protein Data Bank in Europe.

    Science.gov (United States)

    Velankar, Sameer; Alhroub, Younes; Alili, Anaëlle; Best, Christoph; Boutselakis, Harry C; Caboche, Ségolène; Conroy, Matthew J; Dana, Jose M; van Ginkel, Glen; Golovin, Adel; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hirshberg, Miriam; John, Melford; Lagerstedt, Ingvar; Mir, Saqib; Newman, Laurence E; Oldfield, Tom J; Penkett, Chris J; Pineda-Castillo, Jorge; Rinaldi, Luana; Sahni, Gaurav; Sawka, Grégoire; Sen, Sanchayita; Slowley, Robert; Sousa da Silva, Alan Wilter; Suarez-Uruena, Antonio; Swaminathan, G Jawahar; Symmons, Martyn F; Vranken, Wim F; Wainwright, Michael; Kleywegt, Gerard J

    2011-01-01

    The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration--it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.

  16. Synthesis and Thermosensitive Behavior of Polyacrylamide Copolymers and Their Applications in Smart Textiles

    Directory of Open Access Journals (Sweden)

    Tao Chen

    2015-05-01

    Full Text Available We tuned the lower critical solution temperature (LCST of amphiphilic poly(N-isopropylacrylamide (PNIPAAm via copolymerization with a hydrophilic comonomer of N-hydroxymethyl acrylamide (NHMAAm. A series of copolymers P(NIPAAm-co-NHMAAm were synthesized by atom transfer radical polymerization (ATRP using CuBr/(N,N,N',N',N''-Pentamethyldiethylenetriamine (PMDETA as a catalyst system and 2-bromo ethyl isobutyrate (EBiB as an initiator. The copolymers were well characterized by Fourier transform infrared spectroscopy (FT-IR, 1H Nuclear magnetic resonance (NMR, and Thermogravimetric analysis (TGA. The copolymers followed a simple rule in their thermosensitive behaviors and have a linear increase in the LCST as a function of NHMAAm mol%. The thermosensitive properties of the copolymer films were investigated and demonstrated hydrophilic-hydrophobic transitions. Finally, the copolymer was grafted onto cotton fabrics using citric acid (CA as a crosslinking agent and sodium hypophosphite (SHP as a catalyst following a two dipping, two padding process. The large number of hydroxyl groups in the copolymer makes grafting convenient and firm. The grafted cotton fabrics show obvious thermosensitive behaviors. The results demonstrate that the cotton fabrics become more hydrophobic when the temperature is higher than the LCST. This study presents a valuable route towards temperature-responsive smart textiles and their potential applications.

  17. Cutting edge: Human regulatory T cells require IL-35 to mediate suppression and infectious tolerance.

    Science.gov (United States)

    Chaturvedi, Vandana; Collison, Lauren W; Guy, Clifford S; Workman, Creg J; Vignali, Dario A A

    2011-06-15

    Human regulatory T cells (T(reg)) are essential for the maintenance of immune tolerance. However, the mechanisms they use to mediate suppression remain controversial. Although IL-35 has been shown to play an important role in T(reg)-mediated suppression in mice, recent studies have questioned its relevance in human T(reg). In this study, we show that human T(reg) express and require IL-35 for maximal suppressive capacity. Substantial upregulation of EBI3 and IL12A, but not IL10 and TGFB, was observed in activated human T(reg) compared with conventional T cells (T(conv)). Contact-independent T(reg)-mediated suppression was IL-35 dependent and did not require IL-10 or TGF-β. Lastly, human T(reg)-mediated suppression led to the conversion of the suppressed T(conv) into iTr35 cells, an IL-35-induced T(reg) population, in an IL-35-dependent manner. Thus, IL-35 contributes to human T(reg)-mediated suppression, and its conversion of suppressed target T(conv) into IL-35-induced T(reg) may contribute to infectious tolerance.

  18. IL-35 and Autoimmunity: a Comprehensive Perspective.

    Science.gov (United States)

    Choi, Jinjung; Leung, Patrick S C; Bowlus, Christopher; Gershwin, M Eric

    2015-12-01

    Interleukin 35 (IL-35) is the most recently identified member of the IL-12 family of cytokines and offers the potential to be a target for new therapies for autoimmune, inflammatory, and infectious diseases. Similar to other members of the IL-12 family including IL-12, IL-23, and IL-27, IL-35 is composed of a heterodimer of α and β chains, which in the case of IL-35 are the p35 and Epstein-Barr virus-induced gene 3 (EBI3) proteins. However, unlike its proinflammatory relatives, IL-35 has immunosuppressive effects that are mediated through regulatory T and B cells. Although there are limited data available regarding the role of IL-35 in human autoimmunity, several murine models of autoimmunity suggest that IL-35 may have potent effects in regulating immunoreactivity via IL-10-dependent mechanisms. We suggest that similar effects are operational in human disease and IL-35-directed therapies hold significant promise. In particular, we emphasize that IL-35 has immunosuppressive ability that are mediated via regulatory T and B cells that are IL-10 dependent. Further, although deletion of IL-35 does not result in spontaneous breach of tolerance, recombinant IL-35 can improve autoimmune responses in several experimental models.

  19. Elevated IL-35 in bone marrow of the patients with acute myeloid leukemia.

    Science.gov (United States)

    Wang, Jia; Tao, Qianshan; Wang, Huiping; Wang, Zhitao; Wu, Fan; Pan, Ying; Tao, Lili; Xiong, Shudao; Wang, Yiping; Zhai, Zhimin

    2015-09-01

    Acute myeloid leukemia (AML) is the most common hematological malignancy in adults, but the etiology of it remains poorly understood. IL-35 is a recently described cytokine composed of an IL-12 subunit p35 and an IL-27 subunit Epstein-Barr virus induced gene 3 (EBI3), and has an immunosuppressive effect on inflammation through induction of regulatory T cells (Tregs) and suppression of Th1 and Th17. Recently, we have illustrated that concentrations of IL-35 in peripheral blood are up-regulated in newly diagnosed (ND) AML patients. However, whether IL-35 in bone marrow is increased in AML patients is not clear. In this study, we examined IL-35 in bone marrow by various methods including RT-PCR, ELISA, FCM and IHC, and found that IL-35 levels are also increased significantly in bone marrow of adult AML patients. Furthermore, we investigated that concentrations of bone marrow IL-35 in ND group were higher than that in complete remission (CR) group and control group, but there was no significant difference compared to that in relapse group. In conclusion, IL-35 was elevated in bone marrow of adult AML patients and this increase was correlated with the clinical stages of malignancy, suggesting that IL-35 is involved in pathogenesis of AML.

  20. IL-35 over-expression increases apoptosis sensitivity and suppresses cell growth in human cancer cells.

    Science.gov (United States)

    Long, Jun; Zhang, Xulong; Wen, Mingjie; Kong, Qingli; Lv, Zhe; An, Yunqing; Wei, Xiao-Qing

    2013-01-01

    Interleukin (IL)-35 is a novel heterodimeric cytokine in the IL-12 family and is composed of two subunits: Epstein-Barr virus-induced gene 3 (EBI3) and IL-12p35. IL-35 is expressed in T regulatory (Treg) cells and contributes to the immune suppression function of these cells. In contrast, we found that both IL-35 subunits were expressed concurrently in most human cancer cell lines compared to normal cell lines. In addition, we found that TNF-α and IFN-γ stimulation led to increased IL-35 expression in human cancer cells. Furthermore, over-expression of IL-35 in human cancer cells suppressed cell growth in vitro, induced cell cycle arrest at the G1 phase, and mediated robust apoptosis induced by serum starvation, TNF-α, and IFN-γ stimulation through the up-regulation of Fas and concurrent down-regulation of cyclinD1, survivin, and Bcl-2 expression. In conclusion, our results reveal a novel functional role for IL-35 in suppressing cancer activity, inhibiting cancer cell growth, and increasing the apoptosis sensitivity of human cancer cells through the regulation of genes related to the cell cycle and apoptosis. Thus, this research provides new insights into IL-35 function and presents a possible target for the development of novel cancer therapies.

  1. IL-35, an anti-inflammatory cytokine which expands CD4+CD25+ Treg Cells.

    Science.gov (United States)

    Castellani, Maria Luisa; Anogeianaki, A; Felaco, P; Toniato, E; De Lutiis, M A; Shaik, B; Fulcheri, M; Vecchiet, J; Tetè, S; Salini, V; Theoharides, T C; Caraffa, A; Antinolfi, P; Frydas, I; Conti, P; Cuccurullo, C; Ciampoli, C; Cerulli, G; Kempuraj, D

    2010-01-01

    Interleukin 12 (IL 12) p35/p40 is a heterodimeric cytokine which plays a critical role in inflammation, immunity and tissue proliferation, and also plays a relevant function in T helper (Th) cell polarization and Th1 T-cell differentiation. IL-12 family members, IL-12p70, IL-23, IL-27 and IL-35, play an important role in influencing helper T-cell differentiation. EBV-induced gene 3 can be associated with the p35 subunit of IL-12 to form the EBI3/p35 heterodimer, also called IL-35. It has been shown that IL-35 has biological activity and able to expand CD4+CD25+ Treg cells, suppress the proliferation of CD4+CD25- effector cells and inhibit Th17 cell polarization. IL-35 has been shown to be constitutively expressed by regulatory T (Treg) cells CD4(+)CD25(+)Foxp3(+) and suggested to contribute to their suppressive activity. IL-35 is a crucial mediator which provokes CD4+CD25+ T cell proliferation and IL-10 generation, another well-known anti-inflammatory cytokine, along with TGFbeta cytokine. These studies suggest that IL-35, together with other successfully discovered cytokine inhibitors, represents a new potential therapeutic cytokine for chronic inflammation, autoimmunity and other immunological disorders.

  2. Circulating IL-35 in pancreatic ductal adenocarcinoma patients.

    Science.gov (United States)

    Jin, Peng; Ren, He; Sun, Wei; Xin, Wen; Zhang, Huan; Hao, Jihui

    2014-01-01

    IL-35 is a novel inhibitory cytokine that is mainly produced by regulatory T-cells (Tregs) and is required for Treg-mediated immunosuppression. However, the plasma levels of IL-35 in patients with pancreatic ductal adenocarcinoma (PDAC) have never been investigated. In this study, we found that plasma IL-35 levels more significantly increased in PDAC patients than in normal controls (134.53 ± 92.45 pg/mL vs. 14.26 ± 6.56 pg/mL). IL-35 mRNA levels were positively correlated with plasma IL-35 levels (EBI3, R = 0.925, pIL-35 expression levels were associated with lymph node metastasis (p = 0.001) and late tumor stage (p = 0.002). For the resected patients, high IL-35 expression levels were associated with large tumor size (pIL-35 in PDAC patients significantly increased, suggesting that regulating the expression of IL-35 may provide a new possible target for the treatment of PDAC patients, especially for the resectable ones.

  3. Human placental trophoblasts express the immunosuppressive cytokine IL-35.

    Science.gov (United States)

    Mao, Haiting; Gao, Wenjuan; Ma, Chao; Sun, Jintang; Liu, Jia; Shao, Qianqian; Song, Bingfeng; Qu, Xun

    2013-07-01

    Studies of maternal-fetal tolerance focus on defining mechanisms for establishment of immunological privilege within the uterus during pregnancy. Fetal trophoblasts play a key role in maternal tolerance, in part through cytokines production. As a novel inhibitory cytokine, IL-35 is produced by Foxp3(+) regulatory T cells (Tregs) and mediates maximal suppression of Tregs. The purpose of the study is to analyze the expression of IL-35 in first-trimester human placental trophoblasts. IL-35 expression was detected at both protein and mRNA levels by immunohistochemical staining and quantitative real-time PCR method, respectively and secretion of IL-35 was measured by ELISA assay. Our results demonstrated that human trophoblasts constitutively expressed IL-35. Ebi3 and p35 (two subunits of IL-35) mRNA was shown to be co-expressed in trophoblast cells. Moreover, large amounts of secreted IL-35 were detected in the supernatants of trophoblast cells. But we did not detect the constitutive expression of IL-35 in decidual stromal cells. Our findings confirmed for the first time that first-trimester human trophoblast cells expressed and secreted IL-35, which might contribute to their suppressive capacity to maternal immune cells. Therefore, IL-35 may be an important factor of the cytokine network regulating local immune responses during human pregnancy.

  4. The possible role of the novel cytokines il-35 and il-37 in inflammatory bowel disease.

    Science.gov (United States)

    Li, Yanmei; Wang, Yanan; Liu, Ying; Wang, Yatian; Zuo, Xiuli; Li, Yanqing; Lu, Xuefeng

    2014-01-01

    Interleukin- (IL-) 35 and IL-37 are newly discovered immune-suppressing cytokines. They have been described in inflammatory diseases such as collagen-induced arthritis and asthma. However, their expressions in inflammatory bowel disease (IBD) patients have not been yet explored. Our aim was to evaluate serum and inflamed mucosal levels in IBD patients. In 20 ulcerative colitis (UC) patients, 7 Crohn's disease (CD) patients, and 15 healthy subjects, cytokine levels in serum were determined using ELISA and mucosal expression studies were performed by immunohistochemistry, quantitative real-time PCR, and Western blot. The results showed that serums IL-35 and IL-37 levels were significantly decreased in UC and CD patients compared with healthy subjects. The cytokines levels correlated inversely with UC activity. IL-35 was expressed in infiltrating immune cells while IL-37 in intestinal epithelial cells as well as inflammatory cells. IBD patients had significantly higher Ebi3, p35 (two subunits of IL-35), and IL-37b gene expressions; IL-35 and IL-37 protein expressions were higher in IBD patients compared with controls. The study showed that serums IL-35 and IL-37 might be potentially novel biomarkers for IBD. Intestinal IL-35 and IL-37 proteins are upregulated, suggesting that regulating the expression of the two cytokines may provide a new possible target for the treatment of IBD.

  5. Detectable expression of IL-35 in CD4+ T cells from peripheral blood of chronic hepatitis B patients.

    Science.gov (United States)

    Liu, Fen; Tong, Fuyi; He, Yan; Liu, Haiyan

    2011-04-01

    Epstein-Barr virus-induced gene 3 (Ebi3) and the p35 subunit of IL-12 have been reported to form a heterodimeric cytokine, named IL-35, in human and mouse. In mice, IL-35 has been shown to be constitutively expressed by CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs) and suggested to contribute to their suppressive activity. However, human CD4(+)CD25(+)Foxp3(+) Tregs do not constitutively express detectable amounts of IL-35 in both mRNA and protein levels. Circulating CD4(+)CD25(+) Treg frequency of chronic Hepatitis B patients significantly correlates with serum viral load. In this study, we investigated whether IL-35 expression could be detected in CD4(+) T cells from peripheral blood of chronic Hepatitis B patients. Using both RT-PCR and immunoprecipitation plus Western blot analysis, we demonstrated that IL-35 expression could be detected in the CD4(+) T cells from peripheral blood of Chronic Hepatitis B patients.

  6. The composition and signaling of the IL-35 receptor are unconventional.

    Science.gov (United States)

    Collison, Lauren W; Delgoffe, Greg M; Guy, Clifford S; Vignali, Kate M; Chaturvedi, Vandana; Fairweather, DeLisa; Satoskar, Abhay R; Garcia, K Christopher; Hunter, Christopher A; Drake, Charles G; Murray, Peter J; Vignali, Dario A A

    2012-02-05

    Interleukin 35 (IL-35) belongs to the IL-12 family of heterodimeric cytokines but has a distinct functional profile. IL-35 suppresses T cell proliferation and converts naive T cells into IL-35-producing induced regulatory T cells (iTr35 cells). Here we found that IL-35 signaled through a unique heterodimer of receptor chains IL-12Rβ2 and gp130 or homodimers of each chain. Conventional T cells were sensitive to IL-35-mediated suppression in the absence of one receptor chain but not both receptor chains, whereas signaling through both chains was required for IL-35 expression and conversion into iTr35 cells. Signaling through the IL-35 receptor required the transcription factors STAT1 and STAT4, which formed a unique heterodimer that bound to distinct sites in the promoters of the genes encoding the IL-12 subunits p35 and Ebi3. This unconventional mode of signaling, distinct from that of other members of the IL-12 family, may broaden the spectrum and specificity of IL-35-mediated suppression.

  7. Charge Breeding of Radioactive Ions

    CERN Document Server

    Wenander, F J C

    2013-01-01

    Charge breeding is a technique to increase the charge state of ions, in many cases radioactive ions. The singly charged radioactive ions, produced in an isotope separator on-line facility, and extracted with a low kinetic energy of some tens of keV, are injected into a charge breeder, where the charge state is increased to Q. The transformed ions are either directed towards a dedicated experiment requiring highly charged ions, or post-accelerated to higher beam energies. In this paper the physics processes involved in the production of highly charged ions will be introduced, and the injection and extraction beam parameters of the charge breeder defined. A description of the three main charge-breeding methods is given, namely: electron stripping in gas jet or foil; external ion injection into an electron-beam ion source/trap (EBIS/T); and external ion injection into an electron cyclotron resonance ion source (ECRIS). In addition, some preparatory devices for charge breeding and practical beam delivery aspects ...

  8. Interleukin-35: Expanding Its Job Profile

    Science.gov (United States)

    Sawant, Deepali V.; Hamilton, Kristia

    2015-01-01

    Counter-regulation afforded by specialized regulatory cell populations and immunosuppressive cytokines is critical for balancing immune outcome. The inhibitory potential of the established suppressive cytokines, IL-10 and TGFβ, has been well elucidated in diverse inflammatory scenarios in conjunction with their key roles in Treg development and function. Despite the early predictions for an immunomodulatory role for the Ebi3/p35 heterodimer in placental trophoblasts, IL-35 biology remained elusive until 2007 when it was established as a Treg-restricted inhibitory cytokine. Since then, Treg-derived IL-35 has been shown to exhibit its suppressive activities in a range of autoimmune diseases and cancer models. Recent studies are beginning to explore other cellular sources of IL-35, such as Bregs and CD8+ Tregs. Despite these new cellular sources and targets, the mode of IL-35 suppression remains restricted to inhibition of proliferation and induction of an IL-35-producing induced regulatory T cell population referred to as iTr35. In this review, we explore the early beginnings, status quo, and future prospects of IL-35 biology. The unparalleled opportunity of targeting multiple immunosuppressive populations (Tregs, Bregs, CD8+ Tregs) through IL-35 is highly exciting and offers tremendous promise from a translational standpoint, particularly for cancer immunotherapies. PMID:25919641

  9. OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

    Science.gov (United States)

    Adamusiak, Tomasz; Burdett, Tony; Kurbatova, Natalja; Joeri van der Velde, K; Abeygunawardena, Niran; Antonakaki, Despoina; Kapushesky, Misha; Parkinson, Helen; Swertz, Morris A

    2011-05-29

    Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. http://www.ontocat.org.

  10. Nomenclature for factors of the SLA system, update 2008.

    Science.gov (United States)

    Ho, C-S; Lunney, J K; Ando, A; Rogel-Gaillard, C; Lee, J-H; Schook, L B; Smith, D M

    2009-04-01

    This report summarizes the new swine leukocyte antigen (SLA) allele sequences and haplotypes designated by the SLA Nomenclature Committee of the International Society for Animal Genetics. There have been 74 new SLA alleles, comprising 18 SLA-1 alleles, 11 SLA-2 alleles, six SLA-3 alleles, two SLA-6 alleles, one SLA-DRA allele, 20 SLA-DRB1 alleles, three SLA-DQA alleles and 13 SLA-DQB1 alleles. Twelve new SLA class I and four new class II haplotypes have also been designated. This is the first official update since the 2005 reports on the nomenclature for factors of the SLA class I and II systems. This report also summarizes recent updates to the Immunopolymorphism Database-Major Histocompatibility Complex (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/). All information has now been integrated to the SLA section of the IPD-MHC database, which serves as the repository for maintaining a list of all recognized SLA genes and their allelic sequences.

  11. Molecular genetics of the swine major histocompatibility complex, the SLA complex.

    Science.gov (United States)

    Lunney, Joan K; Ho, Chak-Sum; Wysocki, Michal; Smith, Douglas M

    2009-03-01

    The swine major histocompatibility complex (MHC) or swine leukocyte antigen (SLA) complex is one of the most gene-dense regions in the swine genome. It consists of three major gene clusters, the SLA class I, class III and class II regions, that span approximately 1.1, 0.7 and 0.5Mb, respectively, making the swine MHC the smallest among mammalian MHC so far examined and the only one known to span the centromere. This review summarizes recent updates to the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/) which serves as the repository for maintaining a list of all SLA recognized genes and their allelic sequences. It reviews the expression of SLA proteins on cell subsets and their role in antigen presentation and regulating immune responses. It concludes by discussing the role of SLA genes in swine models of transplantation, xenotransplantation, cancer and allergy and in swine production traits and responses to infectious disease and vaccines.

  12. A uvbyCaHbeta CCD Analysis of the Open Cluster Standard, NGC 752

    CERN Document Server

    Twarog, B A; Deliyannis, C P; Thomas, D T

    2015-01-01

    Precision uvbyCaHbeta photometry of the nearby old open cluster, NGC 752, is presented. The mosaic of CCD fields covers an area ~42' on a side with internal precision at the 0.005 to 0.010 mag level for the majority of stars down to V~15. The CCD photometry is tied to the standard system using an extensive set of published photoelectric observations adopted as secondary standards within the cluster. Multicolor indices are used to eliminate as nonmembers a large fraction of the low probability proper-motion members near the faint end of the main sequence, while identifying 24 potential dwarf members between V=15.0 and 16.5, eight of which have been noted before from Vilnius photometry. From 68 highly probable F dwarf members, we derive a reddening estimate of E(b-y)= 0.025 +/- 0.003 (E(B-V) = 0.034 +/- 0.004), where the error includes the internal photometric uncertainty and the systematic error arising from the choice of the standard (b-y), Hbeta relation. With reddening fixed, [Fe/H] is derived from the F dw...

  13. Pulsating electromagnetic fields (PEMF) used to treat full thickness defects in the rabbit model

    Energy Technology Data Exchange (ETDEWEB)

    Andino, R.V.; Feldman, D. (Univ. of Alabama, Birmingham (United States))

    1991-03-15

    Skin ulcers have historically been treated by passive therapy. One active treatment, PEMF, has shown promise. The objective of this study was, therefore, to examine the effects of a current induced by a PEMF on full thickness defects in white New Zealand rabbits. It was hypothesized that the induced current would increase neutrophil, macrophage, and fibroblast proliferation during the wound healing process. This in turn, would lead to an increase in collagen deposition in the wound and thus increase the healing rate. A device which produces a 2.8 mTesla magnetic field at a frequency of 75 Hz was donated by the EBI Corp. and modified so that a rabbit could be fit between its two induction coils. Two rabbits with four 3 x 3 cm wounds each were stimulated for 3.5 hours/day for 1 week and two rabbits with identical wounds were stimulated for the same time period daily but for 2 weeks. These wounds were compared to unstimulated controls. Preliminary results indicate that the healing rate in the PEMF animals increased by about 25-30% and the number of neutrophils is greater in the one week stimulated group. In the two week stimulated group, the collagen deposition is greater, denser and in alignment.

  14. Universal main magnetic focus ion source: A new tool for laboratory research of astrophysics and Tokamak microplasma

    Science.gov (United States)

    Ovsyannikov, V. P.; Nefiodov, A. V.; Levin, A. A.

    2017-01-01

    A novel room-temperature ion source for the production of atomic ions in electron beam within wide ranges of electron energy and current density is developed. The device can operate both as conventional Electron Beam Ion Source/Trap (EBIS/T) and novel Main Magnetic Focus Ion Source. The ion source is suitable for generation of the low-, medium- and high-density microplasma in steady state, which can be employed for investigation of a wide range of physical problems in ordinary university laboratory, in particular, for microplasma simulations relevant to astrophysics and ITER reactor. For the electron beam characterized by the incident energy Ee = 10 keV, the current density je ∼ 20 kA/cm2 and the number density ne ∼ 2 × 1013 cm‑3 were achieved experimentally. For Ee ∼ 60 keV, the value of electron number density ne ∼ 1014 cm‑3 is feasible. The efficiency of the novel ion source for laboratory astrophysics significantly exceeds that of other existing warm and superconducting EBITs.

  15. Protein folds and families: sequence and structure alignments.

    Science.gov (United States)

    Holm, L; Sander, C

    1999-01-01

    Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/

  16. Classical scattering theory of waves from the view point of an eigenvalue problem and application to target identification

    Energy Technology Data Exchange (ETDEWEB)

    Bottcher, C.; Strayer, M.R. [Oak Ridge National Lab., TN (United States); Werby, M.F. [Naval Research Lab. Detachment, Stennis Space Center, MS (United States)

    1993-10-01

    The Helmholtz-Poincare Wave Equation (H-PWE) arises in many areas of classical wave scattering theory. In particular it can be found for the cases of acoustical scattering from submerged bounded objects and electromagnetic scattering from objects. The extended boundary integral equations (EBIE) method is derived from considering both the exterior and interior solutions of the H-PWE`s. This coupled set of expressions has the advantage of not only offering a prescription for obtaining a solution for the exterior scattering problem, but it also obviates the problem of irregular values corresponding to fictitious interior eigenvalues. Once the coupled equations are derived, they can by obtained in matrix form be expanding all relevant terms in partial wave expansions, including a biorthogonal expansion of the Green function. However some freedom of choice in the choice of the surface expansion is available since the unknown surface quantities may be expanded in a variety of ways to long as closure is obtained. Out of many possible choices, we develop an optimal method to obtain such expansions which is based on the optimum eigenfunctions related to the surface of the object. In effect, we convert part of the problem (that associated with the Fredholms integral equation of the first kind) an eigenvalue problem of a related Hermition operator. The methodology will be explained in detail and examples will be presented.

  17. Social reintegration of traumatic brain-injured: the French experience.

    Science.gov (United States)

    Truelle, J-L; Wild, K Von; Onillon, M; Montreuil, M

    2010-01-01

    Traumatic Brain Injury (TBI) may lead to specific handicap, often hidden, mainly due to cognitive and behavioural sequelae. Social re-entry is a long-term, fluctuant and precarious process. The French experience will be illustrated by 6 initiatives answering to 6 challenges to do with TBI specificities:1. bridging the gap, between initial rehabilitation and community re-entry, via transitional units dealing with assessment, retraining, social/vocational orientation and follow-up. Today, there are 30 such units based on multidisciplinary teams.2. assessing recovery by TBI-specific and validated evaluation tools: EBIS holistic document, BNI Screening of higher cerebral functions, Glasgow outcome extended, and QOLIBRI, a TBI-specific quality of life tool.3. promoting specific re-entry programmes founded on limited medication, ecological neuro-psychological rehabilitation, exchange groups and workshops, violence prevention, continuity of care, environmental structuration, and "resocialisation".4. taking into account the "head injured family"5. facilitating recovery after sports-related concussion6. facing medico-legal consequences and compensation: In that perspective, we developed guidelines for TBI-specific expert appraisal, including mandatory neuro-psychological assessment, family interview and an annual forum gathering lawyers and health professionals.

  18. Biomartr: genomic data retrieval with R.

    Science.gov (United States)

    Drost, Hajk-Georg; Paszkowski, Jerzy

    2017-04-15

    Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, biomartr , which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses. The biomartr package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, biomartr communicates with the BioMart database for functional annotation of retrieved sequences. Comprehensive documentation of biomartr functions and five tutorial vignettes provide step-by-step instructions on how to use the package in a reproducible manner. The open source biomartr package is available at https://github.com/HajkD/biomartr and https://cran.r-project.org/web/packages/biomartr/index.html . hgd23@cam.ac.uk. Supplementary data are available at Bioinformatics online.

  19. Auto-transfusion tourniquets: the next evolution of tourniquets

    Directory of Open Access Journals (Sweden)

    Tang DH

    2013-12-01

    Full Text Available David H Tang,1,2,3 Bohdan T Olesnicky,1,3 Michael W Eby,1,4 Lawrence E Heiskell1,51International School of Tactical Medicine, Palm Springs, CA, USA; 2Eisenhower Medical Center, Rancho Mirage, CA, USA; 3High Desert Medical Center, Joshua Tree, CA, USA; 4Veterans Administration Loma Linda Healthcare System, Loma Linda, CA, USA; 5Fallbrook Community Hospital, Fallbrook, CA, USAAbstract: In this article, we discuss the relationship between hemorrhagic shock and the pathophysiology of shock using conventional tourniquets. We will focus on corollary benefits with the use of HemaClear®, a self-contained, sterile, exsanguinating auto-transfusion tourniquet. This discussion will demonstrate that the use of auto-transfusion tourniquets is a practical evidence-based approach in fluid resuscitation: it shortens the duration of shock after hemorrhage and trauma compared with conventional tourniquets. Emphasis is placed on the use of the HemaClear® as an alternative fluid resuscitation tool which is more efficient in the battlefield, pre-hospital and in-hospital settings.Keywords: auto-transfusion tourniquet, field exsanguination, hemorrhagic shock, tourniquet, perfusion requirement, HemaClear® ATT

  20. Desarrollo de la Educación intercultural en Ecuador. El pueblo de Shwar

    Directory of Open Access Journals (Sweden)

    Juan Botasso

    Full Text Available Una fecha significativa es el año 1980, pues es en este año que el Estado asume por primera vez la problemática de la Educación lndigéna, hasta entonces delegada a otras instituciones, a través del Plan Nacional de Alfabetización en Quichua, firmándose un convenio con la Universidad Católica de Quito para la formulación de Curriculum de Educación lndigéna para la escuela primaria, secundaria y alfabetización. Este convenio se suspende en 1982 por problemas con organizaciones indígenas que no participaron en las decisiones, reanudándose en 1985 con la institución EBI (Educación Bilingüe BicuItural creada por el Estado y apoyada técnica y financieramente por dos instancias alemanas.